@base . @prefix rdf: . @prefix : <#> . @prefix dc: . @prefix obo: <.> . @prefix owl: . @prefix xml: . @prefix xsd: . @prefix foaf: . @prefix rdfs: . @prefix dcterms: . @prefix protege: . @prefix oboInOwl: . protege:defaultLanguage a owl:AnnotationProperty . obo:BFO_0000001 obo:BFO_0000179 "entity" ; obo:BFO_0000180 "Entity" ; obo:IAO_0000112 "Julius Caesar"@en, "Verdi’s Requiem"@en, "the Second World War"@en, "your body mass index"@en ; obo: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"@en, "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"@en ; obo:IAO_0000600 "An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])"@en ; a owl:Class ; rdfs:isDefinedBy ; rdfs:label "entity"@en ; rdfs:subClassOf owl:Thing . obo:BFO_0000002 obo:BFO_0000179 "continuant" ; obo:BFO_0000180 "Continuant" ; obo:IAO_0000115 "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."@en ; obo: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"@en, "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"@en ; obo: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])"@en ; obo: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])"@en, "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])"@en, "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])"@en ; obo:IAO_0000602 "(forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] ", "(forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] ", "(forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] ", "(forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] " ; a owl:Class ; rdfs:isDefinedBy ; rdfs:label "continuant"@en ; rdfs:subClassOf obo:BFO_0000001 ; owl:disjointWith obo:BFO_0000003, [ a owl:Restriction ; owl:onProperty obo:BFO_0000050 ; owl:someValuesFrom obo:BFO_0000003 ] . obo:BFO_0000003 obo:BFO_0000179 "occurrent" ; obo:BFO_0000180 "Occurrent" ; obo:IAO_0000115 "An entity that has temporal parts and that happens, unfolds or develops through time."@en ; obo: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"@en, "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."@en, "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."@en, "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." ; obo: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])"@en ; obo:IAO_0000601 "Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])"@en, "b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])"@en ; obo:IAO_0000602 "(forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] ", "(forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] " ; a owl:Class ; rdfs:isDefinedBy ; rdfs:label "occurrent"@en ; rdfs:subClassOf obo:BFO_0000001 ; owl:disjointWith [ a owl:Restriction ; owl:onProperty obo:BFO_0000050 ; owl:someValuesFrom obo:BFO_0000002 ] . obo:BFO_0000004 obo:BFO_0000179 "ic" ; obo:BFO_0000180 "IndependentContinuant" ; obo:IAO_0000112 "a chair"@en, "a heart"@en, "a leg"@en, "a molecule"@en, "a spatial region"@en, "an atom"@en, "an orchestra."@en, "an organism"@en, "the bottom right portion of a human torso"@en, "the interior of your mouth"@en ; obo:IAO_0000115 "A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything."@en, "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])"@en ; obo: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])"@en, "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])"@en ; obo:IAO_0000602 "(forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] ", "(forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] ", "(iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] " ; a owl:Class ; rdfs:isDefinedBy ; rdfs:label "independent continuant"@en ; rdfs:subClassOf obo:BFO_0000002 ; owl:disjointWith obo:BFO_0000020, obo:BFO_0000031 . obo:BFO_0000005 obo:IAO_0000115 "A continuant that is either dependent on one or other independent continuant bearers or inheres in or is borne by other entities."@en ; a owl:Class ; rdfs:label "obsolete dependent continuant"@en ; rdfs:subClassOf oboInOwl:ObsoleteClass ; owl:deprecated true . obo:BFO_0000006 obo:BFO_0000179 "s-region" ; obo:BFO_0000180 "SpatialRegion" ; obo:IAO_0000116 "BFO 2 Reference: Spatial regions do not participate in processes."@en, "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."@en ; obo: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])"@en ; obo:IAO_0000601 "All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001])"@en ; obo:IAO_0000602 "(forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001] ", "(forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001] " ; a owl:Class ; rdfs:isDefinedBy ; rdfs:label "spatial region"@en ; rdfs:subClassOf obo:BFO_0000141 ; owl:disjointWith obo:BFO_0000029, obo:BFO_0000140 . obo:BFO_0000008 obo:BFO_0000179 "t-region" ; obo:BFO_0000180 "TemporalRegion" ; obo: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"@en ; obo: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])"@en ; obo:IAO_0000601 "All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001])"@en, "Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002])"@en ; obo:IAO_0000602 "(forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002] ", "(forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001] ", "(forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001] " ; a owl:Class ; rdfs:isDefinedBy ; rdfs:label "temporal region"@en ; rdfs:subClassOf obo:BFO_0000003 ; owl:disjointWith obo:BFO_0000011, obo:BFO_0000015, obo:BFO_0000035 . obo:BFO_0000009 obo:BFO_0000179 "2d-s-region" ; obo:BFO_0000180 "TwoDimensionalSpatialRegion" ; obo:IAO_0000112 "an infinitely thin plane in space."@en, "the surface of a sphere-shaped part of space"@en ; obo:IAO_0000600 "A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001])"@en ; obo:IAO_0000602 "(forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001] " ; a owl:Class ; rdfs:isDefinedBy ; rdfs:label "two-dimensional spatial region"@en ; rdfs:subClassOf obo:BFO_0000006 ; owl:disjointWith obo:BFO_0000028 . obo:BFO_0000011 obo:BFO_0000179 "st-region" ; obo:BFO_0000180 "SpatiotemporalRegion" ; obo:IAO_0000112 "the spatiotemporal region occupied by a human life"@en, "the spatiotemporal region occupied by a process of cellular meiosis."@en, "the spatiotemporal region occupied by the development of a cancer tumor"@en ; obo:IAO_0000600 "A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001])"@en ; obo:IAO_0000601 "All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001])"@en, "Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001])"@en, "Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001])"@en, "Every spatiotemporal region occupies_spatiotemporal_region itself."@en, "Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002])"@en ; obo:IAO_0000602 "(forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002] ", "(forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001] ", "(forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001] ", "(forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001] ", "(forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001] " ; a owl:Class ; rdfs:isDefinedBy ; rdfs:label "spatiotemporal region"@en ; rdfs:subClassOf obo:BFO_0000003 . obo:BFO_0000015 obo:BFO_0000179 "process" ; obo:BFO_0000180 "Process" ; obo:IAO_0000112 "a process of cell-division, \\ a beating of the heart"@en, "a process of meiosis"@en, "a process of sleeping"@en, "the course of a disease"@en, "the flight of a bird"@en, "the life of an organism"@en, "your process of aging."@en ; obo:IAO_0000115 "An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t."@en, "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])"@en ; obo: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)"@en ; obo: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] " ; a owl:Class ; rdfs:isDefinedBy ; rdfs:label "process"@en ; rdfs:subClassOf obo:BFO_0000003 . obo:BFO_0000016 obo:BFO_0000179 "disposition" ; obo:BFO_0000180 "Disposition" ; obo:IAO_0000112 "an atom of element X has the disposition to decay to an atom of element Y"@en, "certain people have a predisposition to colon cancer"@en, "children are innately disposed to categorize objects in certain ways."@en, "the cell wall is disposed to filter chemicals in endocytosis and exocytosis"@en ; obo: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."@en ; obo: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])"@en ; obo: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])"@en ; obo: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] ", "(forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] " ; a owl:Class ; rdfs:isDefinedBy ; rdfs:label "disposition"@en ; rdfs:subClassOf obo:BFO_0000017 ; owl:disjointWith obo:BFO_0000023 . obo:BFO_0000017 obo:BFO_0000179 "realizable" ; obo:BFO_0000180 "RealizableEntity" ; obo:IAO_0000112 "the disposition of this piece of metal to conduct electricity."@en, "the disposition of your blood to coagulate"@en, "the function of your reproductive organs"@en, "the role of being a doctor"@en, "the role of this boundary to delineate where Utah and Colorado meet"@en ; obo:IAO_0000115 "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."@en ; obo: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])"@en ; obo:IAO_0000601 "All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])"@en ; obo: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] ", "(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] " ; a owl:Class ; rdfs:isDefinedBy ; rdfs:label "realizable entity"@en ; rdfs:subClassOf obo:BFO_0000020 ; owl:disjointWith obo:BFO_0000019 . obo:BFO_0000018 obo:BFO_0000179 "0d-s-region" ; obo:BFO_0000180 "ZeroDimensionalSpatialRegion" ; obo:IAO_0000600 "A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001])"@en ; obo:IAO_0000602 "(forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001] " ; a owl:Class ; rdfs:isDefinedBy ; rdfs:label "zero-dimensional spatial region"@en ; rdfs:subClassOf obo:BFO_0000006 ; owl:disjointWith obo:BFO_0000028 . obo:BFO_0000019 obo:BFO_0000179 "quality" ; obo:BFO_0000180 "Quality" ; obo:IAO_0000112 "the ambient temperature of this portion of air"@en, "the color of a tomato"@en, "the length of the circumference of your waist"@en, "the mass of this piece of gold."@en, "the shape of your nose"@en, "the shape of your nostril"@en ; obo: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])"@en ; obo: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])"@en ; obo:IAO_0000602 "(forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] ", "(forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] " ; a owl:Class ; rdfs:isDefinedBy ; rdfs:label "quality"@en ; rdfs:subClassOf obo:BFO_0000020 . obo:BFO_0000020 obo:BFO_0000179 "sdc" ; obo:BFO_0000180 "SpecificallyDependentContinuant" ; obo: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"@en, "of one-sided specifically dependent continuants: the mass of this tomato"@en, "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."@en, "the disposition of this fish to decay"@en, "the function of this heart: to pump blood"@en, "the mutual dependence of proton donors and acceptors in chemical reactions [79"@en, "the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction"@en, "the pink color of a medium rare piece of grilled filet mignon at its center"@en, "the role of being a doctor"@en, "the shape of this hole."@en, "the smell of this portion of mozzarella"@en ; obo:IAO_0000115 "A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same."@en, "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])"@en ; obo: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."@en ; obo: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] " ; a owl:Class ; rdfs:isDefinedBy ; rdfs:label "specifically dependent continuant"@en ; rdfs:subClassOf obo:BFO_0000002 ; owl:disjointWith obo:BFO_0000031 . obo:BFO_0000023 obo:BFO_0000179 "role" ; obo:BFO_0000180 "Role" ; obo: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."@en, "the priest role"@en, "the role of a boundary to demarcate two neighboring administrative territories"@en, "the role of a building in serving as a military target"@en, "the role of a stone in marking a property boundary"@en, "the role of subject in a clinical trial"@en, "the student role"@en ; obo:IAO_0000115 "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."@en ; obo: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."@en ; obo: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])"@en ; obo:IAO_0000602 "(forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] " ; a owl:Class ; rdfs:isDefinedBy ; rdfs:label "role"@en ; rdfs:subClassOf obo:BFO_0000017 . obo:BFO_0000024 obo:BFO_0000179 "fiat-object-part" ; obo:BFO_0000180 "FiatObjectPart" ; obo: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"@en, "the FMA:regional parts of an intact human body."@en, "the Western hemisphere of the Earth"@en, "the division of the brain into regions"@en, "the division of the planet into hemispheres"@en, "the dorsal and ventral surfaces of the body"@en, "the upper and lower lobes of the left lung"@en ; obo:IAO_0000116 "BFO 2 Reference: Most examples of fiat object parts are associated with theoretically drawn divisions"@en ; obo: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])"@en ; obo: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] " ; a owl:Class ; rdfs:isDefinedBy ; rdfs:label "fiat object part"@en ; rdfs:subClassOf obo:BFO_0000040 . obo:BFO_0000026 obo:BFO_0000179 "1d-s-region" ; obo:BFO_0000180 "OneDimensionalSpatialRegion" ; obo:IAO_0000112 "an edge of a cube-shaped portion of space."@en ; obo: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])"@en ; obo:IAO_0000602 "(forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001] " ; a owl:Class ; rdfs:isDefinedBy ; rdfs:label "one-dimensional spatial region"@en ; rdfs:subClassOf obo:BFO_0000006 ; owl:disjointWith obo:BFO_0000028 . obo:BFO_0000027 obo:BFO_0000179 "object-aggregate" ; obo:BFO_0000180 "ObjectAggregate" ; obo:IAO_0000112 "a collection of cells in a blood biobank."@en, "a swarm of bees is an aggregate of members who are linked together through natural bonds"@en, "a symphony orchestra"@en, "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)"@en, "defined by fiat: the aggregate of members of an organization"@en, "defined through physical attachment: the aggregate of atoms in a lump of granite"@en, "defined through physical containment: the aggregate of molecules of carbon dioxide in a sealed container"@en, "defined via attributive delimitations such as: the patients in this hospital"@en, "the aggregate of bearings in a constant velocity axle joint"@en, "the aggregate of blood cells in your body"@en, "the nitrogen atoms in the atmosphere"@en, "the restaurants in Palo Alto"@en, "your collection of Meissen ceramic plates."@en ; obo: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 ", "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)."@en ; obo: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." ; obo: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])"@en ; obo: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] " ; a owl:Class ; rdfs:isDefinedBy ; rdfs:label "object aggregate"@en ; rdfs:subClassOf obo:BFO_0000040 . obo:BFO_0000028 obo:BFO_0000179 "3d-s-region" ; obo:BFO_0000180 "ThreeDimensionalSpatialRegion" ; obo:IAO_0000112 "a cube-shaped region of space"@en, "a sphere-shaped region of space,"@en ; obo:IAO_0000600 "A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001])"@en ; obo:IAO_0000602 "(forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001] " ; a owl:Class ; rdfs:isDefinedBy ; rdfs:label "three-dimensional spatial region"@en ; rdfs:subClassOf obo:BFO_0000006 . obo:BFO_0000029 obo:BFO_0000179 "site" ; obo:BFO_0000180 "Site" ; obo:IAO_0000112 "Manhattan Canyon)"@en, "a hole in the interior of a portion of cheese"@en, "a rabbit hole"@en, "an air traffic control region defined in the airspace above an airport"@en, "the Grand Canyon"@en, "the Piazza San Marco"@en, "the cockpit of an aircraft"@en, "the hold of a ship"@en, "the interior of a kangaroo pouch"@en, "the interior of the trunk of your car"@en, "the interior of your bedroom"@en, "the interior of your office"@en, "the interior of your refrigerator"@en, "the lumen of your gut"@en, "your left nostril (a fiat part – the opening – of your left nasal cavity)"@en ; obo: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])"@en ; obo:IAO_0000602 "(forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002] " ; a owl:Class ; rdfs:isDefinedBy ; rdfs:label "site"@en ; rdfs:subClassOf obo:BFO_0000141 . obo:BFO_0000030 obo:BFO_0000179 "object" ; obo:BFO_0000180 "Object" ; obo:IAO_0000112 "atom"@en, "cell"@en, "cells and organisms"@en, "engineered artifacts"@en, "grain of sand"@en, "molecule"@en, "organelle"@en, "organism"@en, "planet"@en, "solid portions of matter"@en, "star"@en ; obo: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."@en, "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)."@en, "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"@en, "BFO 2 Reference: an object is a maximal causally unified material entity"@en, "BFO 2 Reference: ‘objects’ are sometimes referred to as ‘grains’ [74"@en ; obo: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])"@en ; a owl:Class ; rdfs:isDefinedBy ; rdfs:label "object"@en ; rdfs:subClassOf obo:BFO_0000040 . obo:BFO_0000031 obo:BFO_0000179 "gdc" ; obo:BFO_0000180 "GenericallyDependentContinuant" ; obo: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."@en, "the pdf file on your laptop, the pdf file that is a copy thereof on my laptop"@en, "the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule."@en ; obo:IAO_0000115 "A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time."@en, "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])"@en ; obo:IAO_0000602 "(iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] " ; a owl:Class ; rdfs:isDefinedBy ; rdfs:label "generically dependent continuant"@en ; rdfs:subClassOf obo:BFO_0000002 . obo:BFO_0000034 obo:BFO_0000179 "function" ; obo:BFO_0000180 "Function" ; obo:IAO_0000112 "the function of a hammer to drive in nails"@en, "the function of a heart pacemaker to regulate the beating of a heart through electricity"@en, "the function of amylase in saliva to break down starch into sugar"@en ; obo: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."@en ; obo: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])"@en ; obo:IAO_0000602 "(forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] " ; a owl:Class ; rdfs:isDefinedBy ; rdfs:label "function"@en ; rdfs:subClassOf obo:BFO_0000016 . obo:BFO_0000035 obo:BFO_0000179 "p-boundary" ; obo:BFO_0000180 "ProcessBoundary" ; obo:IAO_0000112 "the boundary between the 2nd and 3rd year of your life."@en ; obo:IAO_0000115 "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])"@en ; obo:IAO_0000601 "Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002])"@en ; obo:IAO_0000602 "(forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002] ", "(iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001] " ; a owl:Class ; rdfs:isDefinedBy ; rdfs:label "process boundary"@en ; rdfs:subClassOf obo:BFO_0000003 . obo:BFO_0000038 obo:BFO_0000179 "1d-t-region" ; obo:BFO_0000180 "OneDimensionalTemporalRegion" ; obo:IAO_0000112 "the temporal region during which a process occurs."@en ; obo: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)."@en ; obo:IAO_0000600 "A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001])"@en ; obo:IAO_0000602 "(forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001] " ; a owl:Class ; rdfs:isDefinedBy ; rdfs:label "one-dimensional temporal region"@en ; rdfs:subClassOf obo:BFO_0000008 ; owl:disjointWith obo:BFO_0000148 . obo:BFO_0000040 obo:BFO_0000179 "material" ; obo:BFO_0000180 "MaterialEntity" ; obo:IAO_0000112 "a flame"@en, "a forest fire"@en, "a human being"@en, "a hurricane"@en, "a photon"@en, "a puff of smoke"@en, "a sea wave"@en, "a tornado"@en, "an aggregate of human beings."@en, "an energy wave"@en, "an epidemic"@en, "the undetached arm of a human being"@en ; obo:IAO_0000115 "An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time."@en ; obo: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"@en, "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."@en, "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."@en ; obo: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])"@en ; obo:IAO_0000601 "Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])"@en, "every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])"@en ; obo:IAO_0000602 "(forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] ", "(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] ", "(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] " ; a owl:Class ; rdfs:isDefinedBy ; rdfs:label "material entity"@en ; rdfs:subClassOf obo:BFO_0000004 ; owl:disjointWith obo:BFO_0000141 . obo:BFO_0000050 obo:IAO_0000111 "is part of"@en ; obo:IAO_0000112 "my brain is part of my body (continuant parthood, two material entities)"@en, "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)"@en, "this day is part of this year (occurrent parthood)"@en ; obo:IAO_0000115 "a core relation that holds between a part and its whole"@en ; obo: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."@en, "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"@en, """Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'."""@en ; obo:IAO_0000118 "part_of"@en ; obo:RO_0001900 obo:RO_0001901 ; a owl:ObjectProperty, owl:TransitiveProperty ; rdfs:label "part of"@en ; rdfs:seeAlso "http://www.obofoundry.org/ro/#OBO_REL:part_of" ; owl:inverseOf obo:BFO_0000051 . obo:BFO_0000051 obo:IAO_0000111 "has part"@en ; obo:IAO_0000112 "my body has part my brain (continuant parthood, two material entities)"@en, "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)"@en, "this year has part this day (occurrent parthood)"@en ; obo:IAO_0000115 "a core relation that holds between a whole and its part"@en ; obo: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."@en, "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"@en, """Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'."""@en ; obo:IAO_0000118 "has_part"@en ; obo:RO_0001900 obo:RO_0001901 ; a owl:ObjectProperty, owl:TransitiveProperty ; rdfs:label "has part"@en . obo:BFO_0000054 obo:IAO_0000111 "realized in"@en ; obo:IAO_0000112 "this disease is realized in this disease course"@en, "this fragility is realized in this shattering"@en, "this investigator role is realized in this investigation"@en ; obo:IAO_0000118 "is realized by"@en, "realized_in"@en ; obo: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])"@en ; a owl:ObjectProperty ; rdfs: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" ; rdfs:domain obo:BFO_0000017 ; rdfs:isDefinedBy ; rdfs:label "realized in"@en ; rdfs:range obo:BFO_0000015 ; owl:inverseOf obo:BFO_0000055 . obo:BFO_0000055 obo:IAO_0000111 "realizes"@en ; obo:IAO_0000112 "this disease course realizes this disease"@en, "this investigation realizes this investigator role"@en, "this shattering realizes this fragility"@en ; obo: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])"@en ; a owl:ObjectProperty ; rdfs: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" ; rdfs:domain obo:BFO_0000015 ; rdfs:isDefinedBy <> ; rdfs:label "realizes"@en ; rdfs:range obo:BFO_0000017 . obo:BFO_0000066 obo:IAO_0000111 "occurs in"@en ; obo:IAO_0000115 "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"@en ; obo:IAO_0000118 "occurs_in"@en, "unfolds in"@en, "unfolds_in"@en ; a owl:ObjectProperty ; rdfs:comment "Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant" ; rdfs:domain obo:BFO_0000003 ; rdfs:isDefinedBy ; rdfs:label "occurs in"@en ; rdfs:range obo:BFO_0000004 ; owl:inverseOf obo:BFO_0000067 ; owl:propertyChainAxiom (obo:BFO_0000050 obo:BFO_0000066 ), (obo:BFO_0000066 obo:BFO_0000050 ) . obo:BFO_0000067 obo:IAO_0000111 "site of"@en ; obo:IAO_0000115 "[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"@en ; a owl:ObjectProperty ; rdfs:comment "Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant" ; rdfs:isDefinedBy ; rdfs:label "contains process"@en . obo:BFO_0000140 obo:BFO_0000179 "cf-boundary" ; obo:BFO_0000180 "ContinuantFiatBoundary" ; obo:IAO_0000115 "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])"@en ; obo: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."@en, "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"@en, "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."