format-version: 1.2 data-version: 2019-06-07 remark: An information artifact is, loosely, a dependent continuant or its bearer that is created as the result of one or more intentional processes. Examples: uniprot, the english language, the contents of this document or a printout of it, the temperature measurements from a weather balloon. For more information, see the project home page at https://github.com/information-artifact-ontology/IAO remark: IDs allocated to related efforts: PNO: IAO_0020000-IAO_0020999, D_ACTS: IAO_0021000-IAO_0021999 remark: IDs allocated to subdomains of IAO. pno.owl: IAO_0020000-IAO_0020999, d-acts.owl: IAO_0021000-IAO_0021999 ontology: iao property_value: dcterms:license http://creativecommons.org/licenses/by/4.0/ property_value: defaultLanguage "en" xsd:string property_value: http://purl.org/dc/elements/1.1/contributor "Adam Goldstein" xsd:string property_value: http://purl.org/dc/elements/1.1/contributor "Alan Ruttenberg" xsd:string property_value: http://purl.org/dc/elements/1.1/contributor "Albert Goldfain" xsd:string property_value: http://purl.org/dc/elements/1.1/contributor "Barry Smith" xsd:string property_value: http://purl.org/dc/elements/1.1/contributor "Bjoern Peters" xsd:string property_value: http://purl.org/dc/elements/1.1/contributor "Carlo Torniai" xsd:string property_value: http://purl.org/dc/elements/1.1/contributor "Chris Mungall" xsd:string property_value: http://purl.org/dc/elements/1.1/contributor "Chris Stoeckert" xsd:string property_value: http://purl.org/dc/elements/1.1/contributor "Christian A. Boelling" xsd:string property_value: http://purl.org/dc/elements/1.1/contributor "Darren Natale" xsd:string property_value: http://purl.org/dc/elements/1.1/contributor "David Osumi-Sutherland" xsd:string property_value: http://purl.org/dc/elements/1.1/contributor "Gwen Frishkoff" xsd:string property_value: http://purl.org/dc/elements/1.1/contributor "Holger Stenzhorn" xsd:string property_value: http://purl.org/dc/elements/1.1/contributor "James A. Overton" xsd:string property_value: http://purl.org/dc/elements/1.1/contributor "James Malone" xsd:string property_value: http://purl.org/dc/elements/1.1/contributor "Jennifer Fostel" xsd:string property_value: http://purl.org/dc/elements/1.1/contributor "Jie Zheng" xsd:string property_value: http://purl.org/dc/elements/1.1/contributor "Jonathan Rees" xsd:string property_value: http://purl.org/dc/elements/1.1/contributor "Larisa Soldatova" xsd:string property_value: http://purl.org/dc/elements/1.1/contributor "Lawrence Hunter" xsd:string property_value: http://purl.org/dc/elements/1.1/contributor "Mathias Brochhausen" xsd:string property_value: http://purl.org/dc/elements/1.1/contributor "Matt Brush" xsd:string property_value: http://purl.org/dc/elements/1.1/contributor "Melanie Courtot" xsd:string property_value: http://purl.org/dc/elements/1.1/contributor "Michel Dumontier" xsd:string property_value: http://purl.org/dc/elements/1.1/contributor "Paolo Ciccarese" xsd:string property_value: http://purl.org/dc/elements/1.1/contributor "Pat Hayes" xsd:string property_value: http://purl.org/dc/elements/1.1/contributor "Philippe Rocca-Serra" xsd:string property_value: http://purl.org/dc/elements/1.1/contributor "Randy Dipert" xsd:string property_value: http://purl.org/dc/elements/1.1/contributor "Ron Rudnicki" xsd:string property_value: http://purl.org/dc/elements/1.1/contributor "Satya Sahoo" xsd:string property_value: http://purl.org/dc/elements/1.1/contributor "Sivaram Arabandi" xsd:string property_value: http://purl.org/dc/elements/1.1/contributor "Werner Ceusters" xsd:string property_value: http://purl.org/dc/elements/1.1/contributor "William Duncan" xsd:string property_value: http://purl.org/dc/elements/1.1/contributor "William Hogan" xsd:string property_value: http://purl.org/dc/elements/1.1/contributor "Yongqun (Oliver) He" xsd:string property_value: seeAlso https://github.com/information-artifact-ontology/IAO 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(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(DataProperty())\nDeclaration(DataProperty())\nDeclaration(DataProperty())\nDeclaration(DataProperty())\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(NamedIndividual())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\n############################\n# Annotation Properties\n############################\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( rdfs:label)\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( rdfs:label)\n\n# Annotation Property: ()\n\nAnnotationPropertyRange( xsd:dateTime)\n\n\n############################\n# Object Properties\n############################\n\n# Object Property: ()\n\nAnnotationAssertion(rdfs:comment \"\"@en)\n\n# Object Property: ()\n\nObjectPropertyRange( ObjectIntersectionOf( ObjectComplementOf()))\n\n# Object Property: ()\n\nEquivalentObjectProperties( ObjectInverseOf())\n\n# Object Property: ()\n\nEquivalentObjectProperties( ObjectInverseOf())\n\n# Object Property: ()\n\nEquivalentObjectProperties( ObjectInverseOf())\n\n# Object Property: ()\n\nObjectPropertyRange( ObjectIntersectionOf( ObjectComplementOf()))\n\n# Object Property: ()\n\nIrreflexiveObjectProperty()\n\n\n############################\n# Data Properties\n############################\n\n# Data Property: ()\n\nFunctionalDataProperty()\nDataPropertyDomain( )\nDataPropertyRange( xsd:double)\n\n# Data Property: ()\n\nFunctionalDataProperty()\nDataPropertyDomain( )\nDataPropertyRange( xsd:float)\n\n# Data Property: ()\n\nFunctionalDataProperty()\nDataPropertyDomain( )\nDataPropertyRange( xsd:float)\n\n# Data Property: ()\n\nFunctionalDataProperty()\nDataPropertyDomain( )\nDataPropertyRange( xsd:float)\n\n\n\n############################\n# Classes\n############################\n\n# Class: ()\n\nSubClassOf( owl:Thing)\n\n# Class: ()\n\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: ()\n\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: ()\n\nSubClassOf( ObjectMinCardinality(1 ))\nSubClassOf( DataMinCardinality(1 ))\n\n# Class: ()\n\nEquivalentClasses( ObjectOneOf( ))\n\n# Class: ()\n\nEquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( ))))\nSubClassOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( )))\n\n# Class: ()\n\nEquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( ))))\nSubClassOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( )))\n\n# Class: ()\n\nEquivalentClasses( ObjectOneOf( ))\n\n# Class: ()\n\nSubClassOf( ObjectExactCardinality(1 ))\n\n# Class: ()\n\nSubClassOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))))\nSubClassOf( DataExactCardinality(1 ))\n\n# Class: ()\n\nSubClassOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))))\nSubClassOf( DataExactCardinality(1 ))\nSubClassOf( DataExactCardinality(1 ))\n\n# Class: ()\n\nSubClassOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))))\nSubClassOf( DataExactCardinality(1 ))\nSubClassOf( DataExactCardinality(1 ))\nSubClassOf( DataExactCardinality(1 ))\n\n# Class: ()\n\nEquivalentClasses( ObjectOneOf( ))\n\n# Class: ()\n\nSubClassOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( )))\n\n# Class: ()\n\nSubClassOf( owl:Thing)\n\n# Class: ()\n\nEquivalentClasses( ObjectOneOf())\n\n\n############################\n# Named Individuals\n############################\n\n# Individual: ()\n\n\n# Individual: ()\n\n\n# Individual: ()\n\n\n# Individual: ()\n\n\n# Individual: ()\n\n\n# Individual: ()\n\n\n# Individual: ()\n\n\n# Individual: ()\n\n\n# Individual: ()\n\n\n# Individual: ()\n\n\n# Individual: ()\n\n\n# Individual: ()\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 def: "An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts." [] 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 def: "An entity that has temporal parts and that happens, unfolds or develops through time." [] 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:0000005 name: obsolete dependent continuant def: "A continuant that is either dependent on one or other independent continuant bearers or inheres in or is borne by other entities." [] is_a: ObsoleteClass ! Obsolete Class is_obsolete: true [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 def: "A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances." [] 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 def: "A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts." [] 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 def: "An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time." [] 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: DbXref is_a: IAO:0000102 ! data about an ontology part [Term] id: Definition is_a: IAO:0000102 ! data about an ontology part [Term] id: GAZ:00000448 name: geographic location def: "A reference to a place on the Earth, by its name or by its geographical location." [] is_a: BFO:0000029 ! site property_value: IAO:0000412 http://purl.obolibrary.org/obo/gaz.owl [Term] id: IAO:0000001 name: conditional specification def: "a directive information entity that specifies what should happen if the trigger condition is fulfilled" [] is_a: IAO:0000033 ! directive information entity property_value: IAO:0000111 "conditional specification" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "PlanAndPlannedProcess Branch" xsd:string property_value: IAO:0000119 "OBI branch derived" xsd:string property_value: IAO:0000119 "OBI_0000349" xsd:string [Term] id: IAO:0000003 name: measurement unit label def: "A measurement unit label is as a label that is part of a scalar measurement datum and denotes a unit of measure." [] is_a: IAO:0000009 ! datum label property_value: IAO:0000111 "measurement unit label" xsd:string property_value: IAO:0000112 "Examples of measurement unit labels are liters, inches, weight per volume." xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "2009-03-16: provenance: a term measurement unit was\nproposed for OBI (OBI_0000176) , edited by Chris Stoeckert and\nCristian Cocos, and subsequently moved to IAO where the objective for\nwhich the original term was defined was satisfied with the definition\nof this, different, term." xsd:string property_value: IAO:0000116 "2009-03-16: review of this term done during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI." xsd:string property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string property_value: IAO:0000117 "PERSON: Melanie Courtot" xsd:string [Term] id: IAO:0000005 name: objective specification def: "a directive information entity that describes an intended process endpoint. When part of a plan specification the concretization is realized in a planned process in which the bearer tries to effect the world so that the process endpoint is achieved." [] is_a: IAO:0000033 ! directive information entity property_value: IAO:0000111 "objective specification" xsd:string property_value: IAO:0000112 "In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction." xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000116 "2009-03-16: original definition when imported from OBI read: \"objective is an non realizable information entity which can serve as that proper part of a plan towards which the realization of the plan is directed.\"" xsd:string property_value: IAO:0000116 "2014-03-31: In the example of usage (\"In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction\") there is a protocol which is the ChIP assay protocol. In addition to being concretized on paper, the protocol can be concretized as a realizable entity, such as a plan that inheres in a person. The objective specification is the part that says that some protein and DNA interactions are identified. This is a specification of a process endpoint: the boundary in the process before which they are not identified and after which they are. During the realization of the plan, the goal is to get to the point of having the interactions, and participants in the realization of the plan try to do that." xsd:string property_value: IAO:0000116 "Answers the question, why did you do this experiment?" xsd:string property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string property_value: IAO:0000117 "PERSON: Barry Smith" xsd:string property_value: IAO:0000117 "PERSON: Bjoern Peters" xsd:string property_value: IAO:0000117 "PERSON: Jennifer Fostel" xsd:string property_value: IAO:0000118 "goal specification" xsd:string property_value: IAO:0000119 "OBI Plan and Planned Process/Roles Branch" xsd:string property_value: IAO:0000119 "OBI_0000217" xsd:string [Term] id: IAO:0000006 name: narrative object def: "A narrative object is an information content entity that is a set of propositions." [] is_a: IAO:0000030 ! information content entity property_value: IAO:0000111 "narrative object" xsd:string property_value: IAO:0000112 "Examples of narrative objects are reports, journal articles, and patents submission." xsd:string property_value: IAO:0000114 IAO:0000123 property_value: IAO:0000116 "2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'textual entity' and 'figure'. Alan restored as there are OBI dependencies and this merits further discussion" xsd:string property_value: IAO:0000116 "agree - DENRIE. Issue(alan) do we only mean text? What about a story told by mime. Does music count? (no) what about an oral report. Regarding definition, saying it is a set of propositions means we loose the idea that wording matters. Maybe adjust saying a narrative object has some relationshop to a set of propositions" xsd:string property_value: IAO:0000117 "person:Chris Stoeckert" xsd:string property_value: IAO:0000119 group:OBI xsd:string property_value: IAO:0000119 "OBI_0000013" xsd:string [Term] id: IAO:0000007 name: action specification def: "a directive information entity that describes an action the bearer will take" [] is_a: IAO:0000033 ! directive information entity property_value: IAO:0000112 "Pour the contents of flask 1 into flask 2" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "Alan Ruttenberg" xsd:string property_value: IAO:0000119 "OBI Plan and Planned Process branch" xsd:string [Term] id: IAO:0000008 name: obsolete_artifact is_a: ObsoleteClass ! Obsolete Class property_value: IAO:0000231 IAO:0000103 is_obsolete: true [Term] id: IAO:0000009 name: datum label def: "A label is a symbol that is part of some other datum and is used to either partially define the denotation of that datum or to provide a means for identifying the datum as a member of the set of data with the same label" [] is_a: IAO:0000030 ! information content entity property_value: IAO:0000111 "datum label" xsd:string property_value: IAO:0000114 IAO:0000123 property_value: IAO:0000116 http://www.golovchenko.org/cgi-bin/wnsearch?q=label#4n xsd:string property_value: IAO:0000117 "GROUP: IAO" xsd:string property_value: IAO:0000232 "9/22/11 BP: changed the rdfs:label for this class from 'label' to 'datum label' to convey that this class is not intended to cover all kinds of labels (stickers, radiolabels, etc.), and not even all kind of textual labels, but rather the kind of labels occuring in a datum. \n" xsd:string [Term] id: IAO:0000010 name: software def: "Software is a plan specification composed of a series of instructions that can be \ninterpreted by or directly executed by a processing unit." [] is_a: IAO:0000104 ! plan specification property_value: IAO:0000111 "software" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000116 "see sourceforge tracker discussion at http://sourceforge.net/tracker/index.php?func=detail&aid=1958818&group_id=177891&atid=886178" xsd:string property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string property_value: IAO:0000117 "PERSON: Bjoern Peters" xsd:string property_value: IAO:0000117 "PERSON: Chris Stoeckert" xsd:string property_value: IAO:0000117 "PERSON: Melanie Courtot" xsd:string property_value: IAO:0000119 "GROUP: OBI" xsd:string [Term] id: IAO:0000012 name: obsolete2_digital entity def: "A digital entity is an information entity which is a collection of bits that can be interpreted by a computer. Two digital entities are the same if they are bitwise identical." [] is_a: ObsoleteClass ! Obsolete Class property_value: IAO:0000111 "obsolete_digital entity" xsd:string property_value: IAO:0000116 "3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4\n\nSuperclass was 'digitial quality'" xsd:string property_value: IAO:0000117 "person:Chris Stoeckert" xsd:string property_value: IAO:0000119 group:OBI xsd:string property_value: IAO:0000119 "OBI_0000261" xsd:string property_value: IAO:0000231 IAO:0000103 is_obsolete: true [Term] id: IAO:0000013 name: journal article def: "a report that is published in a journal" [] is_a: IAO:0000088 ! report property_value: IAO:0000111 "journal article" xsd:string property_value: IAO:0000112 "Examples are articles published in the journals, Nature and Science. The content can often be cited by reference to a paper based encoding, e.g. Authors, Title of article, Journal name, date or year of publication, volume and page number." xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "person:Alan Ruttenberg" xsd:string property_value: IAO:0000117 "person:Chris Stoeckert" xsd:string property_value: IAO:0000119 group:OBI xsd:string property_value: IAO:0000119 "OBI_0000159" xsd:string [Term] id: IAO:0000015 name: information carrier def: "A quality of an information bearer that imparts the information content" [] is_a: BFO:0000019 ! quality intersection_of: BFO:0000019 ! quality intersection_of: RO:0000059 IAO:0000030 ! concretizes information content entity relationship: RO:0000059 IAO:0000030 ! concretizes information content entity property_value: IAO:0000111 "information carrier" xsd:string property_value: IAO:0000112 "In the case of a printed paperback novel the physicality of the ink and of the paper form part of the information bearer. The qualities of appearing black and having a certain pattern for the ink and appearing white for the paper form part of the information carrier in this case." xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "12/15/09: There is a concern that some ways that carry information may be processes rather than qualities, such as in a 'delayed wave carrier'." xsd:string property_value: IAO:0000116 "2014-03-10: We are not certain that all information carriers are qualities. There was a discussion of dropping it." xsd:string property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string property_value: IAO:0000119 "Smith, Ceusters, Ruttenberg, 2000 years of philosophy" xsd:string [Term] id: IAO:0000017 name: model number def: "A model number is an information content entity specifically borne by catalogs, design specifications, advertising materials, inventory systems and similar that is about manufactured objects of the same class. The model number is an alternative term for the class. The manufactered objects may or may not also bear the model number. Model numbers can be encoded in a variety of other information objects, such as bar codes, numerals, or patterns of dots." [] is_a: IAO:0000028 ! symbol property_value: IAO:0000111 "model number" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "manufactered items may have more than one model number, sometimes by rebranding, or because companies are sold and the products issued new model numbers" xsd:string property_value: IAO:0000117 "Person: Alan Ruttenberg" xsd:string [Term] id: IAO:0000018 name: obsolete_material_entity is_a: ObsoleteClass ! Obsolete Class property_value: IAO:0000231 IAO:0000226 is_obsolete: true [Term] id: IAO:0000019 name: obsolete2_binary digital entity def: "A binary digital entity is a digital entity that is encoded in a way that is not easily human readable and that contains other than text characters." [] is_a: ObsoleteClass ! Obsolete Class property_value: IAO:0000111 "binary digital entity" xsd:string property_value: IAO:0000112 "MS Word document, ZIP file, DICOM file, JPEG file" xsd:string property_value: IAO:0000116 "3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4\nSuperclass was 'digital entity'" xsd:string property_value: IAO:0000116 "digital_entity" xsd:string property_value: IAO:0000117 "person:Chris Stoeckert" xsd:string property_value: IAO:0000119 group:OBI xsd:string property_value: IAO:0000119 "OBI_0000244" xsd:string property_value: IAO:0000231 IAO:0000103 is_obsolete: true [Term] id: IAO:0000024 name: obsolete_unit of measure def: "a unit of measure is the quality of some material entity compared to which another quality is some multiple of." [] is_a: ObsoleteClass ! Obsolete Class property_value: IAO:0000112 "The length of a ruler." xsd:string property_value: IAO:0000117 "Alan Ruttenberg" xsd:string property_value: IAO:0000119 "Smith, Ceusters, Ruttenberg, 2000 years of philosophy" xsd:string property_value: IAO:0000231 IAO:0000103 is_obsolete: true [Term] id: IAO:0000025 name: programming language def: "A language in which source code is written that is intended to be executed/run by a software interpreter. Programming languages are ways to write instructions that specify what to do, and sometimes, how to do it." [] is_a: IAO:0000104 ! plan specification property_value: IAO:0000111 "programming language" xsd:string property_value: IAO:0000112 "R, Perl, Java" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "person:Alan Ruttenberg" xsd:string property_value: IAO:0000117 "person:Chris Stoeckert" xsd:string property_value: IAO:0000119 group:OBI xsd:string property_value: IAO:0000119 "OBI_0000058" xsd:string [Term] id: IAO:0000027 name: data item def: "a data item is 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:0000112 "Data items include counts of things, analyte concentrations, and statistical summaries." xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers." xsd:string property_value: IAO:0000116 "2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum." xsd:string property_value: IAO:0000116 "2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym." xsd:string property_value: IAO:0000116 "2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/" xsd:string property_value: IAO:0000116 "JAR: datum -- well, this will be very tricky to define, but maybe some \ninformation-like stuff that might be put into a computer and that is \nmeant, by someone, to denote and/or to be interpreted by some \nprocess... I would include lists, tables, sentences... I think I might \ndefer to Barry, or to Brian Cantwell Smith\n\nJAR: A data item is an approximately justified approximately true approximate belief" xsd:string property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string property_value: IAO:0000117 "PERSON: Chris Stoeckert" xsd:string property_value: IAO:0000117 "PERSON: Jonathan Rees" xsd:string property_value: IAO:0000118 "data" xsd:string [Term] id: IAO:0000028 name: symbol def: "An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity." [] is_a: IAO:0000030 ! information content entity property_value: IAO:0000111 "symbol" xsd:string property_value: IAO:0000112 "a serial number such as \"12324X\"" xsd:string property_value: IAO:0000112 "a stop sign" xsd:string property_value: IAO:0000112 "a written proper name such as \"OBI\"" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "20091104, MC: this needs work and will most probably change" xsd:string property_value: IAO:0000116 "2014-03-31: We would like to have a deeper analysis of 'mark' and 'sign' in the future (see https://github.com/information-artifact-ontology/IAO/issues/154)." xsd:string property_value: IAO:0000117 "PERSON: James A. Overton" xsd:string property_value: IAO:0000117 "PERSON: Jonathan Rees" xsd:string property_value: IAO:0000119 "based on Oxford English Dictionary" xsd:string [Term] id: IAO:0000029 name: numeral def: "A symbol that denotes a number." [] is_a: IAO:0000028 ! symbol property_value: IAO:0000111 "numeral" xsd:string property_value: IAO:0000114 IAO:0000123 property_value: IAO:0000117 "PERSON: Jonathan Rees" xsd:string [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 relationship: IAO:0000136 BFO:0000001 ! is about entity property_value: IAO:0000111 "information content entity" xsd:string property_value: IAO:0000112 "Examples of information content entites include journal articles, data, graphical layouts, and graphs." xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000116 "2014-03-10: The use of \"thing\" is intended to be general enough to include universals and configurations (see https://groups.google.com/d/msg/information-ontology/GBxvYZCk1oc/-L6B5fSBBTQJ)." xsd:string property_value: IAO:0000116 "information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907).