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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" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. 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See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", "val" : "http://purl.obolibrary.org/obo/agro.owl" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", "val" : "http://purl.obolibrary.org/obo/dron.owl" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", "val" : "http://purl.obolibrary.org/obo/ecocore.owl" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", "val" : "http://purl.obolibrary.org/obo/envo.owl" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", "val" : "http://purl.obolibrary.org/obo/obi.owl" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", "val" : "An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" } ] } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000002", "lbl" : "continuant", "type" : "CLASS", "meta" : { "definition" : { "val" : "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." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", "val" : "continuant" }, { "pred" : "http://purl.obolibrary.org/obo/BFO_0000180", "val" : "Continuant" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "continuant" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "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" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "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" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", "val" : "http://purl.obolibrary.org/obo/agro.owl" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", "val" : "http://purl.obolibrary.org/obo/dron.owl" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", "val" : "http://purl.obolibrary.org/obo/envo.owl" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", "val" : "http://purl.obolibrary.org/obo/obi.owl" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", "val" : "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])" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", "val" : "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])" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", "val" : "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])" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", "val" : "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])" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", "val" : "(forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] " }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", "val" : "(forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] " }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", "val" : "(forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] " }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", "val" : "(forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] " }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" } ] } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000003", "lbl" : "occurrent", "type" : "CLASS", "meta" : { "definition" : { "val" : "An entity that has temporal parts and that happens, unfolds or develops through time." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", "val" : "occurrent" }, { "pred" : "http://purl.obolibrary.org/obo/BFO_0000180", "val" : "Occurrent" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "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" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "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." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "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." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "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." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", "val" : "http://purl.obolibrary.org/obo/agro.owl" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", "val" : "http://purl.obolibrary.org/obo/ecocore.owl" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", "val" : "http://purl.obolibrary.org/obo/envo.owl" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", "val" : "http://purl.obolibrary.org/obo/obi.owl" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", "val" : "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])" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", "val" : "Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", "val" : "b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", "val" : "(forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] " }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", "val" : "(forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] " }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" } ] } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000004", "lbl" : "independent continuant", "type" : "CLASS", "meta" : { "definition" : { "val" : "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])" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", "val" : "ic" }, { "pred" : "http://purl.obolibrary.org/obo/BFO_0000180", "val" : "IndependentContinuant" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "a chair" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "a heart" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "a leg" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "a molecule" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "a spatial region" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "an atom" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "an orchestra." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "an organism" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the bottom right portion of a human torso" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the interior of your mouth" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", "val" : "http://purl.obolibrary.org/obo/agro.owl" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", "val" : "http://purl.obolibrary.org/obo/dron.owl" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", "val" : "http://purl.obolibrary.org/obo/envo.owl" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", "val" : "http://purl.obolibrary.org/obo/obi.owl" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", "val" : "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])" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", "val" : "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])" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", "val" : "(forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] " }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", "val" : "(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] " }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", "val" : "(iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] " }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" } ] } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000006", "lbl" : "spatial region", "type" : "CLASS" }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000008", "lbl" : "temporal region", "type" : "CLASS", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", "val" : "t-region" }, { "pred" : "http://purl.obolibrary.org/obo/BFO_0000180", "val" : "TemporalRegion" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "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" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", "val" : "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])" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", "val" : "All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001])" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", "val" : "Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002])" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", "val" : "(forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002] " }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", "val" : "(forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001] " }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", "val" : "(forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001] " }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" } ] } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000015", "lbl" : "process", "type" : "CLASS", "meta" : { "definition" : { "val" : "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])" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", "val" : "process" }, { "pred" : "http://purl.obolibrary.org/obo/BFO_0000180", "val" : "Process" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "a process of cell-division, \\ a beating of the heart" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "a process of meiosis" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "a process of sleeping" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the course of a disease" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the flight of a bird" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the life of an organism" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "your process of aging." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "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)" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", "val" : "http://purl.obolibrary.org/obo/agro.owl" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", "val" : "http://purl.obolibrary.org/obo/cob.owl" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", "val" : "http://purl.obolibrary.org/obo/ecocore.owl" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", "val" : "http://purl.obolibrary.org/obo/envo.owl" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", "val" : "http://purl.obolibrary.org/obo/obi.owl" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", "val" : "(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] " }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "source" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" } ] } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000016", "lbl" : "disposition", "type" : "CLASS", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", "val" : "disposition" }, { "pred" : "http://purl.obolibrary.org/obo/BFO_0000180", "val" : "Disposition" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "an atom of element X has the disposition to decay to an atom of element Y" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "certain people have a predisposition to colon cancer" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "children are innately disposed to categorize objects in certain ways." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the cell wall is disposed to filter chemicals in endocytosis and exocytosis" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "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." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", "val" : "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])" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", "val" : "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])" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", "val" : "(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] " }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", "val" : "(forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] " }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" } ] } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000017", "lbl" : "realizable entity", "type" : "CLASS", "meta" : { "definition" : { "val" : "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." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", "val" : "realizable" }, { "pred" : "http://purl.obolibrary.org/obo/BFO_0000180", "val" : "RealizableEntity" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the disposition of this piece of metal to conduct electricity." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the disposition of your blood to coagulate" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the function of your reproductive organs" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the role of being a doctor" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the role of this boundary to delineate where Utah and Colorado meet" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", "val" : "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])" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", "val" : "All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", "val" : "(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] " }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", "val" : "(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] " }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" } ] } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000019", "lbl" : "quality", "type" : "CLASS", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", "val" : "quality" }, { "pred" : "http://purl.obolibrary.org/obo/BFO_0000180", "val" : "Quality" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the ambient temperature of this portion of air" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the color of a tomato" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the length of the circumference of your waist" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the mass of this piece of gold." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the shape of your nose" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the shape of your nostril" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", "val" : "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])" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", "val" : "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])" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", "val" : "(forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] " }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", "val" : "(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] " }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" } ] } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000020", "lbl" : "specifically dependent continuant", "type" : "CLASS", "meta" : { "definition" : { "val" : "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])" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", "val" : "sdc" }, { "pred" : "http://purl.obolibrary.org/obo/BFO_0000180", "val" : "SpecificallyDependentContinuant" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "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" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "of one-sided specifically dependent continuants: the mass of this tomato" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "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." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the disposition of this fish to decay" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the function of this heart: to pump blood" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the mutual dependence of proton donors and acceptors in chemical reactions [79" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the pink color of a medium rare piece of grilled filet mignon at its center" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the role of being a doctor" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the shape of this hole." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the smell of this portion of mozzarella" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "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." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", "val" : "(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] " }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" } ] } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000023", "lbl" : "role", "type" : "CLASS", "meta" : { "definition" : { "val" : "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." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", "val" : "role" }, { "pred" : "http://purl.obolibrary.org/obo/BFO_0000180", "val" : "Role" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "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." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the priest role" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the role of a boundary to demarcate two neighboring administrative territories" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the role of a building in serving as a military target" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the role of a stone in marking a property boundary" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the role of subject in a clinical trial" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the student role" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "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." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", "val" : "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])" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", "val" : "(forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] " }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" } ] } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000024", "lbl" : "fiat object part", "type" : "CLASS", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", "val" : "fiat-object-part" }, { "pred" : "http://purl.obolibrary.org/obo/BFO_0000180", "val" : "FiatObjectPart" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "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" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the FMA:regional parts of an intact human body." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the Western hemisphere of the Earth" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the division of the brain into regions" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the division of the planet into hemispheres" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the dorsal and ventral surfaces of the body" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the upper and lower lobes of the left lung" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "BFO 2 Reference: Most examples of fiat object parts are associated with theoretically drawn divisions" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", "val" : "http://purl.obolibrary.org/obo/envo.owl" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", "val" : "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])" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", "val" : "(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] " }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" } ] } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000027", "lbl" : "object aggregate", "type" : "CLASS" }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000029", "lbl" : "site", "type" : "CLASS" }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000030", "lbl" : "object", "type" : "CLASS" }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000031", "lbl" : "generically dependent continuant", "type" : "CLASS", "meta" : { "definition" : { "val" : "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])" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", "val" : "gdc" }, { "pred" : "http://purl.obolibrary.org/obo/BFO_0000180", "val" : "GenericallyDependentContinuant" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "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." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the pdf file on your laptop, the pdf file that is a copy thereof on my laptop" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", "val" : "http://purl.obolibrary.org/obo/obi.owl" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", "val" : "(iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] " }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" } ] } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000034", "lbl" : "function", "type" : "CLASS", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", "val" : "function" }, { "pred" : "http://purl.obolibrary.org/obo/BFO_0000180", "val" : "Function" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the function of a hammer to drive in nails" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the function of a heart pacemaker to regulate the beating of a heart through electricity" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the function of amylase in saliva to break down starch into sugar" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "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." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", "val" : "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])" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", "val" : "(forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] " }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" } ] } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000038", "lbl" : "one-dimensional temporal region", "type" : "CLASS", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", "val" : "1d-t-region" }, { "pred" : "http://purl.obolibrary.org/obo/BFO_0000180", "val" : "OneDimensionalTemporalRegion" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the temporal region during which a process occurs." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "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)." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", "val" : "A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001])" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", "val" : "(forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001] " }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" } ] } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000040", "lbl" : "material entity", "type" : "CLASS", "meta" : { "definition" : { "val" : "An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", "val" : "material" }, { "pred" : "http://purl.obolibrary.org/obo/BFO_0000180", "val" : "MaterialEntity" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "material entity" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "material entity" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "a flame" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "a forest fire" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "a human being" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "a hurricane" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "a photon" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "a puff of smoke" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "a sea wave" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "a tornado" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "an aggregate of human beings." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "an energy wave" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "an epidemic" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the undetached arm of a human being" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "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" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "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." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "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." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", "val" : "http://purl.obolibrary.org/obo/cdno.owl" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", "val" : "http://purl.obolibrary.org/obo/dron.owl" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", "val" : "http://purl.obolibrary.org/obo/envo.owl" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", "val" : "http://purl.obolibrary.org/obo/obi.owl" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", "val" : "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])" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", "val" : "Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", "val" : "every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", "val" : "(forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] " }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", "val" : "(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] " }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", "val" : "(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] " }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "bfo" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" } ] } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000050", "lbl" : "part_of", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "a core relation that holds between a part and its whole" }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_gp2term", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "xrefs" : [ { "val" : "BFO:0000050" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "is part of" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "my brain is part of my body (continuant parthood, two material entities)" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "this day is part of this year (occurrent parthood)" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "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." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "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" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)\n\nA continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "part_of" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", "val" : "http://purl.obolibrary.org/obo/ro.owl" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0040042", "val" : "http://purl.obolibrary.org/obo/BFO_0000002" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0040042", "val" : "http://purl.obolibrary.org/obo/BFO_0000003" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0040042", "val" : "http://purl.obolibrary.org/obo/BFO_0000004" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0040042", "val" : "http://purl.obolibrary.org/obo/BFO_0000017" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0040042", "val" : "http://purl.obolibrary.org/obo/BFO_0000019" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0040042", "val" : "http://purl.obolibrary.org/obo/BFO_0000020" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0040042", "val" : "http://purl.obolibrary.org/obo/BFO_0000031" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "experimental_condition_ontology" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "quality" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "source" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "spatial" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "part_of" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://ontologydesignpatterns.org/wiki/Submissions:PartOf" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://www.obofoundry.org/ro/#OBO_REL:part_of" } ] } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000051", "lbl" : "has_part", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "a core relation that holds between a whole and its part" }, "comments" : [ "We use the has_part relation to relate complex qualities to more primitive ones. A complex quality is a collection of qualities. The complex quality cannot exist without the sub-qualities. For example, the quality 'swollen' necessarily comes with the qualities of 'protruding' and 'increased size'." ], "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "xrefs" : [ { "val" : "BFO:0000051" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "has part" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "my body has part my brain (continuant parthood, two material entities)" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "this year has part this day (occurrent parthood)" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "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." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "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" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)\n\nA continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "has_part" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", "val" : "http://purl.obolibrary.org/obo/obi.owl" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", "val" : "http://purl.obolibrary.org/obo/ro.owl" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "chebi_ontology" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "quality" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "source" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "spatial" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#is_cyclic", "val" : "false" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "has_part" } ] } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000054", "lbl" : "realized in", "type" : "PROPERTY", "meta" : { "comments" : [ "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" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "realized in" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "this disease is realized in this disease course" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "this fragility is realized in this shattering" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "this investigator role is realized in this investigation" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "is realized by" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "realized_in" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", "val" : "[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])" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" } ] } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000055", "lbl" : "realizes", "type" : "PROPERTY", "meta" : { "comments" : [ "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" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "realizes" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "this disease course realizes this disease" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "this investigation realizes this investigator role" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "this shattering realizes this fragility" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", "val" : "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])" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/iao.owl" } ] } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000062", "lbl" : "preceded_by", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "is preceded by", "xrefs" : [ "SIO:000249" ] }, { "pred" : "hasExactSynonym", "val" : "takes place after", "xrefs" : [ "Allen:precedes" ] } ], "xrefs" : [ { "val" : "BFO:0000062" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "preceded by" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "is preceded by" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "preceded_by" }, { "pred" : "http://purl.org/dc/elements/1.1/source", "val" : "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "preceded_by" } ] } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000063", "lbl" : "precedes", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "xrefs" : [ { "val" : "BFO:0000063" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "precedes" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "precedes" } ] } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000066", "lbl" : "occurs in", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "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" }, "comments" : [ "Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant" ], "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "occurs in" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "occurs_in" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "unfolds in" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "unfolds_in" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" } ] } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000067", "lbl" : "contains process", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "[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" }, "comments" : [ "Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "site of" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" } ] } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000140", "lbl" : "continuant fiat boundary", "type" : "CLASS", "meta" : { "definition" : { "val" : "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])" } } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000141", "lbl" : "immaterial entity", "type" : "CLASS" }, { "id" : "http://purl.obolibrary.org/obo/BSPO_0000120", "lbl" : "in left side of", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "X in left side of Y <=> if Y is subdivided into two left and right portions, X is part of the left portion.", "xrefs" : [ "BSPO:PATO_mtg_2009" ] }, "xrefs" : [ { "val" : "BSPO:0000120" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "spatial" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "in_left_side_of" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern" } ] } }, { "id" : "http://purl.obolibrary.org/obo/BSPO_0000121", "lbl" : "in right side of", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "X in right side of Y <=> if Y is subdivided into two left and right portions, X is part of the right portion.", "xrefs" : [ "BSPO:PATO_mtg_2009" ] }, "xrefs" : [ { "val" : "BSPO:0000121" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "spatial" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "in_right_side_of" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern" } ] } }, { "id" : "http://purl.obolibrary.org/obo/BSPO_0000126", "lbl" : "in lateral side of", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "X in lateral side of Y <=> if X is in left side of Y or X is in right side of Y. X is often, but not always a paired structure", "xrefs" : [ "UBERON:cjm" ] }, "xrefs" : [ { "val" : "BSPO:0000126" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "spatial" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "in_lateral_side_of" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://github.com/obophenotype/uberon/issues/2453" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern" } ] } }, { "id" : "http://purl.obolibrary.org/obo/CARO_0000000", "lbl" : "anatomical entity", "type" : "CLASS", "meta" : { "definition" : { "val" : "Biological entity that is either an individual member of a biological species or constitutes the structural organization of an 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