From b986d614efd9533f23fb771c387378dd3255babc Mon Sep 17 00:00:00 2001 From: cmungall Date: Fri, 19 Oct 2018 20:08:29 -0700 Subject: [PATCH] prepared new release --- bfo-classes-minimal.owl | 9 + core.owl | 101 +- ro-base.json | 688 ++-- ro-base.obo | 4 +- ro-base.owl | 500 ++- ro.json | 755 ++-- ro.obo | 244 +- ro.owl | 633 ++-- src/ontology/Makefile | 10 + src/ontology/ro-diff.md | 571 ++- src/ontology/ro.obo | 140 +- src/ontology/ro.owl | 212 +- src/ontology/subsets/ro-causal.obo | 59 +- src/ontology/subsets/ro-causal.owl | 82 +- src/ontology/subsets/ro-chado.obo | 40 +- src/ontology/subsets/ro-chado.obo.tmp | 3852 --------------------- src/ontology/subsets/ro-developmental.obo | 59 +- src/ontology/subsets/ro-developmental.owl | 82 +- src/ontology/subsets/ro-eco.obo | 26 +- src/ontology/subsets/ro-eco.owl | 31 +- src/ontology/subsets/ro-interaction.obo | 59 +- src/ontology/subsets/ro-interaction.owl | 82 +- src/ontology/subsets/ro-mereotopology.obo | 59 +- src/ontology/subsets/ro-mereotopology.owl | 82 +- src/ontology/subsets/ro-sequence.obo | 59 +- src/ontology/subsets/ro-sequence.owl | 82 +- src/ontology/subsets/ro-time-interval.obo | 59 +- src/ontology/subsets/ro-time-interval.owl | 82 +- subsets/ro-causal.obo | 162 +- subsets/ro-causal.owl | 280 +- subsets/ro-chado.obo | 77 +- subsets/ro-developmental.obo | 162 +- subsets/ro-developmental.owl | 280 +- subsets/ro-eco.obo | 99 +- subsets/ro-eco.owl | 207 +- subsets/ro-interaction.obo | 162 +- subsets/ro-interaction.owl | 280 +- subsets/ro-mereotopology.obo | 162 +- subsets/ro-mereotopology.owl | 280 +- subsets/ro-sequence.obo | 162 +- subsets/ro-sequence.owl | 280 +- subsets/ro-time-interval.obo | 162 +- subsets/ro-time-interval.owl | 280 +- temporal-intervals.owl | 283 +- 44 files changed, 5329 insertions(+), 6651 deletions(-) delete mode 100644 src/ontology/subsets/ro-chado.obo.tmp diff --git a/bfo-classes-minimal.owl b/bfo-classes-minimal.owl index 9d1eb52e..28f58d16 100644 --- a/bfo-classes-minimal.owl +++ b/bfo-classes-minimal.owl @@ -76,6 +76,15 @@ A continuant that is either dependent on one or other independent continuant bearers or inheres in or is borne by other entities. + + + + + + + spatial region + + diff --git a/core.owl b/core.owl index bfe8f94b..6643aa65 100644 --- a/core.owl +++ b/core.owl @@ -18,6 +18,71 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/ro-base.json b/ro-base.json index 43a042b1..2bc9998a 100644 --- a/ro-base.json +++ b/ro-base.json @@ -119,6 +119,9 @@ "id" : "http://purl.obolibrary.org/obo/RO_0002297", "meta" : { "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_formation_of" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Chris Mungall" }, { @@ -130,9 +133,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists." - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "results_in_formation_of" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "every \"endocardial cushion formation\" (GO:0003272) results_in_formation_of some \"endocardial cushion\" (UBERON:0002062)" @@ -140,6 +140,16 @@ }, "type" : "PROPERTY", "lbl" : "results in formation of" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002177", + "meta" : { + "definition" : { + "val" : "a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b.", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "attached to part of" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002298", "meta" : { @@ -148,9 +158,6 @@ "xrefs" : [ ] }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "results_in_morphogenesis_of" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723)" }, { @@ -165,20 +172,13 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "GOC:mtg_berkeley_2013" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_morphogenesis_of" } ] }, "type" : "PROPERTY", "lbl" : "results in morphogenesis of" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002177", - "meta" : { - "definition" : { - "val" : "a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b.", - "xrefs" : [ ] - } - }, - "type" : "PROPERTY", - "lbl" : "attached to part of" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002178", "meta" : { @@ -296,14 +296,14 @@ "xrefs" : [ ] }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "results_in_developmental_progression_of" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://wiki.geneontology.org/index.php/Ontology_extensions" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_developmental_progression_of" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Chris Mungall" @@ -363,14 +363,14 @@ "xrefs" : [ ] }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "results_in_development_of" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Chris Mungall" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "every flower development (GO:0009908) results in development of some flower (PO:0009046)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_development_of" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" @@ -654,47 +654,47 @@ "xrefs" : [ ] }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "ancestral_stucture_of" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "evolutionarily_descended_from" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "ancestral_stucture_of" } ] }, "type" : "PROPERTY", "lbl" : "derived by descent from" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002157", + "id" : "http://purl.obolibrary.org/obo/RO_0003003", "meta" : { "definition" : { - "val" : "inverse of derived by descent from", + "val" : "Holds between protein a (a transcription factor) and DNA element b if and only if a activates the process of transcription of b.", "xrefs" : [ ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Logical axioms to be added after the relevant branch of GO is MIREOTed in" } ] }, "type" : "PROPERTY", - "lbl" : "has derived by descendant" + "lbl" : "increases expression of" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0003003", + "id" : "http://purl.obolibrary.org/obo/RO_0002157", "meta" : { "definition" : { - "val" : "Holds between protein a (a transcription factor) and DNA element b if and only if a activates the process of transcription of b.", + "val" : "inverse of derived by descent from", "xrefs" : [ ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Logical axioms to be added after the relevant branch of GO is MIREOTed in" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" } ] }, "type" : "PROPERTY", - "lbl" : "increases expression of" + "lbl" : "has derived by descendant" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002150", "meta" : { @@ -733,9 +733,6 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000426", - "val" : "(forall (?x ?y) \n\t(iff \n\t\t(proper_overlaps ?x ?y)\n\t\t(and \n\t\t\t(overlaps ?x ?y)\n\t\t\t(not (part_of ?x ?y)) \n\t\t\t(not (part_of ?y ?x)))))" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "proper overlaps" }, { @@ -744,6 +741,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000426", + "val" : "(forall (?x ?y) \n\t(iff \n\t\t(proper_overlaps ?x ?y)\n\t\t(and \n\t\t\t(overlaps ?x ?y)\n\t\t\t(not (part_of ?x ?y)) \n\t\t\t(not (part_of ?y ?x)))))" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" @@ -778,15 +778,33 @@ "xrefs" : [ "GOC:dos" ] }, "basicPropertyValues" : [ { + "pred" : "ttp://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-12-07T12:58:06Z" - }, { + } ] + }, + "type" : "PROPERTY", + "lbl" : "in register with" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002029", + "meta" : { + "definition" : { + "val" : "Then percentage of organisms in a population that die during some specified age range (age-specific mortality rate), minus the percentage that die in during the same age range in a wild-type population.", + "xrefs" : [ "PMID:24138933", "Wikipedia:Infant_mortality" ] + }, + "comments" : [ "This could be used to record the increased infant morality rate in some population compared to wild-type. For examples of usage see http://purl.obolibrary.org/obo/FBcv_0000351 and subclasses." ], + "basicPropertyValues" : [ { "pred" : "ttp://www.geneontology.org/formats/oboInOwl#created_by", "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-05-22T16:43:28Z" } ] }, "type" : "PROPERTY", - "lbl" : "in register with" + "lbl" : "has increased age-specific mortality rate" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002380", "meta" : { @@ -896,6 +914,20 @@ }, "type" : "PROPERTY", "lbl" : "acts upstream of or within" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002022", + "meta" : { + "comments" : [ "Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2." ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-09-17T13:52:24Z" + } ] + }, + "type" : "PROPERTY", + "lbl" : "directly regulated by" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002385", "meta" : { @@ -914,19 +946,22 @@ "type" : "PROPERTY", "lbl" : "has potential to developmentally contribute to" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002022", + "id" : "http://purl.obolibrary.org/obo/RO_0002386", "meta" : { - "comments" : [ "Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2." ], + "definition" : { + "val" : "x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y", + "xrefs" : [ ] + }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-09-17T13:52:24Z" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" } ] }, "type" : "PROPERTY", - "lbl" : "directly regulated by" + "lbl" : "has potential to developmentally induce" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002023", "meta" : { @@ -935,32 +970,15 @@ "xrefs" : [ "GOC:dos" ] }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-09-17T13:52:38Z" - } ] - }, - "type" : "PROPERTY", - "lbl" : "directly negatively regulated by" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002386", - "meta" : { - "definition" : { - "val" : "x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y", - "xrefs" : [ ] - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000428" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" } ] }, "type" : "PROPERTY", - "lbl" : "has potential to developmentally induce" + "lbl" : "directly negatively regulated by" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002024", "meta" : { @@ -1021,11 +1039,11 @@ }, "comments" : [ "This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations." ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-09-22T14:14:36Z" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-09-22T14:14:36Z" } ] }, "type" : "PROPERTY", @@ -1213,11 +1231,11 @@ "xrefs" : [ ] }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-07-20T17:19:37Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" } ] }, "type" : "PROPERTY", @@ -1367,11 +1385,11 @@ "meta" : { "comments" : [ "A has necessary component activity B if A and B are GO molecular functions (GO_0003674), A has_component B and B is necessary for A. For example, ATPase coupled transporter activity has necessary component ATPase activity; transcript factor activity has necessary component DNA binding activity." ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-05-24T09:36:08Z" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-05-24T09:36:08Z" } ] }, "type" : "PROPERTY", @@ -1402,11 +1420,11 @@ "xrefs" : [ ] }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-05-24T09:49:21Z" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-05-24T09:49:21Z" } ] }, "type" : "PROPERTY", @@ -1506,6 +1524,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000426", + "val" : "(forall (?x ?y) \n\t(iff \n\t\t(has_fasciculating_neuron_projection ?x ?y)\n\t\t(exists (?nps ?npbs)\t\t\n\t\t\t(and \n\t\t\t\t(\"neuron projection bundle ; CARO_0001001\" ?x)\n\t\t\t\t(\"neuron projection ; GO0043005\" ?y)\n\t\t\t\t(\"neuron projection segment ; CARO_0001502\" ?nps)\n\t\t\t\t(\"neuron projection bundle segment ; CARO_0001500\" ?npbs)\n\t\t\t\t(part_of ?nps ?y)\n\t\t\t\t(part_of ?npbs ?x)\n\t\t\t\t(part_of ?nps ?npbs)\n\t\t\t\t(forall (?npbss)\n\t\t\t\t\t(if\n\t\t\t\t\t\t(and \n\t\t\t\t\t\t\t(\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n\t\t\t\t\t\t\t(part_of ?npbss ?npbs) \n\t\t\t\t\t\t)\n\t\t\t\t\t\t(overlaps ?nps ?npbss)\n\t\t\t\t\t))))))\n\n\n" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "David Osumi-Sutherland" @@ -1518,9 +1539,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000426", - "val" : "(forall (?x ?y) \n\t(iff \n\t\t(has_fasciculating_neuron_projection ?x ?y)\n\t\t(exists (?nps ?npbs)\t\t\n\t\t\t(and \n\t\t\t\t(\"neuron projection bundle ; CARO_0001001\" ?x)\n\t\t\t\t(\"neuron projection ; GO0043005\" ?y)\n\t\t\t\t(\"neuron projection segment ; CARO_0001502\" ?nps)\n\t\t\t\t(\"neuron projection bundle segment ; CARO_0001500\" ?npbs)\n\t\t\t\t(part_of ?nps ?y)\n\t\t\t\t(part_of ?npbs ?x)\n\t\t\t\t(part_of ?nps ?npbs)\n\t\t\t\t(forall (?npbss)\n\t\t\t\t\t(if\n\t\t\t\t\t\t(and \n\t\t\t\t\t\t\t(\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n\t\t\t\t\t\t\t(part_of ?npbss ?npbs) \n\t\t\t\t\t\t)\n\t\t\t\t\t\t(overlaps ?nps ?npbss)\n\t\t\t\t\t))))))\n\n\n" } ] }, "type" : "PROPERTY", @@ -1681,11 +1699,11 @@ "xrefs" : [ ] }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-05-24T09:30:46Z" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-05-24T09:30:46Z" } ] }, "type" : "PROPERTY", @@ -1761,24 +1779,6 @@ }, "type" : "PROPERTY", "lbl" : "developmentally induced by" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002014", - "meta" : { - "definition" : { - "val" : "A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B.", - "xrefs" : [ ] - }, - "comments" : [ "By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'." ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-05-24T09:31:01Z" - } ] - }, - "type" : "PROPERTY", - "lbl" : "has negative regulatory component activity" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002377", "meta" : { @@ -1810,6 +1810,24 @@ }, "type" : "PROPERTY", "lbl" : "distributary of" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002014", + "meta" : { + "definition" : { + "val" : "A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B.", + "xrefs" : [ ] + }, + "comments" : [ "By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'." ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-05-24T09:31:01Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + } ] + }, + "type" : "PROPERTY", + "lbl" : "has negative regulatory component activity" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002491", "meta" : { @@ -2048,6 +2066,16 @@ }, "type" : "PROPERTY", "lbl" : "existence starts during" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002246", + "meta" : { + "definition" : { + "val" : "g is under-expressed in t iff g is expressed in t, and the expression level of g is decreased relative to some background.", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "under-expressed in" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002004", "meta" : { @@ -2062,16 +2090,6 @@ }, "type" : "PROPERTY", "lbl" : "tracheates" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002246", - "meta" : { - "definition" : { - "val" : "g is under-expressed in t iff g is expressed in t, and the expression level of g is decreased relative to some background.", - "xrefs" : [ ] - } - }, - "type" : "PROPERTY", - "lbl" : "under-expressed in" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002005", "meta" : { @@ -6513,9 +6531,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "This class is intended as a grouping for various domain and species-specific exposure classes. The ExO class http://purl.obolibrary.org/obo/ExO_0000002 'exposure event' assumes that all exposures involve stressors, which limits the applicability of this class to 'positive' exposures, e.g. exposing a plant to beneficial growing conditions." - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "cjm" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "An exposure event in which a human is exposed to particulate matter in the air. Here the exposure stimulus/stress is the particulate matter, the receptor is the airways and lungs of the human," @@ -6528,6 +6543,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "An exposure event in which a plant is provided with fertilizer. The exposure receptor is the root system of the plant, the stimulus is the fertilizing chemical, the route is via the soil, possibly mediated by symbotic microbes." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://github.com/oborel/obo-relations/pull/173" @@ -6640,29 +6658,29 @@ "type" : "PROPERTY", "lbl" : "start, days post coitum" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002305", + "id" : "http://purl.obolibrary.org/obo/RO_0002426", "meta" : { - "comments" : [ "holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y" ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", - "val" : "cjm" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0004050", - "val" : "http://purl.obolibrary.org/obo/RO_0002411" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" } ] }, "type" : "PROPERTY", - "lbl" : "causally upstream of, negative effect" + "lbl" : "differs in attribute" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002426", + "id" : "http://purl.obolibrary.org/obo/RO_0002305", "meta" : { + "comments" : [ "holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002411" + }, { + "pred" : "http://purl.org/dc/elements/1.1/creator", + "val" : "cjm" } ] }, "type" : "PROPERTY", - "lbl" : "differs in attribute" + "lbl" : "causally upstream of, negative effect" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002427", "meta" : { @@ -6890,15 +6908,15 @@ "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "Marie Angelique Laporte" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "cjm" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-06-05T17:35:04Z" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "Austin Meier" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "Chris Mungall" @@ -8468,11 +8486,11 @@ }, "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "juvenification", + "val" : "pedomorphosis", "xrefs" : [ ] }, { "pred" : "hasExactSynonym", - "val" : "pedomorphosis", + "val" : "juvenification", "xrefs" : [ ] } ], "basicPropertyValues" : [ { @@ -8596,15 +8614,15 @@ }, { "pred" : "http://purl.org/spar/cito/citesAsAuthority", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000426", + "val" : "(forall (?x ?y) \n\t(iff \n\t\t(downstream_neural_circuit_path ?x ?y)\n\t\t(and\n\t\t\t(\"neuron ; CL_0000540\" ?x)\n\t\t\t(\"neuron ; CL_0000540\" ?y)\n\t\t\t(synapsed_by ?x ?y))))\n\n\n(forall (...s ?x ?y ?z) \n\t(iff \n\t\t(downstream_neural_circuit_path ...s ?x ?y ?z )\n\t\t(and\n\t\t\t(downstream_neural_circuit_path ...s ?x ?y)\n\t\t\t(\"neuron ; CL_0000540\" ?z)\n\t\t\t(synapsed_by ?y ?z))))\n\t\t\t\n(forall (?x ?y) \n\t(iff \n\t\t(downstream_in_neural_circuit_with ?x ?y)\n\t\t(exists (...s)\n\t\t\t(downstream_neural_circuit_path ?x ...s ?y)))) \n\t\t\t" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "David Osumi-Sutherland" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000426", - "val" : "(forall (?x ?y) \n\t(iff \n\t\t(downstream_neural_circuit_path ?x ?y)\n\t\t(and\n\t\t\t(\"neuron ; CL_0000540\" ?x)\n\t\t\t(\"neuron ; CL_0000540\" ?y)\n\t\t\t(synapsed_by ?x ?y))))\n\n\n(forall (...s ?x ?y ?z) \n\t(iff \n\t\t(downstream_neural_circuit_path ...s ?x ?y ?z )\n\t\t(and\n\t\t\t(downstream_neural_circuit_path ...s ?x ?y)\n\t\t\t(\"neuron ; CL_0000540\" ?z)\n\t\t\t(synapsed_by ?y ?z))))\n\t\t\t\n(forall (?x ?y) \n\t(iff \n\t\t(downstream_in_neural_circuit_with ?x ?y)\n\t\t(exists (...s)\n\t\t\t(downstream_neural_circuit_path ?x ...s ?y)))) \n\t\t\t" } ] }, "type" : "PROPERTY", @@ -8678,6 +8696,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000426", + "val" : "(forall (?x ?y) \n\t(iff \n\t\t(upstream_neural_circuit_path ?x ?y)\n\t\t(and\n\t\t\t(\"neuron ; CL_0000540\" ?x)\n\t\t\t(\"neuron ; CL_0000540\" ?y)\n\t\t\t(synapsed_to ?x ?y))))\n\n\n(forall (...s ?x ?y ?z) \n\t(iff \n\t\t(upstream_neural_circuit_path ...s ?x ?y ?z )\n\t\t(and\n\t\t\t(upstream_neural_circuit_path ...s ?x ?y)\n\t\t\t(\"neuron ; CL_0000540\" ?z)\n\t\t\t(synapsed_to ?y ?z))))\n\t\t\t\n(forall (?x ?y) \n\t(iff \n\t\t(upstream_in_neural_circuit_with ?x ?y)\n\t\t(exists (...s)\n\t\t\t(upstream_neural_circuit_path ?x ...s ?y))))" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" @@ -8687,9 +8708,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "David Osumi-Sutherland" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000426", - "val" : "(forall (?x ?y) \n\t(iff \n\t\t(upstream_neural_circuit_path ?x ?y)\n\t\t(and\n\t\t\t(\"neuron ; CL_0000540\" ?x)\n\t\t\t(\"neuron ; CL_0000540\" ?y)\n\t\t\t(synapsed_to ?x ?y))))\n\n\n(forall (...s ?x ?y ?z) \n\t(iff \n\t\t(upstream_neural_circuit_path ...s ?x ?y ?z )\n\t\t(and\n\t\t\t(upstream_neural_circuit_path ...s ?x ?y)\n\t\t\t(\"neuron ; CL_0000540\" ?z)\n\t\t\t(synapsed_to ?y ?z))))\n\t\t\t\n(forall (?x ?y) \n\t(iff \n\t\t(upstream_in_neural_circuit_with ?x ?y)\n\t\t(exists (...s)\n\t\t\t(upstream_neural_circuit_path ?x ...s ?y))))" } ] }, "type" : "PROPERTY", @@ -8735,6 +8753,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.org/spar/cito/citesAsAuthority", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000426", + "val" : "(forall (?x ?y) \n\t(iff \n\t\t(neural_circuit_path ?x ?y)\n\t\t(and\n\t\t\t(\"neuron ; CL_0000540\" ?x)\n\t\t\t(\"neuron ; CL_0000540\" ?y)\n\t\t\t(or \n\t\t\t\t(synapsed_by ?x ?y) \n\t\t\t\t(synapsed_to ?x ?y))))) \n\n(forall (...s ?x ?y ?z) \n\t(iff \n\t\t(neural_circuit_path ...s ?x ?y ?z)\n\t\t(and\n\t\t\t(neural_circuit_path ...s ?x ?y)\n\t\t\t(\"neuron ; CL_0000540\" ?z)\n\t\t\t(or \n\t\t\t\t(synapsed_by ?y ?z) \n\t\t\t\t(synapsed_to ?y ?z))))) \n\n(forall (?x ?y) \n\t(iff \n\t\t(in_neural_circuit_with ?x ?y)\n\t\t(exists (...s)\n\t\t\t(neural_circuit_path ?x ...s ?y)))) " }, { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" @@ -8744,9 +8765,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000426", - "val" : "(forall (?x ?y) \n\t(iff \n\t\t(neural_circuit_path ?x ?y)\n\t\t(and\n\t\t\t(\"neuron ; CL_0000540\" ?x)\n\t\t\t(\"neuron ; CL_0000540\" ?y)\n\t\t\t(or \n\t\t\t\t(synapsed_by ?x ?y) \n\t\t\t\t(synapsed_to ?x ?y))))) \n\n(forall (...s ?x ?y ?z) \n\t(iff \n\t\t(neural_circuit_path ...s ?x ?y ?z)\n\t\t(and\n\t\t\t(neural_circuit_path ...s ?x ?y)\n\t\t\t(\"neuron ; CL_0000540\" ?z)\n\t\t\t(or \n\t\t\t\t(synapsed_by ?y ?z) \n\t\t\t\t(synapsed_to ?y ?z))))) \n\n(forall (?x ?y) \n\t(iff \n\t\t(in_neural_circuit_with ?x ?y)\n\t\t(exists (...s)\n\t\t\t(neural_circuit_path ?x ...s ?y)))) " } ] }, "type" : "PROPERTY", @@ -8790,15 +8808,15 @@ }, "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "many-to-many homology", + "val" : "many to many homologous to", "xrefs" : [ ] }, { "pred" : "hasExactSynonym", - "val" : "many:many homology ", + "val" : "many-to-many homology", "xrefs" : [ ] }, { "pred" : "hasExactSynonym", - "val" : "many to many homologous to", + "val" : "many:many homology ", "xrefs" : [ ] } ], "basicPropertyValues" : [ { @@ -8874,14 +8892,14 @@ "pred" : "hasRelatedSynonym", "val" : "co-orthology", "xrefs" : [ ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "many to 1 orthology", - "xrefs" : [ ] }, { "pred" : "hasExactSynonym", "val" : "1:many orthology", "xrefs" : [ ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "many to 1 orthology", + "xrefs" : [ ] }, { "pred" : "hasExactSynonym", "val" : "1 to many orthologous to", @@ -8981,11 +8999,11 @@ }, "comments" : [ "The term is sometimes also used for anatomical structures." ], "xrefs" : [ { - "val" : "ECO:00000060" - }, { "val" : "SO:0000855" }, { "val" : "SO:0000858" + }, { + "val" : "ECO:00000060" }, { "val" : "SO:orthologous_to" } ], @@ -9072,13 +9090,13 @@ "val" : "SO:non_functional_homolog_of" } ], "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "non functional homologous to", - "xrefs" : [ ] - }, { "pred" : "hasBroadSynonym", "val" : "pseudogene", "xrefs" : [ ] + }, { + "pred" : "hasExactSynonym", + "val" : "non functional homologous to", + "xrefs" : [ ] } ], "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/elements/1.1/source", @@ -9102,15 +9120,15 @@ }, "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "1 to 1 homologous to", + "val" : "one-to-one homology", "xrefs" : [ ] }, { "pred" : "hasExactSynonym", - "val" : "1:1 homology", + "val" : "1 to 1 homologous to", "xrefs" : [ ] }, { "pred" : "hasExactSynonym", - "val" : "one-to-one homology", + "val" : "1:1 homology", "xrefs" : [ ] } ], "basicPropertyValues" : [ { @@ -9135,15 +9153,15 @@ }, "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "1 to 1 orthologous to", + "val" : "one-to-one orthology", "xrefs" : [ ] }, { "pred" : "hasExactSynonym", - "val" : "1:1 orthology", + "val" : "1 to 1 orthologous to", "xrefs" : [ ] }, { "pred" : "hasExactSynonym", - "val" : "one-to-one orthology", + "val" : "1:1 orthology", "xrefs" : [ ] } ], "basicPropertyValues" : [ { @@ -9168,15 +9186,15 @@ }, "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "alloparalogy", + "val" : "out-paralogous to", "xrefs" : [ ] }, { "pred" : "hasExactSynonym", - "val" : "outparalogy", + "val" : "alloparalogy", "xrefs" : [ ] }, { "pred" : "hasExactSynonym", - "val" : "out-paralogous to", + "val" : "outparalogy", "xrefs" : [ ] } ], "basicPropertyValues" : [ { @@ -9259,11 +9277,11 @@ "xrefs" : [ ] }, { "pred" : "hasExactSynonym", - "val" : "in-paralogous to", + "val" : "inparalogy", "xrefs" : [ ] }, { "pred" : "hasExactSynonym", - "val" : "inparalogy", + "val" : "in-paralogous to", "xrefs" : [ ] } ], "basicPropertyValues" : [ { @@ -9291,18 +9309,18 @@ "xrefs" : [ "http://dx.doi.org/10.1016/j.jhevol.2006.11.014", "http://dx.doi.org/10.1146/annurev.es.20.110189.000411", "http://purl.obolibrary.org/obo/HOM_0000006", "ISBN:0123195837" ] }, "xrefs" : [ { - "val" : "ECO:0000071" - }, { "val" : "MI:2163" + }, { + "val" : "ECO:0000071" } ], "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "structural homologous to", - "xrefs" : [ ] - }, { "pred" : "hasRelatedSynonym", "val" : "idealistic homology", "xrefs" : [ ] + }, { + "pred" : "hasExactSynonym", + "val" : "structural homologous to", + "xrefs" : [ ] } ], "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/elements/1.1/creator", @@ -9325,43 +9343,43 @@ "xrefs" : [ "http://dx.doi.org/10.1016/S0169-5347(97)01125-7", "http://purl.obolibrary.org/obo/HOM_0000007", "ISBN:0123195837" ] }, "xrefs" : [ { + "val" : "SO:0000857" + }, { "val" : "SO:0000853" }, { - "val" : "SO:0000857" + "val" : "RO_proposed_relation:homologous_to" }, { - "val" : "SO:0000330" + "val" : "TAO:homologous_to" }, { "val" : "ECO:0000080" }, { - "val" : "SO:homologous_to" - }, { - "val" : "TAO:homologous_to" + "val" : "SO:0000330" }, { - "val" : "RO_proposed_relation:homologous_to" + "val" : "SO:homologous_to" } ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "historical homologous to", + "val" : "phylogenetic homology", "xrefs" : [ ] }, { - "pred" : "hasExactSynonym", - "val" : "taxic homology", + "pred" : "hasRelatedSynonym", + "val" : "true homology", "xrefs" : [ ] }, { - "pred" : "hasBroadSynonym", - "val" : "homology", + "pred" : "hasExactSynonym", + "val" : "historical homologous to", "xrefs" : [ ] }, { "pred" : "hasExactSynonym", - "val" : "cladistic homology", + "val" : "taxic homology", "xrefs" : [ ] }, { "pred" : "hasExactSynonym", - "val" : "phylogenetic homology", + "val" : "cladistic homology", "xrefs" : [ ] }, { - "pred" : "hasRelatedSynonym", - "val" : "true homology", + "pred" : "hasBroadSynonym", + "val" : "homology", "xrefs" : [ ] } ], "basicPropertyValues" : [ { @@ -9470,10 +9488,6 @@ "xrefs" : [ "http://dx.doi.org/10.1016/j.jhevol.2006.11.010", "http://purl.obolibrary.org/obo/HOM_0000009" ] }, "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "rudiment", - "xrefs" : [ ] - }, { "pred" : "hasRelatedSynonym", "val" : "reversion", "xrefs" : [ ] @@ -9481,6 +9495,10 @@ "pred" : "hasExactSynonym", "val" : "atavism", "xrefs" : [ ] + }, { + "pred" : "hasExactSynonym", + "val" : "rudiment", + "xrefs" : [ ] } ], "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/elements/1.1/creator", @@ -9503,20 +9521,20 @@ "xrefs" : [ "http://purl.obolibrary.org/obo/HOM_0000010", "MeSH:Synteny" ] }, "xrefs" : [ { - "val" : "SO:0005858" - }, { "val" : "SO:0000860" + }, { + "val" : "SO:0005858" }, { "val" : "MeSH:Synteny" } ], "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "syntenic homologous to", - "xrefs" : [ ] - }, { "pred" : "hasRelatedSynonym", "val" : "synteny", "xrefs" : [ ] + }, { + "pred" : "hasExactSynonym", + "val" : "syntenic homologous to", + "xrefs" : [ ] } ], "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/elements/1.1/creator", @@ -9565,31 +9583,31 @@ }, "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "fractional homology", + "val" : "partial homologous to", "xrefs" : [ ] }, { "pred" : "hasExactSynonym", - "val" : "segmental homology", + "val" : "fractional homology", "xrefs" : [ ] }, { - "pred" : "hasExactSynonym", - "val" : "partial homologous to", + "pred" : "hasRelatedSynonym", + "val" : "mixed homology", "xrefs" : [ ] }, { "pred" : "hasRelatedSynonym", - "val" : "partial correspondence", + "val" : "percent homology", "xrefs" : [ ] }, { - "pred" : "hasRelatedSynonym", - "val" : "mixed homology", + "pred" : "hasExactSynonym", + "val" : "segmental homology", "xrefs" : [ ] }, { "pred" : "hasRelatedSynonym", - "val" : "modular homology", + "val" : "partial correspondence", "xrefs" : [ ] }, { "pred" : "hasRelatedSynonym", - "val" : "percent homology", + "val" : "modular homology", "xrefs" : [ ] } ], "basicPropertyValues" : [ { @@ -9645,6 +9663,10 @@ "xrefs" : [ "http://dx.doi.org/10.1186/1471-213X-7-100", "http://purl.obolibrary.org/obo/HOM_0000012", "DOI:10.1002/1097-010X(20001215)288:4<345::AID-JEZ7>3.0.CO;2-Y" ] }, "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "duplicon", + "xrefs" : [ ] + }, { "pred" : "hasExactSynonym", "val" : "syntenic paralogous to", "xrefs" : [ ] @@ -9652,10 +9674,6 @@ "pred" : "hasRelatedSynonym", "val" : "paralogon", "xrefs" : [ ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "duplicon", - "xrefs" : [ ] } ], "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/elements/1.1/creator", @@ -9678,13 +9696,13 @@ "xrefs" : [ "http://dx.doi.org/10.1016/j.jhevol.2006.11.010", "http://purl.obolibrary.org/obo/HOM_0000002" ] }, "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "analogy", - "xrefs" : [ ] - }, { "pred" : "hasExactSynonym", "val" : "homoplasous to", "xrefs" : [ ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "analogy", + "xrefs" : [ ] } ], "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/elements/1.1/source", @@ -9742,20 +9760,20 @@ } ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "sameness", + "val" : "similar to", "xrefs" : [ ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "correspondence", - "xrefs" : [ "http://dx.doi.org/10.1007/BF02814479" ] }, { "pred" : "hasExactSynonym", - "val" : "similar to", + "val" : "sameness", "xrefs" : [ ] }, { "pred" : "hasRelatedSynonym", "val" : "resemblance", "xrefs" : [ ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "correspondence", + "xrefs" : [ "http://dx.doi.org/10.1007/BF02814479" ] } ], "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/elements/1.1/creator", @@ -10008,15 +10026,15 @@ }, "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "duplicate xenology", + "val" : "multiple xenology", "xrefs" : [ ] }, { "pred" : "hasExactSynonym", - "val" : "multiple xenology", + "val" : "paraxenologous to", "xrefs" : [ ] }, { "pred" : "hasExactSynonym", - "val" : "paraxenologous to", + "val" : "duplicate xenology", "xrefs" : [ ] } ], "basicPropertyValues" : [ { @@ -10097,15 +10115,15 @@ "xrefs" : [ ] }, { "pred" : "hasExactSynonym", - "val" : "apparent orthologous to", + "val" : "1:1 paralogy", "xrefs" : [ ] }, { "pred" : "hasExactSynonym", - "val" : "1:1 paralogy", + "val" : "apparent 1:1 orthology", "xrefs" : [ ] }, { "pred" : "hasExactSynonym", - "val" : "apparent 1:1 orthology", + "val" : "apparent orthologous to", "xrefs" : [ ] } ], "basicPropertyValues" : [ { @@ -10155,16 +10173,12 @@ "xrefs" : [ "http://dx.doi.org/10.1038/415741a", "http://purl.obolibrary.org/obo/HOM_0000048", "http://www.ensembl.org/info/docs/compara/homology_method.html" ] }, "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "many-to-many orthology", - "xrefs" : [ ] - }, { "pred" : "hasRelatedSynonym", - "val" : "co-orthology", + "val" : "trans-homology", "xrefs" : [ ] }, { "pred" : "hasExactSynonym", - "val" : "many:many orthology", + "val" : "many-to-many orthology", "xrefs" : [ ] }, { "pred" : "hasExactSynonym", @@ -10172,12 +10186,16 @@ "xrefs" : [ ] }, { "pred" : "hasRelatedSynonym", - "val" : "trans-homology", + "val" : "co-orthology", "xrefs" : [ ] }, { "pred" : "hasExactSynonym", "val" : "many to many orthologous to", "xrefs" : [ ] + }, { + "pred" : "hasExactSynonym", + "val" : "many:many orthology", + "xrefs" : [ ] } ], "basicPropertyValues" : [ { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -10325,19 +10343,23 @@ "comments" : [ "Used for structures in closely related taxa." ], "synonyms" : [ { "pred" : "hasRelatedSynonym", - "val" : "re-awakening", + "val" : "homoiology", "xrefs" : [ ] }, { "pred" : "hasExactSynonym", "val" : "cryptic homology", "xrefs" : [ ] + }, { + "pred" : "hasExactSynonym", + "val" : "apomorphic tendency", + "xrefs" : [ ] }, { "pred" : "hasRelatedSynonym", - "val" : "homoplastic tendency", + "val" : "re-awakening", "xrefs" : [ ] }, { "pred" : "hasExactSynonym", - "val" : "apomorphic tendency", + "val" : "underlying synapomorphy", "xrefs" : [ ] }, { "pred" : "hasExactSynonym", @@ -10345,11 +10367,7 @@ "xrefs" : [ ] }, { "pred" : "hasRelatedSynonym", - "val" : "homoiology", - "xrefs" : [ ] - }, { - "pred" : "hasExactSynonym", - "val" : "underlying synapomorphy", + "val" : "homoplastic tendency", "xrefs" : [ ] } ], "basicPropertyValues" : [ { @@ -10403,10 +10421,6 @@ "xrefs" : [ "http://dx.doi.org/10.1016/S0168-9525(00)02005-9", "http://purl.obolibrary.org/obo/HOM_0000055", "ISBN:978-0878932665" ] }, "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "serial paralogy", - "xrefs" : [ ] - }, { "pred" : "hasExactSynonym", "val" : "tandem paralogous to", "xrefs" : [ ] @@ -10414,6 +10428,10 @@ "pred" : "hasRelatedSynonym", "val" : "iterative paralogy", "xrefs" : [ ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "serial paralogy", + "xrefs" : [ ] } ], "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/elements/1.1/creator", @@ -10495,13 +10513,13 @@ "xrefs" : [ "http://purl.obolibrary.org/obo/HOM_0000042", "ISBN:978-0252068140" ] }, "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "synapomorphy", - "xrefs" : [ ] - }, { "pred" : "hasExactSynonym", "val" : "apomorphous to", "xrefs" : [ ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "synapomorphy", + "xrefs" : [ ] } ], "basicPropertyValues" : [ { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -10525,13 +10543,13 @@ }, "comments" : [ "This term is usually contrasted to apomorphy." ], "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "plesiomorphous to", - "xrefs" : [ ] - }, { "pred" : "hasRelatedSynonym", "val" : "symplesiomorphy", "xrefs" : [ ] + }, { + "pred" : "hasExactSynonym", + "val" : "plesiomorphous to", + "xrefs" : [ ] } ], "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/elements/1.1/creator", @@ -10608,20 +10626,20 @@ }, "comments" : [ "Used for structures in distantly related taxa." ], "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "deep homologous to", - "xrefs" : [ ] - }, { "pred" : "hasRelatedSynonym", "val" : "generative homology", "xrefs" : [ ] + }, { + "pred" : "hasExactSynonym", + "val" : "deep genetic homology", + "xrefs" : [ ] }, { "pred" : "hasRelatedSynonym", "val" : "homoiology", "xrefs" : [ ] }, { "pred" : "hasExactSynonym", - "val" : "deep genetic homology", + "val" : "deep homologous to", "xrefs" : [ ] } ], "basicPropertyValues" : [ { @@ -10828,11 +10846,11 @@ "id" : "http://purl.obolibrary.org/obo/RO_0004050", "meta" : { "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2018-03-14T00:03:24Z" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "cjm" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-03-14T00:03:24Z" } ] }, "type" : "PROPERTY", @@ -11098,23 +11116,6 @@ }, "type" : "PROPERTY", "lbl" : "happens during" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0004030", - "meta" : { - "definition" : { - "val" : "A relationship between a disease and an anatomical structure where the material basis of the disease is some pathological change in the structure.", - "xrefs" : [ ] - }, - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "cjm" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-12-26T19:58:44Z" - } ] - }, - "type" : "PROPERTY", - "lbl" : "disease arises from structure" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002093", "meta" : { @@ -11133,6 +11134,23 @@ }, "type" : "PROPERTY", "lbl" : "ends during" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004030", + "meta" : { + "definition" : { + "val" : "A relationship between a disease and an anatomical structure where the material basis of the disease is some pathological change in the structure.