\n\nPrevious. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity." xsd:string property_value: IAO:0000117 "PERSON: Chris Stoeckert" xsd:string property_value: IAO:0000119 "OBI_0000142" xsd:string [Term] id: IAO:0000031 name: integer numeral def: "a numeral that denotes an integer" [] is_a: IAO:0000029 ! numeral property_value: IAO:0000111 "integer numeral" xsd:string property_value: IAO:0000114 IAO:0000123 property_value: IAO:0000117 "PERSON: Jonathan Rees" xsd:string [Term] id: IAO:0000032 name: scalar measurement datum def: "a scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label." [] is_a: IAO:0000109 ! measurement datum property_value: IAO:0000112 "10 feet. 3 ml." xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000116 "2009-03-16: we decided to keep datum singular in scalar measurement datum, as in\nthis case we explicitly refer to the singular form" xsd:string property_value: IAO:0000116 "Would write this as: has_part some 'measurement unit label' and has_part some numeral and has_part exactly 2, except for the fact that this won't let us take advantage of OWL reasoning over the numbers. Instead use has measurment value property to represent the same. Use has measurement unit label (subproperty of has_part) so we can easily say that there is only one of them." xsd:string property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string property_value: IAO:0000117 "PERSON: Melanie Courtot" xsd:string [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 relationship: IAO:0000136 BFO:0000017 ! is about realizable entity property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000116 "2009-03-16: provenance: a term realizable information entity was proposed for OBI (OBI_0000337) , edited by the PlanAndPlannedProcess branch. Original definition was \"is the specification of a process that can be concretized and realized by an actor\" with alternative term \"instruction\".It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term." xsd:string property_value: IAO:0000116 "2013-05-30 Alan Ruttenberg: What differentiates a directive information entity from an information concretization is that it can have concretizations that are either qualities or realizable entities. The concretizations that are realizable entities are created when an individual chooses to take up the direction, i.e. has the intention to (try to) realize it." xsd:string property_value: IAO:0000116 "8/6/2009 Alan Ruttenberg: Changed label from \"information entity about a realizable\" after discussions at ICBO" xsd:string property_value: IAO:0000116 "Werner pushed back on calling it realizable information entity as it isn't realizable. However this name isn't right either. An example would be a recipe. The realizable entity would be a plan, but the information entity isn't about the plan, it, once concretized, *is* the plan. -Alan" xsd:string property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string property_value: IAO:0000117 "PERSON: Bjoern Peters" xsd:string [Term] id: IAO:0000034 name: time trigger def: "revisit?" [] is_a: IAO:0000001 ! conditional specification property_value: IAO:0000111 "time trigger" xsd:string property_value: IAO:0000114 IAO:0000124 property_value: IAO:0000117 "PlanAndPlannedProcess Branch" xsd:string property_value: IAO:0000119 "OBI branch derived" xsd:string property_value: IAO:0000119 "OBI_0000331" xsd:string [Term] id: IAO:0000035 name: obsolete_study interpretation def: "A study interpretation is a textual entity about the implications of a study result. Examples include discussion of whether a hypothesis is false, whether the study failed to address the hypothesis, and whether the study results have led to new hypotheses" [] is_a: ObsoleteClass ! Obsolete Class property_value: IAO:0000111 "obsolete_study interpretation" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "2009-03-16: definition was \"A conclusion is a narrative object which can be published in a paper summerizing and interpreting a protocol application.\"" xsd:string property_value: IAO:0000116 "2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI." xsd:string property_value: IAO:0000116 "The obsoleting of narrative object required a modest change in the definition of this term. Circularity with \"interpretation... interprets\" has been removed, using \"about the implications\" instead." xsd:string property_value: IAO:0000117 "Lawrence Hunter" xsd:string property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string property_value: IAO:0000117 "PERSON: Jennifer Fostel" xsd:string property_value: IAO:0000117 "PERSON: Melanie Courtot" xsd:string property_value: IAO:0000118 "conclusion" xsd:string property_value: IAO:0000119 "OBI_0000005" xsd:string property_value: IAO:0000231 IAO:0000103 is_obsolete: true [Term] id: IAO:0000037 name: dot plot def: "A dot plot is a report graph which is a graphical representation of data where each data point is represented by a single dot placed on coordinates corresponding to data point values in particular dimensions." [] is_a: IAO:0000038 ! graph property_value: IAO:0000111 "dot plot" xsd:string property_value: IAO:0000112 "Dot plot of SSC-H and FSC-H." xsd:string property_value: IAO:0000114 IAO:0000002 property_value: IAO:0000117 "person:Allyson Lister" xsd:string property_value: IAO:0000117 "person:Chris Stoeckert" xsd:string property_value: IAO:0000119 group:OBI xsd:string property_value: IAO:0000119 "OBI_0000123" xsd:string [Term] id: IAO:0000038 name: graph def: "A diagram that presents one or more tuples of information by mapping those tuples in to a two dimensional space in a non arbitrary way." [] is_a: IAO:0000309 ! diagram property_value: IAO:0000111 "graph" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "PERSON: Lawrence Hunter" xsd:string property_value: IAO:0000117 "person:Alan Ruttenberg" xsd:string property_value: IAO:0000117 "person:Allyson Lister" xsd:string property_value: IAO:0000119 group:OBI xsd:string property_value: IAO:0000119 "OBI_0000240" xsd:string [Term] id: IAO:0000047 name: obsolete2_text based digital entity def: "A text based digital entity is a digital entity that is encoded so that it only contains text characters." [] is_a: ObsoleteClass ! Obsolete Class property_value: IAO:0000111 "text based digital entity" xsd:string property_value: IAO:0000112 "XML file, C++ source code file" xsd:string property_value: IAO:0000116 "3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4\nsuperclass was 'digital document'" xsd:string property_value: IAO:0000116 "digital_entity" xsd:string property_value: IAO:0000117 "person:Chris Stoeckert" xsd:string property_value: IAO:0000119 group:OBI xsd:string property_value: IAO:0000119 "OBI_0000132" xsd:string property_value: IAO:0000231 IAO:0000103 is_obsolete: true [Term] id: IAO:0000055 name: rule def: "a rule is an executable which guides, defines, restricts actions" [] is_a: IAO:0000001 ! conditional specification property_value: IAO:0000111 "rule" xsd:string property_value: IAO:0000112 "example to be added" xsd:string property_value: IAO:0000114 IAO:0000123 property_value: IAO:0000116 "MSI" xsd:string property_value: IAO:0000117 "PRS" xsd:string property_value: IAO:0000119 "OBI_0500021" xsd:string property_value: IAO:0000119 "PRS" xsd:string [Term] id: IAO:0000057 name: contour plot is_a: IAO:0000038 ! graph property_value: IAO:0000111 "contour plot" xsd:string property_value: IAO:0000112 "Contour plot of SSC-H, FSC-H, and FL1-H." xsd:string property_value: IAO:0000114 IAO:0000002 property_value: IAO:0000116 "generically_dependent_continuants" xsd:string property_value: IAO:0000117 "person:Allyson Lister" xsd:string property_value: IAO:0000117 "person:Chris Stoeckert" xsd:string property_value: IAO:0000119 "group:Flow Cytometry community" xsd:string property_value: IAO:0000119 "OBI_0000246" xsd:string [Term] id: IAO:0000059 name: obsolete2_report figure def: "A report figure is a report display element that has some aspect of illustration, but may be a composite of figures, images, and other elements" [] is_a: ObsoleteClass ! Obsolete Class property_value: IAO:0000111 "report figure" xsd:string property_value: IAO:0000114 IAO:0000124 property_value: IAO:0000116 "I prepended the 'report ' to make it clear that we mean parts of reports here. We may want a more generic version of 'figure', in which case this would become a defined class - figure and part_of some report" xsd:string property_value: IAO:0000116 "Replaced by defined version of figure" xsd:string property_value: IAO:0000117 "person:Alan Ruttenberg" xsd:string property_value: IAO:0000117 "person:Allyson Lister" xsd:string property_value: IAO:0000119 group:OBI xsd:string property_value: IAO:0000119 "OBI_0000027" xsd:string property_value: IAO:0000231 IAO:0000103 is_obsolete: true [Term] id: IAO:0000064 name: algorithm def: "A plan specification which describes the inputs and output of mathematical functions as well as workflow of execution for achieving an predefined objective. Algorithms are realized usually by means of implementation as computer programs for execution by automata." [] is_a: IAO:0000104 ! plan specification property_value: IAO:0000111 "algorithm" xsd:string property_value: IAO:0000112 "PMID: 18378114.Genomics. 2008 Mar 28. LINKGEN: A new algorithm to process data in genetic linkage studies." xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Philippe Rocca-Serra" xsd:string property_value: IAO:0000117 "PlanAndPlannedProcess Branch" xsd:string property_value: IAO:0000119 "adapted from discussion on OBI list (Matthew Pocock, Christian Cocos, Alan Ruttenberg)" xsd:string property_value: IAO:0000119 "OBI_0000270" xsd:string [Term] id: IAO:0000065 name: software interpreter def: "A software interpreter is a software application that executes some specified input software. " [] is_a: IAO:0000064 ! algorithm property_value: IAO:0000111 "software interpreter" xsd:string property_value: IAO:0000112 "R program, Perl interpreter, Java virtual machine" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000116 "Do we care? Jennifer: Yes, there was a particular version of R that had a bug and it was fixed later. That would imply that we mean specific version of an interpreter. So an instance of this would be a particular version of the interpreter" xsd:string property_value: IAO:0000117 "person:Alan Ruttenberg" xsd:string property_value: IAO:0000117 "person:Chris Stoeckert" xsd:string property_value: IAO:0000119 group:OBI xsd:string property_value: IAO:0000119 "OBI_0000199" xsd:string [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:0000079 name: density plot def: "A density plot is a report graph which is a graphical representation of data where the tint of a particular pixel corresponds to some kind of function corresponding the the amount of data points relativelly with their distance from the the pixel." [] is_a: IAO:0000038 ! graph property_value: IAO:0000111 "density plot" xsd:string property_value: IAO:0000112 "Density plot of SSC-H and FSC-H." xsd:string property_value: IAO:0000114 IAO:0000002 property_value: IAO:0000117 "person:Allyson Lister" xsd:string property_value: IAO:0000117 "person:Chris Stoeckert" xsd:string property_value: IAO:0000119 "group:Flow Cytometry community" xsd:string property_value: IAO:0000119 "OBI_0000179" xsd:string [Term] id: IAO:0000088 name: report def: "a document assembled by an author for the purpose of providing information for the audience. A report is the output of a documenting process and has the objective to be consumed by a specific audience. Topic of the report is on something that has completed. A report is not a single figure. Examples of reports are journal article, patent application, grant progress report, case report (not patient record)" [] is_a: IAO:0000310 ! document property_value: IAO:0000111 "report" xsd:string property_value: IAO:0000112 "Examples of reports are gene lists and investigation reports. These are not published (journal) articles but may be included in a journal article." xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "2009-03-16: comment from Darren Natale: I am slightly uneasy with the sentence \"Topic of the report is on \nsomething that has completed.\" Should it be restricted to those things \nthat are completed? For example, a progress report is (usually) about \nsomething that definitely has *not* been completed, or may include \n(only) projections. I think the definition would not suffer if the \nwhole sentence is deleted." xsd:string property_value: IAO:0000116 "2009-03-16: this was report of results with definition: A report is a narrative object that is a formal statement of the results of an investigation, or of any matter on which definite information is required, made by some person or body instructed or required to do so." xsd:string property_value: IAO:0000116 "2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI." xsd:string property_value: IAO:0000116 "2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'document'. Alan restored as there are OBI dependencies and this merits further discussion" xsd:string property_value: IAO:0000116 "disagreement about where reports go. alan: only some gene lists are reports. Is a report all the content of some document? The example of usage suggests that a report may be part of some article. Term needs clarification" xsd:string property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string property_value: IAO:0000117 "PERSON: Melanie Courtot" xsd:string property_value: IAO:0000117 "PERSON:Chris Stoeckert" xsd:string property_value: IAO:0000119 "GROUP: OBI" xsd:string property_value: IAO:0000119 "OBI_0000099" xsd:string [Term] id: IAO:0000091 name: obsolete_report element def: "A report element is a narrative object in which information is presented and consumed by a human being, and is part of a report. Examples of report elements are figure (dot plot), table, text portion (may include a movie or audio clip on a web page)." [] is_a: ObsoleteClass ! Obsolete Class property_value: IAO:0000111 "report element" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000116 "2009-03-16: needs some more work (clarify relations)." xsd:string property_value: IAO:0000116 "2009-03-16: was report display element with definition: A report display element is a narrative object that is part of a report. Report display elements are set off from the textual parts of a report and are typically given a label(e.g. Figure 2) which is used to refer to the element from the text. Typically the 2d layout is part of the identity of such elements." xsd:string property_value: IAO:0000116 "2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI." xsd:string property_value: IAO:0000116 "2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'textual entity' and 'figure'. Alan restored as there are OBI dependencies and this merits further discussion" xsd:string property_value: IAO:0000116 "Replaced by textual entity and figure" xsd:string property_value: IAO:0000116 "There will be some issue here about whether these are defined classes. As intended these are meant to denote the parts of the report that are not textual but are typically boxed and set within the text, labelled with some identifier, and referred to in the text" xsd:string property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string property_value: IAO:0000117 "PERSON: Allyson Lister" xsd:string property_value: IAO:0000117 "PERSON: Melanie Courtot" xsd:string property_value: IAO:0000119 GROUP:OBI xsd:string property_value: IAO:0000119 "OBI_0000001" xsd:string property_value: IAO:0000231 IAO:0000103 is_obsolete: true [Term] id: IAO:0000093 name: obsolete2_binary executable def: "Binary executable is a digital entity consisting of the binary representation of machine instructions of a specific processor or they may be binary pseudocode for a virtual machine. A non-source executable file is also called an object program. It is assumed that the binary executable file contains properly-formatted computer instructions. (derived from Wikipedia, Nov 1, 2007)" [] is_a: ObsoleteClass ! Obsolete Class property_value: IAO:0000111 "binary executable" xsd:string property_value: IAO:0000116 "3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4\nsuperclass was 'digital entity'" xsd:string property_value: IAO:0000117 "person:Jennifer Fostel" xsd:string property_value: IAO:0000119 group:OBI xsd:string property_value: IAO:0000119 "OBI_0000222" xsd:string property_value: IAO:0000231 IAO:0000103 is_obsolete: true [Term] id: IAO:0000096 name: source code module def: "A source code module is a directive information entity that specifies, using a programming language, some algorithm." [] is_a: IAO:0000033 ! directive information entity property_value: IAO:0000111 "source code module" xsd:string property_value: IAO:0000112 "The written source code that implements part of an algorithm. Test - if you know that it was written in a specific language, then it can be source code module. We mean here, roughly, the wording of a document such as a perl script." xsd:string property_value: IAO:0000114 IAO:0000123 property_value: IAO:0000117 "person:Alan Ruttenberg" xsd:string property_value: IAO:0000117 "person:Chris Stoeckert" xsd:string property_value: IAO:0000119 group:OBI xsd:string property_value: IAO:0000119 "OBI_0000039" xsd:string [Term] id: IAO:0000097 name: obsolete_report table def: "A report table is a report display element consisting of a matrix of cells layed out in a grid, some set of which are filled with some information content" [] is_a: ObsoleteClass ! Obsolete Class property_value: IAO:0000111 "report table" xsd:string property_value: IAO:0000114 IAO:0000002 property_value: IAO:0000116 "2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'textual entity table'. Alan restored as there are OBI dependencies and this merits further discussion" xsd:string property_value: IAO:0000117 "person:Alan Ruttenberg" xsd:string property_value: IAO:0000117 "person:Allyson Lister" xsd:string property_value: IAO:0000119 group:OBI xsd:string property_value: IAO:0000119 "OBI_0000265" xsd:string property_value: IAO:0000231 IAO:0000103 is_obsolete: true [Term] id: IAO:0000098 name: data format specification def: "A data format specification is the information content borne by the document published defining the specification.