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time in which it exists at all, persists through time while maintaining its identity and has no temporal parts.", "xrefs": [] } }, "type": "CLASS" }, { "id": "http://purl.obolibrary.org/obo/BFO_0000003", "lbl": "occurrent", "meta": { "definition": { "val": "An entity that has temporal parts and that happens, unfolds or develops through time.", "xrefs": [] } }, "type": "CLASS" }, { "id": "http://purl.obolibrary.org/obo/BFO_0000004", "lbl": "independent continuant", "meta": { "definition": { "val": "A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything.", "xrefs": [] } }, "type": "CLASS" }, { "id": "http://purl.obolibrary.org/obo/BFO_0000015", "lbl": "process", "meta": { "definition": { "val": "An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t.", "xrefs": [] } }, "type": "CLASS" }, { "id": "http://purl.obolibrary.org/obo/BFO_0000017", "lbl": "realizable entity", "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.", "xrefs": [] } }, "type": "CLASS" }, { "id": "http://purl.obolibrary.org/obo/BFO_0000020", "lbl": "specifically dependent continuant", "meta": { "definition": { "val": "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.", "xrefs": [] } }, "type": "CLASS" }, { "id": "http://purl.obolibrary.org/obo/BFO_0000023", "lbl": "role", "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.", "xrefs": [] } }, "type": "CLASS" }, { "id": "http://purl.obolibrary.org/obo/BFO_0000031", "lbl": "generically dependent continuant", "meta": { "definition": { "val": "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.", "xrefs": [] } }, "type": "CLASS" }, { "id": "http://purl.obolibrary.org/obo/BFO_0000040", "lbl": "material entity", "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.", "xrefs": [] } }, "type": "CLASS" }, { "id": "http://purl.obolibrary.org/obo/BFO_0000050", "lbl": "part of", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "is part of" }, { "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 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": "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_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": "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 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": "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_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_0000118", "val": "part_of" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000412", "val": "http://purl.obolibrary.org/obo/BFO" }, { "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": "external" }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "protein" }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "quality" }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "relationship" }, { "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" } ], "definition": { "val": "a core relation that holds between a part and its whole", "xrefs": [] }, "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" ], "synonyms": [ { "pred": "hasExactSynonym", "val": "part_of", "xrefs": [] } ], "xrefs": [ { "val": "BFO:0000050" }, { "val": "OBO_REL:part_of" } ] }, "type": "PROPERTY" }, { "id": "http://purl.obolibrary.org/obo/BFO_0000051", "lbl": "has part", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "has part" }, { "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 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": "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_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": "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 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": "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_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_0000118", "val": "has_part" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000412", "val": "http://purl.obolibrary.org/obo/BFO" }, { "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": "protein" }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "quality" }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "relationship" }, { "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" } ], "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'." ], "definition": { "val": "a core relation that holds between a whole and its part", "xrefs": [] }, "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" }, { "val": "OBO_REL:has_part" } ] }, "type": "PROPERTY" }, { "id": "http://purl.obolibrary.org/obo/BFO_0000062", "lbl": "preceded by", "meta": { "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" } ], "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.", "xrefs": [] }, "subsets": [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] }, "type": "PROPERTY" }, { "id": "http://purl.obolibrary.org/obo/BFO_0000063", "lbl": "precedes", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "precedes" }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "uberon" }, { "pred": "http://www.geneontology.org/formats/oboInOwl#shorthand", "val": "precedes" }, { "pred": "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val": "http://purl.obolibrary.org/obo/bfo.owl" } ], "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.", "xrefs": [] }, "subsets": [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "xrefs": [ { "val": "BFO:0000063" } ] }, "type": "PROPERTY" }, { "id": "http://purl.obolibrary.org/obo/CARO_0000000", "lbl": "anatomical entity", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000412", "val": "http://purl.obolibrary.org/obo/caro.owl" } ] }, "type": "CLASS" }, { "id": "http://purl.obolibrary.org/obo/CHEBI_10432", "lbl": "2-naphthol", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/chebi/charge", "val": "0" }, { "pred": "http://purl.obolibrary.org/obo/chebi/formula", "val": "C10H8O" }, { "pred": "http://purl.obolibrary.org/obo/chebi/inchi", "val": "InChI=1S/C10H8O/c11-10-6-5-8-3-1-2-4-9(8)7-10/h1-7,11H" }, { "pred": "http://purl.obolibrary.org/obo/chebi/inchikey", "val": "JWAZRIHNYRIHIV-UHFFFAOYSA-N" }, { "pred": "http://purl.obolibrary.org/obo/chebi/mass", "val": "144.173" }, { "pred": "http://purl.obolibrary.org/obo/chebi/monoisotopicmass", "val": "144.05751" }, { "pred": "http://purl.obolibrary.org/obo/chebi/smiles", "val": "OC1=CC2=CC=CC=C2C=C1" }, { "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val": "chebi_ontology" } ], "definition": { "val": "A naphthol carrying a hydroxy group at position 2.", "xrefs": [] }, "subsets": [ "http://purl.obolibrary.org/obo/chebi#3_STAR" ], "synonyms": [ { "pred": "hasExactSynonym", "synonymType": "http://purl.obolibrary.org/obo/chebi#IUPAC_NAME", "val": "naphthalen-2-ol", "xrefs": [ "IUPAC" ] }, { "pred": "hasRelatedSynonym", "synonymType": "http://purl.obolibrary.org/obo/chebi#BRAND_NAME", "val": "Antioxygene BN", "xrefs": [ "HMDB" ] }, { "pred": "hasRelatedSynonym", "synonymType": "http://purl.obolibrary.org/obo/chebi#BRAND_NAME", "val": "Azogen Developer A", "xrefs": [ "HMDB" ] }, { "pred": "hasRelatedSynonym", "synonymType": "http://purl.obolibrary.org/obo/chebi#BRAND_NAME", "val": "C.I. Azoic Coupling Component 1", "xrefs": [ "ChemIDplus" ] }, { "pred": "hasRelatedSynonym", "synonymType": "http://purl.obolibrary.org/obo/chebi#BRAND_NAME", "val": "C.I. 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