{ "_embedded" : { "properties" : [ { "annotation" : { "IAO_0000116" : [ "The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch" ], "IAO_0000117" : [ "Chris Mungall" ], "IAO_0000119" : [ "http://purl.obolibrary.org/obo/ro/docs/causal-relations" ], "IAO_0000232" : [ "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." ] }, "synonyms" : null, "iri" : "http://purl.obolibrary.org/obo/RO_0002506", "label" : "causal relation between entities", "synonym" : null, "description" : null, "ontology_name" : "fbbi", "ontology_prefix" : "FBbi", "ontology_iri" : "http://ontology.data.humancellatlas.org/ontologies/fbbi", "is_obsolete" : false, "is_defining_ontology" : false, "has_children" : true, "is_root" : false, "short_form" : "RO_0002506", "obo_id" : "RO:0002506", "_links" : { "self" : { "href" : "https://ontology.staging.archive.data.humancellatlas.org:443/api/ontologies/fbbi/properties/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FRO_0002506" }, "parents" : { "href" : "https://ontology.staging.archive.data.humancellatlas.org:443/api/ontologies/fbbi/properties/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FRO_0002506/parents" }, "ancestors" : { "href" : "https://ontology.staging.archive.data.humancellatlas.org:443/api/ontologies/fbbi/properties/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FRO_0002506/ancestors" }, "jstree" : { "href" : "https://ontology.staging.archive.data.humancellatlas.org:443/api/ontologies/fbbi/properties/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FRO_0002506/jstree" }, "children" : { "href" : "https://ontology.staging.archive.data.humancellatlas.org:443/api/ontologies/fbbi/properties/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FRO_0002506/children" }, "descendants" : { "href" : "https://ontology.staging.archive.data.humancellatlas.org:443/api/ontologies/fbbi/properties/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FRO_0002506/descendants" } } }, { "annotation" : { "IAO_0000114" : [ "http://purl.obolibrary.org/obo/IAO_0000428" ], "IAO_0000115" : [ "This relation groups causal relations between material entities and causal relations between processes" ], "IAO_0000116" : [ "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative\n\nThe first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.\n\nFor the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.\n\nFor the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." ], "IAO_0000117" : [ "Chris Mungall" ], "IAO_0000232" : [ "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." ] }, "synonyms" : null, "iri" : "http://purl.obolibrary.org/obo/RO_0002410", "label" : "causally related to", "synonym" : null, "description" : null, "ontology_name" : "fbbi", "ontology_prefix" : "FBbi", "ontology_iri" : "http://ontology.data.humancellatlas.org/ontologies/fbbi", "is_obsolete" : false, "is_defining_ontology" : false, "has_children" : true, "is_root" : true, "short_form" : "RO_0002410", "obo_id" : "RO:0002410", "_links" : { "self" : { "href" : "https://ontology.staging.archive.data.humancellatlas.org:443/api/ontologies/fbbi/properties/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FRO_0002410" }, "children" : { "href" : "https://ontology.staging.archive.data.humancellatlas.org:443/api/ontologies/fbbi/properties/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FRO_0002410/children" }, "descendants" : { "href" : "https://ontology.staging.archive.data.humancellatlas.org:443/api/ontologies/fbbi/properties/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FRO_0002410/descendants" } } }, { "annotation" : { }, "synonyms" : null, "iri" : "http://purl.obolibrary.org/obo/IAO_0000114", "label" : "IAO_0000114", "synonym" : null, "description" : null, "ontology_name" : "fbbi", "ontology_prefix" : "FBbi", "ontology_iri" : "http://ontology.data.humancellatlas.org/ontologies/fbbi", "is_obsolete" : false, "is_defining_ontology" : false, "has_children" : false, "is_root" : true, "short_form