\nExample: The ISO document specifying what encompasses an XML document; The instructions in a XSD file" [] is_a: IAO:0000033 ! directive information entity property_value: IAO:0000111 "data format specification" xsd:string property_value: IAO:0000114 IAO:0000123 property_value: IAO:0000116 "2009-03-16: provenance: term imported from OBI_0000187, which had original definition \"A data format specification is a plan which organizes\ninformation. Example: The ISO document specifying what encompasses an\nXML document; The instructions in a XSD file\"" xsd:string property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string property_value: IAO:0000117 "PlanAndPlannedProcess Branch" xsd:string property_value: IAO:0000119 "OBI branch derived" xsd:string property_value: IAO:0000119 "OBI_0000187" xsd:string [Term] id: IAO:0000100 name: data set def: "A data item that is an aggregate of other data items of the same type that have something in common. Averages and distributions can be determined for data sets." [] is_a: IAO:0000027 ! data item property_value: IAO:0000111 "data set" xsd:string property_value: IAO:0000112 "Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves)." xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "2009/10/23 Alan Ruttenberg. The intention is that this term represent collections of like data. So this isn't for, e.g. the whole contents of a cel file, which includes parameters, metadata etc. This is more like java arrays of a certain rather specific type" xsd:string property_value: IAO:0000116 "2014-05-05: Data sets are aggregates and thus must include two or more data items. We have chosen not to add logical axioms to make this restriction." xsd:string property_value: IAO:0000117 "person:Allyson Lister" xsd:string property_value: IAO:0000117 "person:Chris Stoeckert" xsd:string property_value: IAO:0000119 group:OBI xsd:string property_value: IAO:0000119 "OBI_0000042" xsd:string [Term] id: IAO:0000101 name: image def: "An image is an affine projection to a two dimensional surface, of measurements of some quality of an entity or entities repeated at regular intervals across a spatial range, where the measurements are represented as color and luminosity on the projected on surface." [] is_a: IAO:0000308 ! figure property_value: IAO:0000111 "image" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "person:Alan Ruttenberg" xsd:string property_value: IAO:0000117 person:Allyson xsd:string property_value: IAO:0000117 "person:Chris Stoeckert" xsd:string property_value: IAO:0000119 group:OBI xsd:string property_value: IAO:0000119 "OBI_0000030" 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:0000117 "Person:Alan Ruttenberg" xsd:string [Term] id: IAO:0000104 name: plan specification def: "A directive information entity with action specifications and objective specifications as parts that, when concretized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified." [] comment: 2/3/2009 Comment from OBI review.\n\nAction specification not well enough specified.\nConditional specification not well enough specified.\nQuestion whether all plan specifications have objective specifications.\n\nRequest that IAO either clarify these or change definitions not to use them is_a: IAO:0000033 ! directive information entity relationship: BFO:0000051 IAO:0000005 ! has part objective specification relationship: BFO:0000051 IAO:0000007 ! has part action specification property_value: IAO:0000111 "plan specification" xsd:string property_value: IAO:0000112 "PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice." xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000116 "2009-03-16: provenance: a term a plan was proposed for OBI (OBI_0000344) , edited by the PlanAndPlannedProcess branch. Original definition was \" a plan is a specification of a process that is realized by an actor to achieve the objective specified as part of the plan\". It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term." xsd:string property_value: IAO:0000116 "2014-03-31: A plan specification can have other parts, such as conditional specifications." xsd:string property_value: IAO:0000116 "Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved" xsd:string property_value: IAO:0000117 "Alan Ruttenberg" xsd:string property_value: IAO:0000119 "OBI Plan and Planned Process branch" xsd:string property_value: IAO:0000119 "OBI_0000344" xsd:string [Term] id: IAO:0000105 name: obsolete2_digital document def: "A digital document is a digital entity consisting of an electronic file which can be rendered into human-readable form by one or more computational applications. The digital document does not refer to the information content of the document but to an instance of the file." [] is_a: ObsoleteClass ! Obsolete Class property_value: IAO:0000111 "digital document" xsd:string property_value: IAO:0000116 "3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4\nsuperclass was 'digial entity'" xsd:string property_value: IAO:0000117 "person:Jennifer Fostel" xsd:string property_value: IAO:0000119 group:OBI xsd:string property_value: IAO:0000119 "OBI_0000195" xsd:string property_value: IAO:0000231 IAO:0000103 is_obsolete: true [Term] id: IAO:0000109 name: measurement datum def: "A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device." [] is_a: IAO:0000027 ! data item property_value: IAO:0000111 "measurement datum" xsd:string property_value: IAO:0000112 "Examples of measurement data are the recoding of the weight of a mouse as {40,mass,\"grams\"}, the recording of an observation of the behavior of the mouse {,process,\"agitated\"}, the recording of the expression level of a gene as measured through the process of microarray experiment {3.4,luminosity,}." xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "2/2/2009 is_specified_output of some assay?" xsd:string property_value: IAO:0000117 "person:Chris Stoeckert" xsd:string property_value: IAO:0000119 group:OBI xsd:string property_value: IAO:0000119 "OBI_0000305" xsd:string [Term] id: IAO:0000128 name: obsolete_identifier is_a: ObsoleteClass ! Obsolete Class property_value: IAO:0000114 IAO:0000121 property_value: IAO:0000116 "_identifier is a container under information content entity for collecting types of terms to indicate a specific instance or clas of what was used or participated in an investigation. Identifiers are borne by a product or its packaging, and can be encoded in a variety of other information objects, such as bar codes, numerals, or patterns of dots.\n\nNote: everybody agreed that identifier is probably a too general term. We however felt that it would be appropriate to group \"identifiying\" terms under some kind of umbrella. We therefore propose to use _identifier for that purpose. As per OBI conventions, the _ prefixing identifier indicates that this is a helper class and shouldn't be considered as final." xsd:string property_value: IAO:0000231 IAO:0000226 is_obsolete: true [Term] id: IAO:0000129 name: version number def: "A version number is an information content entity which is a sequence of characters borne by part of each of a class of manufactured products or its packaging and indicates its order within a set of other products having the same name." [] is_a: IAO:0000028 ! symbol property_value: IAO:0000111 "version number" xsd:string property_value: IAO:0000114 IAO:0000123 property_value: IAO:0000116 "Note: we feel that at the moment we are happy with a general version number, and that we will subclass as needed in the future. For example, see 7. genome sequence version" xsd:string property_value: IAO:0000117 "GROUP: IAO" xsd:string [Term] id: IAO:0000131 name: serial number def: "A serial number is an information content entity which is a unique sequence of characters borne by part of manufactured product or its packaging that is assigned to each individual in some class of products, and so can serve as a way to identify an individual product within the class. Serial numbers can be encoded in a variety of other information objects, such as bar codes, numerals, or patterns of dots." [] is_a: IAO:0000028 ! symbol property_value: IAO:0000111 "serial number" xsd:string property_value: IAO:0000114 IAO:0000123 property_value: IAO:0000116 "Note: during the call there was some confusion between serial number and model number. We agreed that it would be very helpful for all those terms to have example of usages - please add if you have any :-)" xsd:string property_value: IAO:0000117 "GROUP: IAO" xsd:string [Term] id: IAO:0000132 name: lot number def: "A lot number is an information content entity which is an identical sequence of character borne by part of manufactured product or its packaging for each instances of a product class in a discrete batch of an item. Lot numbers are usually assigned to each separate production run of an item. Manufacturing as a lot might be due to a variety of reasons, for example, a single process during which many individuals are made from the same portion of source material. Lot numbers can be encoded in a pattern of other information objects, such as bar codes, numerals, or patterns of dots." [] is_a: IAO:0000028 ! symbol property_value: IAO:0000111 "lot number" xsd:string property_value: IAO:0000114 IAO:0000123 property_value: IAO:0000117 "GROUP: IAO" xsd:string property_value: IAO:0000118 "batch number" xsd:string [Term] id: IAO:0000140 name: setting datum def: "A settings datum is a datum that denotes some configuration of an instrument." [] is_a: IAO:0000027 ! data item property_value: IAO:0000114 IAO:0000123 property_value: IAO:0000116 "2/3/2009 Feedback from OBI\n\nThis should be a \"setting specification\". There is a question of whether it is information about a realizable or not.\n\nPro other specification are about realizables.\nCons sometimes specifies a quality which is not a realizable." xsd:string property_value: IAO:0000116 "Alan grouped these in placeholder for the moment. Name by analogy to measurement datum." xsd:string [Term] id: IAO:0000141 name: obsolete_digital quality is_a: ObsoleteClass ! Obsolete Class property_value: IAO:0000116 "3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4" xsd:string property_value: IAO:0000116 "Need to rework digital entity. Digital quality was suggested by Barry." xsd:string property_value: IAO:0000231 IAO:0000103 is_obsolete: true [Term] id: IAO:0000144 name: conclusion textual entity def: "A textual entity that expresses the results of reasoning about a problem, for instance as typically found towards the end of scientific papers." [] is_a: IAO:0000300 ! textual entity property_value: IAO:0000111 "conclusion textual entity" xsd:string property_value: IAO:0000112 "that fucoidan has a small statistically significant effect on AT3 level but no useful clinical effect as in-vivo anticoagulant, a paraphrase of part of the last paragraph of the discussion section of the paper 'Pilot clinical study to evaluate the anticoagulant activity of fucoidan', by Lowenthal et. al.PMID:19696660" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000116 "2009/09/28 Alan Ruttenberg. Fucoidan-use-case" xsd:string property_value: IAO:0000116 "2009/10/23 Alan Ruttenberg: We need to work on the definition still" xsd:string property_value: IAO:0000117 "Person:Alan Ruttenberg" xsd:string [Term] id: IAO:0000178 name: material information bearer def: "A material entity in which a concretization of an information content entity inheres." [] is_a: BFO:0000040 ! material entity property_value: IAO:0000111 "material information bearer" xsd:string property_value: IAO:0000112 "a brain" xsd:string property_value: IAO:0000112 "a hard drive" xsd:string property_value: IAO:0000112 "A page of a paperback novel with writing on it. The paper itself is a material information bearer, the pattern of ink is the information carrier." xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "GROUP: IAO" xsd:string [Term] id: IAO:0000179 name: histogram def: "A histogram is a report graph which is a statistical description of a\ndistribution in terms of occurrence frequencies of different event classes." [] is_a: IAO:0000038 ! graph property_value: IAO:0000111 "histogram" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "PERSON:Chris Stoeckert" xsd:string property_value: IAO:0000117 "PERSON:James Malone" xsd:string property_value: IAO:0000117 "PERSON:Melanie Courtot" xsd:string property_value: IAO:0000119 GROUP:OBI xsd:string [Term] id: IAO:0000180 name: heatmap def: "A heatmap is a report graph which is a graphical representation of data\nwhere the values taken by a variable(s) are shown as colors in a\ntwo-dimensional map." [] is_a: IAO:0000038 ! graph property_value: IAO:0000111 "heatmap" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "PERSON:Chris Stoeckert" xsd:string property_value: IAO:0000117 "PERSON:James Malone" xsd:string property_value: IAO:0000117 "PERSON:Melanie Courtot" xsd:string property_value: IAO:0000119 GROUP:OBI xsd:string [Term] id: IAO:0000181 name: Venn diagram def: "A Venn diagram is a report graph showing all hypothetically possible\nlogical relations between a finite collection of sets." [] is_a: IAO:0000038 ! graph property_value: IAO:0000111 "Venn diagram" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "PERSON:Chris Stoeckert" xsd:string property_value: IAO:0000117 "PERSON:James Malone" xsd:string property_value: IAO:0000117 "PERSON:Melanie Courtot" xsd:string property_value: IAO:0000119 "WEB: http://en.wikipedia.org/wiki/Venn_diagram" xsd:string [Term] id: IAO:0000182 name: obsolete_survival curve def: "A survival curve is a report graph which is a graphical representation of data where the percentage of survival is plotted as a function of time." [] is_a: ObsoleteClass ! Obsolete Class property_value: IAO:0000111 "obsolete_survival curve" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "PERSON:Chris Stoeckert" xsd:string property_value: IAO:0000117 "PERSON:James Malone" xsd:string property_value: IAO:0000117 "PERSON:Melanie Courtot" xsd:string property_value: IAO:0000119 "WEB: http://www.graphpad.com/www/book/survive.htm" xsd:string property_value: IAO:0000231 IAO:0000103 is_obsolete: true [Term] id: IAO:0000183 name: dendrogram def: "A dendrogram is a report graph which is a tree diagram\nfrequently used to illustrate the arrangement of the clusters produced by a\nclustering algorithm." [] is_a: IAO:0000038 ! graph property_value: IAO:0000111 "dendrogram" xsd:string property_value: IAO:0000112 "Dendrograms are often used in computational biology to\nillustrate the clustering of genes." xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "PERSON:Chris Stoeckert" xsd:string property_value: IAO:0000117 "PERSON:James Malone" xsd:string property_value: IAO:0000117 "PERSON:Melanie Courtot" xsd:string property_value: IAO:0000119 "WEB: http://en.wikipedia.org/wiki/Dendrogram" xsd:string [Term] id: IAO:0000184 name: scatter plot def: "A scatterplot is a graph which uses Cartesian coordinates to display values for two variables for a set of data. The data is displayed as a collection of points, each having the value of one variable determining the position on the horizontal axis and the value of the other variable determining the position on the vertical axis." [] is_a: IAO:0000038 ! graph property_value: IAO:0000111 "scatter plot" xsd:string property_value: IAO:0000112 "Comparison of gene expression values in two samples can be displayed in a scatter plot" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "PERSON:Chris Stoeckert" xsd:string property_value: IAO:0000117 "PERSON:James Malone" xsd:string property_value: IAO:0000117 "PERSON:Melanie Courtot" xsd:string property_value: IAO:0000118 "scattergraph" xsd:string property_value: IAO:0000119 "WEB: http://en.wikipedia.org/wiki/Scatterplot" xsd:string [Term] id: IAO:0000185 name: photograph def: "A photograph is created by projecting an image onto a photosensitive surface such as a chemically treated plate or film, CCD receptor, etc." [] is_a: IAO:0000101 ! image property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "PERSON:Alan Ruttenberg" xsd:string property_value: IAO:0000117 "PERSON:Joanne Luciano" xsd:string property_value: IAO:0000117 "PERSON:Melanie Courtot" xsd:string property_value: IAO:0000119 "WEB: http://en.wiktionary.org/wiki/photograph" xsd:string [Term] id: IAO:0000186 name: photographic print def: "A photographic print is a material entity upon which a photograph generically depends." [] is_a: IAO:0000178 ! material information bearer property_value: IAO:0000111 "photographic print" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "PERSON:Alan Ruttenberg" xsd:string property_value: IAO:0000117 "PERSON:Melanie Courtot" 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:0000300 name: textual entity def: "A textual entity is a part of a manifestation (FRBR sense), a generically dependent continuant whose concretizations are patterns of glyphs intended to be interpreted as words, formulas, etc." [] is_a: IAO:0000030 ! information content entity property_value: IAO:0000111 "textual entity" xsd:string property_value: IAO:0000112 "Words, sentences, paragraphs, and the written (non-figure) parts of publications are all textual entities" xsd:string property_value: IAO:0000114 IAO:0000123 property_value: IAO:0000116 "AR, (IAO call 2009-09-01): a document as a whole is not typically a textual entity, because it has pictures in it - rather there are parts of it that are textual entities. Examples: The title, paragraph 2 sentence 7, etc." xsd:string property_value: IAO:0000116 "MC, 2009-09-14 (following IAO call 2009-09-01): textual entities live at the FRBR (http://en.wikipedia.org/wiki/Functional_Requirements_for_Bibliographic_Records) manifestation level. Everything is significant: line break, pdf and html versions of same document are different textual entities." xsd:string property_value: IAO:0000117 "PERSON: Lawrence Hunter" xsd:string property_value: IAO:0000118 "text" xsd:string [Term] id: IAO:0000301 name: citation def: "a textual entity intended to identify a particular publication" [] is_a: IAO:0000300 ! textual entity relationship: IAO:0000136 IAO:0000310 ! is about document property_value: IAO:0000111 "citation" xsd:string property_value: IAO:0000112 "Verspoor, K., Cohen, KB., Hunter, L. Textual characteristics of traditional and Open Access scientific journals are similar, BMC Bioinformatics 2009, 10:183." xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "PERSON: Lawrence Hunter" xsd:string [Term] id: IAO:0000302 name: author identification def: "A textual entity intended to identify a particular author" [] is_a: IAO:0000590 ! written name property_value: IAO:0000111 "author identification" xsd:string property_value: IAO:0000112 "L. Hunter" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "PERSON: Lawrence Hunter" xsd:string [Term] id: IAO:0000303 name: institutional identification def: "A textual entity intended to identify a particular institution" [] is_a: IAO:0000300 ! textual entity property_value: IAO:0000111 "institutional identification" xsd:string property_value: IAO:0000112 "University of Colorado Denver School of Medicine" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "PERSON: Lawrence Hunter" xsd:string [Term] id: IAO:0000304 name: caption def: "A textual entity that describes a figure" [] is_a: IAO:0000300 ! textual entity relationship: IAO:0000136 IAO:0000308 ! is about figure property_value: IAO:0000111 "caption" xsd:string property_value: IAO:0000112 "Figure 1: A system diagram describing the modules of the Hanalyzer. Reading methods (green) take external sources of knowledge (blue) and extract information from them, either by parsing structured data or biomedical language processing to extract information from unstructured data. Reading modules are responsible for tracking the provenance of all knowledge. Reasoning methods (yellow) enrich the knowledge that results from reading by, for example, noting two genes that are annotated to the same ontology term or database entry. All knowledge sources, read or reasoned, are assigned a reliability score, and all are combined using that score into a knowledge network (orange) that represents the integration of all sorts of relationship between a pair of genes and a combined reliability score. A data network (also orange) is created from experimental results to be analyzed. The reporting modules (pink) integrate the data and knowledge networks, producing visualizations that can be queried with the associated drill-down tool." xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "PERSON: Lawrence Hunter" xsd:string [Term] id: IAO:0000305 name: document title def: "A textual entity that names a document" [] is_a: IAO:0000300 ! textual entity property_value: IAO:0000111 "document title" xsd:string property_value: IAO:0000112 "Textual characteristics of traditional and Open Access scientific journals are similar" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "PERSON: Lawrence Hunter" xsd:string [Term] id: IAO:0000306 name: table def: "A textual entity that contains a two-dimensional arrangement of texts repeated at regular intervals across a spatial range, such that the spatial relationships among the constituent texts expresses propositions" [] is_a: IAO:0000300 ! textual entity property_value: IAO:0000111 "table" xsd:string property_value: IAO:0000112 "| T F\n--+-----\nT | T F\nF | F F" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "PERSON: Lawrence Hunter" xsd:string [Term] id: IAO:0000307 name: table of abbreviations def: "A table where the constituent texts are abbreviations and their expansions" [] is_a: IAO:0000306 ! table property_value: IAO:0000111 "table of abbreviations" xsd:string property_value: IAO:0000112 "IAO information artifact ontology\nOBI ontology of biomedical investiations\nGO