Alison Wright Barry Smith Janna Hastings Jeanette Alicia Chacón Candia Mark Jensen Neil Otte Paulina Schenk https://creativecommons.org/licenses/by/3.0/ Mental Functioning Ontology The Mental Functioning Ontology (MF) was first described in the publication available at http://www.jbiomedsem.com/content/1/1/10 entitled 'Foundations for a realist ontology of mental disease' (Barry Smith and Werner Ceusters). The Mental Functioning Ontology is an overarching ontology for all aspects of mental functioning, founded on the Basic Formal Ontology (BFO) and related to the Ontology for General Medical Science (OGMS). The OWL representaions of MF and MD were split on 22 May 2012. The release version of the MF is now a single, merged file prepared from the source module files using the ROBOT library's merge function. This OWL version of the MF ontology was originally created by Janna Hastings and is maintained by all committers to the MF ontology project. 2022-07-19 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 term The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English) PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> editor preferred term example example of usage A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> example of usage in branch An annotation property indicating which module the terms belong to. This is currently experimental and not implemented yet. GROUP:OBI OBI_0000277 in branch has curation status PERSON:Alan Ruttenberg PERSON:Bill Bug PERSON:Melanie Courtot OBI_0000281 has curation status definition The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. 2012-04-05: Barry Smith The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. Can you fix to something like: A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. Alan Ruttenberg Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. On the specifics of the proposed definition: We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition 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> editor note term editor Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people 20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> term editor alternative label alternative term 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. An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent) 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 has obsolescence reason Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification. PERSON:Alan Ruttenberg PERSON:Melanie Courtot has obsolescence reason curator note An administrative note of use for a curator but of no use for a user PERSON:Alan Ruttenberg curator note term tracker item term tracker item the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/ 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. 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 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. The 'tracker item' can associate a tracker with a specific ontology term. term tracker item ontology term requester The name of the person, project, or organization that motivated inclusion of an ontology term by requesting its addition. 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 Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg The 'term requester' can credit the person, organization or project who request the ontology term. ontology term requester is denotator type Relates an class defined in an ontology, to the type of it's denotator relates an class defined in an ontology, to the type of it's denotator In OWL 2 add AnnotationPropertyRange('is denotator type' 'denotator type') In OWL 2 add AnnotationPropertyRange('is denotator type' 'denotator type') Alan Ruttenberg Alan Ruttenberg is denotator type is denotator type imported from For external terms/classes, the ontology from which the term was imported PERSON:Alan Ruttenberg PERSON:Melanie Courtot GROUP:OBI:<http://purl.obolibrary.org/obo/obi> imported from expand expression to ObjectProperty: RO_0002104 Label: has plasma membrane part Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.org/obo/owl/GO#GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)" A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones Chris Mungall Chris Mungall expand expression to expand assertion to ObjectProperty: RO??? Label: spatially disjoint from Annotations: expand_assertion_to "DisjointClasses: (http://purl.obolibrary.org/obo/BFO_0000051 some ?X) (http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)" A macro expansion tag applied to an annotation property which can be expanded into a more detailed axiom. Chris Mungall expand assertion to first order logic expression PERSON:Alan Ruttenberg first order logic expression antisymmetric property part_of antisymmetric property xsd:true Use boolean value xsd:true to indicate that the property is an antisymmetric property use boolean value xsd:true to indicate that the property is an antisymmetric property Alan Ruttenberg antisymmetric property OBO foundry unique label An alternative name for a class or property which is unique across the OBO Foundry. The intended usage of that property is as follow: OBO foundry unique labels are automatically generated based on regular expressions provided by each ontology, so that SO could specify unique label = 'sequence ' + [label], etc. , MA could specify 'mouse + [label]' etc. Upon importing terms, ontology developers can choose to use the 'OBO foundry unique label' for an imported term or not. The same applies to tools . The intended usage of that property is as follow: OBO foundry unique labels are automatically generated based on regular expressions provided by each ontology, so that SO could specify unique label = 'sequence ' + [label], etc. , MA could specify 'mouse + [label]' etc. Upon importing terms, ontology developers can choose to use the 'OBO foundry unique label' for an imported term or not. The same applies to tools . PERSON:Alan Ruttenberg PERSON:Bjoern Peters PERSON:Chris Mungall PERSON:Melanie Courtot GROUP:OBO Foundry <http://obofoundry.org/> OBO foundry unique label has ID digit count Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> Annotations: 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" 'has ID digit count' : 7, rdfs:label "RO id policy" 'has ID policy for': "RO" 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) 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 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] 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 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 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" 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 Relating an ontology used to record id policy to the ontology namespace whose policy it manages Person:Alan Ruttenberg Person:Alan Ruttenberg has ID policy for 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" 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. 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 Person:Alan Ruttenberg has ID prefix elucidation person:Alan Ruttenberg Person:Barry Smith Primitive terms in a highest-level ontology such as BFO are terms which are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms elucidation has associated axiom(nl) Person:Alan Ruttenberg Person:Alan Ruttenberg An axiom associated with a term expressed using natural language has associated axiom(nl) has associated axiom(fol) Person:Alan Ruttenberg Person:Alan Ruttenberg An axiom expressed in first order logic using CLIF syntax has associated axiom(fol) is allocated id range Add as annotation triples in the granting ontology Relates an ontology IRI to an (inclusive) range of IRIs in an OBO name space. The range is give as, e.g. "IAO_0020000-IAO_0020999" PERSON:Alan Ruttenberg Add as annotation triples in the granting ontology is allocated id range has ontology root term Ontology annotation property. Relates an ontology to a term that is a designated root term of the ontology. Display tools like OLS can use terms annotated with this property as the starting point for rendering the ontology class hierarchy. There can be more than one root. Nicolas Matentzoglu has ontology root term may be identical to A annotation relationship between two terms in an ontology that may refer to the same (natural) type but where more evidence is required before terms are merged. 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 David Osumi-Sutherland #40 #40 VFB VFB 2018-09-21T16:43:39Z Edges asserting this should be annotated with to record evidence supporting the assertion and its provenance. Edges asserting this should be annotated with to record evidence supporting the assertion and its provenance. may be identical to scheduled for obsoletion on or after Used when the class or object is scheduled for obsoletion/deprecation on or after a particular date. Chris Mungall, Jie Zheng https://github.com/geneontology/go-ontology/issues/15532 https://github.com/information-artifact-ontology/ontology-metadata/issues/32 GO ontology scheduled for obsoletion on or after has axiom id Person:Alan Ruttenberg Person:Alan Ruttenberg A URI that is intended to be unique label for an axiom used for tracking change to the ontology. For an axiom expressed in different languages, each expression is given the same URI has axiom label term replaced by Add as annotation triples in the granting ontology Use on obsolete terms, relating the term to another term that can be used as a substitute Person:Alan Ruttenberg Person:Alan Ruttenberg Add as annotation triples in the granting ontology term replaced by This is an annotation used on an object property to indicate a logical characterstic beyond what is possible in OWL. OBO Operations call logical characteristic of object property 'part disjoint with' 'defined by construct' """ PREFIX owl: <http://www.w3.org/2002/07/owl#> PREFIX : <http://example.org/ CONSTRUCT { [ a owl:Restriction ; owl:onProperty :part_of ; owl:someValuesFrom ?a ; owl:disjointWith [ a owl:Restriction ; owl:onProperty :part_of ; owl:someValuesFrom ?b ] ] } WHERE { ?a :part_disjoint_with ?b . } Links an annotation property to a SPARQL CONSTRUCT query which is meant to provide semantics for a shortcut relation. defined by construct 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 An alternative label for a class or property which has the exact same meaning than the preferred name/primary label. https://github.com/information-artifact-ontology/ontology-metadata/issues/20 has exact synonym https://github.com/information-artifact-ontology/ontology-metadata/issues/20 An alternative label for a class or property which has a more specific meaning than the preferred name/primary label. https://github.com/information-artifact-ontology/ontology-metadata/issues/19 has narrow synonym https://github.com/information-artifact-ontology/ontology-metadata/issues/19 An alternative label for a class or property that has been used synonymously with the primary term name, but the usage is not strictly correct. https://github.com/information-artifact-ontology/ontology-metadata/issues/21 has related synonym https://github.com/information-artifact-ontology/ontology-metadata/issues/21 BFO_0000052 BFO_0000052s BFO_0000052ed inheres in at all times BFO_0000056 BFO_0000056s BFO_0000056ed participates in at some time BFO_0000057 BFO_0000057s BFO_0000057ed has participant at some time BFO_0000110 BFO_0000110s BFO_0000110ed has continuant part at all times BFO_0000111 BFO_0000111s BFO_0000111ed has proper continuant part at all times BFO_0000118 BFO_0000118s BFO_0000118ed has proper occurrent part BFO_0000132 BFO_0000132s BFO_0000132ed part of occurrent BFO_0000163 BFO_0000163s BFO_0000163ed material basis of at all times 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 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 (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 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]) BFO:0000003 occurrent Occurrent 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]) For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] independent continuant b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] 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]) BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war) (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] process p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] 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 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]) Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] specifically dependent continuant b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. per discussion with Barry Smith (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] 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 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). ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158. b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004]) (forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] object aggregate An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158. b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004]) (forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] 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] 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 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 (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] 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] 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 requited 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]) GO:0001661 A conditioned aversion to a specific chemical compound as a result of that compound being coupled with a noxious stimulus. conditioned taste aversion GO:0001662 An acute behavioral change resulting from a perceived external threat. behavioral fear response GO:0001967 Specific behavior of a newborn or infant mammal that results in the derivation of nourishment from the breast. suckling behavior GO:0002023 An eating behavior process whereby detection of a dietary excess results in a decrease in intake of nutrients. reduction of food intake in response to dietary excess GO:0002118 A behavioral interaction between organisms in which one organism has the intention of inflicting physical damage on another individual. aggressive behavior GO:0002120 Aggressive behavior involving attack on prey by a predator. predatory behavior GO:0002121 Aggressive behavior based on competition between males of the same species over access to resources such as females, dominance, status, etc. and characterized by noise, threats, and is often less injurious. inter-male aggressive behavior GO:0002122 Aggressive behavior associated with attempts to flee from a threat. fear-induced aggressive behavior GO:0002123 Aggressive behavior induced by frustration and directed against an available target. irritable aggressive behavior GO:0002124 Aggressive behavior performed in defence of a fixed area against intruders, typically conspecifics. territorial aggressive behavior GO:0002125 Aggressive behavior of a female to protect her offspring from a threat. maternal aggressive behavior GO:0002126 Aggressive behavior directed towards obtaining some goal, considered to be a learned response to a situation. instrumental aggressive behavior GO:0002209 A behavioral response seeking to protect an organism from an a perceived external threat to that organism. behavioral defense response GO:0002210 A behavioral response resulting from wounding. behavioral response to wounding GO:0002211 A behavioral response seeking to protect an organism from an a perceived external threat from an insect or insects to that organism. behavioral defense response to insect GO:0002212 A behavioral response seeking to protect an organism from an a perceived external threat from a nematode or nematodes to that organism. behavioral defense response to nematode GO:0003051 The drinking behavior that is mediated by the action of angiotensin in the brain. Angiotensin stimulates the brain centers that control thirst. angiotensin-mediated drinking behavior GO:0007600 GO:0007610 The internally coordinated responses (actions or inactions) of animals (individuals or groups) to internal or external stimuli, via a mechanism that involves nervous system activity. behavior GO:0007611 The acquisition and processing of information and/or the storage and retrieval of this information over time. learning or memory GO:0007612 Any process in an organism in which a relatively long-lasting adaptive behavioral change occurs as the result of experience. learning GO:0007613 The activities involved in the mental information processing system that receives (registers), modifies, stores, and retrieves informational stimuli. The main stages involved in the formation and retrieval of memory are encoding (processing of received information by acquisition), storage (building a permanent record of received information as a result of consolidation) and retrieval (calling back the stored information and use it in a suitable way to execute a given task). memory GO:0007614 The memory process that deals with the storage, retrieval and modification of information received a short time (up to about 30 minutes) ago. This type of memory is typically dependent on direct, transient effects of second messenger activation. short-term memory GO:0007615 The memory process that results in the formation of consolidated memory resistant to disruption of the patterned activity of the brain, without requiring protein synthesis. anesthesia-resistant memory GO:0007616 The memory process that deals with the storage, retrieval and modification of information a long time (typically weeks, months or years) after receiving that information. This type of memory is typically dependent on gene transcription regulated by second messenger activation. long-term memory GO:0007617 The behavioral interactions between organisms for the purpose of mating, or sexual reproduction resulting in the formation of zygotes. mating behavior GO:0007619 The behavioral interactions between organisms for the purpose of attracting sexual partners. courtship behavior GO:0007621 Any process that stops, prevents or reduces the receptiveness of a female to male advances. negative regulation of female receptivity GO:0007622 The specific behavior of an organism that recur with measured regularity. rhythmic behavior GO:0007625 The specific behavior of an organism relating to grooming, cleaning and brushing to remove dirt and parasites. grooming behavior GO:0007626 The specific movement from place to place of an organism in response to external or internal stimuli. Locomotion of a whole organism in a manner dependent upon some combination of that organism's internal state and external conditions. locomotory behavior GO:0007628 The behavior of an adult relating to the progression of that organism along the ground by the process of lifting and setting down each leg. adult walking behavior GO:0007629 The response to external or internal stimuli that results in the locomotory process of flight. Flight is the self-propelled movement of an organism through the air. flight behavior GO:0007630 The sudden, usually upward, movement off the ground or other surface through sudden muscular effort in the legs, following exposure to an external stimulus. jump response GO:0007631 Behavior associated with the intake of food. feeding behavior GO:0007632 The behavior of an organism in response to a visual stimulus. visual behavior GO:0007633 The actions or reactions of an individual in response to the orientation of a visual pattern. This is exemplified by some classes of insects which are able to detect and learn the orientation of a set of stripes and subsequently behaviorally discriminate between horizontal, vertical or 45 degree stripes. pattern orientation GO:0007634 The behavior of an organism pertaining to movement of the eyes and of objects in the visual field, as in nystagmus. optokinetic behavior GO:0007635 Behavior that is dependent upon the sensation of chemicals. chemosensory behavior GO:0007636 The sudden, usually upward, movement off the ground or other surface through sudden muscular effort in the legs, following exposure to a chemical substance. chemosensory jump behavior GO:0007637 The extension, through direct muscle actions, of the proboscis (the trunk-like extension of the mouthparts on the adult external head) in response to a sugar stimulus. proboscis extension reflex GO:0007638 Behavior that is dependent upon the sensation of a mechanical stimulus. mechanosensory behavior GO:0008049 The behavior of a male, for the purpose of attracting a sexual partner. An example of this process is found in Drosophila melanogaster. male courtship behavior GO:0008050 The behavior of a female, for the purpose of attracting a sexual partner. female courtship behavior GO:0008062 The timing of the emergence of the adult fly from its pupal case, which usually occurs at dawn. eclosion rhythm GO:0008306 Learning by associating a stimulus (the cause) with a particular outcome (the effect). associative learning GO:0008343 Feeding behavior in a fully developed and mature organism. adult feeding behavior GO:0008344 Locomotory behavior in a fully developed and mature organism. adult locomotory behavior GO:0008345 Locomotory behavior in a larval (immature) organism. larval locomotory behavior GO:0008346 The behavior of a larval organism relating to the progression of that organism along the ground by the process of lifting and setting down each leg. larval walking behavior GO:0008355 Any process in an organism in which a relatively long-lasting adaptive behavioral change occurs in response to (repeated) exposure to an olfactory cue. olfactory learning GO:0008542 Any process in an organism in which a change in behavior of an individual occurs in response to repeated exposure to a visual cue. visual learning GO:0016543 The process during courtship, where the male orients towards a potential partner. An example of this is found in Drosophila melanogaster. male courtship behavior, orientation prior to leg tapping and wing vibration GO:0016544 The process during courtship where the male insect taps the female with his frontal leg. An example of this is found in Drosophila melanogaster. male courtship behavior, tapping to detect pheromone GO:0016545 The process during courtship where the male insect vibrates his wings. An example of this is found in Drosophila melanogaster. male courtship behavior, veined wing vibration GO:0016546 The process during courtship where the male fly licks the genitalia of a stationary female fly with his proboscis. An example of this is found in Drosophila melanogaster. male courtship behavior, proboscis-mediated licking GO:0018991 The deposition of eggs (either fertilized or not) upon a surface or into a medium such as water. oviposition GO:0019098 The specific behavior of an organism that is associated with reproduction. reproductive behavior GO:0022410 A behavioral process involved in the cycle from