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-12-26T19:58:44Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" + } ] + }, + "type" : "PROPERTY", + "lbl" : "disease arises from structure" }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000015", "meta" : { @@ -11205,11 +11223,11 @@ "id" : "http://purl.obolibrary.org/obo/RO_0004032", "meta" : { "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within,_positive_effect" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "cjm" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within,_positive_effect" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0004049", "val" : "http://purl.obolibrary.org/obo/RO_0002264" @@ -11294,11 +11312,11 @@ "xrefs" : [ ] }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "cjm" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-12-26T19:50:53Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" } ] }, "type" : "PROPERTY", @@ -11321,11 +11339,11 @@ "xrefs" : [ ] }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-12-26T19:45:49Z" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "cjm" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-12-26T19:45:49Z" } ] }, "type" : "PROPERTY", @@ -11437,11 +11455,11 @@ "id" : "http://purl.obolibrary.org/obo/RO_0004025", "meta" : { "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-11-05T03:58:20Z" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "cjm" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-11-05T03:58:20Z" } ] }, "type" : "PROPERTY", @@ -11468,11 +11486,11 @@ "xrefs" : [ ] }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "cjm" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-11-05T03:51:09Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" } ] }, "type" : "PROPERTY", @@ -11526,12 +11544,12 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "TODO: complete range axiom once more of CARO has been mireoted in to this ontology" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "This relation is intentionally very general, and covers isolated diseases, where the disease is realized as a process occurring in the location, and syndromic diseases, where one or more of the features may be present in that location. Thus any given disease can have multiple locations in the sense defined here." }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "cjm" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This relation is intentionally very general, and covers isolated diseases, where the disease is realized as a process occurring in the location, and syndromic diseases, where one or more of the features may be present in that location. Thus any given disease can have multiple locations in the sense defined here." }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-11-05T04:06:02Z" @@ -11754,11 +11772,11 @@ "xrefs" : [ ] }, "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://www.orpha.net/ORDO/Orphanet_317344" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "cjm" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://www.orpha.net/ORDO/Orphanet_317344" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-11-05T02:57:07Z" @@ -11776,12 +11794,12 @@ "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-11-05T02:56:40Z" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://www.orpha.net/ORDO/Orphanet_317343" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "cjm" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://www.orpha.net/ORDO/Orphanet_317343" } ] }, "type" : "PROPERTY", @@ -11850,14 +11868,14 @@ "xrefs" : [ ] }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "cjm" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://www.orpha.net/ORDO/Orphanet_410295" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-11-05T02:56:06Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" } ] }, "type" : "PROPERTY", @@ -11940,11 +11958,11 @@ "id" : "http://purl.obolibrary.org/obo/RO_0004003", "meta" : { "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://www.orpha.net/ORDO/Orphanet_317343" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "cjm" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://www.orpha.net/ORDO/Orphanet_317343" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-11-05T02:45:54Z" @@ -11982,11 +12000,11 @@ "id" : "http://purl.obolibrary.org/obo/RO_0004004", "meta" : { "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-11-05T02:46:07Z" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "cjm" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-11-05T02:46:07Z" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://www.orpha.net/ORDO/Orphanet_317344" @@ -12000,15 +12018,15 @@ "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-11-05T02:45:20Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://www.orpha.net/ORDO/Orphanet_410296" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://www.orpha.net/ORDO/Orphanet_410295" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "cjm" } ] }, "type" : "PROPERTY", @@ -14967,46 +14985,46 @@ "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/BFO_0000017" } ], - "id" : "http://purl.obolibrary.org/obo/ro/ro-component.owl", + "id" : "http://purl.obolibrary.org/obo/ro/ro-base.owl", "meta" : { "subsets" : [ ], "xrefs" : [ ], "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", - "val" : "Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 18 Logical Axioms: 7]" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", - "val" : "Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 146 Logical Axioms: 45]" - }, { "pred" : "http://purl.org/dc/elements/1.1/description", "val" : "The OBO Relations Ontology (RO) is a collection of OWL relations (ObjectProperties) intended for use across a wide variety of biological ontologies." }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", - "val" : "Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 6 Logical Axioms: 2]" + "pred" : "http://purl.org/dc/elements/1.1/source", + "val" : "http://obofoundry.org/ro" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", - "val" : "Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 278 Logical Axioms: 58]" + "pred" : "http://purl.org/dc/elements/1.1/title", + "val" : "OBO Relations Ontology" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", "val" : "Includes Ontology(OntologyID(Anonymous-21)) [Axioms: 26 Logical Axioms: 0]" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", - "val" : "Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 731 Logical Axioms: 148]" + "val" : "Includes Ontology(OntologyID(Anonymous-21)) [Axioms: 32 Logical Axioms: 0]" }, { - "pred" : "http://xmlns.com/foaf/0.1/homepage", - "val" : " https://github.com/oborel/obo-relations/" + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 18 Logical Axioms: 7]" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", "val" : "Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 53 Logical Axioms: 12]" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", - "val" : "Includes Ontology(OntologyID(Anonymous-21)) [Axioms: 32 Logical Axioms: 0]" + "val" : "Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 278 Logical Axioms: 58]" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", - "val" : "http://obofoundry.org/ro" + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 6 Logical Axioms: 2]" }, { - "pred" : "http://purl.org/dc/elements/1.1/title", - "val" : "OBO Relations Ontology" + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 731 Logical Axioms: 148]" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 146 Logical Axioms: 45]" + }, { + "pred" : "http://xmlns.com/foaf/0.1/homepage", + "val" : " https://github.com/oborel/obo-relations/" } ] }, "equivalentNodesSets" : [ ], diff --git a/ro-base.obo b/ro-base.obo index 77412711..25695e10 100644 --- a/ro-base.obo +++ b/ro-base.obo @@ -9,12 +9,12 @@ remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 6 Logical Axioms: 2] remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 731 Logical Axioms: 148] remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 146 Logical Axioms: 45] -ontology: ro/ro-component +ontology: ro/ro-base property_value: http://purl.org/dc/elements/1.1/description "The OBO Relations Ontology (RO) is a collection of OWL relations (ObjectProperties) intended for use across a wide variety of biological ontologies." xsd:string property_value: http://purl.org/dc/elements/1.1/source http://obofoundry.org/ro property_value: http://purl.org/dc/elements/1.1/title "OBO Relations Ontology" xsd:string property_value: http://xmlns.com/foaf/0.1/homepage " https://github.com/oborel/obo-relations/" xsd:anyURI -owl-axioms: Prefix(owl:=)\nPrefix(rdf:=)\nPrefix(xml:=)\nPrefix(xsd:=)\nPrefix(rdfs:=)\n\n\nOntology(\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\n############################\n# Annotation Properties\n############################\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (never in taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (mutually spatially disjoint with)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (taxonomic class assertion)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (ambiguous for taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (dubious for taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (present in taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (annotation property cardinality)\n\nSubAnnotationPropertyOf( )\nAnnotationPropertyRange( xsd:nonNegativeInteger)\n\n# Annotation Property: (logical macro assertion on a class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on a property)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on an object property)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on an annotation property)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (dispositional interpretation)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has no connections with)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (curator guidance link)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (always present in taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (temporal logical macro assertion on a class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (measurement property has unit)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has start time value)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has end time value)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, days post fertilization)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, days post fertilization)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, years post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, years post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, months post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, months post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (month of gestation)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has developmental stage marker)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, days post coitum)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, days post coitum)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, weeks post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, weeks post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is asymmetric relational form of process class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is symmetric relational form of process class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is relational form of process class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is direct form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is indirect form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on an axiom)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is a defining property chain axiom)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is a defining property chain axiom where second argument is reflexive)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is relational form of a class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion involving identity)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (in approximate one to one relationship with)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is approximately equivalent to)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is opposite of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is indistinguishable from)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (evidential logical macro assertion on an axiom)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (axiom has evidence)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (axiom contradicted by evidence)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is representative IRI for equivalence set)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is directional form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is positive form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is negative form of)\n\nSubAnnotationPropertyOf( )\n\n\n############################\n# Object Properties\n############################\n\n# Object Property: (coincident with)\n\nObjectPropertyRange( ObjectIntersectionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (synapsed by)\n\nObjectPropertyRange( ObjectUnionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (has fasciculating neuron projection)\n\nObjectPropertyRange( ObjectUnionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (connected to)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (connects)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (directly develops from)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (enabled by)\n\nSubObjectPropertyOf( ObjectInverseOf())\n\n# Object Property: (has member)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (anabranch of)\n\nSubObjectPropertyOf( ObjectInverseOf())\n\n# Object Property: (branching part of)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (differs in attribute of)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (condition has genetic basis in)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has feature)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (has substance added)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (has substance removed)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (immersed in)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (has primary substance added)\n\nIrreflexiveObjectProperty()\n\n\n\n############################\n# Classes\n############################\n\n# Class: (continuant)\n\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: (occurrent)\n\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: (material entity)\n\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: (immaterial entity)\n\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: ()\n\nSubClassOf( ObjectHasSelf())\n\n# Class: ()\n\nSubClassOf( ObjectHasSelf())\n\n# Class: ()\n\nSubClassOf( ObjectHasSelf())\n\n# Class: ()\n\nSubClassOf( ObjectHasSelf())\n\n# Class: ()\n\nSubClassOf( ObjectHasSelf())\n\n# Class: ()\n\nSubClassOf( ObjectHasSelf())\n\n\nSubClassOf(ObjectSomeValuesFrom( ) ObjectUnionOf(ObjectSomeValuesFrom( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( ObjectSomeValuesFrom( ObjectSomeValuesFrom( )))))\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain(ObjectInverseOf() ) )\nSubObjectPropertyOf(ObjectPropertyChain(ObjectInverseOf() ) )\nDLSafeRule(Annotation( \"true\"^^xsd:boolean) Annotation(rdfs:comment \"MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z\"^^xsd:string) Annotation(rdfs:label \"infer input from direct reg\"^^xsd:string) Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z),\ne.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity'\") Annotation(rdfs:label \"enabling an MF enables its parts\") Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation( \"true\"^^xsd:boolean) Annotation(rdfs:comment \"GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction'\"^^xsd:string) Annotation(rdfs:label \"involved in BP\"^^xsd:string) Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"From ligand activity to has_ligand\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"This rule is dubious: added as a quick fix for expected inference in GO-CAM. The problem is most acute for transmembrane proteins, such as receptors or cell adhesion molecules, which have some subfunctions inside the cell (e.g. kinase activity) and some subfunctions outside (e.g. ligand binding). Correct annotation of where these functions occurs leads to incorrect inference about the location of the whole protein. This should probably be weakened to \\\"... -> overlaps\\\"\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this.\") Annotation(rdfs:label \"inferring direct reg edge from input to regulatory subfunction\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"inferring direct neg reg edge from input to regulatory subfunction\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"inferring direct positive reg edge from input to regulatory subfunction\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"From has_ligand to ligand activity\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"effector input is compound function input\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"Input of effector is input of its parent MF\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"if effector directly regulates X, its parent MF directly regulates X\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"if effector directly positively regulates X, its parent MF directly positively regulates X\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"if effector directly negatively regulates X, its parent MF directly negatively regulates X\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nAnnotationAssertion(rdfs:comment \"\")\n) +owl-axioms: Prefix(owl:=)\nPrefix(rdf:=)\nPrefix(xml:=)\nPrefix(xsd:=)\nPrefix(rdfs:=)\n\n\nOntology(\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(DataProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\n############################\n# Annotation Properties\n############################\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (never in taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (mutually spatially disjoint with)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (taxonomic class assertion)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (ambiguous for taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (dubious for taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (present in taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (annotation property cardinality)\n\nSubAnnotationPropertyOf( )\nAnnotationPropertyRange( xsd:nonNegativeInteger)\n\n# Annotation Property: (logical macro assertion on a class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on a property)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on an object property)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on an annotation property)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (dispositional interpretation)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has no connections with)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (curator guidance link)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (always present in taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (temporal logical macro assertion on a class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (measurement property has unit)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has start time value)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has end time value)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, days post fertilization)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, days post fertilization)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, years post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, years post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, months post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, months post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (month of gestation)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has developmental stage marker)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, days post coitum)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, days post coitum)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, weeks post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, weeks post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is asymmetric relational form of process class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is symmetric relational form of process class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is relational form of process class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is direct form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is indirect form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on an axiom)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is a defining property chain axiom)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is a defining property chain axiom where second argument is reflexive)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is relational form of a class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion involving identity)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (in approximate one to one relationship with)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is approximately equivalent to)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is opposite of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is indistinguishable from)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (evidential logical macro assertion on an axiom)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (axiom has evidence)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (axiom contradicted by evidence)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is representative IRI for equivalence set)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is directional form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is positive form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is negative form of)\n\nSubAnnotationPropertyOf( )\n\n\n############################\n# Object Properties\n############################\n\n# Object Property: (coincident with)\n\nObjectPropertyRange( ObjectIntersectionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (synapsed by)\n\nObjectPropertyRange( ObjectUnionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (has fasciculating neuron projection)\n\nObjectPropertyRange( ObjectUnionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (connected to)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (connects)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (directly develops from)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (has member)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (anabranch of)\n\nSubObjectPropertyOf( ObjectInverseOf())\n\n# Object Property: (branching part of)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (differs in attribute of)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (condition has genetic basis in)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has feature)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (has substance added)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (has substance removed)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (immersed in)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (has primary substance added)\n\nIrreflexiveObjectProperty()\n\n\n############################\n# Data Properties\n############################\n\n# Data Property: (has increased age-specific mortality rate)\n\nDataPropertyRange( DatatypeRestriction(xsd:short xsd:minInclusive \"0\"^^xsd:short xsd:maxInclusive \"100\"^^xsd:short))\n\n\n\n############################\n# Classes\n############################\n\n# Class: (continuant)\n\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: (occurrent)\n\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: (material entity)\n\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: (immaterial entity)\n\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: ()\n\nSubClassOf( ObjectHasSelf())\n\n# Class: ()\n\nSubClassOf( ObjectHasSelf())\n\n# Class: ()\n\nSubClassOf( ObjectHasSelf())\n\n# Class: ()\n\nSubClassOf( ObjectHasSelf())\n\n# Class: ()\n\nSubClassOf( ObjectHasSelf())\n\n# Class: ()\n\nSubClassOf( ObjectHasSelf())\n\n\nSubClassOf(ObjectSomeValuesFrom( ) ObjectUnionOf(ObjectSomeValuesFrom( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( ObjectSomeValuesFrom( ObjectSomeValuesFrom( )))))\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain(ObjectInverseOf() ) )\nSubObjectPropertyOf(ObjectPropertyChain(ObjectInverseOf() ) )\nDLSafeRule(Annotation( \"true\"^^xsd:boolean) Annotation(rdfs:comment \"MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z\"^^xsd:string) Annotation(rdfs:label \"infer input from direct reg\"^^xsd:string) Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z),\ne.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity'\") Annotation(rdfs:label \"enabling an MF enables its parts\") Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation( \"true\"^^xsd:boolean) Annotation(rdfs:comment \"GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction'\"^^xsd:string) Annotation(rdfs:label \"involved in BP\"^^xsd:string) Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"From ligand activity to has_ligand\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"This rule is dubious: added as a quick fix for expected inference in GO-CAM. The problem is most acute for transmembrane proteins, such as receptors or cell adhesion molecules, which have some subfunctions inside the cell (e.g. kinase activity) and some subfunctions outside (e.g. ligand binding). Correct annotation of where these functions occurs leads to incorrect inference about the location of the whole protein. This should probably be weakened to \\\"... -> overlaps\\\"\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this.\") Annotation(rdfs:label \"inferring direct reg edge from input to regulatory subfunction\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"inferring direct neg reg edge from input to regulatory subfunction\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"inferring direct positive reg edge from input to regulatory subfunction\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"From has_ligand to ligand activity\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"effector input is compound function input\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"Input of effector is input of its parent MF\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"if effector directly regulates X, its parent MF directly regulates X\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"if effector directly positively regulates X, its parent MF directly positively regulates X\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"if effector directly negatively regulates X, its parent MF directly negatively regulates X\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nAnnotationAssertion(rdfs:comment \"\")\n) [Term] id: BFO:0000002 diff --git a/ro-base.owl b/ro-base.owl index 224eaa00..c4cc98ee 100644 --- a/ro-base.owl +++ b/ro-base.owl @@ -1,6 +1,6 @@ - - + The OBO Relations Ontology (RO) is a collection of OWL relations (ObjectProperties) intended for use across a wide variety of biological ontologies. Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/ro/bfo-axioms.owl>) VersionIRI(<null>))) [Axioms: 18 Logical Axioms: 7] Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/ro/temporal-intervals.owl>) VersionIRI(<null>))) [Axioms: 146 Logical Axioms: 45] + Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/ro/bfo-classes-minimal.owl>) VersionIRI(<null>))) [Axioms: 56 Logical Axioms: 13] Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/ro/el-constraints.owl>) VersionIRI(<null>))) [Axioms: 6 Logical Axioms: 2] - Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/ro/core.owl>) VersionIRI(<null>))) [Axioms: 278 Logical Axioms: 58] + Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/ro/chemical.owl>) VersionIRI(<null>))) [Axioms: 9 Logical Axioms: 3] Includes Ontology(OntologyID(Anonymous-21)) [Axioms: 26 Logical Axioms: 0] https://github.com/oborel/obo-relations/ + Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/ro/core.owl>) VersionIRI(<null>))) [Axioms: 291 Logical Axioms: 62] Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/ro/rohom.owl>) VersionIRI(<null>))) [Axioms: 731 Logical Axioms: 148] - Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/ro/bfo-classes-minimal.owl>) VersionIRI(<null>))) [Axioms: 53 Logical Axioms: 12] Includes Ontology(OntologyID(Anonymous-21)) [Axioms: 32 Logical Axioms: 0] OBO Relations Ontology @@ -1004,6 +1005,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. accidentally included in BFO 1.2 proposal - should have been BFO_0000062 obsolete preceded by + true @@ -1336,6 +1338,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. + + A relation that holds between two neurons connected directly via a synapse, or indirectly via a series of synaptically connected neurons. David Osumi-Sutherland @@ -1583,6 +1587,28 @@ range: spatial region or site (immaterial continuant) + + + + + + + + + + + + + + + + + + + + + + located in my brain is located in my head this rat is located in this cage @@ -1594,6 +1620,18 @@ range: spatial region or site (immaterial continuant) http://www.obofoundry.org/ro/#OBO_REL:located_in located in + + + + + This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation. + + + + + + This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation. + @@ -1621,6 +1659,7 @@ range: spatial region or site (immaterial continuant) + May be obsoleted, see https://github.com/oborel/obo-relations/issues/260 David Osumi-Sutherland aligned with @@ -1663,6 +1702,8 @@ range: spatial region or site (immaterial continuant) + + The relationship that holds between a trachea or tracheole and an antomical structure that is contained in (and so provides an oxygen supply to). David Osumi-Sutherland tracheates @@ -1674,6 +1715,8 @@ range: spatial region or site (immaterial continuant) + + David Osumi-Sutherland http://www.ncbi.nlm.nih.gov/pubmed/22402613 innervated_by @@ -2244,6 +2287,7 @@ Examples include: the relationship between two channels collected simultaneously + @@ -2506,6 +2550,7 @@ Examples include: the relationship between two channels collected simultaneously + has neurotransmitter releases neurotransmitter @@ -2911,7 +2956,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - + @@ -3044,13 +3089,14 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - - + + a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b. + attached to part of (anatomical structure to anatomical structure) attached to part of @@ -3110,7 +3156,16 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - + + + + + + + + + + A relationship that holds between a biological entity and a phenotype. Here a phenotype is construed broadly as any kind of quality of an organism part, a collection of these qualities, or a change in quality or qualities (e.g. abnormally increased temperature). The subject of this relationship can be an organism (where the organism has the phenotype, i.e. the qualities inhere in parts of this organism), a genomic entity such as a gene or genotype (if modifications of the gene or the genotype causes the phenotype), or a condition such as a disease (such that if the condition inheres in an organism, then the organism has the phenotype). Chris Mungall @@ -3219,7 +3274,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - + @@ -3382,6 +3437,14 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. + + + + + + + + 'human p53 protein' SubClassOf some ('has prototype' some ('participates in' some 'DNA repair')) heart SubClassOf 'has prototype' some ('participates in' some 'blood circulation') @@ -3433,6 +3496,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.has function in RO_0000053 some (RO_0000054 only (BFO_0000050 some ?Y)) capable of part of + @@ -4153,8 +4217,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - + every flower development (GO:0009908) results in development of some flower (PO:0009046) p 'results in development of' c if and only if p is a developmental process and p results in the state of c changing from its initial state as a primordium or anlage through its mature state and to its final state. @@ -4186,8 +4250,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - + an annotation of gene X to cell morphogenesis with results_in_morphogenesis_of CL:0000540 (neuron) means that at the end of the process an input neuron has attained its shape. tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723) @@ -4203,8 +4267,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - + an annotation of gene X to cell maturation with results_in_maturation_of CL:0000057 (fibroblast) means that the fibroblast is mature at the end of the process bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474) @@ -4261,7 +4325,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - + Hydrozoa (NCBITaxon_6074) SubClassOf 'has habitat' some 'Hydrozoa habitat' where @@ -4331,8 +4395,8 @@ where - + @@ -4363,6 +4427,7 @@ where inheres in part of + @@ -4379,9 +4444,9 @@ where - - + + an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast. The relationship that links a specified entity with the process that results in an unspecified entity acquiring the features and characteristics of the specified entity Chris Mungall @@ -4407,6 +4472,7 @@ where A relationship that is mediated in some way by the environment or environmental feature (ENVO:00002297) + Awaiting class for domain/range constraint, see: https://github.com/OBOFoundry/Experimental-OBO-Core/issues/6 Chris Mungall Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving ecological interactions @@ -4419,6 +4485,7 @@ where + An experimental relation currently used to connect a feature possessed by an organism (e.g. anatomical structure, biological process, phenotype or quality) to a habitat or environment in which that feature is well suited, adapted or provides a reproductive advantage for the organism. For example, fins to an aquatic environment. Usually this will mean that the structure is adapted for this environment, but we avoid saying this directly - primitive forms of the structure may not have evolved specifically for that environment (for example, early wings were not necessarily adapted for an aerial environment). Note also that this is a statement about the general class of structures - not every instance of a limb need confer an advantage for a terrestrial environment, e.g. if the limb is vestigial. Chris Mungall adapted for @@ -4525,6 +4592,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities. Chris Mungall This is a grouping relation that collects relations used for the purpose of connecting structure and function functionally related to @@ -4611,11 +4679,6 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - - - - - inverse of enables Chris Mungall enabled by @@ -4746,8 +4809,8 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - + 'pollen tube growth' results_in growth_of some 'pollen tube' Chris Mungall results in growth of @@ -4877,8 +4940,8 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - + A relationship between a process and an anatomical entity such that the process contributes to the act of creating the structural organization of the anatomical entity. Chris Mungall results in structural organization of @@ -4929,6 +4992,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a Chris Mungall + attached to (anatomical structure to anatomical structure) attached to @@ -4940,12 +5004,19 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to. Chris Mungall Wikipedia:Insertion_(anatomy) has muscle origin + + + + + We need to import uberon muscle to create a stricter domain constraint + @@ -4954,27 +5025,35 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone. Chris Mungall Wikipedia:Insertion_(anatomy) has muscle insertion + + + + + We need to import uberon muscle into RO to use as a stricter domain constraint + - + false x has_fused_element y iff: there exists some z : x has_part z, z homologous_to y, and y is a distinct element, the boundary between x and z is largely fiat Chris Mungall Chris Mungall + has fused element A has_fused_element B does not imply that A has_part some B: rather than A has_part some B', where B' that has some evolutionary relationship to B. - has fused element + derived from ancestral fusion of @@ -5253,7 +5332,6 @@ https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/ - @@ -5382,7 +5460,6 @@ https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/ - This relation groups causal relations between material entities and causal relations between processes 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. @@ -5610,6 +5687,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p + OWL does not allow defining object properties via a Union Chris Mungall involved in or reguates involved in or involved in regulation of @@ -6153,7 +6231,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different Chris Mungall This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning. - helper property + helper property (not for use in curation) @@ -6390,6 +6468,14 @@ the a supports either the existence of b, or the truth value of b. + + + + + + + + Chris Mungall Do not use this relation directly. It is ended as a grouping for a diverse set of relations, typically connecting an anatomical entity to a biological process or developmental stage. @@ -7080,8 +7166,8 @@ the a supports either the existence of b, or the truth value of b. - + p results in the end of s if p results in a change of state in s whereby s either ceases to exist, or s becomes functionally impaired or s has its fate committed such that it is put on a path to be degraded. Chris Mungall results in ending of @@ -7221,7 +7307,7 @@ the a supports either the existence of b, or the truth value of b. - + Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c Chris Mungall @@ -7257,6 +7343,8 @@ the a supports either the existence of b, or the truth value of b. + + A relation that holds between elements of a musculoskeletal system or its analogs. Chris Mungall Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes. @@ -7337,6 +7425,7 @@ the a supports either the existence of b, or the truth value of b. + A relation that holds between an attribute or a qualifier and another attribute. Chris Mungall @@ -7351,6 +7440,8 @@ the a supports either the existence of b, or the truth value of b. + + Chris Mungall participates in a biotic-biotic interaction with @@ -7418,8 +7509,8 @@ the a supports either the existence of b, or the truth value of b. - + p 'results in closure of' c if and only if p is a developmental process and p results in a state of c changing from open to closed. results in closure of @@ -7488,7 +7579,7 @@ the a supports either the existence of b, or the truth value of b. - + p results in organization of c iff p results in the assembly, arrangement of constituent parts, or disassembly of c results in organization of @@ -7640,7 +7731,8 @@ the a supports either the existence of b, or the truth value of b. A relationship that holds between two entities, where the relationship holds based on the presence or absence of statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. - related via dependence to + obsolete related via dependence to + true @@ -7648,7 +7740,6 @@ the a supports either the existence of b, or the truth value of b. - A relationship that holds between two entities, where the entities exhibit a statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes. Groups both positive and negative correlation correlated with @@ -8308,7 +8399,7 @@ Environmental exposures include those imposed by natural environments, experimen - + cjm 2017-11-05T03:26:47Z disease has basis in @@ -8320,8 +8411,9 @@ Environmental exposures include those imposed by natural environments, experimen - + A relation that holds between the disease and a material entity where the physical basis of the disease is a disorder of that material entity that affects its function. + disease has basis in dysfunction of (disease to anatomical structure) cjm 2017-11-05T03:29:32Z disease has basis in dysfunction of @@ -8335,6 +8427,7 @@ Environmental exposures include those imposed by natural environments, experimen A relation that holds between the disease and a process where the physical basis of the disease disrupts execution of a key biological process. + disease has basis in disruption of (disease to process) cjm 2017-11-05T03:37:52Z disease has basis in disruption of @@ -8347,6 +8440,15 @@ Environmental exposures include those imposed by natural environments, experimen + + + + + + + + + A relation that holds between the disease and a feature (a phenotype or other disease) where the physical basis of the disease is the feature. cjm 2017-11-05T03:46:07Z @@ -8359,7 +8461,8 @@ Environmental exposures include those imposed by natural environments, experimen - + + After import upper level from OGMS, make domain more specific. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all of which have a disease as the subject. cjm @@ -8373,12 +8476,14 @@ Environmental exposures include those imposed by natural environments, experimen + A relationship between a disease and a process where the disease process disrupts the execution of the process. + disease causes disruption of (disease to process) cjm 2017-11-05T03:51:09Z disease causes disruption of @@ -8390,11 +8495,13 @@ Environmental exposures include those imposed by natural environments, experimen - + + + disease causes dysfunction of (disease to anatomical entity) cjm 2017-11-05T03:58:20Z disease causes dysfunction of @@ -8405,8 +8512,17 @@ Environmental exposures include those imposed by natural environments, experimen - + + + + + + + + + + A relationship between a disease and an anatomical entity where the disease has one or more features that are located in that entity. TODO: complete range axiom once more of CARO has been mireoted in to this ontology This relation is intentionally very general, and covers isolated diseases, where the disease is realized as a process occurring in the location, and syndromic diseases, where one or more of the features may be present in that location. Thus any given disease can have multiple locations in the sense defined here. @@ -8421,6 +8537,8 @@ Environmental exposures include those imposed by natural environments, experimen + + A relationship between a disease and an anatomical entity where the disease is triggered by an inflammatory response to stimuli occurring in the anatomical entity cjm 2017-12-26T19:37:31Z @@ -8450,12 +8568,13 @@ Environmental exposures include those imposed by natural environments, experimen - + + - - + + @@ -8641,6 +8760,8 @@ Environmental exposures include those imposed by natural environments, experimen + + An interaction relationship wherein one organism creates a structure or environment that is lived in by another organism. creates habitat for @@ -8652,8 +8773,10 @@ Environmental exposures include those imposed by natural environments, experimen + + An interaction relationship describing organisms that often occur together at the same time and space or in the same environment. - co-occurs + ecologically co-occurs with @@ -8683,6 +8806,8 @@ Environmental exposures include those imposed by natural environments, experimen + + muffin 'has substance added' some 'baking soda' "has substance added" is a relation existing between a (physical) entity and a substance in which the entity has had the substance added to it at some point in time. @@ -8697,6 +8822,8 @@ Environmental exposures include those imposed by natural environments, experimen + + 'egg white' 'has substance removed' some 'egg yolk' "has substance removed" is a relation existing between two physical entities in which the first entity has had the second entity (a substance) removed from it at some point in time. @@ -8710,6 +8837,8 @@ Environmental exposures include those imposed by natural environments, experimen + + sardines 'immersed in' some 'oil and mustard' "immersed in" is a relation between a (physical) entity and a fluid substance in which the entity is wholely or substantially surrounded by the substance. @@ -8764,6 +8893,80 @@ Environmental exposures include those imposed by natural environments, experimen + + + + + + + + + + + Genetic information generically depend on molecules of DNA. + The novel *War and Peace* generically depends on this copy of the novel. + The pattern shared by chess boards generically depends on any chess board. + The score of a symphony g-depends on a copy of the score. + This pdf file generically depends on this server. + A generically dependent continuant *b* generically depends on an independent continuant *c* at time *t* means: there inheres in *c* a specifically deendent continuant which concretizes *b* at *t*. + [072-ISO] + g-depends on + generically depends on + + + + + + + + + + + + + + Molecules of DNA are carriers of genetic information. + This copy of *War and Peace* is carrier of the novel written by Tolstoy. + This hard drive is carrier of these data items. + *b* is carrier of *c* at time *t* if and only if *c* *g-depends on* *b* at *t* + [072-ISO] + is carrier of + + + + + + + + This relation groups relations between diseases and any other kind of entity. + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, in which the subject or object is a disease. + cjm + 2018-09-26T00:00:32Z + disease relationship + + + + + + + + + + + + + + + + + p has anatomical participant c iff p has participant c, and c is an anatomical entity + cjm + 2018-09-26T01:08:58Z + has anatomical participant + + + + @@ -10370,6 +10573,55 @@ Environmental exposures include those imposed by natural environments, experimen + + + + + + + + + + + + + + + + + + + + 0 + + + 100 + + + + + Then percentage of organisms in a population that die during some specified age range (age-specific mortality rate), minus the percentage that die in during the same age range in a wild-type population. + 2018-05-22T16:43:28Z + This could be used to record the increased infant morality rate in some population compared to wild-type. For examples of usage see http://purl.obolibrary.org/obo/FBcv_0000351 and subclasses. + has increased age-specific mortality rate + dos + + + + + Then percentage of organisms in a population that die during some specified age range (age-specific mortality rate), minus the percentage that die in during the same age range in a wild-type population. + PMID:24138933 + Wikipedia:Infant_mortality + + + + + + + + + + + + + + + + @@ -10400,6 +10664,12 @@ Environmental exposures include those imposed by natural environments, experimen + + + + + + @@ -10435,10 +10705,25 @@ Environmental exposures include those imposed by natural environments, experimen + + + + + spatial region + + + + + + + + + + An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. process @@ -10555,7 +10840,20 @@ Environmental exposures include those imposed by natural environments, experimen - + + + + + + + + + + + + + + @@ -10565,6 +10863,12 @@ Environmental exposures include those imposed by natural environments, experimen + + + + + + @@ -10697,6 +11001,12 @@ Environmental exposures include those imposed by natural environments, experimen + + + + + + @@ -10785,6 +11095,12 @@ Environmental exposures include those imposed by natural environments, experimen + + + + + + @@ -10869,6 +11185,18 @@ Environmental exposures include those imposed by natural environments, experimen + + + + + + + + + + + + @@ -11082,6 +11410,76 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + From ligand activity to has_ligand @@ -11368,9 +11766,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -11379,9 +11777,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + diff --git a/ro.json b/ro.json index 028bdec0..f90d9220 100644 --- a/ro.json +++ b/ro.json @@ -175,7 +175,11 @@ "definition" : { "val" : "a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b.", "xrefs" : [ ] - } + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "attached to part of (anatomical structure to anatomical structure)" + } ] }, "type" : "PROPERTY", "lbl" : "attached to part of" @@ -801,6 +805,24 @@ }, "type" : "PROPERTY", "lbl" : "in register with" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002029", + "meta" : { + "definition" : { + "val" : "Then percentage of organisms in a population that die during some specified age range (age-specific mortality rate), minus the percentage that die in during the same age range in a wild-type population.", + "xrefs" : [ "PMID:24138933", "Wikipedia:Infant_mortality" ] + }, + "comments" : [ "This could be used to record the increased infant morality rate in some population compared to wild-type. For examples of usage see http://purl.obolibrary.org/obo/FBcv_0000351 and subclasses." ], + "basicPropertyValues" : [ { + "pred" : "ttp://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-05-22T16:43:28Z" + } ] + }, + "type" : "PROPERTY", + "lbl" : "has increased age-specific mortality rate" }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000412", "meta" : { @@ -1476,6 +1498,16 @@ "id" : "http://purl.obolibrary.org/obo/IAO_0000425", "type" : "PROPERTY", "lbl" : "expand assertion to" + }, { + "id" : "http://purl.obolibrary.org/obo/CARO_0000000", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/caro.owl" + } ] + }, + "type" : "CLASS", + "lbl" : "anatomical entity" }, { "id" : "http://purl.obolibrary.org/obo/CARO_0000003", "meta" : { @@ -1485,7 +1517,7 @@ } ] }, "type" : "CLASS", - "lbl" : "anatomical structure" + "lbl" : "connected anatomical structure" }, { "id" : "http://purl.obolibrary.org/obo/CARO_0000007", "type" : "CLASS", @@ -1523,6 +1555,11 @@ "xrefs" : [ ] }, "comments" : [ "A has_fused_element B does not imply that A has_part some B: rather than A has_part some B', where B' that has some evolutionary relationship to B." ], + "synonyms" : [ { + "pred" : "hasBroadSynonym", + "val" : "has fused element", + "xrefs" : [ ] + } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" @@ -1541,7 +1578,7 @@ } ] }, "type" : "PROPERTY", - "lbl" : "has fused element" + "lbl" : "derived from ancestral fusion of" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002495", "meta" : { @@ -1923,6 +1960,9 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "attached to (anatomical structure to anatomical structure)" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Chris Mungall" } ] @@ -2381,6 +2421,9 @@ "id" : "http://purl.obolibrary.org/obo/RO_0002001", "meta" : { "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "May be obsoleted, see https://github.com/oborel/obo-relations/issues/260" + }, { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" }, { @@ -4376,7 +4419,7 @@ } ] }, "type" : "PROPERTY", - "lbl" : "helper property" + "lbl" : "helper property (not for use in curation)" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002585", "meta" : { @@ -5063,6 +5106,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", "val" : "RO_0000053 some (RO_0000054 only (BFO_0000050 some ?Y))" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/oborel/obo-relations/wiki/ROGuide#defining-property-chains-involving-reflexivity" } ] }, "type" : "PROPERTY", @@ -5081,6 +5127,10 @@ }, "type" : "PROPERTY", "lbl" : "related via localization to" + }, { + "id" : "http://purl.obolibrary.org/obo/CARO_0001010", + "type" : "CLASS", + "lbl" : "organism or virus or viroid" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002451", "meta" : { @@ -5655,6 +5705,10 @@ }, { "id" : "http://purl.obolibrary.org/obo/RO_0002328", "meta" : { + "definition" : { + "val" : "A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities.", + "xrefs" : [ ] + }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Chris Mungall" @@ -6164,6 +6218,26 @@ }, "type" : "PROPERTY", "lbl" : "symbiotically interacts with" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0040035", + "meta" : { + "definition" : { + "val" : "This relation groups relations between diseases and any other kind of entity.