gene ontology" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "PERSON: Lawrence Hunter" xsd:string [Term] id: IAO:0000308 name: figure def: "An information content entity consisting of a two dimensional arrangement of information content entities such that the arrangement itself is about something." [] is_a: IAO:0000030 ! information content entity property_value: IAO:0000111 "figure" xsd:string property_value: IAO:0000112 "Any picture, diagram or table" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "PERSON: Lawrence Hunter" xsd:string [Term] id: IAO:0000309 name: diagram def: "A figure that expresses one or more propositions" [] is_a: IAO:0000308 ! figure property_value: IAO:0000111 "diagram" xsd:string property_value: IAO:0000112 "A molecular structure ribbon cartoon showing helices, turns and sheets and their relations to each other in space." xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "PERSON: Lawrence Hunter" xsd:string [Term] id: IAO:0000310 name: document def: "A collection of information content entities intended to be understood together as a whole" [] is_a: IAO:0000030 ! information content entity property_value: IAO:0000111 "document" xsd:string property_value: IAO:0000112 "A journal article, patent application, laboratory notebook, or a book" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "PERSON: Lawrence Hunter" xsd:string [Term] id: IAO:0000311 name: publication def: "A document that has been accepted by a publisher" [] is_a: IAO:0000310 ! document property_value: IAO:0000111 "publication" xsd:string property_value: IAO:0000112 "A journal article or book" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "PERSON: Lawrence Hunter" xsd:string [Term] id: IAO:0000312 name: publication about an investigation def: "A publication that is about an investigation" [] is_a: IAO:0000311 ! publication relationship: IAO:0000136 OBI:0000066 ! is about investigation property_value: IAO:0000111 "publication about an investigation" xsd:string property_value: IAO:0000112 "Most scientific journal articles" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "PERSON: Lawrence Hunter" xsd:string property_value: IAO:0000118 "scientific publication" xsd:string [Term] id: IAO:0000313 name: patent def: "A document that has been accepted by a patent authority" [] is_a: IAO:0000310 ! document property_value: IAO:0000111 "patent" xsd:string property_value: IAO:0000112 "US Patent 6,449,603" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "PERSON: Lawrence Hunter" xsd:string [Term] id: IAO:0000314 name: document part def: "an information content entity that is part of a document" [] is_a: IAO:0000030 ! information content entity relationship: BFO:0000050 IAO:0000310 ! part of document property_value: IAO:0000111 "document part" xsd:string property_value: IAO:0000112 "An abstract, introduction, method or results section." xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "PERSON: Lawrence Hunter" xsd:string [Term] id: IAO:0000315 name: abstract def: "A summary of the entire document that is substantially smaller than the document it summarizes. It is about the document it summarizes." [] is_a: IAO:0000314 ! document part relationship: IAO:0000136 IAO:0000310 ! is about document property_value: IAO:0000111 "abstract" xsd:string property_value: IAO:0000112 "The profusion of high-throughput instruments and the explosion of new results in the scientific literature, particularly in molecular biomedicine, is both a blessing and a curse to the bench researcher. Even knowledgeable and experienced scientists can benefit from computational tools that help navigate this vast and rapidly evolving terrain. In this paper, we describe a novel computational approach to this challenge, a knowledge-based system that combines reading, reasoning and reporting methods to facilitate analysis of experimental data. Reading methods extract information from external resources, either by parsing structured data or biomedical language processing to extract information from unstructured data, and track knowledge provenance. Reasoning methods enrich the knowledge that results from reading by, for example, noting two genes that are annotated to the same ontology term or database entry. Reasoning is also used to combine all sources into a knowledge network that represents the integration of all sorts of relationships between a pair of genes, and to calculate a combined reliability score. Reporting methods combine the knowledge network with a congruent network constructed from experimental data and visualize the combined network in a tool that facilitates the knowledge-based analysis of that data." xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "PERSON: Lawrence Hunter" xsd:string [Term] id: IAO:0000316 name: introduction to a publication about an investigation def: "A part of a publication about an investigation that is about the objective specification (why the investigation is being done)" [] is_a: IAO:0000314 ! document part relationship: IAO:0000136 IAO:0000005 ! is about objective specification property_value: IAO:0000111 "introduction to a publication about an investigation" xsd:string property_value: IAO:0000112 "Section labelled 'introduction' of a typical scientific journal article" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "PERSON: Lawrence Hunter" xsd:string property_value: IAO:0000118 "background" xsd:string property_value: IAO:0000118 "introduction" xsd:string [Term] id: IAO:0000317 name: methods section def: "A part of a publication about an investigation that is about the study design of the investigation" [] is_a: IAO:0000314 ! document part relationship: IAO:0000136 OBI:0500000 ! is about study design property_value: IAO:0000111 "methods section" xsd:string property_value: IAO:0000112 "The section labelled 'Methods' or 'Materials and Methods' in a typical scientific journal article." xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "PERSON: Lawrence Hunter" xsd:string property_value: IAO:0000118 "experimental" xsd:string property_value: IAO:0000118 "experimental procedures" xsd:string property_value: IAO:0000118 "experimental section" xsd:string property_value: IAO:0000118 "methods" xsd:string [Term] id: IAO:0000318 name: results section def: "A part of a publication about an investigation that is about a study design execution" [] is_a: IAO:0000314 ! document part relationship: IAO:0000136 OBI:0000471 ! is about study design execution property_value: IAO:0000111 "results section" xsd:string property_value: IAO:0000112 "The section labelled 'results' in a typical scientific journal article" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "PERSON: Lawrence Hunter" xsd:string property_value: IAO:0000118 "results" xsd:string [Term] id: IAO:0000319 name: discussion section of a publication about an investigation def: "A part of a publication about an investigation that is about the study interpretation of the investigation" [] is_a: IAO:0000314 ! document part property_value: IAO:0000111 "discussion section of a publication about an investigation" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "PERSON: Lawrence Hunter" xsd:string property_value: IAO:0000118 "discussion" xsd:string property_value: IAO:0000118 "discussion section" xsd:string [Term] id: IAO:0000320 name: references section def: "A part of a document that has citations as parts" [] is_a: IAO:0000314 ! document part relationship: BFO:0000051 IAO:0000301 ! has part citation property_value: IAO:0000111 "references section" xsd:string property_value: IAO:0000112 "The list of citations found at the end of a scientific publication, grant proposal or patent application, sometimes called \"literature cited\" or \"bibliography\"" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "PERSON: Lawrence Hunter" xsd:string [Term] id: IAO:0000321 name: author list def: "part of a document that enumerates the authors of the document" [] is_a: IAO:0000314 ! document part relationship: BFO:0000051 IAO:0000302 ! has part author identification property_value: IAO:0000111 "author list" xsd:string property_value: IAO:0000112 "Lawrence Hunter and Kevin Brettonel Cohen" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "PERSON: Lawrence Hunter" xsd:string [Term] id: IAO:0000322 name: institution list def: "part of a document that has parts that are institution identifications associated with the authors of the document" [] is_a: IAO:0000314 ! document part relationship: BFO:0000051 IAO:0000303 ! has part institutional identification property_value: IAO:0000111 "institution list" xsd:string property_value: IAO:0000112 "The University of Colorado Denver School of Medicine and the University of Colorado Boulder." xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "PERSON: Lawrence Hunter" xsd:string [Term] id: IAO:0000323 name: author contributions section def: "A part of a publication that is about the specific contributions of each author" [] is_a: IAO:0000314 ! document part property_value: IAO:0000111 "author contributions section" xsd:string property_value: IAO:0000112 "LH conceived of the hypothesis, designed the study and contributed to the writing of the manuscript. KBC executed the experiments, analyzed the data, and contributed to the writing of the manuscript." xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "PERSON: Lawrence Hunter" xsd:string property_value: IAO:0000118 "author contributions" xsd:string property_value: IAO:0000118 "contributions by the authors" xsd:string [Term] id: IAO:0000324 name: acknowledgements section def: "Part of a publication that is about the contributions of people or institutions other than the authors." [] is_a: IAO:0000314 ! document part property_value: IAO:0000111 "acknowledgements section" xsd:string property_value: IAO:0000112 "The authors wish to thank Alan Ruttenberg for his constructive comments about an earlier draft of this manuscript" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "PERSON: Lawrence Hunter" xsd:string property_value: IAO:0000118 "acknowledgements" xsd:string property_value: IAO:0000118 "acknowledgments" xsd:string [Term] id: IAO:0000325 name: footnote def: "A part of a document that is about a specific other part of the document. Usually footnotes are spatially segregated from the rest of the document." [] is_a: IAO:0000314 ! document part relationship: IAO:0000136 IAO:0000314 ! is about document part property_value: IAO:0000111 "footnote" xsd:string property_value: IAO:0000112 "The referent in the text is usually indicated by a special typographic character such as * or a superscripted number, which is also used to indicate the footnote that refers to that text." xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "PERSON: Lawrence Hunter" xsd:string property_value: IAO:0000118 "endnote" xsd:string [Term] id: IAO:0000326 name: supplementary material to a document def: "part of a document that is segregated from the rest of the document due to its size" [] is_a: IAO:0000314 ! document part property_value: IAO:0000111 "supplementary material to a document" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "PERSON: Lawrence Hunter" xsd:string property_value: IAO:0000118 "additional information" xsd:string property_value: IAO:0000118 "appendix" xsd:string property_value: IAO:0000118 "supplemental information" xsd:string property_value: IAO:0000118 "supplementary material" xsd:string property_value: IAO:0000118 "supporting information" xsd:string [Term] id: IAO:0000327 name: table of contents def: "A table that relates document parts to specific locations in a document (usually page numbers). This is also a document part (subsumption there should be inferred)." [] is_a: IAO:0000306 ! table property_value: IAO:0000111 "table of contents" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "PERSON: Lawrence Hunter" xsd:string [Term] id: IAO:0000328 name: table of figures def: "A table that relates figures in a document to specific locations in that document (usually page numbers). This is also a document part (subsumption there should be inferred)." [] is_a: IAO:0000306 ! table property_value: IAO:0000111 "table of figures" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "PERSON: Lawrence Hunter" xsd:string [Term] id: IAO:0000329 name: running title def: "A shorter version of a document title" [] is_a: IAO:0000305 ! document title property_value: IAO:0000111 "running title" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "PERSON: Lawrence Hunter" xsd:string [Term] id: IAO:0000330 name: copyright section def: "A document part that describes legal restrictions on making or distributing copies of the document" [] is_a: IAO:0000314 ! document part property_value: IAO:0000111 "copyright section" xsd:string property_value: IAO:0000112 "This work is licensed under a Creative Commons Attribution-Share Alike 3.0 United States License." xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "PERSON: Lawrence Hunter" xsd:string [Term] id: IAO:0000400 name: cartesian spatial coordinate datum def: "A cartesian spatial coordinate datum is a representation of a point in a spatial region, in which equal changes in the magnitude of a coordinate value denote length qualities with the same magnitude" [] is_a: IAO:0000027 ! data item relationship: IAO:0000219 BFO:0000018 ! denotes zero-dimensional spatial region property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000116 "2009-08-18 Alan Ruttenberg - question to BFO list about whether the BFO sense of the lower dimensional regions is that they are always part of actual space (the three dimensional sort) http://groups.google.com/group/bfo-discuss/browse_thread/thread/9d04e717e39fb617" xsd:string property_value: IAO:0000117 "Alan Ruttenberg" xsd:string property_value: IAO:0000232 "AR notes: We need to discuss whether it should include site." xsd:string property_value: seeAlso http://groups.google.com/group/bfo-discuss/browse_thread/thread/9d04e717e39fb617 xsd:string [Term] id: IAO:0000401 name: one dimensional cartesian spatial coordinate datum def: "A cartesion spatial coordinate datum that uses one value to specify a position along a one dimensional spatial region" [] is_a: IAO:0000400 ! cartesian spatial coordinate datum property_value: IAO:0000114 IAO:0000123 property_value: IAO:0000117 "Alan Ruttenberg" xsd:string [Term] id: IAO:0000402 name: two dimensional cartesian spatial coordinate datum def: "A cartesion spatial coordinate datum that uses two values to specify a position within a two dimensional spatial region" [] is_a: IAO:0000400 ! cartesian spatial coordinate datum property_value: IAO:0000114 IAO:0000123 property_value: IAO:0000117 "Alan Ruttenberg" xsd:string [Term] id: IAO:0000403 name: three dimensional cartesian spatial coordinate datum def: "A cartesion spatial coordinate datum that uses three values to specify a position within a three dimensional spatial region" [] is_a: IAO:0000400 ! cartesian spatial coordinate datum property_value: IAO:0000114 IAO:0000123 property_value: IAO:0000117 "Alan Ruttenberg" xsd:string [Term] id: IAO:0000408 name: length measurement datum def: "A scalar measurement datum that is the result of measurement of length quality" [] is_a: IAO:0000032 ! scalar measurement datum relationship: IAO:0000039 UO:0000001 ! has measurement unit label length unit relationship: IAO:0000221 PATO:0000122 ! is quality measurement of length property_value: IAO:0000114 IAO:0000123 property_value: IAO:0000117 "Alan Ruttenberg" 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: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:0000414 name: mass measurement datum def: "A scalar measurement datum that is the result of measurement of mass quality" [] is_a: IAO:0000032 ! scalar measurement datum relationship: IAO:0000039 UO:0000002 ! has measurement unit label mass unit relationship: IAO:0000221 PATO:0000125 ! is quality measurement of mass property_value: IAO:0000114 IAO:0000123 property_value: IAO:0000116 "2009/09/28 Alan Ruttenberg. Fucoidan-use-case" xsd:string property_value: IAO:0000117 "Person:Alan Ruttenberg" xsd:string [Term] id: IAO:0000415 name: hypothesis textual entity def: "A textual entity that expresses an assertion that is intended to be tested." [] is_a: IAO:0000300 ! textual entity property_value: IAO:0000111 "hypothesis textual entity" xsd:string property_value: IAO:0000112 "that fucoidan has a small statistically significant effect on AT3 level but no useful clinical effect as in-vivo anticoagulant, a paraphrase of part of the last paragraph of the discussion section of the paper 'Pilot clinical study to evaluate the anticoagulant activity of fucoidan', by Lowenthal et. al.PMID:19696660" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000116 "2009/09/28 Alan Ruttenberg. Fucoidan-use-case" xsd:string property_value: IAO:0000117 "Person:Alan Ruttenberg" xsd:string [Term] id: IAO:0000416 name: time measurement datum def: "A scalar measurement datum that is the result of measuring a temporal interval" [] is_a: IAO:0000032 ! scalar measurement datum relationship: IAO:0000039 UO:0000003 ! has measurement unit label time unit relationship: IAO:0000413 BFO:0000015 ! is duration of process property_value: IAO:0000114 IAO:0000123 property_value: IAO:0000116 "2009/09/28 Alan Ruttenberg. Fucoidan-use-case" xsd:string property_value: IAO:0000117 "Person:Alan Ruttenberg" xsd:string [Term] id: IAO:0000422 name: postal address def: "A textual entity that is used as directive to deliver something to a person, or organization" [] is_a: IAO:0000300 ! textual entity relationship: IAO:0000136 GAZ:00000448 ! is about geographic location property_value: IAO:0000114 IAO:0000123 property_value: IAO:0000116 "2010-05-24 Alan Ruttenberg. Use label for the string representation. See issue https://github.com/information-artifact-ontology/IAO/issues/59" xsd:string [Term] id: IAO:0000429 name: email address is_a: IAO:0000030 ! information content entity property_value: IAO:0000111 "email address" xsd:string property_value: IAO:0000114 IAO:0000123 property_value: IAO:0000116 "Alan Ruttenberg 1/3/2012 - Provisional id, see issue at https://github.com/information-artifact-ontology/IAO/issues/130&thanks=130&ts=1325636583" xsd:string property_value: IAO:0000117 "Person:Alan Ruttenberg" xsd:string property_value: IAO:0000117 "Person:Chris Stoeckart" xsd:string [Term] id: IAO:0000442 name: author role def: "A role inhering in a person or organization that is realized when the bearer participates in the work which is the basis of the document, in the writing of the document, and signs it with their name." [] is_a: BFO:0000023 ! role property_value: IAO:0000111 "author role" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string property_value: IAO:0000117 "PERSON: Melanie Courtot" xsd:string [Term] id: IAO:0000443 name: data item extraction from journal article def: "a planned process in which journal articles are read or processed and data items are extracted, typically for further analysis or indexing" [] is_a: OBI:0000011 ! planned process relationship: OBI:0000293 IAO:0000013 ! has_specified_input journal article relationship: OBI:0000299 IAO:0000027 ! has_specified_output data item property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Person:Alan Ruttenberg" xsd:string [Term] id: IAO:0000572 name: documenting def: "a planned process in which a document is created or added to by including the specified input in it." [] is_a: OBI:0000011 ! planned process relationship: OBI:0000293 IAO:0000030 ! has_specified_input information content entity relationship: OBI:0000299 IAO:0000310 ! has_specified_output document property_value: IAO:0000112 "Recording the current temperature in a laboratory notebook. Writing a journal article. Updating a patient record in a database." xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "6/11/9: Edited at OBI workshop. We need to be able identify a child form of information artifact which corresponds to something enduring (not brain like). This used to be restricted to physical document or digital entity as the output, but that excludes e.g. an audio cassette tape" xsd:string property_value: IAO:0000117 "Bjoern Peters" xsd:string property_value: IAO:0000119 "wikipedia http://en.wikipedia.org/wiki/Documenting" xsd:string [Term] id: IAO:0000573 name: line graph def: "A line graph is a type of graph created by connecting a series of data\npoints together with a line." [] is_a: IAO:0000038 ! graph property_value: IAO:0000111 "line graph" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "PERSON:Chris Stoeckert" xsd:string property_value: IAO:0000117 "PERSON:Melanie Courtot" xsd:string property_value: IAO:0000118 "line chart" xsd:string property_value: IAO:0000119 GROUP:OBI xsd:string property_value: IAO:0000119 "WEB: http://en.wikipedia.org/wiki/Line_chart" xsd:string [Term] id: IAO:0000574 name: assigning a centrally registered identifier def: "a planned process in which a new CRID is created, associated with an entity, and stored in the CRID registry thereby registering it as being associated with some entity" [] is_a: OBI:0000011 ! planned process relationship: OBI:0000299 IAO:0000577 ! has_specified_output centrally registered identifier symbol relationship: RO:0000057 IAO:0000579 ! has participant centrally registered identifier registry property_value: IAO:0000112 "A new pubmed ID being created for a journal article, and the associated pubmed record containing information to the journal article. A license plate number registered at the DMV to be belonging to a specific vehicle and owner. Placing a barcode on a product and entering information in a database that this barcode is assigned." xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000116 "2014-05-05: It is the CRID registry that assigns CRIDs, not the users of the registry." xsd:string property_value: IAO:0000117 "Person:Alan Ruttenberg" xsd:string property_value: IAO:0000117 "Person:Bjoern Peters" xsd:string property_value: IAO:0000117 "Person:Melanie Courtot" xsd:string property_value: IAO:0000118 "assigning a CRID" xsd:string [Term] id: IAO:0000575 name: associating information with a centrally registered identifier in its registry def: "A planned process in which a CRID registry associates an information content entity with a CRID symbol" [] is_a: OBI:0000011 ! planned process relationship: OBI:0000293 IAO:0000030 ! has_specified_input information content entity relationship: OBI:0000293 IAO:0000577 ! has_specified_input centrally registered identifier symbol relationship: RO:0000057 IAO:0000579 ! has participant centrally registered identifier registry property_value: IAO:0000112 "Articles in Pubmed are reviewed by curators who add MESH terms to the Pubmed records in order to categorize them better and improve the ability to search for them. " xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "PERSON:Alan Ruttenberg" xsd:string property_value: IAO:0000118 "associating information with a CRID in the CRID registry" xsd:string [Term] id: IAO:0000576 name: obsolete_establishing a CRID registry def: "a planned process with the objective to establish a system that allows to refer to specific entities of a certain kind and store information about them, by establishing a CRID registry and plan specifications for the process of 1) assigning a CRID and 2) looking up a CRID." [] is_a: ObsoleteClass ! Obsolete Class property_value: IAO:0000116 "MC, 20101124: deprecated following discussion at IAO call 20101124. Term was deemed not necessary - no use case for now." xsd:string property_value: IAO:0000231 IAO:0000103 is_obsolete: true [Term] id: IAO:0000577 name: centrally registered identifier symbol def: "A symbol that is part of a CRID and that is sufficient to look up a record from the CRID's registry." [] is_a: IAO:0000028 ! symbol relationship: BFO:0000050 IAO:0000578 ! part of centrally registered identifier property_value: IAO:0000112 "The sentence \"The article has Pubmed ID 12345.