@en ; obo:IAO_0000601 "Every continuant fiat boundary is located at some spatial region at every time at which it exists"@en ; obo: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] " ; a owl:Class ; rdfs:isDefinedBy ; rdfs:label "continuant fiat boundary"@en ; rdfs:subClassOf obo:BFO_0000141 . obo:BFO_0000141 obo:BFO_0000179 "immaterial" ; obo:BFO_0000180 "ImmaterialEntity" ; obo: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"@en ; a owl:Class ; rdfs:isDefinedBy ; rdfs:label "immaterial entity"@en ; rdfs:subClassOf obo:BFO_0000004 . obo:BFO_0000142 obo:BFO_0000179 "1d-cf-boundary" ; obo:BFO_0000180 "OneDimensionalContinuantFiatBoundary" ; obo:IAO_0000112 "The Equator"@en, "all geopolitical boundaries"@en, "all lines of latitude and longitude"@en, "the line separating the outer surface of the mucosa of the lower lip from the outer surface of the skin of the chin."@en, "the median sulcus of your tongue"@en ; obo: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])"@en ; obo: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] " ; a owl:Class ; rdfs:isDefinedBy ; rdfs:label "one-dimensional continuant fiat boundary"@en ; rdfs:subClassOf obo:BFO_0000140 ; owl:disjointWith obo:BFO_0000146, obo:BFO_0000147 . obo:BFO_0000144 obo:BFO_0000179 "process-profile" ; obo:BFO_0000180 "ProcessProfile" ; obo: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"@en, "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."@en, "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."@en ; obo:IAO_0000115 "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])"@en ; obo: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])"@en ; obo: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] ", "(iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002] " ; a owl:Class ; rdfs:isDefinedBy ; rdfs:label "process profile"@en ; rdfs:subClassOf obo:BFO_0000015 ; owl:disjointWith obo:BFO_0000182 . obo:BFO_0000145 obo:BFO_0000179 "r-quality" ; obo:BFO_0000180 "RelationalQuality" ; obo: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."@en, "a marriage bond, an instance of requited love, an obligation between one person and another."@en ; obo:IAO_0000115 "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])"@en ; obo: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] " ; a owl:Class ; rdfs:isDefinedBy ; rdfs:label "relational quality"@en ; rdfs:subClassOf obo:BFO_0000019 . obo:BFO_0000146 obo:BFO_0000179 "2d-cf-boundary" ; obo:BFO_0000180 "TwoDimensionalContinuantFiatBoundary" ; obo: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])"@en ; obo: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] " ; a owl:Class ; rdfs:isDefinedBy ; rdfs:label "two-dimensional continuant fiat boundary"@en ; rdfs:subClassOf obo:BFO_0000140 . obo:BFO_0000147 obo:BFO_0000179 "0d-cf-boundary" ; obo:BFO_0000180 "ZeroDimensionalContinuantFiatBoundary" ; obo:IAO_0000112 "the geographic North Pole"@en, "the point of origin of some spatial coordinate system."@en, "the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet"@en ; obo: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."@en ; obo: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])"@en ; obo: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] " ; a owl:Class ; rdfs:isDefinedBy ; rdfs:label "zero-dimensional continuant fiat boundary"@en ; rdfs:subClassOf obo:BFO_0000140 . obo:BFO_0000148 obo:BFO_0000179 "0d-t-region" ; obo:BFO_0000180 "ZeroDimensionalTemporalRegion" ; obo:IAO_0000112 "a temporal region that is occupied by a process boundary"@en, "right now"@en, "the moment at which a child is born"@en, "the moment at which a finger is detached in an industrial accident"@en, "the moment of death."@en ; obo:IAO_0000118 "temporal instant."@en ; obo:IAO_0000600 "A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001])"@en ; obo:IAO_0000602 "(forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001] " ; a owl:Class ; rdfs:isDefinedBy ; rdfs:label "zero-dimensional temporal region"@en ; rdfs:subClassOf obo:BFO_0000008 . obo:BFO_0000179 obo:IAO_0000115 "Relates an entity in the ontology to the name of the variable that is used to represent it in the code that generates the BFO OWL file from the lispy specification."@en ; obo:IAO_0000232 "Really of interest to developers only"@en ; a owl:AnnotationProperty ; rdfs:label "BFO OWL specification label"@en ; rdfs:subPropertyOf rdfs:label . obo:BFO_0000180 obo:IAO_0000115 "Relates an entity in the ontology to the term that is used to represent it in the the CLIF specification of BFO2"@en ; obo:IAO_0000119 "Person:Alan Ruttenberg" ; obo:IAO_0000232 "Really of interest to developers only"@en ; a owl:AnnotationProperty ; rdfs:label "BFO CLIF specification label"@en ; rdfs:subPropertyOf rdfs:label . obo:BFO_0000182 obo:BFO_0000179 "history" ; obo:BFO_0000180 "History" ; obo: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])"@en ; a owl:Class ; rdfs:isDefinedBy ; rdfs:label "history"@en ; rdfs:subClassOf obo:BFO_0000015 . obo:GAZ_00000448 obo:IAO_0000115 "A reference to a place on the Earth, by its name or by its geographical location."^^xsd:string ; obo:IAO_0000412 ; a owl:Class, owl:NamedIndividual ; rdfs:label "geographic location"^^xsd:string ; rdfs:subClassOf obo:BFO_0000029 . obo:IAO_0000001 obo:IAO_0000111 "conditional specification"@en ; obo:IAO_0000114 obo:IAO_0000120 ; obo:IAO_0000115 "a directive information entity that specifies what should happen if the trigger condition is fulfilled"@en ; obo:IAO_0000117 "PlanAndPlannedProcess Branch"@en ; obo:IAO_0000119 "OBI branch derived"@en, "OBI_0000349"@en ; a owl:Class ; rdfs:label "conditional specification"@en ; rdfs:subClassOf obo:IAO_0000033 . obo:IAO_0000002 a obo:IAO_0000078, owl:NamedIndividual ; rdfs:label "example to be eventually removed"@en . obo:IAO_0000003 obo:IAO_0000111 "measurement unit label"@en ; obo:IAO_0000112 "Examples of measurement unit labels are liters, inches, weight per volume."@en ; obo:IAO_0000114 obo:IAO_0000125 ; obo:IAO_0000115 "A measurement unit label is as a label that is part of a scalar measurement datum and denotes a unit of measure."@en ; obo:IAO_0000116 """2009-03-16: provenance: a term measurement unit was proposed for OBI (OBI_0000176) , edited by Chris Stoeckert and Cristian Cocos, and subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definition of this, different, term."""@en, "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."@en ; obo:IAO_0000117 "PERSON: Alan Ruttenberg"@en, "PERSON: Melanie Courtot"@en ; a owl:Class ; rdfs:label "measurement unit label"@en ; rdfs:subClassOf obo:IAO_0000009 . obo:IAO_0000004 a owl:DatatypeProperty, owl:FunctionalProperty ; rdfs:domain obo:IAO_0000032 ; rdfs:label "has measurement value"@en ; rdfs:range xsd:double . obo:IAO_0000005 obo:IAO_0000111 "objective specification"@en ; obo:IAO_0000112 "In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction."@en ; obo:IAO_0000114 obo:IAO_0000122 ; obo:IAO_0000115 "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."@en ; obo: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.\""@en, "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."@en, "Answers the question, why did you do this experiment?"@en ; obo:IAO_0000117 "PERSON: Alan Ruttenberg"@en, "PERSON: Barry Smith"@en, "PERSON: Bjoern Peters"@en, "PERSON: Jennifer Fostel"@en ; obo:IAO_0000118 "goal specification"@en ; obo:IAO_0000119 "OBI Plan and Planned Process/Roles Branch"@en, "OBI_0000217"@en ; a owl:Class ; rdfs:label "objective specification"@en ; rdfs:subClassOf obo:IAO_0000033 . obo:IAO_0000006 obo:IAO_0000111 "narrative object"@en ; obo:IAO_0000112 "Examples of narrative objects are reports, journal articles, and patents submission."@en ; obo:IAO_0000114 obo:IAO_0000123 ; obo:IAO_0000115 "A narrative object is an information content entity that is a set of propositions."@en ; obo: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"@en, "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"@en ; obo:IAO_0000117 "person:Chris Stoeckert"@en ; obo:IAO_0000119 "OBI_0000013"@en, "group:OBI"@en ; a owl:Class ; rdfs:label "narrative object"@en ; rdfs:subClassOf obo:IAO_0000030 . obo:IAO_0000007 obo:IAO_0000112 "Pour the contents of flask 1 into flask 2"@en ; obo:IAO_0000114 obo:IAO_0000122 ; obo:IAO_0000115 "a directive information entity that describes an action the bearer will take"@en ; obo:IAO_0000117 "Alan Ruttenberg"@en ; obo:IAO_0000119 "OBI Plan and Planned Process branch"@en ; a owl:Class ; rdfs:label "action specification"@en ; rdfs:subClassOf obo:IAO_0000033 . obo:IAO_0000008 obo:IAO_0000231 obo:IAO_0000103 ; a owl:Class ; rdfs:label "obsolete_artifact"^^xsd:string ; rdfs:subClassOf oboInOwl:ObsoleteClass ; owl:deprecated true . obo:IAO_0000009 obo:IAO_0000111 "datum label"@en ; obo:IAO_0000114 obo:IAO_0000123 ; obo:IAO_0000115 "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"@en ; obo:IAO_0000116 "http://www.golovchenko.org/cgi-bin/wnsearch?q=label#4n"@en ; obo:IAO_0000117 "GROUP: IAO"@en ; obo: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. """ ; a owl:Class ; rdfs:label "datum label"@en ; rdfs:subClassOf obo:IAO_0000030 . obo:IAO_0000010 obo:IAO_0000111 "software"@en ; obo:IAO_0000114 obo:IAO_0000120 ; obo:IAO_0000115 """Software is a plan specification composed of a series of instructions that can be interpreted by or directly executed by a processing unit."""@en ; obo:IAO_0000116 "see sourceforge tracker discussion at http://sourceforge.net/tracker/index.php?func=detail&aid=1958818&group_id=177891&atid=886178"@en ; obo:IAO_0000117 "PERSON: Alan Ruttenberg"@en, "PERSON: Bjoern Peters"@en, "PERSON: Chris Stoeckert"@en, "PERSON: Melanie Courtot"@en ; obo:IAO_0000119 "GROUP: OBI"@en ; a owl:Class ; rdfs:label "software"@en ; rdfs:subClassOf obo:IAO_0000104 . obo:IAO_0000012 obo:IAO_0000111 "obsolete_digital entity"@en ; obo:IAO_0000115 "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."@en ; obo:IAO_0000116 """3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 Superclass was 'digitial quality'"""@en ; obo:IAO_0000117 "person:Chris Stoeckert"@en ; obo:IAO_0000119 "OBI_0000261"^^xsd:string, "group:OBI"@en ; obo:IAO_0000231 obo:IAO_0000103 ; a owl:Class ; rdfs:label "obsolete2_digital entity"@en ; rdfs:subClassOf oboInOwl:ObsoleteClass ; owl:deprecated true . obo:IAO_0000013 obo:IAO_0000111 "journal article"@en ; obo: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."@en ; obo:IAO_0000114 obo:IAO_0000120 ; obo:IAO_0000115 "a report that is published in a journal"@en ; obo:IAO_0000117 "person:Alan Ruttenberg"@en, "person:Chris Stoeckert"@en ; obo:IAO_0000119 "OBI_0000159"@en, "group:OBI"@en ; a owl:Class ; rdfs:label "journal article"@en ; rdfs:subClassOf obo:IAO_0000088 . obo:IAO_0000015 obo:IAO_0000111 "information carrier"@en ; obo: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."@en ; obo:IAO_0000114 obo:IAO_0000125 ; obo:IAO_0000115 "A quality of an information bearer that imparts the information content"@en ; obo: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'."@en, "2014-03-10: We are not certain that all information carriers are qualities. There was a discussion of dropping it." ; obo:IAO_0000117 "PERSON: Alan Ruttenberg"@en ; obo:IAO_0000119 "Smith, Ceusters, Ruttenberg, 2000 years of philosophy"@en ; a owl:Class ; rdfs:label "information carrier"@en ; rdfs:subClassOf obo:BFO_0000019 ; owl:equivalentClass [ a owl:Class ; owl:intersectionOf (obo:BFO_0000019 [ a owl:Restriction ; owl:onProperty obo:RO_0000059 ; owl:someValuesFrom obo:IAO_0000030 ] ) ] . obo:IAO_0000017 obo:IAO_0000111 "model number"@en ; obo:IAO_0000114 obo:IAO_0000125 ; obo:IAO_0000115 "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."@en ; obo: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"@en ; obo:IAO_0000117 "Person: Alan Ruttenberg"@en ; a owl:Class ; rdfs:label "model number"@en ; rdfs:subClassOf obo:IAO_0000028 . obo:IAO_0000018 obo:IAO_0000231 obo:IAO_0000226 ; a owl:Class ; rdfs:label "obsolete_material_entity"^^xsd:string ; rdfs:subClassOf oboInOwl:ObsoleteClass ; owl:deprecated true . obo:IAO_0000019 obo:IAO_0000111 "binary digital entity"@en ; obo:IAO_0000112 "MS Word document, ZIP file, DICOM file, JPEG file"@en ; obo:IAO_0000115 "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."@en ; obo:IAO_0000116 """3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 Superclass was 'digital entity'"""@en, "digital_entity"@en ; obo:IAO_0000117 "person:Chris Stoeckert"@en ; obo:IAO_0000119 "OBI_0000244"^^xsd:string, "group:OBI"@en ; obo:IAO_0000231 obo:IAO_0000103 ; a owl:Class ; rdfs:label "obsolete2_binary digital entity"@en ; rdfs:subClassOf oboInOwl:ObsoleteClass ; owl:deprecated true . obo:IAO_0000024 obo:IAO_0000112 "The length of a ruler."^^xsd:string ; obo:IAO_0000115 "a unit of measure is the quality of some material entity compared to which another quality is some multiple of."^^xsd:string ; obo:IAO_0000117 "Alan Ruttenberg"^^xsd:string ; obo:IAO_0000119 "Smith, Ceusters, Ruttenberg, 2000 years of philosophy"^^xsd:string ; obo:IAO_0000231 obo:IAO_0000103 ; a owl:Class ; rdfs:label "obsolete_unit of measure"^^xsd:string ; rdfs:subClassOf oboInOwl:ObsoleteClass ; owl:deprecated true . obo:IAO_0000025 obo:IAO_0000111 "programming language"@en ; obo:IAO_0000112 "R, Perl, Java"@en ; obo:IAO_0000114 obo:IAO_0000120 ; obo:IAO_0000115 "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."@en ; obo:IAO_0000117 "person:Alan Ruttenberg"@en, "person:Chris Stoeckert"@en ; obo:IAO_0000119 "OBI_0000058"@en, "group:OBI"@en ; a owl:Class ; rdfs:label "programming language"@en ; rdfs:subClassOf obo:IAO_0000104 . obo:IAO_0000027 obo:IAO_0000111 "data item"@en ; obo:IAO_0000112 "Data items include counts of things, analyte concentrations, and statistical summaries."@en ; obo:IAO_0000114 obo:IAO_0000125 ; obo:IAO_0000115 "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."@en ; obo: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."@en, "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."@en, "2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym."@en, "2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/", """JAR: datum -- well, this will be very tricky to define, but maybe some information-like stuff that might be put into a computer and that is meant, by someone, to denote and/or to be interpreted by some process... I would include lists, tables, sentences... I think I might defer to Barry, or to Brian Cantwell Smith JAR: A data item is an approximately justified approximately true approximate belief"""@en ; obo:IAO_0000117 "PERSON: Alan Ruttenberg"@en, "PERSON: Chris Stoeckert"@en, "PERSON: Jonathan Rees"@en ; obo:IAO_0000118 "data"@en ; a owl:Class ; rdfs:label "data item"@en ; rdfs:subClassOf obo:IAO_0000030 . obo:IAO_0000028 obo:IAO_0000111 "symbol"@en ; obo:IAO_0000112 "a serial number such as \"12324X\""@en, "a stop sign"@en, "a written proper name such as \"OBI\""@en ; obo:IAO_0000114 obo:IAO_0000125 ; obo:IAO_0000115 "An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity."@en ; obo:IAO_0000116 "20091104, MC: this needs work and will most probably change"@en, "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)."@en ; obo:IAO_0000117 "PERSON: James A. Overton"@en, "PERSON: Jonathan Rees"@en ; obo:IAO_0000119 "based on Oxford English Dictionary"@en ; a owl:Class ; rdfs:label "symbol"@en ; rdfs:subClassOf obo:IAO_0000030 . obo:IAO_0000029 obo:IAO_0000111 "numeral"@en ; obo:IAO_0000114 obo:IAO_0000123 ; obo:IAO_0000115 "A symbol that denotes a number."@en ; obo:IAO_0000117 "PERSON: Jonathan Rees"@en ; a owl:Class ; rdfs:label "numeral"@en ; rdfs:subClassOf obo:IAO_0000028 . obo:IAO_0000030 obo:IAO_0000111 "information content entity"@en ; obo:IAO_0000112 "Examples of information content entites include journal articles, data, graphical layouts, and graphs."@en ; obo:IAO_0000114 obo:IAO_0000122 ; obo:IAO_0000115 "A generically dependent continuant that is about some thing."@en ; obo: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)."@en, """information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907). Previous. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity."""@en ; obo:IAO_0000117 "PERSON: Chris Stoeckert"@en ; obo:IAO_0000119 "OBI_0000142"@en ; a owl:Class ; rdfs:label "information content entity"@en ; rdfs:subClassOf obo:BFO_0000031, [ a owl:Restriction ; owl:onProperty obo:IAO_0000136 ; owl:someValuesFrom obo:BFO_0000001 ] . obo:IAO_0000031 obo:IAO_0000111 "integer numeral"@en ; obo:IAO_0000114 obo:IAO_0000123 ; obo:IAO_0000115 "a numeral that denotes an integer"@en ; obo:IAO_0000117 "PERSON: Jonathan Rees"@en ; a owl:Class ; rdfs:label "integer numeral"@en ; rdfs:subClassOf obo:IAO_0000029 . obo:IAO_0000032 obo:IAO_0000112 "10 feet. 3 ml."@en ; obo:IAO_0000114 obo:IAO_0000120 ; obo:IAO_0000115 "a scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label."@en ; obo:IAO_0000116 """2009-03-16: we decided to keep datum singular in scalar measurement datum, as in this case we explicitly refer to the singular form"""@en, "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."@en ; obo:IAO_0000117 "PERSON: Alan Ruttenberg"@en, "PERSON: Melanie Courtot"@en ; a owl:Class ; rdfs:label "scalar measurement datum"@en ; rdfs:subClassOf obo:IAO_0000109, [ a owl:Restriction ; owl:minCardinality "1"^^xsd:nonNegativeInteger ; owl:onProperty obo:IAO_0000039 ], [ a owl:Restriction ; owl:minCardinality "1"^^xsd:nonNegativeInteger ; owl:onProperty obo:IAO_0000004 ] . obo:IAO_0000033 obo:IAO_0000114 obo:IAO_0000122 ; obo:IAO_0000115 "An information content entity whose concretizations indicate to their bearer how to realize them in a process."@en ; obo: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."@en, "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."@en, "8/6/2009 Alan Ruttenberg: Changed label from \"information entity about a realizable\" after discussions at ICBO"@en, "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"@en ; obo:IAO_0000117 "PERSON: Alan Ruttenberg"@en, "PERSON: Bjoern Peters"@en ; a owl:Class ; rdfs:label "directive information entity"@en ; rdfs:subClassOf obo:IAO_0000030, [ a owl:Restriction ; owl:onProperty obo:IAO_0000136 ; owl:someValuesFrom obo:BFO_0000017 ] . obo:IAO_0000034 obo:IAO_0000111 "time trigger"@en ; obo:IAO_0000114 obo:IAO_0000124 ; obo:IAO_0000115 "revisit?"@en ; obo:IAO_0000117 "PlanAndPlannedProcess Branch"@en ; obo:IAO_0000119 "OBI branch derived"@en, "OBI_0000331"@en ; a owl:Class ; rdfs:label "time trigger"@en ; rdfs:subClassOf obo:IAO_0000001 . obo:IAO_0000035 obo:IAO_0000111 "obsolete_study interpretation"@en ; obo:IAO_0000114 obo:IAO_0000125 ; obo:IAO_0000115 "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"@en ; obo: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, "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, "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."@en ; obo:IAO_0000117 "Lawrence Hunter"@en, "PERSON: Alan Ruttenberg"^^xsd:string, "PERSON: Jennifer Fostel"@en, "PERSON: Melanie Courtot"^^xsd:string ; obo:IAO_0000118 "conclusion"^^xsd:string ; obo:IAO_0000119 "OBI_0000005"^^xsd:string ; obo:IAO_0000231 obo:IAO_0000103 ; a owl:Class ; rdfs:label "obsolete_study interpretation"@en ; rdfs:subClassOf oboInOwl:ObsoleteClass ; owl:deprecated true . obo:IAO_0000037 obo:IAO_0000111 "dot plot"@en ; obo:IAO_0000112 "Dot plot of SSC-H and FSC-H."@en ; obo:IAO_0000114 obo:IAO_0000002 ; obo:IAO_0000115 "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."@en ; obo:IAO_0000117 "person:Allyson Lister"@en, "person:Chris Stoeckert"@en ; obo:IAO_0000119 "OBI_0000123"@en, "group:OBI"@en ; a owl:Class ; rdfs:label "dot plot"@en ; rdfs:subClassOf obo:IAO_0000038 . obo:IAO_0000038 obo:IAO_0000111 "graph"@en ; obo:IAO_0000114 obo:IAO_0000125 ; obo:IAO_0000115 "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."@en ; obo:IAO_0000117 "PERSON: Lawrence Hunter"@en, "person:Alan Ruttenberg"@en, "person:Allyson Lister"@en ; obo:IAO_0000119 "OBI_0000240"@en, "group:OBI"@en ; a owl:Class ; rdfs:label "graph"@en ; rdfs:subClassOf obo:IAO_0000309 . obo:IAO_0000039 a owl:FunctionalProperty, owl:ObjectProperty ; rdfs:label "has measurement unit label"@en ; rdfs:range obo:IAO_0000003 ; rdfs:subPropertyOf obo:BFO_0000051 . obo:IAO_0000047 obo:IAO_0000111 "text based digital entity"@en ; obo:IAO_0000112 "XML file, C++ source code file"@en ; obo:IAO_0000115 "A text based digital entity is a digital entity that is encoded so that it only contains text characters."@en ; obo:IAO_0000116 """3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 superclass was 'digital document'"""@en, "digital_entity"@en ; obo:IAO_0000117 "person:Chris Stoeckert"@en ; obo:IAO_0000119 "OBI_0000132"^^xsd:string, "group:OBI"^^xsd:string ; obo:IAO_0000231 obo:IAO_0000103 ; a owl:Class ; rdfs:label "obsolete2_text based digital entity"@en ; rdfs:subClassOf oboInOwl:ObsoleteClass ; owl:deprecated true . obo:IAO_0000055 obo:IAO_0000111 "rule"@en ; obo:IAO_0000112 "example to be added"@en ; obo:IAO_0000114 obo:IAO_0000123 ; obo:IAO_0000115 "a rule is an executable which guides, defines, restricts actions"@en ; obo:IAO_0000116 "MSI"@en ; obo:IAO_0000117 "PRS"@en ; obo:IAO_0000119 "OBI_0500021"@en, "PRS"@en ; a owl:Class ; rdfs:label "rule"@en ; rdfs:subClassOf obo:IAO_0000001 . obo:IAO_0000057 obo:IAO_0000111 "contour plot"@en ; obo:IAO_0000112 "Contour plot of SSC-H, FSC-H, and FL1-H."@en ; obo:IAO_0000114 obo:IAO_0000002 ; obo:IAO_0000116 "generically_dependent_continuants"@en ; obo:IAO_0000117 "person:Allyson Lister"@en, "person:Chris Stoeckert"@en ; obo:IAO_0000119 "OBI_0000246"@en, "group:Flow Cytometry community"@en ; a owl:Class ; rdfs:label "contour plot"@en ; rdfs:subClassOf obo:IAO_0000038 . obo:IAO_0000059 obo:IAO_0000111 "report figure"@en ; obo:IAO_0000114 obo:IAO_0000124 ; obo:IAO_0000115 "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"@en ; obo: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"@en, "Replaced by defined version of figure"@en ; obo:IAO_0000117 "person:Alan Ruttenberg"@en, "person:Allyson Lister"@en ; obo:IAO_0000119 "OBI_0000027"^^xsd:string, "group:OBI"@en ; obo:IAO_0000231 obo:IAO_0000103 ; a owl:Class ; rdfs:label "obsolete2_report figure"@en ; rdfs:subClassOf oboInOwl:ObsoleteClass ; owl:deprecated true . obo:IAO_0000064 obo:IAO_0000111 "algorithm"@en ; obo:IAO_0000112 "PMID: 18378114.Genomics. 2008 Mar 28. LINKGEN: A new algorithm to process data in genetic linkage studies."@en ; obo:IAO_0000114 obo:IAO_0000120 ; obo:IAO_0000115 "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."@en ; obo:IAO_0000117 "Philippe Rocca-Serra"@en, "PlanAndPlannedProcess Branch"@en ; obo:IAO_0000119 "OBI_0000270"@en, "adapted from discussion on OBI list (Matthew Pocock, Christian Cocos, Alan Ruttenberg)"@en ; a owl:Class ; rdfs:label "algorithm"@en ; rdfs:subClassOf obo:IAO_0000104 . obo:IAO_0000065 obo:IAO_0000111 "software interpreter"@en ; obo:IAO_0000112 "R program, Perl interpreter, Java virtual machine"@en ; obo:IAO_0000114 obo:IAO_0000120 ; obo:IAO_0000115 "A software interpreter is a software application that executes some specified input software. "@en ; obo: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"@en ; obo:IAO_0000117 "person:Alan Ruttenberg"@en, "person:Chris Stoeckert"@en ; obo:IAO_0000119 "OBI_0000199"@en, "group:OBI"@en ; a owl:Class ; rdfs:label "software interpreter"@en ; rdfs:subClassOf obo:IAO_0000064 . obo:IAO_0000078 obo:IAO_0000111 "curation status specification"@en ; obo:IAO_0000114 obo:IAO_0000125 ; obo:IAO_0000115 "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."@en ; obo:IAO_0000116 "Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)"@en ; obo:IAO_0000117 "PERSON:Bill Bug"@en ; obo:IAO_0000119 "GROUP:OBI:"@en, "OBI_0000266"@en ; a owl:Class ; rdfs:label "curation status specification"@en ; rdfs:subClassOf obo:IAO_0000102 ; owl:equivalentClass [ a owl:Class ; owl:oneOf (obo:IAO_0000002 obo:IAO_0000120 obo:IAO_0000121 obo:IAO_0000122 obo:IAO_0000123 obo:IAO_0000124 obo:IAO_0000125 obo:IAO_0000423 obo:IAO_0000428 ) ] . obo:IAO_0000079 obo:IAO_0000111 "density plot"@en ; obo:IAO_0000112 "Density plot of SSC-H and FSC-H."@en ; obo:IAO_0000114 obo:IAO_0000002 ; obo:IAO_0000115 "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."@en ; obo:IAO_0000117 "person:Allyson Lister"@en, "person:Chris Stoeckert"@en ; obo:IAO_0000119 "OBI_0000179"@en, "group:Flow Cytometry community"@en ; a owl:Class ; rdfs:label "density plot"@en ; rdfs:subClassOf obo:IAO_0000038 . obo:IAO_0000088 obo:IAO_0000111 "report"@en ; obo: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."@en ; obo:IAO_0000114 obo:IAO_0000125 ; obo:IAO_0000115 "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)"@en ; obo:IAO_0000116 """2009-03-16: comment from Darren Natale: I am slightly uneasy with the sentence \"Topic of the report is on something that has completed.\" Should it be restricted to those things that are completed? For example, a progress report is (usually) about something that definitely has *not* been completed, or may include (only) projections. I think the definition would not suffer if the whole sentence is deleted."""@en, "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."@en, "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."