wakefulness through an orderly succession of sleep states and stages that occurs on an approximately 24 hour rhythm. circadian sleep/wake cycle process GO:0030534 Behavior in a fully developed and mature organism. adult behavior GO:0030536 Feeding behavior in a larval (immature) organism. larval feeding behavior GO:0030537 Behavior in a larval form of an organism, an immature organism that must undergo metamorphosis to assume adult characteristics. larval behavior GO:0031223 The behavior of an organism in response to a sound. auditory behavior GO:0032537 The specific behavior of an organism that are associated with finding a host organism; may include behavioral responses to light, temperature, or chemical emanations from the prospective host. host-seeking behavior GO:0034606 The response by the male to a hermaphrodite after initial contact following mate finding. The male stops forward locomotion, presses the ventral side of his tail against his partner's body, and begins moving backward along the hermaphrodite. Male response behavior is initiated when sensory neurons located in the rays of his tail contact a potential mate. response to hermaphrodite contact GO:0034607 The sharp ventral turn performed by the male as he approaches either the hermaphrodite head or tail, whilst trying to locate his partner's vulva. Turning occurs via a sharp ventral coil of the male's tail. turning behavior involved in mating GO:0034608 Location, by the male, of his partner's vulva when backing along the ventral side of the hermaphrodite during mating. The male stops at the vulva, coordinates his movements to the hermaphrodite's, and positions his tail precisely over the vulva so that he may insert his spicules and ejaculate. vulval location GO:0034609 Insertion of the male copulatory spicules into the hermaphrodite. Spicule insertion behavior initiates when the male cloaca contacts the vulva. During most mating encounters, the spicule tips will prod the vulva continuously until they partially penetrate, which then causes the protractors to contract completely so that the spicules extend through the vulva. spicule insertion GO:0035095 Any process that results in a change in the behavior of an organism as a result of a nicotine stimulus. behavioral response to nicotine GO:0035106 Learning to anticipate future events on the basis of past experience with the consequences of one's own behavior. operant conditioning GO:0035176 Behavior directed towards society, or taking place between members of the same species. Occurs predominantly, or only, in individuals that are part of a group. social behavior GO:0035177 The movement of a larva through a feeding substrate whilst feeding on food. larval foraging behavior GO:0035178 Fine-tuning the spatial position of an organism in response to variability in their environment. For example, reorientation of an organism in the direction of a food source. turning behavior GO:0035179 Fine-tuning the spatial position of a larva in response to variability in their environment. For example, reorientation of a larva in the direction of a food source. larval turning behavior GO:0035180 The movement of a third instar larva through a substrate in search of a pupation site. This movement occurs without feeding and is characterized by short bursts of forward movement, separated by stops and repeated side-to-side head probes, followed normally by a change in direction. larval wandering behavior GO:0035181 Digging into the substrate by non-feeding larvae in search for food-free sites suitable for pupation. larval burrowing behavior GO:0035187 The specific behavior of an organism during the emergence from an egg shell. In Drosophila for example, the larva swings its head reiteratively through a semicircular arc, using its mouth hooks to tear apart the chorion in front of it and thus free itself from within the egg shell. hatching behavior GO:0035199 The specific avoidance actions or reactions of an organism in response to the perception of salt. salt aversion GO:0035640 The specific behavior of an organism in response to a novel environment or stimulus. exploration behavior GO:0035641 The specific movement from place to place of an organism in response to a novel environment. locomotory exploration behavior GO:0035648 The fluctuation in mating behavior that occurs over an approximately 24 hour cycle. circadian mating behavior GO:0035737 The process of forcing a substance into another organism, either by penetrating the skin of the other organism or by applying the substance externally to a sensitive tissue such as those that surround the eyes. injection of substance in to other organism GO:0035738 The process which begins with venom being forced into an organism by the bite or sting of another organism, and ends with the manifestation of some change or damage to the bitten organism. envenomation resulting in modification of morphology or physiology of other organism GO:0036269 The response to external or internal stimuli that results in the locomotory process of swimming. Swimming is the self-propelled movement of an organism through the water. swimming behavior GO:0036343 The specific behavior of an organism that combines cognitive functions and physical movement. For example, driving a car, throwing a ball, or playing a musical instrument. psychomotor behavior GO:0040040 Behavior that is dependent upon the sensation of temperature. thermosensory behavior GO:0042048 The behavior of an organism in response to an odor. olfactory behavior GO:0042297 A behavioral process whose outcome is a relatively long-lasting behavioral change whereby an organism modifies innate vocalizations to imitate sounds produced by others. vocal learning GO:0042628 The deposition of a plug of sperm or other gelatinous material into the opening of the vulva by a male at the termination of copulation. Probably acts to prevent subsequent matings by other males. mating plug formation GO:0042630 Any process that results in a change in the behavior of an organism as a result of deprivation of water. behavioral response to water deprivation GO:0042711 Female behaviors associated with the care and rearing of offspring. maternal behavior GO:0042712 Male behaviors associated with the care and rearing offspring. paternal behavior GO:0042745 The cycle from wakefulness through an orderly succession of sleep states and stages that occurs on an approximately 24 hour rhythm. circadian sleep/wake cycle GO:0042746 The part of the circadian sleep/wake cycle where the organism is not asleep. circadian sleep/wake cycle, wakefulness GO:0042747 A stage in the circadian sleep cycle during which dreams occur and the body undergoes marked changes including rapid eye movement, loss of reflexes, and increased pulse rate and brain activity. circadian sleep/wake cycle, REM sleep GO:0042748 All sleep stages in the circadian sleep/wake cycle other than REM sleep. These stages are characterized by a slowing of brain waves and other physiological functions. circadian sleep/wake cycle, non-REM sleep GO:0042755 The specific behavior of an organism relating to the intake of food, any substance (usually solid) that can be metabolized by an organism to give energy and build tissue. eating behavior GO:0042756 The specific behavior of an organism relating to the intake of liquids, especially water. drinking behavior GO:0043050 The contraction and relaxation movements of the pharyngeal muscle that mediate feeding in nematodes. pharyngeal pumping GO:0044358 A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with vascular damage and hemorrhage in the bitten organism. envenomation resulting in hemorrhagic damage to other organism GO:0044365 A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with a resultant change to the frequency, rate or extent of platelet aggregation in the bitten organism. envenomation resulting in modulation of platelet aggregation in other organism GO:0044370 The process of forcing a substance into the bloodstream of another organism, whilst feeding on blood of other organism. The substance may facilitate the feeding process, e.g. by preventing the blood from clotting. injection of substance into other organism during feeding on blood of other organism GO:0044398 A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with the swelling of soft tissues of the bitten organism as a result of excess water accumulation. envenomation resulting in induction of edema in other organism GO:0044468 A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with the modulation of the frequency, rate or extent of blood coagulation in the bitten organism. envenomation resulting in modulation of blood coagulation in other organism GO:0044469 A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with the resultant activation, maintenance or an increase in the frequency, rate or extent of blood coagulation in the bitten organism. envenomation resulting in positive regulation of blood coagulation in other organism GO:0044470 A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with the resultant stopping, prevention or reduction in the frequency, rate or extent of blood coagulation in the bitten organism. envenomation resulting in negative regulation of blood coagulation in other organism GO:0044471 A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with the aggregation, arrangement and bonding together of a set of components to form a pore complex in a membrane of the bitten organism. envenomation resulting in pore formation in membrane of other organism GO:0044472 A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with a resultant change in the activity of a calcium channel in the bitten organism. envenomation resulting in modulation of calcium channel activity in other organism GO:0044473 A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with the resultant stopping, prevention or reduction of the activity of a calcium channel in the bitten organism. envenomation resulting in negative regulation of calcium channel activity in other organism GO:0044474 A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with the resultant stopping, prevention or reduction of the activity of a voltage-gated calcium channel in the bitten organism. envenomation resulting in negative regulation of voltage-gated calcium channel activity in other organism GO:0044475 A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with the resultant stopping, prevention or reduction of the activity of a high voltage-gated calcium channel in the bitten organism. envenomation resulting in negative regulation of high voltage-gated calcium channel activity in other organism GO:0044476 A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with the resultant stopping, prevention or reduction of the activity of a low voltage-gated calcium channel in the bitten organism. envenomation resulting in negative regulation of low voltage-gated calcium channel activity in other organism GO:0044477 A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with the resultant stopping, prevention or reduction in the frequency, rate or extent of platelet aggregation in the bitten organism. envenomation resulting in negative regulation of platelet aggregation in other organism GO:0044478 A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with the resultant activation, maintenance or an increase in the frequency, rate or extent of platelet aggregation in the bitten organism. envenomation resulting in positive regulation of platelet aggregation in other organism GO:0044479 