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, in which the subject or object is a disease." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-09-26T00:00:32Z" + } ] + }, + "type" : "PROPERTY", + "lbl" : "disease relationship" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002561", "meta" : { @@ -6216,6 +6290,23 @@ }, "type" : "PROPERTY", "lbl" : "commensually interacts with" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0040036", + "meta" : { + "definition" : { + "val" : "p has anatomical participant c iff p has participant c, and c is an anatomical entity", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-09-26T01:08:58Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" + } ] + }, + "type" : "PROPERTY", + "lbl" : "has anatomical participant" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002562", "meta" : { @@ -6239,6 +6330,9 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Awaiting class for domain/range constraint, see: https://github.com/OBOFoundry/Experimental-OBO-Core/issues/6" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Chris Mungall" }, { @@ -6636,6 +6730,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/oborel/obo-relations/wiki/ROGuide#defining-property-chains-involving-reflexivity" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Chris Mungall" @@ -6862,6 +6959,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "involved in or reguates" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "OWL does not allow defining object properties via a Union" } ] }, "type" : "PROPERTY", @@ -9356,10 +9456,11 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." - } ] + } ], + "deprecated" : true }, "type" : "PROPERTY", - "lbl" : "related via dependence to" + "lbl" : "obsolete related via dependence to" }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000078", "meta" : { @@ -9369,6 +9470,63 @@ } ] }, "lbl" : "curation status specification" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0010002", + "meta" : { + "definition" : { + "val" : "*b* is carrier of *c* at time *t* if and only if *c* *g-depends on* *b* at *t*", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Molecules of DNA are carriers of genetic information." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "This hard drive is carrier of these data items." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "[072-ISO]" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "This copy of *War and Peace* is carrier of the novel written by Tolstoy." + } ] + }, + "type" : "PROPERTY", + "lbl" : "is carrier of" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0010001", + "meta" : { + "definition" : { + "val" : "A generically dependent continuant *b* generically depends on an independent continuant *c* at time *t* means: there inheres in *c* a specifically deendent continuant which concretizes *b* at *t*.", + "xrefs" : [ ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "g-depends on", + "xrefs" : [ ] + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Genetic information generically depend on molecules of DNA." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The pattern shared by chess boards generically depends on any chess board." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "This pdf file generically depends on this server." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "[072-ISO]" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The novel *War and Peace* generically depends on this copy of the novel." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The score of a symphony g-depends on a copy of the score." + } ] + }, + "type" : "PROPERTY", + "lbl" : "generically depends on" }, { "id" : "http://purl.obolibrary.org/obo/RO_HOM0000017", "meta" : { @@ -10075,10 +10233,6 @@ }, "type" : "PROPERTY", "lbl" : "in syntenic paralogy relationship with" - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0004872", - "type" : "CLASS", - "lbl" : "receptor activity" }, { "id" : "http://purl.obolibrary.org/obo/RO_HOM0000002", "meta" : { @@ -10798,6 +10952,10 @@ }, "type" : "PROPERTY", "lbl" : "in latent homology relationship with" + }, { + "id" : "http://purl.obolibrary.org/obo/CARO_0030000", + "type" : "CLASS", + "lbl" : "biological entity" }, { "id" : "http://purl.obolibrary.org/obo/RO_HOM0000058", "meta" : { @@ -11373,6 +11531,10 @@ "id" : "http://www.geneontology.org/formats/oboInOwl#hasOBOFormatVersion", "type" : "PROPERTY", "lbl" : "has_obo_format_version" + }, { + "id" : "http://purl.obolibrary.org/obo/UPHENO_0001001", + "type" : "CLASS", + "lbl" : "phenotype" }, { "id" : "http://purl.obolibrary.org/obo/GO_0051702", "type" : "CLASS", @@ -11409,6 +11571,16 @@ }, "type" : "PROPERTY", "lbl" : "causally upstream of or within, negative effect" + }, { + "id" : "http://purl.obolibrary.org/obo/OGMS_0000031", + "meta" : { + "definition" : { + "val" : "A disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "disease" }, { "id" : "http://purl.obolibrary.org/obo/RO_0004049", "meta" : { @@ -11450,7 +11622,8 @@ }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000060", "meta" : { - "comments" : [ "accidentally included in BFO 1.2 proposal\n - should have been BFO_0000062" ] + "comments" : [ "accidentally included in BFO 1.2 proposal\n - should have been BFO_0000062" ], + "deprecated" : true }, "type" : "PROPERTY", "lbl" : "obsolete preceded by" @@ -11843,7 +12016,7 @@ } }, "type" : "PROPERTY", - "lbl" : "co-occurs" + "lbl" : "ecologically co-occurs with" }, { "id" : "http://purl.obolibrary.org/obo/RO_0008505", "meta" : { @@ -11914,6 +12087,10 @@ }, "type" : "CLASS", "lbl" : "obsolete dependent continuant" + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000006", + "type" : "CLASS", + "lbl" : "spatial region" }, { "id" : "http://purl.obolibrary.org/obo/RO_0008504", "meta" : { @@ -11925,22 +12102,13 @@ }, "type" : "PROPERTY", "lbl" : "kleptoparasitized by" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002088", - "meta" : { - "comments" : [ "Previously had ID http://purl.obolibrary.org/obo/RO_0002123 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range." ], - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "David Osumi-Sutherland" - } ] - }, - "type" : "PROPERTY", - "lbl" : "during which starts" }, { "id" : "http://purl.obolibrary.org/obo/RO_0004025", "meta" : { "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "disease causes dysfunction of (disease to anatomical entity)" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-11-05T03:58:20Z" }, { @@ -11950,6 +12118,18 @@ }, "type" : "PROPERTY", "lbl" : "disease causes dysfunction of" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002088", + "meta" : { + "comments" : [ "Previously had ID http://purl.obolibrary.org/obo/RO_0002123 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range." ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + } ] + }, + "type" : "PROPERTY", + "lbl" : "during which starts" }, { "id" : "http://purl.obolibrary.org/obo/RO_0008503", "meta" : { @@ -11977,6 +12157,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-11-05T03:51:09Z" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "disease causes disruption of (disease to process)" } ] }, "type" : "PROPERTY", @@ -12070,6 +12253,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "cjm" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "disease has basis in disruption of (disease to process)" } ] }, "type" : "PROPERTY", @@ -12108,6 +12294,9 @@ "xrefs" : [ ] }, "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "disease has basis in dysfunction of (disease to anatomical structure)" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-11-05T03:29:32Z" }, { @@ -12732,10 +12921,6 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002436", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002434" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002299", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0000057" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002200", "pred" : "subPropertyOf", @@ -12836,6 +13021,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002453", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002440" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002374", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002156" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002522", "pred" : "subPropertyOf", @@ -12844,10 +13033,6 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002584", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002595" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002585", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0000057" }, { "sub" : "http://purl.obolibrary.org/obo/BFO_0000141", "pred" : "is_a", @@ -12856,14 +13041,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002572", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002571" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002520", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002524" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002521", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002514" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002520", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002524" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002571", "pred" : "subPropertyOf", @@ -12900,10 +13085,18 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002411", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002418" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0010001", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0010002" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002451", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002321" + }, { + "sub" : "http://purl.obolibrary.org/obo/OGMS_0000031", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000016" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002313", "pred" : "subPropertyOf", @@ -12968,10 +13161,6 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002120", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0000302" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0004029", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0004023" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002338", "pred" : "subPropertyOf", @@ -12988,10 +13177,6 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002356", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002295" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002410", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002609" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002206", "pred" : "subPropertyOf", @@ -13092,6 +13277,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002106", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002112" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0004029", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0040035" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002437", "pred" : "subPropertyOf", @@ -13108,6 +13297,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002459", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002460" + }, { + "sub" : "http://purl.obolibrary.org/obo/CARO_0030000", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000004" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002632", "pred" : "subPropertyOf", @@ -13204,6 +13397,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002441", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002440" + }, { + "sub" : "http://purl.obolibrary.org/obo/UPHENO_0001001", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0000001" }, { "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000010", "pred" : "subPropertyOf", @@ -13212,14 +13409,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002287", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002286" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0004004", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0004000" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002440", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002574" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0004004", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0004000" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002291", "pred" : "subPropertyOf", @@ -13320,6 +13517,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002492", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002497" + }, { + "sub" : "http://purl.obolibrary.org/obo/CARO_0001010", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000040" }, { "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000057", "pred" : "subPropertyOf", @@ -13360,14 +13561,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000036", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_HOM0000007" + }, { + "sub" : "http://purl.obolibrary.org/obo/CARO_0000000", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CARO_0030000" }, { "sub" : "http://purl.obolibrary.org/obo/CARO_0000007", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/BFO_0000141" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002315", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0000057" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002105", "pred" : "inverseOf", @@ -13384,18 +13585,22 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002339", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002344" - }, { - "sub" : "http://purl.obolibrary.org/obo/BFO_0000015", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000003" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002012", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002418" + }, { + "sub" : "http://purl.obolibrary.org/obo/BFO_0000015", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000003" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002209", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002445" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0004026", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0040035" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0085030", "pred" : "is_a", @@ -13521,17 +13726,17 @@ "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002131" }, { - "sub" : "http://purl.obolibrary.org/obo/GO_0030425", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_0043005" + "sub" : "http://purl.obolibrary.org/obo/RO_0008502", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002440" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001199", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000052" }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0008502", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002440" + "sub" : "http://purl.obolibrary.org/obo/GO_0030425", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GO_0043005" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002478", "pred" : "subPropertyOf", @@ -13573,29 +13778,33 @@ "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002629" }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002455", + "sub" : "http://purl.obolibrary.org/obo/RO_0002315", "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002442" + "obj" : "http://purl.obolibrary.org/obo/RO_0040036" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002466", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002465" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002252", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002375" }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002466", + "sub" : "http://purl.obolibrary.org/obo/RO_0002455", "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002465" + "obj" : "http://purl.obolibrary.org/obo/RO_0002442" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002263", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002264" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002310", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000015" }, { "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000007", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_HOM0000001" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002310", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000015" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002442", "pred" : "subPropertyOf", @@ -13608,14 +13817,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002469", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002438" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_0044456", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CARO_0000014" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002578", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002412" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0044456", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CARO_0000014" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002016", "pred" : "subPropertyOf", @@ -13736,14 +13945,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002430", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002428" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002114", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002120" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002113", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002130" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002114", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002120" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002379", "pred" : "subPropertyOf", @@ -13896,10 +14105,6 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002229", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002230" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002592", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0000057" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002533", "pred" : "is_a", @@ -14092,6 +14297,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002101", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002131" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002592", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0040036" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002439", "pred" : "inverseOf", @@ -14168,14 +14377,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002229", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/BFO_0000050" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_0042734", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_0044456" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0004002", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0004012" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0042734", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GO_0044456" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002384", "pred" : "subPropertyOf", @@ -14268,6 +14477,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002468", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002465" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002313", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0040036" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002589", "pred" : "subPropertyOf", @@ -14276,14 +14489,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002526", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002514" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0002009", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0000052" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002160", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002162" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0002009", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0000052" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002261", "pred" : "subPropertyOf", @@ -14296,14 +14509,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002245", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002206" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002180", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000051" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002231", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002479" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002180", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000051" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002230", "pred" : "subPropertyOf", @@ -14312,14 +14525,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002088", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002091" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002007", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000050" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0004012", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0004010" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002007", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000050" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0004024", "pred" : "subPropertyOf", @@ -14332,6 +14545,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000075", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_HOM0000007" + }, { + "sub" : "http://purl.obolibrary.org/obo/BFO_0000006", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000141" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002211", "pred" : "subPropertyOf", @@ -14364,10 +14581,6 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002084", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002093" - }, { - "sub" : "http://purl.obolibrary.org/obo/CARO_0000011", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CARO_0000006" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002444", "pred" : "subPropertyOf", @@ -14384,14 +14597,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002004", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0001018" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002476", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002258" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002458", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002438" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002476", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002258" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002233", "pred" : "subPropertyOf", @@ -14432,14 +14645,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002000", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002002" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002216", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002500" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002495", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002494" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002216", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002500" }, { "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000044", "pred" : "subPropertyOf", @@ -14520,10 +14733,6 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002530", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002515" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002610", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002609" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0004030", "pred" : "subPropertyOf", @@ -14532,10 +14741,18 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0000081", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0000087" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002299", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0040036" }, { "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000069", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_HOM0000011" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0004023", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0040035" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0000080", "pred" : "inverseOf", @@ -14580,10 +14797,6 @@ "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000057", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_HOM0000005" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002403", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002234" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002500", "pred" : "subPropertyOf", @@ -14612,10 +14825,6 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002219", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002221" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002296", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0000057" }, { "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000025", "pred" : "subPropertyOf", @@ -14632,14 +14841,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002380", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002375" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_0044464", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CARO_0000014" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002485", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002170" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0044464", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CARO_0000014" }, { "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000002", "pred" : "subPropertyOf", @@ -14664,14 +14873,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002348", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002295" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_0085031", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_0044403" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0008503", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0008504" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0085031", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GO_0044403" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0000052", "pred" : "is_a", @@ -14820,26 +15029,26 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002624", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002618" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002355", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0000057" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0000079", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0000085" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002159", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002320" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002090", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/BFO_0000063" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002159", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002320" }, { "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000045", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_HOM0000007" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002585", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0040036" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002618", "pred" : "subPropertyOf", @@ -15028,14 +15237,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002459", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002574" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002177", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002323" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0003305", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0003304" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002177", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002323" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002551", "pred" : "inverseOf", @@ -15052,10 +15261,18 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0008505", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002321" + }, { + "sub" : "http://purl.obolibrary.org/obo/CARO_0000011", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CARO_0010000" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002000", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002323" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002296", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0040036" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002341", "pred" : "subPropertyOf", @@ -15064,14 +15281,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000016", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_HOM0000006" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000054", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_HOM0000062" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002349", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002295" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000054", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_HOM0000062" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002445", "pred" : "subPropertyOf", @@ -15140,14 +15357,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002331", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002431" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002286", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002384" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002026", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002323" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002286", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002384" }, { "sub" : "http://purl.obolibrary.org/obo/BFO_0000050", "pred" : "inverseOf", @@ -15156,6 +15373,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0009005", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0009001" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0040036", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0000057" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002243", "pred" : "subPropertyOf", @@ -15176,6 +15397,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0000087", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0000053" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002355", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0040036" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0004015", "pred" : "subPropertyOf", @@ -15192,10 +15417,6 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002570", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002131" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002343", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0000057" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002636", "pred" : "inverseOf", @@ -15212,10 +15433,6 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002371", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002170" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002552", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0000057" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002237", "pred" : "subPropertyOf", @@ -15256,10 +15473,6 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002640", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002634" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002565", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0000057" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002342", "pred" : "subPropertyOf", @@ -15424,10 +15637,6 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002448", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002566" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002298", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0000057" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0007610", "pred" : "is_a", @@ -15452,10 +15661,6 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002515", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002527" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002374", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002320" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002104", "pred" : "subPropertyOf", @@ -15548,14 +15753,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000060", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_HOM0000050" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002297", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002295" }, { "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000065", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_HOM0000000" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002297", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002295" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0051705", "pred" : "is_a", @@ -15596,6 +15801,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000032", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_HOM0000029" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002343", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0040036" }, { "sub" : "http://purl.obolibrary.org/obo/CARO_0000006", "pred" : "is_a", @@ -15628,6 +15837,10 @@ "sub" : "http://purl.obolibrary.org/obo/ENVO_00000428", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/ENVO_01000254" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002552", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0040036" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002208", "pred" : "inverseOf", @@ -15645,13 +15858,13 @@ "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/BFO_0000050" }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0000086", + "sub" : "http://purl.obolibrary.org/obo/RO_0002565", "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0000053" + "obj" : "http://purl.obolibrary.org/obo/RO_0040036" }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0004026", + "sub" : "http://purl.obolibrary.org/obo/RO_0000086", "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0004023" + "obj" : "http://purl.obolibrary.org/obo/RO_0000053" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0004014", "pred" : "subPropertyOf", @@ -15681,13 +15894,17 @@ "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002258" }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002313", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0000057" + "sub" : "http://purl.obolibrary.org/obo/CARO_0000006", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CARO_0000000" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002596", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002500" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002298", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0040036" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002556", "pred" : "inverseOf", @@ -15785,6 +16002,9 @@ }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", "val" : "Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 42 Logical Axioms: 16]" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 56 Logical Axioms: 13]" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", "val" : "Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 20 Logical Axioms: 6]" @@ -15799,7 +16019,7 @@ "val" : "Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 6 Logical Axioms: 2]" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", - "val" : "Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 278 Logical Axioms: 58]" + "val" : "Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 9 Logical Axioms: 3]" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", "val" : "Includes Ontology(OntologyID(Anonymous-21)) [Axioms: 26 Logical Axioms: 0]" @@ -15808,13 +16028,13 @@ "val" : " https://github.com/oborel/obo-relations/" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", - "val" : "Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 61 Logical Axioms: 0]" + "val" : "Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 291 Logical Axioms: 62]" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", - "val" : "Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 731 Logical Axioms: 148]" + "val" : "Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 61 Logical Axioms: 0]" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", - "val" : "Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 53 Logical Axioms: 12]" + "val" : "Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 731 Logical Axioms: 148]" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", "val" : "Includes Ontology(OntologyID(Anonymous-21)) [Axioms: 32 Logical Axioms: 0]" @@ -15824,12 +16044,23 @@ }, { "pred" : "http://purl.org/dc/elements/1.1/title", "val" : "OBO Relations Ontology" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 110 Logical Axioms: 27]" } ], - "version" : "http://purl.obolibrary.org/obo/ro/releases/2018-05-11/ro.owl" + "version" : "http://purl.obolibrary.org/obo/ro/releases/2018-10-19/ro.owl" }, "equivalentNodesSets" : [ ], "logicalDefinitionAxioms" : [ ], "domainRangeAxioms" : [ { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0009002", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0009001", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ] + }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002176", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000004" ] }, { @@ -15841,15 +16072,27 @@ "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000141" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002177", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002573", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000020" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000020" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000020" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002574", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001010" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001010" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002211", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002179", + "allValuesFromEdges" : [ { + "sub" : "http://purl.obolibrary.org/obo/CARO_0000006", + "pred" : "http://purl.obolibrary.org/obo/RO_0002179", + "obj" : "http://purl.obolibrary.org/obo/CARO_0000003" + } ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002295", "domainClassIds" : [ "http://purl.obolibrary.org/obo/GO_0008150" ], @@ -15858,24 +16101,32 @@ "predicateId" : "http://purl.obolibrary.org/obo/RO_0002570", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0009003", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002571", "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002206", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000002" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000004" ] + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000006" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002207", "allValuesFromEdges" : [ { - "sub" : "http://purl.obolibrary.org/obo/CL_0000000", - "pred" : "http://purl.obolibrary.org/obo/RO_0002207", - "obj" : "http://purl.obolibrary.org/obo/CL_0000000" - }, { "sub" : "http://purl.obolibrary.org/obo/CARO_0010000", "pred" : "http://purl.obolibrary.org/obo/RO_0002207", "obj" : "http://purl.obolibrary.org/obo/CARO_0010000" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000000", + "pred" : "http://purl.obolibrary.org/obo/RO_0002207", + "obj" : "http://purl.obolibrary.org/obo/CL_0000000" } ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0000300", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/CL_0000540" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CL_0000540" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002202", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000004" ], @@ -15888,6 +16139,10 @@ "predicateId" : "http://purl.obolibrary.org/obo/RO_0002325", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002567", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002205", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000002" ], @@ -15900,12 +16155,23 @@ "predicateId" : "http://purl.obolibrary.org/obo/BFO_0000054", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000017" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0010002", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000004" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000031" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0010001", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000031" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000004" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002200", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000002" ] + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UPHENO_0001001" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002322", + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/ENVO_01000254" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000004" ] + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001010" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002437", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ], @@ -15916,7 +16182,7 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002315", - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CL_0000000" ] + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000091", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000004" ], @@ -15946,7 +16212,7 @@ "rangeClassIds" : [ "http://xmlns.com/foaf/0.1/image" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002303", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000006" ], + "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001010" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/ENVO_01000254" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000085", @@ -15956,6 +16222,10 @@ "predicateId" : "http://purl.obolibrary.org/obo/RO_0000087", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000004" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000023" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002384", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000000" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000000" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000086", "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000019" ] @@ -15969,6 +16239,17 @@ "predicateId" : "http://purl.obolibrary.org/obo/RO_0002258", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000002" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000002" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_HOM0000000", + "allValuesFromEdges" : [ { + "sub" : "http://purl.obolibrary.org/obo/BFO_0000003", + "pred" : "http://purl.obolibrary.org/obo/RO_HOM0000000", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000003" + }, { + "sub" : "http://purl.obolibrary.org/obo/BFO_0000002", + "pred" : "http://purl.obolibrary.org/obo/RO_HOM0000000", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000002" + } ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002414", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ], @@ -16001,8 +16282,8 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002254", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000004" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000000" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000000" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002375", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ], @@ -16014,29 +16295,60 @@ "predicateId" : "http://purl.obolibrary.org/obo/RO_0002256", "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002372", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002010", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002373", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002009", "domainClassIds" : [ "http://purl.obolibrary.org/obo/CL_0000000" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002004", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0004029", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/OGMS_0000031" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0004028", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000017" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002005", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001001" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0008506", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001010" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001010" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002007", "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ] }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0004025", - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000004" ] + "predicateId" : "http://purl.obolibrary.org/obo/RO_0008505", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001010" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001010" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002121", "domainClassIds" : [ "http://purl.obolibrary.org/obo/CL_0000540" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0004025", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/OGMS_0000031" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000006" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0004024", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/OGMS_0000031" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0004027", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/OGMS_0000031" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002244", "domainClassIds" : [ "http://purl.obolibrary.org/obo/RO_0002310" ] @@ -16050,16 +16362,20 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0004026", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/OGMS_0000031" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000004" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0004021", "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0004020", - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ] + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000006" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0004023", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000016" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/OGMS_0000031" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0004022", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/OGMS_0000031" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002514", "domainClassIds" : [ "http://purl.obolibrary.org/obo/RO_0002532" ], @@ -16076,6 +16392,10 @@ "predicateId" : "http://purl.obolibrary.org/obo/RO_0000057", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000002" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0001025", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000004" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000004" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002356", "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CL_0000000" ] @@ -16085,7 +16405,7 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000004" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0004019", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000016" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/OGMS_0000031" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0001021", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ] @@ -16096,6 +16416,9 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0001022", "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002111", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002232", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ], @@ -16141,7 +16464,7 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002226", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000000" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002501", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ], @@ -16163,7 +16486,8 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000004" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002100", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CL_0000540" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/CL_0000540" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002222", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ], @@ -16185,6 +16509,17 @@ "predicateId" : "http://purl.obolibrary.org/obo/RO_0002334", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002214", + "allValuesFromEdges" : [ { + "sub" : "http://purl.obolibrary.org/obo/BFO_0000015", + "pred" : "http://purl.obolibrary.org/obo/RO_0002214", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000015" + }, { + "sub" : "http://purl.obolibrary.org/obo/BFO_0000002", + "pred" : "http://purl.obolibrary.org/obo/RO_0002214", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000002" + } ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002215", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000004" ], @@ -16344,6 +16679,9 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/BFO_0000050", "http://purl.obolibrary.org/obo/RO_0002162" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0010002", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0000059", "http://purl.obolibrary.org/obo/RO_0000053" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0004028", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0009501", "http://purl.obolibrary.org/obo/RO_0002233" ] @@ -16374,6 +16712,9 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0009501", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/BFO_0000054", "http://purl.obolibrary.org/obo/RO_0002404" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0010001", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0000052", "http://purl.obolibrary.org/obo/RO_0000058" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002314", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002314", "http://purl.obolibrary.org/obo/BFO_0000050" ] diff --git a/ro.obo b/ro.obo index 328cb1ff..0b0d4d01 100644 --- a/ro.obo +++ b/ro.obo @@ -1,17 +1,19 @@ format-version: 1.2 -data-version: releases/2018-05-11 +data-version: releases/2018-10-19 subsetdef: ro-eco "" subsetdef: RO:0002259 "" remark: Includes Ontology(OntologyID(Anonymous-21)) [Axioms: 26 Logical Axioms: 0] remark: Includes Ontology(OntologyID(Anonymous-21)) [Axioms: 32 Logical Axioms: 0] remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 61 Logical Axioms: 0] remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 18 Logical Axioms: 7] -remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 53 Logical Axioms: 12] -remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 278 Logical Axioms: 58] +remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 56 Logical Axioms: 13] +remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 9 Logical Axioms: 3] +remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 291 Logical Axioms: 62] remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 6 Logical Axioms: 2] remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 42 Logical Axioms: 16] remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 49 Logical Axioms: 14] remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 29 Logical Axioms: 9] +remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 110 Logical Axioms: 27] remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 20 Logical Axioms: 6] remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 731 Logical Axioms: 148] remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 146 Logical Axioms: 45] @@ -20,18 +22,21 @@ property_value: http://purl.org/dc/elements/1.1/description "The OBO Relations O property_value: http://purl.org/dc/elements/1.1/source http://obofoundry.org/ro property_value: http://purl.org/dc/elements/1.1/title "OBO Relations Ontology" xsd:string property_value: http://xmlns.com/foaf/0.1/homepage " https://github.com/oborel/obo-relations/" xsd:anyURI -owl-axioms: Prefix(owl:=)\nPrefix(rdf:=)\nPrefix(xml:=)\nPrefix(xsd:=)\nPrefix(rdfs:=)\n\n\nOntology(\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\n############################\n# Annotation Properties\n############################\n\n# Annotation Property: (first order logic expression)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (temporal interpretation)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (never in taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (mutually spatially disjoint with)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (taxonomic class assertion)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (ambiguous for taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (dubious for taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (present in taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (annotation property cardinality)\n\nSubAnnotationPropertyOf( )\nAnnotationPropertyRange( xsd:nonNegativeInteger)\n\n# Annotation Property: (logical macro assertion on a class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on a property)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on an object property)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on an annotation property)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (dispositional interpretation)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has no connections with)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (curator guidance link)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (always present in taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (temporal logical macro assertion on a class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (measurement property has unit)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has start time value)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has end time value)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, days post fertilization)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, days post fertilization)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, years post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, years post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, months post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, months post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (month of gestation)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has developmental stage marker)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, days post coitum)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, days post coitum)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, weeks post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, weeks post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is asymmetric relational form of process class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is symmetric relational form of process class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is relational form of process class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is direct form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is indirect form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on an axiom)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is a defining property chain axiom)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is a defining property chain axiom where second argument is reflexive)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is relational form of a class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion involving identity)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (in approximate one to one relationship with)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is approximately equivalent to)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is opposite of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is indistinguishable from)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (evidential logical macro assertion on an axiom)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (axiom has evidence)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (axiom contradicted by evidence)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is representative IRI for equivalence set)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is directional form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is positive form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is negative form of)\n\nSubAnnotationPropertyOf( )\n\n\n############################\n# Object Properties\n############################\n\n# Object Property: (coincident with)\n\nObjectPropertyRange( ObjectIntersectionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (synapsed by)\n\nObjectPropertyRange( ObjectUnionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (has fasciculating neuron projection)\n\nObjectPropertyRange( ObjectUnionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (connected to)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (connects)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (directly develops from)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (enabled by)\n\nSubObjectPropertyOf( ObjectInverseOf())\n\n# Object Property: (has member)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (anabranch of)\n\nSubObjectPropertyOf( ObjectInverseOf())\n\n# Object Property: (branching part of)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (differs in attribute of)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (condition has genetic basis in)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has feature)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (has substance added)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (has substance removed)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (immersed in)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (has primary substance added)\n\nIrreflexiveObjectProperty()\n\n\n\n############################\n# Classes\n############################\n\n# Class: (continuant)\n\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: (occurrent)\n\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: (material entity)\n\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: (immaterial entity)\n\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: (ubiquitin-protein ligase activity)\n\nSubClassOf( ObjectHasSelf())\n\n# Class: (kinase activity)\n\nSubClassOf( ObjectHasSelf())\n\n# Class: (symbiosis, encompassing mutualism through parasitism)\n\nSubClassOf( ObjectHasSelf())\n\n# Class: (parasitism)\n\nSubClassOf( ObjectHasSelf())\n\n# Class: (mutualism)\n\nSubClassOf( ObjectHasSelf())\n\n# Class: (commensalism)\n\nSubClassOf( ObjectHasSelf())\n\n\nSubClassOf(ObjectSomeValuesFrom( ) ObjectUnionOf(ObjectSomeValuesFrom( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( ObjectSomeValuesFrom( ObjectSomeValuesFrom( )))))\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain(ObjectInverseOf() ) )\nSubObjectPropertyOf(ObjectPropertyChain(ObjectInverseOf() ) )\nDLSafeRule(Annotation( \"true\"^^xsd:boolean) Annotation(rdfs:comment \"MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z\"^^xsd:string) Annotation(rdfs:label \"infer input from direct reg\"^^xsd:string) Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z),\ne.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity'\") Annotation(rdfs:label \"enabling an MF enables its parts\") Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation( \"true\"^^xsd:boolean) Annotation(rdfs:comment \"GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction'\"^^xsd:string) Annotation(rdfs:label \"involved in BP\"^^xsd:string) Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"From ligand activity to has_ligand\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"This rule is dubious: added as a quick fix for expected inference in GO-CAM. The problem is most acute for transmembrane proteins, such as receptors or cell adhesion molecules, which have some subfunctions inside the cell (e.g. kinase activity) and some subfunctions outside (e.g. ligand binding). Correct annotation of where these functions occurs leads to incorrect inference about the location of the whole protein. This should probably be weakened to \\\"... -> overlaps\\\"\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this.\") Annotation(rdfs:label \"inferring direct reg edge from input to regulatory subfunction\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"inferring direct neg reg edge from input to regulatory subfunction\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"inferring direct positive reg edge from input to regulatory subfunction\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"From has_ligand to ligand activity\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"effector input is compound function input\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"Input of effector is input of its parent MF\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"if effector directly regulates X, its parent MF directly regulates X\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"if effector directly positively regulates X, its parent MF directly positively regulates X\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"if effector directly negatively regulates X, its parent MF directly negatively regulates X\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nAnnotationAssertion(rdfs:comment \"\")\n) +owl-axioms: Prefix(owl:=)\nPrefix(rdf:=)\nPrefix(xml:=)\nPrefix(xsd:=)\nPrefix(rdfs:=)\n\n\nOntology(\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(DataProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\n############################\n# Annotation Properties\n############################\n\n# Annotation Property: (first order logic expression)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (temporal interpretation)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (never in taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (mutually spatially disjoint with)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (taxonomic class assertion)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (ambiguous for taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (dubious for taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (present in taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (annotation property cardinality)\n\nSubAnnotationPropertyOf( )\nAnnotationPropertyRange( xsd:nonNegativeInteger)\n\n# Annotation Property: (logical macro assertion on a class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on a property)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on an object property)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on an annotation property)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (dispositional interpretation)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has no connections with)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (curator guidance link)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (always present in taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (temporal logical macro assertion on a class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (measurement property has unit)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has start time value)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has end time value)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, days post fertilization)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, days post fertilization)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, years post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, years post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, months post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, months post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (month of gestation)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has developmental stage marker)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, days post coitum)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, days post coitum)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, weeks post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, weeks post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is asymmetric relational form of process class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is symmetric relational form of process class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is relational form of process class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is direct form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is indirect form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on an axiom)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is a defining property chain axiom)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is a defining property chain axiom where second argument is reflexive)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is relational form of a class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion involving identity)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (in approximate one to one relationship with)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is approximately equivalent to)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is opposite of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is indistinguishable from)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (evidential logical macro assertion on an axiom)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (axiom has evidence)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (axiom contradicted by evidence)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is representative IRI for equivalence set)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is directional form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is positive form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is negative form of)\n\nSubAnnotationPropertyOf( )\n\n\n############################\n# Object Properties\n############################\n\n# Object Property: (located in)\n\nObjectPropertyRange( ObjectIntersectionOf( ObjectComplementOf()))\n\n# Object Property: (coincident with)\n\nObjectPropertyRange( ObjectIntersectionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (synapsed by)\n\nObjectPropertyRange( ObjectUnionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (has fasciculating neuron projection)\n\nObjectPropertyRange( ObjectUnionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (connected to)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (connects)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (directly develops from)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (has member)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (anabranch of)\n\nSubObjectPropertyOf( ObjectInverseOf())\n\n# Object Property: (branching part of)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (differs in attribute of)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (condition has genetic basis in)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has basis in feature)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has location)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has feature)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (has substance added)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (has substance removed)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (immersed in)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (has primary substance added)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (has anatomical participant)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n\n############################\n# Data Properties\n############################\n\n# Data Property: (has increased age-specific mortality rate)\n\nDataPropertyRange( DatatypeRestriction(xsd:short xsd:minInclusive \"0\"^^xsd:short xsd:maxInclusive \"100\"^^xsd:short))\n\n\n\n############################\n# Classes\n############################\n\n# Class: (continuant)\n\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: (occurrent)\n\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: (material entity)\n\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: (immaterial entity)\n\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: (ubiquitin-protein ligase activity)\n\nSubClassOf( ObjectHasSelf())\n\n# Class: (kinase activity)\n\nSubClassOf( ObjectHasSelf())\n\n# Class: (symbiosis, encompassing mutualism through parasitism)\n\nSubClassOf( ObjectHasSelf())\n\n# Class: (parasitism)\n\nSubClassOf( ObjectHasSelf())\n\n# Class: (mutualism)\n\nSubClassOf( ObjectHasSelf())\n\n# Class: (commensalism)\n\nSubClassOf( ObjectHasSelf())\n\n\nSubClassOf(ObjectSomeValuesFrom( ) ObjectUnionOf(ObjectSomeValuesFrom( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( ObjectSomeValuesFrom( ObjectSomeValuesFrom( )))))\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain(ObjectInverseOf() ) )\nSubObjectPropertyOf(ObjectPropertyChain(ObjectInverseOf() ) )\nDLSafeRule(Annotation( \"true\"^^xsd:boolean) Annotation(rdfs:comment \"MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z\"^^xsd:string) Annotation(rdfs:label \"infer input from direct reg\"^^xsd:string) Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z),\ne.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity'\") Annotation(rdfs:label \"enabling an MF enables its parts\") Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation( \"true\"^^xsd:boolean) Annotation(rdfs:comment \"GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction'\"^^xsd:string) Annotation(rdfs:label \"involved in BP\"^^xsd:string) Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"From ligand activity to has_ligand\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"This rule is dubious: added as a quick fix for expected inference in GO-CAM. The problem is most acute for transmembrane proteins, such as receptors or cell adhesion molecules, which have some subfunctions inside the cell (e.g. kinase activity) and some subfunctions outside (e.g. ligand binding). Correct annotation of where these functions occurs leads to incorrect inference about the location of the whole protein. This should probably be weakened to \\\"... -> overlaps\\\"\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this.\") Annotation(rdfs:label \"inferring direct reg edge from input to regulatory subfunction\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"inferring direct neg reg edge from input to regulatory subfunction\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"inferring direct positive reg edge from input to regulatory subfunction\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"From has_ligand to ligand activity\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"effector input is compound function input\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"Input of effector is input of its parent MF\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"if effector directly regulates X, its parent MF directly regulates X\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"if effector directly positively regulates X, its parent MF directly positively regulates X\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"if effector directly negatively regulates X, its parent MF directly negatively regulates X\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nAnnotationAssertion(rdfs:comment \"\")\n) [Term] id: BFO:0000002 name: continuant def: "An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts." [] disjoint_from: BFO:0000003 ! occurrent +relationship: RO:0002214 BFO:0000002 ! has prototype continuant +relationship: RO:HOM0000000 BFO:0000002 ! continuant [Term] id: BFO:0000003 name: occurrent def: "An entity that has temporal parts and that happens, unfolds or develops through time." [] +relationship: RO:HOM0000000 BFO:0000003 ! occurrent [Term] id: BFO:0000004 @@ -48,11 +53,17 @@ def: "A continuant that is either dependent on one or other independent continu is_a: ObsoleteClass ! Obsolete Class is_obsolete: true +[Term] +id: BFO:0000006 +name: spatial region +is_a: BFO:0000141 ! immaterial entity + [Term] id: BFO:0000015 name: process def: "An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t." [] is_a: BFO:0000003 ! occurrent +relationship: RO:0002214 BFO:0000015 ! has prototype process [Term] id: BFO:0000016 @@ -108,9 +119,15 @@ id: BFO:0000141 name: immaterial entity is_a: BFO:0000004 ! independent continuant +[Term] +id: CARO:0000000 +name: anatomical entity +is_a: CARO:0030000 ! biological entity +property_value: IAO:0000412 http://purl.obolibrary.org/obo/caro.owl + [Term] id: CARO:0000003 -name: anatomical structure +name: connected anatomical structure is_a: CARO:0000006 ! material anatomical entity property_value: IAO:0000412 http://purl.obolibrary.org/obo/caro.owl @@ -118,6 +135,8 @@ property_value: IAO:0000412 http://purl.obolibrary.org/obo/caro.owl id: CARO:0000006 name: material anatomical entity is_a: BFO:0000040 ! material entity +is_a: CARO:0000000 ! anatomical entity +relationship: RO:0002179 CARO:0000003 ! drains connected anatomical structure property_value: IAO:0000412 http://purl.obolibrary.org/obo/caro.owl [Term] @@ -128,20 +147,20 @@ is_a: BFO:0000141 ! immaterial entity [Term] id: CARO:0000011 name: connected anatomical system -is_a: CARO:0000006 ! material anatomical entity +is_a: CARO:0010000 ! multicellular anatomical structure is_a: RO:0002577 ! system [Term] id: CARO:0000014 name: cell part -is_a: CARO:0000003 ! anatomical structure +is_a: CARO:0000003 ! connected anatomical structure property_value: IAO:0000412 http://purl.obolibrary.org/obo/caro.owl property_value: IAO:0000589 "cell part (CARO)" xsd:string [Term] id: CARO:0001000 name: multi-cell-part structure -is_a: CARO:0000003 ! anatomical structure +is_a: CARO:0000003 ! connected anatomical structure property_value: IAO:0000412 http://purl.obolibrary.org/obo/caro.owl [Term] @@ -150,17 +169,27 @@ name: neuron projection bundle is_a: CARO:0001000 ! multi-cell-part structure property_value: IAO:0000412 http://purl.obolibrary.org/obo/caro.owl +[Term] +id: CARO:0001010 +name: organism or virus or viroid +is_a: BFO:0000040 ! material entity + [Term] id: CARO:0010000 name: multicellular anatomical structure -is_a: CARO:0000003 ! anatomical structure +is_a: CARO:0000003 ! connected anatomical structure relationship: RO:0002207 CARO:0010000 ! directly develops from multicellular anatomical structure property_value: IAO:0000412 http://purl.obolibrary.org/obo/caro.owl +[Term] +id: CARO:0030000 +name: biological entity +is_a: BFO:0000004 ! independent continuant + [Term] id: CL:0000000 name: cell -is_a: CARO:0000003 ! anatomical structure +is_a: CARO:0000003 ! connected anatomical structure relationship: RO:0002207 CL:0000000 ! directly develops from cell property_value: IAO:0000412 http://purl.obolibrary.org/obo/cl.owl @@ -196,10 +225,6 @@ id: GO:0004842 name: ubiquitin-protein ligase activity is_a: GO:0019787 ! small conjugating protein ligase activity -[Term] -id: GO:0004872 -name: receptor activity - [Term] id: GO:0005634 name: nucleus @@ -376,6 +401,12 @@ id: GO:0085031 name: commensalism is_a: GO:0044403 ! symbiosis, encompassing mutualism through parasitism +[Term] +id: OGMS:0000031 +name: disease +def: "A disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism." [] +is_a: BFO:0000016 ! disposition + [Term] id: ObsoleteClass name: Obsolete Class @@ -472,6 +503,11 @@ property_value: IAO:0000116 "May be replaced by a BFO class, as discussed in htt property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://www.jbiomedsem.com/content/4/1/43 xsd:string +[Term] +id: UPHENO:0001001 +name: phenotype +is_a: PATO:0000001 ! quality + [Typedef] id: BFO:0000050 name: part of @@ -542,6 +578,7 @@ id: BFO:0000060 name: obsolete preceded by comment: accidentally included in BFO 1.2 proposal\n - should have been BFO_0000062 is_transitive: true +is_obsolete: true [Typedef] id: BFO:0000062 @@ -771,6 +808,8 @@ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string property_value: IAO:0000426 "(forall (?x ?y) \n (iff \n (neural_circuit_path ?x ?y)\n (and\n (\"neuron ; CL_0000540\" ?x)\n (\"neuron ; CL_0000540\" ?y)\n (or \n (synapsed_by ?x ?y) \n (synapsed_to ?x ?y))))) \n\n(forall (...s ?x ?y ?z) \n (iff \n (neural_circuit_path ...s ?x ?y ?z)\n (and\n (neural_circuit_path ...s ?x ?y)\n (\"neuron ; CL_0000540\" ?z)\n (or \n (synapsed_by ?y ?z) \n (synapsed_to ?y ?z))))) \n\n(forall (?x ?y) \n (iff \n (in_neural_circuit_with ?x ?y)\n (exists (...s)\n (neural_circuit_path ?x ...s ?y)))) " xsd:string property_value: RO:0001900 RO:0001901 +domain: CL:0000540 ! neuron +range: CL:0000540 ! neuron is_transitive: true [Typedef] @@ -900,6 +939,8 @@ property_value: IAO:0000116 "Location as a relation between instances: The primi property_value: IAO:0000116 "Most location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime" xsd:string property_value: IAO:0000118 "located_in" xsd:string property_value: RO:0001900 RO:0001901 +domain: BFO:0000004 {http://purl.obolibrary.org/obo/IAO_0000116="This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation."} ! independent continuant +range: BFO:0000004 {http://purl.obolibrary.org/obo/IAO_0000116="This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation."} ! independent continuant is_transitive: true [Typedef] @@ -921,6 +962,7 @@ inverse_of: RO:0002002 ! has 2D boundary id: RO:0002001 name: aligned with property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000116 "May be obsoleted, see https://github.com/oborel/obo-relations/issues/260" xsd:string property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string property_value: RO:0001900 RO:0001901 is_transitive: true @@ -953,6 +995,8 @@ id: RO:0002004 name: tracheates def: "The relationship that holds between a trachea or tracheole and an antomical structure that is contained in (and so provides an oxygen supply to)." [] property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +domain: CARO:0000003 ! connected anatomical structure +range: CARO:0000003 ! connected anatomical structure is_a: RO:0001018 ! contained in [Typedef] @@ -960,6 +1004,8 @@ id: RO:0002005 name: innervated_by property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 xsd:anyURI property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +domain: CARO:0000003 ! connected anatomical structure +range: CARO:0001001 ! neuron projection bundle inverse_of: RO:0002134 ! innervates [Typedef] @@ -1082,7 +1128,7 @@ creation_date: 2017-05-24T09:49:21Z id: RO:0002019 name: has ligand def: "A relationship that holds between between a receptor and an chemical entity, typically a small molecule or peptide, that carries information between cells or compartments of a cell and which binds the receptor and regulates its effector function." [] -domain: GO:0004872 ! receptor activity +domain: GO:0004872 is_a: RO:0002233 ! has input created_by: dos creation_date: 2017-07-19T17:30:36Z @@ -1287,6 +1333,7 @@ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string property_value: RO:0001900 RO:0001901 domain: CL:0000540 ! neuron +range: CARO:0000003 ! connected anatomical structure is_a: RO:0002131 ! overlaps transitive_over: BFO:0000050 ! part of expand_expression_to: "BFO_0000051 some (\n GO_0043025 and BFO_0000050 some ?Y)" [] @@ -1434,6 +1481,7 @@ id: RO:0002111 name: releases neurotransmitter property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000118 "has neurotransmitter" xsd:string +domain: CARO:0000003 ! connected anatomical structure [Typedef] id: RO:0002112 @@ -1650,7 +1698,7 @@ property_value: IAO:0000117 "Jennifer Deegan" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/17921072 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20973947 property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Taxon-constraints -range: BFO:0000004 ! independent continuant +range: CARO:0001010 ! organism or virus or viroid holds_over_chain: BFO:0000050 RO:0002162 holds_over_chain: BFO:0000051 RO:0002162 holds_over_chain: results_in_developmental_progression_of RO:0002162 @@ -1704,8 +1752,9 @@ is_a: RO:0002323 ! mereotopologically related to id: RO:0002177 name: attached to part of def: "a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b." [] -domain: BFO:0000040 ! material entity -range: BFO:0000040 ! material entity +property_value: IAO:0000589 "attached to part of (anatomical structure to anatomical structure)" xsd:string +domain: CARO:0000003 ! connected anatomical structure +range: CARO:0000003 ! connected anatomical structure holds_over_chain: RO:0002371 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"} is_a: RO:0002323 ! mereotopologically related to is_a: RO:0002567 ! biomechanically related to @@ -1745,7 +1794,7 @@ def: "A relationship that holds between a biological entity and a phenotype. Her subset: ro-eco property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string -domain: BFO:0000002 ! continuant +range: UPHENO:0001001 ! phenotype inverse_of: RO:0002201 ! phenotype of [Typedef] @@ -1822,7 +1871,7 @@ property_value: IAO:0000112 "'neural crest cell' SubClassOf expresses some 'Wnt property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string domain: BFO:0000002 ! continuant -range: BFO:0000004 ! independent continuant +range: CARO:0000006 ! material anatomical entity is_a: RO:0002330 ! genomically related to inverse_of: RO:0002292 ! expresses transitive_over: BFO:0000050 ! part of @@ -1949,6 +1998,7 @@ name: capable of part of def: "c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p." [] property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "has function in" xsd:string +property_value: seeAlso "defining-property-chains-involving-reflexivity" holds_over_chain: RO:0002215 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"} is_a: RO:0002328 ! functionally related to is_a: RO:0002500 ! causal agent in process @@ -2066,7 +2116,7 @@ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 "EHDAA2" xsd:string property_value: IAO:0000119 "Jonathan Bard, EHDAA2" xsd:string -domain: CARO:0000003 ! anatomical structure +domain: CARO:0000000 ! anatomical entity holds_over_chain: RO:0002207 RO:0001025 is_a: RO:0002258 ! developmentally preceded by @@ -2261,8 +2311,8 @@ def: "x has developmental contribution from y iff x has some part z such that z property_value: IAO:0000112 "Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string -domain: BFO:0000004 ! independent continuant -range: CARO:0000003 ! anatomical structure +domain: CARO:0000000 ! anatomical entity +range: CARO:0000000 ! anatomical entity holds_over_chain: BFO:0000051 RO:0002202 is_a: RO:0002258 ! developmentally preceded by inverse_of: RO:0002255 ! developmentally contributes to @@ -2291,8 +2341,8 @@ property_value: IAO:0000119 " Developmental Biology, Gilbert, 8th edition, figur property_value: IAO:0000119 GO:0001759 xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 property_value: IAO:0000232 "We place this under 'developmentally preceded by'. This placement should be examined in the context of reciprocal inductions[cjm]" xsd:string -domain: CARO:0000003 ! anatomical structure -range: CARO:0000003 ! anatomical structure +domain: CARO:0000003 ! connected anatomical structure +range: CARO:0000003 ! connected anatomical structure is_a: RO:0002258 ! developmentally preceded by inverse_of: RO:0002257 ! developmentally induces @@ -2438,7 +2488,7 @@ property_value: IAO:0000112 "Hydrozoa (NCBITaxon_6074) SubClassOf 'has habitat' property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Pier Buttigieg" xsd:string property_value: IAO:0000118 "adapted for living in" xsd:string -domain: CARO:0000006 ! material anatomical entity +domain: CARO:0001010 ! organism or virus or viroid range: ENVO:01000254 ! environmental system is_a: RO:0002321 ! ecologically related to @@ -2483,8 +2533,8 @@ name: transports or maintains localization of def: "Holds between p and c when p is a localization process (localization covers maintenance of localization as well as its establishment) and the outcome of this process is to regulate the localization of c." [] property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "regulates localization of" xsd:string -is_a: RO:0000057 ! has participant is_a: RO:0002337 ! related via localization to +is_a: RO:0040036 ! has anatomical participant transitive_over: BFO:0000051 ! has part [Typedef] @@ -2495,6 +2545,7 @@ property_value: IAO:0000116 "Because part_of is transitive, inheres in is a sub- property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 property_value: RO:0001900 RO:0001901 +property_value: seeAlso "defining-property-chains-involving-reflexivity" holds_over_chain: RO:0000052 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"} is_a: RO:0002502 ! depends on transitive_over: BFO:0000050 ! part of @@ -2511,6 +2562,7 @@ id: RO:0002321 name: ecologically related to def: "A relationship that is mediated in some way by the environment or environmental feature (ENVO:00002297)" [] subset: ro-eco +property_value: IAO:0000116 "Awaiting class for domain/range constraint, see: https://github.com/OBOFoundry/Experimental-OBO-Core/issues/6" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving ecological interactions" xsd:string @@ -2521,6 +2573,7 @@ subset: ro-eco property_value: IAO:0000116 "An experimental relation currently used to connect a feature possessed by an organism (e.g. anatomical structure, biological process, phenotype or quality) to a habitat or environment in which that feature is well suited, adapted or provides a reproductive advantage for the organism. For example, fins to an aquatic environment. Usually this will mean that the structure is adapted for this environment, but we avoid saying this directly - primitive forms of the structure may not have evolved specifically for that environment (for example, early wings were not necessarily adapted for an aerial environment). Note also that this is a statement about the general class of structures - not every instance of a limb need confer an advantage for a terrestrial environment, e.g. if the limb is vestigial." xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "adapted for" xsd:string +range: ENVO:01000254 ! environmental system is_a: RO:0002321 ! ecologically related to [Typedef] @@ -2584,6 +2637,7 @@ transitive_over: RO:0002017 ! has component activity [Typedef] id: RO:0002328 name: functionally related to +def: "A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities." [] property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000232 "This is a grouping relation that collects relations used for the purpose of connecting structure and function" xsd:string @@ -2716,7 +2770,7 @@ name: results in growth of property_value: IAO:0000112 "'pollen tube growth' results_in growth_of some 'pollen tube'" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: results_in_developmental_progression_of ! results in developmental progression of -is_a: RO:0000057 ! has participant +is_a: RO:0040036 ! has anatomical participant [Typedef] id: RO:0002344 @@ -2803,7 +2857,7 @@ name: results in structural organization of def: "A relationship between a process and an anatomical entity such that the process contributes to the act of creating the structural organization of the anatomical entity." [] property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: results_in_developmental_progression_of ! results in developmental progression of -is_a: RO:0000057 ! has participant +is_a: RO:0040036 ! has anatomical participant [Typedef] id: RO:0002356 @@ -2834,6 +2888,7 @@ name: attached to def: "a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a" [] subset: ro-eco property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000589 "attached to (anatomical structure to anatomical structure)" xsd:string is_symmetric: true is_a: RO:0002170 ! connected to is_a: RO:0002177 ! attached to part of @@ -2845,6 +2900,7 @@ def: "m has_muscle_origin s iff m is attached_to s, and it is the case that when property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 Wikipedia:Insertion_(anatomy) xsd:string property_value: seeAlso http://dbpedia.org/property/origin +domain: CARO:0000003 {comment="We need to import uberon muscle to create a stricter domain constraint"} ! connected anatomical structure is_a: RO:0002371 ! attached to is_a: RO:0002567 ! biomechanically related to @@ -2855,20 +2911,22 @@ def: "m has_muscle_insertion s iff m is attaches_to s, and it is the case that w property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 Wikipedia:Insertion_(anatomy) xsd:string property_value: seeAlso http://dbpedia.org/property/insertion +domain: CARO:0000003 {http://purl.obolibrary.org/obo/IAO_0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} ! connected anatomical structure is_a: RO:0002371 ! attached to is_a: RO:0002567 ! biomechanically related to [Typedef] id: RO:0002374 -name: has fused element +name: derived from ancestral fusion of def: "x has_fused_element y iff: there exists some z : x has_part z, z homologous_to y, and y is a distinct element, the boundary between x and z is largely fiat" [] comment: A has_fused_element B does not imply that A has_part some B: rather than A has_part some B', where B' that has some evolutionary relationship to B. +synonym: "has fused element" BROAD [] property_value: IAO:0000112 "false" xsd:boolean property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 -is_a: RO:0002320 ! evolutionarily related to +is_a: RO:0002156 ! derived by descent from [Typedef] id: RO:0002375 @@ -2985,6 +3043,8 @@ name: has developmental potential involving def: "x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction)." [] property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Chris Mungall" xsd:string +domain: CARO:0000000 ! anatomical entity +range: CARO:0000000 ! anatomical entity is_a: RO:0002324 ! developmentally related to [Typedef] @@ -3056,7 +3116,6 @@ comment: Likely to be obsoleted. See:\nhttps://docs.google.com/document/d/1QMhs9 property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Chris Mungall" xsd:string holds_over_chain: RO:0002411 RO:0002402 -is_a: RO:0002234 ! has output is_obsolete: true [Typedef] @@ -3133,7 +3192,6 @@ property_value: IAO:0000114 IAO:0000428 property_value: 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." xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: 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." xsd:string -is_a: RO:0002609 ! related via dependence to [Typedef] id: RO:0002411 @@ -3258,6 +3316,7 @@ is_a: RO:0002428 ! involved in regulation of id: RO:0002431 name: involved in or involved in regulation of def: "c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p" [] +property_value: IAO:0000116 "OWL does not allow defining object properties via a Union" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "involved in or reguates" xsd:string is_a: RO:0002264 ! acts upstream of or within @@ -3593,7 +3652,7 @@ is_a: RO:0002461 ! partner in [Typedef] id: RO:0002464 -name: helper property +name: helper property (not for use in curation) property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000232 "This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning." xsd:string @@ -4190,7 +4249,7 @@ name: results in ending of def: "p results in the end of s if p results in a change of state in s whereby s either ceases to exist, or s becomes functionally impaired or s has its fate committed such that it is put on a path to be degraded." [] property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: results_in_developmental_progression_of ! results in developmental progression of -is_a: RO:0000057 ! has participant +is_a: RO:0040036 ! has anatomical participant [Typedef] id: RO:0002553 @@ -4271,7 +4330,7 @@ name: interaction relation helper property property_value: http://xmlns.com/foaf/0.1/page https://github.com/oborel/obo-relations/wiki/InteractionRelations xsd:anyURI property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:N-Ary_Relation_Pattern_%28OWL_2%29 -is_a: RO:0002464 ! helper property +is_a: RO:0002464 ! helper property (not for use in curation) [Typedef] id: RO:0002564 @@ -4285,7 +4344,7 @@ name: results in movement of def: "Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c" [] property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000232 "" xsd:string -is_a: RO:0000057 ! has participant +is_a: RO:0040036 ! has anatomical participant [Typedef] id: RO:0002566 @@ -4302,6 +4361,8 @@ name: biomechanically related to def: "A relation that holds between elements of a musculoskeletal system or its analogs." [] property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes." xsd:string +domain: CARO:0000003 ! connected anatomical structure +range: CARO:0000003 ! connected anatomical structure is_a: RO:0002328 ! functionally related to [Typedef] @@ -4361,6 +4422,7 @@ property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 property_value: IAO:0000232 "This relation is intended to be used in combination with PATO, to be able to refine PATO quality classes using modifiers such as 'abnormal' and 'normal'. It has yet to be formally aligned into an ontological framework; it's not clear what the ontological status of the \"modifiers\" are." xsd:string domain: BFO:0000020 ! specifically dependent continuant +range: BFO:0000020 ! specifically dependent continuant [Typedef] id: RO:0002574 @@ -4368,6 +4430,8 @@ name: participates in a biotic-biotic interaction with subset: ro-eco property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: seeAlso http://dx.doi.org/10.1016/j.ecoinf.2014.08.005 +domain: CARO:0001010 ! organism or virus or viroid +range: CARO:0001010 ! organism or virus or viroid is_a: RO:0002437 ! biotically interacts with [Typedef] @@ -4376,8 +4440,8 @@ name: skeleton of def: "inverse of has skeleton" [] subset: RO:0002259 property_value: IAO:0000117 "Chris Mungall" xsd:string -domain: CARO:0000003 ! anatomical structure -range: CARO:0000003 ! anatomical structure +domain: CARO:0000003 ! connected anatomical structure +range: CARO:0000003 ! connected anatomical structure is_a: BFO:0000050 ! part of [Typedef] @@ -4412,7 +4476,7 @@ id: RO:0002585 name: results in closure of property_value: IAO:0000116 "p 'results in closure of' c if and only if p is a developmental process and p results in a state of c changing from open to closed." xsd:string is_a: results_in_developmental_progression_of ! results in developmental progression of -is_a: RO:0000057 ! has participant +is_a: RO:0040036 ! has anatomical participant [Typedef] id: RO:0002586 @@ -4453,7 +4517,7 @@ is_a: RO:0002592 ! results in organization of id: RO:0002592 name: results in organization of def: "p results in organization of c iff p results in the assembly, arrangement of constituent parts, or disassembly of c" [] -is_a: RO:0000057 ! has participant +is_a: RO:0040036 ! has anatomical participant [Typedef] id: RO:0002593 @@ -4542,16 +4606,16 @@ is_a: RO:0002410 ! causally related to [Typedef] id: RO:0002609 -name: related via dependence to +name: obsolete related via dependence to def: "A relationship that holds between two entities, where the relationship holds based on the presence or absence of statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes." [] property_value: 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." xsd:string +is_obsolete: true [Typedef] id: RO:0002610 name: correlated with def: "A relationship that holds between two entities, where the entities exhibit a statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes." [] property_value: IAO:0000232 "Groups both positive and negative correlation" xsd:string -is_a: RO:0002609 ! related via dependence to [Typedef] id: RO:0002614 @@ -4966,7 +5030,7 @@ creation_date: 2017-11-05T03:20:29Z [Typedef] id: RO:0004019 name: disease has basis in -domain: BFO:0000016 ! disposition +domain: OGMS:0000031 ! disease is_a: RO:0004017 ! realizable has basis in is_a: RO:0004023 ! causal relationship with disease as subject created_by: cjm @@ -4976,7 +5040,8 @@ creation_date: 2017-11-05T03:26:47Z id: RO:0004020 name: disease has basis in dysfunction of def: "A relation that holds between the disease and a material entity where the physical basis of the disease is a disorder of that material entity that affects its function." [] -range: BFO:0000040 ! material entity +property_value: IAO:0000589 "disease has basis in dysfunction of (disease to anatomical structure)" xsd:string +range: CARO:0000006 ! material anatomical entity is_a: RO:0004019 ! disease has basis in created_by: cjm creation_date: 2017-11-05T03:29:32Z @@ -4985,6 +5050,7 @@ creation_date: 2017-11-05T03:29:32Z id: RO:0004021 name: disease has basis in disruption of def: "A relation that holds between the disease and a process where the physical basis of the disease disrupts execution of a key biological process." [] +property_value: IAO:0000589 "disease has basis in disruption of (disease to process)" xsd:string range: BFO:0000015 ! process is_a: RO:0004019 ! disease has basis in created_by: cjm @@ -4994,6 +5060,7 @@ creation_date: 2017-11-05T03:37:52Z id: RO:0004022 name: disease has basis in feature def: "A relation that holds between the disease and a feature (a phenotype or other disease) where the physical basis of the disease is the feature." [] +domain: OGMS:0000031 ! disease is_a: RO:0002200 ! has phenotype is_a: RO:0004019 ! disease has basis in created_by: cjm @@ -5004,8 +5071,9 @@ id: RO:0004023 name: causal relationship with disease as subject property_value: IAO:0000116 "After import upper level from OGMS, make domain more specific." xsd:string property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all of which have a disease as the subject." xsd:string -domain: BFO:0000016 ! disposition +domain: OGMS:0000031 ! disease is_a: RO:0002410 ! causally related to +is_a: RO:0040035 ! disease relationship created_by: cjm creation_date: 2017-11-05T03:50:54Z @@ -5013,6 +5081,8 @@ creation_date: 2017-11-05T03:50:54Z id: RO:0004024 name: disease causes disruption of def: "A relationship between a disease and a process where the disease process disrupts the execution of the process." [] +property_value: IAO:0000589 "disease causes disruption of (disease to process)" xsd:string +domain: OGMS:0000031 ! disease range: BFO:0000015 ! process is_a: RO:0004023 ! causal relationship with disease as subject transitive_over: BFO:0000050 ! part of @@ -5022,7 +5092,9 @@ creation_date: 2017-11-05T03:51:09Z [Typedef] id: RO:0004025 name: disease causes dysfunction of -range: BFO:0000004 ! independent continuant +property_value: IAO:0000589 "disease causes dysfunction of (disease to anatomical entity)" xsd:string +domain: OGMS:0000031 ! disease +range: CARO:0000006 ! material anatomical entity is_a: RO:0004023 ! causal relationship with disease as subject transitive_over: BFO:0000050 ! part of created_by: cjm @@ -5034,8 +5106,9 @@ name: disease has location def: "A relationship between a disease and an anatomical entity where the disease has one or more features that are located in that entity." [] property_value: IAO:0000116 "TODO: complete range axiom once more of CARO has been mireoted in to this ontology" xsd:string property_value: IAO:0000232 "This relation is intentionally very general, and covers isolated diseases, where the disease is realized as a process occurring in the location, and syndromic diseases, where one or more of the features may be present in that location. Thus any given disease can have multiple locations in the sense defined here." xsd:string +domain: OGMS:0000031 ! disease range: BFO:0000004 ! independent continuant -is_a: RO:0004023 ! causal relationship with disease as subject +is_a: RO:0040035 ! disease relationship created_by: cjm creation_date: 2017-11-05T04:06:02Z @@ -5043,6 +5116,8 @@ creation_date: 2017-11-05T04:06:02Z id: RO:0004027 name: disease has inflammation site def: "A relationship between a disease and an anatomical entity where the disease is triggered by an inflammatory response to stimuli occurring in the anatomical entity" [] +domain: OGMS:0000031 ! disease +range: CARO:0000003 ! connected anatomical structure is_a: RO:0004026 ! disease has location created_by: cjm creation_date: 2017-12-26T19:37:31Z @@ -5062,7 +5137,8 @@ creation_date: 2017-12-26T19:45:49Z id: RO:0004029 name: disease has feature def: "A relationship between a disease and some feature of that disease, where the feature is either a phenotype or an isolated disease." [] -is_a: RO:0004023 ! causal relationship with disease as subject +domain: OGMS:0000031 ! disease +is_a: RO:0040035 ! disease relationship created_by: cjm creation_date: 2017-12-26T19:50:53Z @@ -5070,7 +5146,7 @@ creation_date: 2017-12-26T19:50:53Z id: RO:0004030 name: disease arises from structure def: "A relationship between a disease and an anatomical structure where the material basis of the disease is some pathological change in the structure." [] -range: CARO:0000003 ! anatomical structure +range: CARO:0000003 ! connected anatomical structure is_a: RO:0004019 ! disease has basis in created_by: cjm creation_date: 2017-12-26T19:58:44Z @@ -5177,12 +5253,16 @@ is_a: RO:0002445 ! parasitized by id: RO:0008505 name: creates habitat for def: "An interaction relationship wherein one organism creates a structure or environment that is lived in by another organism." [] +domain: CARO:0001010 ! organism or virus or viroid +range: CARO:0001010 ! organism or virus or viroid is_a: RO:0002321 ! ecologically related to [Typedef] id: RO:0008506 -name: co-occurs +name: ecologically co-occurs with def: "An interaction relationship describing organisms that often occur together at the same time and space or in the same environment." [] +domain: CARO:0001010 ! organism or virus or viroid +range: CARO:0001010 ! organism or virus or viroid is_symmetric: true is_a: RO:0002321 ! ecologically related to @@ -5207,6 +5287,8 @@ property_value: IAO:0000112 "muffin 'has substance added' some 'baking soda'" xs property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000116 "The relation X 'has substance added' some Y doesn't imply that X still has Y in any detectable fashion subsequent to the addition. Water in dehydrated food or ice cubes are examples, as is food that undergoes chemical transformation. This definition should encompass recipe ingredients." xsd:string property_value: IAO:0000117 "Damion Dooley" xsd:string +domain: BFO:0000040 ! material entity +range: BFO:0000040 ! material entity [Typedef] id: RO:0009002 @@ -5215,6 +5297,8 @@ def: "\"has substance removed\" is a relation existing between two physical enti property_value: IAO:0000112 "'egg white' 'has substance removed' some 'egg yolk'" xsd:string property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Damion Dooley" xsd:string +domain: BFO:0000040 ! material entity +range: BFO:0000040 ! material entity [Typedef] id: RO:0009003 @@ -5223,6 +5307,8 @@ def: "\"immersed in\" is a relation between a (physical) entity and a fluid subs property_value: IAO:0000112 "sardines 'immersed in' some 'oil and mustard'" xsd:string property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Damion Dooley" xsd:string +domain: BFO:0000040 ! material entity +range: BFO:0000040 ! material entity [Typedef] id: RO:0009005 @@ -5251,6 +5337,50 @@ range: BFO:0000015 ! process holds_over_chain: BFO:0000054 RO:0002404 is_a: RO:0002410 ! causally related to +[Typedef] +id: RO:0010001 +name: generically depends on +def: "A generically dependent continuant *b* generically depends on an independent continuant *c* at time *t* means: there inheres in *c* a specifically deendent continuant which concretizes *b* at *t*." [] +synonym: "g-depends on" EXACT [] +property_value: IAO:0000112 "Genetic information generically depend on molecules of DNA." xsd:string +property_value: IAO:0000112 "The novel *War and Peace* generically depends on this copy of the novel." xsd:string +property_value: IAO:0000112 "The pattern shared by chess boards generically depends on any chess board." xsd:string +property_value: IAO:0000112 "The score of a symphony g-depends on a copy of the score." xsd:string +property_value: IAO:0000112 "This pdf file generically depends on this server." xsd:string +property_value: IAO:0000119 "[072-ISO]" xsd:string +domain: BFO:0000031 ! generically dependent continuant +range: BFO:0000004 ! independent continuant +holds_over_chain: RO:0000052 RO:0000058 +inverse_of: RO:0010002 ! is carrier of + +[Typedef] +id: RO:0010002 +name: is carrier of +def: "*b* is carrier of *c* at time *t* if and only if *c* *g-depends on* *b* at *t*" [] +property_value: IAO:0000112 "Molecules of DNA are carriers of genetic information." xsd:string +property_value: IAO:0000112 "This copy of *War and Peace* is carrier of the novel written by Tolstoy." xsd:string +property_value: IAO:0000112 "This hard drive is carrier of these data items." xsd:string +property_value: IAO:0000119 "[072-ISO]" xsd:string +domain: BFO:0000004 ! independent continuant +range: BFO:0000031 ! generically dependent continuant +holds_over_chain: RO:0000059 RO:0000053 + +[Typedef] +id: RO:0040035 +name: disease relationship +def: "This relation groups relations between diseases and any other kind of entity." [] +property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, in which the subject or object is a disease." xsd:string +created_by: cjm +creation_date: 2018-09-26T00:00:32Z + +[Typedef] +id: RO:0040036 +name: has anatomical participant +def: "p has anatomical participant c iff p has participant c, and c is an anatomical entity" [] +is_a: RO:0000057 ! has participant +created_by: cjm +creation_date: 2018-09-26T01:08:58Z + [Typedef] id: RO:HOM0000000 name: in similarity relationship with @@ -6104,9 +6234,9 @@ def: "The relationship that links a specified entity with the process that resul property_value: IAO:0000112 "an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast." xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string -range: CL:0000000 ! cell +range: CARO:0000003 ! connected anatomical structure is_a: results_in_developmental_progression_of ! results in developmental progression of -is_a: RO:0000057 ! has participant +is_a: RO:0040036 ! has anatomical participant [Typedef] id: results_in_development_of @@ -6117,7 +6247,7 @@ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://www.geneontology.org/GO.doc.development.shtml xsd:anyURI is_a: results_in_developmental_progression_of ! results in developmental progression of -is_a: RO:0000057 ! has participant +is_a: RO:0040036 ! has anatomical participant [Typedef] id: results_in_developmental_progression_of @@ -6128,7 +6258,7 @@ property_value: IAO:0000116 "This property and its subproperties are being used property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: seeAlso Ontology:extensions domain: GO:0008150 ! biological_process -range: CARO:0000003 ! anatomical structure +range: CARO:0000003 ! connected anatomical structure is_a: RO:0002324 ! developmentally related to [Typedef] @@ -6162,7 +6292,7 @@ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string is_a: results_in_developmental_progression_of ! results in developmental progression of -is_a: RO:0000057 ! has participant +is_a: RO:0040036 ! has anatomical participant [Typedef] id: results_in_morphogenesis_of @@ -6174,5 +6304,5 @@ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string is_a: results_in_developmental_progression_of ! results in developmental progression of -is_a: RO:0000057 ! has participant +is_a: RO:0040036 ! has anatomical participant diff --git a/ro.owl b/ro.owl index 747dd01f..9d59e0e3 100644 --- a/ro.owl +++ b/ro.owl @@ -17,14 +17,16 @@ xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:subsets="http://purl.obolibrary.org/obo/ro/subsets#"> - + + + The OBO Relations Ontology (RO) is a collection of OWL relations (ObjectProperties) intended for use across a wide variety of biological ontologies. @@ -65,10 +67,7 @@ - - - OBO foundry unique label - + @@ -842,6 +841,8 @@ Where we have an annotation assertion + + A relation that holds between two neurons connected directly via a synapse, or indirectly via a series of synaptically connected neurons. David Osumi-Sutherland @@ -1049,6 +1050,7 @@ range: spatial region or site (immaterial continuant) + May be obsoleted, see https://github.com/oborel/obo-relations/issues/260 David Osumi-Sutherland aligned with @@ -1081,6 +1083,8 @@ range: spatial region or site (immaterial continuant) + + The relationship that holds between a trachea or tracheole and an antomical structure that is contained in (and so provides an oxygen supply to). David Osumi-Sutherland tracheates @@ -1092,6 +1096,8 @@ range: spatial region or site (immaterial continuant) + + David Osumi-Sutherland http://www.ncbi.nlm.nih.gov/pubmed/22402613 innervated_by @@ -1534,6 +1540,7 @@ Examples include: the relationship between two channels collected simultaneously + @@ -1796,6 +1803,7 @@ Examples include: the relationship between two channels collected simultaneously + has neurotransmitter releases neurotransmitter @@ -2201,7 +2209,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - + @@ -2334,13 +2342,14 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - - + + a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b. + attached to part of (anatomical structure to anatomical structure) attached to part of @@ -2400,7 +2409,16 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - + + + + + + + + + + A relationship that holds between a biological entity and a phenotype. Here a phenotype is construed broadly as any kind of quality of an organism part, a collection of these qualities, or a change in quality or qualities (e.g. abnormally increased temperature). The subject of this relationship can be an organism (where the organism has the phenotype, i.e. the qualities inhere in parts of this organism), a genomic entity such as a gene or genotype (if modifications of the gene or the genotype causes the phenotype), or a condition such as a disease (such that if the condition inheres in an organism, then the organism has the phenotype). Chris Mungall @@ -2509,7 +2527,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - + @@ -2672,6 +2690,14 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. + + + + + + + + 'human p53 protein' SubClassOf some ('has prototype' some ('participates in' some 'DNA repair')) heart SubClassOf 'has prototype' some ('participates in' some 'blood circulation') @@ -2723,6 +2749,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.has function in RO_0000053 some (RO_0000054 only (BFO_0000050 some ?Y)) capable of part of + @@ -2870,7 +2897,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - + @@ -3163,8 +3190,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - - + + @@ -3251,31 +3278,19 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - - - c has-biological-role r iff c has-role r and r is a biological role (CHEBI:24432) - has biological role - + - - - c has-application-role r iff c has-role r and r is an application role (CHEBI:33232) - has application role - + - - - c has-chemical-role r iff c has-role r and r is a chemical role (CHEBI:51086) - has chemical role - + @@ -3413,8 +3428,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - + every flower development (GO:0009908) results in development of some flower (PO:0009046) p 'results in development of' c if and only if p is a developmental process and p results in the state of c changing from its initial state as a primordium or anlage through its mature state and to its final state. @@ -3446,8 +3461,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - + an annotation of gene X to cell morphogenesis with results_in_morphogenesis_of CL:0000540 (neuron) means that at the end of the process an input neuron has attained its shape. tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723) @@ -3463,8 +3478,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - + an annotation of gene X to cell maturation with results_in_maturation_of CL:0000057 (fibroblast) means that the fibroblast is mature at the end of the process bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474) @@ -3521,7 +3536,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - + Hydrozoa (NCBITaxon_6074) SubClassOf 'has habitat' some 'Hydrozoa habitat' where @@ -3591,8 +3606,8 @@ where - + @@ -3623,6 +3638,7 @@ where inheres in part of + @@ -3639,9 +3655,9 @@ where - - + + an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast. The relationship that links a specified entity with the process that results in an unspecified entity acquiring the features and characteristics of the specified entity Chris Mungall @@ -3667,6 +3683,7 @@ where A relationship that is mediated in some way by the environment or environmental feature (ENVO:00002297) + Awaiting class for domain/range constraint, see: https://github.com/OBOFoundry/Experimental-OBO-Core/issues/6 Chris Mungall Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving ecological interactions @@ -3679,6 +3696,7 @@ where + An experimental relation currently used to connect a feature possessed by an organism (e.g. anatomical structure, biological process, phenotype or quality) to a habitat or environment in which that feature is well suited, adapted or provides a reproductive advantage for the organism. For example, fins to an aquatic environment. Usually this will mean that the structure is adapted for this environment, but we avoid saying this directly - primitive forms of the structure may not have evolved specifically for that environment (for example, early wings were not necessarily adapted for an aerial environment). Note also that this is a statement about the general class of structures - not every instance of a limb need confer an advantage for a terrestrial environment, e.g. if the limb is vestigial. Chris Mungall adapted for @@ -3785,6 +3803,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities. Chris Mungall This is a grouping relation that collects relations used for the purpose of connecting structure and function functionally related to @@ -3871,11 +3890,6 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - - - - - inverse of enables Chris Mungall enabled by @@ -4006,8 +4020,8 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - + 'pollen tube growth' results_in growth_of some 'pollen tube' Chris Mungall results in growth of @@ -4108,8 +4122,8 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - + A relationship between a process and an anatomical entity such that the process contributes to the act of creating the structural organization of the anatomical entity. Chris Mungall results in structural organization of @@ -4160,6 +4174,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a Chris Mungall + attached to (anatomical structure to anatomical structure) attached to @@ -4171,12 +4186,19 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to. Chris Mungall Wikipedia:Insertion_(anatomy) has muscle origin + + + + + We need to import uberon muscle to create a stricter domain constraint + @@ -4185,27 +4207,35 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone. Chris Mungall Wikipedia:Insertion_(anatomy) has muscle insertion + + + + + We need to import uberon muscle into RO to use as a stricter domain constraint + - + false x has_fused_element y iff: there exists some z : x has_part z, z homologous_to y, and y is a distinct element, the boundary between x and z is largely fiat Chris Mungall Chris Mungall + has fused element A has_fused_element B does not imply that A has_part some B: rather than A has_part some B', where B' that has some evolutionary relationship to B. - has fused element + derived from ancestral fusion of @@ -4379,6 +4409,8 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + + x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction). Chris Mungall @@ -4484,7 +4516,6 @@ https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/ - @@ -4613,7 +4644,6 @@ https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/ - This relation groups causal relations between material entities and causal relations between processes 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. @@ -4841,6 +4871,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p + OWL does not allow defining object properties via a Union Chris Mungall involved in or reguates involved in or involved in regulation of @@ -5384,7 +5415,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different Chris Mungall This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning. - helper property + helper property (not for use in curation) @@ -5621,6 +5652,14 @@ the a supports either the existence of b, or the truth value of b. + + + + + + + + Chris Mungall Do not use this relation directly. It is ended as a grouping for a diverse set of relations, typically connecting an anatomical entity to a biological process or developmental stage. @@ -6311,8 +6350,8 @@ the a supports either the existence of b, or the truth value of b. - + p results in the end of s if p results in a change of state in s whereby s either ceases to exist, or s becomes functionally impaired or s has its fate committed such that it is put on a path to be degraded. Chris Mungall results in ending of @@ -6452,7 +6491,7 @@ the a supports either the existence of b, or the truth value of b. - + Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c Chris Mungall @@ -6488,6 +6527,8 @@ the a supports either the existence of b, or the truth value of b. + + A relation that holds between elements of a musculoskeletal system or its analogs. Chris Mungall Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes. @@ -6568,6 +6609,7 @@ the a supports either the existence of b, or the truth value of b. + A relation that holds between an attribute or a qualifier and another attribute. Chris Mungall @@ -6582,6 +6624,8 @@ the a supports either the existence of b, or the truth value of b. + + Chris Mungall participates in a biotic-biotic interaction with @@ -6649,8 +6693,8 @@ the a supports either the existence of b, or the truth value of b. - + p 'results in closure of' c if and only if p is a developmental process and p results in a state of c changing from open to closed. results in closure of @@ -6719,7 +6763,7 @@ the a supports either the existence of b, or the truth value of b. - + p results in organization of c iff p results in the assembly, arrangement of constituent parts, or disassembly of c results in organization of @@ -6871,7 +6915,8 @@ the a supports either the existence of b, or the truth value of b. A relationship that holds between two entities, where the relationship holds based on the presence or absence of statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. - related via dependence to + obsolete related via dependence to + true @@ -6879,7 +6924,6 @@ the a supports either the existence of b, or the truth value of b. - A relationship that holds between two entities, where the entities exhibit a statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes. Groups both positive and negative correlation correlated with @@ -7539,7 +7583,7 @@ Environmental exposures include those imposed by natural environments, experimen - + cjm 2017-11-05T03:26:47Z disease has basis in @@ -7551,8 +7595,9 @@ Environmental exposures include those imposed by natural environments, experimen - + A relation that holds between the disease and a material entity where the physical basis of the disease is a disorder of that material entity that affects its function. + disease has basis in dysfunction of (disease to anatomical structure) cjm 2017-11-05T03:29:32Z disease has basis in dysfunction of @@ -7566,6 +7611,7 @@ Environmental exposures include those imposed by natural environments, experimen A relation that holds between the disease and a process where the physical basis of the disease disrupts execution of a key biological process. + disease has basis in disruption of (disease to process) cjm 2017-11-05T03:37:52Z disease has basis in disruption of @@ -7578,6 +7624,15 @@ Environmental exposures include those imposed by natural environments, experimen + + + + + + + + + A relation that holds between the disease and a feature (a phenotype or other disease) where the physical basis of the disease is the feature. cjm 2017-11-05T03:46:07Z @@ -7590,7 +7645,8 @@ Environmental exposures include those imposed by natural environments, experimen - + + After import upper level from OGMS, make domain more specific. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all of which have a disease as the subject. cjm @@ -7604,12 +7660,14 @@ Environmental exposures include those imposed by natural environments, experimen + A relationship between a disease and a process where the disease process disrupts the execution of the process. + disease causes disruption of (disease to process) cjm 2017-11-05T03:51:09Z disease causes disruption of @@ -7621,11 +7679,13 @@ Environmental exposures include those imposed by natural environments, experimen - + + + disease causes dysfunction of (disease to anatomical entity) cjm 2017-11-05T03:58:20Z disease causes dysfunction of @@ -7636,8 +7696,17 @@ Environmental exposures include those imposed by natural environments, experimen - + + + + + + + + + + A relationship between a disease and an anatomical entity where the disease has one or more features that are located in that entity. TODO: complete range axiom once more of CARO has been mireoted in to this ontology This relation is intentionally very general, and covers isolated diseases, where the disease is realized as a process occurring in the location, and syndromic diseases, where one or more of the features may be present in that location. Thus any given disease can have multiple locations in the sense defined here. @@ -7652,6 +7721,8 @@ Environmental exposures include those imposed by natural environments, experimen + + A relationship between a disease and an anatomical entity where the disease is triggered by an inflammatory response to stimuli occurring in the anatomical entity cjm 2017-12-26T19:37:31Z @@ -7681,12 +7752,13 @@ Environmental exposures include those imposed by natural environments, experimen - + + - - + + @@ -7872,6 +7944,8 @@ Environmental exposures include those imposed by natural environments, experimen + + An interaction relationship wherein one organism creates a structure or environment that is lived in by another organism. creates habitat for @@ -7883,8 +7957,10 @@ Environmental exposures include those imposed by natural environments, experimen + + An interaction relationship describing organisms that often occur together at the same time and space or in the same environment. - co-occurs + ecologically co-occurs with @@ -7914,6 +7990,8 @@ Environmental exposures include those imposed by natural environments, experimen + + muffin 'has substance added' some 'baking soda' "has substance added" is a relation existing between a (physical) entity and a substance in which the entity has had the substance added to it at some point in time. @@ -7928,6 +8006,8 @@ Environmental exposures include those imposed by natural environments, experimen + + 'egg white' 'has substance removed' some 'egg yolk' "has substance removed" is a relation existing between two physical entities in which the first entity has had the second entity (a substance) removed from it at some point in time. @@ -7941,6 +8021,8 @@ Environmental exposures include those imposed by natural environments, experimen + + sardines 'immersed in' some 'oil and mustard' "immersed in" is a relation between a (physical) entity and a fluid substance in which the entity is wholely or substantially surrounded by the substance. @@ -7995,175 +8077,217 @@ Environmental exposures include those imposed by natural environments, experimen - - - - - - - - - + - - - + + + + + + + + + Genetic information generically depend on molecules of DNA. + The novel *War and Peace* generically depends on this copy of the novel. + The pattern shared by chess boards generically depends on any chess board. + The score of a symphony g-depends on a copy of the score. + This pdf file generically depends on this server. + A generically dependent continuant *b* generically depends on an independent continuant *c* at time *t* means: there inheres in *c* a specifically deendent continuant which concretizes *b* at *t*. + [072-ISO] + g-depends on + generically depends on + - + - + + + + + + + + Molecules of DNA are carriers of genetic information. + This copy of *War and Peace* is carrier of the novel written by Tolstoy. + This hard drive is carrier of these data items. + *b* is carrier of *c* at time *t* if and only if *c* *g-depends on* *b* at *t* + [072-ISO] + is carrier of + - + + + This relation groups relations between diseases and any other kind of entity. + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, in which the subject or object is a disease. + cjm + 2018-09-26T00:00:32Z + disease relationship + - + - - - - anatomical structure - + + + + + + + + + + + p has anatomical participant c iff p has participant c, and c is an anatomical entity + cjm + 2018-09-26T01:08:58Z + has anatomical participant + - + - - - - material anatomical entity - + + + - + - - - immaterial anatomical entity - + + + - + - - - - connected anatomical system - + - + - - - - cell part (CARO) - cell part - - + - - - - multi-cell-part structure - + + + + + + + 0 + + + 100 + + + + + Then percentage of organisms in a population that die during some specified age range (age-specific mortality rate), minus the percentage that die in during the same age range in a wild-type population. + 2018-05-22T16:43:28Z + This could be used to record the increased infant morality rate in some population compared to wild-type. For examples of usage see http://purl.obolibrary.org/obo/FBcv_0000351 and subclasses. + has increased age-specific mortality rate + dos + + + + + Then percentage of organisms in a population that die during some specified age range (age-specific mortality rate), minus the percentage that die in during the same age range in a wild-type population. + PMID:24138933 + Wikipedia:Infant_mortality + - + - - - - neuron projection bundle - - + - - + - - + + - - multicellular anatomical structure - - - - - - - - - - + + - - cell - + - + - - - - neuron - + + + + + + + + - + - - - biome - + + + + + + + + - + - - - environmental system - + + + + + + + + - + - - - molecular process - + @@ -8182,21 +8306,7 @@ Environmental exposures include those imposed by natural environments, experimen - - receptor activity - - - - - - - - - - - - - + @@ -8271,56 +8381,6 @@ Environmental exposures include those imposed by natural environments, experimen - - - - - quality (PATO) - - - - - - - - - - - - - - - - - shape - - - - - - - - - branched - - - - - - - - - - - - - - - branchiness - - - - @@ -8380,14 +8440,14 @@ Environmental exposures include those imposed by natural environments, experimen - + A material entity consisting of multiple components that are causally integrated. May be replaced by a BFO class, as discussed in http://www.jbiomedsem.com/content/4/1/43 Chris Mungall http://www.jbiomedsem.com/content/4/1/43 system - + @@ -8405,29 +8465,8 @@ Environmental exposures include those imposed by natural environments, experimen /////////////////////////////////////////////////////////////////////////////////////// --> - - - curation status specification - - - ready for release - - - - - pending final vetting - - - - obsolescence reason specification - - - requires discussion - - - - - term replaced by + + true inverse of has disposition @@ -8543,6 +8582,18 @@ Environmental exposures include those imposed by natural environments, experimen + + + + + + + + + + + + @@ -8756,6 +8807,76 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + From ligand activity to has_ligand diff --git a/src/ontology/Makefile b/src/ontology/Makefile index 4a4defd6..09a1a020 100644 --- a/src/ontology/Makefile +++ b/src/ontology/Makefile @@ -116,6 +116,16 @@ subsets/ro-hom.owl: ro.owl subsets/ro-chado.obo: ro.obo owltools --use-catalog $< --merge-imports-closure --remove-tbox --remove-annotation-assertions -r -l -s -d --remove-dangling --set-ontology-id $(OBO)/ro/$@ -o -f obo $@.tmp && ../tools/translate-to-chado-obo.pl $@.tmp > $@ +# ======================================== +# REPORTING (EXPERIMENTAL) +# ======================================== +# requires sparqlprog + +usage.tsv: ro-base.owl + pq-ontobee -f tsv -e -i $< "owl:objectProperty(P), label(P,PN), (ontobee ?? aggregate_group(count(Restr),[P,G],rdf(Restr,owl:onProperty,P,G),Num))" "x(P,PN,G,Num)" > $@.tmp && mv $@.tmp $@ +usage-full.tsv: + pq-ontobee -f tsv -e -i ro.owl "owl:objectProperty(P), (ontobee ?? rdf(Restr,owl:onProperty,P,G),label(P,PN))" "x(Restr,P,PN,G)" > $@.tmp && mv $@.tmp $@ + # ======================================== # EXPERIMENTAL # ======================================== diff --git a/src/ontology/ro-diff.md b/src/ontology/ro-diff.md index 62694f56..00105f07 100644 --- a/src/ontology/ro-diff.md +++ b/src/ontology/ro-diff.md @@ -1,185 +1,550 @@ ---- -comments: true -layout: post -title: "/releases/2018-03-13/ro.owl" -date: 2018-03-13 -summary: "" -categories: release -image: '/anatomy/images/u-logo.jpg' -tags: - - release ---- - -# Ontology Diff Report ## Original Ontology * IRI: http://purl.obolibrary.org/obo/ro.owl - * VersionIRI: http://purl.obolibrary.org/obo/ro/releases/2018-01-05b/ro.owl + * VersionIRI: http://purl.obolibrary.org/obo/ro/releases/2018-05-11/ro.owl ## New Ontology * IRI: http://purl.obolibrary.org/obo/ro.owl - * VersionIRI: http://purl.obolibrary.org/obo/ro/releases/2018-03-13/ro.owl + * VersionIRI: http://purl.obolibrary.org/obo/ro/releases/2018-10-01/ro.owl # Report for classes -## Class objects lost from source: 0 +## Class objects lost from source: 10 + + * [branchiness](http://purl.obolibrary.org/obo/PATO_0002009) + * [morphology](http://purl.obolibrary.org/obo/PATO_0000051) + * [shape](http://purl.obolibrary.org/obo/PATO_0000052) + * [biome](http://purl.obolibrary.org/obo/ENVO_00000428) + * [cell part](http://purl.obolibrary.org/obo/CARO_0000014) + * [disposition](http://purl.obolibrary.org/obo/BFO_0000016) + * [quality](http://purl.obolibrary.org/obo/PATO_0000001) + * [connected anatomical system](http://purl.obolibrary.org/obo/CARO_0000011) + * [multi-cell-part structure](http://purl.obolibrary.org/obo/CARO_0001000) + * [null](http://purl.obolibrary.org/obo/GO_0005515) + +## Class objects new in target: 4 + + +### New Class : [generically dependent continuant](http://purl.obolibrary.org/obo/BFO_0000031) + + * [generically dependent continuant](http://purl.obolibrary.org/obo/BFO_0000031) *[definition](http://purl.obolibrary.org/obo/IAO_0000115)* A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time. + * [generically dependent continuant](http://purl.obolibrary.org/obo/BFO_0000031) **SubClassOf** [continuant](http://purl.obolibrary.org/obo/BFO_0000002) + * DisjointClasses( [independent continuant](http://purl.obolibrary.org/obo/BFO_0000004) [generically dependent continuant](http://purl.obolibrary.org/obo/BFO_0000031) ) + * DisjointClasses( [specifically dependent continuant](http://purl.obolibrary.org/obo/BFO_0000020) [generically dependent continuant](http://purl.obolibrary.org/obo/BFO_0000031) ) + * [generically dependent continuant](http://purl.obolibrary.org/obo/BFO_0000031) *[label](http://www.w3.org/2000/01/rdf-schema#label)* generically dependent continuant + +### New Class : [organism or virus or viroid](http://purl.obolibrary.org/obo/CARO_0001010) + + * [organism or virus or viroid](http://purl.obolibrary.org/obo/CARO_0001010) **SubClassOf** [material entity](http://purl.obolibrary.org/obo/BFO_0000040) + * [organism or virus or viroid](http://purl.obolibrary.org/obo/CARO_0001010) *[label](http://www.w3.org/2000/01/rdf-schema#label)* organism or virus or viroid + +### New Class : [disease](http://purl.obolibrary.org/obo/OGMS_0000031) + + * [disease](http://purl.obolibrary.org/obo/OGMS_0000031) *[label](http://www.w3.org/2000/01/rdf-schema#label)* disease + * [disease](http://purl.obolibrary.org/obo/OGMS_0000031) **SubClassOf** [disposition](http://purl.obolibrary.org/obo/BFO_0000016) + * [disease](http://purl.obolibrary.org/obo/OGMS_0000031) *[definition](http://purl.obolibrary.org/obo/IAO_0000115)* A disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism. + +### New Class : [phenotype](http://purl.obolibrary.org/obo/UPHENO_0001001) + + * [phenotype](http://purl.obolibrary.org/obo/UPHENO_0001001) **SubClassOf** [quality](http://purl.obolibrary.org/obo/PATO_0000001) + * [phenotype](http://purl.obolibrary.org/obo/UPHENO_0001001) *[label](http://www.w3.org/2000/01/rdf-schema#label)* phenotype + +## Changed Class objects: 5 + + +### Changes for: [material anatomical entity](http://purl.obolibrary.org/obo/CARO_0000006) + + * _Added_ + * **+** [material anatomical entity](http://purl.obolibrary.org/obo/CARO_0000006) **SubClassOf** ObjectAllValuesFrom( [drains](http://purl.obolibrary.org/obo/RO_0002179) [anatomical structure](http://purl.obolibrary.org/obo/CARO_0000003) ) + +### Changes for: [occurrent](http://purl.obolibrary.org/obo/BFO_0000003) + + * _Added_ + * **+** [occurrent](http://purl.obolibrary.org/obo/BFO_0000003) **SubClassOf** ObjectAllValuesFrom( [in similarity relationship with](http://purl.obolibrary.org/obo/RO_HOM0000000) [occurrent](http://purl.obolibrary.org/obo/BFO_0000003) ) + +### Changes for: [null](http://purl.obolibrary.org/obo/GO_0004872) + * _Deleted_ + * **-** [receptor activity](http://purl.obolibrary.org/obo/GO_0004872) *[label](http://www.w3.org/2000/01/rdf-schema#label)* receptor activity -## Class objects new in target: 0 +### Changes for: [process](http://purl.obolibrary.org/obo/BFO_0000015) + * _Added_ + * **+** [process](http://purl.obolibrary.org/obo/BFO_0000015) **SubClassOf** ObjectAllValuesFrom( [has prototype](http://purl.obolibrary.org/obo/RO_0002214) [process](http://purl.obolibrary.org/obo/BFO_0000015) ) -## Changed Class objects: 0 +### Changes for: [continuant](http://purl.obolibrary.org/obo/BFO_0000002) + * _Added_ + * **+** [continuant](http://purl.obolibrary.org/obo/BFO_0000002) **SubClassOf** ObjectAllValuesFrom( [has prototype](http://purl.obolibrary.org/obo/RO_0002214) [continuant](http://purl.obolibrary.org/obo/BFO_0000002) ) + * **+** [continuant](http://purl.obolibrary.org/obo/BFO_0000002) **SubClassOf** ObjectAllValuesFrom( [in similarity relationship with](http://purl.obolibrary.org/obo/RO_HOM0000000) [continuant](http://purl.obolibrary.org/obo/BFO_0000002) ) # Report for properties -## ObjectProperty objects lost from source: 0 +## ObjectProperty objects lost from source: 1 + * [has role](http://purl.obolibrary.org/obo/RO_0000087) ## ObjectProperty objects new in target: 7 -### New ObjectProperty : [causally upstream of or within, negative effect](http://purl.obolibrary.org/obo/RO_0004046) +### New ObjectProperty : [has anatomical participant](http://purl.obolibrary.org/obo/RO_0040036) + + * ObjectPropertyRange( [has anatomical participant](http://purl.obolibrary.org/obo/RO_0040036) [material anatomical entity](http://purl.obolibrary.org/obo/CARO_0000006) **or** [immaterial anatomical entity](http://purl.obolibrary.org/obo/CARO_0000007) ) + * [has anatomical participant](http://purl.obolibrary.org/obo/RO_0040036) *[creation date](http://www.geneontology.org/formats/oboInOwl#creation_date)* 2018-09-26T01:08:58Z + * [has anatomical participant](http://purl.obolibrary.org/obo/RO_0040036) *[definition](http://purl.obolibrary.org/obo/IAO_0000115)* p has anatomical participant c iff p has participant c, and c is an anatomical entity + * SubObjectPropertyOf( [has anatomical participant](http://purl.obolibrary.org/obo/RO_0040036) [has participant](http://purl.obolibrary.org/obo/RO_0000057) ) + * [has anatomical participant](http://purl.obolibrary.org/obo/RO_0040036) *[label](http://www.w3.org/2000/01/rdf-schema#label)* has anatomical participant + * [has anatomical participant](http://purl.obolibrary.org/obo/RO_0040036) *[created by](http://www.geneontology.org/formats/oboInOwl#created_by)* cjm + +### New ObjectProperty : [disease relationship](http://purl.obolibrary.org/obo/RO_0040035) + + * [disease relationship](http://purl.obolibrary.org/obo/RO_0040035) *[created by](http://www.geneontology.org/formats/oboInOwl#created_by)* cjm + * [disease relationship](http://purl.obolibrary.org/obo/RO_0040035) *[creation date](http://www.geneontology.org/formats/oboInOwl#creation_date)* 2018-09-26T00:00:32Z + * [disease relationship](http://purl.obolibrary.org/obo/RO_0040035) *[label](http://www.w3.org/2000/01/rdf-schema#label)* disease relationship + * [disease relationship](http://purl.obolibrary.org/obo/RO_0040035) *[definition](http://purl.obolibrary.org/obo/IAO_0000115)* This relation groups relations between diseases and any other kind of entity. + * [disease relationship](http://purl.obolibrary.org/obo/RO_0040035) *[curator note](http://purl.obolibrary.org/obo/IAO_0000232)* Do not use this relation directly. It is intended as a grouping for a diverse set of relations, in which the subject or object is a disease. + +### New ObjectProperty : [in similarity relationship with](http://purl.obolibrary.org/obo/RO_HOM0000000) + + * [in similarity relationship with](http://purl.obolibrary.org/obo/RO_HOM0000000) *[database cross reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref)* ECO:0000041 + * [in similarity relationship with](http://purl.obolibrary.org/obo/RO_HOM0000000) *[definition](http://purl.obolibrary.org/obo/IAO_0000115)* Relation between biological objects that resemble or are related to each other sufficiently to warrant a comparison. { [database cross reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref)=[http://purl.obolibrary.org/obo/HOM_0000000](http://purl.obolibrary.org/obo/HOM_0000000) , [database cross reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref)=BGEE:curator } + * [in similarity relationship with](http://purl.obolibrary.org/obo/RO_HOM0000000) *[http://purl.org/dc/elements/1.1/creator](http://purl.org/dc/elements/1.1/creator)* [http://bgee.unil.ch](http://bgee.unil.ch) + * [in similarity relationship with](http://purl.obolibrary.org/obo/RO_HOM0000000) *[has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym)* sameness + * [in similarity relationship with](http://purl.obolibrary.org/obo/RO_HOM0000000) *[database cross reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref)* SO:similar_to + * [in similarity relationship with](http://purl.obolibrary.org/obo/RO_HOM0000000) *[has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym)* similar to + * [in similarity relationship with](http://purl.obolibrary.org/obo/RO_HOM0000000) *[seeAlso](http://www.w3.org/2000/01/rdf-schema#seeAlso)* [http://purl.obolibrary.org/obo/HOM_0000000](http://purl.obolibrary.org/obo/HOM_0000000) + * [in similarity relationship with](http://purl.obolibrary.org/obo/RO_HOM0000000) *[label](http://www.w3.org/2000/01/rdf-schema#label)* in similarity relationship with + * SymmetricObjectProperty( [in similarity relationship with](http://purl.obolibrary.org/obo/RO_HOM0000000) ) + * [in similarity relationship with](http://purl.obolibrary.org/obo/RO_HOM0000000) *[has related synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym)* resemblance + * [in similarity relationship with](http://purl.obolibrary.org/obo/RO_HOM0000000) *[has related synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym)* correspondence { [database cross reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref)=[http://dx.doi.org/10.1007/BF02814479](http://dx.doi.org/10.1007/BF02814479) } + * [in similarity relationship with](http://purl.obolibrary.org/obo/RO_HOM0000000) *[http://purl.org/dc/elements/1.1/source](http://purl.org/dc/elements/1.1/source)* [http://www.ncbi.nlm.nih.gov/pubmed/20116127](http://www.ncbi.nlm.nih.gov/pubmed/20116127) + +### New ObjectProperty : [is concretized as](http://purl.obolibrary.org/obo/RO_0000058) + + * [is concretized as](http://purl.obolibrary.org/obo/RO_0000058) *[definition](http://purl.obolibrary.org/obo/IAO_0000115)* A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants. + * [is concretized as](http://purl.obolibrary.org/obo/RO_0000058) *[example of usage](http://purl.obolibrary.org/obo/IAO_0000112)* A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant). + * ObjectPropertyRange( [is concretized as](http://purl.obolibrary.org/obo/RO_0000058) [specifically dependent continuant](http://purl.obolibrary.org/obo/BFO_0000020) ) + * [is concretized as](http://purl.obolibrary.org/obo/RO_0000058) *[example of usage](http://purl.obolibrary.org/obo/IAO_0000112)* An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process). + * InverseObjectProperties( [is concretized as](http://purl.obolibrary.org/obo/RO_0000058) [concretizes](http://purl.obolibrary.org/obo/RO_0000059) ) + * ObjectPropertyDomain( [is concretized as](http://purl.obolibrary.org/obo/RO_0000058) [generically dependent continuant](http://purl.obolibrary.org/obo/BFO_0000031) ) + * [is concretized as](http://purl.obolibrary.org/obo/RO_0000058) *[label](http://www.w3.org/2000/01/rdf-schema#label)* is concretized as + +### New ObjectProperty : [concretizes](http://purl.obolibrary.org/obo/RO_0000059) + + * [concretizes](http://purl.obolibrary.org/obo/RO_0000059) *[example of usage](http://purl.obolibrary.org/obo/IAO_0000112)* A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant). + * [concretizes](http://purl.obolibrary.org/obo/RO_0000059) *[definition](http://purl.obolibrary.org/obo/IAO_0000115)* A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant. + * ObjectPropertyDomain( [concretizes](http://purl.obolibrary.org/obo/RO_0000059) [specifically dependent continuant](http://purl.obolibrary.org/obo/BFO_0000020) ) + * [concretizes](http://purl.obolibrary.org/obo/RO_0000059) *[example of usage](http://purl.obolibrary.org/obo/IAO_0000112)* An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process). + * [concretizes](http://purl.obolibrary.org/obo/RO_0000059) *[label](http://www.w3.org/2000/01/rdf-schema#label)* concretizes + * InverseObjectProperties( [is concretized as](http://purl.obolibrary.org/obo/RO_0000058) [concretizes](http://purl.obolibrary.org/obo/RO_0000059) ) + * ObjectPropertyRange( [concretizes](http://purl.obolibrary.org/obo/RO_0000059) [generically dependent continuant](http://purl.obolibrary.org/obo/BFO_0000031) ) + +### New ObjectProperty : [generically depends on](http://purl.obolibrary.org/obo/RO_0010001) + + * ObjectPropertyRange( [generically depends on](http://purl.obolibrary.org/obo/RO_0010001) [independent continuant](http://purl.obolibrary.org/obo/BFO_0000004) ) + * [generically depends on](http://purl.obolibrary.org/obo/RO_0010001) *[example of usage](http://purl.obolibrary.org/obo/IAO_0000112)* The novel *War and Peace* generically depends on this copy of the novel. + * [generically depends on](http://purl.obolibrary.org/obo/RO_0010001) *[label](http://www.w3.org/2000/01/rdf-schema#label)* generically depends on + * [generically depends on](http://purl.obolibrary.org/obo/RO_0010001) *[example of usage](http://purl.obolibrary.org/obo/IAO_0000112)* The score of a symphony g-depends on a copy of the score. + * [generically depends on](http://purl.obolibrary.org/obo/RO_0010001) *[definition source](http://purl.obolibrary.org/obo/IAO_0000119)* [072-ISO] + * [generically depends on](http://purl.obolibrary.org/obo/RO_0010001) *[example of usage](http://purl.obolibrary.org/obo/IAO_0000112)* This pdf file generically depends on this server. + * InverseObjectProperties( [generically depends on](http://purl.obolibrary.org/obo/RO_0010001) [is carrier of](http://purl.obolibrary.org/obo/RO_0010002) ) + * [generically depends on](http://purl.obolibrary.org/obo/RO_0010001) *[example of usage](http://purl.obolibrary.org/obo/IAO_0000112)* The pattern shared by chess boards generically depends on any chess board. + * ObjectPropertyDomain( [generically depends on](http://purl.obolibrary.org/obo/RO_0010001) [generically dependent continuant](http://purl.obolibrary.org/obo/BFO_0000031) ) + * [generically depends on](http://purl.obolibrary.org/obo/RO_0010001) *[example of usage](http://purl.obolibrary.org/obo/IAO_0000112)* Genetic information generically depend on molecules of DNA. + * [generically depends on](http://purl.obolibrary.org/obo/RO_0010001) *[definition](http://purl.obolibrary.org/obo/IAO_0000115)* A generically dependent continuant *b* generically depends on an independent continuant *c* at time *t* means: there inheres in *c* a specifically deendent continuant which concretizes *b* at *t*. + * [generically depends on](http://purl.obolibrary.org/obo/RO_0010001) *[has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym)* g-depends on + +### New ObjectProperty : [is carrier of](http://purl.obolibrary.org/obo/RO_0010002) + + * [is carrier of](http://purl.obolibrary.org/obo/RO_0010002) *[definition source](http://purl.obolibrary.org/obo/IAO_0000119)* [072-ISO] + * [is carrier of](http://purl.obolibrary.org/obo/RO_0010002) *[example of usage](http://purl.obolibrary.org/obo/IAO_0000112)* This hard drive is carrier of these data items. + * [is carrier of](http://purl.obolibrary.org/obo/RO_0010002) *[label](http://www.w3.org/2000/01/rdf-schema#label)* is carrier of + * ObjectPropertyDomain( [is carrier of](http://purl.obolibrary.org/obo/RO_0010002) [independent continuant](http://purl.obolibrary.org/obo/BFO_0000004) ) + * InverseObjectProperties( [generically depends on](http://purl.obolibrary.org/obo/RO_0010001) [is carrier of](http://purl.obolibrary.org/obo/RO_0010002) ) + * [is carrier of](http://purl.obolibrary.org/obo/RO_0010002) *[definition](http://purl.obolibrary.org/obo/IAO_0000115)* *b* is carrier of *c* at time *t* if and only if *c* *g-depends on* *b* at *t* + * [is carrier of](http://purl.obolibrary.org/obo/RO_0010002) *[example of usage](http://purl.obolibrary.org/obo/IAO_0000112)* This copy of *War and Peace* is carrier of the novel written by Tolstoy. + * ObjectPropertyRange( [is carrier of](http://purl.obolibrary.org/obo/RO_0010002) [generically dependent continuant](http://purl.obolibrary.org/obo/BFO_0000031) ) + * [is carrier of](http://purl.obolibrary.org/obo/RO_0010002) *[example of usage](http://purl.obolibrary.org/obo/IAO_0000112)* Molecules of DNA are carriers of genetic information. + +## Changed ObjectProperty objects: 58 + + +### Changes for: [in taxon](http://purl.obolibrary.org/obo/RO_0002162) + + * _Deleted_ + * **-** ObjectPropertyRange( [in taxon](http://purl.obolibrary.org/obo/RO_0002162) [independent continuant](http://purl.obolibrary.org/obo/BFO_0000004) ) + * _Added_ + * **+** ObjectPropertyRange( [in taxon](http://purl.obolibrary.org/obo/RO_0002162) [organism or virus or viroid](http://purl.obolibrary.org/obo/CARO_0001010) ) + +### Changes for: [results in maturation of](http://purl.obolibrary.org/obo/RO_0002299) + + * _Deleted_ + * **-** SubObjectPropertyOf( [results in maturation of](http://purl.obolibrary.org/obo/RO_0002299) [has participant](http://purl.obolibrary.org/obo/RO_0000057) ) + * _Added_ + * **+** SubObjectPropertyOf( [results in maturation of](http://purl.obolibrary.org/obo/RO_0002299) [has anatomical participant](http://purl.obolibrary.org/obo/RO_0040036) ) + +### Changes for: [attached to part of](http://purl.obolibrary.org/obo/RO_0002177) + + * _Deleted_ + * **-** ObjectPropertyDomain( [attached to part of](http://purl.obolibrary.org/obo/RO_0002177) [material entity](http://purl.obolibrary.org/obo/BFO_0000040) ) + * **-** ObjectPropertyRange( [attached to part of](http://purl.obolibrary.org/obo/RO_0002177) [material entity](http://purl.obolibrary.org/obo/BFO_0000040) ) + * _Added_ + * **+** ObjectPropertyDomain( [attached to part of](http://purl.obolibrary.org/obo/RO_0002177) [anatomical structure](http://purl.obolibrary.org/obo/CARO_0000003) ) + * **+** ObjectPropertyRange( [attached to part of](http://purl.obolibrary.org/obo/RO_0002177) [anatomical structure](http://purl.obolibrary.org/obo/CARO_0000003) ) + * **+** [attached to part of](http://purl.obolibrary.org/obo/RO_0002177) *[OBO foundry unique label](http://purl.obolibrary.org/obo/IAO_0000589)* attached to part of (anatomical structure to anatomical structure) + +### Changes for: [results in morphogenesis of](http://purl.obolibrary.org/obo/RO_0002298) + + * _Deleted_ + * **-** SubObjectPropertyOf( [results in morphogenesis of](http://purl.obolibrary.org/obo/RO_0002298) [has participant](http://purl.obolibrary.org/obo/RO_0000057) ) + * _Added_ + * **+** SubObjectPropertyOf( [results in morphogenesis of](http://purl.obolibrary.org/obo/RO_0002298) [has anatomical participant](http://purl.obolibrary.org/obo/RO_0040036) ) + +### Changes for: [results in development of](http://purl.obolibrary.org/obo/RO_0002296) + + * _Deleted_ + * **-** SubObjectPropertyOf( [results in development of](http://purl.obolibrary.org/obo/RO_0002296) [has participant](http://purl.obolibrary.org/obo/RO_0000057) ) + * _Added_ + * **+** SubObjectPropertyOf( [results in development of](http://purl.obolibrary.org/obo/RO_0002296) [has anatomical participant](http://purl.obolibrary.org/obo/RO_0040036) ) + +### Changes for: [disease has inflammation site](http://purl.obolibrary.org/obo/RO_0004027) + + * _Added_ + * **+** ObjectPropertyDomain( [disease has inflammation site](http://purl.obolibrary.org/obo/RO_0004027) [disease](http://purl.obolibrary.org/obo/OGMS_0000031) ) + * **+** ObjectPropertyRange( [disease has inflammation site](http://purl.obolibrary.org/obo/RO_0004027) [anatomical structure](http://purl.obolibrary.org/obo/CARO_0000003) ) + +### Changes for: [creates habitat for](http://purl.obolibrary.org/obo/RO_0008505) + + * _Added_ + * **+** ObjectPropertyDomain( [creates habitat for](http://purl.obolibrary.org/obo/RO_0008505) [organism or virus or viroid](http://purl.obolibrary.org/obo/CARO_0001010) ) + * **+** ObjectPropertyRange( [creates habitat for](http://purl.obolibrary.org/obo/RO_0008505) [organism or virus or viroid](http://purl.obolibrary.org/obo/CARO_0001010) ) + +### Changes for: [disease has feature](http://purl.obolibrary.org/obo/RO_0004029) + + * _Deleted_ + * **-** ObjectPropertyRange( [disease has feature](http://purl.obolibrary.org/obo/RO_0004029) [disposition](http://purl.obolibrary.org/obo/BFO_0000016) **or** [quality](http://purl.obolibrary.org/obo/BFO_0000019) ) + * **-** SubObjectPropertyOf( [disease has feature](http://purl.obolibrary.org/obo/RO_0004029) [causal relationship with disease as subject](http://purl.obolibrary.org/obo/RO_0004023) ) + * _Added_ + * **+** ObjectPropertyDomain( [disease has feature](http://purl.obolibrary.org/obo/RO_0004029) [disease](http://purl.obolibrary.org/obo/OGMS_0000031) ) + * **+** ObjectPropertyRange( [disease has feature](http://purl.obolibrary.org/obo/RO_0004029) [disease](http://purl.obolibrary.org/obo/OGMS_0000031) **or** [phenotype](http://purl.obolibrary.org/obo/UPHENO_0001001) ) + * **+** SubObjectPropertyOf( [disease has feature](http://purl.obolibrary.org/obo/RO_0004029) [disease relationship](http://purl.obolibrary.org/obo/RO_0040035) ) + +### Changes for: [ecologically co-occurs with](http://purl.obolibrary.org/obo/RO_0008506) + + * _Deleted_ + * **-** [co-occurs](http://purl.obolibrary.org/obo/RO_0008506) *[label](http://www.w3.org/2000/01/rdf-schema#label)* co-occurs + * _Added_ + * **+** ObjectPropertyDomain( [ecologically co-occurs with](http://purl.obolibrary.org/obo/RO_0008506) [organism or virus or viroid](http://purl.obolibrary.org/obo/CARO_0001010) ) + * **+** ObjectPropertyRange( [ecologically co-occurs with](http://purl.obolibrary.org/obo/RO_0008506) [organism or virus or viroid](http://purl.obolibrary.org/obo/CARO_0001010) ) + * **+** [ecologically co-occurs with](http://purl.obolibrary.org/obo/RO_0008506) *[label](http://www.w3.org/2000/01/rdf-schema#label)* ecologically co-occurs with + +### Changes for: [disease has basis in dysfunction of](http://purl.obolibrary.org/obo/RO_0004020) + + * _Deleted_ + * **-** ObjectPropertyRange( [disease has basis in dysfunction of](http://purl.obolibrary.org/obo/RO_0004020) [material entity](http://purl.obolibrary.org/obo/BFO_0000040) ) + * _Added_ + * **+** ObjectPropertyRange( [disease has basis in dysfunction of](http://purl.obolibrary.org/obo/RO_0004020) [material anatomical entity](http://purl.obolibrary.org/obo/CARO_0000006) ) + * **+** [disease has basis in dysfunction of](http://purl.obolibrary.org/obo/RO_0004020) *[OBO foundry unique label](http://purl.obolibrary.org/obo/IAO_0000589)* disease has basis in dysfunction of (disease to anatomical structure) + +### Changes for: [disease has basis in disruption of](http://purl.obolibrary.org/obo/RO_0004021) + + * _Added_ + * **+** [disease has basis in disruption of](http://purl.obolibrary.org/obo/RO_0004021) *[OBO foundry unique label](http://purl.obolibrary.org/obo/IAO_0000589)* disease has basis in disruption of (disease to process) + +### Changes for: [disease has basis in feature](http://purl.obolibrary.org/obo/RO_0004022) + + * _Added_ + * **+** ObjectPropertyDomain( [disease has basis in feature](http://purl.obolibrary.org/obo/RO_0004022) [disease](http://purl.obolibrary.org/obo/OGMS_0000031) ) + * **+** ObjectPropertyRange( [disease has basis in feature](http://purl.obolibrary.org/obo/RO_0004022) [disease](http://purl.obolibrary.org/obo/OGMS_0000031) **or** [phenotype](http://purl.obolibrary.org/obo/UPHENO_0001001) ) + +### Changes for: [causal relationship with disease as subject](http://purl.obolibrary.org/obo/RO_0004023) + + * _Deleted_ + * **-** ObjectPropertyDomain( [causal relationship with disease as subject](http://purl.obolibrary.org/obo/RO_0004023) [disposition](http://purl.obolibrary.org/obo/BFO_0000016) ) + * _Added_ + * **+** ObjectPropertyDomain( [causal relationship with disease as subject](http://purl.obolibrary.org/obo/RO_0004023) [disease](http://purl.obolibrary.org/obo/OGMS_0000031) ) + * **+** SubObjectPropertyOf( [causal relationship with disease as subject](http://purl.obolibrary.org/obo/RO_0004023) [disease relationship](http://purl.obolibrary.org/obo/RO_0040035) ) + +### Changes for: [disease causes disruption of](http://purl.obolibrary.org/obo/RO_0004024) + + * _Added_ + * **+** ObjectPropertyDomain( [disease causes disruption of](http://purl.obolibrary.org/obo/RO_0004024) [disease](http://purl.obolibrary.org/obo/OGMS_0000031) ) + * **+** [disease causes disruption of](http://purl.obolibrary.org/obo/RO_0004024) *[OBO foundry unique label](http://purl.obolibrary.org/obo/IAO_0000589)* disease causes disruption of (disease to process) + +### Changes for: [disease causes dysfunction of](http://purl.obolibrary.org/obo/RO_0004025) + + * _Deleted_ + * **-** ObjectPropertyRange( [disease causes dysfunction of](http://purl.obolibrary.org/obo/RO_0004025) [independent continuant](http://purl.obolibrary.org/obo/BFO_0000004) ) + * _Added_ + * **+** ObjectPropertyDomain( [disease causes dysfunction of](http://purl.obolibrary.org/obo/RO_0004025) [disease](http://purl.obolibrary.org/obo/OGMS_0000031) ) + * **+** ObjectPropertyRange( [disease causes dysfunction of](http://purl.obolibrary.org/obo/RO_0004025) [material anatomical entity](http://purl.obolibrary.org/obo/CARO_0000006) ) + * **+** [disease causes dysfunction of](http://purl.obolibrary.org/obo/RO_0004025) *[OBO foundry unique label](http://purl.obolibrary.org/obo/IAO_0000589)* disease causes dysfunction of (disease to anatomical entity) + +### Changes for: [disease has location](http://purl.obolibrary.org/obo/RO_0004026) + + * _Deleted_ + * **-** SubObjectPropertyOf( [disease has location](http://purl.obolibrary.org/obo/RO_0004026) [causal relationship with disease as subject](http://purl.obolibrary.org/obo/RO_0004023) ) + * _Added_ + * **+** ObjectPropertyDomain( [disease has location](http://purl.obolibrary.org/obo/RO_0004026) [disease](http://purl.obolibrary.org/obo/OGMS_0000031) ) + * **+** ObjectPropertyRange( [disease has location](http://purl.obolibrary.org/obo/RO_0004026) [material anatomical entity](http://purl.obolibrary.org/obo/CARO_0000006) **or** [immaterial anatomical entity](http://purl.obolibrary.org/obo/CARO_0000007) ) + * **+** SubObjectPropertyOf( [disease has location](http://purl.obolibrary.org/obo/RO_0004026) [disease relationship](http://purl.obolibrary.org/obo/RO_0040035) ) + +### Changes for: [disease has basis in](http://purl.obolibrary.org/obo/RO_0004019) + + * _Deleted_ + * **-** ObjectPropertyDomain( [disease has basis in](http://purl.obolibrary.org/obo/RO_0004019) [disposition](http://purl.obolibrary.org/obo/BFO_0000016) ) + * _Added_ + * **+** ObjectPropertyDomain( [disease has basis in](http://purl.obolibrary.org/obo/RO_0004019) [disease](http://purl.obolibrary.org/obo/OGMS_0000031) ) + +### Changes for: [has phenotype](http://purl.obolibrary.org/obo/RO_0002200) + + * _Deleted_ + * **-** ObjectPropertyDomain( [has phenotype](http://purl.obolibrary.org/obo/RO_0002200) [continuant](http://purl.obolibrary.org/obo/BFO_0000002) ) + * _Added_ + * **+** ObjectPropertyDomain( [has phenotype](http://purl.obolibrary.org/obo/RO_0002200) [generically dependent continuant](http://purl.obolibrary.org/obo/BFO_0000031) **or** [material anatomical entity](http://purl.obolibrary.org/obo/CARO_0000006) **or** [disease](http://purl.obolibrary.org/obo/OGMS_0000031) ) + * **+** ObjectPropertyRange( [has phenotype](http://purl.obolibrary.org/obo/RO_0002200) [phenotype](http://purl.obolibrary.org/obo/UPHENO_0001001) ) + +### Changes for: [ecologically related to](http://purl.obolibrary.org/obo/RO_0002321) + + * _Added_ + * **+** [ecologically related to](http://purl.obolibrary.org/obo/RO_0002321) *[editor note](http://purl.obolibrary.org/obo/IAO_0000116)* Awaiting class for domain/range constraint, see: https://github.com/OBOFoundry/Experimental-OBO-Core/issues/6 + +### Changes for: [functionally related to](http://purl.obolibrary.org/obo/RO_0002328) + + * _Added_ + * **+** [functionally related to](http://purl.obolibrary.org/obo/RO_0002328) *[definition](http://purl.obolibrary.org/obo/IAO_0000115)* A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities. + +### Changes for: [expressed in](http://purl.obolibrary.org/obo/RO_0002206) + + * _Deleted_ + * **-** ObjectPropertyRange( [expressed in](http://purl.obolibrary.org/obo/RO_0002206) [independent continuant](http://purl.obolibrary.org/obo/BFO_0000004) ) + * _Added_ + * **+** ObjectPropertyRange( [expressed in](http://purl.obolibrary.org/obo/RO_0002206) [material anatomical entity](http://purl.obolibrary.org/obo/CARO_0000006) ) + +### Changes for: [biomechanically related to](http://purl.obolibrary.org/obo/RO_0002567) + + * _Added_ + * **+** ObjectPropertyDomain( [biomechanically related to](http://purl.obolibrary.org/obo/RO_0002567) [anatomical structure](http://purl.obolibrary.org/obo/CARO_0000003) ) + * **+** ObjectPropertyRange( [biomechanically related to](http://purl.obolibrary.org/obo/RO_0002567) [anatomical structure](http://purl.obolibrary.org/obo/CARO_0000003) ) + +### Changes for: [results in movement of](http://purl.obolibrary.org/obo/RO_0002565) + + * _Deleted_ + * **-** SubObjectPropertyOf( [results in movement of](http://purl.obolibrary.org/obo/RO_0002565) [has participant](http://purl.obolibrary.org/obo/RO_0000057) ) + * _Added_ + * **+** SubObjectPropertyOf( [results in movement of](http://purl.obolibrary.org/obo/RO_0002565) [has anatomical participant](http://purl.obolibrary.org/obo/RO_0040036) ) + +### Changes for: [confers advantage in](http://purl.obolibrary.org/obo/RO_0002322) + + * _Added_ + * **+** ObjectPropertyRange( [confers advantage in](http://purl.obolibrary.org/obo/RO_0002322) [environmental system](http://purl.obolibrary.org/obo/ENVO_01000254) ) + +### Changes for: [involved in or involved in regulation of](http://purl.obolibrary.org/obo/RO_0002431) + + * _Added_ + * **+** [involved in or involved in regulation of](http://purl.obolibrary.org/obo/RO_0002431) *[editor note](http://purl.obolibrary.org/obo/IAO_0000116)* OWL does not allow defining object properties via a Union + +### Changes for: [results in ending of](http://purl.obolibrary.org/obo/RO_0002552) + + * _Deleted_ + * **-** SubObjectPropertyOf( [results in ending of](http://purl.obolibrary.org/obo/RO_0002552) [has participant](http://purl.obolibrary.org/obo/RO_0000057) ) + * _Added_ + * **+** SubObjectPropertyOf( [results in ending of](http://purl.obolibrary.org/obo/RO_0002552) [has anatomical participant](http://purl.obolibrary.org/obo/RO_0040036) ) + +### Changes for: [results in acquisition of features of](http://purl.obolibrary.org/obo/RO_0002315) + + * _Deleted_ + * **-** ObjectPropertyRange( [results in acquisition of features of](http://purl.obolibrary.org/obo/RO_0002315) [cell](http://purl.obolibrary.org/obo/CL_0000000) ) + * **-** SubObjectPropertyOf( [results in acquisition of features of](http://purl.obolibrary.org/obo/RO_0002315) [has participant](http://purl.obolibrary.org/obo/RO_0000057) ) + * _Added_ + * **+** ObjectPropertyRange( [results in acquisition of features of](http://purl.obolibrary.org/obo/RO_0002315) [anatomical structure](http://purl.obolibrary.org/obo/CARO_0000003) ) + * **+** SubObjectPropertyOf( [results in acquisition of features of](http://purl.obolibrary.org/obo/RO_0002315) [has anatomical participant](http://purl.obolibrary.org/obo/RO_0040036) ) + +### Changes for: [inheres in part of](http://purl.obolibrary.org/obo/RO_0002314) + + * _Added_ + * **+** [inheres in part of](http://purl.obolibrary.org/obo/RO_0002314) *[seeAlso](http://www.w3.org/2000/01/rdf-schema#seeAlso)* [defining-property-chains-involving-reflexivity](https://github.com/oborel/obo-relations/wiki/ROGuide#defining-property-chains-involving-reflexivity) + +### Changes for: [transports or maintains localization of](http://purl.obolibrary.org/obo/RO_0002313) + + * _Deleted_ + * **-** SubObjectPropertyOf( [transports or maintains localization of](http://purl.obolibrary.org/obo/RO_0002313) [has participant](http://purl.obolibrary.org/obo/RO_0000057) ) + * _Added_ + * **+** SubObjectPropertyOf( [transports or maintains localization of](http://purl.obolibrary.org/obo/RO_0002313) [has anatomical participant](http://purl.obolibrary.org/obo/RO_0040036) ) - * [causally upstream of or within, negative effect](http://purl.obolibrary.org/obo/RO_0004046) *[label](http://www.w3.org/2000/01/rdf-schema#label)* causally upstream of or within, negative effect - * SubObjectPropertyOf( [causally upstream of or within, negative effect](http://purl.obolibrary.org/obo/RO_0004046) [causally upstream of or within](http://purl.obolibrary.org/obo/RO_0002418) ) - * [causally upstream of or within, negative effect](http://purl.obolibrary.org/obo/RO_0004046) *[created by](http://www.geneontology.org/formats/oboInOwl#created_by)* cjm - * [causally upstream of or within, negative effect](http://purl.obolibrary.org/obo/RO_0004046) *[is negative form of](http://purl.obolibrary.org/obo/RO_0004050)* [causally upstream of or within](http://purl.obolibrary.org/obo/RO_0002418) - * [causally upstream of or within, negative effect](http://purl.obolibrary.org/obo/RO_0004046) *[creation date](http://www.geneontology.org/formats/oboInOwl#creation_date)* 2018-03-13T23:55:05Z +### Changes for: [results in growth of](http://purl.obolibrary.org/obo/RO_0002343) -### New ObjectProperty : [causally upstream of or within, positive effect](http://purl.obolibrary.org/obo/RO_0004047) + * _Deleted_ + * **-** SubObjectPropertyOf( [results in growth of](http://purl.obolibrary.org/obo/RO_0002343) [has participant](http://purl.obolibrary.org/obo/RO_0000057) ) + * _Added_ + * **+** SubObjectPropertyOf( [results in growth of](http://purl.obolibrary.org/obo/RO_0002343) [has anatomical participant](http://purl.obolibrary.org/obo/RO_0040036) ) - * [causally upstream of or within, positive effect](http://purl.obolibrary.org/obo/RO_0004047) *[label](http://www.w3.org/2000/01/rdf-schema#label)* causally upstream of or within, positive effect - * [causally upstream of or within, positive effect](http://purl.obolibrary.org/obo/RO_0004047) *[created by](http://www.geneontology.org/formats/oboInOwl#created_by)* cjm - * SubObjectPropertyOf( [causally upstream of or within, positive effect](http://purl.obolibrary.org/obo/RO_0004047) [causally upstream of or within](http://purl.obolibrary.org/obo/RO_0002418) ) - * [causally upstream of or within, positive effect](http://purl.obolibrary.org/obo/RO_0004047) *[is positive form of](http://purl.obolibrary.org/obo/RO_0004049)* [causally upstream of or within](http://purl.obolibrary.org/obo/RO_0002418) - * [causally upstream of or within, positive effect](http://purl.obolibrary.org/obo/RO_0004047) *[creation date](http://www.geneontology.org/formats/oboInOwl#creation_date)* 2018-03-13T23:55:19Z +### Changes for: [helper property (not for use in curation)](http://purl.obolibrary.org/obo/RO_0002464) -### New ObjectProperty : [enables subfunction](http://purl.obolibrary.org/obo/RO_0004031) + * _Deleted_ + * **-** [helper property](http://purl.obolibrary.org/obo/RO_0002464) *[label](http://www.w3.org/2000/01/rdf-schema#label)* helper property + * _Added_ + * **+** [helper property (not for use in curation)](http://purl.obolibrary.org/obo/RO_0002464) *[label](http://www.w3.org/2000/01/rdf-schema#label)* helper property (not for use in curation) - * SubObjectPropertyOf( [enables subfunction](http://purl.obolibrary.org/obo/RO_0004031) [functionally related to](http://purl.obolibrary.org/obo/RO_0002328) ) - * [enables subfunction](http://purl.obolibrary.org/obo/RO_0004031) *[label](http://www.w3.org/2000/01/rdf-schema#label)* enables subfunction - * [enables subfunction](http://purl.obolibrary.org/obo/RO_0004031) *[definition](http://purl.obolibrary.org/obo/IAO_0000115)* Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P. - * [enables subfunction](http://purl.obolibrary.org/obo/RO_0004031) *[created by](http://www.geneontology.org/formats/oboInOwl#created_by)* cjm - * [enables subfunction](http://purl.obolibrary.org/obo/RO_0004031) *[creation date](http://www.geneontology.org/formats/oboInOwl#creation_date)* 2018-01-25T23:20:13Z +### Changes for: [results in closure of](http://purl.obolibrary.org/obo/RO_0002585) -### New ObjectProperty : [acts upstream of or within, positive effect](http://purl.obolibrary.org/obo/RO_0004032) + * _Deleted_ + * **-** SubObjectPropertyOf( [results in closure of](http://purl.obolibrary.org/obo/RO_0002585) [has participant](http://purl.obolibrary.org/obo/RO_0000057) ) + * _Added_ + * **+** SubObjectPropertyOf( [results in closure of](http://purl.obolibrary.org/obo/RO_0002585) [has anatomical participant](http://purl.obolibrary.org/obo/RO_0040036) ) - * [acts upstream of or within, positive effect](http://purl.obolibrary.org/obo/RO_0004032) *[is positive form of](http://purl.obolibrary.org/obo/RO_0004049)* [acts upstream of or within](http://purl.obolibrary.org/obo/RO_0002264) - * [acts upstream of or within, positive effect](http://purl.obolibrary.org/obo/RO_0004032) *[created by](http://www.geneontology.org/formats/oboInOwl#created_by)* cjm - * [acts upstream of or within, positive effect](http://purl.obolibrary.org/obo/RO_0004032) *[creation date](http://www.geneontology.org/formats/oboInOwl#creation_date)* 2018-01-26T23:49:30Z - * SubObjectPropertyOf( [acts upstream of or within, positive effect](http://purl.obolibrary.org/obo/RO_0004032) [acts upstream of or within](http://purl.obolibrary.org/obo/RO_0002264) ) - * [acts upstream of or within, positive effect](http://purl.obolibrary.org/obo/RO_0004032) *[seeAlso](http://www.w3.org/2000/01/rdf-schema#seeAlso)* [http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within,_positive_effect](http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within,_positive_effect) - * [acts upstream of or within, positive effect](http://purl.obolibrary.org/obo/RO_0004032) *[label](http://www.w3.org/2000/01/rdf-schema#label)* acts upstream of or within, positive effect +### Changes for: [has soma location](http://purl.obolibrary.org/obo/RO_0002100) -### New ObjectProperty : [acts upstream of or within, negative effect](http://purl.obolibrary.org/obo/RO_0004033) + * _Added_ + * **+** ObjectPropertyRange( [has soma location](http://purl.obolibrary.org/obo/RO_0002100) [anatomical structure](http://purl.obolibrary.org/obo/CARO_0000003) ) - * [acts upstream of or within, negative effect](http://purl.obolibrary.org/obo/RO_0004033) *[is negative form of](http://purl.obolibrary.org/obo/RO_0004050)* [acts upstream of or within](http://purl.obolibrary.org/obo/RO_0002264) - * [acts upstream of or within, negative effect](http://purl.obolibrary.org/obo/RO_0004033) *[label](http://www.w3.org/2000/01/rdf-schema#label)* acts upstream of or within, negative effect - * [acts upstream of or within, negative effect](http://purl.obolibrary.org/obo/RO_0004033) *[creation date](http://www.geneontology.org/formats/oboInOwl#creation_date)* 2018-01-26T23:49:51Z - * SubObjectPropertyOf( [acts upstream of or within, negative effect](http://purl.obolibrary.org/obo/RO_0004033) [acts upstream of or within](http://purl.obolibrary.org/obo/RO_0002264) ) - * [acts upstream of or within, negative effect](http://purl.obolibrary.org/obo/RO_0004033) *[created by](http://www.geneontology.org/formats/oboInOwl#created_by)* cjm +### Changes for: [participates in a biotic-biotic interaction with](http://purl.obolibrary.org/obo/RO_0002574) -### New ObjectProperty : [acts upstream of, positive effect](http://purl.obolibrary.org/obo/RO_0004034) + * _Added_ + * **+** ObjectPropertyDomain( [participates in a biotic-biotic interaction with](http://purl.obolibrary.org/obo/RO_0002574) [organism or virus or viroid](http://purl.obolibrary.org/obo/CARO_0001010) ) + * **+** ObjectPropertyRange( [participates in a biotic-biotic interaction with](http://purl.obolibrary.org/obo/RO_0002574) [organism or virus or viroid](http://purl.obolibrary.org/obo/CARO_0001010) ) - * [acts upstream of, positive effect](http://purl.obolibrary.org/obo/RO_0004034) *[definition](http://purl.obolibrary.org/obo/IAO_0000115)* c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive - * SubObjectPropertyOf( [acts upstream of, positive effect](http://purl.obolibrary.org/obo/RO_0004034) [acts upstream of or within, positive effect](http://purl.obolibrary.org/obo/RO_0004032) ) - * SubObjectPropertyOf( [acts upstream of, positive effect](http://purl.obolibrary.org/obo/RO_0004034) [acts upstream of](http://purl.obolibrary.org/obo/RO_0002263) ) - * [acts upstream of, positive effect](http://purl.obolibrary.org/obo/RO_0004034) *[seeAlso](http://www.w3.org/2000/01/rdf-schema#seeAlso)* [http://wiki.geneontology.org/index.php/Acts_upstream_of,_positive_effect](http://wiki.geneontology.org/index.php/Acts_upstream_of,_positive_effect) - * [acts upstream of, positive effect](http://purl.obolibrary.org/obo/RO_0004034) *[label](http://www.w3.org/2000/01/rdf-schema#label)* acts upstream of, positive effect - * [acts upstream of, positive effect](http://purl.obolibrary.org/obo/RO_0004034) *[creation date](http://www.geneontology.org/formats/oboInOwl#creation_date)* 2018-01-26T23:53:14Z - * [acts upstream of, positive effect](http://purl.obolibrary.org/obo/RO_0004034) *[is positive form of](http://purl.obolibrary.org/obo/RO_0004049)* [acts upstream of](http://purl.obolibrary.org/obo/RO_0002263) - * [acts upstream of, positive effect](http://purl.obolibrary.org/obo/RO_0004034) *[created by](http://www.geneontology.org/formats/oboInOwl#created_by)* cjm +### Changes for: [has modifier](http://purl.obolibrary.org/obo/RO_0002573) -### New ObjectProperty : [acts upstream of, negative effect](http://purl.obolibrary.org/obo/RO_0004035) + * _Added_ + * **+** ObjectPropertyRange( [has modifier](http://purl.obolibrary.org/obo/RO_0002573) [specifically dependent continuant](http://purl.obolibrary.org/obo/BFO_0000020) ) - * [acts upstream of, negative effect](http://purl.obolibrary.org/obo/RO_0004035) *[definition](http://purl.obolibrary.org/obo/IAO_0000115)* c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative - * [acts upstream of, negative effect](http://purl.obolibrary.org/obo/RO_0004035) *[label](http://www.w3.org/2000/01/rdf-schema#label)* acts upstream of, negative effect - * [acts upstream of, negative effect](http://purl.obolibrary.org/obo/RO_0004035) *[creation date](http://www.geneontology.org/formats/oboInOwl#creation_date)* 2018-01-26T23:53:22Z - * SubObjectPropertyOf( [acts upstream of, negative effect](http://purl.obolibrary.org/obo/RO_0004035) [acts upstream of](http://purl.obolibrary.org/obo/RO_0002263) ) - * [acts upstream of, negative effect](http://purl.obolibrary.org/obo/RO_0004035) *[seeAlso](http://www.w3.org/2000/01/rdf-schema#seeAlso)* [http://wiki.geneontology.org/index.php/Acts_upstream_of,_negative_effect](http://wiki.geneontology.org/index.php/Acts_upstream_of,_negative_effect) - * [acts upstream of, negative effect](http://purl.obolibrary.org/obo/RO_0004035) *[is negative form of](http://purl.obolibrary.org/obo/RO_0004050)* [acts upstream of](http://purl.obolibrary.org/obo/RO_0002263) - * SubObjectPropertyOf( [acts upstream of, negative effect](http://purl.obolibrary.org/obo/RO_0004035) [acts upstream of or within, negative effect](http://purl.obolibrary.org/obo/RO_0004033) ) - * [acts upstream of, negative effect](http://purl.obolibrary.org/obo/RO_0004035) *[created by](http://www.geneontology.org/formats/oboInOwl#created_by)* cjm +### Changes for: [capable of part of](http://purl.obolibrary.org/obo/RO_0002216) -## Changed ObjectProperty objects: 12 + * _Added_ + * **+** [capable of part of](http://purl.obolibrary.org/obo/RO_0002216) *[seeAlso](http://www.w3.org/2000/01/rdf-schema#seeAlso)* [defining-property-chains-involving-reflexivity](https://github.com/oborel/obo-relations/wiki/ROGuide#defining-property-chains-involving-reflexivity) + +### Changes for: [has prototype](http://purl.obolibrary.org/obo/RO_0002214) + + * _Added_ + * **+** ObjectPropertyDomain( [has prototype](http://purl.obolibrary.org/obo/RO_0002214) [independent continuant](http://purl.obolibrary.org/obo/BFO_0000004) **or** [process](http://purl.obolibrary.org/obo/BFO_0000015) ) + +### Changes for: [enabled by](http://purl.obolibrary.org/obo/RO_0002333) + * _Deleted_ + * **-** SubObjectPropertyOf( [enabled by](http://purl.obolibrary.org/obo/RO_0002333) undefined( ) ) -### Changes for: [involved in positive regulation of](http://purl.obolibrary.org/obo/RO_0002429) +### Changes for: [aligned with](http://purl.obolibrary.org/obo/RO_0002001) * _Added_ - * **+** [involved in positive regulation of](http://purl.obolibrary.org/obo/RO_0002429) *[is positive form of](http://purl.obolibrary.org/obo/RO_0004049)* [involved in regulation of](http://purl.obolibrary.org/obo/RO_0002428) + * **+** [aligned with](http://purl.obolibrary.org/obo/RO_0002001) *[editor note](http://purl.obolibrary.org/obo/IAO_0000116)* May be obsoleted, see https://github.com/oborel/obo-relations/issues/260 -### Changes for: [involved in negative regulation of](http://purl.obolibrary.org/obo/RO_0002430) +### Changes for: [innervated_by](http://purl.obolibrary.org/obo/RO_0002005) * _Added_ - * **+** [involved in negative regulation of](http://purl.obolibrary.org/obo/RO_0002430) *[is negative form of](http://purl.obolibrary.org/obo/RO_0004050)* [involved in regulation of](http://purl.obolibrary.org/obo/RO_0002428) + * **+** ObjectPropertyDomain( [innervated by](http://purl.obolibrary.org/obo/RO_0002005) [anatomical structure](http://purl.obolibrary.org/obo/CARO_0000003) ) + * **+** ObjectPropertyRange( [innervated by](http://purl.obolibrary.org/obo/RO_0002005) [neuron projection bundle](http://purl.obolibrary.org/obo/CARO_0001001) ) -### Changes for: [involved in](http://purl.obolibrary.org/obo/RO_0002331) +### Changes for: [tracheates](http://purl.obolibrary.org/obo/RO_0002004) * _Added_ - * **+** [involved in](http://purl.obolibrary.org/obo/RO_0002331) *[seeAlso](http://www.w3.org/2000/01/rdf-schema#seeAlso)* [http://wiki.geneontology.org/index.php/Involved_in](http://wiki.geneontology.org/index.php/Involved_in) + * **+** ObjectPropertyDomain( [tracheates](http://purl.obolibrary.org/obo/RO_0002004) [anatomical structure](http://purl.obolibrary.org/obo/CARO_0000003) ) + * **+** ObjectPropertyRange( [tracheates](http://purl.obolibrary.org/obo/RO_0002004) [anatomical structure](http://purl.obolibrary.org/obo/CARO_0000003) ) -### Changes for: [positively regulates](http://purl.obolibrary.org/obo/RO_0002213) +### Changes for: [relation between structure and stage](http://purl.obolibrary.org/obo/RO_0002487) * _Added_ - * **+** [positively regulates](http://purl.obolibrary.org/obo/RO_0002213) *[is positive form of](http://purl.obolibrary.org/obo/RO_0004049)* [regulates](http://purl.obolibrary.org/obo/RO_0002211) + * **+** ObjectPropertyDomain( [relation between structure and stage](http://purl.obolibrary.org/obo/RO_0002487) [material anatomical entity](http://purl.obolibrary.org/obo/CARO_0000006) **or** [immaterial anatomical entity](http://purl.obolibrary.org/obo/CARO_0000007) ) + +### Changes for: [releases neurotransmitter](http://purl.obolibrary.org/obo/RO_0002111) -### Changes for: [negatively regulates](http://purl.obolibrary.org/obo/RO_0002212) + * _Added_ + * **+** ObjectPropertyDomain( [releases neurotransmitter](http://purl.obolibrary.org/obo/RO_0002111) [anatomical structure](http://purl.obolibrary.org/obo/CARO_0000003) ) + +### Changes for: [results in organization of](http://purl.obolibrary.org/obo/RO_0002592) * _Deleted_ - * **-** [negatively regulates](http://purl.obolibrary.org/obo/RO_0002212) *[has curation status](http://purl.obolibrary.org/obo/IAO_0000114)* [pending final vetting](http://purl.obolibrary.org/obo/IAO_0000125) + * **-** SubObjectPropertyOf( [results in organization of](http://purl.obolibrary.org/obo/RO_0002592) [has participant](http://purl.obolibrary.org/obo/RO_0000057) ) * _Added_ - * **+** [negatively regulates](http://purl.obolibrary.org/obo/RO_0002212) *[is negative form of](http://purl.obolibrary.org/obo/RO_0004050)* [regulates](http://purl.obolibrary.org/obo/RO_0002211) + * **+** SubObjectPropertyOf( [results in organization of](http://purl.obolibrary.org/obo/RO_0002592) [has anatomical participant](http://purl.obolibrary.org/obo/RO_0040036) ) -### Changes for: [acts upstream of or within](http://purl.obolibrary.org/obo/RO_0002264) +### Changes for: [results in structural organization of](http://purl.obolibrary.org/obo/RO_0002355) * _Deleted_ - * **-** [acts upstream of or within](http://purl.obolibrary.org/obo/RO_0002264) *[definition](http://purl.obolibrary.org/obo/IAO_0000115)* c acts upstream of or within p if c is enables 'p' and p' causally upstream of or within p + * **-** SubObjectPropertyOf( [results in structural organization of](http://purl.obolibrary.org/obo/RO_0002355) [has participant](http://purl.obolibrary.org/obo/RO_0000057) ) * _Added_ - * **+** [acts upstream of or within](http://purl.obolibrary.org/obo/RO_0002264) *[definition](http://purl.obolibrary.org/obo/IAO_0000115)* c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process. - * **+** [acts upstream of or within](http://purl.obolibrary.org/obo/RO_0002264) *[example of usage](http://purl.obolibrary.org/obo/IAO_0000112)* A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway. - * **+** [acts upstream of or within](http://purl.obolibrary.org/obo/RO_0002264) *[seeAlso](http://www.w3.org/2000/01/rdf-schema#seeAlso)* [http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within](http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within) + * **+** SubObjectPropertyOf( [results in structural organization of](http://purl.obolibrary.org/obo/RO_0002355) [has anatomical participant](http://purl.obolibrary.org/obo/RO_0040036) ) -### Changes for: [acts upstream of](http://purl.obolibrary.org/obo/RO_0002263) +### Changes for: [derived from ancestral fusion of](http://purl.obolibrary.org/obo/RO_0002374) * _Deleted_ - * **-** [acts upstream of](http://purl.obolibrary.org/obo/RO_0002263) *[definition](http://purl.obolibrary.org/obo/IAO_0000115)* c involved in regulation of p if c enables 'p' and p' causally upstream of p + * **-** SubObjectPropertyOf( [has fused element](http://purl.obolibrary.org/obo/RO_0002374) [evolutionarily related to](http://purl.obolibrary.org/obo/RO_0002320) ) + * **-** [has fused element](http://purl.obolibrary.org/obo/RO_0002374) *[label](http://www.w3.org/2000/01/rdf-schema#label)* has fused element + * _Added_ + * **+** SubObjectPropertyOf( [derived from ancestral fusion of](http://purl.obolibrary.org/obo/RO_0002374) [derived by descent from](http://purl.obolibrary.org/obo/RO_0002156) ) + * **+** [derived from ancestral fusion of](http://purl.obolibrary.org/obo/RO_0002374) *[has broad synonym](http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym)* has fused element + * **+** [derived from ancestral fusion of](http://purl.obolibrary.org/obo/RO_0002374) *[label](http://www.w3.org/2000/01/rdf-schema#label)* derived from ancestral fusion of + +### Changes for: [has muscle insertion](http://purl.obolibrary.org/obo/RO_0002373) + + * _Added_ + * **+** ObjectPropertyDomain( [has muscle insertion](http://purl.obolibrary.org/obo/RO_0002373) [anatomical structure](http://purl.obolibrary.org/obo/CARO_0000003) ) { [editor note](http://purl.obolibrary.org/obo/IAO_0000116)=We need to import uberon muscle into RO to use as a stricter domain constraint } + +### Changes for: [has muscle origin](http://purl.obolibrary.org/obo/RO_0002372) + * _Added_ - * **+** [acts upstream of](http://purl.obolibrary.org/obo/RO_0002263) *[definition](http://purl.obolibrary.org/obo/IAO_0000115)* c involved in regulation of p if c enables f and f causally upstream of p - * **+** [acts upstream of](http://purl.obolibrary.org/obo/RO_0002263) *[example of usage](http://purl.obolibrary.org/obo/IAO_0000112)* A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision. - * **+** [acts upstream of](http://purl.obolibrary.org/obo/RO_0002263) *[seeAlso](http://www.w3.org/2000/01/rdf-schema#seeAlso)* [http://wiki.geneontology.org/index.php/Acts_upstream_of](http://wiki.geneontology.org/index.php/Acts_upstream_of) + * **+** ObjectPropertyDomain( [has muscle origin](http://purl.obolibrary.org/obo/RO_0002372) [anatomical structure](http://purl.obolibrary.org/obo/CARO_0000003) ) { [comment](http://www.w3.org/2000/01/rdf-schema#comment)=We need to import uberon muscle to create a stricter domain constraint } -### Changes for: [directly positively regulates](http://purl.obolibrary.org/obo/RO_0002629) +### Changes for: [attached to](http://purl.obolibrary.org/obo/RO_0002371) * _Added_ - * **+** [directly positively regulates](http://purl.obolibrary.org/obo/RO_0002629) *[is positive form of](http://purl.obolibrary.org/obo/RO_0004049)* [directly regulates](http://purl.obolibrary.org/obo/RO_0002578) + * **+** [attached to](http://purl.obolibrary.org/obo/RO_0002371) *[OBO foundry unique label](http://purl.obolibrary.org/obo/IAO_0000589)* attached to (anatomical structure to anatomical structure) -### Changes for: [directly negatively regulates](http://purl.obolibrary.org/obo/RO_0002630) +### Changes for: [in neural circuit with](http://purl.obolibrary.org/obo/RO_0000300) * _Added_ - * **+** [directly negatively regulates](http://purl.obolibrary.org/obo/RO_0002630) *[is negative form of](http://purl.obolibrary.org/obo/RO_0004050)* [directly regulates](http://purl.obolibrary.org/obo/RO_0002578) + * **+** ObjectPropertyDomain( [in neural circuit with](http://purl.obolibrary.org/obo/RO_0000300) [neuron](http://purl.obolibrary.org/obo/CL_0000540) ) + * **+** ObjectPropertyRange( [in neural circuit with](http://purl.obolibrary.org/obo/RO_0000300) [neuron](http://purl.obolibrary.org/obo/CL_0000540) ) -### Changes for: [involved in regulation of](http://purl.obolibrary.org/obo/RO_0002428) +### Changes for: [obsolete related via dependence to](http://purl.obolibrary.org/obo/RO_0002609) * _Deleted_ - * **-** [involved in regulation of](http://purl.obolibrary.org/obo/RO_0002428) *[definition](http://purl.obolibrary.org/obo/IAO_0000115)* c involved in regulation of p if c is involved in some 'p' and p' regulates some p + * **-** [related via dependence to](http://purl.obolibrary.org/obo/RO_0002609) *[label](http://www.w3.org/2000/01/rdf-schema#label)* related via dependence to * _Added_ - * **+** [involved in regulation of](http://purl.obolibrary.org/obo/RO_0002428) *[definition](http://purl.obolibrary.org/obo/IAO_0000115)* c involved in regulation of p if c is involved in some p' and p' regulates some p + * **+** [obsolete related via dependence to](http://purl.obolibrary.org/obo/RO_0002609) *[deprecated](http://www.w3.org/2002/07/owl#deprecated)* true + * **+** [obsolete related via dependence to](http://purl.obolibrary.org/obo/RO_0002609) *[label](http://www.w3.org/2000/01/rdf-schema#label)* obsolete related via dependence to -### Changes for: [causally upstream of, negative effect](http://purl.obolibrary.org/obo/RO_0002305) +### Changes for: [has substance added](http://purl.obolibrary.org/obo/RO_0009001) * _Added_ - * **+** SubObjectPropertyOf( [causally upstream of, negative effect](http://purl.obolibrary.org/obo/RO_0002305) [causally upstream of or within, negative effect](http://purl.obolibrary.org/obo/RO_0004046) ) - * **+** [causally upstream of, negative effect](http://purl.obolibrary.org/obo/RO_0002305) *[is negative form of](http://purl.obolibrary.org/obo/RO_0004050)* [causally upstream of](http://purl.obolibrary.org/obo/RO_0002411) + * **+** ObjectPropertyDomain( [has substance added](http://purl.obolibrary.org/obo/RO_0009001) [material entity](http://purl.obolibrary.org/obo/BFO_0000040) ) + * **+** ObjectPropertyRange( [has substance added](http://purl.obolibrary.org/obo/RO_0009001) [material entity](http://purl.obolibrary.org/obo/BFO_0000040) ) -### Changes for: [causally upstream of, positive effect](http://purl.obolibrary.org/obo/RO_0002304) +### Changes for: [has substance removed](http://purl.obolibrary.org/obo/RO_0009002) * _Added_ - * **+** SubObjectPropertyOf( [causally upstream of, positive effect](http://purl.obolibrary.org/obo/RO_0002304) [causally upstream of or within, positive effect](http://purl.obolibrary.org/obo/RO_0004047) ) - * **+** [causally upstream of, positive effect](http://purl.obolibrary.org/obo/RO_0002304) *[is positive form of](http://purl.obolibrary.org/obo/RO_0004049)* [causally upstream of](http://purl.obolibrary.org/obo/RO_0002411) + * **+** ObjectPropertyDomain( [has substance removed](http://purl.obolibrary.org/obo/RO_0009002) [material entity](http://purl.obolibrary.org/obo/BFO_0000040) ) + * **+** ObjectPropertyRange( [has substance removed](http://purl.obolibrary.org/obo/RO_0009002) [material entity](http://purl.obolibrary.org/obo/BFO_0000040) ) + +### Changes for: [immersed in](http://purl.obolibrary.org/obo/RO_0009003) + + * _Added_ + * **+** ObjectPropertyDomain( [immersed in](http://purl.obolibrary.org/obo/RO_0009003) [material entity](http://purl.obolibrary.org/obo/BFO_0000040) ) + * **+** ObjectPropertyRange( [immersed in](http://purl.obolibrary.org/obo/RO_0009003) [material entity](http://purl.obolibrary.org/obo/BFO_0000040) ) + +### Changes for: [correlated with](http://purl.obolibrary.org/obo/RO_0002610) + + * _Deleted_ + * **-** SubObjectPropertyOf( [correlated with](http://purl.obolibrary.org/obo/RO_0002610) [related via dependence to](http://purl.obolibrary.org/obo/RO_0002609) ) + +### Changes for: [obsolete has indirect output](http://purl.obolibrary.org/obo/RO_0002403) + + * _Deleted_ + * **-** SubObjectPropertyOf( [obsolete has indirect output](http://purl.obolibrary.org/obo/RO_0002403) [has output](http://purl.obolibrary.org/obo/RO_0002234) ) + +### Changes for: [has habitat](http://purl.obolibrary.org/obo/RO_0002303) + + * _Deleted_ + * **-** ObjectPropertyDomain( [has habitat](http://purl.obolibrary.org/obo/RO_0002303) [material anatomical entity](http://purl.obolibrary.org/obo/CARO_0000006) ) + * _Added_ + * **+** ObjectPropertyDomain( [has habitat](http://purl.obolibrary.org/obo/RO_0002303) [organism or virus or viroid](http://purl.obolibrary.org/obo/CARO_0001010) ) + +### Changes for: [causally related to](http://purl.obolibrary.org/obo/RO_0002410) + + * _Deleted_ + * **-** SubObjectPropertyOf( [causally related to](http://purl.obolibrary.org/obo/RO_0002410) [related via dependence to](http://purl.obolibrary.org/obo/RO_0002609) ) diff --git a/src/ontology/ro.obo b/src/ontology/ro.obo index 89d2d685..0b0d4d01 100644 --- a/src/ontology/ro.obo +++ b/src/ontology/ro.obo @@ -1,19 +1,19 @@ format-version: 1.2 -data-version: releases/2018-09-25 +data-version: releases/2018-10-19 subsetdef: ro-eco "" subsetdef: RO:0002259 "" remark: Includes Ontology(OntologyID(Anonymous-21)) [Axioms: 26 Logical Axioms: 0] remark: Includes Ontology(OntologyID(Anonymous-21)) [Axioms: 32 Logical Axioms: 0] remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 61 Logical Axioms: 0] remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 18 Logical Axioms: 7] -remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 53 Logical Axioms: 12] +remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 56 Logical Axioms: 13] remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 9 Logical Axioms: 3] -remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 289 Logical Axioms: 60] +remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 291 Logical Axioms: 62] remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 6 Logical Axioms: 2] remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 42 Logical Axioms: 16] remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 49 Logical Axioms: 14] remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 29 Logical Axioms: 9] -remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 102 Logical Axioms: 24] +remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 110 Logical Axioms: 27] remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 20 Logical Axioms: 6] remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 731 Logical Axioms: 148] remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 146 Logical Axioms: 45] @@ -22,7 +22,7 @@ property_value: http://purl.org/dc/elements/1.1/description "The OBO Relations O property_value: http://purl.org/dc/elements/1.1/source http://obofoundry.org/ro property_value: http://purl.org/dc/elements/1.1/title "OBO Relations Ontology" xsd:string property_value: http://xmlns.com/foaf/0.1/homepage " https://github.com/oborel/obo-relations/" xsd:anyURI -owl-axioms: Prefix(owl:=)\nPrefix(rdf:=)\nPrefix(xml:=)\nPrefix(xsd:=)\nPrefix(rdfs:=)\n\n\nOntology(\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(DataProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\n############################\n# Annotation Properties\n############################\n\n# Annotation Property: (first order logic expression)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (temporal interpretation)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (never in taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (mutually spatially disjoint with)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (taxonomic class assertion)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (ambiguous for taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (dubious for taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (present in taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (annotation property cardinality)\n\nSubAnnotationPropertyOf( )\nAnnotationPropertyRange( xsd:nonNegativeInteger)\n\n# Annotation Property: (logical macro assertion on a class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on a property)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on an object property)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on an annotation property)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (dispositional interpretation)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has no connections with)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (curator guidance link)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (always present in taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (temporal logical macro assertion on a class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (measurement property has unit)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has start time value)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has end time value)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, days post fertilization)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, days post fertilization)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, years post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, years post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, months post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, months post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (month of gestation)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has developmental stage marker)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, days post coitum)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, days post coitum)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, weeks post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, weeks post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is asymmetric relational form of process class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is symmetric relational form of process class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is relational form of process class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is direct form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is indirect form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on an axiom)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is a defining property chain axiom)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is a defining property chain axiom where second argument is reflexive)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is relational form of a class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion involving identity)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (in approximate one to one relationship with)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is approximately equivalent to)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is opposite of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is indistinguishable from)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (evidential logical macro assertion on an axiom)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (axiom has evidence)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (axiom contradicted by evidence)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is representative IRI for equivalence set)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is directional form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is positive form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is negative form of)\n\nSubAnnotationPropertyOf( )\n\n\n############################\n# Object Properties\n############################\n\n# Object Property: (coincident with)\n\nObjectPropertyRange( ObjectIntersectionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (synapsed by)\n\nObjectPropertyRange( ObjectUnionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (has fasciculating neuron projection)\n\nObjectPropertyRange( ObjectUnionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (connected to)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (connects)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (directly develops from)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (has member)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (anabranch of)\n\nSubObjectPropertyOf( ObjectInverseOf())\n\n# Object Property: (branching part of)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (differs in attribute of)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (condition has genetic basis in)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has basis in feature)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has location)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has feature)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (has substance added)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (has substance removed)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (immersed in)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (has primary substance added)\n\nIrreflexiveObjectProperty()\n\n\n############################\n# Data Properties\n############################\n\n# Data Property: (has increased age-specific mortality rate)\n\nDataPropertyRange( DatatypeRestriction(xsd:short xsd:minInclusive \"0\"^^xsd:short xsd:maxInclusive \"100\"^^xsd:short))\n\n\n\n############################\n# Classes\n############################\n\n# Class: (continuant)\n\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: (occurrent)\n\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: (material entity)\n\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: (immaterial entity)\n\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: (ubiquitin-protein ligase activity)\n\nSubClassOf( ObjectHasSelf())\n\n# Class: (kinase activity)\n\nSubClassOf( ObjectHasSelf())\n\n# Class: (symbiosis, encompassing mutualism through parasitism)\n\nSubClassOf( ObjectHasSelf())\n\n# Class: (parasitism)\n\nSubClassOf( ObjectHasSelf())\n\n# Class: (mutualism)\n\nSubClassOf( ObjectHasSelf())\n\n# Class: (commensalism)\n\nSubClassOf( ObjectHasSelf())\n\n\nSubClassOf(ObjectSomeValuesFrom( ) ObjectUnionOf(ObjectSomeValuesFrom( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( ObjectSomeValuesFrom( ObjectSomeValuesFrom( )))))\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain(ObjectInverseOf() ) )\nSubObjectPropertyOf(ObjectPropertyChain(ObjectInverseOf() ) )\nDLSafeRule(Annotation( \"true\"^^xsd:boolean) Annotation(rdfs:comment \"MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z\"^^xsd:string) Annotation(rdfs:label \"infer input from direct reg\"^^xsd:string) Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z),\ne.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity'\") Annotation(rdfs:label \"enabling an MF enables its parts\") Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation( \"true\"^^xsd:boolean) Annotation(rdfs:comment \"GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction'\"^^xsd:string) Annotation(rdfs:label \"involved in BP\"^^xsd:string) Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"From ligand activity to has_ligand\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"This rule is dubious: added as a quick fix for expected inference in GO-CAM. The problem is most acute for transmembrane proteins, such as receptors or cell adhesion molecules, which have some subfunctions inside the cell (e.g. kinase activity) and some subfunctions outside (e.g. ligand binding). Correct annotation of where these functions occurs leads to incorrect inference about the location of the whole protein. This should probably be weakened to \\\"... -> overlaps\\\"\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this.\") Annotation(rdfs:label \"inferring direct reg edge from input to regulatory subfunction\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"inferring direct neg reg edge from input to regulatory subfunction\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"inferring direct positive reg edge from input to regulatory subfunction\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"From has_ligand to ligand activity\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"effector input is compound function input\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"Input of effector is input of its parent MF\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"if effector directly regulates X, its parent MF directly regulates X\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"if effector directly positively regulates X, its parent MF directly positively regulates X\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"if effector directly negatively regulates X, its parent MF directly negatively regulates X\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nAnnotationAssertion(rdfs:comment \"\")\n) +owl-axioms: Prefix(owl:=)\nPrefix(rdf:=)\nPrefix(xml:=)\nPrefix(xsd:=)\nPrefix(rdfs:=)\n\n\nOntology(\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(DataProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\n############################\n# Annotation Properties\n############################\n\n# Annotation Property: (first order logic expression)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (temporal interpretation)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (never in taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (mutually spatially disjoint with)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (taxonomic class assertion)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (ambiguous for taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (dubious for taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (present in taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (annotation property cardinality)\n\nSubAnnotationPropertyOf( )\nAnnotationPropertyRange( xsd:nonNegativeInteger)\n\n# Annotation Property: (logical macro assertion on a class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on a property)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on an object property)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on an annotation property)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (dispositional interpretation)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has no connections with)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (curator guidance link)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (always present in taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (temporal logical macro assertion on a class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (measurement property has unit)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has start time value)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has end time value)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, days post fertilization)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, days post fertilization)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, years post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, years post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, months post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, months post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (month of gestation)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has developmental stage marker)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, days post coitum)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, days post coitum)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, weeks post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, weeks post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is asymmetric relational form of process class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is symmetric relational form of process class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is relational form of process class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is direct form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is indirect form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on an axiom)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is a defining property chain axiom)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is a defining property chain axiom where second argument is reflexive)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is relational form of a class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion involving identity)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (in approximate one to one relationship with)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is approximately equivalent to)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is opposite of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is indistinguishable from)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (evidential logical macro assertion on an axiom)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (axiom has evidence)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (axiom contradicted by evidence)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is representative IRI for equivalence set)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is directional form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is positive form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is negative form of)\n\nSubAnnotationPropertyOf( )\n\n\n############################\n# Object Properties\n############################\n\n# Object Property: (located in)\n\nObjectPropertyRange( ObjectIntersectionOf( ObjectComplementOf()))\n\n# Object Property: (coincident with)\n\nObjectPropertyRange( ObjectIntersectionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (synapsed by)\n\nObjectPropertyRange( ObjectUnionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (has fasciculating neuron projection)\n\nObjectPropertyRange( ObjectUnionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (connected to)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (connects)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (directly develops from)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (has member)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (anabranch of)\n\nSubObjectPropertyOf( ObjectInverseOf())\n\n# Object Property: (branching part of)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (differs in attribute of)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (condition has genetic basis in)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has basis in feature)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has location)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has feature)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (has substance added)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (has substance removed)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (immersed in)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (has primary substance added)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (has anatomical participant)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n\n############################\n# Data Properties\n############################\n\n# Data Property: (has increased age-specific mortality rate)\n\nDataPropertyRange( DatatypeRestriction(xsd:short xsd:minInclusive \"0\"^^xsd:short xsd:maxInclusive \"100\"^^xsd:short))\n\n\n\n############################\n# Classes\n############################\n\n# Class: (continuant)\n\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: (occurrent)\n\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: (material entity)\n\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: (immaterial entity)\n\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: (ubiquitin-protein ligase activity)\n\nSubClassOf( ObjectHasSelf())\n\n# Class: (kinase activity)\n\nSubClassOf( ObjectHasSelf())\n\n# Class: (symbiosis, encompassing mutualism through parasitism)\n\nSubClassOf( ObjectHasSelf())\n\n# Class: (parasitism)\n\nSubClassOf( ObjectHasSelf())\n\n# Class: (mutualism)\n\nSubClassOf( ObjectHasSelf())\n\n# Class: (commensalism)\n\nSubClassOf( ObjectHasSelf())\n\n\nSubClassOf(ObjectSomeValuesFrom( ) ObjectUnionOf(ObjectSomeValuesFrom( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( ObjectSomeValuesFrom( ObjectSomeValuesFrom( )))))\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain(ObjectInverseOf() ) )\nSubObjectPropertyOf(ObjectPropertyChain(ObjectInverseOf() ) )\nDLSafeRule(Annotation( \"true\"^^xsd:boolean) Annotation(rdfs:comment \"MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z\"^^xsd:string) Annotation(rdfs:label \"infer input from direct reg\"^^xsd:string) Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z),\ne.