format-version: 1.2 data-version: 2021-08-19 remark: The Ontology for General Medical Science (OGMS) is based on the papers Toward an Ontological Treatment of Disease and Diagnosis and On Carcinomas and Other Pathological Entities. The ontology attempts to address some of the issues raised at the Workshop on Ontology of Diseases (Dallas, TX). OGMS was formerly called the clinical phenotype ontology. Terms from OGMS hang from the Basic Formal Ontology.\n\nThe latest version of OGMS is available at http://purl.obolibrary.org/obo/ogms.owl\n\nThe OGMS developer site is https://github.com/OGMS/ogms\n\nIf you are interested in participating in the development of OGMS, please send email to baeverma ontology: ogms property_value: http://purl.org/dc/elements/1.1/creator "Alan Ruttenberg" xsd:string property_value: http://purl.org/dc/elements/1.1/creator "Albert Goldfain" xsd:string property_value: http://purl.org/dc/elements/1.1/creator "Anand Kumar" xsd:string property_value: http://purl.org/dc/elements/1.1/creator "Barry Smith" xsd:string property_value: http://purl.org/dc/elements/1.1/creator "Bill Hogan" xsd:string property_value: http://purl.org/dc/elements/1.1/creator "Brian Aevermann" xsd:string property_value: http://purl.org/dc/elements/1.1/creator "Cornelius Rosse" xsd:string property_value: http://purl.org/dc/elements/1.1/creator "Daniel Merico" xsd:string property_value: http://purl.org/dc/elements/1.1/creator "Jie Zheng" xsd:string property_value: http://purl.org/dc/elements/1.1/creator "Lindsay Cowell" xsd:string property_value: http://purl.org/dc/elements/1.1/creator "Richard Scheuermann" xsd:string property_value: http://purl.org/dc/elements/1.1/creator "Sivaram Arabandi" xsd:string property_value: http://purl.org/dc/elements/1.1/creator "Werner Ceusters" xsd:string property_value: http://purl.org/dc/elements/1.1/date "2009-08-07" xsd:string property_value: http://purl.org/dc/elements/1.1/description "The Ontology for General Medical Science (OGMS) is an ontology of entities involved in a clinical encounter. OGMS includes very general terms that are used across medical disciplines, including: 'disease', 'disorder', 'disease course', 'diagnosis', 'patient', and 'healthcare provider'. OGMS uses the Basic Formal Ontology (BFO) as an upper-level ontology. The scope of OGMS is restricted to humans, but many terms can be applied to a variety of organisms. OGMS provides a formal theory of disease that can be further elaborated by specific disease ontologies. This theory is implemented using OWL-DL and OBO Relation Ontology relations and is available in OWL and OBO formats.\n\nOGMS is based on the papers Toward an Ontological Treatment of Disease and Diagnosis and On Carcinomas and Other Pathological Entities. The ontology attempts to address some of the issues raised at the Workshop on Ontology of Diseases (Dallas, TX) and the Signs, Symptoms, and Findings Workshop(Milan, Italy). OGMS was formerly called the clinical phenotype ontology. Terms from OGMS hang from the Basic Formal Ontology." xsd:string property_value: http://purl.org/dc/elements/1.1/title "Ontology for General Medical Science" xsd:string property_value: http://purl.org/dc/terms/license http://creativecommons.org/licenses/by/4.0/ xsd:string property_value: owl:versionInfo "2021-08-19" xsd:string owl-axioms: Prefix(owl:=)\nPrefix(rdf:=)\nPrefix(xml:=)\nPrefix(xsd:=)\nPrefix(rdfs:=)\n\n\nOntology(\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(NamedIndividual())\nDeclaration(NamedIndividual())\nDeclaration(NamedIndividual())\nDeclaration(NamedIndividual())\nDeclaration(NamedIndividual())\nDeclaration(NamedIndividual())\nDeclaration(NamedIndividual())\nDeclaration(NamedIndividual())\nDeclaration(NamedIndividual())\nDeclaration(NamedIndividual())\nDeclaration(NamedIndividual())\nDeclaration(NamedIndividual())\nDeclaration(NamedIndividual())\nDeclaration(NamedIndividual())\nDeclaration(NamedIndividual())\nDeclaration(NamedIndividual())\nDeclaration(NamedIndividual())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\n############################\n# Annotation Properties\n############################\n\n# Annotation Property: (BFO OWL specification label)\n\nSubAnnotationPropertyOf( rdfs:label)\n\n# Annotation Property: (BFO CLIF specification label)\n\nSubAnnotationPropertyOf( rdfs:label)\n\n# Annotation Property: (scheduled for obsoletion on or after)\n\nAnnotationPropertyRange( xsd:dateTime)\n\n\n############################\n# Classes\n############################\n\n# Class: (entity)\n\nSubClassOf( owl:Thing)\n\n# Class: (curation status specification)\n\nEquivalentClasses( ObjectOneOf( ))\n\n# Class: (obsolescence reason specification)\n\nEquivalentClasses( ObjectOneOf( ))\n\n# Class: (denotator type)\n\nEquivalentClasses( ObjectOneOf( ))\n\n# Class: (obsolete_sign)\n\nSubClassOf( owl:Thing)\n\n\n############################\n# Named Individuals\n############################\n\n# Individual: (metadata complete)\n\n\n# Individual: (organizational term)\n\n\n# Individual: (ready for release)\n\n\n# Individual: (metadata incomplete)\n\n\n# Individual: (uncurated)\n\n\n# Individual: (pending final vetting)\n\n\n# Individual: (placeholder removed)\n\n\n# Individual: (terms merged)\n\n\n# Individual: (term imported)\n\n\n# Individual: (term split)\n\n\n# Individual: (to be replaced with external ontology term)\n\n\n# Individual: (requires discussion)\n\n\n\nDifferentIndividuals( )\nDifferentIndividuals( )\n) [Term] id: BFO:0000001 name: entity property_value: BFO:0000179 "entity" xsd:string property_value: BFO:0000180 "Entity" xsd:string property_value: IAO:0000112 "Julius Caesar" xsd:string property_value: IAO:0000112 "the Second World War" xsd:string property_value: IAO:0000112 "Verdi’s Requiem" xsd:string property_value: IAO:0000112 "your body mass index" xsd:string property_value: IAO:0000116 "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" xsd:string property_value: IAO:0000116 "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" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000004", comment="per discussion with Barry Smith", http://www.w3.org/2000/01/rdf-schema#seeAlso="http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf"} property_value: IAO:0000600 "An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/001-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000002 name: continuant is_a: BFO:0000001 ! entity disjoint_from: BFO:0000003 ! occurrent property_value: BFO:0000179 "continuant" xsd:string property_value: BFO:0000180 "Continuant" xsd:string property_value: IAO:0000116 "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" xsd:string property_value: IAO:0000116 "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" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000007"} property_value: IAO:0000600 "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])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/008-002"} property_value: IAO:0000601 "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])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/126-001"} property_value: IAO:0000601 "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])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/009-002"} property_value: IAO:0000601 "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])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/011-002"} property_value: IAO:0000602 "(forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/009-002"} property_value: IAO:0000602 "(forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/126-001"} property_value: IAO:0000602 "(forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/008-002"} property_value: IAO:0000602 "(forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/011-002"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000003 name: occurrent is_a: BFO:0000001 ! entity property_value: BFO:0000179 "occurrent" xsd:string property_value: BFO:0000180 "Occurrent" xsd:string property_value: IAO:0000116 "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" xsd:string property_value: IAO:0000116 "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." xsd:string property_value: IAO:0000116 "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." xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000006", comment="per discussion with Barry Smith"} property_value: IAO:0000116 "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." xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000012"} property_value: IAO:0000600 "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])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/077-002"} property_value: IAO:0000601 "b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/079-001"} property_value: IAO:0000601 "Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/108-001"} property_value: IAO:0000602 "(forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/108-001"} property_value: IAO:0000602 "(forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/079-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000004 name: independent continuant def: "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])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/017-002"} is_a: BFO:0000002 ! continuant disjoint_from: BFO:0000020 ! specifically dependent continuant disjoint_from: BFO:0000031 ! generically dependent continuant property_value: BFO:0000179 "ic" xsd:string property_value: BFO:0000180 "IndependentContinuant" xsd:string property_value: IAO:0000112 "a chair" xsd:string property_value: IAO:0000112 "a heart" xsd:string property_value: IAO:0000112 "a leg" xsd:string property_value: IAO:0000112 "a molecule" xsd:string property_value: IAO:0000112 "a spatial region" xsd:string property_value: IAO:0000112 "an atom" xsd:string property_value: IAO:0000112 "an orchestra." xsd:string property_value: IAO:0000112 "an organism" xsd:string property_value: IAO:0000112 "the bottom right portion of a human torso" xsd:string property_value: IAO:0000112 "the interior of your mouth" xsd:string property_value: IAO:0000601 "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])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/134-001"} property_value: IAO:0000601 "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])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/018-002"} property_value: IAO:0000602 "(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] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/018-002"} property_value: IAO:0000602 "(forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/134-001"} property_value: IAO:0000602 "(iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/017-002"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000006 name: spatial region is_a: BFO:0000141 ! immaterial entity disjoint_from: BFO:0000029 ! site disjoint_from: BFO:0000140 ! continuant fiat boundary property_value: BFO:0000179 "s-region" xsd:string property_value: BFO:0000180 "SpatialRegion" xsd:string property_value: IAO:0000116 "BFO 2 Reference: Spatial regions do not participate in processes." xsd:string property_value: IAO:0000116 "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." xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000002", comment="per discussion with Barry Smith"} property_value: IAO:0000600 "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])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/035-001"} property_value: IAO:0000601 "All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/036-001"} property_value: IAO:0000602 "(forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/036-001"} property_value: IAO:0000602 "(forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/035-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000008 name: temporal region is_a: BFO:0000003 ! occurrent disjoint_from: BFO:0000011 ! spatiotemporal region disjoint_from: BFO:0000015 ! process disjoint_from: BFO:0000035 ! process boundary property_value: BFO:0000179 "t-region" xsd:string property_value: BFO:0000180 "TemporalRegion" xsd:string property_value: IAO:0000116 "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" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000003", comment="per discussion with Barry Smith"} property_value: IAO:0000600 "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])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/100-001"} property_value: IAO:0000601 "All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/101-001"} property_value: IAO:0000601 "Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/119-002"} property_value: IAO:0000602 "(forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/119-002"} property_value: IAO:0000602 "(forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/101-001"} property_value: IAO:0000602 "(forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/100-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000009 name: two-dimensional spatial region is_a: BFO:0000006 ! spatial region disjoint_from: BFO:0000028 ! three-dimensional spatial region property_value: BFO:0000179 "2d-s-region" xsd:string property_value: BFO:0000180 "TwoDimensionalSpatialRegion" xsd:string property_value: IAO:0000112 "an infinitely thin plane in space." xsd:string property_value: IAO:0000112 "the surface of a sphere-shaped part of space" xsd:string property_value: IAO:0000600 "A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/039-001"} property_value: IAO:0000602 "(forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/039-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000011 name: spatiotemporal region is_a: BFO:0000003 ! occurrent property_value: BFO:0000179 "st-region" xsd:string property_value: BFO:0000180 "SpatiotemporalRegion" xsd:string property_value: IAO:0000112 "the spatiotemporal region occupied by a human life" xsd:string property_value: IAO:0000112 "the spatiotemporal region occupied by a process of cellular meiosis." xsd:string property_value: IAO:0000112 "the spatiotemporal region occupied by the development of a cancer tumor" xsd:string property_value: IAO:0000600 "A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/095-001"} property_value: IAO:0000601 "All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/096-001"} property_value: IAO:0000601 "Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/099-001"} property_value: IAO:0000601 "Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/098-001"} property_value: IAO:0000601 "Every spatiotemporal region occupies_spatiotemporal_region itself." xsd:string property_value: IAO:0000601 "Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/107-002"} property_value: IAO:0000602 "(forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/107-002"} property_value: IAO:0000602 "(forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/099-001"} property_value: IAO:0000602 "(forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/096-001"} property_value: IAO:0000602 "(forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/098-001"} property_value: IAO:0000602 "(forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/095-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000015 name: process def: "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])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/083-003"} is_a: BFO:0000003 ! occurrent property_value: BFO:0000179 "process" xsd:string property_value: BFO:0000180 "Process" xsd:string property_value: IAO:0000112 "a process of cell-division, \\ a beating of the heart" xsd:string property_value: IAO:0000112 "a process of meiosis" xsd:string property_value: IAO:0000112 "a process of sleeping" xsd:string property_value: IAO:0000112 "the course of a disease" xsd:string property_value: IAO:0000112 "the flight of a bird" xsd:string property_value: IAO:0000112 "the life of an organism" xsd:string property_value: IAO:0000112 "your process of aging." xsd:string property_value: IAO:0000116 "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)" xsd:string property_value: IAO:0000602 "(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] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/083-003"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000016 name: disposition is_a: BFO:0000017 ! realizable entity disjoint_from: BFO:0000023 ! role property_value: BFO:0000179 "disposition" xsd:string property_value: BFO:0000180 "Disposition" xsd:string property_value: IAO:0000112 "an atom of element X has the disposition to decay to an atom of element Y" xsd:string property_value: IAO:0000112 "certain people have a predisposition to colon cancer" xsd:string property_value: IAO:0000112 "children are innately disposed to categorize objects in certain ways." xsd:string property_value: IAO:0000112 "the cell wall is disposed to filter chemicals in endocytosis and exocytosis" xsd:string property_value: IAO:0000116 "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." xsd:string property_value: IAO:0000600 "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])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/062-002"} property_value: IAO:0000601 "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])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/063-002"} property_value: IAO:0000602 "(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] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/063-002"} property_value: IAO:0000602 "(forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/062-002"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000017 name: realizable entity is_a: BFO:0000020 ! specifically dependent continuant disjoint_from: BFO:0000019 ! quality property_value: BFO:0000179 "realizable" xsd:string property_value: BFO:0000180 "RealizableEntity" xsd:string property_value: IAO:0000112 "the disposition of this piece of metal to conduct electricity." xsd:string property_value: IAO:0000112 "the disposition of your blood to coagulate" xsd:string property_value: IAO:0000112 "the function of your reproductive organs" xsd:string property_value: IAO:0000112 "the role of being a doctor" xsd:string property_value: IAO:0000112 "the role of this boundary to delineate where Utah and Colorado meet" xsd:string property_value: IAO:0000600 "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])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/058-002"} property_value: IAO:0000601 "All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/060-002"} property_value: IAO:0000602 "(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] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/060-002"} property_value: IAO:0000602 "(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] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/058-002"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000018 name: zero-dimensional spatial region is_a: BFO:0000006 ! spatial region disjoint_from: BFO:0000028 ! three-dimensional spatial region property_value: BFO:0000179 "0d-s-region" xsd:string property_value: BFO:0000180 "ZeroDimensionalSpatialRegion" xsd:string property_value: IAO:0000600 "A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/037-001"} property_value: IAO:0000602 "(forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/037-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000019 name: quality is_a: BFO:0000020 ! specifically dependent continuant property_value: BFO:0000179 "quality" xsd:string property_value: BFO:0000180 "Quality" xsd:string property_value: IAO:0000112 "the ambient temperature of this portion of air" xsd:string property_value: IAO:0000112 "the color of a tomato" xsd:string property_value: IAO:0000112 "the length of the circumference of your waist" xsd:string property_value: IAO:0000112 "the mass of this piece of gold." xsd:string property_value: IAO:0000112 "the shape of your nose" xsd:string property_value: IAO:0000112 "the shape of your nostril" xsd:string property_value: IAO:0000600 "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])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/055-001"} property_value: IAO:0000601 "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])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/105-001"} property_value: IAO:0000602 "(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] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/105-001"} property_value: IAO:0000602 "(forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/055-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000020 name: specifically dependent continuant def: "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])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/050-003"} is_a: BFO:0000002 ! continuant disjoint_from: BFO:0000031 ! generically dependent continuant property_value: BFO:0000179 "sdc" xsd:string property_value: BFO:0000180 "SpecificallyDependentContinuant" xsd:string property_value: IAO:0000112 "of one-sided specifically dependent continuants: the mass of this tomato" xsd:string property_value: IAO:0000112 "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." xsd:string property_value: IAO:0000112 "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" xsd:string property_value: IAO:0000112 "the disposition of this fish to decay" xsd:string property_value: IAO:0000112 "the function of this heart: to pump blood" xsd:string property_value: IAO:0000112 "the mutual dependence of proton donors and acceptors in chemical reactions [79" xsd:string property_value: IAO:0000112 "the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction" xsd:string property_value: IAO:0000112 "the pink color of a medium rare piece of grilled filet mignon at its center" xsd:string property_value: IAO:0000112 "the role of being a doctor" xsd:string property_value: IAO:0000112 "the shape of this hole." xsd:string property_value: IAO:0000112 "the smell of this portion of mozzarella" xsd:string property_value: IAO:0000116 "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." xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000005", comment="per discussion with Barry Smith"} property_value: IAO:0000602 "(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] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/050-003"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000023 name: role is_a: BFO:0000017 ! realizable entity property_value: BFO:0000179 "role" xsd:string property_value: BFO:0000180 "Role" xsd:string property_value: IAO:0000112 "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." xsd:string property_value: IAO:0000112 "the priest role" xsd:string property_value: IAO:0000112 "the role of a boundary to demarcate two neighboring administrative territories" xsd:string property_value: IAO:0000112 "the role of a building in serving as a military target" xsd:string property_value: IAO:0000112 "the role of a stone in marking a property boundary" xsd:string property_value: IAO:0000112 "the role of subject in a clinical trial" xsd:string property_value: IAO:0000112 "the student role" xsd:string property_value: IAO:0000116 "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." xsd:string property_value: IAO:0000600 "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])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/061-001"} property_value: IAO:0000602 "(forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/061-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000024 name: fiat object part is_a: BFO:0000040 ! material entity property_value: BFO:0000179 "fiat-object-part" xsd:string property_value: BFO:0000180 "FiatObjectPart" xsd:string property_value: IAO:0000112 "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" xsd:string property_value: IAO:0000112 "the division of the brain into regions" xsd:string property_value: IAO:0000112 "the division of the planet into hemispheres" xsd:string property_value: IAO:0000112 "the dorsal and ventral surfaces of the body" xsd:string property_value: IAO:0000112 "the FMA:regional parts of an intact human body." xsd:string property_value: IAO:0000112 "the upper and lower lobes of the left lung" xsd:string property_value: IAO:0000112 "the Western hemisphere of the Earth" xsd:string property_value: IAO:0000116 "BFO 2 Reference: Most examples of fiat object parts are associated with theoretically drawn divisions" xsd:string property_value: IAO:0000600 "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])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/027-004"} property_value: IAO:0000602 "(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] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/027-004"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000026 name: one-dimensional spatial region is_a: BFO:0000006 ! spatial region disjoint_from: BFO:0000028 ! three-dimensional spatial region property_value: BFO:0000179 "1d-s-region" xsd:string