A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with the resultant modulation of blood mast cell degranulation in the bitten organism. envenomation resulting in modulation of mast cell degranulation in other organism GO:0044480 A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with the resultant positive regulation of blood mast cell degranulation in the bitten organism. envenomation resulting in positive regulation of mast cell degranulation in other organism GO:0044481 A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with the resultant hydrolysis of proteins in of the bitten organism. envenomation resulting in proteolysis in other organism GO:0044482 A process that begins with venom being forced into an organism by the bite or sting of another organism which causes damage to the extracellular matrix of the blood vessels of the bitten organism, ultimately resulting in hemorrhage in the bitten organism. envenomation resulting in blood vessel extracellular matrix damage, causing hemorrhagic damage in other organism GO:0044483 A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with the inhibition of the process of hemostasis - the stopping of bleeding or the arrest of the circulation to an organ or part - in the bitten organism. envenomation resulting in impairment of hemostasis in other organism GO:0044484 The process which begins with venom being forced into an organism by the bite or sting of another organism, and ends with fibrinolysis, a process that solubilizes fibrin, chiefly by the proteolytic action of plasmin, in the bloodstream of the bitten/stung organism. envenomation resulting in fibrinolysis in other organism GO:0044485 The process which begins with venom being forced into an organism by the bite or sting of another organism, and ends with fibrinogenolysis, a process that degrades fibrinogen at a variety of Arg-Lys bonds, thus impairing fibrinogen clotting in the bloodstream of the bitten/stung organism. envenomation resulting in fibrinogenolysis in other organism GO:0044487 A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with the resultant modulation of the transmission of nerve impulses in the bitten organism. envenomation resulting in modulation of transmission of nerve impulse in other organism GO:0044492 A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with a resultant change in the activity of a voltage-gated sodium channel in the bitten organism. envenomation resulting in modulation of voltage-gated sodium channel activity in other organism GO:0044493 A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with the resultant stopping, prevention or reduction of the activity of a voltage-gated sodium channel in the bitten organism. envenomation resulting in negative regulation of voltage-gated sodium channel activity in other organism GO:0044494 A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with the resultant activation or increase in the activity of the activity of a voltage-gated sodium channel in the bitten organism. envenomation resulting in positive regulation of voltage-gated sodium channel activity in other organism GO:0044498 A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with the resultant modulation of the force with which blood travels through the circulatory system of the bitten/stung organism. envenomation resulting in modulation of blood pressure in other organism GO:0044499 A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with the resultant increase of the force with which blood travels through the circulatory system of the bitten/stung organism. envenomation resulting in positive regulation of blood pressure in other organism GO:0044500 A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with the resultant decrease of the force with which blood travels through the circulatory system of the bitten/stung organism. envenomation resulting in negative regulation of blood pressure in other organism GO:0044509 A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with the resultant modulation of signal transduction in the bitten organism. envenomation resulting in modulation of signal transduction in other organism GO:0044510 A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with the resultant positive regulation of signal transduction in the bitten organism. envenomation resulting in positive regulation of signal transduction in other organism GO:0044511 A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with the resultant modulation of receptor activity in of the bitten organism. envenomation resulting in modulation of receptor activity in other organism GO:0044512 A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with the resultant modulation of glucagon-like peptide receptor 1 activity in of the bitten organism. envenomation resulting in modulation of glucagon-like peptide receptor 1 activity in other organism GO:0044513 A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with the resultant modulation of G-protein coupled receptor activity in of the bitten organism. envenomation resulting in modulation of G-protein coupled receptor activity in other organism GO:0044514 A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with the resultant positive regulation of G-protein coupled receptor activity in of the bitten organism. envenomation resulting in positive regulation of G-protein coupled receptor activity in other organism GO:0044515 A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with the resultant positive regulation of glucagon-like peptide receptor 1 activity in of the bitten organism. envenomation resulting in positive regulation of glucagon-like peptide receptor 1 activity in other organism GO:0044519 A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with the resultant modulation of the activity of a vasoactive intestinal polypeptide receptor in the bitten organism. envenomation resulting in modulation of vasoactive intestinal polypeptide receptor activity in other organism GO:0044520 A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with the resultant positive regulation of the activity of a vasoactive intestinal polypeptide receptor in the bitten organism. envenomation resulting in positive regulation of vasoactive intestinal polypeptide receptor activity in other organism GO:0044521 A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with resultant muscle damage in the bitten organism. envenomation resulting in muscle damage in other organism GO:0044522 A process that begins with venom being forced into an organism by the bite or sting of another organism, killing heart myocytes and ultimately resulting in muscle damage in the bitten organism. envenomation resulting in myocyte killing in other organism GO:0044523 A process that begins with venom being forced into an organism by the bite or sting of another organism, damaging the extracellular matrix of muscle cells and ultimately resulting in muscle necrosis in the bitten organism. envenomation resulting in damage of muscle extracellular matrix in other organism GO:0044534 A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with the resultant modulation of apoptosis in the bitten organism. envenomation resulting in modulation of apoptotic process in other organism GO:0044536 The process which begins with venom being forced into an organism by the bite or sting of another organism, and ends with a reduction in the quantity of fibrinogen found in the bloodstream of the bitten/stung organism. envenomation resulting in depletion of circulating fibrinogen in other organism GO:0044543 The process which begins with venom being forced into an organism by the bite or sting of another organism, and ends with the proteolytic processing of an inactive enzyme to an active form. envenomation resulting in zymogen activation in other organism GO:0044544 The process which begins with venom being forced into an organism by the bite or sting of another organism, and ends with the activation of plasminogen into plasmin in the bitten organism. This process includes cleavage at an internal Arg-Val site to form an N-terminal A-chain and C-terminal B-chain held together by a disulfide bond, and can include further proteolytic cleavage events to remove the preactivation peptide. envenomation resulting in plasminogen activation in other organism GO:0044551 A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with resultant vasodilation of blood vessels, usually causing a reduction in blood pressure, in the bitten/stung organism. envenomation resulting in vasodilation in other organism GO:0044556 A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with the negative regulation of the heart rate of the bitten/stung organism. envenomation resulting in negative regulation of heart rate of other organism GO:0044559 A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with a resultant change in the activity of a voltage-gated potassium channel in the bitten/stung organism. envenomation resulting in modulation of voltage-gated potassium channel activity in other organism GO:0044560 A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with a resultant change in the activity of an ion channel in the bitten organism. envenomation resulting in modulation of ion channel activity in other organism GO:0044562 A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with a resultant negative regulation of the activity of a voltage-gated potassium channel in the bitten/stung organism. envenomation resulting in negative regulation of voltage-gated potassium channel activity in other organism GO:0044563 A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with a resultant slowing of the activation kinetics of the activity of a voltage-gated potassium channel in the bitten/stung organism. envenomation resulting in slowing of activation kinetics of voltage-gated potassium channel in other organism GO:0044564 A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with a resultant blocking of a voltage-gated potassium channel, inhibiting the pore's activity, in the bitten/stung organism. envenomation resulting in occlusion of the pore of voltage-gated potassium channel in other organism GO:0044624 A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with the modulation of cell migration in the bitten organism. envenomation resulting in modulation of cell migration in other organism GO:0044625 A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with the negative regulation of cell migration in the bitten organism. envenomation resulting in negative regulation of cell migration in other organism GO:0044626 A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with the positive regulation of cell migration in the bitten organism. envenomation resulting in positive regulation of cell migration in other organism GO:0044636 A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with the regulation of complement activation via the classical pathway of the bitten/stung organism. envenomation resulting in modulation of complement activation, classical pathway in other organism GO:0044637 A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with the negative regulation of complement activation via the classical pathway of the bitten/stung organism. envenomation resulting in negative regulation of complement activation, classical pathway in other organism GO:0044638 A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with the positive regulation of complement activation via the classical pathway of the bitten/stung organism. envenomation resulting in positive regulation of complement