@en, "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"@en, "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"@en ; obo:IAO_0000117 "PERSON: Alan Ruttenberg"@en, "PERSON: Melanie Courtot"@en, "PERSON:Chris Stoeckert"@en ; obo:IAO_0000119 "GROUP: OBI"@en, "OBI_0000099"@en ; a owl:Class ; rdfs:label "report"@en ; rdfs:subClassOf obo:IAO_0000310 . obo:IAO_0000091 obo:IAO_0000111 "report element"@en ; obo:IAO_0000114 obo:IAO_0000120 ; obo:IAO_0000115 "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)."@en ; obo:IAO_0000116 "2009-03-16: needs some more work (clarify relations)."^^xsd:string, "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, "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, "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, "Replaced by textual entity and figure"^^xsd:string, "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"@en ; obo:IAO_0000117 "PERSON: Alan Ruttenberg"@en, "PERSON: Allyson Lister"@en, "PERSON: Melanie Courtot"^^xsd:string ; obo:IAO_0000119 "GROUP:OBI"@en, "OBI_0000001"^^xsd:string ; obo:IAO_0000231 obo:IAO_0000103 ; a owl:Class ; rdfs:label "obsolete_report element"@en ; rdfs:subClassOf oboInOwl:ObsoleteClass ; owl:deprecated true . obo:IAO_0000093 obo:IAO_0000111 "binary executable"@en ; obo:IAO_0000115 "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)"@en ; obo:IAO_0000116 """3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 superclass was 'digital entity'"""@en ; obo:IAO_0000117 "person:Jennifer Fostel"@en ; obo:IAO_0000119 "OBI_0000222"^^xsd:string, "group:OBI"@en ; obo:IAO_0000231 obo:IAO_0000103 ; a owl:Class ; rdfs:label "obsolete2_binary executable"@en ; rdfs:subClassOf oboInOwl:ObsoleteClass ; owl:deprecated true . obo:IAO_0000096 obo:IAO_0000111 "source code module"@en ; obo: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."@en ; obo:IAO_0000114 obo:IAO_0000123 ; obo:IAO_0000115 "A source code module is a directive information entity that specifies, using a programming language, some algorithm."@en ; obo:IAO_0000117 "person:Alan Ruttenberg"@en, "person:Chris Stoeckert"@en ; obo:IAO_0000119 "OBI_0000039"@en, "group:OBI"@en ; a owl:Class ; rdfs:label "source code module"@en ; rdfs:subClassOf obo:IAO_0000033 . obo:IAO_0000097 obo:IAO_0000111 "report table"@en ; obo:IAO_0000114 obo:IAO_0000002 ; obo:IAO_0000115 "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"@en ; obo: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 ; obo:IAO_0000117 "person:Alan Ruttenberg"@en, "person:Allyson Lister"@en ; obo:IAO_0000119 "OBI_0000265"^^xsd:string, "group:OBI"@en ; obo:IAO_0000231 obo:IAO_0000103 ; a owl:Class ; rdfs:label "obsolete_report table"@en ; rdfs:subClassOf oboInOwl:ObsoleteClass ; owl:deprecated true . obo:IAO_0000098 obo:IAO_0000111 "data format specification"@en ; obo:IAO_0000114 obo:IAO_0000123 ; obo:IAO_0000115 """A data format specification is the information content borne by the document published defining the specification. Example: The ISO document specifying what encompasses an XML document; The instructions in a XSD file"""@en ; obo:IAO_0000116 """2009-03-16: provenance: term imported from OBI_0000187, which had original definition \"A data format specification is a plan which organizes information. Example: The ISO document specifying what encompasses an XML document; The instructions in a XSD file\""""@en ; obo:IAO_0000117 "PERSON: Alan Ruttenberg"@en, "PlanAndPlannedProcess Branch"@en ; obo:IAO_0000119 "OBI branch derived"@en, "OBI_0000187"@en ; a owl:Class ; rdfs:label "data format specification"@en ; rdfs:subClassOf obo:IAO_0000033 . obo:IAO_0000100 obo:IAO_0000111 "data set"@en ; obo:IAO_0000112 "Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves)."@en ; obo:IAO_0000114 obo:IAO_0000125 ; obo:IAO_0000115 "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."@en ; obo: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"@en, "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." ; obo:IAO_0000117 "person:Allyson Lister"@en, "person:Chris Stoeckert"@en ; obo:IAO_0000119 "OBI_0000042"@en, "group:OBI"@en ; a owl:Class ; rdfs:label "data set"@en ; rdfs:subClassOf obo:IAO_0000027 . obo:IAO_0000101 obo:IAO_0000111 "image"@en ; obo:IAO_0000114 obo:IAO_0000122 ; obo:IAO_0000115 "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."@en ; obo:IAO_0000117 "person:Alan Ruttenberg"@en, "person:Allyson"@en, "person:Chris Stoeckert"@en ; obo:IAO_0000119 "OBI_0000030"@en, "group:OBI"@en ; a owl:Class ; rdfs:label "image"@en ; rdfs:subClassOf obo:IAO_0000308 . obo:IAO_0000102 obo:IAO_0000115 "data about an ontology part is a data item about a part of an ontology, for example a term"@en ; obo:IAO_0000117 "Person:Alan Ruttenberg"^^xsd:string ; a owl:Class ; rdfs:label "data about an ontology part"@en ; rdfs:subClassOf obo:IAO_0000027 . obo:IAO_0000103 obo:IAO_0000115 "The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job"@en ; obo:IAO_0000117 "Person:Alan Ruttenberg"^^xsd:string ; a obo:IAO_0000225, owl:NamedIndividual, owl:Thing ; rdfs:label "failed exploratory term"@en . obo:IAO_0000104 obo:IAO_0000111 "plan specification"@en ; obo:IAO_0000112 "PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice."@en ; obo:IAO_0000114 obo:IAO_0000122 ; obo:IAO_0000115 "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."@en ; obo: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."@en, "2014-03-31: A plan specification can have other parts, such as conditional specifications."@en, "Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved"@en ; obo:IAO_0000117 "Alan Ruttenberg"@en ; obo:IAO_0000119 "OBI Plan and Planned Process branch"@en, "OBI_0000344"@en ; a owl:Class ; rdfs:comment """2/3/2009 Comment from OBI review. Action specification not well enough specified. Conditional specification not well enough specified. Question whether all plan specifications have objective specifications. Request that IAO either clarify these or change definitions not to use them"""@en ; rdfs:label "plan specification"@en ; rdfs:subClassOf obo:IAO_0000033, [ a owl:Restriction ; owl:onProperty obo:BFO_0000051 ; owl:someValuesFrom obo:IAO_0000005 ], [ a owl:Restriction ; owl:onProperty obo:BFO_0000051 ; owl:someValuesFrom obo:IAO_0000007 ] . obo:IAO_0000105 obo:IAO_0000111 "digital document"@en ; obo:IAO_0000115 "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."@en ; obo:IAO_0000116 """3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 superclass was 'digial entity'"""@en ; obo:IAO_0000117 "person:Jennifer Fostel"@en ; obo:IAO_0000119 "OBI_0000195"^^xsd:string, "group:OBI"@en ; obo:IAO_0000231 obo:IAO_0000103 ; a owl:Class ; rdfs:label "obsolete2_digital document"@en ; rdfs:subClassOf oboInOwl:ObsoleteClass ; owl:deprecated true . obo:IAO_0000109 obo:IAO_0000111 "measurement datum"@en ; obo: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,}."@en ; obo:IAO_0000114 obo:IAO_0000125 ; obo:IAO_0000115 "A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device."@en ; obo:IAO_0000116 "2/2/2009 is_specified_output of some assay?"@en ; obo:IAO_0000117 "person:Chris Stoeckert"@en ; obo:IAO_0000119 "OBI_0000305"@en, "group:OBI"@en ; a owl:Class ; rdfs:label "measurement datum"@en ; rdfs:subClassOf obo:IAO_0000027 . obo:IAO_0000111 obo:IAO_0000111 "editor preferred label", "editor preferred label"@en, "editor preferred term", "editor preferred term"@en, "editor preferred term~editor preferred label" ; obo:IAO_0000114 obo:IAO_0000122 ; obo:IAO_0000115 "The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English)"@en ; obo:IAO_0000117 "PERSON:Daniel Schober"@en ; obo:IAO_0000119 "GROUP:OBI:"@en ; a owl:AnnotationProperty ; rdfs:isDefinedBy <> ; rdfs:label "editor preferred label", "editor preferred label"@en, "editor preferred term", "editor preferred term"@en, "editor preferred term~editor preferred label" . obo:IAO_0000112 obo:IAO_0000111 "example"@en ; obo:IAO_0000114 obo:IAO_0000122 ; obo:IAO_0000115 "A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold."@en ; obo:IAO_0000117 "PERSON:Daniel Schober"@en ; obo:IAO_0000119 "GROUP:OBI:"@en ; a owl:AnnotationProperty ; rdfs:isDefinedBy <> ; rdfs:label "example of usage"@en . obo:IAO_0000113 obo:IAO_0000111 "in branch"@en ; obo:IAO_0000115 "An annotation property indicating which module the terms belong to. This is currently experimental and not implemented yet."@en ; obo:IAO_0000117 "GROUP:OBI"@en ; obo:IAO_0000119 "OBI_0000277"@en ; a owl:AnnotationProperty ; rdfs:label "in branch"@en . obo:IAO_0000114 obo:IAO_0000111 "has curation status"@en ; obo:IAO_0000117 "PERSON:Alan Ruttenberg"@en, "PERSON:Bill Bug"@en, "PERSON:Melanie Courtot"@en ; obo:IAO_0000119 "OBI_0000281"@en ; a owl:AnnotationProperty ; rdfs:label "has curation status"@en . obo:IAO_0000115 obo:IAO_0000111 "definition"^^xsd:string, "definition"@en, "textual definition"^^xsd:string ; obo:IAO_0000114 obo:IAO_0000122 ; obo:IAO_0000115 "The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions."@en, "The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions."@en ; obo:IAO_0000116 """2012-04-05: Barry Smith The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. Can you fix to something like: A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. Alan Ruttenberg Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. On the specifics of the proposed definition: We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. """@en ; obo:IAO_0000117 "PERSON:Daniel Schober"@en ; obo:IAO_0000119 "GROUP:OBI:"@en ; a owl:AnnotationProperty ; rdfs:isDefinedBy <> ; rdfs:label "definition"^^xsd:string, "definition"@en, "textual definition"^^xsd:string . obo:IAO_0000116 obo:IAO_0000111 "editor note"@en ; obo:IAO_0000114 obo:IAO_0000122 ; obo:IAO_0000115 "An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology."@en ; obo:IAO_0000117 "PERSON:Daniel Schober"@en ; obo:IAO_0000119 "GROUP:OBI:"@en ; a owl:AnnotationProperty ; rdfs:isDefinedBy <> ; rdfs:label "editor note"@en . obo:IAO_0000117 obo:IAO_0000111 "term editor"@en ; obo:IAO_0000114 obo:IAO_0000122 ; obo:IAO_0000115 "Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people"@en ; obo:IAO_0000116 "20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115."@en ; obo:IAO_0000117 "PERSON:Daniel Schober"@en ; obo:IAO_0000119 "GROUP:OBI:"@en ; a owl:AnnotationProperty ; rdfs:isDefinedBy <> ; rdfs:label "term editor"@en . obo:IAO_0000118 obo:IAO_0000111 "alternative term"@en ; obo:IAO_0000114 obo:IAO_0000125 ; obo:IAO_0000115 "An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent)"@en ; obo:IAO_0000117 "PERSON:Daniel Schober"@en ; obo:IAO_0000119 "GROUP:OBI:"@en ; a owl:AnnotationProperty ; rdfs:isDefinedBy <> ; rdfs:label "alternative term"@en . obo:IAO_0000119 obo:IAO_0000111 "definition source"@en ; obo:IAO_0000114 obo:IAO_0000122 ; obo:IAO_0000115 "formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007"@en ; obo:IAO_0000117 "PERSON:Daniel Schober"@en ; obo:IAO_0000119 "Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w"^^xsd:string, "GROUP:OBI:"@en ; a owl:AnnotationProperty ; rdfs:isDefinedBy <> ; rdfs:label "definition source"@en . obo:IAO_0000120 obo:IAO_0000115 "Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete."@en ; a obo:IAO_0000078, owl:NamedIndividual ; rdfs:label "metadata complete"@en . obo:IAO_0000121 obo:IAO_0000115 "term created to ease viewing/sort terms for development purpose, and will not be included in a release"@en ; a obo:IAO_0000078, owl:NamedIndividual ; rdfs:label "organizational term"@en . obo:IAO_0000122 obo:IAO_0000115 "Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking \"ready_for_release\" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed \"ready_for_release\" will also derived from a chain of ancestor classes that are also \"ready_for_release.\""@en ; a obo:IAO_0000078, owl:NamedIndividual ; rdfs:label "ready for release"@en . obo:IAO_0000123 obo:IAO_0000115 "Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors."@en ; a obo:IAO_0000078, owl:NamedIndividual ; rdfs:label "metadata incomplete"@en . obo:IAO_0000124 obo:IAO_0000115 "Nothing done yet beyond assigning a unique class ID and proposing a preferred term."@en ; a obo:IAO_0000078, owl:NamedIndividual ; rdfs:label "uncurated"@en . obo:IAO_0000125 obo:IAO_0000115 "All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor."@en ; a obo:IAO_0000078, owl:NamedIndividual ; rdfs:label "pending final vetting"@en . obo:IAO_0000128 obo:IAO_0000114 obo:IAO_0000121 ; obo: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. Note: 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 ; obo:IAO_0000231 obo:IAO_0000226 ; a owl:Class ; rdfs:label "obsolete_identifier"^^xsd:string ; rdfs:subClassOf oboInOwl:ObsoleteClass ; owl:deprecated true . obo:IAO_0000129 obo:IAO_0000111 "version number"@en ; obo:IAO_0000114 obo:IAO_0000123 ; obo:IAO_0000115 "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."@en ; obo: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"@en ; obo:IAO_0000117 "GROUP: IAO"@en ; a owl:Class ; rdfs:label "version number"@en ; rdfs:subClassOf obo:IAO_0000028 . obo:IAO_0000131 obo:IAO_0000111 "serial number"@en ; obo:IAO_0000114 obo:IAO_0000123 ; obo:IAO_0000115 "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."@en ; obo: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 :-)"@en ; obo:IAO_0000117 "GROUP: IAO"@en ; a owl:Class ; rdfs:label "serial number"@en ; rdfs:subClassOf obo:IAO_0000028 . obo:IAO_0000132 obo:IAO_0000111 "lot number"@en ; obo:IAO_0000114 obo:IAO_0000123 ; obo:IAO_0000115 "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."@en ; obo:IAO_0000117 "GROUP: IAO"@en ; obo:IAO_0000118 "batch number"@en ; a owl:Class ; rdfs:label "lot number"@en ; rdfs:subClassOf obo:IAO_0000028 . obo:IAO_0000135 obo: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. Here the ink + paper is the independent continuant and the carrier is the pattern in the ink. c = pattern in the ink b = paper + ink r = friend"""^^xsd:string ; obo:IAO_0000114 obo:IAO_0000125 ; obo:IAO_0000115 """c specifically denotes r =def r is a portion of reality & c is a particular quality & c depends specifically on some independent continuant b & b acquired c as the result of the achievement of an objective to enable pointing to r repeatedly. Marked means there is a changed or additional quality of the bearer - the quality is the information carrier. Case 1 Memory trace as mark created when reading some description of some friend. The trace can denote. Case 2 Pattern of ink arrayed on paper as mark when writing down a friend's name Case 3 Pattern of magnetic domains on scattered pieces of a hard disk platter as mark when saving a file."""^^xsd:string ; obo: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, "see https://github.com/information-artifact-ontology/IAO/issues/25&q=denote"^^xsd:string ; obo:IAO_0000117 "Alan Ruttenberg"^^xsd:string ; obo:IAO_0000119 "Smith, Ceusters, Ruttenberg, 2000 years of philosophy"^^xsd:string ; obo:IAO_0000231 obo:IAO_0000103 ; a owl:ObjectProperty ; rdfs:label "obsolete_specifically denotes"^^xsd:string ; rdfs:subPropertyOf oboInOwl:ObsoleteProperty ; owl:deprecated true . obo:IAO_0000136 obo:IAO_0000112 "This document is about information artifacts and their representations"@en ; obo:IAO_0000114 obo:IAO_0000125 ; obo:IAO_0000115 "is_about is a (currently) primitive relation that relates an information artifact to an entity."@en ; obo: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. We will try to build it back up by elaborating the various subproperties that are more precisely defined. Some 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."""@en ; obo:IAO_0000117 "person:Alan Ruttenberg"@en ; obo:IAO_0000119 "Smith, Ceusters, Ruttenberg, 2000 years of philosophy"@en ; a owl:ObjectProperty ; rdfs:domain obo:IAO_0000030 ; rdfs:label "is about"@en . obo:IAO_0000140 obo:IAO_0000114 obo:IAO_0000123 ; obo:IAO_0000115 "A settings datum is a datum that denotes some configuration of an instrument."@en ; obo:IAO_0000116 """2/3/2009 Feedback from OBI This should be a \"setting specification\". There is a question of whether it is information about a realizable or not. Pro other specification are about realizables. Cons sometimes specifies a quality which is not a realizable."""@en, "Alan grouped these in placeholder for the moment. Name by analogy to measurement datum."@en ; a owl:Class ; rdfs:label "setting datum"@en ; rdfs:subClassOf obo:IAO_0000027 . obo:IAO_0000141 obo:IAO_0000116 "3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4", "Need to rework digital entity. Digital quality was suggested by Barry."^^xsd:string ; obo:IAO_0000231 obo:IAO_0000103 ; a owl:Class ; rdfs:label "obsolete_digital quality"^^xsd:string ; rdfs:subClassOf oboInOwl:ObsoleteClass ; owl:deprecated true . obo:IAO_0000142 obo:IAO_0000114 obo:IAO_0000125 ; obo:IAO_0000115 "An information artifact IA mentions an entity E exactly when it has a component/part that denotes E"@en ; obo: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)"@en, "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"@en ; obo:IAO_0000117 "PERSON: Jonathan Rees"@en, "Person: Alan Ruttenberg"@en ; a owl:ObjectProperty ; rdfs:label "mentions"@en ; rdfs:subPropertyOf obo:IAO_0000136 . obo:IAO_0000144 obo:IAO_0000111 "conclusion textual entity"@en ; obo: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"@en ; obo:IAO_0000114 obo:IAO_0000120 ; obo:IAO_0000115 "A textual entity that expresses the results of reasoning about a problem, for instance as typically found towards the end of scientific papers."@en ; obo:IAO_0000116 "2009/09/28 Alan Ruttenberg. Fucoidan-use-case"@en, "2009/10/23 Alan Ruttenberg: We need to work on the definition still"@en ; obo:IAO_0000117 "Person:Alan Ruttenberg"@en ; a owl:Class ; rdfs:label "conclusion textual entity"@en ; rdfs:subClassOf obo:IAO_0000300 . obo:IAO_0000178 obo:IAO_0000111 "material information bearer"@en ; obo: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."@en, "a brain"@en, "a hard drive"@en ; obo:IAO_0000114 obo:IAO_0000122 ; obo:IAO_0000115 "A material entity in which a concretization of an information content entity inheres."@en ; obo:IAO_0000117 "GROUP: IAO"@en ; a owl:Class ; rdfs:label "material information bearer"@en ; rdfs:subClassOf obo:BFO_0000040 ; owl:equivalentClass [ a owl:Class ; owl:intersectionOf (obo:BFO_0000040 [ a owl:Restriction ; owl:onProperty obo:RO_0000053 ; owl:someValuesFrom [ a owl:Restriction ; owl:onProperty obo:RO_0000059 ; owl:someValuesFrom obo:IAO_0000030 ] ] ) ] . obo:IAO_0000179 obo:IAO_0000111 "histogram"@en ; obo:IAO_0000114 obo:IAO_0000122 ; obo:IAO_0000115 """A histogram is a report graph which is a statistical description of a distribution in terms of occurrence frequencies of different event classes."""@en ; obo:IAO_0000117 "PERSON:Chris Stoeckert"@en, "PERSON:James Malone"@en, "PERSON:Melanie Courtot"@en ; obo:IAO_0000119 "GROUP:OBI"@en ; a owl:Class ; rdfs:label "histogram"@en ; rdfs:subClassOf obo:IAO_0000038 . obo:IAO_0000180 obo:IAO_0000111 "heatmap"@en ; obo:IAO_0000114 obo:IAO_0000122 ; obo:IAO_0000115 """A heatmap is a report graph which is a graphical representation of data where the values taken by a variable(s) are shown as colors in a two-dimensional map."""@en ; obo:IAO_0000117 "PERSON:Chris Stoeckert"@en, "PERSON:James Malone"@en, "PERSON:Melanie Courtot"@en ; obo:IAO_0000119 "GROUP:OBI"@en ; a owl:Class ; rdfs:label "heatmap"@en ; rdfs:subClassOf obo:IAO_0000038 . obo:IAO_0000181 obo:IAO_0000111 "Venn diagram"@en ; obo:IAO_0000114 obo:IAO_0000122 ; obo:IAO_0000115 """A Venn diagram is a report graph showing all hypothetically possible logical relations between a finite collection of sets."""@en ; obo:IAO_0000117 "PERSON:Chris Stoeckert"@en, "PERSON:James Malone"@en, "PERSON:Melanie Courtot"@en ; obo:IAO_0000119 "WEB: http://en.wikipedia.org/wiki/Venn_diagram"@en ; a owl:Class ; rdfs:label "Venn diagram"@en ; rdfs:subClassOf obo:IAO_0000038 . obo:IAO_0000182 obo:IAO_0000111 "obsolete_survival curve"@en ; obo:IAO_0000114 obo:IAO_0000122 ; obo:IAO_0000115 "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."@en ; obo:IAO_0000117 "PERSON:Chris Stoeckert"@en, "PERSON:James Malone"@en, "PERSON:Melanie Courtot"@en ; obo:IAO_0000119 "WEB: http://www.graphpad.com/www/book/survive.htm"@en ; obo:IAO_0000231 obo:IAO_0000103 ; a owl:Class ; rdfs:label "obsolete_survival curve"@en ; rdfs:subClassOf oboInOwl:ObsoleteClass ; owl:deprecated true . obo:IAO_0000183 obo:IAO_0000111 "dendrogram"@en ; obo:IAO_0000112 """Dendrograms are often used in computational biology to illustrate the clustering of genes."""@en ; obo:IAO_0000114 obo:IAO_0000122 ; obo:IAO_0000115 """A dendrogram is a report graph which is a tree diagram frequently used to illustrate the arrangement of the clusters produced by a clustering algorithm."""@en ; obo:IAO_0000117 "PERSON:Chris Stoeckert"@en, "PERSON:James Malone"@en, "PERSON:Melanie Courtot"@en ; obo:IAO_0000119 "WEB: http://en.wikipedia.org/wiki/Dendrogram"@en ; a owl:Class ; rdfs:label "dendrogram"@en ; rdfs:subClassOf obo:IAO_0000038 . obo:IAO_0000184 obo:IAO_0000111 "scatter plot"@en ; obo:IAO_0000112 "Comparison of gene expression values in two samples can be displayed in a scatter plot"@en ; obo:IAO_0000114 obo:IAO_0000122 ; obo:IAO_0000115 "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."@en ; obo:IAO_0000117 "PERSON:Chris Stoeckert"@en, "PERSON:James Malone"@en, "PERSON:Melanie Courtot"@en ; obo:IAO_0000118 "scattergraph"@en ; obo:IAO_0000119 "WEB: http://en.wikipedia.org/wiki/Scatterplot"@en ; a owl:Class ; rdfs:label "scatter plot"@en ; rdfs:subClassOf obo:IAO_0000038 . obo:IAO_0000185 obo:IAO_0000114 obo:IAO_0000122 ; obo:IAO_0000115 "A photograph is created by projecting an image onto a photosensitive surface such as a chemically treated plate or film, CCD receptor, etc."@en ; obo:IAO_0000117 "PERSON:Alan Ruttenberg"@en, "PERSON:Joanne Luciano"@en, "PERSON:Melanie Courtot"@en ; obo:IAO_0000119 "WEB: http://en.wiktionary.org/wiki/photograph"@en ; a owl:Class ; rdfs:label "photograph"@en ; rdfs:subClassOf obo:IAO_0000101 . obo:IAO_0000186 obo:IAO_0000111 "photographic print"@en ; obo:IAO_0000114 obo:IAO_0000125 ; obo:IAO_0000115 "A photographic print is a material entity upon which a photograph generically depends."@en ; obo:IAO_0000117 "PERSON:Alan Ruttenberg"@en, "PERSON:Melanie Courtot"@en ; a owl:Class ; rdfs:label "photographic print"@en ; rdfs:subClassOf obo:IAO_0000178 ; owl:equivalentClass [ a owl:Class ; owl:intersectionOf (obo:BFO_0000040 [ a owl:Restriction ; owl:onProperty obo:RO_0000053 ; owl:someValuesFrom [ a owl:Restriction ; owl:onProperty obo:RO_0000059 ; owl:someValuesFrom obo:IAO_0000185 ] ] ) ] . obo:IAO_0000219 obo: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."@en ; obo:IAO_0000115 "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"@en ; obo: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. g denotes r =def r is a portion of reality there is some c that is a concretization of g every c that is a concretization of g specifically denotes r"""@en ; obo:IAO_0000117 "person:Alan Ruttenberg"@en ; obo:IAO_0000119 "Conversations with Barry Smith, Werner Ceusters, Bjoern Peters, Michel Dumontier, Melanie Courtot, James Malone, Bill Hogan"@en ; a owl:ObjectProperty ; rdfs:comment ""@en ; rdfs:domain obo:IAO_0000030 ; rdfs:label "denotes"@en ; rdfs:range obo:BFO_0000001 ; rdfs:subPropertyOf obo:IAO_0000136 ; owl:inverseOf obo:IAO_0000235 . obo:IAO_0000220 obo:IAO_0000116 "see https://github.com/information-artifact-ontology/IAO/issues/25&q=denote"^^xsd:string ; obo:IAO_0000231 obo:IAO_0000103 ; a owl:ObjectProperty ; rdfs:label "obsolete_materially denotes"^^xsd:string ; rdfs:subPropertyOf oboInOwl:ObsoleteProperty ; owl:deprecated true . obo:IAO_0000221 obo:IAO_0000115 """m is a quality measurement of q at t when q is a quality there is a measurement process p that has specified output m, a measurement datum, that is about q"""@en ; obo: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"@en, """From the second IAO workshop [Alan Ruttenberg 8/6/2009: not completely current, though bringing in comparison is probably important] 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. Werner suggests a solution based on \"Magnitudes\" a proposal for which we are awaiting details. -- From the second IAO workshop, various comments, [commented on by Alan Ruttenberg 8/6/2009] unit of measure is a quality, e.g. the length of a ruler. [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] [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] a represents b means either a denotes b or a describes describe: a describes b means a is about b and a allows an inference of at least one quality of b We have had a long discussion about denotes versus describes."""@en, """From the second IAO workshop: An attempt at tieing the quality to the measurement datum more carefully. a 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."""