\" contains a CRID that has two parts: one part is the CRID symbol, which is '12345'; the other part denotes the CRID registry, which is Pubmed." xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string property_value: IAO:0000117 "PERSON: Bill Hogan" xsd:string property_value: IAO:0000117 "PERSON: Bjoern Peters" xsd:string property_value: IAO:0000117 "PERSON: Melanie Courtot" xsd:string property_value: IAO:0000118 "CRID symbol" xsd:string property_value: IAO:0000119 "Original proposal from Bjoern, discussions at IAO calls" xsd:string [Term] id: IAO:0000578 name: centrally registered identifier def: "An information content entity that consists of a CRID symbol and additional information about the CRID registry to which it belongs." [] is_a: IAO:0000030 ! information content entity relationship: BFO:0000051 IAO:0000577 ! has part centrally registered identifier symbol property_value: IAO:0000112 "The sentence \"The article has Pubmed ID 12345.\" contains a CRID that has two parts: one part is the CRID symbol, which is '12345'; the other part denotes the CRID registry, which is Pubmed." xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000116 "2014-05-05: In defining this term we take no position on what the CRID denotes. In particular do not assume it denotes a *record* in the CRID registry (since the registry might not have 'records')." xsd:string property_value: IAO:0000116 "Alan, IAO call 20101124: potentially the CRID denotes the instance it was associated with during creation. \n" xsd:string property_value: IAO:0000116 "Note, IAO call 20101124: URIs are not always CRID, as not centrally registered. We acknowledge that CRID is a subset of a larger identifier class, but this subset fulfills our current needs. OBI PURLs are CRID as they are registered with OCLC. UPCs (Universal Product Codes from AC Nielsen)are not CRID as they are not centrally registered." xsd:string property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string property_value: IAO:0000117 "PERSON: Bill Hogan" xsd:string property_value: IAO:0000117 "PERSON: Bjoern Peters" xsd:string property_value: IAO:0000117 "PERSON: Melanie Courtot" xsd:string property_value: IAO:0000118 "CRID" xsd:string property_value: IAO:0000119 "Original proposal from Bjoern, discussions at IAO calls" xsd:string [Term] id: IAO:0000579 name: centrally registered identifier registry def: "A CRID registry is a dataset of CRID records, each consisting of a CRID symbol and additional information which was recorded in the dataset through a assigning a centrally registered identifier process." [] is_a: IAO:0000100 ! data set property_value: IAO:0000112 "PubMed is a CRID registry. It has a dataset of PubMed identifiers associated with journal articles. " xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string property_value: IAO:0000117 "PERSON: Bill Hogan" xsd:string property_value: IAO:0000117 "PERSON: Bjoern Peters" xsd:string property_value: IAO:0000117 "PERSON: Melanie Courtot" xsd:string property_value: IAO:0000118 "CRID registry" xsd:string property_value: IAO:0000119 "Original proposal from Bjoern, discussions at IAO calls" xsd:string [Term] id: IAO:0000580 name: looking up a centrally registered identifier def: "A planned process in which a request to a CRID registry is made to return the information associated with a CRID symbol" [] is_a: OBI:0000011 ! planned process relationship: OBI:0000293 IAO:0000577 ! has_specified_input centrally registered identifier symbol relationship: OBI:0000299 IAO:0000030 ! has_specified_output information content entity relationship: RO:0000057 IAO:0000579 ! has participant centrally registered identifier registry property_value: IAO:0000112 "Going to the PubMed website and entering a PubMed ID in order to retrieve the Pubmed information associated with that ID. " xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string property_value: IAO:0000117 "PERSON: Bill Hogan" xsd:string property_value: IAO:0000117 "PERSON: Bjoern Peters" xsd:string property_value: IAO:0000117 "PERSON: Melanie Courtot" xsd:string property_value: IAO:0000118 "looking up a CRID" xsd:string [Term] id: IAO:0000582 name: time stamped measurement datum is_a: IAO:0000109 ! measurement datum relationship: IAO:0000581 IAO:0000416 ! has time stamp time measurement datum relationship: IAO:0000583 IAO:0000109 ! has measurement datum measurement datum property_value: IAO:0000114 IAO:0000123 [Term] id: IAO:0000584 name: time sampled measurement data set def: "A data set that is an aggregate of data recording some measurement at a number of time points. The time series data set is an ordered list of pairs of time measurement data and the corresponding measurement data acquired at that time." [] is_a: IAO:0000100 ! data set relationship: BFO:0000051 IAO:0000582 ! has part time stamped measurement datum property_value: IAO:0000112 "pmid:20604925 - time-lapse live cell microscopy" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Alan Ruttenberg" xsd:string property_value: IAO:0000118 "experimental time series" xsd:string [Term] id: IAO:0000590 name: written name def: "A textual entity that denotes a particular in reality." [] is_a: IAO:0000300 ! textual entity property_value: IAO:0000111 "written name" xsd:string property_value: IAO:0000112 "\"Bill Clinton\"" xsd:string property_value: IAO:0000112 "\"The Eiffel Tower\"" xsd:string property_value: IAO:0000112 "\"United States of America\"" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "PERSON: Bill Hogan" xsd:string property_value: IAO:0000119 https://github.com/information-artifact-ontology/IAO/issues/114 xsd:string property_value: IAO:0000232 "The qualifier \"written\" is to set it apart from spoken names. Also, note the restrictions to particulars. We are not naming universals. We could however, be naming, attributive collections which are particulars, so \"All people located in the boundaries of the city of Little Rock, AR on June 18, 2011 at 9:50a CDT\" would be a name." xsd:string [Term] id: IAO:0000591 name: software method def: "A software method (also called subroutine, subprogram, procedure, method, function, or routine) is software designed to execute a specific task." [] is_a: IAO:0000010 ! software property_value: IAO:0000114 IAO:0000123 property_value: IAO:0000117 "PERSON: Melanie Courtot" xsd:string property_value: IAO:0000117 "PERSON: Michel Dumontier" xsd:string property_value: IAO:0000119 https://github.com/information-artifact-ontology/IAO/issues/80 xsd:string [Term] id: IAO:0000592 name: software module def: " A software module is software composed of a collection of software methods." [] is_a: IAO:0000010 ! software property_value: IAO:0000114 IAO:0000123 property_value: IAO:0000117 "PERSON: Melanei Courtot" xsd:string property_value: IAO:0000117 "PERSON: Michel Dumontier" xsd:string property_value: IAO:0000119 https://github.com/information-artifact-ontology/IAO/issues/80 xsd:string [Term] id: IAO:0000593 name: software library def: "A software library is software composed of a collection of software modules and/or software methods in a form that can be statically or dynamically linked to some software application." [] is_a: IAO:0000010 ! software property_value: IAO:0000114 IAO:0000123 property_value: IAO:0000117 "PERSON: Melanie Courtot" xsd:string property_value: IAO:0000117 "PERSON: Michel Dumontier" xsd:string property_value: IAO:0000119 https://github.com/information-artifact-ontology/IAO/issues/80 xsd:string [Term] id: IAO:0000594 name: software application def: "A software application is software that can be directly executed by some processing unit." [] is_a: IAO:0000010 ! software property_value: IAO:0000114 IAO:0000123 property_value: IAO:0000117 "PERSON: Melanie Courtot" xsd:string property_value: IAO:0000117 "PERSON: Michel Dumontier" xsd:string property_value: IAO:0000119 https://github.com/information-artifact-ontology/IAO/issues/80 xsd:string [Term] id: IAO:0000595 name: software script def: " A software script is software whose instructions can be executed using a software \ninterpreter." [] is_a: IAO:0000010 ! software property_value: IAO:0000114 IAO:0000123 property_value: IAO:0000117 "PERSON: Melanie Courtot" xsd:string property_value: IAO:0000117 "PERSON: Michel Dumontier" xsd:string property_value: IAO:0000119 https://github.com/information-artifact-ontology/IAO/issues/80 xsd:string [Term] id: IAO:0000605 name: abbreviation textual entity def: "A textual entity listing abbreviations and their expansions that are used in a document." [] is_a: IAO:0000300 ! textual entity property_value: IAO:0000111 "abbreviation textual entity" xsd:string property_value: IAO:0000112 "From Shiba et al. Acta Neuropathol Commun. 2013; 1: 45. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3893467/):\n\nBAC: Bacterial artificial chromosome; CR: Calretinin; GFAP: Glial fibrillary acidic protein; MAP: Microtubule-associated protein; MRI: Magnetic resonance imaging; NSC: Neural stem cell; PDA: Patent ductus arteriosus; PMG: Polymicrogyria; PNH: Periventricular nodular heterotopia; VSD: Ventricular septal defect." xsd:string property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183 [Term] id: IAO:0000606 name: abbreviations section def: "A part of a document where abbreviations and their long-forms used within the document are listed." [] is_a: IAO:0000314 ! document part relationship: BFO:0000051 IAO:0000605 ! has part abbreviation textual entity property_value: IAO:0000111 "abbreviations section" xsd:string property_value: IAO:0000112 "The section labelled 'abbreviations' in a typical scientific journal article." xsd:string property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string property_value: IAO:0000118 "abbreviations" xsd:string property_value: IAO:0000118 "abbreviations list" xsd:string property_value: IAO:0000118 "abbreviations used" xsd:string property_value: IAO:0000118 "list of abbreviations" xsd:string property_value: IAO:0000118 "list of abbreviations used" xsd:string property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183 [Term] id: IAO:0000607 name: author information section def: "A part of a document about the authors that provides biographical information and may discuss how the authors' professional experiences are relevant to the work described in the document." [] is_a: IAO:0000314 ! document part relationship: BFO:0000051 IAO:0000608 ! has part author information textual entity property_value: IAO:0000111 "author information section" xsd:string property_value: IAO:0000112 "The section labelled 'author information' in a typical scientific journal article, e.g. in Takon. Ann Gen Psychiatry. 2011; 10: 25. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3204268/)" xsd:string property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string property_value: IAO:0000118 "author information" xsd:string property_value: IAO:0000118 "authors’ information" xsd:string property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183 [Term] id: IAO:0000608 name: author information textual entity def: "A textual entity expression information about an author of a document. This information may include biographical information and may discuss how the authors' professional experiences are relevant to the work described in the document." [] is_a: IAO:0000300 ! textual entity property_value: IAO:0000111 "author information textual entity" xsd:string property_value: IAO:0000112 "From Takon. Ann Gen Psychiatry. 2011; 10: 25. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3204268/):\n\nIT [the author] is the lead paediatrician for ADHD services in East Hertfordshire, UK, where she runs a weekly joint ADHD clinic with the Child and Adolescent psychiatrist and works within an ADHD specialist team. IT also sees children with other neurodisability issues who may have comorbid ADHD, where the presentation may be more complex and challenging to manage. IT has vast experience in managing children with complex ADHD. She has 18 years of experience in paediatrics and also has extensive experience in the use of psychopharmacologic agents in managing children with ADHD." xsd:string property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183 [Term] id: IAO:0000609 name: author summary section def: "A part of a document, distinct from the abstract, that describes the significance and broader context of the document content. The author summary is often written in a non-technical manner and is aimed at both scientists and non-scientist readers." [] is_a: IAO:0000314 ! document part relationship: BFO:0000051 IAO:0000610 ! has part author summary textual entity property_value: IAO:0000111 "author summary section" xsd:string property_value: IAO:0000112 "The section labelled 'synopsis' in a typical scientific journal article, e.g. in Pendse et al. BMC Genomics. 2013; 14: 136. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3608171/)" xsd:string property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string property_value: IAO:0000118 "author summary" xsd:string property_value: IAO:0000118 "summary" xsd:string property_value: IAO:0000118 "synopsis" xsd:string property_value: IAO:0000119 "Article submission guidelines for PLoS Genetics (http://journals.plos.org/plosgenetics/s/submission-guidelines)" xsd:string property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183 [Term] id: IAO:0000610 name: author summary textual entity def: "A textual entity, distinct from the abstract, that describes the significance and broader context of the document content. The author summary is often written in a non-technical manner and is aimed at both scientists and non-scientist readers, e.g as described in the article submission guidelines for PLoS Genetics (http://journals.plos.org/plosgenetics/s/submission-guidelines)." [] is_a: IAO:0000300 ! textual entity property_value: IAO:0000111 "author summary textual entity" xsd:string property_value: IAO:0000112 "From Pendse et al. BMC Genomics. 2013; 14: 136. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3608171/):\n\n\nThe search for genetic risk factors for common human diseases often relies on the use of linkage and association studies to establish correlation between genomic markers and disease risk. These studies require additional functional evaluation of candidate genes, including their possible interaction with diet and environment. The number of candidate genes is typically large and the development of appropriate genetic tools in mammalian systems is slow. By contrast, large-scale genetic screens, using widely available genetic tools, are routinely conducted in the fruit fly Drosophila melanogaster. In this study, we used Drosophila to screen candidate genes identified in human genome-wide scans as associated with risk of metabolic abnormalities such as type 2 diabetes. We show that a number of human candidate genes have fly orthologs that play an important role in Drosophila tolerance to high dietary sucrose. We further explored some of the specific metabolic abnormalities that can result when these genes’ activities are reduced in flies, focusing on a gene we call dHHEX (CG7056), the fly ortholog of human HHEX." xsd:string property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string property_value: IAO:0000119 "Article submission guidelines for PLoS Genetics (http://journals.plos.org/plosgenetics/s/submission-guidelines)." xsd:string property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183 [Term] id: IAO:0000611 name: availability section def: "A part of a document about a resource described in the document, e.g. software, that describes where and/or how that resource can be obtained." [] is_a: IAO:0000314 ! document part relationship: BFO:0000051 IAO:0000612 ! has part availability textual entity property_value: IAO:0000111 "availability section" xsd:string property_value: IAO:0000112 "The section labelled 'availability and requirements' in a typical scientific journal article, e.g. Qi et al. BMC Bioinformatics. 2014; 15: 11. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3897912/)." xsd:string property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string property_value: IAO:0000118 "availability" xsd:string property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183 [Term] id: IAO:0000612 name: availability textual entity def: "A textual entity expressing the location of a resource, e.g. software, or the manner in which a resource can be obtained." [] is_a: IAO:0000300 ! textual entity property_value: IAO:0000111 "availability textual entity" xsd:string property_value: IAO:0000112 "From Qi et al. BMC Bioinformatics. 2014; 15: 11. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3897912/):\n\nProject home page:http://krux.googlecode.com" xsd:string property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183 [Term] id: IAO:0000613 name: case report section def: "A part of a document about the medical history of a specific patient as it relates to the topic of the document." [] is_a: IAO:0000314 ! document part relationship: BFO:0000051 IAO:0000614 ! has part case report textual entity property_value: IAO:0000111 "case report section" xsd:string property_value: IAO:0000112 "The section labelled 'case report' in a typical scientific journal article, e.g. in Taglia et al. Acta Myol. 2012 Dec; 31(3): 201–203. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3631801/)" xsd:string property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string property_value: IAO:0000118 "case presentation" xsd:string property_value: IAO:0000118 "case report" xsd:string property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183 [Term] id: IAO:0000614 name: case report textual entity def: "A textual entity that expresses a detailed account of a portion of the medical history for a specific patient." [] is_a: IAO:0000300 ! textual entity property_value: IAO:0000111 "case report textual entity" xsd:string property_value: IAO:0000112 "Excerpt from Taglia et al. Acta Myol. 2012 Dec; 31(3): 201–203. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3631801/):\n\nThe patient is a 50-year-old man. His medical history was not contributory. At the age of 37 years, he complained of persistent fatigue and dyspnoea even for modest efforts and oedema of lower limbs. The patient was examined at the department of internal medicine of the local hospital, and hospitalised with a diagnosis of dilated cardiomyopathy probably consequence of a myocarditis process. Soon after he was transferred to the cardiologic department of the regional hospital, and pharmacologically treated for heart failure and pulmonary hypertension." xsd:string property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183 [Term] id: IAO:0000615 name: conclusion section def: "A part of a document used to summarize the findings discussed in the document. The conclusion section is typically found near the end of a document. " [] is_a: IAO:0000314 ! document part relationship: BFO:0000051 IAO:0000144 ! has part conclusion textual entity property_value: IAO:0000111 "conclusion section" xsd:string property_value: IAO:0000112 "The section labelled 'conclusion' in a typical scientific journal article." xsd:string property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string property_value: IAO:0000118 "concluding remarks" xsd:string property_value: IAO:0000118 "conclusion" xsd:string property_value: IAO:0000118 "conclusions" xsd:string property_value: IAO:0000118 "findings" xsd:string property_value: IAO:0000118 "summary" xsd:string property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183 [Term] id: IAO:0000616 name: conflict of interest section def: "A part of a document used to declare any competing interests regarding the authors and/or funding organization for the work described in the document." [] is_a: IAO:0000314 ! document part relationship: BFO:0000051 IAO:0000617 ! has part conflict of interest textual entity property_value: IAO:0000111 "conflict of interest section" xsd:string property_value: IAO:0000112 "The section labelled 'conflict of interest statement' in a typical scientific journal article." xsd:string property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string property_value: IAO:0000118 "competing interests" xsd:string property_value: IAO:0000118 "conflict of interest" xsd:string property_value: IAO:0000118 "conflict of interest statement" xsd:string property_value: IAO:0000118 "declaration of competing interests" xsd:string property_value: IAO:0000118 "disclosure of potential conflicts of interest" xsd:string property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183 [Term] id: IAO:0000617 name: conflict of interest textual entity def: "A textual entity that expresses a situation involving one or more of the authors, or the funding source of a document whereby the authors or funding source stand to potentially gain (typically financially) from the results reported in the document." [] is_a: IAO:0000300 ! textual entity property_value: IAO:0000111 "conflict of interest statement" xsd:string property_value: IAO:0000112 "SD [an author] is a Merck employee and Merck is the sponsor of this study. [Taken from 'Effects of obstructive sleep apnoea risk on postoperative respiratory complications: protocol for a hospital-based registry study' Shin et al. 2016 (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4735131/)] " xsd:string property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183 [Term] id: IAO:0000618 name: consent section def: "A part of a document about the consent process that was used to enroll patients in a study." [] is_a: IAO:0000314 ! document part relationship: BFO:0000051 IAO:0000619 ! has part consent textual entity property_value: IAO:0000111 "consent section" xsd:string property_value: IAO:0000112 "The section labelled 'consent' in a typical scientific journal article, e.g. Shiba et al. Acta Neuropathol Commun. 2013; 1: 45. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3893467/)" xsd:string property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string property_value: IAO:0000118 "consent" xsd:string property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183 [Term] id: IAO:0000619 name: consent textual entity def: "A textual entity that documents the consenting process used to enroll patients in a study." [] is_a: IAO:0000300 ! textual entity property_value: IAO:0000111 "consent textual entity" xsd:string property_value: IAO:0000112 "From Shiba et al. Acta Neuropathol Commun. 2013; 1: 45. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3893467/):\n\nWritten informed consent was obtained from the patient’s parents for publication of this Case report and any accompanying images. A copy of the written consent is available for review by the Editor-in chief of this journal." xsd:string property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183 [Term] id: IAO:0000620 name: ethical approval section def: "A part of a document about the governance body responsible for approving the work discussed in a document on an ethical basis." [] is_a: IAO:0000314 ! document part relationship: BFO:0000051 IAO:0000621 ! has part ethical approval textual entity property_value: IAO:0000111 "ethical approval section" xsd:string property_value: IAO:0000112 "The section labelled 'ethical approval' in a typical scientific journal article." xsd:string property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string property_value: IAO:0000118 "ethical approval" xsd:string property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183 [Term] id: IAO:0000621 name: ethical approval textual entity def: "A textual entity that documents the ethical approval of some study design." [] is_a: IAO:0000300 ! textual entity relationship: IAO:0000136 OBI:0500000 ! is about study design property_value: IAO:0000111 "ethical approval textual entity" xsd:string property_value: IAO:0000112 "From McLean et al. Br J Gen Pract. 2014 Jul; 64(624): e440–e447 (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4073730/):\n\nThe NHS National Research Ethics Service had previously approved the use of these anonymised data for research purposes and this analysis did not require independent review." xsd:string property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183 [Term] id: IAO:0000622 name: figures section def: "A part of a document that contains one or more figures." [] is_a: IAO:0000314 ! document part relationship: BFO:0000051 IAO:0000308 ! has part figure property_value: IAO:0000111 "figures section" xsd:string property_value: IAO:0000112 "The section labelled 'figures' in a typical scientific journal article." xsd:string property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string property_value: IAO:0000118 "figures" xsd:string property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183 [Term] id: IAO:0000623 name: funding source declaration section def: "A part of a document used to detail information regarding the source of funding used in support of the generation of the document content." [] is_a: IAO:0000314 ! document part relationship: BFO:0000051 IAO:0000624 ! has part funding source declaration textual entity property_value: IAO:0000111 "funding source declaration section" xsd:string property_value: IAO:0000112 "The section labelled 'funding' in a typical scientific journal article." xsd:string property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string property_value: IAO:0000118 "funding" xsd:string property_value: IAO:0000118 "funding information" xsd:string property_value: IAO:0000118 "funding sources" xsd:string property_value: IAO:0000118 "funding statement" xsd:string property_value: IAO:0000118 "funding/support" xsd:string property_value: IAO:0000118 "source of funding" xsd:string property_value: IAO:0000118 "sources of funding" xsd:string property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183 [Term] id: IAO:0000624 name: funding source declaration textual entity def: "A textual entity documenting the source of funding that supported some study." [] is_a: IAO:0000300 ! textual entity property_value: IAO:0000111 "funding souce declaration textual entity" xsd:string property_value: IAO:0000112 "From Stephan et al. Accid Anal Prev. 2011 May; 43(3): 1062–1067. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3062852/):\n\nThis study was supported by the International Collaborative Research Grants Scheme with joint grants from the Wellcome Trust UK (GR071587MA) and the Australian NHMRC (268055). The funding sources played no role in study design, data collection, analysis or interpretation, writing the report, or the decision to submit the paper for publication." xsd:string property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183 [Term] id: IAO:0000625 name: future directions section def: "A part of a document detailing extensions of the described work that may be implemented at some future point in time." [] is_a: IAO:0000314 ! document part relationship: BFO:0000051 IAO:0000626 ! has part future directions textual entity property_value: IAO:0000111 "future directions section" xsd:string property_value: IAO:0000112 "The section labelled 'future directions' in a typical scientific journal article." xsd:string property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string property_value: IAO:0000118 "future challenges" xsd:string property_value: IAO:0000118 "future considerations" xsd:string property_value: IAO:0000118 "future developments" xsd:string property_value: IAO:0000118 "future directions" xsd:string property_value: IAO:0000118 "future outlook" xsd:string property_value: IAO:0000118 "future perspectives" xsd:string property_value: IAO:0000118 "future plans" xsd:string property_value: IAO:0000118 "future prospects" xsd:string property_value: IAO:0000118 "future research" xsd:string property_value: IAO:0000118 "future research directions" xsd:string property_value: IAO:0000118 "future studies" xsd:string property_value: IAO:0000118 "future work" xsd:string property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183 [Term] id: IAO:0000626 name: future directions textual entity def: "A textual entity expressing ideas regarding future work relevant to work described in a document that could be done." [] is_a: IAO:0000300 ! textual entity property_value: IAO:0000111 "future directions textual entity" xsd:string property_value: IAO:0000112 "Excerpt from Wang and Li. Acta Pharmacol Sin. 2016 Jan; 37(1): 25–33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4722976/):\n\nIn the future, several questions will need to be resolved regarding the physiological assembly of KCNQ channels and their functional implications in complex neural circuits. First, we still lack sufficiently selective inhibitors and activators among the KCNQ family members." xsd:string property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183 [Term] id: IAO:0000627 name: genome announcement section def: "A document part announcing the publication of a novel draft genome sequence." [] is_a: IAO:0000314 ! document part relationship: BFO:0000051 IAO:0000628 ! has part genome announcement textual entity property_value: IAO:0000111 "genome announcement section" xsd:string property_value: IAO:0000112 "The section labelled 'genome announcement' in a typical scientific journal article, e.g. in Kim et al. J Bacteriol. 2011 Oct; 193(19): 5537. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3187466/)" xsd:string property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string property_value: IAO:0000118 "genome announcement" xsd:string property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183 [Term] id: IAO:0000628 name: genome announcement textual entity def: "A textual entity that describes the generation and public release of a novel, draft genome sequence." [] is_a: IAO:0000300 ! textual entity property_value: IAO:0000111 "genome announcement textual entity" xsd:string property_value: IAO:0000112 "Excerpt from Kim et al. J Bacteriol. 2011 Oct; 193(19): 5537. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3187466/):\n\nHere we report the genome sequence of Lactobacillus malefermentans KCTC 3548, which we obtained using a whole-genome shotgun strategy (4) with Roche 454 GS (FLX Titanium) pyrosequencing (257,559 reads totaling ∼89.8 Mb; ∼45-fold coverage of the genome) at the Genome Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB)." xsd:string property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183 [Term] id: IAO:0000629 name: keyword textual entity def: "A textual entity listing keywords indicating the major theme(s) of a document." [] is_a: IAO:0000300 ! textual entity property_value: IAO:0000111 "keyword textual entity" xsd:string property_value: IAO:0000112 "From: Fu and Lin. Identification of gene-oriented exon orthology between human and mouse. BMC Genomics. 2012; 13(Suppl 1): S10. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3303729/):\n\nExon orthology; alternative splicing; exon duplication; intron-exon structure." xsd:string property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183 [Term] id: IAO:0000630 name: keywords section def: "A part of a document where keywords selected by the author to categorize the major theme(s) of a document are listed." [] is_a: IAO:0000314 ! document part relationship: BFO:0000051 IAO:0000629 ! has part keyword textual entity property_value: IAO:0000111 "keywords section" xsd:string property_value: IAO:0000112 "The section labelled 'keywords' in a typical scientific journal article." xsd:string property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string property_value: IAO:0000118 "keywords" xsd:string property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183 [Term] id: IAO:0000631 name: study limitations section def: "A part of a document about biases or short comings related to the study design and execution." [] is_a: IAO:0000314 ! document part relationship: BFO:0000051 IAO:0000632 ! has part study limitations textual entity relationship: IAO:0000136 OBI:0500000 ! is about study design property_value: IAO:0000111 "study limitations section" xsd:string property_value: IAO:0000112 "The section labelled 'limitations' in a typical scientific journal article." xsd:string property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string property_value: IAO:0000118 "limitations" xsd:string property_value: IAO:0000118 "study limitations" xsd:string property_value: IAO:0000119 "Author guidelines published by The Society for Academic Emergency Medicine. (http://onlinelibrary.wiley.com/journal/10.1111/(ISSN)1553-2712/homepage/ForAuthors.html)" xsd:string property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183 [Term] id: IAO:0000632 name: study limitations textual entity def: "A textual entity addressing a shortcoming or bias of a study design or execution." [] is_a: IAO:0000300 ! textual entity property_value: IAO:0000111 "study limitations textual entity" xsd:string property_value: IAO:0000112 "Excerpt from the Limitations section of Fermann et al 2015, Acad Emerg Med. 2015 Mar; 22(3): 299–307 (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4405051/). \n\nOwing to the nature of a post hoc study, any significant values must be interpreted with caution. In the current analysis, no multiple testing was conducted and p-values remain unadjusted. Moreover, a selection bias arising from the randomized open-label design of the original EINSTEIN PE study cannot be ruled out." xsd:string property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string property_value: IAO:0000119 "Author guidelines published by The Society for Academic Emergency Medicine. (http://onlinelibrary.wiley.com/journal/10.1111/(ISSN)1553-2712/homepage/ForAuthors.html)" xsd:string property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183 [Term] id: IAO:0000633 name: materials section def: "A part of a document about the materials required to reproduce the content of the document." [] is_a: IAO:0000314 ! document part property_value: IAO:0000111 "materials section" xsd:string property_value: IAO:0000112 "The section labelled 'materials' in a typical scientific journal article, e.g. Nguyen et al. BMC Bioinformatics. 2010; 11: 279. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2889936/)" xsd:string property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string property_value: IAO:0000118 "materials" xsd:string property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183 [Term] id: IAO:0000634 name: notes section def: "A part of a document containing typically short notes about the document itself and/or the authors. Often the notes section contains subsections related to funding, competing interests, ethical approval, etc." [] is_a: IAO:0000314 ! document part property_value: IAO:0000111 "notes section" xsd:string property_value: IAO:0000112 "The section labelled 'notes' in a typical scientific journal article, e.g. McLean et al. Br J Gen Pract. 2014 Jul; 64(624): e440–e447 (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4073730/):" xsd:string property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string property_value: IAO:0000118 "footnotes" xsd:string property_value: IAO:0000118 "notes" xsd:string property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183 [Term] id: IAO:0000635 name: patients section def: "A part of a document about the patients that participated in a study." [] is_a: IAO:0000314 ! document part relationship: BFO:0000051 IAO:0000636 ! has part patients textual entity property_value: IAO:0000111 "patients section" xsd:string property_value: IAO:0000112 "The section labelled 'patients' in a typical scientific journal article, e.g. in Citak et al. Acta Orthop. 2013 Jun; 84(3): 326–327. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3715825/)" xsd:string property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183 [Term] id: IAO:0000636 name: patients textual entity def: "A textual entity expressing information regarding the patients used in a study." [] is_a: IAO:0000300 ! textual entity property_value: IAO:0000111 "patients textual entity" xsd:string property_value: IAO:0000112 "Excerpt from Citak et al. Acta Orthop. 2013 Jun; 84(3): 326–327. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3715825/):\n\nBetween January 1996 and February 2012, we treated 4 patients with interprosthetic femoral fractures (3 of them women) (Figure 2) using a custom-made interposition device (Waldemar Link GmbH, Hamburg, Germany) (Figure 1). Mean age was 74 (59–86) years. The fractures occurred mean 18 (13–28) years after primary THA and mean 14 (10–17) years after primary TKA. At the latest follow-up, after mean 8 (0.5–16) years, revision surgery with a total femur replacement was required in 1 case due to aseptic loosening. No other complications requiring revision surgery occurred." xsd:string property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183 [Term] id: IAO:0000637 name: pre-publication history section def: "A part of the document about the publication history of a document. This section typically details dates of document submission to a journal and dates of any re-submissions as well as reviewer comments and responses to reviewers by the authors." [] is_a: IAO:0000314 ! document part relationship: BFO:0000051 IAO:0000638 ! has part pre-publication history textual entity property_value: IAO:0000111 "pre-publication history section" xsd:string property_value: IAO:0000112 "The section labelled 'pre-publication history' in a typical scientific journal article, e.g. in Xiao et al. BMC Anesthesiol. 2013; 13: 33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4016475/)" xsd:string property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string property_value: IAO:0000118 "notice of republication" xsd:string property_value: IAO:0000118 "pre-publication history" xsd:string property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183 [Term] id: IAO:0000638 name: pre-publication history textual entity def: "A textual entity that expresses the pre-publication history (submission dates, reviewer comments, etc) for a document, often including a hyperlink to a web page detailing the information." [] is_a: IAO:0000300 ! textual entity property_value: IAO:0000111 "pre-publication history textual entity" xsd:string property_value: IAO:0000112 "From Xiao et al. BMC Anesthesiol. 2013; 13: 33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4016475/):\n\nThe pre-publication history for this paper can be accessed here:\nhttp://www.biomedcentral.com/1471-2253/13/33/prepub" xsd:string property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183 [Term] id: IAO:0000639 name: related work section def: "A part of a document about work in other publications that is relevant to the content of the document." [] is_a: IAO:0000314 ! document part relationship: BFO:0000051 IAO:0000640 ! has part related work textual entity property_value: IAO:0000111 "related work section" xsd:string property_value: IAO:0000112 "The section labelled 'related work' in a typical scientific journal article, e.g. Žitnik and Zupan. Bioinformatics. 2015 Jun 15; 31(12): i230–i239. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4542780/)" xsd:string property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string property_value: IAO:0000118 "related literature" xsd:string property_value: IAO:0000118 "related work" xsd:string property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183 [Term] id: IAO:0000640 name: related work textual entity def: "A textual entity that discusses work from other publications and expresses their relevancy to the content of a document." [] is_a: IAO:0000300 ! textual entity property_value: IAO:0000111 "related work textual entity" xsd:string property_value: IAO:0000112 "Excerpt from Žitnik and Zupan. Bioinformatics. 2015 Jun 15; 31(12): i230–i239. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4542780/):\n\nOur work presented here is similar in spirit to our recently developed methodology for data fusion via collective matrix factorization (Žitnik and Zupan, 2015).\n\n" xsd:string property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183 [Term] id: IAO:0000641 name: requirements section def: "A part of a document about a resource described in the document, e.g. software, that describes the requirements necessary to use the resource, e.g. operating systems, hardware, etc. in the case of a software resource." [] is_a: IAO:0000314 ! document part relationship: BFO:0000051 IAO:0000642 ! has part requirements textual entity property_value: IAO:0000111 "requirements section" xsd:string property_value: IAO:0000112 "The section labelled 'availability and requirements' in a typical scientific journal article, e.g. Qi et al. BMC Bioinformatics. 