activation, classical pathway in other organism GO:0044639 A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with the resultant modulation of complement activation via the lectin pathway in the bitten/stung organism. envenomation resulting in modulation of complement activation, lectin pathway in other organism GO:0044640 A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with the resultant negative regulation of complement activation via the lectin pathway in the bitten/stung organism. envenomation resulting in negative regulation of complement activation, lectin pathway in other organism GO:0044641 A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with the resultant positive regulation of complement activation via the lectin pathway in the bitten/stung organism. envenomation resulting in positive regulation of complement activation, lectin pathway in other organism GO:0044642 A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with the resultant modulation of complement activation via the alternative pathway in the bitten/stung organism. envenomation resulting in modulation of complement activation, alternative pathway in other organism GO:0044643 A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with the resultant positive regulation of complement activation via the alternative pathway in the bitten/stung organism. envenomation resulting in positive regulation of complement activation, alternative pathway in other organism GO:0044644 A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with the resultant negative regulation of complement activation via the alternative pathway in the bitten/stung organism. envenomation resulting in negative regulation of complement activation, alternative pathway in other organism GO:0044646 A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with the resultant modulation of complement activation in the bitten/stung organism. envenomation resulting in modulation of complement activation in other organism GO:0044649 A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with cytolysis in the bitten organism. envenomation resulting in cytolysis in other organism GO:0044705 The specific behavior of an organism that is associated with reproduction involving another organism of the same or different species. multi-organism reproductive behavior GO:0044733 A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with a resultant change in the activity of an acid-sensing ion channel (ASIC) in the bitten organism. envenomation resulting in modulation of acid-sensing ion channel activity in other organism GO:0044734 A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with a resultant positive regulation in the activity of an acid-sensing ion channel (ASIC) in the bitten organism. envenomation resulting in positive regulation of acid-sensing ion channel activity in other organism GO:0044735 A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with a resultant negative regulation in the activity of an acid-sensing ion channel (ASIC) in the bitten organism. envenomation resulting in negative regulation of acid-sensing ion channel activity in other organism GO:0044741 A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with the inhibition of the sensory perception of pain in the bitten organism. envenomation resulting in negative regulation of sensory perception of pain in other organism GO:0044742 A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with the modulation of the sensory perception of pain in the bitten organism. envenomation resulting in modulation of sensory perception of pain in other organism GO:0045297 The specific behavior of an organism following mating. post-mating behavior GO:0045433 The process during wing vibration where the male insect produces a species-specific acoustic signal called a love song. male courtship behavior, veined wing generated song production GO:0045434 Any process that stops, prevents or reduces the receptiveness of a female to male advances subsequent to mating. negative regulation of female receptivity, post-mating GO:0045475 The rhythm of the locomotor activity of an organism during its 24 hour activity cycle. locomotor rhythm GO:0045924 Any process that modulates the frequency, rate or extent of the willingness or readiness of a female to receive male advances. regulation of female receptivity GO:0045925 Any process that activates or increases the receptiveness of a female to male advances. positive regulation of female receptivity GO:0046008 Any process that modulates the receptiveness of a female to male advances subsequent to mating. regulation of female receptivity, post-mating GO:0046009 Any process that increases the receptiveness of a female to male advances subsequent to mating. positive regulation of female receptivity, post-mating GO:0046958 A simple form of learning whereby the repeated presence of a stimulus leads to a change in the probability or strength of the response to that stimulus. There is no association of one type of stimulus with another, rather it is a generalized response to the environment. nonassociative learning GO:0046959 A decrease in a behavioral response to a repeated stimulus. This is exemplified by the failure of a person to show a startle response to a loud noise that has been repeatedly presented. habituation GO:0046960 An increased in a behavioral response to a repeated stimulus. For example, a shock to the tail of the marine snail Aplysia, to which the snail responds by withdrawing its gill, will result in increased gill withdrawal the next time the skin is touched. sensitization GO:0048047 The behavior of individuals for the purpose of discriminating between the sexes, for the purpose of finding a suitable mating partner. mating behavior, sex discrimination GO:0048065 The process during courtship where the male insect extends his wings. An example of this process is found in Drosophila melanogaster. male courtship behavior, veined wing extension GO:0048148 Any process that results in a change in the behavior of an organism as a result of a cocaine stimulus. behavioral response to cocaine GO:0048149 Any process that results in a change in the behavior of an organism as a result of an ethanol stimulus. behavioral response to ethanol GO:0048150 Any process that results in a change in the behavior of an organism as a result of an ether stimulus. behavioral response to ether GO:0048266 Any process that results in a change in the behavior of an organism as a result of a pain stimulus. Pain stimuli cause activation of nociceptors, peripheral receptors for pain, include receptors which are sensitive to painful mechanical stimuli, extreme heat or cold, and chemical stimuli. behavioral response to pain GO:0048512 The specific behavior of an organism that recurs with a regularity of approximately 24 hours. circadian behavior GO:0050802 The part of the circadian sleep/wake cycle where the organism is asleep. circadian sleep/wake cycle, sleep GO:0051705 Any process in which an organism has a behavioral effect on another organism of the same or different species. multi-organism behavior GO:0051780 Any process that results in a change in the behavior of an organism as a result of a nutrient stimulus. behavioral response to nutrient GO:0051867 The set of behavioral processes that occur as part of the general adaptation syndrome, the response of the body to a strong, stressful stimulus. general adaptation syndrome, behavioral process GO:0060179 The specific behavior of a male organism that is associated with reproduction. male mating behavior GO:0060180 The specific behavior of a female organism that is associated with reproduction. female mating behavior GO:0060273 The behavior in which an organism sheds tears, often accompanied by non-verbal vocalizations and in response to external or internal stimuli. crying behavior GO:0060403 The deposition of eggs, either fertilized or not, upon a surface or into a medium, following mating. post-mating oviposition GO:0060746 A reproductive behavior in which a parent cares for and rears offspring. parental behavior GO:0060747 A parental behavior in which fertilized eggs are taken into the mouth and held until hatching. oral incubation GO:0060756 Behavior by which an organism locates food. foraging behavior GO:0060757 Behavior by which an adult locates food. adult foraging behavior GO:0060758 Foraging behavior in which an anatomical part of the organism is inserted into the substrate to locate food. foraging behavior by probing substrate GO:0061366 Any process that results in a change in the behaviour of an organism as a result of a chemical pain stimulus. behavioral response to chemical pain GO:0061367 Any process that results in a change in the behaviour of an organism as a result of an acetic acid pain stimulus. behavioral response to acetic acid induced pain GO:0061368 Any process that results in a change in the behaviour of an organism as a result of a formalin pain stimulus. behavioral response to formalin induced pain GO:0061743 Any process in which an organism acquires a novel neuromuscular action or movement as the result of experience. motor learning GO:0061744 The specific neuromuscular movement of a single organism in response to external or internal stimuli. motor behavior GO:0071625 The behavior in which an organism produces sounds by a mechanism involving its respiratory system. vocalization behavior GO:0071632 Eye, head or whole body movements that help to compensate movements of the environment in order to stabilize its image on the retina. In the case of whole body movements, these motor actions may also stabilize a locomotor course in response to some disturbance. Examples include: the optokinetic reflex, which allows human eyes to follow objects in motion while the head remains stationary reflex; the optomotor responses of flying insects and swimming fish. optomotor response GO:0072375 The memory process that deals with the storage, retrieval and modification of information received at a time ago that is intermediate between that of short and long term memory (30min - 7hrs in Drosophila melanogaster). medium-term memory GO:0090659 The behavior of an organism relating to the progression of that organism along the ground by the process of lifting and setting down each leg. walking behavior GO:0097270 The temporary recovery of response to a stimulus when a novel stimulus is added. dishabituation GO:0098582 A vocalisation behavior that is innate, i.e. that does not need to be learned in order to occur. innate vocalization behavior GO:0098583 A vocalization behavior that is the result of learning. learned vocalization behavior GO:0098596 Learning in which new behaviors are acquired through imitation. imitative learning GO:0098597 Learning that occurs through observing the behavior of others. observational learning GO:0098598 Vocalisation behavior that is the result of learning, or the process by which new vocalizations are learned. learned vocalization behavior or vocal learning GO:0099127 A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with the activation of the cytosolic argininosuccinate synthase in the bitten organism. envenomation resulting in positive regulation of argininosuccinate synthase activity in other organism GO:1990142 A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with hemolysis in the bitten organism. envenomation resulting in hemolysis in other organism GO:1990708 The associative learning process by which an animal learns and remembers an association between a neutral, unchanging environment and a putatively rewarding, internal state produced by a xenobiotic or drug. conditioned place preference IAO:0000027 data item data item IAO:0000030 information content entity information content entity IAO:0000078 curation status specification The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting) PERSON:Bill Bug GROUP:OBI:<http://purl.obolibrary.org/obo/obi> OBI_0000266 curation status specification IAO:0000102 data about an ontology part Data about an ontology part is a data item about a part of an ontology, for example a term data about an ontology part is a data item about a part of an ontology, for example a term Person:Alan Ruttenberg Person:Alan Ruttenberg data about an ontology part IAO:0000225 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 IAO:0000409 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. 