@en, """From the second meeting on IAO: An attempt at defining assay using Barry's \"reliability\" wording assay: process and has_input some material entity and has_output some information content entity and which is such that instances of this process type reliably generate outputs that describes the input."""@en, """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. Werner suggests a solution based on \"Magnitudes\" a proposal for which we are awaiting details."""@en ; obo:IAO_0000117 "Alan Ruttenberg"@en ; a owl:ObjectProperty ; rdfs:domain obo:IAO_0000109 ; rdfs:label "is quality measurement of"@en ; rdfs:range obo:BFO_0000019 ; rdfs:subPropertyOf obo:IAO_0000136 ; owl:inverseOf obo:IAO_0000417 . obo:IAO_0000222 obo:IAO_0000231 obo:IAO_0000103 ; a owl:ObjectProperty ; rdfs:label "obsolete_describes"^^xsd:string ; rdfs:subPropertyOf oboInOwl:ObsoleteProperty ; owl:deprecated true . obo:IAO_0000223 obo:IAO_0000231 obo:IAO_0000103 ; a owl:ObjectProperty ; rdfs:label "obsolete_represents"^^xsd:string ; rdfs:subPropertyOf oboInOwl:ObsoleteProperty ; owl:deprecated true . obo:IAO_0000224 obo:IAO_0000115 "Core is an instance of a grouping of terms from an ontology or ontologies. It is used by the ontology to identify main classes."@en ; obo:IAO_0000117 "PERSON: Alan Ruttenberg"@en, "PERSON: Melanie Courtot"@en ; a oboInOwl:Subset, owl:NamedIndividual ; rdfs:label "core"@en . obo:IAO_0000225 obo:IAO_0000111 "obsolescence reason specification"@en ; obo:IAO_0000114 obo:IAO_0000125 ; obo:IAO_0000115 "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."@en ; obo:IAO_0000116 "The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology."@en ; obo:IAO_0000117 "PERSON: Alan Ruttenberg"@en, "PERSON: Melanie Courtot"@en ; a owl:Class ; rdfs:label "obsolescence reason specification"@en ; rdfs:subClassOf obo:IAO_0000102 ; owl:equivalentClass [ a owl:Class ; owl:oneOf (obo:IAO_0000103 obo:IAO_0000226 obo:IAO_0000227 obo:IAO_0000228 obo:IAO_0000229 ) ] . obo:IAO_0000226 a obo:IAO_0000225, owl:NamedIndividual, owl:Thing ; rdfs:label "placeholder removed"@en . obo:IAO_0000227 obo:IAO_0000116 "An editor note should explain what were the merged terms and the reason for the merge."@en ; a obo:IAO_0000225, owl:NamedIndividual ; rdfs:label "terms merged"@en . obo:IAO_0000228 obo:IAO_0000116 "This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use."@en ; a obo:IAO_0000225, owl:NamedIndividual ; rdfs:label "term imported"@en . obo:IAO_0000229 obo:IAO_0000116 "This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created."@en ; a obo:IAO_0000225, owl:NamedIndividual ; rdfs:label "term split"@en . obo:IAO_0000230 obo:IAO_0000116 "This is to be used if none of the existing instances cover the reason for obsolescence. An editor note should indicate this new reason."@en, "We expect to be able to mine these new reasons and add instances as required."@en ; a obo:IAO_0000225, owl:NamedIndividual ; rdfs:label "other"@en ; owl:deprecated true . obo:IAO_0000231 obo:IAO_0000111 "has obsolescence reason"@en ; obo:IAO_0000115 "Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification."@en ; obo:IAO_0000117 "PERSON:Alan Ruttenberg"@en, "PERSON:Melanie Courtot"@en ; a owl:AnnotationProperty ; rdfs:label "has obsolescence reason"@en . obo:IAO_0000232 obo:IAO_0000111 "curator note"@en ; obo:IAO_0000114 obo:IAO_0000122 ; obo:IAO_0000115 "An administrative note of use for a curator but of no use for a user"@en ; obo:IAO_0000117 "PERSON:Alan Ruttenberg"@en ; a owl:AnnotationProperty ; rdfs:isDefinedBy <> ; rdfs:label "curator note"@en . obo:IAO_0000233 obo:IAO_0000111 "term tracker item" ; obo:IAO_0000112 "the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/" ; obo:IAO_0000114 obo:IAO_0000125 ; obo:IAO_0000115 "An IRI or similar locator for a request or discussion of an ontology term." ; obo:IAO_0000117 "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg" ; obo:IAO_0000119 "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg" ; a owl:AnnotationProperty ; rdfs:comment "The 'tracker item' can associate a tracker with a specific ontology term." ; rdfs:label "term tracker item"@en . obo:IAO_0000234 obo:IAO_0000114 obo:IAO_0000125 ; obo:IAO_0000115 "The name of the person, project, or organization that motivated inclusion of an ontology term by requesting its addition." ; obo:IAO_0000117 "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg" ; obo:IAO_0000119 "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg" ; a owl:AnnotationProperty ; rdfs:comment "The 'term requester' can credit the person, organization or project who request the ontology term." ; rdfs:label "ontology term requester"@en . obo:IAO_0000235 obo:IAO_0000115 "inverse of the relation 'denotes'"@en ; obo:IAO_0000117 "Person: Jie Zheng, Chris Stoeckert, Mike Conlon"@en ; obo:IAO_0000233 ; a owl:ObjectProperty ; rdfs:domain obo:BFO_0000001 ; rdfs:label "denoted by"@en ; rdfs:range obo:IAO_0000030 . obo:IAO_0000300 obo:IAO_0000111 "textual entity"@en ; obo:IAO_0000112 "Words, sentences, paragraphs, and the written (non-figure) parts of publications are all textual entities"@en ; obo:IAO_0000114 obo:IAO_0000123 ; obo:IAO_0000115 "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."@en ; obo: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."@en, "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."@en ; obo:IAO_0000117 "PERSON: Lawrence Hunter"@en ; obo:IAO_0000118 "text"@en ; a owl:Class ; rdfs:label "textual entity"@en ; rdfs:subClassOf obo:IAO_0000030 . obo:IAO_0000301 obo:IAO_0000111 "citation"@en ; obo:IAO_0000112 "Verspoor, K., Cohen, KB., Hunter, L. Textual characteristics of traditional and Open Access scientific journals are similar, BMC Bioinformatics 2009, 10:183."@en ; obo:IAO_0000114 obo:IAO_0000125 ; obo:IAO_0000115 "a textual entity intended to identify a particular publication"@en ; obo:IAO_0000117 "PERSON: Lawrence Hunter"@en ; a owl:Class ; rdfs:label "citation"@en ; rdfs:subClassOf obo:IAO_0000300, [ a owl:Restriction ; owl:onProperty obo:IAO_0000136 ; owl:someValuesFrom obo:IAO_0000310 ] . obo:IAO_0000302 obo:IAO_0000111 "author identification"@en ; obo:IAO_0000112 "L. Hunter"@en ; obo:IAO_0000114 obo:IAO_0000125 ; obo:IAO_0000115 "A textual entity intended to identify a particular author"@en ; obo:IAO_0000117 "PERSON: Lawrence Hunter"@en ; a owl:Class ; rdfs:label "author identification"@en ; rdfs:subClassOf obo:IAO_0000590 . obo:IAO_0000303 obo:IAO_0000111 "institutional identification"@en ; obo:IAO_0000112 "University of Colorado Denver School of Medicine"@en ; obo:IAO_0000114 obo:IAO_0000125 ; obo:IAO_0000115 "A textual entity intended to identify a particular institution"@en ; obo:IAO_0000117 "PERSON: Lawrence Hunter"@en ; a owl:Class ; rdfs:label "institutional identification"@en ; rdfs:subClassOf obo:IAO_0000300 . obo:IAO_0000304 obo:IAO_0000111 "caption"@en ; obo: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."@en ; obo:IAO_0000114 obo:IAO_0000125 ; obo:IAO_0000115 "A textual entity that describes a figure"@en ; obo:IAO_0000117 "PERSON: Lawrence Hunter"@en ; a owl:Class ; rdfs:label "caption"@en ; rdfs:subClassOf obo:IAO_0000300, [ a owl:Restriction ; owl:onProperty obo:IAO_0000136 ; owl:someValuesFrom obo:IAO_0000308 ] . obo:IAO_0000305 obo:IAO_0000111 "document title"@en ; obo:IAO_0000112 "Textual characteristics of traditional and Open Access scientific journals are similar"@en ; obo:IAO_0000114 obo:IAO_0000125 ; obo:IAO_0000115 "A textual entity that names a document"@en ; obo:IAO_0000117 "PERSON: Lawrence Hunter"@en ; a owl:Class ; rdfs:label "document title"@en ; rdfs:subClassOf obo:IAO_0000300 . obo:IAO_0000306 obo:IAO_0000111 "table"@en ; obo:IAO_0000112 """| T F --+----- T | T F F | F F"""@en ; obo:IAO_0000114 obo:IAO_0000125 ; obo:IAO_0000115 "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"@en ; obo:IAO_0000117 "PERSON: Lawrence Hunter"@en ; a owl:Class ; rdfs:label "table"@en ; rdfs:subClassOf obo:IAO_0000300 . obo:IAO_0000307 obo:IAO_0000111 "table of abbreviations"@en ; obo:IAO_0000112 """IAO information artifact ontology OBI ontology of biomedical investiations GO gene ontology"""@en ; obo:IAO_0000114 obo:IAO_0000125 ; obo:IAO_0000115 "A table where the constituent texts are abbreviations and their expansions"@en ; obo:IAO_0000117 "PERSON: Lawrence Hunter"@en ; a owl:Class ; rdfs:label "table of abbreviations"@en ; rdfs:subClassOf obo:IAO_0000306 . obo:IAO_0000308 obo:IAO_0000111 "figure"@en ; obo:IAO_0000112 "Any picture, diagram or table"@en ; obo:IAO_0000114 obo:IAO_0000120 ; obo:IAO_0000115 "An information content entity consisting of a two dimensional arrangement of information content entities such that the arrangement itself is about something."@en ; obo:IAO_0000117 "PERSON: Lawrence Hunter"@en ; a owl:Class ; rdfs:label "figure"@en ; rdfs:subClassOf obo:IAO_0000030 . obo:IAO_0000309 obo:IAO_0000111 "diagram"@en ; obo:IAO_0000112 "A molecular structure ribbon cartoon showing helices, turns and sheets and their relations to each other in space."@en ; obo:IAO_0000114 obo:IAO_0000120 ; obo:IAO_0000115 "A figure that expresses one or more propositions"@en ; obo:IAO_0000117 "PERSON: Lawrence Hunter"@en ; a owl:Class ; rdfs:label "diagram"@en ; rdfs:subClassOf obo:IAO_0000308 . obo:IAO_0000310 obo:IAO_0000111 "document"@en ; obo:IAO_0000112 "A journal article, patent application, laboratory notebook, or a book"@en ; obo:IAO_0000114 obo:IAO_0000120 ; obo:IAO_0000115 "A collection of information content entities intended to be understood together as a whole"@en ; obo:IAO_0000117 "PERSON: Lawrence Hunter"@en ; a owl:Class ; rdfs:label "document"@en ; rdfs:subClassOf obo:IAO_0000030 . obo:IAO_0000311 obo:IAO_0000111 "publication"@en ; obo:IAO_0000112 "A journal article or book"@en ; obo:IAO_0000114 obo:IAO_0000120 ; obo:IAO_0000115 "A document that has been accepted by a publisher"@en ; obo:IAO_0000117 "PERSON: Lawrence Hunter"@en ; a owl:Class ; rdfs:label "publication"@en ; rdfs:subClassOf obo:IAO_0000310 . obo:IAO_0000312 obo:IAO_0000111 "publication about an investigation"@en ; obo:IAO_0000112 "Most scientific journal articles"@en ; obo:IAO_0000114 obo:IAO_0000120 ; obo:IAO_0000115 "A publication that is about an investigation"@en ; obo:IAO_0000117 "PERSON: Lawrence Hunter"@en ; obo:IAO_0000118 "scientific publication"@en ; a owl:Class ; rdfs:label "publication about an investigation"@en ; rdfs:subClassOf obo:IAO_0000311, [ a owl:Restriction ; owl:onProperty obo:IAO_0000136 ; owl:someValuesFrom obo:OBI_0000066 ] . obo:IAO_0000313 obo:IAO_0000111 "patent"@en ; obo:IAO_0000112 "US Patent 6,449,603"@en ; obo:IAO_0000114 obo:IAO_0000120 ; obo:IAO_0000115 "A document that has been accepted by a patent authority"@en ; obo:IAO_0000117 "PERSON: Lawrence Hunter"@en ; a owl:Class ; rdfs:label "patent"@en ; rdfs:subClassOf obo:IAO_0000310 . obo:IAO_0000314 obo:IAO_0000111 "document part"@en ; obo:IAO_0000112 "An abstract, introduction, method or results section."@en ; obo:IAO_0000114 obo:IAO_0000120 ; obo:IAO_0000115 "an information content entity that is part of a document"@en ; obo:IAO_0000117 "PERSON: Lawrence Hunter"@en ; a owl:Class ; rdfs:label "document part"@en ; rdfs:subClassOf obo:IAO_0000030, [ a owl:Restriction ; owl:onProperty obo:BFO_0000050 ; owl:someValuesFrom obo:IAO_0000310 ] . obo:IAO_0000315 obo:IAO_0000111 "abstract"@en ; obo: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."@en ; obo:IAO_0000114 obo:IAO_0000120 ; obo:IAO_0000115 "A summary of the entire document that is substantially smaller than the document it summarizes. It is about the document it summarizes."@en ; obo:IAO_0000117 "PERSON: Lawrence Hunter"@en ; a owl:Class ; rdfs:label "abstract"@en ; rdfs:subClassOf obo:IAO_0000314, [ a owl:Restriction ; owl:onProperty obo:IAO_0000136 ; owl:someValuesFrom obo:IAO_0000310 ] . obo:IAO_0000316 obo:IAO_0000111 "introduction to a publication about an investigation"@en ; obo:IAO_0000112 "Section labelled 'introduction' of a typical scientific journal article"@en ; obo:IAO_0000114 obo:IAO_0000120 ; obo:IAO_0000115 "A part of a publication about an investigation that is about the objective specification (why the investigation is being done)"@en ; obo:IAO_0000117 "PERSON: Lawrence Hunter"@en ; obo:IAO_0000118 "background"@en, "introduction"@en ; a owl:Class ; rdfs:label "introduction to a publication about an investigation"@en ; rdfs:subClassOf obo:IAO_0000314, [ a owl:Restriction ; owl:onProperty obo:IAO_0000136 ; owl:someValuesFrom obo:IAO_0000005 ] . obo:IAO_0000317 obo:IAO_0000111 "methods section"@en ; obo:IAO_0000112 "The section labelled 'Methods' or 'Materials and Methods' in a typical scientific journal article."@en ; obo:IAO_0000114 obo:IAO_0000120 ; obo:IAO_0000115 "A part of a publication about an investigation that is about the study design of the investigation"@en ; obo:IAO_0000117 "PERSON: Lawrence Hunter"@en ; obo:IAO_0000118 "experimental"@en, "experimental procedures"@en, "experimental section"@en, "methods"@en ; a owl:Class ; rdfs:label "methods section"@en ; rdfs:subClassOf obo:IAO_0000314, [ a owl:Restriction ; owl:onProperty obo:IAO_0000136 ; owl:someValuesFrom obo:OBI_0500000 ] . obo:IAO_0000318 obo:IAO_0000111 "results section"@en ; obo:IAO_0000112 "The section labelled 'results' in a typical scientific journal article"@en ; obo:IAO_0000114 obo:IAO_0000120 ; obo:IAO_0000115 "A part of a publication about an investigation that is about a study design execution"@en ; obo:IAO_0000117 "PERSON: Lawrence Hunter"@en ; obo:IAO_0000118 "results"@en ; a owl:Class ; rdfs:label "results section"@en ; rdfs:subClassOf obo:IAO_0000314, [ a owl:Restriction ; owl:onProperty obo:IAO_0000136 ; owl:someValuesFrom obo:OBI_0000471 ] . obo:IAO_0000319 obo:IAO_0000111 "discussion section of a publication about an investigation"@en ; obo:IAO_0000114 obo:IAO_0000120 ; obo:IAO_0000115 "A part of a publication about an investigation that is about the study interpretation of the investigation"@en ; obo:IAO_0000117 "PERSON: Lawrence Hunter"@en ; obo:IAO_0000118 "discussion"@en, "discussion section"@en ; a owl:Class ; rdfs:label "discussion section of a publication about an investigation"@en ; rdfs:subClassOf obo:IAO_0000314 . obo:IAO_0000320 obo:IAO_0000111 "references section"@en ; obo: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\""@en ; obo:IAO_0000114 obo:IAO_0000120 ; obo:IAO_0000115 "A part of a document that has citations as parts"@en ; obo:IAO_0000117 "PERSON: Lawrence Hunter"@en ; a owl:Class ; rdfs:label "references section"@en ; rdfs:subClassOf obo:IAO_0000314, [ a owl:Restriction ; owl:onProperty obo:BFO_0000051 ; owl:someValuesFrom obo:IAO_0000301 ] . obo:IAO_0000321 obo:IAO_0000111 "author list"@en ; obo:IAO_0000112 "Lawrence Hunter and Kevin Brettonel Cohen"@en ; obo:IAO_0000114 obo:IAO_0000120 ; obo:IAO_0000115 "part of a document that enumerates the authors of the document"@en ; obo:IAO_0000117 "PERSON: Lawrence Hunter"@en ; a owl:Class ; rdfs:label "author list"@en ; rdfs:subClassOf obo:IAO_0000314, [ a owl:Restriction ; owl:onProperty obo:BFO_0000051 ; owl:someValuesFrom obo:IAO_0000302 ] . obo:IAO_0000322 obo:IAO_0000111 "institution list"@en ; obo:IAO_0000112 "The University of Colorado Denver School of Medicine and the University of Colorado Boulder."@en ; obo:IAO_0000114 obo:IAO_0000120 ; obo:IAO_0000115 "part of a document that has parts that are institution identifications associated with the authors of the document"@en ; obo:IAO_0000117 "PERSON: Lawrence Hunter"@en ; a owl:Class ; rdfs:label "institution list"@en ; rdfs:subClassOf obo:IAO_0000314, [ a owl:Restriction ; owl:onProperty obo:BFO_0000051 ; owl:someValuesFrom obo:IAO_0000303 ] . obo:IAO_0000323 obo:IAO_0000111 "author contributions section"@en ; obo: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."@en ; obo:IAO_0000114 obo:IAO_0000120 ; obo:IAO_0000115 "A part of a publication that is about the specific contributions of each author"@en ; obo:IAO_0000117 "PERSON: Lawrence Hunter"@en ; obo:IAO_0000118 "author contributions"@en, "contributions by the authors"@en ; a owl:Class ; rdfs:label "author contributions section"@en ; rdfs:subClassOf obo:IAO_0000314 . obo:IAO_0000324 obo:IAO_0000111 "acknowledgements section"@en ; obo:IAO_0000112 "The authors wish to thank Alan Ruttenberg for his constructive comments about an earlier draft of this manuscript"@en ; obo:IAO_0000114 obo:IAO_0000120 ; obo:IAO_0000115 "Part of a publication that is about the contributions of people or institutions other than the authors."@en ; obo:IAO_0000117 "PERSON: Lawrence Hunter"@en ; obo:IAO_0000118 "acknowledgements"@en, "acknowledgments"@en ; a owl:Class ; rdfs:label "acknowledgements section"@en ; rdfs:subClassOf obo:IAO_0000314 . obo:IAO_0000325 obo:IAO_0000111 "footnote"@en ; obo: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."@en ; obo:IAO_0000114 obo:IAO_0000120 ; obo:IAO_0000115 "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."@en ; obo:IAO_0000117 "PERSON: Lawrence Hunter"@en ; obo:IAO_0000118 "endnote"@en ; a owl:Class ; rdfs:label "footnote"@en ; rdfs:subClassOf obo:IAO_0000314, [ a owl:Restriction ; owl:onProperty obo:IAO_0000136 ; owl:someValuesFrom obo:IAO_0000314 ] . obo:IAO_0000326 obo:IAO_0000111 "supplementary material to a document"@en ; obo:IAO_0000114 obo:IAO_0000120 ; obo:IAO_0000115 "part of a document that is segregated from the rest of the document due to its size"@en ; obo:IAO_0000117 "PERSON: Lawrence Hunter"@en ; obo:IAO_0000118 "additional information"@en, "appendix"@en, "supplemental information"@en, "supplementary material"@en, "supporting information"@en ; a owl:Class ; rdfs:label "supplementary material to a document"@en ; rdfs:subClassOf obo:IAO_0000314 . obo:IAO_0000327 obo:IAO_0000111 "table of contents"@en ; obo:IAO_0000114 obo:IAO_0000125 ; obo:IAO_0000115 "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)."@en ; obo:IAO_0000117 "PERSON: Lawrence Hunter"@en ; a owl:Class ; rdfs:label "table of contents"@en ; rdfs:subClassOf obo:IAO_0000306 . obo:IAO_0000328 obo:IAO_0000111 "table of figures"@en ; obo:IAO_0000114 obo:IAO_0000125 ; obo:IAO_0000115 "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)."@en ; obo:IAO_0000117 "PERSON: Lawrence Hunter"@en ; a owl:Class ; rdfs:label "table of figures"@en ; rdfs:subClassOf obo:IAO_0000306 . obo:IAO_0000329 obo:IAO_0000111 "running title"@en ; obo:IAO_0000114 obo:IAO_0000125 ; obo:IAO_0000115 "A shorter version of a document title"@en ; obo:IAO_0000117 "PERSON: Lawrence Hunter"@en ; a owl:Class ; rdfs:label "running title"@en ; rdfs:subClassOf obo:IAO_0000305 . obo:IAO_0000330 obo:IAO_0000111 "copyright section"@en ; obo:IAO_0000112 "This work is licensed under a Creative Commons Attribution-Share Alike 3.0 United States License."@en ; obo:IAO_0000114 obo:IAO_0000120 ; obo:IAO_0000115 "A document part that describes legal restrictions on making or distributing copies of the document"@en ; obo:IAO_0000117 "PERSON: Lawrence Hunter"@en ; a owl:Class ; rdfs:label "copyright section"@en ; rdfs:subClassOf obo:IAO_0000314 . obo:IAO_0000400 obo:IAO_0000114 obo:IAO_0000120 ; obo:IAO_0000115 "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"@en ; obo: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"@en ; obo:IAO_0000117 "Alan Ruttenberg"@en ; obo:IAO_0000232 "AR notes: We need to discuss whether it should include site." ; a owl:Class ; rdfs:label "cartesian spatial coordinate datum"@en ; rdfs:seeAlso "http://groups.google.com/group/bfo-discuss/browse_thread/thread/9d04e717e39fb617"@en ; rdfs:subClassOf obo:IAO_0000027, [ a owl:Restriction ; owl:onProperty obo:IAO_0000219 ; owl:someValuesFrom obo:BFO_0000018 ], [ a owl:Restriction ; owl:cardinality "1"^^xsd:nonNegativeInteger ; owl:onProperty obo:IAO_0000407 ] . obo:IAO_0000401 obo:IAO_0000114 obo:IAO_0000123 ; obo:IAO_0000115 "A cartesion spatial coordinate datum that uses one value to specify a position along a one dimensional spatial region"@en ; obo:IAO_0000117 "Alan Ruttenberg"@en ; a owl:Class ; rdfs:label "one dimensional cartesian spatial coordinate datum"@en ; rdfs:subClassOf obo:IAO_0000400, [ a owl:Restriction ; owl:onProperty obo:IAO_0000219 ; owl:someValuesFrom [ a owl:Class ; owl:intersectionOf (obo:BFO_0000018 [ a owl:Restriction ; owl:onProperty obo:BFO_0000050 ; owl:someValuesFrom obo:BFO_0000026 ] ) ] ], [ a owl:Restriction ; owl:cardinality "1"^^xsd:nonNegativeInteger ; owl:onProperty obo:IAO_0000404 ] . obo:IAO_0000402 obo:IAO_0000114 obo:IAO_0000123 ; obo:IAO_0000115 "A cartesion spatial coordinate datum that uses two values to specify a position within a two dimensional spatial region"@en ; obo:IAO_0000117 "Alan Ruttenberg"@en ; a owl:Class ; rdfs:label "two dimensional cartesian spatial coordinate datum"@en ; rdfs:subClassOf obo:IAO_0000400, [ a owl:Restriction ; owl:onProperty obo:IAO_0000219 ; owl:someValuesFrom [ a owl:Class ; owl:intersectionOf (obo:BFO_0000018 [ a owl:Restriction ; owl:onProperty obo:BFO_0000050 ; owl:someValuesFrom obo:BFO_0000009 ] ) ] ], [ a owl:Restriction ; owl:cardinality "1"^^xsd:nonNegativeInteger ; owl:onProperty obo:IAO_0000404 ], [ a owl:Restriction ; owl:cardinality "1"^^xsd:nonNegativeInteger ; owl:onProperty obo:IAO_0000406 ] . obo:IAO_0000403 obo:IAO_0000114 obo:IAO_0000123 ; obo:IAO_0000115 "A cartesion spatial coordinate datum that uses three values to specify a position within a three dimensional spatial region"@en ; obo:IAO_0000117 "Alan Ruttenberg"@en ; a owl:Class ; rdfs:label "three dimensional cartesian spatial coordinate datum"@en ; rdfs:subClassOf obo:IAO_0000400, [ a owl:Restriction ; owl:onProperty obo:IAO_0000219 ; owl:someValuesFrom [ a owl:Class ; owl:intersectionOf (obo:BFO_0000018 [ a owl:Restriction ; owl:onProperty obo:BFO_0000050 ; owl:someValuesFrom obo:BFO_0000028 ] ) ] ], [ a owl:Restriction ; owl:cardinality "1"^^xsd:nonNegativeInteger ; owl:onProperty obo:IAO_0000404 ], [ a owl:Restriction ; owl:cardinality "1"^^xsd:nonNegativeInteger ; owl:onProperty obo:IAO_0000405 ], [ a owl:Restriction ; owl:cardinality "1"^^xsd:nonNegativeInteger ; owl:onProperty obo:IAO_0000406 ] . obo:IAO_0000404 a owl:DatatypeProperty, owl:FunctionalProperty ; rdfs:domain obo:IAO_0000400 ; rdfs:label "has x coordinate value"@en ; rdfs:range xsd:float . obo:IAO_0000405 a owl:DatatypeProperty, owl:FunctionalProperty ; rdfs:domain obo:IAO_0000400 ; rdfs:label "has z coordinate value"@en ; rdfs:range xsd:float . obo:IAO_0000406 a owl:DatatypeProperty, owl:FunctionalProperty ; rdfs:domain obo:IAO_0000400 ; rdfs:label "has y coordinate value"@en ; rdfs:range xsd:float . obo:IAO_0000407 a owl:FunctionalProperty, owl:ObjectProperty ; rdfs:comment "relating a cartesian spatial coordinate datum to a unit label that together with the values represent a point"@en ; rdfs:domain obo:IAO_0000400 ; rdfs:label "has coordinate unit label"@en ; rdfs:range obo:UO_0000001 ; rdfs:subPropertyOf obo:BFO_0000051 . obo:IAO_0000408 obo:IAO_0000114 obo:IAO_0000123 ; obo:IAO_0000115 "A scalar measurement datum that is the result of measurement of length quality"@en ; obo:IAO_0000117 "Alan Ruttenberg"@en ; a owl:Class ; rdfs:label "length measurement datum"@en ; rdfs:subClassOf obo:IAO_0000032, [ a owl:Restriction ; owl:onProperty obo:IAO_0000039 ; owl:someValuesFrom obo:UO_0000001 ], [ a owl:Restriction ; owl:onProperty obo:IAO_0000221 ; owl:someValuesFrom obo:PATO_0000122 ] . obo:IAO_0000409 obo: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 ; obo:IAO_0000115 "A denotator type indicates how a term should be interpreted from an ontological perspective."^^xsd:string ; obo:IAO_0000117 "Alan Ruttenberg"^^xsd:string ; obo:IAO_0000119 "Barry Smith, Werner Ceusters"^^xsd:string ; a owl:Class ; rdfs:label "denotator type"^^xsd:string ; rdfs:subClassOf obo:IAO_0000102 ; owl:equivalentClass [ a owl:Class ; owl:oneOf (obo:IAO_0000410 obo:IAO_0000420 obo:IAO_0000421 ) ] . obo:IAO_0000410 obo:IAO_0000116 "Hard to give a definition for. Intuitively a \"natural kind\" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents."^^xsd:string ; obo:IAO_0000117 "Alan Ruttenberg"^^xsd:string ; obo:IAO_0000119 "A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf"^^xsd:string ; a obo:IAO_0000409, owl:NamedIndividual ; rdfs:label "universal"^^xsd:string . obo:IAO_0000411 obo:IAO_0000111 "is denotator type"@en ; obo:IAO_0000115 "relates an class defined in an ontology, to the type of it's denotator"^^xsd:string ; obo:IAO_0000116 "In OWL 2 add AnnotationPropertyRange('is denotator type' 'denotator type')"^^xsd:string ; obo:IAO_0000117 "Alan Ruttenberg"^^xsd:string ; a owl:AnnotationProperty ; rdfs:label "is denotator type"^^xsd:string . obo:IAO_0000412 obo:IAO_0000111 "imported from"@en ; obo:IAO_0000114 obo:IAO_0000125 ; obo:IAO_0000115 "For external terms/classes, the ontology from which the term was imported"@en ; obo:IAO_0000117 "PERSON:Alan Ruttenberg"@en, "PERSON:Melanie Courtot"@en ; obo:IAO_0000119 "GROUP:OBI:"@en ; a owl:AnnotationProperty ; rdfs:isDefinedBy <> ; rdfs:label "imported from"@en . obo:IAO_0000413 obo:IAO_0000114 obo:IAO_0000120 ; obo:IAO_0000115 "relates a process to a time-measurement-datum that represents the duration of the process"@en ; obo:IAO_0000117 "Person:Alan Ruttenberg"@en ; a owl:ObjectProperty ; rdfs:domain obo:IAO_0000416 ; rdfs:label "is duration of"@en ; rdfs:range obo:BFO_0000015 ; rdfs:subPropertyOf obo:IAO_0000136 . obo:IAO_0000414 obo:IAO_0000114 obo:IAO_0000123 ; obo:IAO_0000115 "A scalar measurement datum that is the result of measurement of mass quality"@en ; obo:IAO_0000116 "2009/09/28 Alan Ruttenberg. Fucoidan-use-case"@en ; obo:IAO_0000117 "Person:Alan Ruttenberg"@en ; a owl:Class ; rdfs:label "mass measurement datum"@en ; rdfs:subClassOf obo:IAO_0000032, [ a owl:Class ; owl:intersectionOf ([ a owl:Restriction ; owl:allValuesFrom obo:UO_0000002 ; owl:onProperty obo:IAO_0000039 ] [ a owl:Restriction ; owl:allValuesFrom obo:PATO_0000125 ; owl:onProperty obo:IAO_0000221 ] ) ] . obo:IAO_0000415 obo:IAO_0000111 "hypothesis textual entity"@en ; obo: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"@en ; obo:IAO_0000114 obo:IAO_0000120 ; obo:IAO_0000115 "A textual entity that expresses an assertion that is intended to be tested."@en ; obo:IAO_0000116 "2009/09/28 Alan Ruttenberg. Fucoidan-use-case"@en ; obo:IAO_0000117 "Person:Alan Ruttenberg"@en ; a owl:Class ; rdfs:label "hypothesis textual entity"@en ; rdfs:subClassOf obo:IAO_0000300 . obo:IAO_0000416 obo:IAO_0000114 obo:IAO_0000123 ; obo:IAO_0000115 "A scalar measurement datum that is the result of measuring a temporal interval"@en ; obo:IAO_0000116 "2009/09/28 Alan Ruttenberg. Fucoidan-use-case"@en ; obo:IAO_0000117 "Person:Alan Ruttenberg"@en ; a owl:Class ; rdfs:label "time measurement datum"@en ; rdfs:subClassOf obo:IAO_0000032, [ a owl:Class ; owl:intersectionOf ([ a owl:Restriction ; owl:allValuesFrom obo:UO_0000003 ; owl:onProperty obo:IAO_0000039 ] [ a owl:Restriction ; owl:allValuesFrom obo:BFO_0000015 ; owl:onProperty obo:IAO_0000413 ] ) ] . obo:IAO_0000417 obo:IAO_0000114 obo:IAO_0000120 ; obo:IAO_0000115 "inverse of the relation of is quality measurement of"@en ; obo:IAO_0000116 "2009/10/19 Alan Ruttenberg. Named 'junk' relation useful in restrictions, but not a real instance relationship"@en ; obo:IAO_0000117 "Person:Alan Ruttenberg"@en ; a owl:ObjectProperty ; rdfs:label "is quality measured as"@en . obo:IAO_0000418 obo:IAO_0000114 obo:IAO_0000120 ; obo:IAO_0000115 "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."@en ; obo:IAO_0000117 "Person:Alan Ruttenberg"@en, "Person:Bjoern Peters"@en ; a owl:ObjectProperty ; rdfs:label "is quality specification of"@en ; rdfs:subPropertyOf obo:IAO_0000136 ; owl:inverseOf obo:IAO_0000419 . obo:IAO_0000419 obo:IAO_0000114 obo:IAO_0000120 ; obo:IAO_0000115 "inverse of the relation of is quality specification of"@en ; obo:IAO_0000116 "2009/10/19 Alan Ruttenberg. Named 'junk' relation useful in restrictions, but not a real instance relationship"@en ; obo:IAO_0000117 "Person:Alan Ruttenberg"@en, "Person:Bjoern Peters"@en ; a owl:ObjectProperty ; rdfs:label "quality is specified as"@en . obo:IAO_0000420 obo:IAO_0000115 "A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal"^^xsd:string ; obo:IAO_0000116 "\"definitions\", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal."^^xsd:string ; obo:IAO_0000117 "Alan Ruttenberg"^^xsd:string ; a obo:IAO_0000409, owl:NamedIndividual ; rdfs:label "defined class"^^xsd:string . obo:IAO_0000421 obo:IAO_0000115 "A named class expression is a logical expression that is given a name. The name can be used in place of the expression."^^xsd:string ; obo:IAO_0000116 "named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions"^^xsd:string ; obo:IAO_0000117 "Alan Ruttenberg"^^xsd:string ; a obo:IAO_0000409, owl:NamedIndividual ; rdfs:label "named class expression"^^xsd:string . obo:IAO_0000422 obo:IAO_0000114 obo:IAO_0000123 ; obo:IAO_0000115 "A textual entity that is used as directive to deliver something to a person, or organization" ; obo:IAO_0000116 "2010-05-24 Alan Ruttenberg. Use label for the string representation. See issue https://github.com/information-artifact-ontology/IAO/issues/59" ; a owl:Class ; rdfs:label "postal address"@en ; rdfs:subClassOf obo:IAO_0000300, [ a owl:Restriction ; owl:onProperty obo:IAO_0000136 ; owl:someValuesFrom obo:GAZ_00000448 ] . obo:IAO_0000423 obo:IAO_0000115 "Terms with this status should eventually replaced with a term from another ontology."@en ; obo:IAO_0000117 "Alan Ruttenberg"@en ; obo:IAO_0000119 "group:OBI"@en ; a obo:IAO_0000078, owl:NamedIndividual ; rdfs:label "to be replaced with external ontology term"@en . obo:IAO_0000424 obo:IAO_0000111 "expand expression to"@en ; obo:IAO_0000112 """ObjectProperty: RO_0002104 Label: has plasma membrane part Annotations: IAO_0000424 \"http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.org/obo/owl/GO#GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)\" """@en ; obo:IAO_0000115 "A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones"@en ; obo:IAO_0000117 "Chris Mungall"^^xsd:string ; a owl:AnnotationProperty ; rdfs:label "expand expression to"@en . obo:IAO_0000425 obo:IAO_0000111 "expand assertion to"@en ; obo:IAO_0000112 """ObjectProperty: RO??? Label: spatially disjoint from Annotations: expand_assertion_to \"DisjointClasses: (http://purl.obolibrary.org/obo/BFO_0000051 some ?X) (http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)\" """@en ; obo:IAO_0000115 "A macro expansion tag applied to an annotation property which can be expanded into a more detailed axiom."@en ; obo:IAO_0000117 "Chris Mungall"@en ; a owl:AnnotationProperty ; rdfs:label "expand assertion to"@en . obo:IAO_0000426 obo:IAO_0000111 "first order logic expression"@en ; obo:IAO_0000117 "PERSON:Alan Ruttenberg"@en ; a owl:AnnotationProperty ; rdfs:label "first order logic expression"@en . obo:IAO_0000427 obo:IAO_0000111 "antisymmetric property"@en ; obo:IAO_0000112 "part_of antisymmetric property xsd:true"@en ; obo:IAO_0000115 "use boolean value xsd:true to indicate that the property is an antisymmetric property"@en ; obo:IAO_0000117 "Alan Ruttenberg"@en ; a owl:AnnotationProperty ; rdfs:label "antisymmetric property"@en . obo:IAO_0000428 obo:IAO_0000115 "A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues."@en ; obo:IAO_0000117 "Alan Ruttenberg"@en ; obo:IAO_0000119 "group:OBI"@en ; a obo:IAO_0000078, owl:NamedIndividual ; rdfs:label "requires discussion"@en . obo:IAO_0000429 obo:IAO_0000111 "email address"@en ; obo:IAO_0000114 obo:IAO_0000123 ; obo: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"@en ; obo:IAO_0000117 "Person:Alan Ruttenberg"@en, "Person:Chris Stoeckart"@en ; a owl:Class ; rdfs:label "email address"@en ; rdfs:subClassOf obo:IAO_0000030 . obo:IAO_0000442 obo:IAO_0000111 "author role"@en ; obo:IAO_0000114 obo:IAO_0000125 ; obo:IAO_0000115 "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."@en ; obo:IAO_0000117 "PERSON: Alan Ruttenberg"@en, "PERSON: Melanie Courtot"@en ; a owl:Class ; rdfs:label "author role"@en ; rdfs:subClassOf obo:BFO_0000023 . obo:IAO_0000443 obo:IAO_0000114 obo:IAO_0000120 ; obo:IAO_0000115 "a planned process in which journal articles are read or processed and data items are extracted, typically for further analysis or indexing" ; obo:IAO_0000117 "Person:Alan Ruttenberg" ; a owl:Class ; rdfs:label "data item extraction from journal article" ; rdfs:subClassOf obo:OBI_0000011, [ a owl:Restriction ; owl:onProperty obo:OBI_0000293 ; owl:someValuesFrom obo:IAO_0000013 ], [ a owl:Restriction ; owl:onProperty obo:OBI_0000299 ; owl:someValuesFrom obo:IAO_0000027 ] . obo:IAO_0000572 obo:IAO_0000112 "Recording the current temperature in a laboratory notebook. Writing a journal article. Updating a patient record in a database."@en ; obo:IAO_0000114 obo:IAO_0000125 ; obo:IAO_0000115 "a planned process in which a document is created or added to by including the specified input in it."@en ; obo: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"@en ; obo:IAO_0000117 "Bjoern Peters"@en ; obo:IAO_0000119 "wikipedia http://en.wikipedia.org/wiki/Documenting"@en ; a owl:Class ; rdfs:label "documenting"@en ; rdfs:subClassOf obo:OBI_0000011, [ a owl:Restriction ; owl:onProperty obo:OBI_0000293 ; owl:someValuesFrom obo:IAO_0000030 ], [ a owl:Restriction ; owl:onProperty obo:OBI_0000299 ; owl:someValuesFrom obo:IAO_0000310 ] . obo:IAO_0000573 obo:IAO_0000111 "line graph"@en ; obo:IAO_0000114 obo:IAO_0000122 ; obo:IAO_0000115 """A line graph is a type of graph created by connecting a series of data points together with a line."""@en ; obo:IAO_0000117 "PERSON:Chris Stoeckert"@en, "PERSON:Melanie Courtot"@en ; obo:IAO_0000118 "line chart"@en ; obo:IAO_0000119 "GROUP:OBI"@en, "WEB: http://en.wikipedia.org/wiki/Line_chart"@en ; a owl:Class ; rdfs:label "line graph"@en ; rdfs:subClassOf obo:IAO_0000038 . obo:IAO_0000574 obo: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."@en ; obo:IAO_0000114 obo:IAO_0000120 ; obo:IAO_0000115 "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"@en ; obo:IAO_0000116 "2014-05-05: It is the CRID registry that assigns CRIDs, not the users of the registry."@en ; obo:IAO_0000117 "Person:Alan Ruttenberg"@en, "Person:Bjoern Peters"@en, "Person:Melanie Courtot"@en ; obo:IAO_0000118 "assigning a CRID" ; a owl:Class ; rdfs:label "assigning a centrally registered identifier"@en ; rdfs:subClassOf obo:OBI_0000011, [ a owl:Restriction ; owl:onProperty obo:OBI_0000299 ; owl:someValuesFrom obo:IAO_0000577 ], [ a owl:Restriction ; owl:onProperty obo:RO_0000057 ; owl:someValuesFrom obo:IAO_0000579 ] . obo:IAO_0000575 obo: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. " ; obo:IAO_0000114 obo:IAO_0000120 ; obo:IAO_0000115 "A planned process in which a CRID registry associates an information content entity with a CRID symbol"@en ; obo:IAO_0000117 "PERSON:Alan Ruttenberg"@en ; obo:IAO_0000118 "associating information with a CRID in the CRID registry" ; a owl:Class ; rdfs:label "associating information with a centrally registered identifier in its registry"@en ; rdfs:subClassOf obo:OBI_0000011, [ a owl:Restriction ; owl:onProperty obo:OBI_0000293 ; owl:someValuesFrom obo:IAO_0000030 ], [ a owl:Restriction ; owl:onProperty obo:OBI_0000293 ; owl:someValuesFrom obo:IAO_0000577 ], [ a owl:Restriction ; owl:onProperty obo:RO_0000057 ; owl:someValuesFrom obo:IAO_0000579 ] . obo:IAO_0000576 obo:IAO_0000115 "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."^^xsd:string ; obo:IAO_0000116 "MC, 20101124: deprecated following discussion at IAO call 20101124. Term was deemed not necessary - no use case for now." ; obo:IAO_0000231 obo:IAO_0000103 ; a owl:Class ; rdfs:label "obsolete_establishing a CRID registry"^^xsd:string ; rdfs:subClassOf oboInOwl:ObsoleteClass ; owl:deprecated true . obo:IAO_0000577 obo: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."@en ; obo:IAO_0000114 obo:IAO_0000120 ; obo:IAO_0000115 "A symbol that is part of a CRID and that is sufficient to look up a record from the CRID's registry."@en ; obo:IAO_0000117 "PERSON: Alan Ruttenberg"@en, "PERSON: Bill Hogan"@en, "PERSON: Bjoern Peters"@en, "PERSON: Melanie Courtot"@en ; obo:IAO_0000118 "CRID symbol" ; obo:IAO_0000119 "Original proposal from Bjoern, discussions at IAO calls"@en ; a owl:Class ; rdfs:label "centrally registered identifier symbol"@en ; rdfs:subClassOf obo:IAO_0000028, [ a owl:Restriction ; owl:onProperty obo:BFO_0000050 ; owl:someValuesFrom obo:IAO_0000578 ] . obo:IAO_0000578 obo: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."@en ; obo:IAO_0000114 obo:IAO_0000120 ; obo:IAO_0000115 "An information content entity that consists of a CRID symbol and additional information about the CRID registry to which it belongs."@en ; obo: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')."@en, """Alan, IAO call 20101124: potentially the CRID denotes the instance it was associated with during creation. """@en, "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."@en ; obo:IAO_0000117 "PERSON: Alan Ruttenberg"@en, "PERSON: Bill Hogan"@en, "PERSON: Bjoern Peters"@en, "PERSON: Melanie Courtot"@en ; obo:IAO_0000118 "CRID" ; obo:IAO_0000119 "Original proposal from Bjoern, discussions at IAO calls"@en ; a owl:Class ; rdfs:label "centrally registered identifier"@en ; rdfs:subClassOf obo:IAO_0000030, [ a owl:Restriction ; owl:onProperty obo:BFO_0000051 ; owl:someValuesFrom obo:IAO_0000577 ], [ a owl:Restriction ; owl:onProperty obo:BFO_0000051 ; owl:someValuesFrom [ a owl:Restriction ; owl:onProperty obo:IAO_0000219 ; owl:someValuesFrom obo:IAO_0000579 ] ] . obo:IAO_0000579 obo:IAO_0000112 "PubMed is a CRID registry. It has a dataset of PubMed identifiers associated with journal articles. "@en ; obo:IAO_0000114 obo:IAO_0000120 ; obo:IAO_0000115 "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."@en ; obo:IAO_0000117 "PERSON: Alan Ruttenberg"@en, "PERSON: Bill Hogan"@en, "PERSON: Bjoern Peters"@en, "PERSON: Melanie Courtot"@en ; obo:IAO_0000118 "CRID registry" ; obo:IAO_0000119 "Original proposal from Bjoern, discussions at IAO calls"@en ; a owl:Class ; rdfs:label "centrally registered identifier registry"@en ; rdfs:subClassOf obo:IAO_0000100 . obo:IAO_0000580 obo:IAO_0000112 "Going to the PubMed website and entering a PubMed ID in order to retrieve the Pubmed information associated with that ID. " ; obo:IAO_0000114 obo:IAO_0000120 ; obo:IAO_0000115 "A planned process in which a request to a CRID registry is made to return the information associated with a CRID symbol"@en ; obo:IAO_0000117 "PERSON: Alan Ruttenberg"@en, "PERSON: Bill Hogan"@en, "PERSON: Bjoern Peters"@en, "PERSON: Melanie Courtot"@en ; obo:IAO_0000118 "looking up a CRID" ; a owl:Class ; rdfs:label "looking up a centrally registered identifier"@en ; rdfs:subClassOf obo:OBI_0000011, [ a owl:Restriction ; owl:onProperty obo:OBI_0000293 ; owl:someValuesFrom obo:IAO_0000577 ], [ a owl:Restriction ; owl:onProperty obo:OBI_0000299 ; owl:someValuesFrom obo:IAO_0000030 ], [ a owl:Restriction ; owl:onProperty obo:RO_0000057 ; owl:someValuesFrom obo:IAO_0000579 ] . obo:IAO_0000581 obo:IAO_0000114 obo:IAO_0000123 ; obo:IAO_0000115 "relates a time stamped measurement datum to the time measurement datum that denotes the time when the measurement was taken"@en ; obo:IAO_0000117 "Alan Ruttenberg"@en ; a owl:FunctionalProperty, owl:ObjectProperty ; rdfs:domain obo:IAO_0000582 ; rdfs:label "has time stamp"@en ; rdfs:range obo:IAO_0000416 ; rdfs:subPropertyOf obo:BFO_0000051 . obo:IAO_0000582 obo:IAO_0000114 obo:IAO_0000123 ; a owl:Class ; rdfs:label "time stamped measurement datum"@en ; rdfs:subClassOf obo:IAO_0000109, [ a owl:Class ; owl:intersectionOf ([ a owl:Restriction ; owl:onProperty obo:IAO_0000581 ; owl:someValuesFrom obo:IAO_0000416 ] [ a owl:Restriction ; owl:onProperty obo:IAO_0000583 ; owl:someValuesFrom obo:IAO_0000109 ] ) ] . obo:IAO_0000583 obo:IAO_0000114 obo:IAO_0000123 ; obo:IAO_0000115 "relates a time stamped measurement datum to the measurement datum that was measured"@en ; obo:IAO_0000117 "Alan Ruttenberg"@en ; a owl:ObjectProperty ; rdfs:domain obo:IAO_0000582 ; rdfs:label "has measurement datum"@en ; rdfs:range [ a owl:Class ; owl:intersectionOf (obo:IAO_0000109 [ a owl:Class ; owl:complementOf obo:IAO_0000416 ] ) ] ; rdfs:subPropertyOf obo:BFO_0000051 . obo:IAO_0000584 obo:IAO_0000112 "pmid:20604925 - time-lapse live cell microscopy"@en ; obo:IAO_0000114 obo:IAO_0000120 ; obo:IAO_0000115 "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."@en ; obo:IAO_0000117 "Alan Ruttenberg"@en ; obo:IAO_0000118 "experimental time series"@en ; a owl:Class ; rdfs:label "time sampled measurement data set"@en ; rdfs:subClassOf obo:IAO_0000100, [ a owl:Restriction ; owl:onProperty obo:BFO_0000051 ; owl:someValuesFrom obo:IAO_0000582 ] . obo:IAO_0000589 obo:IAO_0000111 "OBO foundry unique label"@en ; obo:IAO_0000114 obo:IAO_0000125 ; obo:IAO_0000115 "An alternative name for a class or property which is unique across the OBO Foundry."@en ; obo:IAO_0000116 "The intended usage of that property is as follow: OBO foundry unique labels are automatically generated based on regular expressions provided by each ontology, so that SO could specify unique label = 'sequence ' + [label], etc. , MA could specify 'mouse + [label]' etc. Upon importing terms, ontology developers can choose to use the 'OBO foundry unique label' for an imported term or not. The same applies to tools ."^^xsd:string ; obo:IAO_0000117 "PERSON:Alan Ruttenberg"@en, "PERSON:Bjoern Peters"@en, "PERSON:Chris Mungall"@en, "PERSON:Melanie Courtot"@en ; obo:IAO_0000119 "GROUP:OBO Foundry "@en ; a owl:AnnotationProperty ; rdfs:label "OBO foundry unique label"@en . obo:IAO_0000590 obo:IAO_0000111 "written name"@en ; obo:IAO_0000112 "\"Bill Clinton\""@en, "\"The Eiffel Tower\""@en, "\"United States of America\""@en ; obo:IAO_0000114 obo:IAO_0000125 ; obo:IAO_0000115 "A textual entity that denotes a particular in reality."@en ; obo:IAO_0000117 "PERSON: Bill Hogan"@en ; obo:IAO_0000119 "https://github.com/information-artifact-ontology/IAO/issues/114"@en ; obo: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."@en ; a owl:Class ; rdfs:label "written name"@en ; rdfs:subClassOf obo:IAO_0000300 . obo:IAO_0000591 obo:IAO_0000114 obo:IAO_0000123 ; obo:IAO_0000115 "A software method (also called subroutine, subprogram, procedure, method, function, or routine) is software designed to execute a specific task."@en ; obo:IAO_0000117 "PERSON: Melanie Courtot"@en, "PERSON: Michel Dumontier"@en ; obo:IAO_0000119 "https://github.com/information-artifact-ontology/IAO/issues/80"@en ; a owl:Class ; rdfs:label "software method"@en ; rdfs:subClassOf obo:IAO_0000010 . obo:IAO_0000592 obo:IAO_0000114 obo:IAO_0000123 ; obo:IAO_0000115 " A software module is software composed of a collection of software methods."@en ; obo:IAO_0000117 "PERSON: Melanei Courtot"@en, "PERSON: Michel Dumontier"@en ; obo:IAO_0000119 "https://github.com/information-artifact-ontology/IAO/issues/80"@en ; a owl:Class ; rdfs:label "software module"@en ; rdfs:subClassOf obo:IAO_0000010 . obo:IAO_0000593 obo:IAO_0000114 obo:IAO_0000123 ; obo:IAO_0000115 "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."@en ; obo:IAO_0000117 "PERSON: Melanie Courtot"@en, "PERSON: Michel Dumontier"@en ; obo:IAO_0000119 "https://github.com/information-artifact-ontology/IAO/issues/80"@en ; a owl:Class ; rdfs:label "software library"@en ; rdfs:subClassOf obo:IAO_0000010 . obo:IAO_0000594 obo:IAO_0000114 obo:IAO_0000123 ; obo:IAO_0000115 "A software application is software that can be directly executed by some processing unit."@en ; obo:IAO_0000117 "PERSON: Melanie Courtot"@en, "PERSON: Michel Dumontier"@en ; obo:IAO_0000119 "https://github.com/information-artifact-ontology/IAO/issues/80"@en ; a owl:Class ; rdfs:label "software application"@en ; rdfs:subClassOf obo:IAO_0000010 . obo:IAO_0000595 obo:IAO_0000114 obo:IAO_0000123 ; obo:IAO_0000115 """ A software script is software whose instructions can be executed using a software interpreter."""@en ; obo:IAO_0000117 "PERSON: Melanie Courtot"@en, "PERSON: Michel Dumontier"@en ; obo:IAO_0000119 "https://github.com/information-artifact-ontology/IAO/issues/80"@en ; a owl:Class ; rdfs:label "software script"@en ; rdfs:subClassOf obo:IAO_0000010 . obo:IAO_0000596 obo:IAO_0000112 """Ontology: Annotations: 'has ID prefix': \"http://purl.obolibrary.org/obo/RO_\" 'has ID digit count' : 7, rdfs:label \"RO id policy\" 'has ID policy for': \"RO\"""" ; obo:IAO_0000115 "Relates an ontology used to record id policy to the number of digits in the URI. The URI is: the 'has ID prefix\" annotation property value concatenated with an integer in the id range (left padded with \"0\"s to make this many digits)" ; obo:IAO_0000117 "Person:Alan Ruttenberg" ; a owl:AnnotationProperty ; rdfs:label "has ID digit count"@en . obo:IAO_0000597 obo:IAO_0000112 """Datatype: idrange:1 Annotations: 'has ID range allocated to': \"Chris Mungall\" EquivalentTo: xsd:integer[> 2151 , <= 2300] """ ; obo:IAO_0000115 "Relates a datatype that encodes a range of integers to the name of the person or organization who can use those ids constructed in that range to define new terms" ; obo:IAO_0000117 "Person:Alan Ruttenberg" ; a owl:AnnotationProperty ; rdfs:label "has ID range allocated to"@en . obo:IAO_0000598 obo:IAO_0000112 """Ontology: Annotations: 'has ID prefix': \"http://purl.obolibrary.org/obo/RO_\" 'has ID digit count' : 7, rdfs:label \"RO id policy\" 'has ID policy for': \"RO\"""" ; obo:IAO_0000115 "Relating an ontology used to record id policy to the ontology namespace whose policy it manages" ; obo:IAO_0000117 "Person:Alan Ruttenberg" ; a owl:AnnotationProperty ; rdfs:label "has ID policy for" . obo:IAO_0000599 obo:IAO_0000112 """Ontology: Annotations: 'has ID prefix': \"http://purl.obolibrary.org/obo/RO_\" 'has ID digit count' : 7, rdfs:label \"RO id policy\" 'has ID policy for': \"RO\"""" ; obo:IAO_0000115 "Relates an ontology used to record id policy to a prefix concatenated with an integer in the id range (left padded with \"0\"s to make this many digits) to construct an ID for a term being created." ; obo:IAO_0000117 "Person:Alan Ruttenberg" ; a owl:AnnotationProperty ; rdfs:label "has ID prefix"@en . obo:IAO_0000600 obo:IAO_0000111 "elucidation"@en ; obo:IAO_0000117 "person:Alan Ruttenberg"@en ; obo:IAO_0000119 "Person:Barry Smith"@en ; obo:IAO_0000600 "Primitive terms in a highest-level ontology such as BFO are terms which are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms"@en ; a owl:AnnotationProperty ; rdfs:isDefinedBy <> ; rdfs:label "elucidation"@en . obo:IAO_0000601 obo:IAO_0000111 "has associated axiom(nl)"@en ; obo:IAO_0000117 "Person:Alan Ruttenberg"@en ; obo:IAO_0000119 "Person:Alan Ruttenberg"@en ; obo:IAO_0000600 "An axiom associated with a term expressed using natural language"@en ; a owl:AnnotationProperty ; rdfs:isDefinedBy <> ; rdfs:label "has associated axiom(nl)"@en . obo:IAO_0000602 obo:IAO_0000111 "has associated axiom(fol)"@en ; obo:IAO_0000117 "Person:Alan Ruttenberg"@en ; obo:IAO_0000119 "Person:Alan Ruttenberg"@en ; obo:IAO_0000600 "An axiom expressed in first order logic using CLIF syntax"@en ; a owl:AnnotationProperty ; rdfs:isDefinedBy <> ; rdfs:label "has associated axiom(fol)"@en . obo:IAO_0000603 obo:IAO_0000111 "is allocated id range"@en ; obo:IAO_0000115 "Add as annotation triples in the granting ontology"@en, "Relates an ontology IRI to an (inclusive) range of IRIs in an OBO name space. The range is give as, e.g. \"IAO_0020000-IAO_0020999\""@en ; obo:IAO_0000117 "PERSON:Alan Ruttenberg"@en ; a owl:AnnotationProperty ; rdfs:label "is allocated id range"@en . obo:IAO_0000604 obo:IAO_0000111 "retired from use as of"@en ; obo:IAO_0000115 "relates a class of CRID to the date after which further instances should not be made, according to the central authority"^^xsd:string ; obo:IAO_0000116 "In OWL 2 add AnnotationPropertyRange xsd:dateTimeStamp"^^xsd:string ; obo:IAO_0000117 "Alan Ruttenberg"^^xsd:string ; a owl:AnnotationProperty ; rdfs:label "retired from use as of"^^xsd:string . obo:IAO_0000605 obo:IAO_0000111 "abbreviation textual entity"@en ; obo:IAO_0000112 """From Shiba et al. Acta Neuropathol Commun. 2013; 1: 45. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3893467/): BAC: 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."""@en ; obo:IAO_0000115 "A textual entity listing abbreviations and their expansions that are used in a document."@en ; obo:IAO_0000117 "PERSON: Bill Baumgartner"@en ; obo:IAO_0000233 ; a owl:Class ; rdfs:label "abbreviation textual entity"@en ; rdfs:subClassOf obo:IAO_0000300 . obo:IAO_0000606 obo:IAO_0000111 "abbreviations section"@en ; obo:IAO_0000112 "The section labelled 'abbreviations' in a typical scientific journal article."@en ; obo:IAO_0000115 "A part of a document where abbreviations and their long-forms used within the document are listed."@en ; obo:IAO_0000117 "PERSON: Bill Baumgartner"@en ; obo:IAO_0000118 "abbreviations"@en, "abbreviations list"@en, "abbreviations used"@en, "list of abbreviations"@en, "list of abbreviations used"@en ; obo:IAO_0000233 ; a owl:Class ; rdfs:label "abbreviations section"@en ; rdfs:subClassOf obo:IAO_0000314, [ a owl:Restriction ; owl:onProperty obo:BFO_0000051 ; owl:someValuesFrom obo:IAO_0000605 ] . obo:IAO_0000607 obo:IAO_0000111 "author information section"@en ; obo: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/)"@en ; obo:IAO_0000115 "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."@en ; obo:IAO_0000117 "PERSON: Bill Baumgartner"@en ; obo:IAO_0000118 "author information"@en, "authors’ information"@en ; obo:IAO_0000233 ; a owl:Class ; rdfs:label "author information section"@en ; rdfs:subClassOf obo:IAO_0000314, [ a owl:Restriction ; owl:onProperty obo:BFO_0000051 ; owl:someValuesFrom obo:IAO_0000608 ] . obo:IAO_0000608 obo:IAO_0000111 "author information textual entity"@en ; obo:IAO_0000112 """From Takon. Ann Gen Psychiatry. 2011; 10: 25. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3204268/): IT [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."""@en ; obo:IAO_0000115 "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."@en ; obo:IAO_0000117 "PERSON: Bill Baumgartner"@en ; obo:IAO_0000233 ; a owl:Class ; rdfs:label "author information textual entity"@en ; rdfs:subClassOf obo:IAO_0000300 . obo:IAO_0000609 obo:IAO_0000111 "author summary section"@en ; obo: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/)"@en ; obo:IAO_0000115 "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."@en ; obo:IAO_0000117 "PERSON: Bill Baumgartner"@en ; obo:IAO_0000118 "author summary"@en, "summary"@en, "synopsis"@en ; obo:IAO_0000119 "Article submission guidelines for PLoS Genetics (http://journals.plos.org/plosgenetics/s/submission-guidelines)"@en ; obo:IAO_0000233 ; a owl:Class ; rdfs:label "author summary section"@en ; rdfs:subClassOf obo:IAO_0000314, [ a owl:Restriction ; owl:onProperty obo:BFO_0000051 ; owl:someValuesFrom obo:IAO_0000610 ] . obo:IAO_0000610 obo:IAO_0000111 "author summary textual entity"@en ; obo:IAO_0000112 """From Pendse et al. BMC Genomics. 2013; 14: 136. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3608171/): The 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."""@en ; obo:IAO_0000115 "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)."@en ; obo:IAO_0000117 "PERSON: Bill Baumgartner"@en ; obo:IAO_0000119 "Article submission guidelines for PLoS Genetics (http://journals.plos.org/plosgenetics/s/submission-guidelines)."@en ; obo:IAO_0000233 ; a owl:Class ; rdfs:label "author summary textual entity"@en ; rdfs:subClassOf obo:IAO_0000300 . obo:IAO_0000611 obo:IAO_0000111 "availability section"@en ; obo: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/)."@en ; obo:IAO_0000115 "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."@en ; obo:IAO_0000117 "PERSON: Bill Baumgartner"@en ; obo:IAO_0000118 "availability"@en ; obo:IAO_0000233 ; a owl:Class ; rdfs:label "availability section"@en ; rdfs:subClassOf obo:IAO_0000314, [ a owl:Restriction ; owl:onProperty obo:BFO_0000051 ; owl:someValuesFrom obo:IAO_0000612 ] . obo:IAO_0000612 obo:IAO_0000111 "availability textual entity"@en ; obo:IAO_0000112 """From Qi et al. BMC Bioinformatics. 2014; 15: 11. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3897912/): Project home page:http://krux.googlecode.com"""@en ; obo:IAO_0000115 "A textual entity expressing the location of a resource, e.g. software, or the manner in which a resource can be obtained."@en ; obo:IAO_0000117 "PERSON: Bill Baumgartner"@en ; obo:IAO_0000233 ; a owl:Class ; rdfs:label "availability textual entity"@en ; rdfs:subClassOf obo:IAO_0000300 . obo:IAO_0000613 obo:IAO_0000111 "case report section"@en ; obo: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/)"@en ; obo:IAO_0000115 "A part of a document about the medical history of a specific patient as it relates to the topic of the document."@en ; obo:IAO_0000117 "PERSON: Bill Baumgartner"@en ; obo:IAO_0000118 "case presentation"@en, "case report"@en ; obo:IAO_0000233 ; a owl:Class ; rdfs:label "case report section"@en ; rdfs:subClassOf obo:IAO_0000314, [ a owl:Restriction ; owl:onProperty obo:BFO_0000051 ; owl:someValuesFrom obo:IAO_0000614 ] . obo:IAO_0000614 obo:IAO_0000111 "case report textual entity"@en ; obo:IAO_0000112 """Excerpt from Taglia et al. Acta Myol. 2012 Dec; 31(3): 201–203. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3631801/): The 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."""@en ; obo:IAO_0000115 "A textual entity that expresses a detailed account of a portion of the medical history for a specific patient."@en ; obo:IAO_0000117 "PERSON: Bill Baumgartner"@en ; obo:IAO_0000233 ; a owl:Class ; rdfs:label "case report textual entity"@en ; rdfs:subClassOf obo:IAO_0000300 . obo:IAO_0000615 obo:IAO_0000111 "conclusion section"@en ; obo:IAO_0000112 "The section labelled 'conclusion' in a typical scientific journal article."@en ; obo:IAO_0000115 "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. "@en ; obo:IAO_0000117 "PERSON: Bill Baumgartner"@en ; obo:IAO_0000118 "concluding remarks"@en, "conclusion"@en, "conclusions"@en, "findings"@en, "summary"@en ; obo:IAO_0000233 ; a owl:Class ; rdfs:label "conclusion section"@en ; rdfs:subClassOf obo:IAO_0000314, [ a owl:Restriction ; owl:onProperty obo:BFO_0000051 ; owl:someValuesFrom obo:IAO_0000144 ] . obo:IAO_0000616 obo:IAO_0000111 "conflict of interest section"@en ; obo:IAO_0000112 "The section labelled 'conflict of interest statement' in a typical scientific journal article."@en ; obo:IAO_0000115 "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."@en ; obo:IAO_0000117 "PERSON: Bill Baumgartner"@en ; obo:IAO_0000118 "competing interests"@en, "conflict of interest"@en, "conflict of interest statement"@en, "declaration of competing interests"@en, "disclosure of potential conflicts of interest"@en ; obo:IAO_0000233 ; a owl:Class ; rdfs:label "conflict of interest section"@en ; rdfs:subClassOf obo:IAO_0000314, [ a owl:Restriction ; owl:onProperty obo:BFO_0000051 ; owl:someValuesFrom obo:IAO_0000617 ] . obo:IAO_0000617 obo:IAO_0000111 "conflict of interest statement"@en ; obo: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/)] "@en ; obo:IAO_0000115 "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."@en ; obo:IAO_0000117 "PERSON: Bill Baumgartner"@en ; obo:IAO_0000233 ; a owl:Class ; rdfs:label "conflict of interest textual entity"@en ; rdfs:subClassOf obo:IAO_0000300 . obo:IAO_0000618 obo:IAO_0000111 "consent section"@en ; obo: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/)"@en ; obo:IAO_0000115 "A part of a document about the consent process that was used to enroll patients in a study."@en ; obo:IAO_0000117 "PERSON: Bill Baumgartner"@en ; obo:IAO_0000118 "consent"@en ; obo:IAO_0000233 ; a owl:Class ; rdfs:label "consent section"@en ; rdfs:subClassOf obo:IAO_0000314, [ a owl:Restriction ; owl:onProperty obo:BFO_0000051 ; owl:someValuesFrom obo:IAO_0000619 ] . obo:IAO_0000619 obo:IAO_0000111 "consent textual entity"@en ; obo:IAO_0000112 """From Shiba et al. Acta Neuropathol Commun. 2013; 1: 45. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3893467/): Written 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."""@en ; obo:IAO_0000115 "A textual entity that documents the consenting process used to enroll patients in a study."@en ; obo:IAO_0000117 "PERSON: Bill Baumgartner"@en ; obo:IAO_0000233 ; a owl:Class ; rdfs:label "consent textual entity"@en ; rdfs:subClassOf obo:IAO_0000300 . obo:IAO_0000620 obo:IAO_0000111 "ethical approval section"@en ; obo:IAO_0000112 "The section labelled 'ethical approval' in a typical scientific journal article."@en ; obo:IAO_0000115 "A part of a document about the governance body responsible for approving the work discussed in a document on an ethical basis."@en ; obo:IAO_0000117 "PERSON: Bill Baumgartner"@en ; obo:IAO_0000118 "ethical approval"@en ; obo:IAO_0000233 ; a owl:Class ; rdfs:label "ethical approval section"@en ; rdfs:subClassOf obo:IAO_0000314, [ a owl:Restriction ; owl:onProperty obo:BFO_0000051 ; owl:someValuesFrom obo:IAO_0000621 ] . obo:IAO_0000621 obo:IAO_0000111 "ethical approval textual entity"@en ; obo: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/): The 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."""@en ; obo:IAO_0000115 "A textual entity that documents the ethical approval of some study design."@en ; obo:IAO_0000117 "PERSON: Bill Baumgartner"@en ; obo:IAO_0000233 ; a owl:Class ; rdfs:label "ethical approval textual entity"@en ; rdfs:subClassOf obo:IAO_0000300, [ a owl:Restriction ; owl:onProperty obo:IAO_0000136 ; owl:someValuesFrom obo:OBI_0500000 ] . obo:IAO_0000622 obo:IAO_0000111 "figures section"@en ; obo:IAO_0000112 "The section labelled 'figures' in a typical scientific journal article."@en ; obo:IAO_0000115 "A part of a document that contains one or more figures."@en ; obo:IAO_0000117 "PERSON: Bill Baumgartner"@en ; obo:IAO_0000118 "figures"@en ; obo:IAO_0000233 ; a owl:Class ; rdfs:label "figures section"@en ; rdfs:subClassOf obo:IAO_0000314, [ a owl:Restriction ; owl:onProperty obo:BFO_0000051 ; owl:someValuesFrom obo:IAO_0000308 ] . obo:IAO_0000623 obo:IAO_0000111 "funding source declaration section"@en ; obo:IAO_0000112 "The section labelled 'funding' in a typical scientific journal article."@en ; obo:IAO_0000115 "A part of a document used to detail information regarding the source of funding used in support of the generation of the document content."@en ; obo:IAO_0000117 "PERSON: Bill Baumgartner"@en ; obo:IAO_0000118 "funding"@en, "funding information"@en, "funding sources"@en, "funding statement"@en, "funding/support"@en, "source of funding"@en, "sources of funding"@en ; obo:IAO_0000233 ; a owl:Class ; rdfs:label "funding source declaration section"@en ; rdfs:subClassOf obo:IAO_0000314, [ a owl:Restriction ; owl:onProperty obo:BFO_0000051 ; owl:someValuesFrom obo:IAO_0000624 ] . obo:IAO_0000624 obo:IAO_0000111 "funding souce declaration textual entity"@en ; obo:IAO_0000112 """From Stephan et al. Accid Anal Prev. 2011 May; 43(3): 1062–1067. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3062852/): This 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."""@en ; obo:IAO_0000115 "A textual entity documenting the source of funding that supported some study."@en ; obo:IAO_0000117 "PERSON: Bill Baumgartner"@en ; obo:IAO_0000233 ; a owl:Class ; rdfs:label "funding source declaration textual entity"@en ; rdfs:subClassOf obo:IAO_0000300 . obo:IAO_0000625 obo:IAO_0000111 "future directions section"@en ; obo:IAO_0000112 "The section labelled 'future directions' in a typical scientific journal article."@en ; obo:IAO_0000115 "A part of a document detailing extensions of the described work that may be implemented at some future point in time."@en ; obo:IAO_0000117 "PERSON: Bill Baumgartner"@en ; obo:IAO_0000118 "future challenges"@en, "future considerations"@en, "future developments"@en, "future directions"@en, "future outlook"@en, "future perspectives"@en, "future plans"@en, "future prospects"@en, "future research"@en, "future research directions"@en, "future studies"@en, "future work"@en ; obo:IAO_0000233 ; a owl:Class ; rdfs:label "future directions section"@en ; rdfs:subClassOf obo:IAO_0000314, [ a owl:Restriction ; owl:onProperty obo:BFO_0000051 ; owl:someValuesFrom obo:IAO_0000626 ] . obo:IAO_0000626 obo:IAO_0000111 "future directions textual entity"@en ; obo: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/): In 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."""@en ; obo:IAO_0000115 "A textual entity expressing ideas regarding future work relevant to work described in a document that could be done."@en ; obo:IAO_0000117 "PERSON: Bill Baumgartner"@en ; obo:IAO_0000233 ; a owl:Class ; rdfs:label "future directions textual entity"@en ; rdfs:subClassOf obo:IAO_0000300 . obo:IAO_0000627 obo:IAO_0000111 "genome announcement section"@en ; obo: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/)"@en ; obo:IAO_0000115 "A document part announcing the publication of a novel draft genome sequence."@en ; obo:IAO_0000117 "PERSON: Bill Baumgartner"@en ; obo:IAO_0000118 "genome announcement"@en ; obo:IAO_0000233 ; a owl:Class ; rdfs:label "genome announcement section"@en ; rdfs:subClassOf obo:IAO_0000314, [ a owl:Restriction ; owl:onProperty obo:BFO_0000051 ; owl:someValuesFrom obo:IAO_0000628 ] . obo:IAO_0000628 obo:IAO_0000111 "genome announcement textual entity"@en ; obo:IAO_0000112 """Excerpt from Kim et al. J Bacteriol. 2011 Oct; 193(19): 5537. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3187466/): Here 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)."""@en ; obo:IAO_0000115 "A textual entity that describes the generation and public release of a novel, draft genome sequence."@en ; obo:IAO_0000117 "PERSON: Bill Baumgartner"@en ; obo:IAO_0000233 ; a owl:Class ; rdfs:label "genome announcement textual entity"@en ; rdfs:subClassOf obo:IAO_0000300 . obo:IAO_0000629 obo:IAO_0000111 "keyword textual entity"@en ; obo: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/): Exon orthology; alternative splicing; exon duplication; intron-exon structure."""@en ; obo:IAO_0000115 "A textual entity listing keywords indicating the major theme(s) of a document."@en ; obo:IAO_0000117 "PERSON: Bill Baumgartner"@en ; obo:IAO_0000233 ; a owl:Class ; rdfs:label "keyword textual entity"@en ; rdfs:subClassOf obo:IAO_0000300 . obo:IAO_0000630 obo:IAO_0000111 "keywords section"@en ; obo:IAO_0000112 "The section labelled 'keywords' in a typical scientific journal article."@en ; obo:IAO_0000115 "A part of a document where keywords selected by the author to categorize the major theme(s) of a document are listed."@en ; obo:IAO_0000117 "PERSON: Bill Baumgartner"@en ; obo:IAO_0000118 "keywords"@en ; obo:IAO_0000233 ; a owl:Class ; rdfs:label "keywords section"@en ; rdfs:subClassOf obo:IAO_0000314, [ a owl:Restriction ; owl:onProperty obo:BFO_0000051 ; owl:someValuesFrom obo:IAO_0000629 ] . obo:IAO_0000631 obo:IAO_0000111 "study limitations section"@en ; obo:IAO_0000112 "The section labelled 'limitations' in a typical scientific journal article."@en ; obo:IAO_0000115 "A part of a document about biases or short comings related to the study design and execution."@en ; obo:IAO_0000117 "PERSON: Bill Baumgartner"@en ; obo:IAO_0000118 "limitations"@en, "study limitations"@en ; obo: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)"@en ; obo:IAO_0000233 ; a owl:Class ; rdfs:label "study limitations section"@en ; rdfs:subClassOf obo:IAO_0000314, [ a owl:Restriction ; owl:onProperty obo:BFO_0000051 ; owl:someValuesFrom obo:IAO_0000632 ], [ a owl:Restriction ; owl:onProperty obo:IAO_0000136 ; owl:someValuesFrom obo:OBI_0500000 ] . obo:IAO_0000632 obo:IAO_0000111 "study limitations textual entity"@en ; obo: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/). Owing 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."""@en ; obo:IAO_0000115 "A textual entity addressing a shortcoming or bias of a study design or execution."@en ; obo:IAO_0000117 "PERSON: Bill Baumgartner"@en ; obo: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)"@en ; obo:IAO_0000233 ; a owl:Class ; rdfs:label "study limitations textual entity"@en ; rdfs:subClassOf obo:IAO_0000300 . obo:IAO_0000633 obo:IAO_0000111 "materials section"@en ; obo: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/)"@en ; obo:IAO_0000115 "A part of a document about the materials required to reproduce the content of the document."@en ; obo:IAO_0000117 "PERSON: Bill Baumgartner"@en ; obo:IAO_0000118 "materials"@en ; obo:IAO_0000233 ; a owl:Class ; rdfs:label "materials section"@en ; rdfs:subClassOf obo:IAO_0000314 . obo:IAO_0000634 obo:IAO_0000111 "notes section"@en ; obo: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/):"@en ; obo:IAO_0000115 "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."@en ; obo:IAO_0000117 "PERSON: Bill Baumgartner"@en ; obo:IAO_0000118 "footnotes"@en, "notes"@en ; obo:IAO_0000233 ; a owl:Class ; rdfs:label "notes section"@en ; rdfs:subClassOf obo:IAO_0000314 . obo:IAO_0000635 obo:IAO_0000111 "patients section"@en ; obo: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/)"@en ; obo:IAO_0000115 "A part of a document about the patients that participated in a study."@en ; obo:IAO_0000117 "PERSON: Bill Baumgartner"@en ; obo:IAO_0000233 ; a owl:Class ; rdfs:label "patients section"@en ; rdfs:subClassOf obo:IAO_0000314, [ a owl:Restriction ; owl:onProperty obo:BFO_0000051 ; owl:someValuesFrom obo:IAO_0000636 ] . obo:IAO_0000636 obo:IAO_0000111 "patients textual entity"@en ; obo:IAO_0000112 """Excerpt from Citak et al. Acta Orthop. 2013 Jun; 84(3): 326–327. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3715825/): Between 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."""@en ; obo:IAO_0000115 "A textual entity expressing information regarding the patients used in a study."@en ; obo:IAO_0000117 "PERSON: Bill Baumgartner"@en ; obo:IAO_0000233 ; a owl:Class ; rdfs:label "patients textual entity"@en ; rdfs:subClassOf obo:IAO_0000300 . obo:IAO_0000637 obo:IAO_0000111 "pre-publication history section"@en ; obo: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/)"@en ; obo:IAO_0000115 "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."@en ; obo:IAO_0000117 "PERSON: Bill Baumgartner"@en ; obo:IAO_0000118 "notice of republication"@en, "pre-publication history"@en ; obo:IAO_0000233 ; a owl:Class ; rdfs:label "pre-publication history section"@en ; rdfs:subClassOf obo:IAO_0000314, [ a owl:Restriction ; owl:onProperty obo:BFO_0000051 ; owl:someValuesFrom obo:IAO_0000638 ] . obo:IAO_0000638 obo:IAO_0000111 "pre-publication history textual entity"@en ; obo:IAO_0000112 """From Xiao et al. BMC Anesthesiol. 2013; 13: 33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4016475/): The pre-publication history for this paper can be accessed here: http://www.biomedcentral.com/1471-2253/13/33/prepub"""@en ; obo:IAO_0000115 "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."@en ; obo:IAO_0000117 "PERSON: Bill Baumgartner"@en ; obo:IAO_0000233 ; a owl:Class ; rdfs:label "pre-publication history textual entity"@en ; rdfs:subClassOf obo:IAO_0000300 . obo:IAO_0000639 obo:IAO_0000111 "related work section"@en ; obo: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/)"@en ; obo:IAO_0000115 "A part of a document about work in other publications that is relevant to the content of the document."@en ; obo:IAO_0000117 "PERSON: Bill Baumgartner"@en ; obo:IAO_0000118 "related literature"@en, "related work"@en ; obo:IAO_0000233 ; a owl:Class ; rdfs:label "related work section"@en ; rdfs:subClassOf obo:IAO_0000314, [ a owl:Restriction ; owl:onProperty obo:BFO_0000051 ; owl:someValuesFrom obo:IAO_0000640 ] . obo:IAO_0000640 obo:IAO_0000111 "related work textual entity"@en ; obo:IAO_0000112 """Excerpt from Žitnik and Zupan. Bioinformatics. 2015 Jun 15; 31(12): i230–i239. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4542780/): Our work presented here is similar in spirit to our recently developed methodology for data fusion via collective matrix factorization (Žitnik and Zupan, 2015). """@en ; obo:IAO_0000115 "A textual entity that discusses work from other publications and expresses their relevancy to the content of a document."@en ; obo:IAO_0000117 "PERSON: Bill Baumgartner"@en ; obo:IAO_0000233 ; a owl:Class ; rdfs:label "related work textual entity"@en ; rdfs:subClassOf obo:IAO_0000300 . obo:IAO_0000641 obo:IAO_0000111 "requirements section"@en ; obo: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/)."@en ; obo:IAO_0000115 "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."@en ; obo:IAO_0000117 "PERSON: Bill Baumgartner"@en ; obo:IAO_0000118 "requirements"@en ; obo:IAO_0000233 ; a owl:Class ; rdfs:label "requirements section"@en ; rdfs:subClassOf obo:IAO_0000314, [ a owl:Restriction ; owl:onProperty obo:BFO_0000051 ; owl:someValuesFrom obo:IAO_0000642 ] . obo:IAO_0000642 obo:IAO_0000111 "requirements textual entity"@en ; obo:IAO_0000112 """From Qi et al. BMC Bioinformatics. 2014; 15: 11. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3897912/): • Operating systems: Platform independent • Programming language: Matlab, R, Python • Other requirements: None • License: GNU GPL v3 • Any restrictions to use by non-academics: None"""@en ; obo:IAO_0000115 "A textual entity that expresses the requirements necessary to use a resource, e.g. software."@en ; obo:IAO_0000117 "PERSON: Bill Baumgartner"@en ; obo:IAO_0000233 ; a owl:Class ; rdfs:label "requirements textual entity"@en ; rdfs:subClassOf obo:IAO_0000300 . obo:IAO_0000643 obo:IAO_0000111 "statistical analysis textual entity"@en ; obo:IAO_0000112 """From Mondo et al. Cardiovasc J Afr. 2013 Mar; 24(2): 28–33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3734881/): Data 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."""@en ; obo:IAO_0000115 "A textual entity documenting statistical analysis tools and techniques employed."@en ; obo:IAO_0000117 "PERSON: Bill Baumgartner"@en ; obo:IAO_0000233 ; a owl:Class ; rdfs:label "statistical analysis textual entity"@en ; rdfs:subClassOf obo:IAO_0000300 . obo:IAO_0000644 obo:IAO_0000111 "statistical analysis section"@en ; obo: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/)"@en ; obo:IAO_0000115 "A part of the document used to describe the statistical methodologies employed in the work presented in the document."@en ; obo:IAO_0000117 "PERSON: Bill Baumgartner"@en ; obo:IAO_0000118 "statistical analysis"@en ; obo:IAO_0000233 ; a owl:Class ; rdfs:label "statistical analysis section"@en ; rdfs:subClassOf obo:IAO_0000314, [ a owl:Restriction ; owl:onProperty obo:BFO_0000051 ; owl:someValuesFrom obo:IAO_0000643 ] . obo:IAO_0000645 obo:IAO_0000111 "tables section"@en ; obo:IAO_0000112 "The section labelled 'tables' in a typical scientific journal article."@en ; obo:IAO_0000115 "A part of a document that contains one or more tables."@en ; obo:IAO_0000117 "PERSON: Bill Baumgartner"@en ; obo:IAO_0000118 "tables"@en ; obo:IAO_0000233 ; a owl:Class ; rdfs:label "tables section"@en ; rdfs:subClassOf obo:IAO_0000314, [ a owl:Restriction ; owl:onProperty obo:BFO_0000051 ; owl:someValuesFrom obo:IAO_0000306 ] . obo:IAO_0000650 obo:IAO_0000111 "database extract, transform, and load process"@en ; obo:IAO_0000115 "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."@en ; obo: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", "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."@en ; obo:IAO_0000117 "PERSON:Alan Ruttenberg" ; obo:IAO_0000118 "ETL"@en ; obo:IAO_0000119 "WEB:https://en.wikipedia.org/wiki/Extract,_transform,_load" ; obo:IAO_0000233 ; a owl:Class ; rdfs:isDefinedBy ; rdfs:label "database extract, transform, and load process"@en ; rdfs:subClassOf obo:OBI_0000011, [ a owl:Restriction ; owl:onProperty obo:OBI_0000293 ; owl:someValuesFrom obo:IAO_0000030 ], [ a owl:Restriction ; owl:onProperty obo:OBI_0000299 ; owl:someValuesFrom obo:IAO_0000030 ] ; foaf:page . obo:IAO_0006011 obo:IAO_0000115 "A annotation relationship between two terms in an ontology that may refer to the same (natural) type but where more evidence is required before terms are merged." ; obo:IAO_0000117 "David Osumi-Sutherland" ; obo:IAO_0000233 "#40" ; obo:IAO_0000234 "VFB" ; oboInOwl:creation_date "2018-09-21T16:43:39Z"^^xsd:dateTime ; a owl:AnnotationProperty ; rdfs:comment "Edges asserting this should be annotated with to record evidence supporting the assertion and its provenance." ; rdfs:label "may be identical to"@en . obo:IAO_0006012 obo:IAO_0000115 "Used when the class or object is scheduled for obsoletion/deprecation on or after a particular date."