property_value: BFO:0000180 "OneDimensionalSpatialRegion" xsd:string property_value: IAO:0000112 "an edge of a cube-shaped portion of space." xsd:string property_value: IAO:0000600 "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])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/038-001"} property_value: IAO:0000602 "(forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/038-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000027 name: object aggregate is_a: BFO:0000040 ! material entity property_value: BFO:0000179 "object-aggregate" xsd:string property_value: BFO:0000180 "ObjectAggregate" xsd:string property_value: IAO:0000112 "a collection of cells in a blood biobank." xsd:string property_value: IAO:0000112 "a swarm of bees is an aggregate of members who are linked together through natural bonds" xsd:string property_value: IAO:0000112 "a symphony orchestra" xsd:string property_value: IAO:0000112 "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)" xsd:string property_value: IAO:0000112 "defined by fiat: the aggregate of members of an organization" xsd:string property_value: IAO:0000112 "defined through physical attachment: the aggregate of atoms in a lump of granite" xsd:string property_value: IAO:0000112 "defined through physical containment: the aggregate of molecules of carbon dioxide in a sealed container" xsd:string property_value: IAO:0000112 "defined via attributive delimitations such as: the patients in this hospital" xsd:string property_value: IAO:0000112 "the aggregate of bearings in a constant velocity axle joint" xsd:string property_value: IAO:0000112 "the aggregate of blood cells in your body" xsd:string property_value: IAO:0000112 "the nitrogen atoms in the atmosphere" xsd:string property_value: IAO:0000112 "the restaurants in Palo Alto" xsd:string property_value: IAO:0000112 "your collection of Meissen ceramic plates." xsd:string property_value: IAO:0000116 "An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000301"} property_value: IAO:0000116 "An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000011"} property_value: IAO:0000116 "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)." xsd:string property_value: IAO:0000119 "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." xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000300"} property_value: IAO:0000600 "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])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/025-004"} property_value: IAO:0000602 "(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] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/025-004"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000028 name: three-dimensional spatial region is_a: BFO:0000006 ! spatial region property_value: BFO:0000179 "3d-s-region" xsd:string property_value: BFO:0000180 "ThreeDimensionalSpatialRegion" xsd:string property_value: IAO:0000112 "a cube-shaped region of space" xsd:string property_value: IAO:0000112 "a sphere-shaped region of space," xsd:string property_value: IAO:0000600 "A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/040-001"} property_value: IAO:0000602 "(forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/040-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000029 name: site is_a: BFO:0000141 ! immaterial entity property_value: BFO:0000179 "site" xsd:string property_value: BFO:0000180 "Site" xsd:string property_value: IAO:0000112 "a hole in the interior of a portion of cheese" xsd:string property_value: IAO:0000112 "a rabbit hole" xsd:string property_value: IAO:0000112 "an air traffic control region defined in the airspace above an airport" xsd:string property_value: IAO:0000112 "Manhattan Canyon)" xsd:string property_value: IAO:0000112 "the cockpit of an aircraft" xsd:string property_value: IAO:0000112 "the Grand Canyon" xsd:string property_value: IAO:0000112 "the hold of a ship" xsd:string property_value: IAO:0000112 "the interior of a kangaroo pouch" xsd:string property_value: IAO:0000112 "the interior of the trunk of your car" xsd:string property_value: IAO:0000112 "the interior of your bedroom" xsd:string property_value: IAO:0000112 "the interior of your office" xsd:string property_value: IAO:0000112 "the interior of your refrigerator" xsd:string property_value: IAO:0000112 "the lumen of your gut" xsd:string property_value: IAO:0000112 "the Piazza San Marco" xsd:string property_value: IAO:0000112 "your left nostril (a fiat part – the opening – of your left nasal cavity)" xsd:string property_value: IAO:0000600 "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])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/034-002"} property_value: IAO:0000602 "(forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/034-002"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000030 name: object is_a: BFO:0000040 ! material entity property_value: BFO:0000179 "object" xsd:string property_value: BFO:0000180 "Object" xsd:string property_value: IAO:0000112 "atom" xsd:string property_value: IAO:0000112 "cell" xsd:string property_value: IAO:0000112 "cells and organisms" xsd:string property_value: IAO:0000112 "engineered artifacts" xsd:string property_value: IAO:0000112 "grain of sand" xsd:string property_value: IAO:0000112 "molecule" xsd:string property_value: IAO:0000112 "organelle" xsd:string property_value: IAO:0000112 "organism" xsd:string property_value: IAO:0000112 "planet" xsd:string property_value: IAO:0000112 "solid portions of matter" xsd:string property_value: IAO:0000112 "star" xsd:string property_value: IAO:0000116 "BFO 2 Reference: an object is a maximal causally unified material entity" xsd:string property_value: IAO:0000116 "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." xsd:string property_value: IAO:0000116 "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)." xsd:string property_value: IAO:0000116 "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" xsd:string property_value: IAO:0000116 "BFO 2 Reference: ‘objects’ are sometimes referred to as ‘grains’ [74" xsd:string property_value: IAO:0000600 "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])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/024-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000031 name: generically dependent continuant def: "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])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/074-001"} is_a: BFO:0000002 ! continuant property_value: BFO:0000179 "gdc" xsd:string property_value: BFO:0000180 "GenericallyDependentContinuant" xsd:string property_value: IAO:0000112 "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." xsd:string property_value: IAO:0000112 "the pdf file on your laptop, the pdf file that is a copy thereof on my laptop" xsd:string property_value: IAO:0000112 "the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule." xsd:string property_value: IAO:0000602 "(iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/074-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000034 name: function is_a: BFO:0000016 ! disposition property_value: BFO:0000179 "function" xsd:string property_value: BFO:0000180 "Function" xsd:string property_value: IAO:0000112 "the function of a hammer to drive in nails" xsd:string property_value: IAO:0000112 "the function of a heart pacemaker to regulate the beating of a heart through electricity" xsd:string property_value: IAO:0000112 "the function of amylase in saliva to break down starch into sugar" xsd:string property_value: IAO:0000116 "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." xsd:string property_value: IAO:0000600 "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])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/064-001"} property_value: IAO:0000602 "(forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/064-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000035 name: process boundary def: "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])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/084-001"} is_a: BFO:0000003 ! occurrent property_value: BFO:0000179 "p-boundary" xsd:string property_value: BFO:0000180 "ProcessBoundary" xsd:string property_value: IAO:0000112 "the boundary between the 2nd and 3rd year of your life." xsd:string property_value: IAO:0000601 "Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/085-002"} property_value: IAO:0000602 "(forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/085-002"} property_value: IAO:0000602 "(iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/084-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000038 name: one-dimensional temporal region is_a: BFO:0000008 ! temporal region disjoint_from: BFO:0000148 ! zero-dimensional temporal region property_value: BFO:0000179 "1d-t-region" xsd:string property_value: BFO:0000180 "OneDimensionalTemporalRegion" xsd:string property_value: IAO:0000112 "the temporal region during which a process occurs." xsd:string property_value: IAO:0000116 "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)." xsd:string property_value: IAO:0000600 "A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/103-001"} property_value: IAO:0000602 "(forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/103-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000040 name: material entity is_a: BFO:0000004 ! independent continuant disjoint_from: BFO:0000141 ! immaterial entity property_value: BFO:0000179 "material" xsd:string property_value: BFO:0000180 "MaterialEntity" xsd:string property_value: IAO:0000112 "a flame" xsd:string property_value: IAO:0000112 "a forest fire" xsd:string property_value: IAO:0000112 "a human being" xsd:string property_value: IAO:0000112 "a hurricane" xsd:string property_value: IAO:0000112 "a photon" xsd:string property_value: IAO:0000112 "a puff of smoke" xsd:string property_value: IAO:0000112 "a sea wave" xsd:string property_value: IAO:0000112 "a tornado" xsd:string property_value: IAO:0000112 "an aggregate of human beings." xsd:string property_value: IAO:0000112 "an energy wave" xsd:string property_value: IAO:0000112 "an epidemic" xsd:string property_value: IAO:0000112 "the undetached arm of a human being" xsd:string property_value: IAO:0000116 "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" xsd:string property_value: IAO:0000116 "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." xsd:string property_value: IAO:0000116 "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." xsd:string property_value: IAO:0000600 "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])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/019-002"} property_value: IAO:0000601 "every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/021-002"} property_value: IAO:0000601 "Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/020-002"} property_value: IAO:0000602 "(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] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/021-002"} property_value: IAO:0000602 "(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] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/020-002"} property_value: IAO:0000602 "(forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/019-002"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000140 name: continuant fiat boundary def: "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])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/029-001"} is_a: BFO:0000141 ! immaterial entity property_value: BFO:0000179 "cf-boundary" xsd:string property_value: BFO:0000180 "ContinuantFiatBoundary" xsd:string property_value: IAO:0000116 "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" xsd:string property_value: IAO:0000116 "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." xsd:string property_value: IAO:0000116 "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." xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000008"} property_value: IAO:0000601 "Every continuant fiat boundary is located at some spatial region at every time at which it exists" xsd:string property_value: IAO:0000602 "(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] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/029-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000141 name: immaterial entity is_a: BFO:0000004 ! independent continuant property_value: BFO:0000179 "immaterial" xsd:string property_value: BFO:0000180 "ImmaterialEntity" xsd:string property_value: IAO:0000116 "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" xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000142 name: one-dimensional continuant fiat boundary is_a: BFO:0000140 ! continuant fiat boundary disjoint_from: BFO:0000146 ! two-dimensional continuant fiat boundary disjoint_from: BFO:0000147 ! zero-dimensional continuant fiat boundary property_value: BFO:0000179 "1d-cf-boundary" xsd:string property_value: BFO:0000180 "OneDimensionalContinuantFiatBoundary" xsd:string property_value: IAO:0000112 "all geopolitical boundaries" xsd:string property_value: IAO:0000112 "all lines of latitude and longitude" xsd:string property_value: IAO:0000112 "The Equator" xsd:string property_value: IAO:0000112 "the line separating the outer surface of the mucosa of the lower lip from the outer surface of the skin of the chin." xsd:string property_value: IAO:0000112 "the median sulcus of your tongue" xsd:string property_value: IAO:0000600 "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])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/032-001"} property_value: IAO:0000602 "(iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/032-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000144 name: process profile def: "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])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/093-002"} is_a: BFO:0000015 ! process disjoint_from: BFO:0000182 ! history property_value: BFO:0000179 "process-profile" xsd:string property_value: BFO:0000180 "ProcessProfile" xsd:string property_value: IAO:0000112 "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" xsd:string property_value: IAO:0000112 "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." xsd:string property_value: IAO:0000112 "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." xsd:string property_value: IAO:0000600 "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])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/094-005"} property_value: IAO:0000602 "(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] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/094-005"} property_value: IAO:0000602 "(iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/093-002"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000145 name: relational quality def: "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])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/057-001"} is_a: BFO:0000019 ! quality property_value: BFO:0000179 "r-quality" xsd:string property_value: BFO:0000180 "RelationalQuality" xsd:string property_value: IAO:0000112 "a marriage bond, an instance of requited love, an obligation between one person and another." xsd:string property_value: IAO:0000112 "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." xsd:string property_value: IAO:0000602 "(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] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/057-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000146 name: two-dimensional continuant fiat boundary is_a: BFO:0000140 ! continuant fiat boundary property_value: BFO:0000179 "2d-cf-boundary" xsd:string property_value: BFO:0000180 "TwoDimensionalContinuantFiatBoundary" xsd:string property_value: IAO:0000600 "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])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/033-001"} property_value: IAO:0000602 "(iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/033-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000147 name: zero-dimensional continuant fiat boundary is_a: BFO:0000140 ! continuant fiat boundary property_value: BFO:0000179 "0d-cf-boundary" xsd:string property_value: BFO:0000180 "ZeroDimensionalContinuantFiatBoundary" xsd:string property_value: IAO:0000112 "the geographic North Pole" xsd:string property_value: IAO:0000112 "the point of origin of some spatial coordinate system." xsd:string property_value: IAO:0000112 "the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet" xsd:string property_value: IAO:0000116 "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." xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000001", comment="requested by Melanie Courtot", http://www.w3.org/2000/01/rdf-schema#seeAlso="ZDRnpiIi:TUJ"} property_value: IAO:0000600 "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])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/031-001"} property_value: IAO:0000602 "(iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/031-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000148 name: zero-dimensional temporal region is_a: BFO:0000008 ! temporal region property_value: BFO:0000179 "0d-t-region" xsd:string property_value: BFO:0000180 "ZeroDimensionalTemporalRegion" xsd:string property_value: IAO:0000112 "a temporal region that is occupied by a process boundary" xsd:string property_value: IAO:0000112 "right now" xsd:string property_value: IAO:0000112 "the moment at which a child is born" xsd:string property_value: IAO:0000112 "the moment at which a finger is detached in an industrial accident" xsd:string property_value: IAO:0000112 "the moment of death." xsd:string property_value: IAO:0000118 "temporal instant." xsd:string property_value: IAO:0000600 "A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/102-001"} property_value: IAO:0000602 "(forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/102-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000182 name: history is_a: BFO:0000015 ! process property_value: BFO:0000179 "history" xsd:string property_value: BFO:0000180 "History" xsd:string property_value: IAO:0000600 "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])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/138-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: IAO:0000027 name: data item def: "An information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements." [] is_a: IAO:0000030 ! information content entity property_value: IAO:0000111 "data item" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/iao.owl [Term] id: IAO:0000030 name: information content entity def: "A generically dependent continuant that is about some thing." [] is_a: BFO:0000031 ! generically dependent continuant property_value: IAO:0000111 "information content entity" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/iao.owl [Term] id: IAO:0000033 name: directive information entity def: "An information content entity whose concretizations indicate to their bearer how to realize them in a process." [] is_a: IAO:0000030 ! information content entity property_value: IAO:0000412 http://purl.obolibrary.org/obo/iao.owl [Term] id: IAO:0000078 name: curation status specification def: "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." [] is_a: IAO:0000102 ! data about an ontology part property_value: IAO:0000111 "curation status specification" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)" xsd:string property_value: IAO:0000117 "PERSON:Bill Bug" xsd:string property_value: IAO:0000119 GROUP:OBI: xsd:string property_value: IAO:0000119 "OBI_0000266" xsd:string [Term] id: IAO:0000102 name: data about an ontology part def: "Data about an ontology part is a data item about a part of an ontology, for example a term" [] is_a: IAO:0000027 ! data item property_value: IAO:0000111 "data about an ontology part" xsd:string property_value: IAO:0000117 "Person:Alan Ruttenberg" xsd:string [Term] id: IAO:0000225 name: obsolescence reason specification def: "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." [] is_a: IAO:0000102 ! data about an ontology part property_value: IAO:0000111 "obsolescence reason specification" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology." xsd:string property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string property_value: IAO:0000117 "PERSON: Melanie Courtot" xsd:string [Term] id: IAO:0000409 name: denotator type def: "A denotator type indicates how a term should be interpreted from an ontological perspective." [] is_a: IAO:0000102 ! data about an ontology part property_value: IAO:0000111 "denotator type" xsd:string property_value: IAO:0000112 "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." xsd:string property_value: IAO:0000117 "Alan Ruttenberg" xsd:string property_value: IAO:0000119 "Barry Smith, Werner Ceusters" xsd:string [Term] id: IAO:8000000 name: ontology module is_a: IAO:0000102 ! data about an ontology part property_value: IAO:0000111 "ontology module" xsd:string property_value: IAO:0000116 "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." xsd:string property_value: IAO:0000118 "ontology file" xsd:string property_value: IAO:0000232 "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." xsd:string [Term] id: IAO:8000001 name: base ontology module def: "An ontology module that comprises only of asserted axioms local to the ontology, excludes import directives, and excludes axioms or declarations from external ontologies." [] is_a: IAO:8000000 ! ontology module property_value: IAO:0000111 "base ontology module" xsd:string property_value: seeAlso https://github.com/INCATools/ontology-starter-kit/issues/50 [Term] id: IAO:8000002 name: editors ontology module def: "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." [] is_a: IAO:8000000 ! ontology module property_value: IAO:0000111 "editors ontology module" xsd:string property_value: IAO:0000118 "source ontology module" xsd:string [Term] id: IAO:8000003 name: main release ontology module def: "An ontology module that is intended to be the primary release product and the one consumed by the majority of tools." [] is_a: IAO:8000000 ! ontology module property_value: IAO:0000111 "main release ontology module" xsd:string property_value: IAO:0000116 "TODO: Add logical axioms that state that a main release ontology module is derived from (directly or indirectly) an editors module" xsd:string [Term] id: IAO:8000004 name: bridge ontology module def: "An ontology module that consists entirely of axioms that connect or bridge two distinct ontology modules. For example, the Uberon-to-ZFA bridge module." [] is_a: IAO:8000000 ! ontology module property_value: IAO:0000111 "bridge ontology module" xsd:string property_value: seeAlso https://github.com/obophenotype/uberon/wiki/inter-anatomy-ontology-bridge-ontologies [Term] id: IAO:8000005 name: import ontology module def: "A subset ontology module that is intended to be imported from another ontology." [] is_a: IAO:8000006 ! subset ontology module property_value: IAO:0000111 "import ontology module" xsd:string property_value: IAO:0000116 "TODO: add axioms that indicate this is the output of a module extraction process." xsd:string property_value: IAO:0000118 "import file" xsd:string property_value: seeAlso http://robot.obolibrary.org/extract [Term] id: IAO:8000006 name: subset ontology module def: "An ontology module that is extracted from a main ontology module and includes only a subset of entities or axioms." [] is_a: IAO:8000000 ! ontology module property_value: IAO:0000111 "subset ontology module" xsd:string property_value: IAO:0000118 "ontology slim" xsd:string property_value: IAO:0000118 "subset ontology" xsd:string property_value: seeAlso http://robot.obolibrary.org/filter property_value: seeAlso http://www.geneontology.org/page/go-slim-and-subset-guide [Term] id: IAO:8000007 name: curation subset ontology module def: "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." [] is_a: IAO:8000006 ! subset ontology module property_value: IAO:0000111 "curation subset ontology module" xsd:string [Term] id: IAO:8000008 name: analysis subset ontology module def: "An ontology module that is intended for usage in analysis or discovery applications." [] is_a: IAO:8000006 ! subset ontology module property_value: IAO:0000111 "analysis ontology module" xsd:string [Term] id: IAO:8000009 name: single layer subset ontology module def: "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." [] is_a: IAO:8000006 ! subset ontology module property_value: IAO:0000111 "single layer ontology module" xsd:string property_value: IAO:0000118 "ribbon subset" xsd:string [Term] id: IAO:8000010 name: exclusion subset ontology module def: "A subset of an ontology that is intended to be excluded for some purpose. For example, a blacklist of classes." [] is_a: IAO:8000006 ! subset ontology module property_value: IAO:0000111 "exclusion subset ontology module" xsd:string property_value: IAO:0000118 "antislim" xsd:string [Term] id: IAO:8000011 name: external import ontology module def: "An imported ontology module that is derived from an external ontology. Derivation methods include the OWLAPI SLME approach." [] is_a: IAO:8000005 ! import ontology module property_value: IAO:0000111 "external import ontology module" xsd:string property_value: IAO:0000118 "external import" xsd:string [Term] id: IAO:8000012 name: species subset ontology module def: "A subset ontology that is crafted to either include or exclude a taxonomic grouping of species." [] is_a: IAO:8000006 ! subset ontology module property_value: IAO:0000111 "species subset ontology module" xsd:string property_value: IAO:0000118 "taxon subset" xsd:string property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Taxon-constraints [Term] id: IAO:8000013 name: reasoned ontology module def: "An ontology module that contains axioms generated by a reasoner. The generated axioms are typically direct SubClassOf axioms, but other possibilities are available." [] is_a: IAO:8000000 ! ontology module property_value: IAO:0000111 "reasoned ontology module" xsd:string property_value: seeAlso http://robot.obolibrary.org/reason [Term] id: IAO:8000014 name: generated ontology module def: "An ontology module that is automatically generated, for example via a SPARQL query or via template and a CSV." [] is_a: IAO:8000000 ! ontology module property_value: IAO:0000111 "generated ontology module" xsd:string property_value: IAO:0000116 "TODO: Add axioms (using PROV-O?) that indicate this is the output-of some reasoning process" xsd:string [Term] id: IAO:8000015 name: template generated ontology module def: "An ontology module that is automatically generated from a template specification and fillers for slots in that template." [] is_a: IAO:8000014 ! generated ontology module property_value: IAO:0000111 "template generated ontology module" xsd:string property_value: seeAlso http://robot.obolibrary.org/template property_value: seeAlso https://doi.org/10.1186/s13326-017-0126-0 property_value: seeAlso https://github.com/dosumis/dead_simple_owl_design_patterns/ [Term] id: IAO:8000016 name: taxonomic bridge ontology module is_a: IAO:8000004 ! bridge ontology module property_value: IAO:0000111 "taxonomic bridge ontology module" xsd:string [Term] id: IAO:8000017 name: ontology module subsetted by expressivity is_a: IAO:8000006 ! subset ontology module property_value: IAO:0000111 "ontology module subsetted by expressivity" xsd:string [Term] id: IAO:8000018 name: obo basic subset ontology module def: "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.\n\nExamples 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).\n\nAn ontology is OBO Basic if and only if it has the following characteristics:\nDAG\nUnidirectional\nNo Dangling Clauses\nFully Asserted\nFully Labeled\nNo equivalence axioms\nSingly labeled edges\nNo qualifier lists\nNo disjointness axioms\nNo owl-axioms header\nNo imports" [] is_a: IAO:8000017 ! ontology module subsetted by expressivity property_value: IAO:0000111 "obo basic subset ontology module" xsd:string property_value: seeAlso "6.2" [Term] id: IAO:8000019 name: ontology module subsetted by OWL profile is_a: IAO:8000017 ! ontology module subsetted by expressivity property_value: IAO:0000111 "ontology module subsetted by OWL profile" xsd:string [Term] id: IAO:8000020 name: EL++ ontology module is_a: IAO:8000019 ! ontology module subsetted by OWL profile property_value: IAO:0000111 "EL++ ontology module" xsd:string [Term] id: IDO:0000504 name: infectious disorder def: "An infection that is clinically abnormal." [] is_a: OGMS:0000045 ! disorder property_value: IAO:0000412 http://purl.obolibrary.org/obo/ido.owl [Term] id: IDO:0000586 name: infection def: "A part of an extended organism that itself has as part a population of one or more infectious agents and that (1) exists as a result of processes initiated by members of the infectious agent population and is (2) clinically abnormal in virtue of the presence of this infectious agent population, or (3) has a disposition to bring clinical abnormality to immunocompetent organisms of the same Species as the host (the organism corresponding to the extended organism) through transmission of a member or offspring of a member of the infectious agent population." [] is_a: BFO:0000040 ! material entity property_value: IAO:0000412 http://purl.obolibrary.org/obo/ido.owl [Term] id: IDO:0000630 name: hospital-acquired infection def: "An infection resulting from a transmission process that unfolds in a hospital." [] is_a: IDO:0000586 ! infection property_value: IAO:0000412 http://purl.obolibrary.org/obo/ido.owl [Term] id: OBI:0000011 name: planned process def: "A process that realizes a plan which is the concretization of a plan specification." [] is_a: BFO:0000015 ! process property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl [Term] id: OBI:0000278 name: disease stage def: "a part of an occurrence of a disease process which is associated with position in the normal progression of the disease" [] is_a: BFO:0000015 ! process property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl [Term] id: OGMS:0000014 name: clinical finding def: "A representation that is either the output of a clinical history taking or a physical examination or an image finding, or some combination thereof." [] is_a: OGMS:0000123 ! clinical data item property_value: IAO:0000117 "Albert Goldfain" xsd:string property_value: IAO:0000119 http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf xsd:string property_value: IAO:0000232 "creation date: 2010-07-19T10:18:02Z" xsd:string [Term] id: OGMS:0000015 name: clinical history def: "A series of statements representing health-relevant qualities of a patient and of a patient's family." [] is_a: OGMS:0000123 ! clinical data item property_value: IAO:0000117 "Albert Goldfain" xsd:string property_value: IAO:0000119 http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf xsd:string property_value: IAO:0000232 "creation date: 2010-07-19T10:18:59Z" xsd:string [Term] id: OGMS:0000016 name: clinical picture def: "A representation of clinically significant bodily components, dispositions, and/or bodily processes of a human being that is inferred from relevant clinical findings." [] is_a: OGMS:0000123 ! clinical data item property_value: IAO:0000117 "Albert Goldfain" xsd:string property_value: IAO:0000119 http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf xsd:string property_value: IAO:0000232 "creation date: 2010-07-19T10:20:20Z" xsd:string [Term] id: OGMS:0000017 name: image finding def: "A representation of an image that supports an inference to an assertion about some quality of a patient." [] is_a: OGMS:0000014 ! clinical finding property_value: IAO:0000117 "Albert Goldfain" xsd:string property_value: IAO:0000119 http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf xsd:string property_value: IAO:0000232 "creation date: 2009-06-23T10:21:10Z" xsd:string [Term] id: OGMS:0000018 name: laboratory finding def: "A representation of a quality of a specimen that is the output of a laboratory test and that can support an inference to an assertion about some quality of the patient." [] is_a: OGMS:0000014 ! clinical finding property_value: IAO:0000117 "Albert Goldfain" xsd:string property_value: IAO:0000119 http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf xsd:string property_value: IAO:0000232 "creation date: 2009-06-23T10:21:58Z" xsd:string [Term] id: OGMS:0000019 name: preclinical finding def: "A representation of a quality of a patient that is (1) recorded by a clinician because the quality is hypothesized to be of clinical significance and (2) refers to qualities obtaining in the patient prior to their becoming detectable in a clinical history taking or physical examination." [] is_a: IAO:0000027 ! data item property_value: IAO:0000117 "Albert Goldfain" xsd:string property_value: IAO:0000119 http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf xsd:string property_value: IAO:0000232 "creation date: 2009-06-23T10:22:44Z" xsd:string [Term] id: OGMS:0000020 name: symptom def: "A process experienced by the patient, which can only be experienced by the patient, that is hypothesized to be clinically relevant." [] is_a: BFO:0000015 ! process property_value: IAO:0000116 "note: defined class" xsd:string property_value: IAO:0000119 http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf xsd:string property_value: IAO:0000232 "creation date: 2010-11-18T11:02:10Z\nUpdated: 2020-07-06" xsd:string [Term] id: OGMS:0000022 name: manifestation of a disease def: "A quality of a patient that is (a) a deviation from clinical normality that exists in virtue of the realization of a disease and (b) is observable." [] is_a: BFO:0000019 ! quality property_value: IAO:0000117 "Albert Goldfain" xsd:string property_value: IAO:0000119 http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf xsd:string property_value: IAO:0000232 "creation date: 2009-06-23T11:12:33Z" xsd:string [Term] id: OGMS:0000023 name: phenotype def: "A (combination of) quality(ies) of an organism determined by the interaction of its genetic make-up and environment that differentiates specific instances of a species from other instances of the same species." [] is_a: BFO:0000019 ! quality property_value: IAO:0000117 "Albert Goldfain" xsd:string property_value: IAO:0000119 http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf xsd:string property_value: IAO:0000232 "creation date: 2010-07-19T11:13:49Z" xsd:string [Term] id: OGMS:0000024 name: obsolete_sign comment: The class sign has been replaced by three seperate classes which reflect the different types of signs possible. is_obsolete: true [Term] id: OGMS:0000025 name: clinical manifestation of a disease def: "A manifestation of a disease that is detectable in a clinical history taking or physical examination." [] is_a: OGMS:0000022 ! manifestation of a disease property_value: IAO:0000117 "Albert Goldfain" xsd:string property_value: IAO:0000119 http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf xsd:string property_value: IAO:0000232 "creation date: 2009-06-23T11:15:43Z" xsd:string [Term] id: OGMS:0000026 name: preclinical manifestation of a disease def: "A manifestation of a disease that exists prior to the time at which it would be detected in a clinical history taking or physical examination, if the patient were to present to a clinician. A realization of a disease that exists prior to its becoming detectable in a clinical history taking or physical examination." [] is_a: OGMS:0000022 ! manifestation of a disease property_value: IAO:0000117 "Albert Goldfain" xsd:string property_value: IAO:0000119 http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf xsd:string property_value: IAO:0000232 "creation date: 2009-06-23T11:16:50Z" xsd:string [Term] id: OGMS:0000027 name: clinical phenotype def: "A clinically abnormal phenotype." [] is_a: OGMS:0000023 ! phenotype property_value: IAO:0000117 "Albert Goldfain" xsd:string property_value: IAO:0000119 http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf xsd:string property_value: IAO:0000232 "creation date: 2009-06-23T11:18:05Z" xsd:string [Term] id: OGMS:0000028 name: disease phenotype def: "A clinically abnormal phenotype that is characteristic of a single disease." [] is_a: OGMS:0000023 ! phenotype property_value: IAO:0000117 "Albert Goldfain" xsd:string property_value: IAO:0000119 http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf xsd:string property_value: IAO:0000232 "creation date: 2009-06-23T11:18:39Z" xsd:string [Term] id: OGMS:0000029 name: vital sign def: "A physical sign in which a non-zero value is standardly considered to be an indication that the organism is alive." [] is_a: OGMS:0000129 ! physical sign property_value: IAO:0000117 "Albert Goldfain" xsd:string property_value: IAO:0000119 http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf xsd:string property_value: IAO:0000232 "creation date: 2009-06-23T11:19:17Z" xsd:string [Term] id: OGMS:0000030 name: predisposition to disease of type X def: "A disposition in an organism that constitutes an increased risk of the organism's subsequently developing the disease X." [] is_a: BFO:0000016 ! disposition property_value: IAO:0000117 "Albert Goldfain" xsd:string property_value: IAO:0000119 http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf xsd:string property_value: IAO:0000232 "creation date: 