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. A denotator type indicates how a term should be interpreted from an ontological perspective. Alan Ruttenberg Alan Ruttenberg Barry Smith, Werner Ceusters Barry Smith, Werner Ceusters denotator type denotator type IAO:8000000 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. 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 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. 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. cjm 2018-05-20T20:55:03Z ontology module ontology module IAO:8000001 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. An ontology module that comprises only of asserted axioms local to the ontology, excludes import directives, and excludes axioms or declarations from external ontologies. cjm 2018-05-20T20:55:30Z base ontology module base ontology module IAO:8000002 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. 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 source ontology module cjm 2018-05-20T20:55:47Z editors ontology module editors ontology module IAO:8000003 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. 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 TODO: Add logical axioms that state that a main release ontology module is derived from (directly or indirectly) an editors module cjm 2018-05-20T20:56:13Z main release ontology module main release ontology module IAO:8000004 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. An ontology module that consists entirely of axioms that connect or bridge two distinct ontology modules. For example, the Uberon-to-ZFA bridge module. cjm 2018-05-20T20:56:23Z bridge ontology module bridge ontology module IAO:8000005 import ontology module A subset ontology module that is intended to be imported from another ontology. 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. TODO: add axioms that indicate this is the output of a module extraction process. import file import file cjm 2018-05-20T20:56:47Z import ontology module import ontology module IAO:8000006 subset ontology module An ontology module that is extracted from a main ontology module and includes only a subset of entities or axioms. An ontology module that is extracted from a main ontology module and includes only a subset of entities or axioms. ontology slim ontology slim subset ontology subset ontology cjm 2018-05-20T20:58:11Z subset ontology module subset ontology module IAO:8000007 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. 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. cjm 2018-05-20T20:58:38Z curation subset ontology module curation subset ontology module IAO:8000008 analysis ontology module An ontology module that is intended for usage in analysis or discovery applications. An ontology module that is intended for usage in analysis or discovery applications. cjm 2018-05-20T20:58:49Z analysis subset ontology module analysis subset ontology module IAO:8000009 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. 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 ribbon subset cjm 2018-05-20T20:59:19Z single layer subset ontology module single layer subset ontology module IAO:8000010 exclusion subset ontology module A subset of an ontology that is intended to be excluded for some purpose. For example, a blacklist of classes. A subset of an ontology that is intended to be excluded for some purpose. For example, a blacklist of classes. antislim antislim cjm 2018-05-20T20:59:57Z exclusion subset ontology module exclusion subset ontology module IAO:8000011 external import ontology module An imported ontology module that is derived from an external ontology. Derivation methods include the OWLAPI SLME approach. An imported ontology module that is derived from an external ontology. Derivation methods include the OWLAPI SLME approach. external import external import cjm 2018-05-20T21:00:14Z external import ontology module external import ontology module IAO:8000012 species subset ontology module A subset ontology that is crafted to either include or exclude a taxonomic grouping of species. A subset ontology that is crafted to either include or exclude a taxonomic grouping of species. taxon subset taxon subset cjm 2018-05-20T21:14:16Z species subset ontology module species subset ontology module IAO:8000013 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. An ontology module that contains axioms generated by a reasoner. The generated axioms are typically direct SubClassOf axioms, but other possibilities are available. cjm 2018-05-20T21:20:33Z reasoned ontology module reasoned ontology module IAO:8000014 generated ontology module An ontology module that is automatically generated, for example via a SPARQL query or via template and a CSV. 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 TODO: Add axioms (using PROV-O?) that indicate this is the output-of some reasoning process cjm 2018-05-20T21:21:12Z generated ontology module generated ontology module IAO:8000015 template generated ontology module An ontology module that is automatically generated from a template specification and fillers for slots in that template. An ontology module that is automatically generated from a template specification and fillers for slots in that template. cjm 2018-05-20T21:21:21Z template generated ontology module template generated ontology module IAO:8000016 taxonomic bridge ontology module cjm 2018-05-20T21:28:15Z taxonomic bridge ontology module taxonomic bridge ontology module IAO:8000017 ontology module subsetted by expressivity cjm 2018-05-22T04:15:54Z ontology module subsetted by expressivity ontology module subsetted by expressivity IAO:8000018 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 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 cjm 2018-05-22T04:16:10Z obo basic subset ontology module obo basic subset ontology module IAO:8000019 ontology module subsetted by OWL profile cjm 2018-05-22T04:16:28Z ontology module subsetted by OWL profile ontology module subsetted by OWL profile IAO:8000020 EL++ ontology module cjm 2018-05-22T04:16:48Z EL++ ontology module EL++ ontology module MF:0000000 An anatomical structure in which there inheres the disposition to be the agent of a mental process. http://www.jbiomedsem.com/content/1/1/10 mental functioning related anatomical structure MF:0000001 disposition to be agent of mental process MF:0000002 (for the case of remembering X, where X is an event in the organism’s history) a mental process that is a) about X, and b) made possible by the physical traces left by a causal process involving the organism during the event X act of remembering remembering MF:0000003 State of active attention by high sensory awareness such as being watchful and prompt to meet danger or emergency, or being quick to perceive and act. http://en.wikipedia.org/wiki/Alertness state of alertness alertness MFOMD_0000176 MF:0000004 A cognitive process that involves the mental representation of sequential numbers. mental counting MF:0000005 A cognitive process that involves the manipulation of mental representations of numeric entities in order to compute the outcome of a mathematical function. mental calculation MF:0000006 A mental process during which information is evaluated, the outcome of which is a belief or opinion. act of judging judging MF:0000007 A judging process during which an opinion about the gender of a person is determined. A judging that involves forming an opinion about the gender of a person. determining gender MF:0000008 A mental process that creates, modifies or has as participant some cognitive representation. cognitive process GO:0050890, cognition, defined as `The operation of the mind by which an organism becomes aware of objects of thought or perception; it includes the mental activities associated with thinking, learning, and memory.' MF:0000009 A judging that involves the determination of the orientation of some object. determining orientation MF:0000010 mathematical problem solving behavior MF:0000011 visual problem solving behavior MF:0000012 A mental process that is the psychological and physiological state of being awake and reactive to stimuli. arousal MFOMD_0000146 MF:0000013 a mental process that involves the manipulation of mental language and/or mental images act of thinking thinking MF:0000014 language problem solving behavior MF:0000015 A mental process that manipulates mental images and words that go beyond mere memory and thoughts about the objects and entities that the person has encountered, to visualise or consider entities and states of affairs that the person has never encountered and which may not yet exist or obtain in the world. Imagination is the capacity to produce images, ideas and sensations in the mind without any immediate input of the senses. https://en.wikipedia.org/wiki/Imagination imagination MF:0000016 An extended organism that is a member of the species Homo sapiens. person human being MF:0000017 Consciousness is an inseparable part of all mental processes. It is that part of the mental process that: a) confers a subjective perspective, a phenomenology, an experience of the mental process of which it is a part; and b) intends the object or event that the mental process is about, should such exist; i.e., it confers intentionality on the mental process. Note that while there are different modes of consciousness corresponding to the different senses, the whole of conscious experience at any one time is largely experienced as a unity, that is, as a fused whole. Mental processes which are simultaneously ongoing are separable only in fiat, not in essence. consciousness MF:0000018 the process whereby relevant aspects of our mental experience are focused on specific targets attending MF:0000019 A mental process which is a) produced by a causal process involving a part of the environment of the organism, and b) is experienced by the organism as being so caused, and c) in which the relevant part of the environment is thereby represented to the organism. Examples for 'causal processes involving a part of the environment of an organism' that can be perceived are light rays and air vibrations. perception MF:0000020 A bodily process that occurs in the brain, and that can of itself be conscious, or can give rise to a process that can of itself be conscious or can give rise to behaviour. A 'mental process' is a subclass of 'bodily process', as mental processes occur within the body, specifically involving the brain. A bodily process which brings into being, sustains or modifies a cognitive representation or a behavior inducing state. Examples include thinking, feeling pain, remembering and emotion as occurrent experiences. Mental processes can varying in the degree to which they involve consciousness. mental process GO:0050890, cognition, defined as `The operation of the mind by which an organism becomes aware of objects of thought or perception; it includes the mental activities associated with thinking, learning, and memory.' 