@en ; obo:IAO_0000117 "Chris Mungall, Jie Zheng"@en ; obo:IAO_0000233 "https://github.com/geneontology/go-ontology/issues/15532"@en, "https://github.com/information-artifact-ontology/ontology-metadata/issues/32"@en ; obo:IAO_0000234 "GO ontology"@en ; a owl:AnnotationProperty ; rdfs:label "scheduled for obsoletion on or after"@en ; rdfs:range xsd:dateTime . obo:IAO_0010000 obo:IAO_0000111 "has axiom id"@en ; obo:IAO_0000117 "Person:Alan Ruttenberg"@en ; obo:IAO_0000119 "Person:Alan Ruttenberg"@en ; obo:IAO_0000600 "A URI that is intended to be unique label for an axiom used for tracking change to the ontology. For an axiom expressed in different languages, each expression is given the same URI"@en ; a owl:AnnotationProperty ; rdfs:isDefinedBy <> ; rdfs:label "has axiom label"@en . obo:IAO_0100001 obo:IAO_0000111 "term replaced by"@en ; obo:IAO_0000114 obo:IAO_0000125 ; obo:IAO_0000115 "Add as annotation triples in the granting ontology"@en, "Use on obsolete terms, relating the term to another term that can be used as a substitute"@en ; obo:IAO_0000117 "Person:Alan Ruttenberg"@en ; obo:IAO_0000119 "Person:Alan Ruttenberg"@en ; a owl:AnnotationProperty ; rdfs:label "term replaced by"@en . obo:IAO_8000000 obo: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." ; obo:IAO_0000118 "ontology file" ; obo: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." ; oboInOwl:created_by "cjm"^^xsd:string ; oboInOwl:creation_date "2018-05-20T20:55:03Z"^^xsd:dateTime ; a owl:Class ; rdfs:label "ontology module" ; rdfs:subClassOf obo:IAO_0000102 . obo:IAO_8000001 obo:IAO_0000115 "An ontology module that comprises only of asserted axioms local to the ontology, excludes import directives, and excludes axioms or declarations from external ontologies." ; oboInOwl:created_by "cjm"^^xsd:string ; oboInOwl:creation_date "2018-05-20T20:55:30Z"^^xsd:dateTime ; a owl:Class ; rdfs:label "base ontology module" ; rdfs:seeAlso ; rdfs:subClassOf obo:IAO_8000000 . obo:IAO_8000002 obo:IAO_0000115 "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." ; obo:IAO_0000118 "source ontology module" ; oboInOwl:created_by "cjm"^^xsd:string ; oboInOwl:creation_date "2018-05-20T20:55:47Z"^^xsd:dateTime ; a owl:Class ; rdfs:label "editors ontology module" ; rdfs:subClassOf obo:IAO_8000000 . obo:IAO_8000003 obo:IAO_0000115 "An ontology module that is intended to be the primary release product and the one consumed by the majority of tools." ; obo:IAO_0000116 "TODO: Add logical axioms that state that a main release ontology module is derived from (directly or indirectly) an editors module" ; oboInOwl:created_by "cjm"^^xsd:string ; oboInOwl:creation_date "2018-05-20T20:56:13Z"^^xsd:dateTime ; a owl:Class ; rdfs:label "main release ontology module" ; rdfs:subClassOf obo:IAO_8000000 . obo:IAO_8000004 obo:IAO_0000115 "An ontology module that consists entirely of axioms that connect or bridge two distinct ontology modules. For example, the Uberon-to-ZFA bridge module." ; oboInOwl:created_by "cjm"^^xsd:string ; oboInOwl:creation_date "2018-05-20T20:56:23Z"^^xsd:dateTime ; a owl:Class ; rdfs:label "bridge ontology module" ; rdfs:seeAlso ; rdfs:subClassOf obo:IAO_8000000 . obo:IAO_8000005 obo:IAO_0000115 "A subset ontology module that is intended to be imported from another ontology." ; obo:IAO_0000116 "TODO: add axioms that indicate this is the output of a module extraction process." ; obo:IAO_0000118 "import file" ; oboInOwl:created_by "cjm"^^xsd:string ; oboInOwl:creation_date "2018-05-20T20:56:47Z"^^xsd:dateTime ; a owl:Class ; rdfs:label "import ontology module" ; rdfs:seeAlso ; rdfs:subClassOf obo:IAO_8000006 . obo:IAO_8000006 obo:IAO_0000115 "An ontology module that is extracted from a main ontology module and includes only a subset of entities or axioms." ; obo:IAO_0000118 "ontology slim", "subset ontology" ; oboInOwl:created_by "cjm"^^xsd:string ; oboInOwl:creation_date "2018-05-20T20:58:11Z"^^xsd:dateTime ; a owl:Class ; rdfs:label "subset ontology module" ; rdfs:seeAlso , ; rdfs:subClassOf obo:IAO_8000000 . obo:IAO_8000007 obo:IAO_0000115 "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." ; oboInOwl:created_by "cjm"^^xsd:string ; oboInOwl:creation_date "2018-05-20T20:58:38Z"^^xsd:dateTime ; a owl:Class ; rdfs:label "curation subset ontology module" ; rdfs:subClassOf obo:IAO_8000006 . obo:IAO_8000008 obo:IAO_0000115 "An ontology module that is intended for usage in analysis or discovery applications." ; oboInOwl:created_by "cjm"^^xsd:string ; oboInOwl:creation_date "2018-05-20T20:58:49Z"^^xsd:dateTime ; a owl:Class ; rdfs:label "analysis subset ontology module" ; rdfs:subClassOf obo:IAO_8000006 . obo:IAO_8000009 obo:IAO_0000115 "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." ; obo:IAO_0000118 "ribbon subset" ; oboInOwl:created_by "cjm"^^xsd:string ; oboInOwl:creation_date "2018-05-20T20:59:19Z"^^xsd:dateTime ; a owl:Class ; rdfs:label "single layer subset ontology module" ; rdfs:subClassOf obo:IAO_8000006 . obo:IAO_8000010 obo:IAO_0000115 "A subset of an ontology that is intended to be excluded for some purpose. For example, a blacklist of classes." ; obo:IAO_0000118 "antislim" ; oboInOwl:created_by "cjm"^^xsd:string ; oboInOwl:creation_date "2018-05-20T20:59:57Z"^^xsd:dateTime ; a owl:Class ; rdfs:label "exclusion subset ontology module" ; rdfs:subClassOf obo:IAO_8000006 . obo:IAO_8000011 obo:IAO_0000115 "An imported ontology module that is derived from an external ontology. Derivation methods include the OWLAPI SLME approach." ; obo:IAO_0000118 "external import" ; oboInOwl:created_by "cjm"^^xsd:string ; oboInOwl:creation_date "2018-05-20T21:00:14Z"^^xsd:dateTime ; a owl:Class ; rdfs:label "external import ontology module" ; rdfs:subClassOf obo:IAO_8000005 . obo:IAO_8000012 obo:IAO_0000115 "A subset ontology that is crafted to either include or exclude a taxonomic grouping of species." ; obo:IAO_0000118 "taxon subset" ; oboInOwl:created_by "cjm"^^xsd:string ; oboInOwl:creation_date "2018-05-20T21:14:16Z"^^xsd:dateTime ; a owl:Class ; rdfs:label "species subset ontology module" ; rdfs:seeAlso ; rdfs:subClassOf obo:IAO_8000006 . obo:IAO_8000013 obo:IAO_0000115 "An ontology module that contains axioms generated by a reasoner. The generated axioms are typically direct SubClassOf axioms, but other possibilities are available." ; oboInOwl:created_by "cjm"^^xsd:string ; oboInOwl:creation_date "2018-05-20T21:20:33Z"^^xsd:dateTime ; a owl:Class ; rdfs:label "reasoned ontology module" ; rdfs:seeAlso ; rdfs:subClassOf obo:IAO_8000000 . obo:IAO_8000014 obo:IAO_0000115 "An ontology module that is automatically generated, for example via a SPARQL query or via template and a CSV." ; obo:IAO_0000116 "TODO: Add axioms (using PROV-O?) that indicate this is the output-of some reasoning process" ; oboInOwl:created_by "cjm"^^xsd:string ; oboInOwl:creation_date "2018-05-20T21:21:12Z"^^xsd:dateTime ; a owl:Class ; rdfs:label "generated ontology module" ; rdfs:subClassOf obo:IAO_8000000 . obo:IAO_8000015 obo:IAO_0000115 "An ontology module that is automatically generated from a template specification and fillers for slots in that template." ; oboInOwl:created_by "cjm"^^xsd:string ; oboInOwl:creation_date "2018-05-20T21:21:21Z"^^xsd:dateTime ; a owl:Class ; rdfs:label "template generated ontology module" ; rdfs:seeAlso , , ; rdfs:subClassOf obo:IAO_8000014 . obo:IAO_8000016 oboInOwl:created_by "cjm"^^xsd:string ; oboInOwl:creation_date "2018-05-20T21:28:15Z"^^xsd:dateTime ; a owl:Class ; rdfs:label "taxonomic bridge ontology module" ; rdfs:subClassOf obo:IAO_8000004 . obo:IAO_8000017 oboInOwl:created_by "cjm"^^xsd:string ; oboInOwl:creation_date "2018-05-22T04:15:54Z"^^xsd:dateTime ; a owl:Class ; rdfs:label "ontology module subsetted by expressivity" ; rdfs:subClassOf obo:IAO_8000006 . obo:IAO_8000018 obo:IAO_0000115 """A subset ontology that is designed for basic applications to continue to make certain simplifying assumptions; many of these simplifying assumptions were based on the initial version of the Gene Ontology, and have become enshrined in many popular and useful tools such as term enrichment tools. Examples of such assumptions include: traversing the ontology graph ignoring relationship types using a naive algorithm will not lead to cycles (i.e. the ontology is a DAG); every referenced term is declared in the ontology (i.e. there are no dangling clauses). An ontology is OBO Basic if and only if it has the following characteristics: DAG Unidirectional No Dangling Clauses Fully Asserted Fully Labeled No equivalence axioms Singly labeled edges No qualifier lists No disjointness axioms No owl-axioms header No imports""" ; oboInOwl:created_by "cjm"^^xsd:string ; oboInOwl:creation_date "2018-05-22T04:16:10Z"^^xsd:dateTime ; a owl:Class ; rdfs:label "obo basic subset ontology module" ; rdfs:seeAlso ; rdfs:subClassOf obo:IAO_8000017 . obo:IAO_8000019 oboInOwl:created_by "cjm"^^xsd:string ; oboInOwl:creation_date "2018-05-22T04:16:28Z"^^xsd:dateTime ; a owl:Class ; rdfs:label "ontology module subsetted by OWL profile" ; rdfs:subClassOf obo:IAO_8000017 . obo:IAO_8000020 oboInOwl:created_by "cjm"^^xsd:string ; oboInOwl:creation_date "2018-05-22T04:16:48Z"^^xsd:dateTime ; a owl:Class ; rdfs:label "EL++ ontology module" ; rdfs:subClassOf obo:IAO_8000019 . obo:OBI_0000011 obo:IAO_0000111 "planned process"@en ; obo:IAO_0000115 "A processual entity that realizes a plan which is the concretization of a plan specification."@en ; obo:IAO_0000412 ; a owl:Class ; rdfs:label "planned process"@en ; rdfs:subClassOf obo:BFO_0000015 . obo:OBI_0000066 obo:IAO_0000111 "investigation"@en ; obo:IAO_0000115 "a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s)."@en ; obo:IAO_0000412 ; a owl:Class ; rdfs:label "investigation"@en ; rdfs:subClassOf obo:OBI_0000011 . obo:OBI_0000293 obo:IAO_0000111 "has_specified_input"^^xsd:string, "has_specified_input"@en ; obo:IAO_0000112 "see is_input_of example_of_usage"@en ; obo:IAO_0000114 obo:IAO_0000122 ; obo:IAO_0000115 "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."@en ; obo: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 ; obo:IAO_0000117 "PERSON: Alan Ruttenberg"@en, "PERSON: Bjoern Peters"^^xsd:string, "PERSON: Larry Hunter"^^xsd:string, "PERSON: Melanie Coutot"^^xsd:string ; obo:IAO_0000412 ; a owl:ObjectProperty ; rdfs:domain obo:OBI_0000011 ; rdfs:label "has_specified_input"@en ; rdfs:subPropertyOf obo:RO_0000057 ; owl:equivalentProperty [ owl:inverseOf obo:OBI_0000295 ] ; owl:inverseOf obo:OBI_0000295 . obo:OBI_0000295 a owl:ObjectProperty ; rdfs:label "is_specified_input_of"@en . obo:OBI_0000299 obo:IAO_0000111 "has_specified_output"^^xsd:string, "has_specified_output"@en ; obo:IAO_0000114 obo:IAO_0000122 ; obo:IAO_0000115 "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."@en ; obo:IAO_0000117 "PERSON: Alan Ruttenberg"@en, "PERSON: Bjoern Peters"^^xsd:string, "PERSON: Larry Hunter"^^xsd:string, "PERSON: Melanie Courtot"^^xsd:string ; obo:IAO_0000412 ; a owl:ObjectProperty ; rdfs:domain obo:OBI_0000011 ; rdfs:label "has_specified_output"@en ; rdfs:subPropertyOf obo:RO_0000057 ; owl:equivalentProperty [ owl:inverseOf obo:OBI_0000312 ] ; owl:inverseOf obo:OBI_0000312 . obo:OBI_0000312 obo:IAO_0000111 "is_specified_output_of"^^xsd:string, "is_specified_output_of"@en ; obo:IAO_0000114 obo:IAO_0000122 ; obo:IAO_0000115 "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."@en ; obo:IAO_0000117 "Alan Ruttenberg"@en, "PERSON:Bjoern Peters"^^xsd:string ; obo:IAO_0000412 ; a owl:ObjectProperty ; rdfs:label "is_specified_output_of"@en ; rdfs:range obo:OBI_0000011 ; rdfs:subPropertyOf obo:RO_0000056 ; owl:equivalentProperty [ owl:inverseOf obo:OBI_0000299 ] . obo:OBI_0000471 obo:IAO_0000111 "study design execution"^^xsd:string ; obo:IAO_0000115 "a planned process that carries out a study design"^^xsd:string ; obo:IAO_0000412 ; a owl:Class ; rdfs:label "study design execution"^^xsd:string ; rdfs:subClassOf obo:OBI_0000011 . obo:OBI_0500000 obo:IAO_0000111 "study design"@en ; obo:IAO_0000115 "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."^^xsd:string ; obo:IAO_0000412 ; a owl:Class ; rdfs:label "study design"@en ; rdfs:subClassOf obo:IAO_0000104 . obo:PATO_0000051 obo:IAO_0000111 "morphology"^^xsd:string ; obo:IAO_0000115 "A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure."^^xsd:string ; obo:IAO_0000412 ; a owl:Class ; rdfs:label "morphology"^^xsd:string ; rdfs:subClassOf obo:PATO_0001241 . obo:PATO_0000117 obo:IAO_0000111 "size"^^xsd:string ; obo:IAO_0000115 "A morphology quality inhering in a bearer by virtue of the bearer's physical magnitude."^^xsd:string ; obo:IAO_0000412 ; a owl:Class ; rdfs:label "size"^^xsd:string ; rdfs:subClassOf obo:PATO_0000051 . obo:PATO_0000122 obo:IAO_0000111 "length"^^xsd:string ; obo:IAO_0000115 "A 1-D extent quality which is equal to the distance between two points."^^xsd:string ; obo:IAO_0000412 ; a owl:Class ; rdfs:label "length"^^xsd:string ; rdfs:subClassOf obo:PATO_0001708 . obo:PATO_0000125 obo:IAO_0000111 "mass"^^xsd:string ; obo:IAO_0000115 "A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter."^^xsd:string ; obo:IAO_0000412 ; a owl:Class ; rdfs:label "mass"^^xsd:string ; rdfs:subClassOf obo:PATO_0001018 . obo:PATO_0001018 obo:IAO_0000111 "physical quality"^^xsd:string ; obo:IAO_0000115 "A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities."^^xsd:string ; obo:IAO_0000412 ; a owl:Class ; rdfs:label "physical quality"^^xsd:string ; rdfs:subClassOf obo:PATO_0001241 . obo:PATO_0001241 obo:IAO_0000111 "physical object quality"^^xsd:string ; obo:IAO_0000115 "A quality which inheres in a continuant."^^xsd:string ; obo:IAO_0000412 ; a owl:Class ; rdfs:label "physical object quality"^^xsd:string ; rdfs:subClassOf obo:BFO_0000019 . obo:PATO_0001708 obo:IAO_0000111 "1-D extent"^^xsd:string ; obo:IAO_0000115 "A size quality inhering in an bearer by virtue of the bearer's extension in one dimension."^^xsd:string ; obo:IAO_0000412 ; a owl:Class ; rdfs:label "1-D extent"^^xsd:string ; rdfs:subClassOf obo:PATO_0000117 . obo:RO_0000052 obo:IAO_0000111 "inheres in"@en ; obo:IAO_0000112 "this fragility inheres in this vase"@en, "this red color inheres in this apple"@en ; obo:IAO_0000115 "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"@en ; obo:IAO_0000116 "A dependent inheres in its bearer at all times for which the dependent exists."@en ; obo:IAO_0000118 "inheres_in"@en ; obo:RO_0001900 obo:RO_0001901 ; a owl:ObjectProperty ; rdfs:label "inheres in"@en ; owl:inverseOf obo:RO_0000053 . obo:RO_0000053 obo:IAO_0000111 "bearer of"@en ; obo:IAO_0000112 "this apple is bearer of this red color"@en, "this vase is bearer of this fragility"@en ; obo:IAO_0000115 "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"@en ; obo: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."@en ; obo:IAO_0000118 "bearer_of"@en, "is bearer of"@en ; obo:RO_0001900 obo:RO_0001901 ; a owl:ObjectProperty ; rdfs:label "bearer of"@en ; rdfs:range obo:BFO_0000020 . obo:RO_0000056 obo:IAO_0000111 "participates in"@en ; obo:IAO_0000112 "this blood clot participates in this blood coagulation"@en, "this input material (or this output material) participates in this process"@en, "this investigator participates in this investigation"@en ; obo:IAO_0000115 "a relation between a continuant and a process, in which the continuant is somehow involved in the process"@en ; obo:IAO_0000118 "participates_in"@en ; a owl:ObjectProperty ; rdfs:domain obo:BFO_0000002 ; rdfs:label "participates in"@en ; rdfs:range obo:BFO_0000003 ; owl:inverseOf obo:RO_0000057 . obo:RO_0000057 obo:IAO_0000111 "has participant"@en ; obo:IAO_0000112 "this blood coagulation has participant this blood clot"@en, "this investigation has participant this investigator"@en, "this process has participant this input material (or this output material)"@en ; obo:IAO_0000115 "a relation between a process and a continuant, in which the continuant is somehow involved in the process"@en ; obo: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."@en ; obo:IAO_0000118 "has_participant"@en ; dc:source "http://www.obofoundry.org/ro/#OBO_REL:has_participant" ; a owl:ObjectProperty ; rdfs:domain obo:BFO_0000003 ; rdfs:label "has participant"@en ; rdfs:range obo:BFO_0000002 . obo:RO_0000058 obo: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)."@en, "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)."@en ; obo:IAO_0000115 "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."@en ; a owl:ObjectProperty ; rdfs:domain obo:BFO_0000031 ; rdfs:label "is concretized as"@en ; rdfs:range obo:BFO_0000020 ; owl:inverseOf obo:RO_0000059 . obo:RO_0000059 obo: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)."@en, "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)."@en ; obo:IAO_0000115 "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."@en ; a owl:ObjectProperty ; rdfs:domain obo:BFO_0000020 ; rdfs:label "concretizes"@en ; rdfs:range obo:BFO_0000031 . obo:RO_0000079 obo:IAO_0000112 "this catalysis function is a function of this enzyme"@en ; obo:IAO_0000115 "a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence"@en ; obo: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."@en ; obo:IAO_0000118 "function_of"@en, "is function of"@en ; a owl:ObjectProperty ; rdfs:domain obo:BFO_0000034 ; rdfs:label "function of"@en ; rdfs:subPropertyOf obo:RO_0000052 ; owl:inverseOf obo:RO_0000085 . obo:RO_0000080 obo:IAO_0000112 "this red color is a quality of this apple"@en ; obo:IAO_0000115 "a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence"@en ; obo:IAO_0000116 "A quality inheres in its bearer at all times for which the quality exists."@en ; obo:IAO_0000118 "is quality of"@en, "quality_of"@en ; a owl:ObjectProperty ; rdfs:label "quality of"@en ; rdfs:subPropertyOf obo:RO_0000052 ; owl:inverseOf obo:RO_0000086 . obo:RO_0000081 obo:IAO_0000112 "this investigator role is a role of this person"@en ; obo:IAO_0000115 "a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence"@en ; obo: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."@en ; obo:IAO_0000118 "is role of"@en, "role_of"@en ; a owl:ObjectProperty ; rdfs:label "role of"@en ; rdfs:subPropertyOf obo:RO_0000052 ; owl:inverseOf obo:RO_0000087 . obo:RO_0000085 obo:IAO_0000112 "this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)"@en ; obo:IAO_0000115 "a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence"@en ; obo: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."@en ; obo:IAO_0000118 "has_function"@en ; a owl:ObjectProperty ; rdfs:domain obo:BFO_0000004 ; rdfs:label "has function"@en ; rdfs:range obo:BFO_0000034 ; rdfs:subPropertyOf obo:RO_0000053 . obo:RO_0000086 obo:IAO_0000112 "this apple has quality this red color"@en ; obo:IAO_0000115 "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence"@en ; obo: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."@en ; obo:IAO_0000118 "has_quality"@en ; a owl:ObjectProperty ; rdfs:label "has quality"@en ; rdfs:range obo:BFO_0000019 ; rdfs:subPropertyOf obo:RO_0000053 . obo:RO_0000087 obo:IAO_0000112 "this person has role this investigator role (more colloquially: this person has this role of investigator)"@en ; obo:IAO_0000115 "a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence"@en ; obo: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."@en ; obo:IAO_0000118 "has_role"@en ; a owl:ObjectProperty ; rdfs:domain obo:BFO_0000004 ; rdfs:label "has role"@en ; rdfs:range obo:BFO_0000023 ; rdfs:subPropertyOf obo:RO_0000053 . obo:RO_0000091 obo:IAO_0000115 "a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence"@en ; a owl:ObjectProperty ; rdfs:domain obo:BFO_0000004 ; rdfs:label "has disposition"@en ; rdfs:range obo:BFO_0000016 ; rdfs:subPropertyOf obo:RO_0000053 ; owl:inverseOf obo:RO_0000092 . obo:RO_0000092 a owl:ObjectProperty ; rdfs:label "disposition of"@en ; rdfs:subPropertyOf obo:RO_0000052 . obo:RO_0001000 obo:IAO_0000112 "this cell derives from this parent cell (cell division)"@en, "this nucleus derives from this parent nucleus (nuclear division)"@en ; obo:IAO_0000114 obo:IAO_0000125 ; obo:IAO_0000115 "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"@en ; obo:IAO_0000116 "This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'."@en ; obo:IAO_0000118 "derives_from"@en ; a owl:ObjectProperty ; rdfs:label "derives from"@en ; owl:inverseOf obo:RO_0001001 . obo:RO_0001001 obo:IAO_0000112 "this parent cell derives into this cell (cell division)"@en, "this parent nucleus derives into this nucleus (nuclear division)"@en ; obo:IAO_0000114 obo:IAO_0000125 ; obo:IAO_0000115 "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"@en ; obo: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'."@en ; obo:IAO_0000118 "derives_into"@en ; a owl:ObjectProperty ; rdfs:label "derives into"@en . obo:RO_0001015 obo:IAO_0000111 "is location of"@en ; obo:IAO_0000112 "my head is the location of my brain"@en, "this cage is the location of this rat"@en ; obo:IAO_0000115 "a relation between two independent continuants, the location and the target, in which the target is entirely within the location"@en ; obo: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"@en ; obo:IAO_0000118 "location_of"@en ; obo:RO_0001900 obo:RO_0001901 ; a owl:ObjectProperty, owl:TransitiveProperty ; rdfs:label "location of"@en ; owl:inverseOf obo:RO_0001025 . obo:RO_0001025 obo:IAO_0000111 "located in"@en ; obo:IAO_0000112 "my brain is located in my head"@en, "this rat is located in this cage"@en ; obo:IAO_0000115 "a relation between two independent continuants, the target and the location, in which the target is entirely within the location"@en ; obo: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"@en, "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"@en ; obo:IAO_0000118 "located_in"@en ; obo:RO_0001900 obo:RO_0001901 ; dc:source "http://www.obofoundry.org/ro/#OBO_REL:located_in" ; a owl:ObjectProperty, owl:TransitiveProperty ; rdfs:domain obo:BFO_0000004, [ a owl:Class ; owl:intersectionOf (obo:BFO_0000004 [ a owl:Class ; owl:complementOf obo:BFO_0000006 ] ) ] ; rdfs:label "located in"@en ; rdfs:range obo:BFO_0000004, [ a owl:Class ; owl:intersectionOf (obo:BFO_0000004 [ a owl:Class ; owl:complementOf obo:BFO_0000006 ] ) ] . obo:RO_0001900 obo:IAO_0000115 "An assertion that holds between an OWL Object Property and a temporal interpretation that elucidates how OWL Class Axioms that use this property are to be interpreted in a temporal context." ; a owl:AnnotationProperty ; rdfs:label "temporal interpretation"@en . obo:RO_0002000 obo:IAO_0000112 "the surface of my skin is a 2D boundary of my body"@en ; obo:IAO_0000115 "a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity"@en ; obo: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."@en, "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape."@en ; obo:IAO_0000118 "2D_boundary_of"@en, "boundary of"@en, "is 2D boundary of"@en, "is boundary of"@en ; obo:RO_0001900 obo:RO_0001901 ; a owl:ObjectProperty ; rdfs:label "2D boundary of"@en ; owl:inverseOf obo:RO_0002002 . obo:RO_0002002 obo:IAO_0000112 "my body has 2D boundary the surface of my skin"@en ; obo:IAO_0000115 "a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity"@en ; obo: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."@en, "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape."@en ; obo:IAO_0000118 "has boundary"@en, "has_2D_boundary"@en ; obo:RO_0001900 obo:RO_0001901 ; a owl:ObjectProperty ; rdfs:domain obo:BFO_0000040 ; rdfs:label "has 2D boundary"@en ; rdfs:range obo:BFO_0000141 . obo:RO_0002350 obo:IAO_0000112 "An organism that is a member of a population of organisms" ; obo:IAO_0000115 "is member of is a mereological relation between a item and a collection." ; obo:IAO_0000118 "is member of", "member part of" ; obo:IAO_0000119 "SIO" ; obo:RO_0001900 obo:RO_0001901 ; a owl:ObjectProperty ; rdfs:label "member of"@en ; rdfs:subPropertyOf obo:BFO_0000050 ; owl:inverseOf obo:RO_0002351 . obo:RO_0002351 obo:IAO_0000115 "has member is a mereological relation between a collection and an item." ; obo:IAO_0000119 "SIO" ; obo:RO_0001900 obo:RO_0001901 ; a owl:IrreflexiveProperty, owl:ObjectProperty ; rdfs:label "has member"@en ; rdfs:subPropertyOf obo:BFO_0000051 . obo:UO_0000001 obo:IAO_0000111 "length unit"^^xsd:string ; obo:IAO_0000115 "A unit which is a standard measure of the distance between two points."^^xsd:string ; obo:IAO_0000412 ; a owl:Class ; rdfs:label "length unit"^^xsd:string ; rdfs:subClassOf obo:IAO_0000003 . obo:UO_0000002 obo:IAO_0000111 "mass unit"^^xsd:string ; obo:IAO_0000115 "A unit which is a standard measure of the amount of matter/energy of a physical object."^^xsd:string ; obo:IAO_0000412 ; a owl:Class ; rdfs:label "mass unit"^^xsd:string ; rdfs:subClassOf obo:IAO_0000003 . obo:UO_0000003 obo:IAO_0000111 "time unit"^^xsd:string ; obo:IAO_0000115 "A unit which is a standard measure of the dimension in which events occur in sequence."