2009-06-23T11:20:25Z" xsd:string [Term] id: OGMS:0000031 name: disease def: "A disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism." [] is_a: BFO:0000016 ! disposition property_value: IAO:0000117 "Albert Goldfain" xsd:string property_value: IAO:0000119 http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf xsd:string property_value: IAO:0000232 "creation date: 2009-06-23T11:21:20Z" xsd:string [Term] id: OGMS:0000032 name: homeostasis is_a: BFO:0000016 ! disposition property_value: IAO:0000117 "Albert Goldfain" xsd:string property_value: IAO:0000232 "creation date: 2009-06-23T11:22:01Z" xsd:string [Term] id: OGMS:0000033 name: genetic predisposition to disease of type X def: "A predisposition to disease of type X whose physical basis is a constitutional abnormality in an organism's genome. This abnormality is the physical basis for the increased risk of acquiring the disease X." [] is_a: OGMS:0000030 ! predisposition to disease of type X property_value: IAO:0000117 "Albert Goldfain" xsd:string property_value: IAO:0000119 http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf xsd:string property_value: IAO:0000232 "creation date: 2009-06-23T11:23:07Z" xsd:string [Term] id: OGMS:0000034 name: acquired genetic disease def: "A disease whose physical basis is an acquired genetic disorder." [] is_a: OGMS:0000031 ! disease property_value: IAO:0000117 "Albert Goldfain" xsd:string property_value: IAO:0000119 http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf xsd:string property_value: IAO:0000232 "creation date: 2009-06-23T11:24:05Z" xsd:string [Term] id: OGMS:0000035 name: constitutional genetic disease def: "A disease whose physical basis is a constitutional genetic disorder." [] is_a: OGMS:0000031 ! disease property_value: IAO:0000117 "Albert Goldfain" xsd:string property_value: IAO:0000119 http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf xsd:string property_value: IAO:0000232 "creation date: 2009-06-23T11:24:59Z" xsd:string [Term] id: OGMS:0000037 name: abnormal homeostasis def: "Homeostasis that is clinically abnormal for an organism of a given type and age in a given environment." [] is_a: OGMS:0000032 ! homeostasis property_value: IAO:0000117 "Albert Goldfain" xsd:string property_value: IAO:0000119 http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf xsd:string property_value: IAO:0000232 "creation date: 2009-06-23T11:26:44Z" xsd:string [Term] id: OGMS:0000038 name: normal homeostasis def: "Homeostasis of a type that is not clinically abnormal." [] is_a: OGMS:0000032 ! homeostasis property_value: IAO:0000117 "Albert Goldfain" xsd:string property_value: IAO:0000119 http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf xsd:string property_value: IAO:0000232 "creation date: 2009-06-23T11:27:28Z" xsd:string [Term] id: OGMS:0000039 name: configuration def: "A quality which is an spatial arrangement or distribution of a(n) independent continuant(s) across a Three Dimensional Region." [] is_a: BFO:0000019 ! quality property_value: IAO:0000117 "Albert Goldfain" xsd:string property_value: IAO:0000119 http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf xsd:string property_value: IAO:0000232 "creation date: 2009-06-23T11:36:24Z" xsd:string [Term] id: OGMS:0000040 name: pathological physical configuration def: "A configuration which deviates in some way from a canonical configuration for a particular organism." [] is_a: OGMS:0000039 ! configuration property_value: IAO:0000117 "Albert Goldfain" xsd:string property_value: IAO:0000119 http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf xsd:string property_value: IAO:0000232 "creation date: 2009-06-23T11:36:58Z" xsd:string [Term] id: OGMS:0000045 name: disorder def: "A material entity which is clinically abnormal and part of an extended organism. Disorders are the physical basis of disease." [] is_a: BFO:0000040 ! material entity property_value: IAO:0000117 "Albert Goldfain" xsd:string property_value: IAO:0000119 http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf xsd:string property_value: IAO:0000232 "creation date: 2009-06-23T11:39:44Z" xsd:string [Term] id: OGMS:0000046 name: epigenetic disorder def: "A disorder whose etiology involves (1) a modification to the patient's genomic DNA which leads to alterations in the normal expression pattern of the genome, but is (2) not a change in the nucleotide sequence." [] is_a: OGMS:0000045 ! disorder property_value: IAO:0000117 "Albert Goldfain" xsd:string property_value: IAO:0000119 http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf xsd:string property_value: IAO:0000232 "creation date: 2009-06-23T11:40:27Z" xsd:string [Term] id: OGMS:0000047 name: genetic disorder def: "A disorder whose etiology involves an abnormality in the nucleotide sequence of an organism's genome." [] is_a: OGMS:0000045 ! disorder property_value: IAO:0000117 "Albert Goldfain" xsd:string property_value: IAO:0000119 http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf xsd:string property_value: IAO:0000232 "creation date: 2009-06-23T11:41:14Z" xsd:string [Term] id: OGMS:0000050 name: acquired genetic disorder def: "A genetic disorder acquired by a single cell in an organism that leads to a population of cells within the organism bearing the disorder." [] is_a: OGMS:0000047 ! genetic disorder property_value: IAO:0000117 "Albert Goldfain" xsd:string property_value: IAO:0000119 http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf xsd:string property_value: IAO:0000232 "creation date: 2009-06-23T11:43:09Z" xsd:string [Term] id: OGMS:0000051 name: constitutional genetic disorder def: "A genetic disorder inherited during conception that is part of all cells in the organism." [] is_a: OGMS:0000047 ! genetic disorder property_value: IAO:0000117 "Albert Goldfain" xsd:string property_value: IAO:0000119 http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf xsd:string property_value: IAO:0000232 "creation date: 2009-06-23T11:43:44Z" xsd:string [Term] id: OGMS:0000055 name: clinical history taking def: "A health care process in which a clinician elicits a description of previous sign and symptoms of disease from a patient or from a third party who is reporting on behalf of the patient." [] is_a: OGMS:0000108 ! health care process assay property_value: IAO:0000117 "Albert Goldfain" xsd:string property_value: IAO:0000119 http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf xsd:string property_value: IAO:0000232 "creation date: 2009-06-23T11:49:16Z" xsd:string [Term] id: OGMS:0000056 name: clinical laboratory test def: "A measurement assay that has as input a patient-derived specimen and as output a data item that is about a quality of the specimen." [] is_a: OGMS:0000108 ! health care process assay property_value: IAO:0000117 "Albert Goldfain" xsd:string property_value: IAO:0000119 http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf xsd:string property_value: IAO:0000232 "creation date: 2009-06-23T11:49:49Z" xsd:string [Term] id: OGMS:0000057 name: physical examination def: "A sequence of acts of observing and measuring qualities of a patient performed by a clinician; measurements may occur with and without elicitation." [] is_a: OGMS:0000108 ! health care process assay property_value: IAO:0000117 "Albert Goldfain" xsd:string property_value: IAO:0000119 http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf xsd:string property_value: IAO:0000232 "creation date: 2010-07-19T11:50:18Z" xsd:string [Term] id: OGMS:0000059 name: etiological process def: "A process in an organism that leads to a subsequent disorder." [] is_a: BFO:0000015 ! process property_value: IAO:0000117 "Albert Goldfain" xsd:string property_value: IAO:0000119 http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf xsd:string property_value: IAO:0000232 "creation date: 2009-06-23T11:53:07Z" xsd:string [Term] id: OGMS:0000060 name: bodily process is_a: BFO:0000015 ! process property_value: IAO:0000117 "Albert Goldfain" xsd:string property_value: IAO:0000232 "creation date: 2009-06-23T11:53:49Z" xsd:string [Term] id: OGMS:0000061 name: pathological bodily process def: "A bodily process that is clinically abnormal." [] is_a: OGMS:0000060 ! bodily process property_value: IAO:0000117 "Albert Goldfain" xsd:string property_value: IAO:0000119 http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf xsd:string property_value: IAO:0000232 "creation date: 2009-06-23T11:54:29Z" xsd:string [Term] id: OGMS:0000063 name: disease course def: "The totality of all processes through which a given disease instance is realized." [] is_a: BFO:0000015 ! process property_value: IAO:0000117 "Albert Goldfain" xsd:string property_value: IAO:0000119 http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf xsd:string property_value: IAO:0000232 "creation date: 2009-06-23T11:55:44Z" xsd:string [Term] id: OGMS:0000064 name: chronic disease course def: "A disease course that (a) does not terminate in a return to normal homeostasis and (b) would, absent intervention, fall within abnormal homeostatic range." [] is_a: OGMS:0000063 ! disease course property_value: IAO:0000117 "Albert Goldfain" xsd:string property_value: IAO:0000119 http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf xsd:string property_value: IAO:0000232 "creation date: 2009-06-23T11:56:26Z\n\n10212020\n\nfor definition use: \nhttp://purl.obolibrary.org/obo/PATO_0001863" xsd:string [Term] id: OGMS:0000065 name: progressive disease course def: "A disease course that (a) does not terminate in a return to normal homeostasis and (b) would, absent intervention, involve an increasing deviation from homeostasis." [] is_a: OGMS:0000063 ! disease course property_value: IAO:0000117 "Albert Goldfain" xsd:string property_value: IAO:0000119 http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf xsd:string property_value: IAO:0000232 "creation date: 2009-06-23T11:57:09Z" xsd:string [Term] id: OGMS:0000066 name: transient disease course def: "A disease course that terminates in a return to normal homeostasis." [] is_a: OGMS:0000063 ! disease course property_value: IAO:0000117 "Albert Goldfain" xsd:string property_value: IAO:0000119 http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf xsd:string property_value: IAO:0000232 "creation date: 2009-06-23T11:57:44Z" xsd:string [Term] id: OGMS:0000067 name: _undefined primitive term is_a: BFO:0000001 ! entity property_value: IAO:0000117 "Albert Goldfain" xsd:string property_value: IAO:0000232 "creation date: 2009-06-23T11:58:22Z" xsd:string [Term] id: OGMS:0000069 name: clinically abnormal is_a: OGMS:0000067 ! _undefined primitive term property_value: IAO:0000117 "Albert Goldfain" xsd:string property_value: IAO:0000232 "creation date: 2009-06-23T11:59:24Z" xsd:string [Term] id: OGMS:0000070 name: physical basis is_a: OGMS:0000067 ! _undefined primitive term property_value: IAO:0000117 "Albert Goldfain" xsd:string property_value: IAO:0000232 "creation date: 2009-06-23T12:00:09Z" xsd:string [Term] id: OGMS:0000071 name: realization is_a: OGMS:0000067 ! _undefined primitive term property_value: IAO:0000117 "Albert Goldfain" xsd:string property_value: IAO:0000232 "creation date: 2009-06-23T12:00:39Z" xsd:string [Term] id: OGMS:0000073 name: diagnosis def: "The representation of a conclusion of a diagnostic process." [] is_a: OGMS:0000123 ! clinical data item property_value: IAO:0000117 "Albert Goldfain" xsd:string property_value: IAO:0000119 http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf xsd:string property_value: IAO:0000232 "creation date: 2009-06-23T12:42:23Z" xsd:string [Term] id: OGMS:0000074 name: normal value def: "A value for a quality reported in a lab report and asserted by the testing lab or the kit manufacturer to be normal based on a statistical treatment of values from a reference population." [] is_a: BFO:0000031 ! generically dependent continuant property_value: IAO:0000117 "Albert Goldfain" xsd:string property_value: IAO:0000119 http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf xsd:string property_value: IAO:0000232 "creation date: 2009-06-26T10:31:34Z" xsd:string [Term] id: OGMS:0000077 name: pathological formation def: "TODO: Define, relate to disorder, and place in the OGMS hierarchy." [] is_a: BFO:0000040 ! material entity property_value: IAO:0000117 "Albert Goldfain" xsd:string property_value: IAO:0000119 http://ontology.buffalo.edu/bio/ISMB/ISMB_Bio-ontologies.pdf xsd:string property_value: IAO:0000232 "creation date: 2009-07-13T02:14:59Z" xsd:string [Term] id: OGMS:0000078 name: pathological anatomical structure def: "An anatomical structure (FMA) is pathological whenever (1) it has come into being as a result of changes in some pre-existing canonical anatomical structure, (2) through processes other than the expression of the normal complement of genes of an organism of the given type, and (3) is predisposed to have health-related consequences for the organism in question manifested by symptoms and signs." [] is_a: BFO:0000040 ! material entity property_value: IAO:0000117 "Albert Goldfain" xsd:string property_value: IAO:0000119 http://ontology.buffalo.edu/bio/ISMB/ISMB_Bio-ontologies.pdf xsd:string property_value: IAO:0000232 "creation date: 2009-07-13T02:14:05Z" xsd:string [Term] id: OGMS:0000079 name: portion of pathological body substance def: "TODO: Define, relate to disorder, and place in the OGMS hierarchy." [] is_a: BFO:0000040 ! material entity property_value: IAO:0000117 "Albert Goldfain" xsd:string property_value: IAO:0000119 http://ontology.buffalo.edu/bio/ISMB/ISMB_Bio-ontologies.pdf xsd:string property_value: IAO:0000232 "creation date: 2009-07-13T02:15:17Z" xsd:string [Term] id: OGMS:0000080 name: pathological transformation def: "A pathological bodily process in which a canonical anatomical structure becomes a pathological anatomical structure." [] is_a: OGMS:0000061 ! pathological bodily process property_value: IAO:0000117 "Albert Goldfain" xsd:string property_value: IAO:0000119 http://ontology.buffalo.edu/bio/ISMB/ISMB_Bio-ontologies.pdf xsd:string property_value: IAO:0000232 "creation date: 2009-07-13T02:17:07Z" xsd:string [Term] id: OGMS:0000081 name: pathological derivation def: "A pathological bodily process in which matter is reorganized in such a way as to give rise to new pathological formations which take the place of entities existing earlier." [] is_a: OGMS:0000061 ! pathological bodily process property_value: IAO:0000117 "Albert Goldfain" xsd:string property_value: IAO:0000119 http://ontology.buffalo.edu/bio/ISMB/ISMB_Bio-ontologies.pdf xsd:string property_value: IAO:0000232 "creation date: 2009-07-13T02:17:24Z" xsd:string [Term] id: OGMS:0000082 name: pathological invasion def: "TODO: Define." [] is_a: OGMS:0000061 ! pathological bodily process property_value: IAO:0000117 "Albert Goldfain" xsd:string property_value: IAO:0000119 http://ontology.buffalo.edu/bio/ISMB/ISMB_Bio-ontologies.pdf xsd:string property_value: IAO:0000232 "creation date: 2009-07-13T02:17:47Z" xsd:string [Term] id: OGMS:0000083 name: physical examination finding def: "TODO: Define." [] is_a: OGMS:0000014 ! clinical finding property_value: IAO:0000117 "Albert Goldfain" xsd:string property_value: IAO:0000119 http://code.google.com/p/ogms/issues/detail?id=26 xsd:string property_value: IAO:0000232 "creation date: 2009-11-24T04:51:11Z" xsd:string [Term] id: OGMS:0000084 name: organism population def: "An aggregate of organisms of the same type." [] is_a: BFO:0000040 ! material entity property_value: IAO:0000117 "Albert Goldfain" xsd:string property_value: IAO:0000119 http://code.google.com/p/ogms/issues/detail?id=33 xsd:string property_value: IAO:0000232 "creation date: 2009-11-24T04:51:11Z" xsd:string [Term] id: OGMS:0000085 name: pain def: "A bodily process in an organism S involving two integrated levels: (a) activation of the nociceptive system and associated emotion generating brain components of S, and (b) a simultaneous aversive sensory and emotional experience on the part of S, where (b) is phenomenologically similar to the sort of aversive experience involved in pain with concordant tissue damage." [] is_a: OGMS:0000020 ! symptom property_value: IAO:0000117 "Albert Goldfain" xsd:string property_value: IAO:0000119 http://www.referent-tracking.com/RTU/sendfile/?file=painTokyo1_27_2011.pdf xsd:string property_value: IAO:0000232 "creation date: 2009-11-24T04:51:11Z" xsd:string [Term] id: OGMS:0000086 name: syndrome def: "A pattern of signs and symptoms that typically co-occur." [] is_a: BFO:0000019 ! quality property_value: IAO:0000117 "Albert Goldfain" xsd:string property_value: IAO:0000119 http://code.google.com/p/ogms/issues/detail?id=32 xsd:string property_value: IAO:0000232 "creation date: 2009-11-24T04:51:11Z" xsd:string [Term] id: OGMS:0000087 name: extended organism def: "An object aggregate consisting of an organism and all material entities located within the organism, overlapping the organism, or occupying sites formed in part by the organism." [] is_a: BFO:0000040 ! material entity property_value: IAO:0000117 "Albert Goldfain" xsd:string property_value: IAO:0000119 http://code.google.com/p/ogms/issues/detail?id=3 xsd:string property_value: IAO:0000232 "creation date: 2010-01-25T04:51:11Z" xsd:string [Term] id: OGMS:0000088 name: patient symptom report def: "A communication from a patient about something they perceive as being abnormal about their body or life." [] is_a: IAO:0000030 ! information content entity property_value: IAO:0000117 "Albert Goldfain" xsd:string property_value: IAO:0000119 http://code.google.com/p/ogms/issues/detail?id=12 xsd:string property_value: IAO:0000232 "creation date: 2010-01-25T04:51:11Z" xsd:string [Term] id: OGMS:0000089 name: congenital disorder def: "A structurally anomalous part of an organism acquired during fetal development and present at birth (but not necessarily hereditary) which is hypothesized to be harmful for the organism." [] is_a: BFO:0000040 ! material entity property_value: IAO:0000117 "Albert Goldfain" xsd:string property_value: IAO:0000118 "congenital malformation" xsd:string property_value: IAO:0000119 http://code.google.com/p/ogms/issues/detail?id=28 xsd:string property_value: IAO:0000232 "creation date: 2010-03-31T04:51:11Z" xsd:string [Term] id: OGMS:0000090 name: treatment def: "A planned process whose completion is hypothesized by a health care provider to eliminate, prevent, or alleviate a disorder, the signs and symptoms of a disorder, or a pathological process" [] is_a: OGMS:0000096 ! health care process property_value: IAO:0000117 "Albert Goldfain" xsd:string property_value: IAO:0000119 http://code.google.com/p/ogms/issues/detail?id=35 xsd:string property_value: IAO:0000232 "creation date: 2010-03-31T04:51:11Z" xsd:string [Term] id: OGMS:0000091 name: convalescence def: "A processual entity during which a patient participating in a disease course gradually returns to participating in a canonical life course." [] is_a: BFO:0000015 ! process property_value: IAO:0000117 "Albert Goldfain" xsd:string property_value: IAO:0000119 http://code.google.com/p/ogms/issues/detail?id=35 xsd:string property_value: IAO:0000232 "creation date: 2010-03-31T04:51:11Z" xsd:string [Term] id: OGMS:0000092 name: life course def: "A process which has as parts all the processes in which a given organism is participant." [] is_a: BFO:0000015 ! process property_value: IAO:0000117 "Albert Goldfain\nRichard Scheuermann\nSagar Jain" xsd:string property_value: IAO:0000119 http://code.google.com/p/ogms/issues/detail?id=38 xsd:string property_value: IAO:0000232 "creation date: 2010-03-31T04:51:11Z\n\nEDIT: 10 NOV 2015" xsd:string [Term] id: OGMS:0000093 name: prognosis def: "A hypothesis about some future part of a disease course." [] is_a: IAO:0000027 ! data item property_value: IAO:0000117 "Albert Goldfain" xsd:string property_value: IAO:0000119 http://code.google.com/p/ogms/issues/detail?id=35 xsd:string property_value: IAO:0000232 "creation date: 2010-03-31T12:42:23Z" xsd:string [Term] id: OGMS:0000094 name: acute disease course def: "A disease course with an acute onset" [] is_a: OGMS:0000063 ! disease course property_value: IAO:0000117 "Albert Goldfain" xsd:string property_value: IAO:0000119 http://code.google.com/p/ogms/wiki/Meeting_notes_20100513 xsd:string property_value: IAO:0000232 "creation date: 2010-07-19T11:57:44Z\n\n10212020\n\nfor definition use\n\nhttp://purl.obolibrary.org/obo/PATO_0000389" xsd:string [Term] id: OGMS:0000095 name: inflammatory process def: "A bodily process caused by some disorder that results in recruitment of leukocytes into a localized tissue site, typically causing localized pain and swelling." [] is_a: OGMS:0000060 ! bodily process property_value: IAO:0000117 "Albert Goldfain\nRichard Scheuermann\nSagar Jain" xsd:string property_value: IAO:0000119 http://code.google.com/p/ogms/wiki/Meeting_notes_20100513 xsd:string property_value: IAO:0000232 "creation date: 2010-07-19T11:57:44Z\n\nUpdated: 10 NOV 2015" xsd:string [Term] id: OGMS:0000096 name: health care process def: "A planned process with the objective to improve the health status of a patient that directly involves the treatment, diagnosis, or prevention of disease or injury of a patient" [] is_a: OBI:0000011 ! planned process property_value: IAO:0000117 "Albert Goldfain\nSagar Jain" xsd:string property_value: IAO:0000119 http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6 xsd:string property_value: IAO:0000232 "creation date: 2011-02-21T09:57:44Z\neditor date: 2017-04-18" xsd:string [Term] id: OGMS:0000097 name: health care encounter def: "A temporally-connected health care process that has as participants an organization or person realizing the health care provider role and a person realizing the patient role. The health care provider role and patient are realized during the health care encounter" [] is_a: OGMS:0000096 ! health care process property_value: IAO:0000117 "Albert Goldfain" xsd:string property_value: IAO:0000119 http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6 xsd:string property_value: IAO:0000232 "creation date: 2011-02-21T09:57:44Z" xsd:string [Term] id: OGMS:0000098 name: hospitalization def: "TODO" [] comment: 09/16/2020\nIs this same as admission? \nIs this the same as inpatient encounter? is_a: OGMS:0000096 ! health care process property_value: IAO:0000117 "Albert Goldfain" xsd:string property_value: IAO:0000119 http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6 xsd:string property_value: IAO:0000232 "creation date: 2011-02-21T09:57:44Z" xsd:string [Term] id: OGMS:0000099 name: outpatient encounter def: "TODO" [] is_a: OGMS:0000097 ! health care encounter property_value: IAO:0000117 "Albert Goldfain" xsd:string property_value: IAO:0000119 http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6 xsd:string property_value: IAO:0000232 "creation date: 2011-02-21T09:57:44Z" xsd:string [Term] id: OGMS:0000100 name: inpatient encounter def: "A health care encounter involving a patient who has been admitted to a health care facility and remains in a hospital facility for at least one night." [] is_a: OGMS:0000097 ! health care encounter property_value: IAO:0000117 "Albert Goldfain" xsd:string property_value: IAO:0000119 http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6 xsd:string property_value: IAO:0000232 "creation date: 2011-02-21T09:57:44Z" xsd:string [Term] id: OGMS:0000101 name: emergency department encounter def: "A health care encounter in which care is provided for undifferentiated and unscheduled patients with illnesses or injuries requiring immediate medical attention." [] is_a: OGMS:0000097 ! health care encounter property_value: IAO:0000117 "Albert Goldfain" xsd:string property_value: IAO:0000119 http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6 xsd:string property_value: IAO:0000232 "creation date: 2011-02-21T09:57:44Z" xsd:string [Term] id: OGMS:0000102 name: injury def: "A disorder that involves some structural damage that is immediately caused by a catastrophic external force." [] is_a: OGMS:0000045 ! disorder property_value: IAO:0000116 "At the scale of organism (as opposed to the cellular scale or the population scale), an injury is typically the result of a catastrophic event. Consider the implications of making 'injury' a subtype of 'disorder'.