2014; 15: 11. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3897912/)." xsd:string property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string property_value: IAO:0000118 "requirements" xsd:string property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183 [Term] id: IAO:0000642 name: requirements textual entity def: "A textual entity that expresses the requirements necessary to use a resource, e.g. software." [] is_a: IAO:0000300 ! textual entity property_value: IAO:0000111 "requirements textual entity" xsd:string property_value: IAO:0000112 "From Qi et al. BMC Bioinformatics. 2014; 15: 11. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3897912/):\n\n• Operating systems: Platform independent\n\n• Programming language: Matlab, R, Python\n\n• Other requirements: None\n\n• License: GNU GPL v3\n\n• Any restrictions to use by non-academics: None" xsd:string property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183 [Term] id: IAO:0000643 name: statistical analysis textual entity def: "A textual entity documenting statistical analysis tools and techniques employed." [] is_a: IAO:0000300 ! textual entity property_value: IAO:0000111 "statistical analysis textual entity" xsd:string property_value: IAO:0000112 "From Mondo et al. Cardiovasc J Afr. 2013 Mar; 24(2): 28–33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3734881/):\n\nData were captured into EPI-DATA (version 3.1), cleaned and then exported to Stata version 10 for analysis. Continuous variables were summarised as mean (± standard deviation) and median (inter-quartile range), and presented in the tables. Categorical data were analysed using frequency and percentages, and results are presented in frequency tables and bar charts. Test of significance (p-value) was determined using the chi-square test. A p-value of less than 0.05 was considered significant." xsd:string property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183 [Term] id: IAO:0000644 name: statistical analysis section def: "A part of the document used to describe the statistical methodologies employed in the work presented in the document." [] is_a: IAO:0000314 ! document part relationship: BFO:0000051 IAO:0000643 ! has part statistical analysis textual entity property_value: IAO:0000111 "statistical analysis section" xsd:string property_value: IAO:0000112 "The section labelled 'statistical analysis' in a typical scientific journal article, e.g. Mondo et al. Cardiovasc J Afr. 2013 Mar; 24(2): 28–33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3734881/)" xsd:string property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string property_value: IAO:0000118 "statistical analysis" xsd:string property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183 [Term] id: IAO:0000645 name: tables section def: "A part of a document that contains one or more tables." [] is_a: IAO:0000314 ! document part relationship: BFO:0000051 IAO:0000306 ! has part table property_value: IAO:0000111 "tables section" xsd:string property_value: IAO:0000112 "The section labelled 'tables' in a typical scientific journal article." xsd:string property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string property_value: IAO:0000118 "tables" xsd:string property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183 [Term] id: IAO:0000650 name: database extract, transform, and load process def: "A planned process which takes as input a database and fills another database by extracting concretizations of information entities from the first, transforming them, and loading the transformed concretizations into the second." [] is_a: OBI:0000011 ! planned process relationship: OBI:0000293 IAO:0000030 ! has_specified_input information content entity relationship: OBI:0000299 IAO:0000030 ! has_specified_output information content entity property_value: http://xmlns.com/foaf/0.1/page https://en.wikipedia.org/wiki/Extract,_transform,_load property_value: IAO:0000111 "database extract, transform, and load process" xsd:string property_value: IAO:0000116 "Alan Ruttenberg 12/21/16: Maybe this definition instead: A planned process which takes as input a database and copies concretizations from the first, optionally transforms then copies the result to the second" xsd:string property_value: IAO:0000116 "Alan Ruttenberg 12/21/16: We don't define database in IAO, currently, as the bare word is ambiguous. Reasonable interpretations of the word might be the material entity, an information structure, an information content entity. However this definition commits, at least, to there being some material thing which bear concretizations of information entities and that there are new concretizations created during the process. We consider the ETL process in terms of information entities rather than the concretizations. No committment is made as to whether the specified output." xsd:string property_value: IAO:0000117 "PERSON:Alan Ruttenberg" xsd:string property_value: IAO:0000118 "ETL" xsd:string property_value: IAO:0000119 WEB:https://en.wikipedia.org/wiki/Extract,_transform,_load xsd:string property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/187 property_value: isDefinedBy https://github.com/information-artifact-ontology/IAO [Term] id: IAO:8000000 name: ontology module is_a: IAO:0000102 ! data about an ontology part 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 created_by: cjm creation_date: 2018-05-20T20:55:03Z [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: seeAlso https://github.com/INCATools/ontology-starter-kit/issues/50 created_by: cjm creation_date: 2018-05-20T20:55:30Z [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:0000118 "source ontology module" xsd:string created_by: cjm creation_date: 2018-05-20T20:55:47Z [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:0000116 "TODO: Add logical axioms that state that a main release ontology module is derived from (directly or indirectly) an editors module" xsd:string created_by: cjm creation_date: 2018-05-20T20:56:13Z [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: seeAlso https://github.com/obophenotype/uberon/wiki/inter-anatomy-ontology-bridge-ontologies created_by: cjm creation_date: 2018-05-20T20:56:23Z [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: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 created_by: cjm creation_date: 2018-05-20T20:56:47Z [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: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 created_by: cjm creation_date: 2018-05-20T20:58:11Z [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 created_by: cjm creation_date: 2018-05-20T20:58:38Z [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 created_by: cjm creation_date: 2018-05-20T20:58:49Z [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:0000118 "ribbon subset" xsd:string created_by: cjm creation_date: 2018-05-20T20:59:19Z [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:0000118 "antislim" xsd:string created_by: cjm creation_date: 2018-05-20T20:59:57Z [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:0000118 "external import" xsd:string created_by: cjm creation_date: 2018-05-20T21:00:14Z [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:0000118 "taxon subset" xsd:string property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Taxon-constraints created_by: cjm creation_date: 2018-05-20T21:14:16Z [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: seeAlso http://robot.obolibrary.org/reason created_by: cjm creation_date: 2018-05-20T21:20:33Z [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:0000116 "TODO: Add axioms (using PROV-O?) that indicate this is the output-of some reasoning process" xsd:string created_by: cjm creation_date: 2018-05-20T21:21:12Z [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: 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/ created_by: cjm creation_date: 2018-05-20T21:21:21Z [Term] id: IAO:8000016 name: taxonomic bridge ontology module is_a: IAO:8000004 ! bridge ontology module created_by: cjm creation_date: 2018-05-20T21:28:15Z [Term] id: IAO:8000017 name: ontology module subsetted by expressivity is_a: IAO:8000006 ! subset ontology module created_by: cjm creation_date: 2018-05-22T04:15:54Z [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: seeAlso "6.2" created_by: cjm creation_date: 2018-05-22T04:16:10Z [Term] id: IAO:8000019 name: ontology module subsetted by OWL profile is_a: IAO:8000017 ! ontology module subsetted by expressivity created_by: cjm creation_date: 2018-05-22T04:16:28Z [Term] id: IAO:8000020 name: EL++ ontology module is_a: IAO:8000019 ! ontology module subsetted by OWL profile created_by: cjm creation_date: 2018-05-22T04:16:48Z [Term] id: OBI:0000011 name: planned process def: "A processual entity that realizes a plan which is the concretization of a plan specification." [] is_a: BFO:0000015 ! process property_value: IAO:0000111 "planned process" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl [Term] id: OBI:0000066 name: investigation def: "a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s)." [] is_a: OBI:0000011 ! planned process property_value: IAO:0000111 "investigation" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl [Term] id: OBI:0000471 name: study design execution def: "a planned process that carries out a study design" [] is_a: OBI:0000011 ! planned process property_value: IAO:0000111 "study design execution" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl [Term] id: OBI:0500000 name: study design def: "A plan specification comprised of protocols (which may specify how and what kinds of data will be gathered) that are executed as part of an investigation and is realized during a study design execution." [] is_a: IAO:0000104 ! plan specification property_value: IAO:0000111 "study design" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl [Term] id: ObsoleteClass name: Obsolete Class [Term] id: PATO:0000051 name: morphology def: "A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure." [] is_a: PATO:0001241 ! physical object quality property_value: IAO:0000111 "morphology" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/pato.owl [Term] id: PATO:0000117 name: size def: "A morphology quality inhering in a bearer by virtue of the bearer's physical magnitude." [] is_a: PATO:0000051 ! morphology property_value: IAO:0000111 "size" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/pato.owl [Term] id: PATO:0000122 name: length def: "A 1-D extent quality which is equal to the distance between two points." [] is_a: PATO:0001708 ! 1-D extent property_value: IAO:0000111 "length" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/pato.owl [Term] id: PATO:0000125 name: mass def: "A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter." [] is_a: PATO:0001018 ! physical quality property_value: IAO:0000111 "mass" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/pato.owl [Term] id: PATO:0001018 name: physical quality def: "A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities." [] is_a: PATO:0001241 ! physical object quality property_value: IAO:0000111 "physical quality" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/pato.owl [Term] id: PATO:0001241 name: physical object quality def: "A quality which inheres in a continuant." [] is_a: BFO:0000019 ! quality property_value: IAO:0000111 "physical object quality" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/pato.owl [Term] id: PATO:0001708 name: 1-D extent def: "A size quality inhering in an bearer by virtue of the bearer's extension in one dimension." [] is_a: PATO:0000117 ! size property_value: IAO:0000111 "1-D extent" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/pato.owl [Term] id: Subset is_a: IAO:0000102 ! data about an ontology part [Term] id: Synonym is_a: IAO:0000102 ! data about an ontology part [Term] id: SynonymType is_a: IAO:0000102 ! data about an ontology part [Term] id: UO:0000001 name: length unit def: "A unit which is a standard measure of the distance between two points." [] is_a: IAO:0000003 ! measurement unit label property_value: IAO:0000111 "length unit" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uo.owl [Term] id: UO:0000002 name: mass unit def: "A unit which is a standard measure of the amount of matter/energy of a physical object." [] is_a: IAO:0000003 ! measurement unit label property_value: IAO:0000111 "mass unit" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uo.owl [Term] id: UO:0000003 name: time unit def: "A unit which is a standard measure of the dimension in which events occur in sequence." [] is_a: IAO:0000003 ! measurement unit label property_value: IAO:0000111 "time unit" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uo.owl [Typedef] id: BFO:0000050 name: part of def: "a core relation that holds between a part and its whole" [] property_value: IAO:0000111 "is part of" xsd:string property_value: IAO:0000112 "my brain is part of my body (continuant parthood, two material entities)" xsd:string property_value: IAO:0000112 "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)" xsd:string property_value: IAO:0000112 "this day is part of this year (occurrent parthood)" xsd:string property_value: IAO:0000116 "Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other." xsd:string property_value: IAO:0000116 "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime" xsd:string property_value: IAO:0000116 "Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)\n\nA continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'." xsd:string property_value: IAO:0000118 "part_of" xsd:string property_value: RO:0001900 RO:0001901 property_value: seeAlso http://www.obofoundry.org/ro/#OBO_REL:part_of xsd:string is_transitive: true inverse_of: BFO:0000051 ! has part [Typedef] id: BFO:0000051 name: has part def: "a core relation that holds between a whole and its part" [] property_value: IAO:0000111 "has part" xsd:string property_value: IAO:0000112 "my body has part my brain (continuant parthood, two material entities)" xsd:string property_value: IAO:0000112 "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)" xsd:string property_value: IAO:0000112 "this year has part this day (occurrent parthood)" xsd:string property_value: IAO:0000116 "Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part." xsd:string property_value: IAO:0000116 "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime" xsd:string property_value: IAO:0000116 "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)\n\nA continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'." xsd:string property_value: IAO:0000118 "has_part" xsd:string property_value: RO:0001900 RO:0001901 is_transitive: true [Typedef] id: BFO:0000054 name: realized in comment: Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process property_value: IAO:0000111 "realized in" xsd:string property_value: IAO:0000112 "this disease is realized in this disease course" xsd:string property_value: IAO:0000112 "this fragility is realized in this shattering" xsd:string property_value: IAO:0000112 "this investigator role is realized in this investigation" xsd:string property_value: IAO:0000118 "is realized by" xsd:string property_value: IAO:0000118 "realized_in" xsd:string property_value: IAO:0000600 "[copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])" xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl domain: BFO:0000017 ! realizable entity range: BFO:0000015 ! process inverse_of: BFO:0000055 ! realizes [Typedef] id: BFO:0000055 name: realizes comment: Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process property_value: IAO:0000111 "realizes" xsd:string property_value: IAO:0000112 "this disease course realizes this disease" xsd:string property_value: IAO:0000112 "this investigation realizes this investigator role" xsd:string property_value: IAO:0000112 "this shattering realizes this fragility" xsd:string property_value: IAO:0000600 "to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])" xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/iao.owl domain: BFO:0000015 ! process range: BFO:0000017 ! realizable entity [Typedef] id: BFO:0000066 name: occurs in def: "b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" [] comment: Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant property_value: IAO:0000111 "occurs in" xsd:string property_value: IAO:0000118 "occurs_in" xsd:string property_value: IAO:0000118 "unfolds in" xsd:string property_value: IAO:0000118 "unfolds_in" xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl domain: BFO:0000003 ! occurrent range: BFO:0000004 ! independent continuant holds_over_chain: BFO:0000050 BFO:0000066 inverse_of: BFO:0000067 ! contains process transitive_over: BFO:0000050 ! part of [Typedef] id: BFO:0000067 name: contains process def: "[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" [] comment: Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant property_value: IAO:0000111 "site of" xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Typedef] id: IAO:0000039 name: has measurement unit label range: IAO:0000003 ! measurement unit label is_functional: true is_a: BFO:0000051 ! has part [Typedef] id: IAO:0000135 name: obsolete_specifically denotes def: "c specifically denotes r =def \nr is a portion of reality\n& c is a particular quality\n& c depends specifically on some independent continuant b \n& b acquired c as the result of the achievement of an objective to enable pointing to r repeatedly. \n\nMarked means there is a changed or additional quality of the bearer - the quality is the information carrier.\n\nCase 1\nMemory trace as mark created when reading some description of some friend. The trace can denote.\n\nCase 2\nPattern of ink arrayed on paper as mark when writing down a friend's name\n\nCase 3\nPattern of magnetic domains on scattered pieces of a hard disk platter as mark when saving a file." [] property_value: IAO:0000112 "The process of creation is, for example, writing down on paper the name of a friend by deliberately creating a certain pattern using ink.\n\nHere the ink + paper is the independent continuant and the carrier is the pattern in the ink.\n\nc = pattern in the ink\nb = paper + ink\nr = friend" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "8/6/2009 Alan Ruttenberg: The suggestions is to deprecate specific and generically denotes in favor of a single denote relationship that corresponds to the generic sense" xsd:string property_value: IAO:0000116 "see https://github.com/information-artifact-ontology/IAO/issues/25&q=denote" xsd:string property_value: IAO:0000117 "Alan Ruttenberg" xsd:string property_value: IAO:0000119 "Smith, Ceusters, Ruttenberg, 2000 years of philosophy" xsd:string property_value: IAO:0000231 IAO:0000103 is_a: ObsoleteProperty is_obsolete: true [Typedef] id: IAO:0000136 name: is about def: "is_about is a (currently) primitive relation that relates an information artifact to an entity." [] property_value: IAO:0000112 "This document is about information artifacts and their representations" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of \"mentions\" relation. Weaken the is_about relationship to be primitive. \n\nWe will try to build it back up by elaborating the various subproperties that are more precisely defined.\n\nSome currently missing phenomena that should be considered \"about\" are predications - \"The only person who knows the answer is sitting beside me\" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic." xsd:string property_value: IAO:0000117 "person:Alan Ruttenberg" xsd:string property_value: IAO:0000119 "Smith, Ceusters, Ruttenberg, 2000 years of philosophy" xsd:string domain: IAO:0000030 ! information content entity [Typedef] id: IAO:0000142 name: mentions def: "An information artifact IA mentions an entity E exactly when it has a component/part that denotes E" [] property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "7/6/2009 Alan Ruttenberg. P4 RC1 munges our GCI so remove it for now: mentions some entity equivalentTo has_part some ('generically denotes' some entity)" xsd:string property_value: IAO:0000116 "7/6/2009 Alan Ruttenberg: Add this relation following conversation with Jonathan Rees that N&S GCI for is_about was too strong. Really it was simply sufficient. To effect this change we introduce this relation, which is subproperty of is_about, and have previous GCI use this relation \"mentions\" in it's (logical) definition" xsd:string property_value: IAO:0000117 "Person: Alan Ruttenberg" xsd:string property_value: IAO:0000117 "PERSON: Jonathan Rees" xsd:string is_a: IAO:0000136 ! is about [Typedef] id: IAO:0000219 name: denotes def: "denotes is a primitive, instance-level, relation obtaining between an information content entity and some portion of reality. Denotation is what happens when someone creates an information content entity E in order to specifically refer to something. The only relation between E and the thing is that E can be used to 'pick out' the thing. This relation connects those two together. Freedictionary.com sense 3: To signify directly; refer to specifically" [] property_value: IAO:0000112 "A person's name denotes the person. A variable name in a computer program denotes some piece of memory. Lexically equivalent strings can denote different things, for instance \"Alan\" can denote different people. In each case of use, there is a case of the denotation relation obtaining, between \"Alan\" and the person that is being named." xsd:string property_value: IAO:0000116 "2009-11-10 Alan Ruttenberg. Old definition said the following to emphasize the generic nature of this relation. We no longer have 'specifically denotes', which would have been primitive, so make this relation primitive.