" : "IAO_0000114", "obo_id" : "IAO:0000114", "_links" : { "self" : { "href" : "https://ontology.staging.archive.data.humancellatlas.org:443/api/ontologies/fbbi/properties/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FIAO_0000114" } } }, { "annotation" : { }, "synonyms" : null, "iri" : "http://www.w3.org/2002/07/owl#TopObjectProperty", "label" : "TopObjectProperty", "synonym" : null, "description" : null, "ontology_name" : "fbbi", "ontology_prefix" : "FBbi", "ontology_iri" : "http://ontology.data.humancellatlas.org/ontologies/fbbi", "is_obsolete" : false, "is_defining_ontology" : false, "has_children" : false, "is_root" : true, "short_form" : "TopObjectProperty", "obo_id" : null, "_links" : { "self" : { "href" : "https://ontology.staging.archive.data.humancellatlas.org:443/api/ontologies/fbbi/properties/http%253A%252F%252Fwww.w3.org%252F2002%252F07%252Fowl%2523TopObjectProperty" } } }, { "annotation" : { }, "synonyms" : null, "iri" : "http://purl.obolibrary.org/obo/IAO_0000115", "label" : "IAO_0000115", "synonym" : null, "description" : null, "ontology_name" : "fbbi", "ontology_prefix" : "FBbi", "ontology_iri" : "http://ontology.data.humancellatlas.org/ontologies/fbbi", "is_obsolete" : false, "is_defining_ontology" : false, "has_children" : false, "is_root" : true, "short_form" : "IAO_0000115", "obo_id" : "IAO:0000115", "_links" : { "self" : { "href" : "https://ontology.staging.archive.data.humancellatlas.org:443/api/ontologies/fbbi/properties/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FIAO_0000115" } } }, { "annotation" : { "IAO_0000111" : [ "preceded by" ], "IAO_0000115" : [ "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." ], "IAO_0000116" : [ "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." ], "IAO_0000118" : [ "is preceded by", "preceded_by" ], "source" : [ "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" ] }, "synonyms" : null, "iri" : "http://purl.obolibrary.org/obo/BFO_0000062", "label" : "preceded by", "synonym" : null, "description" : null, "ontology_name" : "fbbi", "ontology_prefix" : "FBbi", "ontology_iri" : "http://ontology.data.humancellatlas.org/ontologies/fbbi", "is_obsolete" : false, "is_defining_ontology" : false, "has_children" : true, "is_root" : false, "short_form" : "BFO_0000062", "obo_id" : "BFO:0000062", "_links" : { "self" : { "href" : "https://ontology.staging.archive.data.humancellatlas.org:443/api/ontologies/fbbi/properties/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FBFO_0000062" }, "parents" : { "href" : "https://ontology.staging.archive.data.humancellatlas.org:443/api/ontologies/fbbi/properties/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FBFO_0000062/parents" }, "ancestors" : { "href" : "https://ontology.staging.archive.data.humancellatlas.org:443/api/ontologies/fbbi/properties/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FBFO_0000062/ancestors" }, "jstree" : { "href" : "https://ontology.staging.archive.data.humancellatlas.org:443/api/ontologies/fbbi/properties/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FBFO_0000062/jstree" }, "children" : { "href" : "https://ontology.staging.archive.data.humancellatlas.org:443/api/ontologies/fbbi/properties/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FBFO_0000062/children" }, "descendants" : { "href" : "https://ontology.staging.archive.data.humancellatlas.org:443/api/ontologies/fbbi/properties/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FBFO_0000062/descendants" } } }, { "annotation" : { "IAO_0000117" : [ "David Osumi-Sutherland" ], "comment" : [ "X ends_after Y iff: end(Y) before_or_simultaneous_with end(X)" ] }, "synonyms" : null, "iri" : "http://purl.obolibrary.org/obo/RO_0002086", "label" : "ends