\n\nNote: Adopted subtype of disorder, and injury can occur at the scale of organism down to cellular level." xsd:string property_value: IAO:0000117 "Albert Goldfain\nSagar Jain" xsd:string property_value: IAO:0000119 "http://groups.google.com/group/ogms-discuss/browse_thread/thread/ca0ad373f27774c5\n\nOGMS call adoption- 16 SEPT 2015\nhttps://docs.google.com/document/d/1iiV1-fTS7BUUSzDw3N_Afx42698YWf54-FOTY2NkAxo/edit" xsd:string property_value: IAO:0000232 "creation date: 2011-09-20T09:57:44Z\nedited date: 30 SEPT 2015" xsd:string [Term] id: OGMS:0000103 name: disease prophylaxis def: "A planned process whose completion is hypothesized by a health care provider to reduce the risk of developing a disorder or the signs and symptoms of a disorder." [] is_a: OBI:0000011 ! planned process property_value: IAO:0000116 "Whether or not 'prophylaxis' and 'treatment' classes are disjoint is an open question." xsd:string property_value: IAO:0000117 "Albert Goldfain" xsd:string property_value: IAO:0000119 http://groups.google.com/group/ogms-discuss/browse_thread/thread/e42bde79218ee34e xsd:string property_value: IAO:0000232 "creation date: 2011-09-20T09:57:44Z" xsd:string [Term] id: OGMS:0000104 name: diagnostic process def: "A health care process that involves the interpretation of a clinical picture from a given patient (input) and the assertion to the effect that the patient has a disease, disorder, or syndrome of a certain type, or none of these (output)." [] is_a: OGMS:0000096 ! health care process property_value: IAO:0000117 "Albert Goldfain" xsd:string property_value: IAO:0000119 http://groups.google.com/group/ogms-discuss/browse_thread/thread/2a7008f311fac766/e7de486c94dfd82e xsd:string property_value: IAO:0000232 "creation date: 2011-09-20T09:57:44Z" xsd:string [Term] id: OGMS:0000105 name: relapse def: "A disease stage which is preceded by a remission and characterized by the return of a manifestation of a disease." [] is_a: OBI:0000278 ! disease stage property_value: http://purl.org/dc/elements/1.1/date "10 NOV 2015" xsd:string property_value: IAO:0000116 "A pathological bodily process which is part of a disease couse that occurs after an incomplete remission and that is similar to earlier parts of the disease course." xsd:string property_value: IAO:0000117 "Albert Goldfain\nRichard Scheuermann\nSagar Jain" xsd:string property_value: IAO:0000118 "recurrent" xsd:string property_value: IAO:0000119 http://code.google.com/p/ogms/issues/detail?id=73 xsd:string [Term] id: OGMS:0000106 name: remission def: "A disease stage which is characterized by the lack of a manifestation of a disease" [] is_a: OBI:0000278 ! disease stage property_value: http://purl.org/dc/elements/1.1/date "10 NOV 2015" xsd:string property_value: IAO:0000116 "A part of a disease course in which the extent or rate of change of the signs and symptoms of a disorder has decreased." xsd:string property_value: IAO:0000117 "Albert Goldfain\nRichard Scheuermann\nSagar Jain" xsd:string property_value: IAO:0000119 http://code.google.com/p/ogms/issues/detail?id=73 xsd:string [Term] id: OGMS:0000107 name: ancillary health care process def: "A planned process that has the objective to support the objective of a health care process without directly involving the treatment, diagnosis, or prevention of disease or injury of a patient." [] is_a: OBI:0000011 ! planned process property_value: http://purl.org/dc/elements/1.1/date "2017-04-18" xsd:string property_value: http://purl.org/dc/elements/1.1/publisher "Sagar Jain" xsd:string [Term] id: OGMS:0000108 name: health care process assay def: "A health care process with the objective to produce information about the material entity that is the evaluant, by physically examining it or its proxies." [] is_a: OGMS:0000096 ! health care process property_value: http://purl.org/dc/elements/1.1/date "creation: 16MAY2017" xsd:string property_value: http://purl.org/dc/elements/1.1/publisher "Sagar Jain" xsd:string [Term] id: OGMS:0000109 name: health care process biomaterial transformation def: "A health care process which results in physical changes in a specified input material" [] is_a: OGMS:0000096 ! health care process property_value: http://purl.org/dc/elements/1.1/date "creation: 16MAY2017" xsd:string property_value: http://purl.org/dc/elements/1.1/publisher "Sagar Jain" xsd:string [Term] id: OGMS:0000110 name: health care process data transformation def: "A health care process that produces output from input data" [] is_a: OGMS:0000096 ! health care process property_value: http://purl.org/dc/elements/1.1/date "creation: 16MAY2017" xsd:string property_value: http://purl.org/dc/elements/1.1/publisher "Sagar Jain" xsd:string [Term] id: OGMS:0000111 name: prophylactic treatment def: "A treatment whose completion is hypothesized by a health care provider to prevent the signs and symptoms of a disorder or pathological process." [] is_a: OGMS:0000090 ! treatment property_value: IAO:0000232 "Creation date: 2018-11-27" xsd:string [Term] id: OGMS:0000112 name: therapeutic procedure def: "A treatment whose completion is hypothesized by a health care provider to eliminate a disorder or to alleviate the signs and symptoms of a disorder or pathological process." [] is_a: OGMS:0000090 ! treatment property_value: IAO:0000232 "Creation data: 2018-11-27" xsd:string [Term] id: OGMS:0000113 name: chemotherapy procedure def: "A therapeutic procedure that uses synthetic or naturally-occurring chemicals" [] is_a: OGMS:0000112 ! therapeutic procedure property_value: IAO:0000232 "creation date: 2018-11-27" xsd:string [Term] id: OGMS:0000114 name: immunotherapy procedure def: "A therapeutic procedure that uses immune system derived entities." [] is_a: OGMS:0000112 ! therapeutic procedure property_value: IAO:0000232 "creation date: 2018-11-27" xsd:string [Term] id: OGMS:0000115 name: physical therapy procedure def: "A therapeutic procedure that uses physical conditioning" [] is_a: OGMS:0000112 ! therapeutic procedure property_value: IAO:0000232 "creation date: 2018-11-27" xsd:string [Term] id: OGMS:0000116 name: radiation therapy procedure def: "A therapeutic procedure that uses radiation." [] is_a: OGMS:0000112 ! therapeutic procedure property_value: IAO:0000232 "creation date: 2018-11-27" xsd:string [Term] id: OGMS:0000117 name: asymptomatic def: "A disease stage characterized by the lack of symptoms associated with a given disease" [] is_a: OBI:0000278 ! disease stage property_value: IAO:0000232 "creation date: 2018-11-27" xsd:string [Term] id: OGMS:0000118 name: onset def: "A disease stage that marks the beginning of a disease" [] is_a: OBI:0000278 ! disease stage property_value: IAO:0000232 "creation date 2018-11-27" xsd:string [Term] id: OGMS:0000119 name: acute onset def: "A disease stage with a rapid unfolding of signs and symptoms" [] is_a: OGMS:0000118 ! onset property_value: IAO:0000232 "creation date 2018-11-27" xsd:string [Term] id: OGMS:0000120 name: complete remission def: "A remission which is characterized by a prolonged lack of all manifestations of a disease" [] is_a: OGMS:0000106 ! remission [Term] id: OGMS:0000121 name: partial remission def: "A remission which is characterized by a prolonged lack of some manifestations of a disease" [] is_a: OGMS:0000106 ! remission [Term] id: OGMS:0000122 name: recovered from disease def: "A quality in which complete clearance of the disorder is attained; however, physiological 'memory' may persist" [] is_a: BFO:0000019 ! quality property_value: IAO:0000232 "creation date: 2018-11-27" xsd:string [Term] id: OGMS:0000123 name: clinical data item def: "A data item that is about a patient and is the specified output of a health care process assay or diagnostic process" [] is_a: IAO:0000027 ! data item property_value: IAO:0000232 "creation date: 2018-11-27" xsd:string [Term] id: OGMS:0000124 name: routine health care encounter def: "A health care encounter that is regularly scheduled for the purpose of health monitoring." [] is_a: OGMS:0000099 ! outpatient encounter property_value: IAO:0000118 "routine clinical visit" xsd:string [Term] id: OGMS:0000125 name: follow-up health care encounter def: "A health care encounter that is scheduled for the purpose of assessing a known set of specific issues" [] is_a: OGMS:0000099 ! outpatient encounter property_value: IAO:0000118 "follow-up clinical visit" xsd:string [Term] id: OGMS:0000126 name: congenital infection def: "A congenital disorder arising as a result of an infectious process" [] is_a: OGMS:0000089 ! congenital disorder [Term] id: OGMS:0000127 name: drug induced congenital malformation def: "A congenital disorder arising as a result of a drug exposure causing an anatomical abnormality" [] is_a: OGMS:0000089 ! congenital disorder [Term] id: OGMS:0000128 name: congenital process def: "A pathological bodily process that occurs in the fetus during fetal development" [] is_a: OGMS:0000061 ! pathological bodily process [Term] id: OGMS:0000129 name: physical sign def: "An abnormal material entity that is part of a patient and hypothesized to be clinically relevant." [] is_a: BFO:0000040 ! material entity property_value: IAO:0000232 "Example: an abnormal growth, an inflammatory infiltrate, swollen tissue, distension" xsd:string [Term] id: OGMS:0000130 name: allergic disease process def: "The process in which an allergic disease unfolds." [] is_a: OGMS:0000061 ! pathological bodily process [Term] id: OGMS:0000131 name: cancer process def: "The process in which cancer unfolds" [] is_a: OGMS:0000061 ! pathological bodily process [Term] id: OGMS:0000132 name: autoimmune disease process def: "The process in which an autoimmune disease unfolds." [] is_a: OGMS:0000061 ! pathological bodily process [Term] id: OGMS:0000133 name: progression stage is_a: OBI:0000278 ! disease stage [Term] id: OGMS:0000134 name: cancer progression stage is_a: OGMS:0000133 ! progression stage [Term] id: OGMS:0000135 name: cancer progression stage 0 def: "A cancer progression stage characterized by abnormal cellular growth contained within normal tissue boundaries (e.g. carcinoma in situ)." [] is_a: OGMS:0000134 ! cancer progression stage [Term] id: OGMS:0000136 name: cancer progression stage I def: "A cancer progression stage characterized by abnormal cellular growth that extends through normal local tissue boundaries as a contiguous mass." [] is_a: OGMS:0000134 ! cancer progression stage [Term] id: OGMS:0000137 name: cancer progression stage II def: "A cancer progression stage characterized by abnormal cellular growth that extends well beyond normal local tissue boundaries as a contiguous mass." [] is_a: OGMS:0000134 ! cancer progression stage [Term] id: OGMS:0000138 name: cancer progression stage III def: "A cancer progression stage characterized by abnormal cellular growth that extends through normal local tissue boundaries as a contiguous mass and includes metastasis to one or more regional draining lymph nodes." [] is_a: OGMS:0000134 ! cancer progression stage [Term] id: OGMS:0000139 name: cancer progression stage IV def: "A cancer progression stage characterized by abnormal cellular growth that extends through normal local tissue boundaries as a contiguous mass and includes metastasis to other distant tissues besides lymph nodes." [] is_a: OGMS:0000134 ! cancer progression stage [Term] id: OGMS:0000140 name: infectious disease process def: "The process in which an infectious disease unfolds" [] is_a: OGMS:0000061 ! pathological bodily process [Term] id: OGMS:0000141 name: processual sign def: "An abnormal processual entity occuring in a patient that is hypothesized to be clinically relevant." [] is_a: BFO:0000015 ! process [Term] id: OGMS:0000142 name: qualitative sign def: "An abnormal observable quality of a part of a patient that is hypothesized to be clinically relevant." [] is_a: BFO:0000019 ! quality property_value: IAO:0000232 "Example: the color of a rash; the shape of a melanoma" xsd:string [Term] id: OGMS:0000143 name: transplantation def: "A therapeutic procedure in which a body part is transferred into a organism" [] is_a: OGMS:0000112 ! therapeutic procedure [Term] id: OGMS:0000144 name: solid organ transplant def: "A transplantation in which the body part is a non-fluid tissue" [] is_a: OGMS:0000143 ! transplantation [Term] id: OGMS:0000145 name: transfusion def: "A transplantation in which the body part is a bodily fluid" [] is_a: OGMS:0000143 ! transplantation [Term] id: OGMS:0000146 name: tissue disorder def: "A disorder of some macroscopic part of a tissue" [] is_a: OGMS:0000045 ! disorder [Term] id: OGMS:0000147 name: neoplasm def: "A tissue disorder that has resulted from a dysregulation of cell proliferation leading to a net increase in mass" [] is_a: OGMS:0000146 ! tissue disorder [Term] id: OGMS:0000148 name: medication role def: "A role borne by some material entity which can be delivered/administrated into some organism and the role is realized during a clinical treatment process aiming to treat symptoms, signs or diagnosed disease." [] is_a: BFO:0000023 ! role property_value: IAO:0000116 "Originally OBIB_0000026" xsd:string