^^xsd:string ; obo:IAO_0000412 ; a owl:Class ; rdfs:label "time unit"^^xsd:string ; rdfs:subClassOf obo:IAO_0000003 . <> dcterms:license ; protege:defaultLanguage "en"^^xsd:string ; dc:contributor "Adam Goldstein"@en, "Alan Ruttenberg"@en, "Albert Goldfain"@en, "Barry Smith"@en, "Bjoern Peters"@en, "Carlo Torniai"@en, "Chris Mungall"@en, "Chris Stoeckert"@en, "Christian A. Boelling"@en, "Darren Natale"@en, "David Osumi-Sutherland"@en, "Gwen Frishkoff"@en, "Holger Stenzhorn"@en, "James A. Overton"@en, "James Malone"@en, "Jennifer Fostel"@en, "Jie Zheng"@en, "Jonathan Rees"@en, "Larisa Soldatova"@en, "Lawrence Hunter"@en, "Mathias Brochhausen"@en, "Matt Brush"@en, "Melanie Courtot"@en, "Michel Dumontier"@en, "Paolo Ciccarese"@en, "Pat Hayes"@en, "Philippe Rocca-Serra"@en, "Randy Dipert"@en, "Ron Rudnicki"@en, "Satya Sahoo"@en, "Sivaram Arabandi"@en, "Werner Ceusters"@en, "William Duncan"@en, "William Hogan"@en, "Yongqun (Oliver) He"@en ; a owl:NamedIndividual, owl:Ontology ; rdfs:comment "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"^^xsd:string, "IDs allocated to related efforts: PNO: IAO_0020000-IAO_0020999, D_ACTS: IAO_0021000-IAO_0021999"^^xsd:string, "IDs allocated to subdomains of IAO. pno.owl: IAO_0020000-IAO_0020999, d-acts.owl: IAO_0021000-IAO_0021999"^^xsd:string ; rdfs:seeAlso ; owl:versionIRI . obo:IAO_0000603 "IAO_0021000-IAO_0021999"^^xsd:string . obo:IAO_0000603 "IAO_0020000-IAO_0020999"^^xsd:string . a owl:NamedIndividual . dc:contributor a owl:AnnotationProperty . dc:coverage a owl:AnnotationProperty . dc:creator a owl:AnnotationProperty . dc:date a owl:AnnotationProperty . dc:description a owl:AnnotationProperty . dc:format a owl:AnnotationProperty . dc:identifier a owl:AnnotationProperty . dc:language a owl:AnnotationProperty . dc:member a owl:AnnotationProperty . dc:publisher a owl:AnnotationProperty . dc:relation a owl:AnnotationProperty . dc:rights a owl:AnnotationProperty . dc:source a owl:AnnotationProperty . dc:subject a owl:AnnotationProperty . dc:title a owl:AnnotationProperty . dc:type a owl:AnnotationProperty . oboInOwl:DbXref a owl:Class ; rdfs:subClassOf obo:IAO_0000102 . oboInOwl:Definition a owl:Class ; rdfs:subClassOf obo:IAO_0000102 . oboInOwl:ObsoleteClass a owl:Class ; rdfs:label "Obsolete Class"^^xsd:string ; rdfs:subClassOf owl:Thing . oboInOwl:ObsoleteProperty a owl:ObjectProperty . oboInOwl:Subset a owl:Class ; rdfs:subClassOf obo:IAO_0000102 ; owl:equivalentClass [ a owl:Class ; owl:oneOf (obo:IAO_0000224 ) ] . oboInOwl:Synonym a owl:Class ; rdfs:subClassOf obo:IAO_0000102 . oboInOwl:SynonymType a owl:Class ; rdfs:subClassOf obo:IAO_0000102 . oboInOwl:created_by a owl:AnnotationProperty . oboInOwl:creation_date a owl:AnnotationProperty . rdf:type a owl:AnnotationProperty . rdfs:comment a owl:AnnotationProperty . rdfs:isDefinedBy a owl:AnnotationProperty . rdfs:label obo:IAO_0000111 "label" ; a owl:AnnotationProperty ; rdfs:label "label" . rdfs:seeAlso a owl:AnnotationProperty . foaf:homepage a owl:AnnotationProperty . foaf:page a owl:AnnotationProperty . [] obo:IAO_0010000 ; a owl:Axiom ; owl:annotatedProperty obo:IAO_0000600 ; owl:annotatedSource obo:BFO_0000027 ; owl:annotatedTarget "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])"@en . [] obo:IAO_0010000 ; a owl:Axiom ; owl:annotatedProperty obo:IAO_0000602 ; owl:annotatedSource obo:BFO_0000027 ; owl:annotatedTarget "(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] " . [] obo:IAO_0010000 ; a owl:Axiom ; owl:annotatedProperty obo:IAO_0000600 ; owl:annotatedSource obo:BFO_0000028 ; owl:annotatedTarget "A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001])"@en . [] obo:IAO_0010000 ; a owl:Axiom ; owl:annotatedProperty obo:IAO_0000602 ; owl:annotatedSource obo:BFO_0000028 ; owl:annotatedTarget "(forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001] " . [] obo:IAO_0010000 ; a owl:Axiom ; owl:annotatedProperty obo:IAO_0000600 ; owl:annotatedSource obo:BFO_0000029 ; owl:annotatedTarget "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])"@en . [] obo:IAO_0010000 ; a owl:Axiom ; owl:annotatedProperty obo:IAO_0000602 ; owl:annotatedSource obo:BFO_0000029 ; owl:annotatedTarget "(forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002] " . [] obo:IAO_0010000 ; a owl:Axiom ; owl:annotatedProperty obo:IAO_0000600 ; owl:annotatedSource obo:BFO_0000030 ; owl:annotatedTarget "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])"@en . [] obo:IAO_0010000 ; a owl:Axiom ; owl:annotatedProperty obo:IAO_0000115 ; owl:annotatedSource obo:BFO_0000031 ; owl:annotatedTarget "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])"@en . [] obo:IAO_0010000 ; a owl:Axiom ; owl:annotatedProperty obo:IAO_0000602 ; owl:annotatedSource obo:BFO_0000031 ; owl:annotatedTarget "(iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] " . [] obo:IAO_0010000 ; a owl:Axiom ; owl:annotatedProperty obo:IAO_0000600 ; owl:annotatedSource obo:BFO_0000034 ; owl:annotatedTarget "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])"@en . [] obo:IAO_0010000 ; a owl:Axiom ; owl:annotatedProperty obo:IAO_0000602 ; owl:annotatedSource obo:BFO_0000034 ; owl:annotatedTarget "(forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] " . [] obo:IAO_0010000 ; a owl:Axiom ; owl:annotatedProperty obo:IAO_0000115 ; owl:annotatedSource obo:BFO_0000035 ; owl:annotatedTarget "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])"@en . [] obo:IAO_0010000 ; a owl:Axiom ; owl:annotatedProperty obo:IAO_0000601 ; owl:annotatedSource obo:BFO_0000035 ; owl:annotatedTarget "Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002])"@en . [] obo:IAO_0010000 ; a owl:Axiom ; owl:annotatedProperty obo:IAO_0000602 ; owl:annotatedSource obo:BFO_0000035 ; owl:annotatedTarget "(forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002] " . [] obo:IAO_0010000 ; a owl:Axiom ; owl:annotatedProperty obo:IAO_0000602 ; owl:annotatedSource obo:BFO_0000035 ; owl:annotatedTarget "(iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001] " . [] obo:IAO_0010000 ; a owl:Axiom ; owl:annotatedProperty obo:IAO_0000600 ; owl:annotatedSource obo:BFO_0000038 ; owl:annotatedTarget "A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001])"@en . [] obo:IAO_0010000 ; a owl:Axiom ; owl:annotatedProperty obo:IAO_0000602 ; owl:annotatedSource obo:BFO_0000038 ; owl:annotatedTarget "(forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001] " . [] obo:IAO_0010000 ; a owl:Axiom ; owl:annotatedProperty obo:IAO_0000600 ; owl:annotatedSource obo:BFO_0000040 ; owl:annotatedTarget "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])"@en . [] obo:IAO_0010000 ; a owl:Axiom ; owl:annotatedProperty obo:IAO_0000601 ; owl:annotatedSource obo:BFO_0000040 ; owl:annotatedTarget "Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])"@en . [] obo:IAO_0010000 ; a owl:Axiom ; owl:annotatedProperty obo:IAO_0000601 ; owl:annotatedSource obo:BFO_0000040 ; owl:annotatedTarget "every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])"@en . [] obo:IAO_0010000 ; a owl:Axiom ; owl:annotatedProperty obo:IAO_0000602 ; owl:annotatedSource obo:BFO_0000040 ; owl:annotatedTarget "(forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] " . [] obo:IAO_0010000 ; a owl:Axiom ; owl:annotatedProperty obo:IAO_0000602 ; owl:annotatedSource obo:BFO_0000040 ; owl:annotatedTarget "(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] " . [] obo:IAO_0010000 ; a owl:Axiom ; owl:annotatedProperty obo:IAO_0000602 ; owl:annotatedSource obo:BFO_0000040 ; owl:annotatedTarget "(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] " . [] obo:IAO_0010000 ; a owl:Axiom ; owl:annotatedProperty obo:IAO_0000115 ; owl:annotatedSource obo:BFO_0000140 ; owl:annotatedTarget "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])"@en . [] obo:IAO_0010000 ; a owl:Axiom ; owl:annotatedProperty obo:IAO_0000116 ; owl:annotatedSource obo:BFO_0000140 ; owl:annotatedTarget "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."@en . [] obo:IAO_0010000 ; a owl:Axiom ; owl:annotatedProperty obo:IAO_0000602 ; owl:annotatedSource obo:BFO_0000140 ; owl:annotatedTarget "(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] " . [] obo:IAO_0010000 ; a owl:Axiom ; owl:annotatedProperty obo:IAO_0000600 ; owl:annotatedSource obo:BFO_0000142 ; owl:annotatedTarget "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])"@en . [] obo:IAO_0010000 ; a owl:Axiom ; owl:annotatedProperty obo:IAO_0000602 ; owl:annotatedSource obo:BFO_0000142 ; owl:annotatedTarget "(iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001] " . [] obo:IAO_0010000 ; a owl:Axiom ; owl:annotatedProperty obo:IAO_0000115 ; owl:annotatedSource obo:BFO_0000144 ; owl:annotatedTarget "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])"@en . [] obo:IAO_0010000 ; a owl:Axiom ; owl:annotatedProperty obo:IAO_0000600 ; owl:annotatedSource obo:BFO_0000144 ; owl:annotatedTarget "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])"@en . [] obo:IAO_0010000 ; a owl:Axiom ; owl:annotatedProperty obo:IAO_0000602 ; owl:annotatedSource obo:BFO_0000144 ; owl:annotatedTarget "(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] " . [] obo:IAO_0010000 ; a owl:Axiom ; owl:annotatedProperty obo:IAO_0000602 ; owl:annotatedSource obo:BFO_0000144 ; owl:annotatedTarget "(iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002] " . [] obo:IAO_0010000 ; a owl:Axiom ; owl:annotatedProperty obo:IAO_0000115 ; owl:annotatedSource obo:BFO_0000145 ; owl:annotatedTarget "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])"@en . [] obo:IAO_0010000 ; a owl:Axiom ; owl:annotatedProperty obo:IAO_0000602 ; owl:annotatedSource obo:BFO_0000145 ; owl:annotatedTarget "(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] " . [] obo:IAO_0010000 ; a owl:Axiom ; owl:annotatedProperty obo:IAO_0000600 ; owl:annotatedSource obo:BFO_0000146 ; owl:annotatedTarget "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])"@en . [] obo:IAO_0010000 ; a owl:Axiom ; owl:annotatedProperty obo:IAO_0000602 ; owl:annotatedSource obo:BFO_0000146 ; owl:annotatedTarget "(iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001] " . [] obo:IAO_0010000 ; a owl:Axiom ; rdfs:comment "requested by Melanie Courtot" ; rdfs:seeAlso ; owl:annotatedProperty obo:IAO_0000116 ; owl:annotatedSource obo:BFO_0000147 ; owl:annotatedTarget "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."@en . [] obo:IAO_0010000 ; a owl:Axiom ; owl:annotatedProperty obo:IAO_0000600 ; owl:annotatedSource obo:BFO_0000147 ; owl:annotatedTarget "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])"@en . [] obo:IAO_0010000 ; a owl:Axiom ; owl:annotatedProperty obo:IAO_0000602 ; owl:annotatedSource obo:BFO_0000147 ; owl:annotatedTarget "(iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001] " . [] obo:IAO_0010000 ; a owl:Axiom ; owl:annotatedProperty obo:IAO_0000600 ; owl:annotatedSource obo:BFO_0000148 ; owl:annotatedTarget "A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001])"@en . [] obo:IAO_0010000 ; a owl:Axiom ; owl:annotatedProperty obo:IAO_0000602 ; owl:annotatedSource obo:BFO_0000148 ; owl:annotatedTarget "(forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001] " . [] obo:IAO_0010000 ; a owl:Axiom ; owl:annotatedProperty obo:IAO_0000600 ; owl:annotatedSource obo:BFO_0000182 ; owl:annotatedTarget "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])"@en . [] 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." ; a owl:Axiom ; owl:annotatedProperty rdfs:domain ; owl:annotatedSource obo:RO_0001025 ; owl:annotatedTarget obo:BFO_0000004 . [] 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." ; a owl:Axiom ; owl:annotatedProperty rdfs:range ; owl:annotatedSource obo:RO_0001025 ; owl:annotatedTarget obo:BFO_0000004 . [] obo:IAO_0010000 ; a owl:Axiom ; rdfs:comment "per discussion with Barry Smith" ; rdfs:seeAlso ; owl:annotatedProperty obo:IAO_0000116 ; owl:annotatedSource obo:BFO_0000001 ; owl:annotatedTarget "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"@en . [] obo:IAO_0010000 ; a owl:Axiom ; owl:annotatedProperty obo:IAO_0000600 ; owl:annotatedSource obo:BFO_0000001 ; owl:annotatedTarget "An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])"@en . [] obo:IAO_0010000 ; a owl:Axiom ; owl:annotatedProperty obo:IAO_0000116 ; owl:annotatedSource obo:BFO_0000002 ; owl:annotatedTarget "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"@en . [] obo:IAO_0010000 ; a owl:Axiom ; owl:annotatedProperty obo:IAO_0000600 ; owl:annotatedSource obo:BFO_0000002 ; owl:annotatedTarget "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])"@en . [] obo:IAO_0010000 ; a owl:Axiom ; owl:annotatedProperty obo:IAO_0000601 ; owl:annotatedSource obo:BFO_0000002 ; owl:annotatedTarget "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])"@en . [] a owl:AllDifferent ; owl:distinctMembers (obo:IAO_0000120 obo:IAO_0000121 obo:IAO_0000122 obo:IAO_0000123 obo:IAO_0000124 obo:IAO_0000125 obo:IAO_0000423 obo:IAO_0000428 ) . [] obo:IAO_0010000 ; a owl:Axiom ; owl:annotatedProperty obo:IAO_0000601 ; owl:annotatedSource obo:BFO_0000002 ; owl:annotatedTarget "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])"@en . [] a owl:AllDifferent ; owl:distinctMembers (obo:IAO_0000226 obo:IAO_0000227 obo:IAO_0000228 obo:IAO_0000229 ) . [] obo:IAO_0010000 ; a owl:Axiom ; owl:annotatedProperty obo:IAO_0000601 ; owl:annotatedSource obo:BFO_0000002 ; owl:annotatedTarget "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])"@en . [] obo:IAO_0010000 ; a owl:Axiom ; owl:annotatedProperty obo:IAO_0000602 ; owl:annotatedSource obo:BFO_0000002 ; owl:annotatedTarget "(forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] " . [] obo:IAO_0010000 ; a owl:Axiom ; owl:annotatedProperty obo:IAO_0000602 ; owl:annotatedSource obo:BFO_0000002 ; owl:annotatedTarget "(forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] " . [] obo:IAO_0010000 ; a owl:Axiom ; owl:annotatedProperty obo:IAO_0000602 ; owl:annotatedSource obo:BFO_0000002 ; owl:annotatedTarget "(forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] " . [] obo:IAO_0010000 ; a owl:Axiom ; owl:annotatedProperty obo:IAO_0000602 ; owl:annotatedSource obo:BFO_0000002 ; owl:annotatedTarget "(forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] " . [] obo:IAO_0010000 ; a owl:Axiom ; rdfs:comment "per discussion with Barry Smith" ; owl:annotatedProperty obo:IAO_0000116 ; owl:annotatedSource obo:BFO_0000003 ; owl:annotatedTarget "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."@en . [] obo:IAO_0010000 ; a owl:Axiom ; owl:annotatedProperty obo:IAO_0000116 ; owl:annotatedSource obo:BFO_0000003 ; owl:annotatedTarget "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." . [] obo:IAO_0010000 ; a owl:Axiom ; owl:annotatedProperty obo:IAO_0000600 ; owl:annotatedSource obo:BFO_0000003 ; owl:annotatedTarget "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])"@en . [] obo:IAO_0010000 ; a owl:Axiom ; owl:annotatedProperty obo:IAO_0000601 ; owl:annotatedSource obo:BFO_0000003 ; owl:annotatedTarget "Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])"@en . [] obo:IAO_0010000 ; a owl:Axiom ; owl:annotatedProperty obo:IAO_0000601 ; owl:annotatedSource obo:BFO_0000003 ; owl:annotatedTarget "b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])"@en . [] obo:IAO_0010000 ; a owl:Axiom ; owl:annotatedProperty obo:IAO_0000602 ; owl:annotatedSource obo:BFO_0000003 ; owl:annotatedTarget "(forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] " . [] obo:IAO_0010000 ; a owl:Axiom ; owl:annotatedProperty obo:IAO_0000602 ; owl:annotatedSource obo:BFO_0000003 ; owl:annotatedTarget "(forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] " . [] obo:IAO_0010000 ; a owl:Axiom ; owl:annotatedProperty obo:IAO_0000115 ; owl:annotatedSource obo:BFO_0000004 ; owl:annotatedTarget "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])"@en . [] obo:IAO_0010000 ; a owl:Axiom ; owl:annotatedProperty obo:IAO_0000601 ; owl:annotatedSource obo:BFO_0000004 ; owl:annotatedTarget "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])"@en . [] obo:IAO_0010000 ; a owl:Axiom ; owl:annotatedProperty obo:IAO_0000601 ; owl:annotatedSource obo:BFO_0000004 ; owl:annotatedTarget "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])"@en . [] obo:IAO_0010000 ; a owl:Axiom ; owl:annotatedProperty obo:IAO_0000602 ; owl:annotatedSource obo:BFO_0000004 ; owl:annotatedTarget "(forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] " . [] obo:IAO_0010000 ; a owl:Axiom ; owl:annotatedProperty obo:IAO_0000602 ; owl:annotatedSource obo:BFO_0000004 ; owl:annotatedTarget "(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] " . [] obo:IAO_0010000 ; a owl:Axiom ; owl:annotatedProperty obo:IAO_0000602 ; owl:annotatedSource obo:BFO_0000004 ; owl:annotatedTarget "(iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] " . [] obo:IAO_0010000 ; a owl:Axiom ; rdfs:comment "per discussion with Barry Smith" ; owl:annotatedProperty obo:IAO_0000116 ; owl:annotatedSource obo:BFO_0000006 ; owl:annotatedTarget "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."@en . [] obo:IAO_0010000 ; a owl:Axiom ; owl:annotatedProperty obo:IAO_0000600 ; owl:annotatedSource obo:BFO_0000006 ; owl:annotatedTarget "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])"@en . [] obo:IAO_0010000 ; a owl:Axiom ; owl:annotatedProperty obo:IAO_0000601 ; owl:annotatedSource obo:BFO_0000006 ; owl:annotatedTarget "All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001])"@en . [] obo:IAO_0010000 ; a owl:Axiom ; owl:annotatedProperty obo:IAO_0000602 ; owl:annotatedSource obo:BFO_0000006 ; owl:annotatedTarget "(forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001] " . [] obo:IAO_0010000 ; a owl:Axiom ; owl:annotatedProperty obo:IAO_0000602 ; owl:annotatedSource obo:BFO_0000006 ; owl:annotatedTarget "(forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001] " . [] obo:IAO_0010000 ; a owl:Axiom ; rdfs:comment "per discussion with Barry Smith" ; owl:annotatedProperty obo:IAO_0000116 ; owl:annotatedSource obo:BFO_0000008 ; owl:annotatedTarget "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"@en . [] obo:IAO_0010000 ; a owl:Axiom ; owl:annotatedProperty obo:IAO_0000600 ; owl:annotatedSource obo:BFO_0000008 ; owl:annotatedTarget "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])"@en . [] obo:IAO_0010000 ; a owl:Axiom ; owl:annotatedProperty obo:IAO_0000601 ; owl:annotatedSource obo:BFO_0000008 ; owl:annotatedTarget "All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001])"@en . [] obo:IAO_0010000 ; a owl:Axiom ; owl:annotatedProperty obo:IAO_0000601 ; owl:annotatedSource obo:BFO_0000008 ; owl:annotatedTarget "Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002])"@en . [] obo:IAO_0010000 ; a owl:Axiom ; owl:annotatedProperty obo:IAO_0000602 ; owl:annotatedSource obo:BFO_0000008 ; owl:annotatedTarget "(forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002] " . [] obo:IAO_0010000 ; a owl:Axiom ; owl:annotatedProperty obo:IAO_0000602 ; owl:annotatedSource obo:BFO_0000008 ; owl:annotatedTarget "(forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001] " . [] obo:IAO_0010000 ; a owl:Axiom ; owl:annotatedProperty obo:IAO_0000602 ; owl:annotatedSource obo:BFO_0000008 ; owl:annotatedTarget "(forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001] " . [] obo:IAO_0010000 ; a owl:Axiom ; owl:annotatedProperty obo:IAO_0000600 ; owl:annotatedSource obo:BFO_0000009 ; owl:annotatedTarget "A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001])"@en . [] obo:IAO_0010000 ; a owl:Axiom ; owl:annotatedProperty obo:IAO_0000602 ; owl:annotatedSource obo:BFO_0000009 ; owl:annotatedTarget "(forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001] " . [] obo:IAO_0010000 ; a owl:Axiom ; owl:annotatedProperty obo:IAO_0000600 ; owl:annotatedSource obo:BFO_0000011 ; owl:annotatedTarget "A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001])"@en . [] obo:IAO_0010000 ; a owl:Axiom ; owl:annotatedProperty obo:IAO_0000601 ; owl:annotatedSource obo:BFO_0000011 ; owl:annotatedTarget "All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001])"@en . [] obo:IAO_0010000 ; a owl:Axiom ; owl:annotatedProperty obo:IAO_0000601 ; owl:annotatedSource obo:BFO_0000011 ; owl:annotatedTarget "Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001])"@en . [] obo:IAO_0010000 ; a owl:Axiom ; owl:annotatedProperty obo:IAO_0000601 ; owl:annotatedSource obo:BFO_0000011 ; owl:annotatedTarget "Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001])"@en . [] obo:IAO_0010000 ; a owl:Axiom ; owl:annotatedProperty obo:IAO_0000601 ; owl:annotatedSource obo:BFO_0000011 ; owl:annotatedTarget "Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002])"@en . [] obo:IAO_0010000 ; a owl:Axiom ; owl:annotatedProperty obo:IAO_0000602 ; owl:annotatedSource obo:BFO_0000011 ; owl:annotatedTarget "(forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002] " . [] obo:IAO_0010000 ; a owl:Axiom ; owl:annotatedProperty obo:IAO_0000602 ; owl:annotatedSource obo:BFO_0000011 ; owl:annotatedTarget "(forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001] " . [] obo:IAO_0010000 ; a owl:Axiom ; owl:annotatedProperty obo:IAO_0000602 ; owl:annotatedSource obo:BFO_0000011 ; owl:annotatedTarget "(forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001] " . [] obo:IAO_0010000 ; a owl:Axiom ; owl:annotatedProperty obo:IAO_0000602 ; owl:annotatedSource obo:BFO_0000011 ; owl:annotatedTarget "(forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001] " . [] obo:IAO_0010000 ; a owl:Axiom ; owl:annotatedProperty obo:IAO_0000602 ; owl:annotatedSource obo:BFO_0000011 ; owl:annotatedTarget "(forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001] " . [] obo:IAO_0010000 ; a owl:Axiom ; owl:annotatedProperty obo:IAO_0000115 ; owl:annotatedSource obo:BFO_0000015 ; owl:annotatedTarget "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])"@en . [] obo:IAO_0010000 ; a owl:Axiom ; owl:annotatedProperty obo:IAO_0000602 ; owl:annotatedSource obo:BFO_0000015 ; owl:annotatedTarget "(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] " . [] obo:IAO_0010000 ; a owl:Axiom ; owl:annotatedProperty obo:IAO_0000600 ; owl:annotatedSource obo:BFO_0000016 ; owl:annotatedTarget "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])"@en . [] obo:IAO_0010000 ; a owl:Axiom ; owl:annotatedProperty obo:IAO_0000601 ; owl:annotatedSource obo:BFO_0000016 ; owl:annotatedTarget "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])"@en . [] obo:IAO_0010000 ; a owl:Axiom ; owl:annotatedProperty obo:IAO_0000602 ; owl:annotatedSource obo:BFO_0000016 ; owl:annotatedTarget "(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] " . [] obo:IAO_0010000 ; a owl:Axiom ; owl:annotatedProperty obo:IAO_0000602 ; owl:annotatedSource obo:BFO_0000016 ; owl:annotatedTarget "(forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] " . [] obo:IAO_0010000 ; a owl:Axiom ; owl:annotatedProperty obo:IAO_0000600 ; owl:annotatedSource obo:BFO_0000017 ; owl:annotatedTarget "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])"@en . [] obo:IAO_0010000 ; a owl:Axiom ; owl:annotatedProperty obo:IAO_0000601 ; owl:annotatedSource obo:BFO_0000017 ; owl:annotatedTarget "All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])"@en . [] obo:IAO_0010000 ; a owl:Axiom ; owl:annotatedProperty obo:IAO_0000602 ; owl:annotatedSource obo:BFO_0000017 ; owl:annotatedTarget "(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] " . [] obo:IAO_0010000 ; a owl:Axiom ; owl:annotatedProperty obo:IAO_0000602 ; owl:annotatedSource obo:BFO_0000017 ; owl:annotatedTarget "(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] " . [] obo:IAO_0010000 ; a owl:Axiom ; owl:annotatedProperty obo:IAO_0000600 ; owl:annotatedSource obo:BFO_0000018 ; owl:annotatedTarget "A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001])"@en . [] obo:IAO_0010000 ; a owl:Axiom ; owl:annotatedProperty obo:IAO_0000602 ; owl:annotatedSource obo:BFO_0000018 ; owl:annotatedTarget "(forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001] " . [] obo:IAO_0010000 ; a owl:Axiom ; owl:annotatedProperty obo:IAO_0000600 ; owl:annotatedSource obo:BFO_0000019 ; owl:annotatedTarget "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])"@en . [] obo:IAO_0010000 ; a owl:Axiom ; owl:annotatedProperty obo:IAO_0000601 ; owl:annotatedSource obo:BFO_0000019 ; owl:annotatedTarget "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])"@en . [] obo:IAO_0010000 ; a owl:Axiom ; owl:annotatedProperty obo:IAO_0000602 ; owl:annotatedSource obo:BFO_0000019 ; owl:annotatedTarget "(forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] " . [] obo:IAO_0010000 ; a owl:Axiom ; owl:annotatedProperty obo:IAO_0000602 ; owl:annotatedSource obo:BFO_0000019 ; owl:annotatedTarget "(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] " . [] obo:IAO_0010000 ; a owl:Axiom ; owl:annotatedProperty obo:IAO_0000115 ; owl:annotatedSource obo:BFO_0000020 ; owl:annotatedTarget "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])"@en . [] obo:IAO_0010000 ; a owl:Axiom ; rdfs:comment "per discussion with Barry Smith" ; owl:annotatedProperty obo:IAO_0000116 ; owl:annotatedSource obo:BFO_0000020 ; owl:annotatedTarget "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."@en . [] obo:IAO_0010000 ; a owl:Axiom ; owl:annotatedProperty obo:IAO_0000602 ; owl:annotatedSource obo:BFO_0000020 ; owl:annotatedTarget "(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] " . [] obo:IAO_0010000 ; a owl:Axiom ; owl:annotatedProperty obo:IAO_0000600 ; owl:annotatedSource obo:BFO_0000023 ; owl:annotatedTarget "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])"@en . [] obo:IAO_0010000 ; a owl:Axiom ; owl:annotatedProperty obo:IAO_0000602 ; owl:annotatedSource obo:BFO_0000023 ; owl:annotatedTarget "(forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] " . [] obo:IAO_0010000 ; a owl:Axiom ; owl:annotatedProperty obo:IAO_0000600 ; owl:annotatedSource obo:BFO_0000024 ; owl:annotatedTarget "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])"@en . [] obo:IAO_0010000 ; a owl:Axiom ; owl:annotatedProperty obo:IAO_0000602 ; owl:annotatedSource obo:BFO_0000024 ; owl:annotatedTarget "(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] " . [] obo:IAO_0010000 ; a owl:Axiom ; owl:annotatedProperty obo:IAO_0000600 ; owl:annotatedSource obo:BFO_0000026 ; owl:annotatedTarget "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])"@en . [] obo:IAO_0010000 ; a owl:Axiom ; owl:annotatedProperty obo:IAO_0000602 ; owl:annotatedSource obo:BFO_0000026 ; owl:annotatedTarget "(forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001] " . [] obo:IAO_0010000 ; a owl:Axiom ; owl:annotatedProperty obo:IAO_0000116 ; owl:annotatedSource obo:BFO_0000027 ; owl:annotatedTarget "An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects " . [] obo:IAO_0010000 ; a owl:Axiom ; owl:annotatedProperty obo:IAO_0000116 ; owl:annotatedSource obo:BFO_0000027 ; owl:annotatedTarget "An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects " . [] obo:IAO_0010000 ; a owl:Axiom ; owl:annotatedProperty obo:IAO_0000119 ; owl:annotatedSource obo:BFO_0000027 ; owl:annotatedTarget "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." .