2 MF:0000021 A process in which at least two human beings are agents. http://www.jbiomedsem.com/content/1/1/10 interpersonal process MF:0000022 A personality trait manifesting itself in individual behavioral characteristics that are perceived as kind, sympathetic, cooperative, warm, and considerate. Development and Validation of International English Big-Five Mini-Markers. Edmund R. Thomspson. Personality and Individual Differences, Volume 45, Issue 6, October 2008. http://www.sciencedirect.com/science/article/pii/S0191886908002195 http://www.github.com/no/ontologies/2017/PAO/Agreeableness Associated adjectives: appreciative, forgiving, generous, kind, sympathetic, and trusting. agreeableness MF:0000023 Behavior having interpersonal processes as parts, each involving the same instances of human being. http://www.jbiomedsem.com/content/1/1/10 interpersonal behavior GO:0051705, multi-organism behaviour, defined as: "Any process in which an organism has a behavioral effect on another organism of the same or different species" (http://amigo.geneontology.org/cgi-bin/amigo/term_details?term=GO:0051705#lineage) MF:0000024 Seeing (visual perception) is a mental process that is a) produced by a causal process involving light rays from a part of the environment of the subject being absorbed by photoreceptors in the retina, and b) is experienced by the subject as being so caused, and c) in which the relevant part of the environment is thereby represented to the subject act of seeing visual perception seeing MF:0000025 A mental capability realised in processes involving understanding complex ideas, adapting effectively to the environment, learning from experience, engaging in various forms of reasoning, and overcome obstacles through the outcome of thinking processes. intelligence MF:0000026 introversion MF:0000027 A mental process that involves mentally manipulating representations of steps in an imagined process which has some goal. act of planning The outcome of this mental process is a plan which has the potential to be followed to bring about the desired outcome. planning MF:0000028 A personality trait manifesting itself in individual behavioral characteristics that are perceived as careful, self-disciplined, dependable, vigilant, dutiful, and goal-oriented. http://www.github.com/no/ontologies/2017/PAO/Conscientiousness Associated adjectives: efficient, organized, planful, reliable, responsible, and thorough. conscientiousness MF:0000029 A mental disposition to frequent or easily incited outbursts of anger. irascibility MF:0000030 A dependent continuant which is about a portion of reality. http://www.jbiomedsem.com/content/1/1/10 representation MF:0000031 A representation which specifically depends on an anatomical structure in the cognitive system of an organism. http://www.jbiomedsem.com/content/1/1/10 cognitive representation MF:0000032 A bodily disposition is a disposition that inheres in some extended organism. Examples are: my disposition to catch a cold when exposed to a virus, my ability to speak the English language. personal disposition Bodily disposition includes features that can be used in a specific context, such as a person's strength, but not a person's weight. A person has a specific weight independent of the circumstances they are in. Extended organism refers to an organism and its microbiome (e.g., the bacteria that live in one's digestive system). bodily disposition MF:0000033 A mental disposition is a bodily disposition that is realized in a mental process. 'Mental disposition' is a subclass of 'bodily disposition', as mental dispositions occur in the body. mental disposition MF:0000034 Visual consciousness is consciousness of a visual stimulus, as experienced through the visual sensory medium as a part of a process of seeing. visual consciousness MF:0000035 Auditory consciousness is consciousness of an auditory stimulus, as a part of a conscious process of hearing. auditory consciousness MF:0000036 Tactile consciousness is consciousness that is experienced in the tactile sensory medium, through the sensory medium of touch and pressure sensation. tactile consciousness MF:0000037 Direct consciousness is consciousness of phenomenal experience, it is the given experience in consciousness of (for example) sounds, tastes, emotions and bodily feelings. pre-reflexive consciousness direct consciousness MF:0000038 Hearing (auditory perception) is a mental process that is a) produced by a causal process involving sound waves from a part of the environment of the subject being absorbed by detectors in the ear, and b) is experienced by the subject as being so caused, and c) in which the relevant part of the environment is thereby represented to the subject act of hearing auditory perception hearing MF:0000039 A cognitive representation sustained by an organsim about its own emotions. http://www.jbiomedsem.com/content/1/1/10 affective representation MF:0000040 A communication process is an interpersonal process that involves the transmission of information between two organisms. communication http://purl.obolibrary.org/obo/OMRSE_00000192 MF:0000041 A mental disposition to represent a proposition to be true. Judging is a mental process that brings a belief into existence. Judging differently may also bring that belief out of existence. An act of believing is just thinking about a belief. Beliefs typically cause us to behave in ways that are characteristic with the content of that belief. However, this is not a necessary feature for the existence of the belief. belief MF:0000042 preference MF:0000043 A bodily disposition whose realization ordinarily brings benefits to an organism or group of organisms, where "ordinarily" means within a typical range or context. personal capability https://github.com/NCOR-US/Capabilities/wiki/The-Account-of-Capabilities Note that, as discussed in https://philpapers.org/archive/MERMC.pdf, both organisms and artifacts can bear capabilities. However, this capability class is just applicable to organismal capabilities (as a subclass of 'bodily disposition') and the definition has been amended from that of the definition source accordingly. The phrase 'ordinarily brings benefits to an organism or group of organism' is used to explain that capabilities normally provide a benefit. For exampoe, having a musical ability is usually an ability that is positive for a person (e.g., they enjoy playing music, they receive positive feedback about their ability). However, in certain exceptional cases (e.g., a neighbour becoming annoyed with a person playing the piano and expressing this annoyance), the ability might not bring benefits. capability MF:0000044 A capability that is realised in an activity of producing or interpreting music. musical capability MF:0000045 A mental process that involves thinking about a state of affairs that is not yet the case together with a desire for that state of affairs to come about. act of wanting wanting MF:0000046 A musical capability that is realised in the production of music using a piano. capability to play piano MF:0000047 A musical capability that is realised in the production of music using a violin. capability to play violin MF:0000048 A personal capability that includes mental processes in its realisation. mental capability MF:0000049 A linguistic capability that is realised by processes in which textual concretisations of linguistic expressions are processed and understood. capability to read MF:0000050 A mental capability that is realised in processes of communication involving language or in expressions of language. linguistic capability MF:0000051 A linguistic capability that is realised in processes in which well-formed expressions in a given language are understood. capability to understand language MF:0000052 A linguistic capability that is realised in processes in which well-formed vocal expressions in a given language are produced. capability to speak MF:0000053 A musical capability that is the ability to interpret the musical instructions represented in a musical score. capability to read music MF:0000054 Taste perception is a mental process which is a) produced by a causal process involving xenobiotic molecules from a part of the environment of the subject binding with specialized sensory cells in the tongue and nasal cavity, and b) is experienced by the subject as being so caused, and c) in which the relevant part of the environment is thereby represented to the subject act of tasting tasting MF:0000055 Smelling (olfactory perception) is a mental process which is a) produced by a causal process involving xenobiotic molecules from a part of the environment of the subject binding with specialized sensory cells in the nasal cavity, and b) is experienced by the subject as being so caused, and c) in which the relevant part of the environment is thereby represented to the subject act of smelling olfactory perception smelling MF:0000056 Touching (tactile perception) is a mental process which is a) produced by a causal process involving pressure on the organism’s skin from a part of the environment of the subject, and b) is experienced by the subject as being so caused, and c) in which the relevant part of the environment is thereby represented to the subject act of touching touching MF:0000057 A cognitive process that involves the manipulation of mental language. thinking with language MF:0000058 Affectional tie that one person or animal forms between himself and another specific one, a tie that binds them together emotionally and endures over time. attachment MFOMF_0000177 MF:0000059 Short-term detachment from one's immediate surroundings, during which a person's contact with reality is blurred and partially substituted by a visionary fantasy, especially one of happy, pleasant thoughts, hopes or ambitions, imagined as coming to pass, and experienced while awake. act of daydreaming http://en.wikipedia.org/wiki/Daydream daydreaming MFOMD_0000148 MF:0000060 The ability to maintain attention and alertness over prolonged periods of time. http://en.wikipedia.org/wiki/Vigilance_%28psychology%29 state of vigilance vigilance MFOMD_0000140 MF:0000061 Orgasm is the sudden discharge of accumulated sexual tension during the sexual response cycle, resulting in rhythmic muscular contractions in the pelvic region characterized by sexual pleasure. http://en.wikipedia.org/wiki/Orgasm sexual climax orgasm MFOMD_0000207 MF:0000062 The psychic energy that drives individuals toward sensual pleasures of all types, especially sexual ones. http://www.apa.org/research/action/glossary.aspx libido MFOMD_0000130 MF:0000063 A personality trait manifesting itself in individual behavioral characteristics that are perceived as positive, assertive, social, and outgoing. http://www.github.com/no/ontologies/2017/PAO/Extraversion Associated Adjectives: active, assertive, energetic, enthusiastic, outgoing, talkative. extraversion MF:0000064 A personality trait manifesting itself in individual behavioral characteristics that are perceived as angry, anxious, depressed, unstable, and vulnerable. http://www.github.com/no/ontologies/2017/PAO/Neuroticism Associated adjectives: anxious, self-pitying, tense, touchy unstable, and worrying. neuroticism MF:0000065 A personality