after", "synonym" : null, "description" : null, "ontology_name" : "fbbi", "ontology_prefix" : "FBbi", "ontology_iri" : "http://ontology.data.humancellatlas.org/ontologies/fbbi", "is_obsolete" : false, "is_defining_ontology" : false, "has_children" : true, "is_root" : false, "short_form" : "RO_0002086", "obo_id" : "RO:0002086", "_links" : { "self" : { "href" : "https://ontology.staging.archive.data.humancellatlas.org:443/api/ontologies/fbbi/properties/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FRO_0002086" }, "parents" : { "href" : "https://ontology.staging.archive.data.humancellatlas.org:443/api/ontologies/fbbi/properties/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FRO_0002086/parents" }, "ancestors" : { "href" : "https://ontology.staging.archive.data.humancellatlas.org:443/api/ontologies/fbbi/properties/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FRO_0002086/ancestors" }, "jstree" : { "href" : "https://ontology.staging.archive.data.humancellatlas.org:443/api/ontologies/fbbi/properties/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FRO_0002086/jstree" }, "children" : { "href" : "https://ontology.staging.archive.data.humancellatlas.org:443/api/ontologies/fbbi/properties/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FRO_0002086/children" }, "descendants" : { "href" : "https://ontology.staging.archive.data.humancellatlas.org:443/api/ontologies/fbbi/properties/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FRO_0002086/descendants" } } }, { "annotation" : { }, "synonyms" : null, "iri" : "http://purl.obolibrary.org/obo/IAO_0000116", "label" : "IAO_0000116", "synonym" : null, "description" : null, "ontology_name" : "fbbi", "ontology_prefix" : "FBbi", "ontology_iri" : "http://ontology.data.humancellatlas.org/ontologies/fbbi", "is_obsolete" : false, "is_defining_ontology" : false, "has_children" : false, "is_root" : true, "short_form" : "IAO_0000116", "obo_id" : "IAO:0000116", "_links" : { "self" : { "href" : "https://ontology.staging.archive.data.humancellatlas.org:443/api/ontologies/fbbi/properties/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FIAO_0000116" } } }, { "annotation" : { "IAO_0000111" : [ "precedes" ], "IAO_0000115" : [ "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." ] }, "synonyms" : null, "iri" : "http://purl.obolibrary.org/obo/BFO_0000063", "label" : "precedes", "synonym" : null, "description" : null, "ontology_name" : "fbbi", "ontology_prefix" : "FBbi", "ontology_iri" : "http://ontology.data.humancellatlas.org/ontologies/fbbi", "is_obsolete" : false, "is_defining_ontology" : false, "has_children" : true, "is_root" : false, "short_form" : "BFO_0000063", "obo_id" : "BFO:0000063", "_links" : { "self" : { "href" : "https://ontology.staging.archive.data.humancellatlas.org:443/api/ontologies/fbbi/properties/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FBFO_0000063" }, "parents" : { "href" : "https://ontology.staging.archive.data.humancellatlas.org:443/api/ontologies/fbbi/properties/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FBFO_0000063/parents" }, "ancestors" : { "href" : "https://ontology.staging.archive.data.humancellatlas.org:443/api/ontologies/fbbi/properties/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FBFO_0000063/ancestors" }, "jstree" : { "href" : "https://ontology.staging.archive.data.humancellatlas.org:443/api/ontologies/fbbi/properties/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FBFO_0000063/jstree" }, "children" : { "href" : "https://ontology.staging.archive.data.humancellatlas.org:443/api/ontologies/fbbi/properties/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FBFO_0000063/children" }, "descendants" : { "href" : "https://ontology.staging.archive.data.humancellatlas.org:443/api/ontologies/fbbi/properties/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FBFO_0000063/descendants" } } }, { "annotation" : { "IAO_0000114" : [ "http://purl.obolibrary.org/obo/IAO_0000125" ], "IAO_0000117" : [ "Chris Mungall" ], "IAO_0000119" : [ "https://en.wikipedia.org/wiki/Allen%27s_interval_algebra" ], "IAO_0000232" : [ "Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends." ], "comment" : [ "A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations." ], "source" : [ "https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1" ] }, "synonyms" : null, "iri" : "http://purl.obolibrary.org/obo/RO_0002222", "label" : "temporally related to", "synonym" : null, "description" : null, "ontology_name" : "fbbi", "ontology_prefix" : "FBbi", "ontology_iri" : "http://ontology.data.humancellatlas.org/ontologies/fbbi", "is_obsolete" : false, "is_defining_ontology" : false, "has_children" : true, "is_root" : true, "short_form" : "RO_0002222", "obo_id" : "RO:0002222", "_links" : { "self" : { "href" : "https://ontology.staging.archive.data.humancellatlas.org:443/api/ontologies/fbbi/properties/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FRO_0002222" }, "children" : { "href" : "https://ontology.staging.archive.data.humancellatlas.org:443/api/ontologies/fbbi/properties/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FRO_0002222/children" }, "descendants" : { "href" : "https://ontology.staging.archive.data.humancellatlas.org:443/api/ontologies/fbbi/properties/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FRO_0002222/descendants" } } }, { "annotation" : { }, "synonyms" : null, "iri" : "http://purl.obolibrary.org/obo/IAO_0000117", "label" : "IAO_0000117", "synonym" : null, "description" : null, "ontology_name" : "fbbi", "ontology_prefix" : "FBbi", "ontology_iri" : "http://ontology.data.humancellatlas.org/ontologies/fbbi", "is_obsolete" : false, "is_defining_ontology" : false, "has_children" : false, "is_root" : true, "short_form" : "IAO_0000117", "obo_id" : "IAO:0000117", "_links" : { "self" : { "href" : "https://ontology.staging.archive.data.humancellatlas.org:443/api/ontologies/fbbi/properties/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FIAO_0000117" } } }, { "annotation" : { "IAO_0000115" : [ "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q." ], "IAO_0000117" : [ "Chris Mungall" ], "IAO_0000119" : [ "http://purl.obolibrary.org/obo/ro/docs/causal-relations" ], "IAO_0000232" : [ "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." ] }, "synonyms" : null, "iri" : "http://purl.obolibrary.org/obo/RO_0002501", "label" : "causal relation between processes", "synonym" : null, "description" : null, "ontology_name" : "fbbi", "ontology_prefix" : "FBbi", "ontology_iri" : "http://ontology.data.humancellatlas.org/ontologies/fbbi", "is_obsolete" : false, "is_defining_ontology" : false, "has_children" : true, "is_root" : false, "short_form" : "RO_0002501", "obo_id" : "RO:0002501", "_links" : { "self" : { "href" : "https://ontology.staging.archive.data.humancellatlas.org:443/api/ontologies/fbbi/properties/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FRO_0002501" }, "parents" : { "href" : "https://ontology.staging.archive.data.humancellatlas.org:443/api/ontologies/fbbi/properties/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FRO_0002501/parents" }, "ancestors" : { "href" : "https://ontology.staging.archive.data.humancellatlas.org:443/api/ontologies/fbbi/properties/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FRO_0002501/ancestors" }, "jstree" : { "href" : "https://ontology.staging.archive.data.humancellatlas.org:443/api/ontologies/fbbi/properties/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FRO_0002501/jstree" }, "children" : { "href" : "https://ontology.staging.archive.data.humancellatlas.org:443/api/ontologies/fbbi/properties/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FRO_0002501/children" }, "descendants" : { "href" : "https://ontology.staging.archive.data.humancellatlas.org:443/api/ontologies/fbbi/properties/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FRO_0002501/descendants" } } }, { "annotation" : { }, "synonyms" : null, "iri" : "http://purl.obolibrary.org/obo/IAO_0000232", "label" : "IAO_0000232", "synonym" : null, "description" : null, "ontology_name" : "fbbi", "ontology_prefix" : "FBbi", "ontology_iri" : 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