\ng denotes r =def \nr is a portion of reality\nthere is some c that is a concretization of g \nevery c that is a concretization of g specifically denotes r" xsd:string property_value: IAO:0000117 "person:Alan Ruttenberg" xsd:string property_value: IAO:0000119 "Conversations with Barry Smith, Werner Ceusters, Bjoern Peters, Michel Dumontier, Melanie Courtot, James Malone, Bill Hogan" xsd:string domain: IAO:0000030 ! information content entity range: BFO:0000001 ! entity is_a: IAO:0000136 ! is about inverse_of: IAO:0000235 ! denoted by [Typedef] id: IAO:0000220 name: obsolete_materially denotes property_value: IAO:0000116 "see https://github.com/information-artifact-ontology/IAO/issues/25&q=denote" xsd:string property_value: IAO:0000231 IAO:0000103 is_a: ObsoleteProperty is_obsolete: true [Typedef] id: IAO:0000221 name: is quality measurement of def: "m is a quality measurement of q at t when\nq is a quality \nthere is a measurement process p that has specified output m, a measurement datum, that is about q" [] property_value: IAO:0000116 "8/6/2009 Alan Ruttenberg: The strategy is to be rather specific with this relationship. There are other kinds of measurements that are not of qualities, such as those that measure time. We will add these as separate properties for the moment and see about generalizing later" xsd:string property_value: IAO:0000116 "From the second IAO workshop [Alan Ruttenberg 8/6/2009: not completely current, though bringing in comparison is probably important]\n\nThis one is the one we are struggling with at the moment. The issue is what a measurement measures. On the one hand saying that it measures the quality would include it \"measuring\" the bearer = referring to the bearer in the measurement. However this makes comparisons of two different things not possible. On the other hand not having it inhere in the bearer, on the face of it, breaks the audit trail.\n\nWerner suggests a solution based on \"Magnitudes\" a proposal for which we are awaiting details.\n--\nFrom the second IAO workshop, various comments, [commented on by Alan Ruttenberg 8/6/2009]\n\nunit of measure is a quality, e.g. the length of a ruler.\n\n[We decided to hedge on what units of measure are, instead talking about measurement unit labels, which are the information content entities that are about whatever measurement units are. For IAO we need that information entity in any case. See the term measurement unit label]\n\n[Some struggling with the various subflavors of is_about. We subsequently removed the relation represents, and describes until and only when we have a better theory]\n\na represents b means either a denotes b or a describes\n\ndescribe:\na describes b means a is about b and a allows an inference of at least one quality of b\n\nWe have had a long discussion about denotes versus describes." xsd:string property_value: IAO:0000116 "From the second IAO workshop: An attempt at tieing the quality to the measurement datum more carefully.\n\na is a magnitude means a is a determinate quality particular inhering in some bearer b existing at a time t that can be represented/denoted by an information content entity e that has parts denoting a unit of measure, a number, and b. The unit of measure is an instance of the determinable quality." xsd:string property_value: IAO:0000116 "From the second meeting on IAO:\n\nAn attempt at defining assay using Barry's \"reliability\" wording\n\nassay:\nprocess and has_input some material entity\nand has_output some information content entity \nand which is such that instances of this process type reliably generate \noutputs that describes the input." xsd:string property_value: IAO:0000116 "This one is the one we are struggling with at the moment. The issue is what a measurement measures. On the one hand saying that it measures the quality would include it \"measuring\" the bearer = referring to the bearer in the measurement. However this makes comparisons of two different things not possible. On the other hand not having it inhere in the bearer, on the face of it, breaks the audit trail.\n\nWerner suggests a solution based on \"Magnitudes\" a proposal for which we are awaiting details." xsd:string property_value: IAO:0000117 "Alan Ruttenberg" xsd:string domain: IAO:0000109 ! measurement datum range: BFO:0000019 ! quality is_a: IAO:0000136 ! is about inverse_of: IAO:0000417 ! is quality measured as [Typedef] id: IAO:0000222 name: obsolete_describes property_value: IAO:0000231 IAO:0000103 is_a: ObsoleteProperty is_obsolete: true [Typedef] id: IAO:0000223 name: obsolete_represents property_value: IAO:0000231 IAO:0000103 is_a: ObsoleteProperty is_obsolete: true [Typedef] id: IAO:0000235 name: denoted by def: "inverse of the relation 'denotes'" [] property_value: IAO:0000117 "Person: Jie Zheng, Chris Stoeckert, Mike Conlon" xsd:string property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/206 domain: BFO:0000001 ! entity range: IAO:0000030 ! information content entity [Typedef] id: IAO:0000407 name: has coordinate unit label comment: relating a cartesian spatial coordinate datum to a unit label that together with the values represent a point domain: IAO:0000400 ! cartesian spatial coordinate datum range: UO:0000001 ! length unit is_functional: true is_a: BFO:0000051 ! has part [Typedef] id: IAO:0000413 name: is duration of def: "relates a process to a time-measurement-datum that represents the duration of the process" [] property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Person:Alan Ruttenberg" xsd:string domain: IAO:0000416 ! time measurement datum range: BFO:0000015 ! process is_a: IAO:0000136 ! is about [Typedef] id: IAO:0000417 name: is quality measured as def: "inverse of the relation of is quality measurement of" [] property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000116 "2009/10/19 Alan Ruttenberg. Named 'junk' relation useful in restrictions, but not a real instance relationship" xsd:string property_value: IAO:0000117 "Person:Alan Ruttenberg" xsd:string [Typedef] id: IAO:0000418 name: is quality specification of def: "a relation between a data item and a quality of a material entity where the material entity is the specified output of a material transformation which achieves an objective specification that indicates the intended value of the specified quality." [] property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Person:Alan Ruttenberg" xsd:string property_value: IAO:0000117 "Person:Bjoern Peters" xsd:string is_a: IAO:0000136 ! is about inverse_of: IAO:0000419 ! quality is specified as [Typedef] id: IAO:0000419 name: quality is specified as def: "inverse of the relation of is quality specification of" [] property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000116 "2009/10/19 Alan Ruttenberg. Named 'junk' relation useful in restrictions, but not a real instance relationship" xsd:string property_value: IAO:0000117 "Person:Alan Ruttenberg" xsd:string property_value: IAO:0000117 "Person:Bjoern Peters" xsd:string [Typedef] id: IAO:0000581 name: has time stamp def: "relates a time stamped measurement datum to the time measurement datum that denotes the time when the measurement was taken" [] property_value: IAO:0000114 IAO:0000123 property_value: IAO:0000117 "Alan Ruttenberg" xsd:string domain: IAO:0000582 ! time stamped measurement datum range: IAO:0000416 ! time measurement datum is_functional: true is_a: BFO:0000051 ! has part [Typedef] id: IAO:0000583 name: has measurement datum def: "relates a time stamped measurement datum to the measurement datum that was measured" [] property_value: IAO:0000114 IAO:0000123 property_value: IAO:0000117 "Alan Ruttenberg" xsd:string domain: IAO:0000582 ! time stamped measurement datum is_a: BFO:0000051 ! has part [Typedef] id: OBI:0000293 name: has_specified_input def: "A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of." [] property_value: IAO:0000111 "has_specified_input" xsd:string property_value: IAO:0000111 "has_specified_input" xsd:string property_value: IAO:0000112 "see is_input_of example_of_usage" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000116 "8/17/09: specified inputs of one process are not necessarily specified inputs of a larger process that it is part of. This is in contrast to how 'has participant' works." xsd:string property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string property_value: IAO:0000117 "PERSON: Bjoern Peters" xsd:string property_value: IAO:0000117 "PERSON: Larry Hunter" xsd:string property_value: IAO:0000117 "PERSON: Melanie Coutot" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl domain: OBI:0000011 ! planned process is_a: RO:0000057 ! has participant inverse_of: OBI:0000295 ! is_specified_input_of [Typedef] id: OBI:0000295 name: is_specified_input_of [Typedef] id: OBI:0000299 name: has_specified_output def: "A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of." [] property_value: IAO:0000111 "has_specified_output" xsd:string property_value: IAO:0000111 "has_specified_output" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string property_value: IAO:0000117 "PERSON: Bjoern Peters" xsd:string property_value: IAO:0000117 "PERSON: Larry Hunter" xsd:string property_value: IAO:0000117 "PERSON: Melanie Courtot" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl domain: OBI:0000011 ! planned process is_a: RO:0000057 ! has participant inverse_of: OBI:0000312 ! is_specified_output_of [Typedef] id: OBI:0000312 name: is_specified_output_of def: "A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of." [] property_value: IAO:0000111 "is_specified_output_of" xsd:string property_value: IAO:0000111 "is_specified_output_of" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "Alan Ruttenberg" xsd:string property_value: IAO:0000117 "PERSON:Bjoern Peters" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl range: OBI:0000011 ! planned process is_a: RO:0000056 ! participates in [Typedef] id: RO:0000052 name: inheres in def: "a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence" [] property_value: IAO:0000111 "inheres in" xsd:string property_value: IAO:0000112 "this fragility inheres in this vase" xsd:string property_value: IAO:0000112 "this red color inheres in this apple" xsd:string property_value: IAO:0000116 "A dependent inheres in its bearer at all times for which the dependent exists." xsd:string property_value: IAO:0000118 "inheres_in" xsd:string property_value: RO:0001900 RO:0001901 inverse_of: RO:0000053 ! bearer of [Typedef] id: RO:0000053 name: bearer of def: "a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence" [] property_value: IAO:0000111 "bearer of" xsd:string property_value: IAO:0000112 "this apple is bearer of this red color" xsd:string property_value: IAO:0000112 "this vase is bearer of this fragility" xsd:string property_value: IAO:0000116 "A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist." xsd:string property_value: IAO:0000118 "bearer_of" xsd:string property_value: IAO:0000118 "is bearer of" xsd:string property_value: RO:0001900 RO:0001901 range: BFO:0000020 ! specifically dependent continuant [Typedef] id: RO:0000056 name: participates in def: "a relation between a continuant and a process, in which the continuant is somehow involved in the process" [] property_value: IAO:0000111 "participates in" xsd:string property_value: IAO:0000112 "this blood clot participates in this blood coagulation" xsd:string property_value: IAO:0000112 "this input material (or this output material) participates in this process" xsd:string property_value: IAO:0000112 "this investigator participates in this investigation" xsd:string property_value: IAO:0000118 "participates_in" xsd:string domain: BFO:0000002 ! continuant range: BFO:0000003 ! occurrent inverse_of: RO:0000057 ! has participant [Typedef] id: RO:0000057 name: has participant def: "a relation between a process and a continuant, in which the continuant is somehow involved in the process" [] property_value: http://purl.org/dc/elements/1.1/source http://www.obofoundry.org/ro/#OBO_REL:has_participant xsd:string property_value: IAO:0000111 "has participant" xsd:string property_value: IAO:0000112 "this blood coagulation has participant this blood clot" xsd:string property_value: IAO:0000112 "this investigation has participant this investigator" xsd:string property_value: IAO:0000112 "this process has participant this input material (or this output material)" xsd:string property_value: IAO:0000116 "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time." xsd:string property_value: IAO:0000118 "has_participant" xsd:string domain: BFO:0000003 ! occurrent range: BFO:0000002 ! continuant [Typedef] id: RO:0000058 name: is concretized as def: "A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants." [] property_value: IAO:0000112 "A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant)." xsd:string property_value: IAO:0000112 "An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process)." xsd:string domain: BFO:0000031 ! generically dependent continuant range: BFO:0000020 ! specifically dependent continuant inverse_of: RO:0000059 ! concretizes [Typedef] id: RO:0000059 name: concretizes def: "A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant." [] property_value: IAO:0000112 "A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant)." xsd:string property_value: IAO:0000112 "An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process)." xsd:string domain: BFO:0000020 ! specifically dependent continuant range: BFO:0000031 ! generically dependent continuant [Typedef] id: RO:0000079 name: function of def: "a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence" [] property_value: IAO:0000112 "this catalysis function is a function of this enzyme" xsd:string property_value: IAO:0000116 "A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists." xsd:string property_value: IAO:0000118 "function_of" xsd:string property_value: IAO:0000118 "is function of" xsd:string domain: BFO:0000034 ! function is_a: RO:0000052 ! inheres in inverse_of: RO:0000085 ! has function [Typedef] id: RO:0000080 name: quality of def: "a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence" [] property_value: IAO:0000112 "this red color is a quality of this apple" xsd:string property_value: IAO:0000116 "A quality inheres in its bearer at all times for which the quality exists." xsd:string property_value: IAO:0000118 "is quality of" xsd:string property_value: IAO:0000118 "quality_of" xsd:string is_a: RO:0000052 ! inheres in inverse_of: RO:0000086 ! has quality [Typedef] id: RO:0000081 name: role of def: "a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence" [] property_value: IAO:0000112 "this investigator role is a role of this person" xsd:string property_value: IAO:0000116 "A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists." xsd:string property_value: IAO:0000118 "is role of" xsd:string property_value: IAO:0000118 "role_of" xsd:string is_a: RO:0000052 ! inheres in inverse_of: RO:0000087 ! has role [Typedef] id: RO:0000085 name: has function def: "a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence" [] property_value: IAO:0000112 "this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)" xsd:string property_value: IAO:0000116 "A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists." xsd:string property_value: IAO:0000118 "has_function" xsd:string domain: BFO:0000004 ! independent continuant range: BFO:0000034 ! function is_a: RO:0000053 ! bearer of [Typedef] id: RO:0000086 name: has quality def: "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence" [] property_value: IAO:0000112 "this apple has quality this red color" xsd:string property_value: IAO:0000116 "A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist." xsd:string property_value: IAO:0000118 "has_quality" xsd:string range: BFO:0000019 ! quality is_a: RO:0000053 ! bearer of [Typedef] id: RO:0000087 name: has role def: "a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence" [] property_value: IAO:0000112 "this person has role this investigator role (more colloquially: this person has this role of investigator)" xsd:string property_value: IAO:0000116 "A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists." xsd:string property_value: IAO:0000118 "has_role" xsd:string domain: BFO:0000004 ! independent continuant range: BFO:0000023 ! role is_a: RO:0000053 ! bearer of [Typedef] id: RO:0000091 name: has disposition def: "a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence" [] domain: BFO:0000004 ! independent continuant range: BFO:0000016 ! disposition is_a: RO:0000053 ! bearer of inverse_of: RO:0000092 ! disposition of [Typedef] id: RO:0000092 name: disposition of is_a: RO:0000052 ! inheres in [Typedef] id: RO:0001000 name: derives from def: "a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity" [] property_value: IAO:0000112 "this cell derives from this parent cell (cell division)" xsd:string property_value: IAO:0000112 "this nucleus derives from this parent nucleus (nuclear division)" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'." xsd:string property_value: IAO:0000118 "derives_from" xsd:string inverse_of: RO:0001001 ! derives into [Typedef] id: RO:0001001 name: derives into def: "a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity" [] property_value: IAO:0000112 "this parent cell derives into this cell (cell division)" xsd:string property_value: IAO:0000112 "this parent nucleus derives into this nucleus (nuclear division)" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'." xsd:string property_value: IAO:0000118 "derives_into" xsd:string [Typedef] id: RO:0001015 name: location of def: "a relation between two independent continuants, the location and the target, in which the target is entirely within the location" [] property_value: IAO:0000111 "is location of" xsd:string property_value: IAO:0000112 "my head is the location of my brain" xsd:string property_value: IAO:0000112 "this cage is the location of this rat" xsd:string property_value: IAO:0000116 "Most location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime" xsd:string property_value: IAO:0000118 "location_of" xsd:string property_value: RO:0001900 RO:0001901 is_transitive: true inverse_of: RO:0001025 ! located in [Typedef] id: RO:0001025 name: located in def: "a relation between two independent continuants, the target and the location, in which the target is entirely within the location" [] property_value: http://purl.org/dc/elements/1.1/source http://www.obofoundry.org/ro/#OBO_REL:located_in xsd:string property_value: IAO:0000111 "located in" xsd:string property_value: IAO:0000112 "my brain is located in my head" xsd:string property_value: IAO:0000112 "this rat is located in this cage" xsd:string property_value: IAO:0000116 "Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus" xsd:string property_value: IAO:0000116 "Most location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime" xsd:string property_value: IAO:0000118 "located_in" xsd:string property_value: RO:0001900 RO:0001901 domain: BFO:0000004 {http://purl.obolibrary.org/obo/IAO_0000116="This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation."} ! independent continuant range: BFO:0000004 {http://purl.obolibrary.org/obo/IAO_0000116="This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation."} ! independent continuant is_transitive: true [Typedef] id: RO:0002000 name: 2D boundary of def: "a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity" [] property_value: IAO:0000112 "the surface of my skin is a 2D boundary of my body" xsd:string property_value: IAO:0000116 "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." xsd:string property_value: IAO:0000116 "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." xsd:string property_value: IAO:0000118 "2D_boundary_of" xsd:string property_value: IAO:0000118 "boundary of" xsd:string property_value: IAO:0000118 "is 2D boundary of" xsd:string property_value: IAO:0000118 "is boundary of" xsd:string property_value: RO:0001900 RO:0001901 inverse_of: RO:0002002 ! has 2D boundary [Typedef] id: RO:0002002 name: has 2D boundary def: "a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity" [] property_value: IAO:0000112 "my body has 2D boundary the surface of my skin" xsd:string property_value: IAO:0000116 "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." xsd:string property_value: IAO:0000116 "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." xsd:string property_value: IAO:0000118 "has boundary" xsd:string property_value: IAO:0000118 "has_2D_boundary" xsd:string property_value: RO:0001900 RO:0001901 domain: BFO:0000040 ! material entity range: BFO:0000141 ! immaterial entity [Typedef] id: RO:0002350 name: member of def: "is member of is a mereological relation between a item and a collection." [] property_value: IAO:0000112 "An organism that is a member of a population of organisms" xsd:string property_value: IAO:0000118 "is member of" xsd:string property_value: IAO:0000118 "member part of" xsd:string property_value: IAO:0000119 "SIO" xsd:string property_value: RO:0001900 RO:0001901 is_a: BFO:0000050 ! part of inverse_of: RO:0002351 ! has member [Typedef] id: RO:0002351 name: has member def: "has member is a mereological relation between a collection and an item." [] property_value: IAO:0000119 "SIO" xsd:string property_value: RO:0001900 RO:0001901 is_a: BFO:0000051 ! has part