trait manifesting itself in individual behavioral characteristics that are perceived as revealing, curiosity, an appreciation of novelty and variety of experiences and ideas, invention, and unpredictability. http://www.github.com/no/ontologies/2017/PAO/OpennessToExperience Associated adjectives: artistic, curious, imaginative, insightful, original, and wide interests. openness to experience MF:0000066 Olfactory consciousness is consciousness of an olfactory stimulus (scent), as experienced through the olfactory sensory medium as a part of a process of smelling. olfactory consciousness MF:0000067 Consciousness of self is the higher order consciousness that reflexively includes the awareness that the organism that is the subject of the conscious experience exists. consciousness of the existence of the self self-consciousness selfhood The implication of Descartes' famous "Cogito ergo sum" is that awareness of one's own existence entails that one exists. This is because consciousness creates a perspective, and awareness of this is a self-reflexive perspective of oneself. This is one aspect of intentionality that cannot fail. Intentionality can fail at all levels of content, but not at the level of intending through awareness the existence of the self that is consciously intending. consciousness of self MF:0000068 Proprioception is a mental process which is a) produced by a causal process specialized internal sensory cells in, for example, skin, muscles and joints, and b) by which their location and state of motion and/or balance are represented to the organism, and c) which is experienced by the subject as being so caused proprioception MF:0000069 Nociception is a mental process which is a) produced by a causal process specialized internal sensory cells in, for example, skin, muscles and joints, and b) by which actual or immanent tissue damage are reported to the organism, and c) which is experienced by the subject as being so caused nociception MF:0000070 A memory is a mental disposition that is realized in a process of remembering, i.e. a memory of X is a disposition realized in the process of remembering X. a memory MF:0000071 problem solving behaviour MF:0000072 The subjective experience of time as a coherent process inhabited by oneself as an embodied thinking being time awareness consciousness of time MF:0000073 Intentionality is the fundamental quality of conscious mental processes of always having content, of being directed towards, or about something. intentionality MF:0000074 A bodily quality is a quality that inheres in some extended organism. bodily quality MF:0000075 A mental quality is a bodily quality that inheres in those structures of the extended organism that are essential for mental functioning. mental quality MF:0000076 An example of an intentional modality is the capacity to represent objects of intentionality as unfolding in time or being time contingent. A structural capacity that shapes how an object of intentionality is represented for the subject. intentional mode intentional structure intentional modality MF:0000077 The subjective experience of the spatial surroundings one inhabits as an embodied entity. space awareness consciousness of space MF:0000078 The subjective experience of being an embodied entity. body awareness consciousness of the body MF:0000079 The subjective experience of other beings as self-aware entities. intersubjectivity MF:0000080 The intentional structural capacity to experience lived time. time intentional modality MF:0000081 The partial structure of time consciousness that relates to linking and projecting the content of immediate moments to future moments (e.g. how the path of a moving object is intuitively projected). protention MF:0000082 The partial structure of time consciousness that relates to retaining past events in memory and linking them to present events (e.g. how the individual tones in a melody is intuitively linked together to form a whole). retention MF:0000083 A mental process that evokes the representation of the sensory characteristics of objects or events when these are not immediately present to the senses. mental imagery MF:0000084 A spoken communication process is a linguistic communication process that: (a) involves as participant at least two linguistically capable organisms; (b) one of whom produces an utterance that is well-formed in a given spoken language; (c) the other of whom perceives and understands that utterance by virtue of their recognition of the meaning of the utterance through their knowledge of the language. spoken communication MF:0000085 A written communication process is an interpersonal process that: (a) involves as participant at least two organisms, (b) one of whom produces a message in writing that is well-formed in a given language; (c) the other of whom reads the message and understands it. written communication MF:0000086 A linguistic communication process is a communication process in which the information that is communicated is encoded in language. linguistic communication MF:0000087 A gestural communication process is a communication process in which information is transferred by means of physical movements. gestural communication MF:0000088 A mental process that involves neuronal activity in response to a sensory stimuli but which is not the subject of consciousness. subliminal process MF:0000089 A communication process in which information is transmitted without being encoded in the meaning units of any language. non-linguistic communication MF:0000090 A linguistic communication in which the meaning units are encoded in a sign language. sign-language communication MF:0000091 A non-linguistic communication process that involves the transmission of information by one participant interpreting the facial expressions of another participant. facial expression communication MF:0000101 Higher order consciousness is consciousness of one's own mental states, a self-reflexive consciousness of the experience of being conscious, of having mental processes ongoing. higher order consciousness MF:0000202 A personality is a complex sum of dispositions and predispositions towards mental processes and behaviour. It inheres in a person. Personality is not the same as mood, although a person may have a personality that includes a predisposition to moods of certain types, moods may come and go but a personality stays relatively constant, not appearing and disappearing. Personality typically changes slowly over time. personality MF:0000203 A personality trait is an individual disposition or predisposition that forms part of an overall personality and is realized in repeated occurrences of a specific mental process type or behavioural profile. personality trait NBO:0000159 rapid eye movement sleep NBO:0000161 "Behavior related to all sleep stages in the circadian sleep/wake cycle other than REM sleep." [NBO:GVG] non-rapid eye movement sleep behavior NBO:0000166 "Endogenously driven roughly 24-hour cycle in biochemical, physiological, or behavioral processes." [GOC:bf] circadian rhythm NBO:0000167 circadian period NBO:0000168 circadian persistence NBO:0000169 circadian phase NBO:0000536 "Any process in which an organism modulates its heart rate at different values with a regularity of approximately 24 hours." [GOC:rl] circadian regulation of heart rate NBO:0000537 "Any process in which an organism modulates its blood pressure at different values with a regularity of approximately 24 hours." [GO:GO\:0003052] circadian regulation of systemic arterial blood pressure NBO:0000538 "Any homeostatic process in which an organism modulates its internal body temperature at different values with a regularity of approximately 24 hours." [GOC:dbh] circadian temperature homeostasis NBO:0000634 irritable aggressive behavior NBO:0020040 Active pursuit of fleeing prey. chase prey NBO:0020045 Behaviors in which predator forces potential prey to emerge from cover. flush prey NBO:0020137 Building of a trap, web, net, or other structure to help ensnare potential food items. construct capturing device NBO:0020160 Approach to prey in manner designed to avoid early detection by prey. stalk prey NBO:0020292 Suite of behaviors involved in securing a prey item once it has been located. capturing behaviour NBO:0020293 Behaviors that result in ending flight of prey with successful predation. capturing prey OGMS:0000060 A process in which at least one bodily component of an organsim participates. http://www.jbiomedsem.com/content/1/1/10 From OGMS: http://purl.obolibrary.org/obo/OGMS_0000060 bodily process OGMS:0000087 From OGMS: http://purl.obolibrary.org/obo/OGMS_0000087 extended organism oboInOwl:DbXref oboInOwl:Definition oboInOwl:Subset oboInOwl:Synonym oboInOwl:SynonymType owl:Thing example to be eventually removed example to be eventually removed 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 Person:Alan Ruttenberg failed exploratory term 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 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 Core is an instance of a grouping of terms from an ontology or ontologies. It is used by the ontology to identify main classes. PERSON: Alan Ruttenberg PERSON: Melanie Courtot core obsolete_core true 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 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. 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 Alan Ruttenberg A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf universal universal 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 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. "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 Alan Ruttenberg defined class 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. 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 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 Alan Ruttenberg named class expression named class expression 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 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. https://github.com/information-artifact-ontology/ontology-metadata/issues/77 https://orcid.org/0000-0001-5208-3432 out of scope 2022-07-19 BFO_0000054 BFO_0000054s BFO_0000054ed realized in BFO_0000055 BFO_0000055s BFO_0000055ed realizes BFO_0000107 BFO_0000107s BFO_0000107ed disposition of at all times BFO_0000112 BFO_0000112s BFO_0000112ed has disposition at some time BFO_0000117 BFO_0000117s BFO_0000117ed has occurrent part BFO_0000167 BFO_0000167s BFO_0000167ed has participant at all times BFO_0000176 BFO_0000176s BFO_0000176ed part of continuant at some time Alison Wright Barry Smith Janna Hastings Jeanette Alicia Chacón Candia Mark Jensen Neil Otte Paulina Schenk https://creativecommons.org/licenses/by/3.0/ Mental Functioning Ontology The Mental Functioning Ontology (MF) was first described in the publication available at http://www.jbiomedsem.com/content/1/1/10 entitled 'Foundations for a realist ontology of mental disease' (Barry Smith and Werner Ceusters). The Mental Functioning Ontology is an overarching ontology for all aspects of mental functioning, founded on the Basic Formal Ontology (BFO) and related to the Ontology for General Medical Science (OGMS). The OWL representaions of MF and MD were split on 22 May 2012. The release version of the MF is now a single, merged file prepared from the source module files using the ROBOT library's merge function. This OWL version of the MF ontology was originally created by Janna Hastings and is maintained by all committers to the MF ontology project. 2022-07-19