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity'\") Annotation(rdfs:label \"enabling an MF enables its parts\") Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation( \"true\"^^xsd:boolean) Annotation(rdfs:comment \"GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction'\"^^xsd:string) Annotation(rdfs:label \"involved in BP\"^^xsd:string) Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"From ligand activity to has_ligand\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"This rule is dubious: added as a quick fix for expected inference in GO-CAM. The problem is most acute for transmembrane proteins, such as receptors or cell adhesion molecules, which have some subfunctions inside the cell (e.g. kinase activity) and some subfunctions outside (e.g. ligand binding). Correct annotation of where these functions occurs leads to incorrect inference about the location of the whole protein. This should probably be weakened to \\\"... -> overlaps\\\"\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this.\") Annotation(rdfs:label \"inferring direct reg edge from input to regulatory subfunction\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"inferring direct neg reg edge from input to regulatory subfunction\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"inferring direct positive reg edge from input to regulatory subfunction\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"From has_ligand to ligand activity\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"effector input is compound function input\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"Input of effector is input of its parent MF\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"if effector directly regulates X, its parent MF directly regulates X\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"if effector directly positively regulates X, its parent MF directly positively regulates X\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"if effector directly negatively regulates X, its parent MF directly negatively regulates X\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nAnnotationAssertion(rdfs:comment \"\")\n) [Term] id: BFO:0000002 @@ -30,11 +30,13 @@ name: continuant def: "An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts." [] disjoint_from: BFO:0000003 ! occurrent relationship: RO:0002214 BFO:0000002 ! has prototype continuant +relationship: RO:HOM0000000 BFO:0000002 ! continuant [Term] id: BFO:0000003 name: occurrent def: "An entity that has temporal parts and that happens, unfolds or develops through time." [] +relationship: RO:HOM0000000 BFO:0000003 ! occurrent [Term] id: BFO:0000004 @@ -51,6 +53,11 @@ def: "A continuant that is either dependent on one or other independent continu is_a: ObsoleteClass ! Obsolete Class is_obsolete: true +[Term] +id: BFO:0000006 +name: spatial region +is_a: BFO:0000141 ! immaterial entity + [Term] id: BFO:0000015 name: process @@ -112,9 +119,15 @@ id: BFO:0000141 name: immaterial entity is_a: BFO:0000004 ! independent continuant +[Term] +id: CARO:0000000 +name: anatomical entity +is_a: CARO:0030000 ! biological entity +property_value: IAO:0000412 http://purl.obolibrary.org/obo/caro.owl + [Term] id: CARO:0000003 -name: anatomical structure +name: connected anatomical structure is_a: CARO:0000006 ! material anatomical entity property_value: IAO:0000412 http://purl.obolibrary.org/obo/caro.owl @@ -122,6 +135,8 @@ property_value: IAO:0000412 http://purl.obolibrary.org/obo/caro.owl id: CARO:0000006 name: material anatomical entity is_a: BFO:0000040 ! material entity +is_a: CARO:0000000 ! anatomical entity +relationship: RO:0002179 CARO:0000003 ! drains connected anatomical structure property_value: IAO:0000412 http://purl.obolibrary.org/obo/caro.owl [Term] @@ -132,20 +147,20 @@ is_a: BFO:0000141 ! immaterial entity [Term] id: CARO:0000011 name: connected anatomical system -is_a: CARO:0000006 ! material anatomical entity +is_a: CARO:0010000 ! multicellular anatomical structure is_a: RO:0002577 ! system [Term] id: CARO:0000014 name: cell part -is_a: CARO:0000003 ! anatomical structure +is_a: CARO:0000003 ! connected anatomical structure property_value: IAO:0000412 http://purl.obolibrary.org/obo/caro.owl property_value: IAO:0000589 "cell part (CARO)" xsd:string [Term] id: CARO:0001000 name: multi-cell-part structure -is_a: CARO:0000003 ! anatomical structure +is_a: CARO:0000003 ! connected anatomical structure property_value: IAO:0000412 http://purl.obolibrary.org/obo/caro.owl [Term] @@ -162,14 +177,19 @@ is_a: BFO:0000040 ! material entity [Term] id: CARO:0010000 name: multicellular anatomical structure -is_a: CARO:0000003 ! anatomical structure +is_a: CARO:0000003 ! connected anatomical structure relationship: RO:0002207 CARO:0010000 ! directly develops from multicellular anatomical structure property_value: IAO:0000412 http://purl.obolibrary.org/obo/caro.owl +[Term] +id: CARO:0030000 +name: biological entity +is_a: BFO:0000004 ! independent continuant + [Term] id: CL:0000000 name: cell -is_a: CARO:0000003 ! anatomical structure +is_a: CARO:0000003 ! connected anatomical structure relationship: RO:0002207 CL:0000000 ! directly develops from cell property_value: IAO:0000412 http://purl.obolibrary.org/obo/cl.owl @@ -558,6 +578,7 @@ id: BFO:0000060 name: obsolete preceded by comment: accidentally included in BFO 1.2 proposal\n - should have been BFO_0000062 is_transitive: true +is_obsolete: true [Typedef] id: BFO:0000062 @@ -787,6 +808,8 @@ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string property_value: IAO:0000426 "(forall (?x ?y) \n (iff \n (neural_circuit_path ?x ?y)\n (and\n (\"neuron ; CL_0000540\" ?x)\n (\"neuron ; CL_0000540\" ?y)\n (or \n (synapsed_by ?x ?y) \n (synapsed_to ?x ?y))))) \n\n(forall (...s ?x ?y ?z) \n (iff \n (neural_circuit_path ...s ?x ?y ?z)\n (and\n (neural_circuit_path ...s ?x ?y)\n (\"neuron ; CL_0000540\" ?z)\n (or \n (synapsed_by ?y ?z) \n (synapsed_to ?y ?z))))) \n\n(forall (?x ?y) \n (iff \n (in_neural_circuit_with ?x ?y)\n (exists (...s)\n (neural_circuit_path ?x ...s ?y)))) " xsd:string property_value: RO:0001900 RO:0001901 +domain: CL:0000540 ! neuron +range: CL:0000540 ! neuron is_transitive: true [Typedef] @@ -916,8 +939,8 @@ property_value: IAO:0000116 "Location as a relation between instances: The primi property_value: IAO:0000116 "Most location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime" xsd:string property_value: IAO:0000118 "located_in" xsd:string property_value: RO:0001900 RO:0001901 -domain: BFO:0000004 ! independent continuant -range: BFO:0000004 ! independent continuant +domain: BFO:0000004 {http://purl.obolibrary.org/obo/IAO_0000116="This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation."} ! independent continuant +range: BFO:0000004 {http://purl.obolibrary.org/obo/IAO_0000116="This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation."} ! independent continuant is_transitive: true [Typedef] @@ -972,8 +995,8 @@ id: RO:0002004 name: tracheates def: "The relationship that holds between a trachea or tracheole and an antomical structure that is contained in (and so provides an oxygen supply to)." [] property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -domain: CARO:0000003 ! anatomical structure -range: CARO:0000003 ! anatomical structure +domain: CARO:0000003 ! connected anatomical structure +range: CARO:0000003 ! connected anatomical structure is_a: RO:0001018 ! contained in [Typedef] @@ -981,6 +1004,8 @@ id: RO:0002005 name: innervated_by property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 xsd:anyURI property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +domain: CARO:0000003 ! connected anatomical structure +range: CARO:0001001 ! neuron projection bundle inverse_of: RO:0002134 ! innervates [Typedef] @@ -1308,6 +1333,7 @@ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string property_value: RO:0001900 RO:0001901 domain: CL:0000540 ! neuron +range: CARO:0000003 ! connected anatomical structure is_a: RO:0002131 ! overlaps transitive_over: BFO:0000050 ! part of expand_expression_to: "BFO_0000051 some (\n GO_0043025 and BFO_0000050 some ?Y)" [] @@ -1455,6 +1481,7 @@ id: RO:0002111 name: releases neurotransmitter property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000118 "has neurotransmitter" xsd:string +domain: CARO:0000003 ! connected anatomical structure [Typedef] id: RO:0002112 @@ -1726,8 +1753,8 @@ id: RO:0002177 name: attached to part of def: "a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b." [] property_value: IAO:0000589 "attached to part of (anatomical structure to anatomical structure)" xsd:string -domain: CARO:0000003 ! anatomical structure -range: CARO:0000003 ! anatomical structure +domain: CARO:0000003 ! connected anatomical structure +range: CARO:0000003 ! connected anatomical structure holds_over_chain: RO:0002371 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"} is_a: RO:0002323 ! mereotopologically related to is_a: RO:0002567 ! biomechanically related to @@ -1844,7 +1871,7 @@ property_value: IAO:0000112 "'neural crest cell' SubClassOf expresses some 'Wnt property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string domain: BFO:0000002 ! continuant -range: BFO:0000004 ! independent continuant +range: CARO:0000006 ! material anatomical entity is_a: RO:0002330 ! genomically related to inverse_of: RO:0002292 ! expresses transitive_over: BFO:0000050 ! part of @@ -1971,6 +1998,7 @@ name: capable of part of def: "c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p." [] property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "has function in" xsd:string +property_value: seeAlso "defining-property-chains-involving-reflexivity" holds_over_chain: RO:0002215 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"} is_a: RO:0002328 ! functionally related to is_a: RO:0002500 ! causal agent in process @@ -2088,7 +2116,7 @@ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 "EHDAA2" xsd:string property_value: IAO:0000119 "Jonathan Bard, EHDAA2" xsd:string -domain: CARO:0000003 ! anatomical structure +domain: CARO:0000000 ! anatomical entity holds_over_chain: RO:0002207 RO:0001025 is_a: RO:0002258 ! developmentally preceded by @@ -2283,8 +2311,8 @@ def: "x has developmental contribution from y iff x has some part z such that z property_value: IAO:0000112 "Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string -domain: BFO:0000004 ! independent continuant -range: CARO:0000003 ! anatomical structure +domain: CARO:0000000 ! anatomical entity +range: CARO:0000000 ! anatomical entity holds_over_chain: BFO:0000051 RO:0002202 is_a: RO:0002258 ! developmentally preceded by inverse_of: RO:0002255 ! developmentally contributes to @@ -2313,8 +2341,8 @@ property_value: IAO:0000119 " Developmental Biology, Gilbert, 8th edition, figur property_value: IAO:0000119 GO:0001759 xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 property_value: IAO:0000232 "We place this under 'developmentally preceded by'. This placement should be examined in the context of reciprocal inductions[cjm]" xsd:string -domain: CARO:0000003 ! anatomical structure -range: CARO:0000003 ! anatomical structure +domain: CARO:0000003 ! connected anatomical structure +range: CARO:0000003 ! connected anatomical structure is_a: RO:0002258 ! developmentally preceded by inverse_of: RO:0002257 ! developmentally induces @@ -2505,8 +2533,8 @@ name: transports or maintains localization of def: "Holds between p and c when p is a localization process (localization covers maintenance of localization as well as its establishment) and the outcome of this process is to regulate the localization of c." [] property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "regulates localization of" xsd:string -is_a: RO:0000057 ! has participant is_a: RO:0002337 ! related via localization to +is_a: RO:0040036 ! has anatomical participant transitive_over: BFO:0000051 ! has part [Typedef] @@ -2517,6 +2545,7 @@ property_value: IAO:0000116 "Because part_of is transitive, inheres in is a sub- property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 property_value: RO:0001900 RO:0001901 +property_value: seeAlso "defining-property-chains-involving-reflexivity" holds_over_chain: RO:0000052 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"} is_a: RO:0002502 ! depends on transitive_over: BFO:0000050 ! part of @@ -2741,7 +2770,7 @@ name: results in growth of property_value: IAO:0000112 "'pollen tube growth' results_in growth_of some 'pollen tube'" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: results_in_developmental_progression_of ! results in developmental progression of -is_a: RO:0000057 ! has participant +is_a: RO:0040036 ! has anatomical participant [Typedef] id: RO:0002344 @@ -2828,7 +2857,7 @@ name: results in structural organization of def: "A relationship between a process and an anatomical entity such that the process contributes to the act of creating the structural organization of the anatomical entity." [] property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: results_in_developmental_progression_of ! results in developmental progression of -is_a: RO:0000057 ! has participant +is_a: RO:0040036 ! has anatomical participant [Typedef] id: RO:0002356 @@ -2871,7 +2900,7 @@ def: "m has_muscle_origin s iff m is attached_to s, and it is the case that when property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 Wikipedia:Insertion_(anatomy) xsd:string property_value: seeAlso http://dbpedia.org/property/origin -domain: CARO:0000003 {comment="We need to import uberon muscle to create a stricter domain constraint"} ! anatomical structure +domain: CARO:0000003 {comment="We need to import uberon muscle to create a stricter domain constraint"} ! connected anatomical structure is_a: RO:0002371 ! attached to is_a: RO:0002567 ! biomechanically related to @@ -2882,7 +2911,7 @@ def: "m has_muscle_insertion s iff m is attaches_to s, and it is the case that w property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 Wikipedia:Insertion_(anatomy) xsd:string property_value: seeAlso http://dbpedia.org/property/insertion -domain: CARO:0000003 {http://purl.obolibrary.org/obo/IAO_0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} ! anatomical structure +domain: CARO:0000003 {http://purl.obolibrary.org/obo/IAO_0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} ! connected anatomical structure is_a: RO:0002371 ! attached to is_a: RO:0002567 ! biomechanically related to @@ -3014,6 +3043,8 @@ name: has developmental potential involving def: "x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction)." [] property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Chris Mungall" xsd:string +domain: CARO:0000000 ! anatomical entity +range: CARO:0000000 ! anatomical entity is_a: RO:0002324 ! developmentally related to [Typedef] @@ -3085,7 +3116,6 @@ comment: Likely to be obsoleted. See:\nhttps://docs.google.com/document/d/1QMhs9 property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Chris Mungall" xsd:string holds_over_chain: RO:0002411 RO:0002402 -is_a: RO:0002234 ! has output is_obsolete: true [Typedef] @@ -3286,6 +3316,7 @@ is_a: RO:0002428 ! involved in regulation of id: RO:0002431 name: involved in or involved in regulation of def: "c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p" [] +property_value: IAO:0000116 "OWL does not allow defining object properties via a Union" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "involved in or reguates" xsd:string is_a: RO:0002264 ! acts upstream of or within @@ -3621,7 +3652,7 @@ is_a: RO:0002461 ! partner in [Typedef] id: RO:0002464 -name: helper property +name: helper property (not for use in curation) property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000232 "This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning." xsd:string @@ -4218,7 +4249,7 @@ name: results in ending of def: "p results in the end of s if p results in a change of state in s whereby s either ceases to exist, or s becomes functionally impaired or s has its fate committed such that it is put on a path to be degraded." [] property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: results_in_developmental_progression_of ! results in developmental progression of -is_a: RO:0000057 ! has participant +is_a: RO:0040036 ! has anatomical participant [Typedef] id: RO:0002553 @@ -4299,7 +4330,7 @@ name: interaction relation helper property property_value: http://xmlns.com/foaf/0.1/page https://github.com/oborel/obo-relations/wiki/InteractionRelations xsd:anyURI property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:N-Ary_Relation_Pattern_%28OWL_2%29 -is_a: RO:0002464 ! helper property +is_a: RO:0002464 ! helper property (not for use in curation) [Typedef] id: RO:0002564 @@ -4313,7 +4344,7 @@ name: results in movement of def: "Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c" [] property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000232 "" xsd:string -is_a: RO:0000057 ! has participant +is_a: RO:0040036 ! has anatomical participant [Typedef] id: RO:0002566 @@ -4330,8 +4361,8 @@ name: biomechanically related to def: "A relation that holds between elements of a musculoskeletal system or its analogs." [] property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes." xsd:string -domain: CARO:0000003 ! anatomical structure -range: CARO:0000003 ! anatomical structure +domain: CARO:0000003 ! connected anatomical structure +range: CARO:0000003 ! connected anatomical structure is_a: RO:0002328 ! functionally related to [Typedef] @@ -4391,6 +4422,7 @@ property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 property_value: IAO:0000232 "This relation is intended to be used in combination with PATO, to be able to refine PATO quality classes using modifiers such as 'abnormal' and 'normal'. It has yet to be formally aligned into an ontological framework; it's not clear what the ontological status of the \"modifiers\" are." xsd:string domain: BFO:0000020 ! specifically dependent continuant +range: BFO:0000020 ! specifically dependent continuant [Typedef] id: RO:0002574 @@ -4408,8 +4440,8 @@ name: skeleton of def: "inverse of has skeleton" [] subset: RO:0002259 property_value: IAO:0000117 "Chris Mungall" xsd:string -domain: CARO:0000003 ! anatomical structure -range: CARO:0000003 ! anatomical structure +domain: CARO:0000003 ! connected anatomical structure +range: CARO:0000003 ! connected anatomical structure is_a: BFO:0000050 ! part of [Typedef] @@ -4444,7 +4476,7 @@ id: RO:0002585 name: results in closure of property_value: IAO:0000116 "p 'results in closure of' c if and only if p is a developmental process and p results in a state of c changing from open to closed." xsd:string is_a: results_in_developmental_progression_of ! results in developmental progression of -is_a: RO:0000057 ! has participant +is_a: RO:0040036 ! has anatomical participant [Typedef] id: RO:0002586 @@ -4485,7 +4517,7 @@ is_a: RO:0002592 ! results in organization of id: RO:0002592 name: results in organization of def: "p results in organization of c iff p results in the assembly, arrangement of constituent parts, or disassembly of c" [] -is_a: RO:0000057 ! has participant +is_a: RO:0040036 ! has anatomical participant [Typedef] id: RO:0002593 @@ -5085,7 +5117,7 @@ id: RO:0004027 name: disease has inflammation site def: "A relationship between a disease and an anatomical entity where the disease is triggered by an inflammatory response to stimuli occurring in the anatomical entity" [] domain: OGMS:0000031 ! disease -range: CARO:0000003 ! anatomical structure +range: CARO:0000003 ! connected anatomical structure is_a: RO:0004026 ! disease has location created_by: cjm creation_date: 2017-12-26T19:37:31Z @@ -5114,7 +5146,7 @@ creation_date: 2017-12-26T19:50:53Z id: RO:0004030 name: disease arises from structure def: "A relationship between a disease and an anatomical structure where the material basis of the disease is some pathological change in the structure." [] -range: CARO:0000003 ! anatomical structure +range: CARO:0000003 ! connected anatomical structure is_a: RO:0004019 ! disease has basis in created_by: cjm creation_date: 2017-12-26T19:58:44Z @@ -5255,6 +5287,8 @@ property_value: IAO:0000112 "muffin 'has substance added' some 'baking soda'" xs property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000116 "The relation X 'has substance added' some Y doesn't imply that X still has Y in any detectable fashion subsequent to the addition. Water in dehydrated food or ice cubes are examples, as is food that undergoes chemical transformation. This definition should encompass recipe ingredients." xsd:string property_value: IAO:0000117 "Damion Dooley" xsd:string +domain: BFO:0000040 ! material entity +range: BFO:0000040 ! material entity [Typedef] id: RO:0009002 @@ -5263,6 +5297,8 @@ def: "\"has substance removed\" is a relation existing between two physical enti property_value: IAO:0000112 "'egg white' 'has substance removed' some 'egg yolk'" xsd:string property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Damion Dooley" xsd:string +domain: BFO:0000040 ! material entity +range: BFO:0000040 ! material entity [Typedef] id: RO:0009003 @@ -5271,6 +5307,8 @@ def: "\"immersed in\" is a relation between a (physical) entity and a fluid subs property_value: IAO:0000112 "sardines 'immersed in' some 'oil and mustard'" xsd:string property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Damion Dooley" xsd:string +domain: BFO:0000040 ! material entity +range: BFO:0000040 ! material entity [Typedef] id: RO:0009005 @@ -5335,6 +5373,14 @@ property_value: IAO:0000232 "Do not use this relation directly. It is intended a created_by: cjm creation_date: 2018-09-26T00:00:32Z +[Typedef] +id: RO:0040036 +name: has anatomical participant +def: "p has anatomical participant c iff p has participant c, and c is an anatomical entity" [] +is_a: RO:0000057 ! has participant +created_by: cjm +creation_date: 2018-09-26T01:08:58Z + [Typedef] id: RO:HOM0000000 name: in similarity relationship with @@ -6188,9 +6234,9 @@ def: "The relationship that links a specified entity with the process that resul property_value: IAO:0000112 "an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast." xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string -range: CL:0000000 ! cell +range: CARO:0000003 ! connected anatomical structure is_a: results_in_developmental_progression_of ! results in developmental progression of -is_a: RO:0000057 ! has participant +is_a: RO:0040036 ! has anatomical participant [Typedef] id: results_in_development_of @@ -6201,7 +6247,7 @@ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://www.geneontology.org/GO.doc.development.shtml xsd:anyURI is_a: results_in_developmental_progression_of ! results in developmental progression of -is_a: RO:0000057 ! has participant +is_a: RO:0040036 ! has anatomical participant [Typedef] id: results_in_developmental_progression_of @@ -6212,7 +6258,7 @@ property_value: IAO:0000116 "This property and its subproperties are being used property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: seeAlso Ontology:extensions domain: GO:0008150 ! biological_process -range: CARO:0000003 ! anatomical structure +range: CARO:0000003 ! connected anatomical structure is_a: RO:0002324 ! developmentally related to [Typedef] @@ -6246,7 +6292,7 @@ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string is_a: results_in_developmental_progression_of ! results in developmental progression of -is_a: RO:0000057 ! has participant +is_a: RO:0040036 ! has anatomical participant [Typedef] id: results_in_morphogenesis_of @@ -6258,5 +6304,5 @@ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string is_a: results_in_developmental_progression_of ! results in developmental progression of -is_a: RO:0000057 ! has participant +is_a: RO:0040036 ! has anatomical participant diff --git a/src/ontology/ro.owl b/src/ontology/ro.owl index 22fdf28f..9d59e0e3 100644 --- a/src/ontology/ro.owl +++ b/src/ontology/ro.owl @@ -17,7 +17,7 @@ xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:subsets="http://purl.obolibrary.org/obo/ro/subsets#"> - + @@ -841,6 +841,8 @@ Where we have an annotation assertion + + A relation that holds between two neurons connected directly via a synapse, or indirectly via a series of synaptically connected neurons. David Osumi-Sutherland @@ -1094,6 +1096,8 @@ range: spatial region or site (immaterial continuant) + + David Osumi-Sutherland http://www.ncbi.nlm.nih.gov/pubmed/22402613 innervated_by @@ -1536,6 +1540,7 @@ Examples include: the relationship between two channels collected simultaneously + @@ -1798,6 +1803,7 @@ Examples include: the relationship between two channels collected simultaneously + has neurotransmitter releases neurotransmitter @@ -2521,7 +2527,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - + @@ -2743,6 +2749,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.has function in RO_0000053 some (RO_0000054 only (BFO_0000050 some ?Y)) capable of part of + @@ -2890,7 +2897,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - + @@ -3183,8 +3190,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - - + + @@ -3421,8 +3428,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - + every flower development (GO:0009908) results in development of some flower (PO:0009046) p 'results in development of' c if and only if p is a developmental process and p results in the state of c changing from its initial state as a primordium or anlage through its mature state and to its final state. @@ -3454,8 +3461,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - + an annotation of gene X to cell morphogenesis with results_in_morphogenesis_of CL:0000540 (neuron) means that at the end of the process an input neuron has attained its shape. tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723) @@ -3471,8 +3478,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - + an annotation of gene X to cell maturation with results_in_maturation_of CL:0000057 (fibroblast) means that the fibroblast is mature at the end of the process bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474) @@ -3599,8 +3606,8 @@ where - + @@ -3631,6 +3638,7 @@ where inheres in part of + @@ -3647,9 +3655,9 @@ where - - + + an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast. The relationship that links a specified entity with the process that results in an unspecified entity acquiring the features and characteristics of the specified entity Chris Mungall @@ -4012,8 +4020,8 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - + 'pollen tube growth' results_in growth_of some 'pollen tube' Chris Mungall results in growth of @@ -4114,8 +4122,8 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - + A relationship between a process and an anatomical entity such that the process contributes to the act of creating the structural organization of the anatomical entity. Chris Mungall results in structural organization of @@ -4401,6 +4409,8 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + + x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction). Chris Mungall @@ -4506,7 +4516,6 @@ https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/ - @@ -4862,6 +4871,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p + OWL does not allow defining object properties via a Union Chris Mungall involved in or reguates involved in or involved in regulation of @@ -5405,7 +5415,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different Chris Mungall This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning. - helper property + helper property (not for use in curation) @@ -5642,6 +5652,14 @@ the a supports either the existence of b, or the truth value of b. + + + + + + + + Chris Mungall Do not use this relation directly. It is ended as a grouping for a diverse set of relations, typically connecting an anatomical entity to a biological process or developmental stage. @@ -6332,8 +6350,8 @@ the a supports either the existence of b, or the truth value of b. - + p results in the end of s if p results in a change of state in s whereby s either ceases to exist, or s becomes functionally impaired or s has its fate committed such that it is put on a path to be degraded. Chris Mungall results in ending of @@ -6473,7 +6491,7 @@ the a supports either the existence of b, or the truth value of b. - + Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c Chris Mungall @@ -6591,6 +6609,7 @@ the a supports either the existence of b, or the truth value of b. + A relation that holds between an attribute or a qualifier and another attribute. Chris Mungall @@ -6674,8 +6693,8 @@ the a supports either the existence of b, or the truth value of b. - + p 'results in closure of' c if and only if p is a developmental process and p results in a state of c changing from open to closed. results in closure of @@ -6744,7 +6763,7 @@ the a supports either the existence of b, or the truth value of b. - + p results in organization of c iff p results in the assembly, arrangement of constituent parts, or disassembly of c results in organization of @@ -7971,6 +7990,8 @@ Environmental exposures include those imposed by natural environments, experimen + + muffin 'has substance added' some 'baking soda' "has substance added" is a relation existing between a (physical) entity and a substance in which the entity has had the substance added to it at some point in time. @@ -7985,6 +8006,8 @@ Environmental exposures include those imposed by natural environments, experimen + + 'egg white' 'has substance removed' some 'egg yolk' "has substance removed" is a relation existing between two physical entities in which the first entity has had the second entity (a substance) removed from it at some point in time. @@ -7998,6 +8021,8 @@ Environmental exposures include those imposed by natural environments, experimen + + sardines 'immersed in' some 'oil and mustard' "immersed in" is a relation between a (physical) entity and a fluid substance in which the entity is wholely or substantially surrounded by the substance. @@ -8106,6 +8131,26 @@ Environmental exposures include those imposed by natural environments, experimen + + + + + + + + + + + + + p has anatomical participant c iff p has participant c, and c is an anatomical entity + cjm + 2018-09-26T01:08:58Z + has anatomical participant + + + + @@ -8191,6 +8236,25 @@ Environmental exposures include those imposed by natural environments, experimen + + + + + + + + + + + + + + + + + + + @@ -8208,6 +8272,19 @@ Environmental exposures include those imposed by natural environments, experimen + + + + + + + + + + + + + @@ -8388,6 +8465,9 @@ Environmental exposures include those imposed by natural environments, experimen /////////////////////////////////////////////////////////////////////////////////////// --> + + true + inverse of has disposition @@ -8502,6 +8582,18 @@ Environmental exposures include those imposed by natural environments, experimen + + + + + + + + + + + + @@ -8715,6 +8807,76 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + From ligand activity to has_ligand @@ -9001,9 +9163,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -9012,9 +9174,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + diff --git a/src/ontology/subsets/ro-causal.obo b/src/ontology/subsets/ro-causal.obo index c7c2198a..c69c7a3b 100644 --- a/src/ontology/subsets/ro-causal.obo +++ b/src/ontology/subsets/ro-causal.obo @@ -1,6 +1,6 @@ format-version: 1.2 ontology: ro/subsets/ro-causal -owl-axioms: Prefix(owl:=)\nPrefix(rdf:=)\nPrefix(xml:=)\nPrefix(xsd:=)\nPrefix(rdfs:=)\n\n\nOntology(\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\n\n############################\n# Object Properties\n############################\n\n# Object Property: (coincident with)\n\nObjectPropertyRange( ObjectIntersectionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (has fasciculating neuron projection)\n\nObjectPropertyRange( ObjectUnionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (connected to)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (connects)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (directly develops from)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (anabranch of)\n\nSubObjectPropertyOf( ObjectInverseOf())\n\n# Object Property: (branching part of)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (condition has genetic basis in)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has basis in feature)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has location)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has feature)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n\n\n\nAnnotationAssertion(rdfs:comment \"\")\n) +owl-axioms: Prefix(owl:=)\nPrefix(rdf:=)\nPrefix(xml:=)\nPrefix(xsd:=)\nPrefix(rdfs:=)\n\n\nOntology(\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\n\n############################\n# Object Properties\n############################\n\n# Object Property: (coincident with)\n\nObjectPropertyRange( ObjectIntersectionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (has fasciculating neuron projection)\n\nObjectPropertyRange( ObjectUnionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (connected to)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (connects)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (directly develops from)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (anabranch of)\n\nSubObjectPropertyOf( ObjectInverseOf())\n\n# Object Property: (branching part of)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (condition has genetic basis in)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has basis in feature)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has location)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has feature)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (has anatomical participant)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n\n\n\nAnnotationAssertion(rdfs:comment \"\")\n) [Typedef] id: 2D_boundary_of @@ -327,6 +327,7 @@ def: "c stands in this relationship to p if and only if there exists some p' suc xref: RO:0002216 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "has function in" xsd:string +property_value: seeAlso "defining-property-chains-involving-reflexivity" is_a: causal_agent_in_process ! causal agent in process is_a: functionally_related_to ! functionally related to expand_expression_to: "RO_0000053 some (RO_0000054 only (BFO_0000050 some ?Y))" [] @@ -948,7 +949,7 @@ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 "EHDAA2" xsd:string property_value: IAO:0000119 "Jonathan Bard, EHDAA2" xsd:string -domain: CARO:0000003 +domain: CARO:0000000 is_a: developmentally_preceded_by ! developmentally preceded by [Typedef] @@ -1449,6 +1450,15 @@ property_value: IAO:0000112 "penicillin allergy (DOID:0060520) has allergic trig range: BFO:0000040 is_a: causes_or_contributes_to_condition ! causes or contributes to condition +[Typedef] +id: has_anatomical_participant +name: has anatomical participant +def: "p has anatomical participant c iff p has participant c, and c is an anatomical entity" [] +xref: RO:0040036 +is_a: has_participant +created_by: cjm +creation_date: 2018-09-26T01:08:58Z + [Typedef] id: has_autoimmune_trigger name: has autoimmune trigger @@ -1522,8 +1532,8 @@ xref: RO:0002254 property_value: IAO:0000112 "Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string -domain: BFO:0000004 -range: CARO:0000003 +domain: CARO:0000000 +range: CARO:0000000 is_a: developmentally_preceded_by ! developmentally preceded by inverse_of: developmentally_contributes_to ! developmentally contributes to @@ -1534,6 +1544,8 @@ def: "x has developmental potential involving y iff x is capable of a developmen xref: RO:0002384 property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Chris Mungall" xsd:string +domain: CARO:0000000 +range: CARO:0000000 is_a: developmentally_related_to ! developmentally related to [Typedef] @@ -2069,6 +2081,7 @@ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string property_value: RO:0001900 RO:0001901 domain: CL:0000540 +range: CARO:0000003 is_a: overlaps ! overlaps expand_expression_to: "BFO_0000051 some (\n GO_0043025 and BFO_0000050 some ?Y)" [] @@ -2324,6 +2337,8 @@ name: innervated_by xref: RO:0002005 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 xsd:anyURI property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +domain: CARO:0000003 +range: CARO:0001001 inverse_of: innervates ! innervates [Typedef] @@ -2422,6 +2437,7 @@ id: involved_in_or_involved_in_regulation_of name: involved in or involved in regulation of def: "c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p" [] xref: RO:0002431 +property_value: IAO:0000116 "OWL does not allow defining object properties via a Union" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "involved in or reguates" xsd:string is_a: acts_upstream_of_or_within ! acts upstream of or within @@ -2861,16 +2877,6 @@ def: "A sub-relation of parasite-of in which the parasite that cannot complete i xref: RO:0002227 is_a: parasite_of ! parasite of -[Typedef] -id: obsolete_has_indirect_output -name: obsolete has indirect output -comment: Likely to be obsoleted. See:\nhttps://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/edit -xref: RO:0002403 -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string -is_a: has_output ! has output -is_obsolete: true - [Typedef] id: occurent_part_of name: occurent part of @@ -3313,6 +3319,7 @@ name: releases neurotransmitter xref: RO:0002111 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000118 "has neurotransmitter" xsd:string +domain: CARO:0000003 [Typedef] id: represses_expression_of @@ -3330,8 +3337,8 @@ xref: RO:0002315 property_value: IAO:0000112 "an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast." xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string -range: CL:0000000 -is_a: has_participant +range: CARO:0000003 +is_a: has_anatomical_participant ! has anatomical participant is_a: results_in_developmental_progression_of ! results in developmental progression of [Typedef] @@ -3360,7 +3367,7 @@ id: results_in_closure_of name: results in closure of xref: RO:0002585 property_value: IAO:0000116 "p 'results in closure of' c if and only if p is a developmental process and p results in a state of c changing from open to closed." xsd:string -is_a: has_participant +is_a: has_anatomical_participant ! has anatomical participant is_a: results_in_developmental_progression_of ! results in developmental progression of [Typedef] @@ -3393,7 +3400,7 @@ property_value: IAO:0000112 "every flower development (GO:0009908) results in de property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://www.geneontology.org/GO.doc.development.shtml xsd:anyURI -is_a: has_participant +is_a: has_anatomical_participant ! has anatomical participant is_a: results_in_developmental_progression_of ! results in developmental progression of [Typedef] @@ -3450,7 +3457,7 @@ name: results in ending of def: "p results in the end of s if p results in a change of state in s whereby s either ceases to exist, or s becomes functionally impaired or s has its fate committed such that it is put on a path to be degraded." [] xref: RO:0002552 property_value: IAO:0000117 "Chris Mungall" xsd:string -is_a: has_participant +is_a: has_anatomical_participant ! has anatomical participant is_a: results_in_developmental_progression_of ! results in developmental progression of [Typedef] @@ -3472,7 +3479,7 @@ name: results in growth of xref: RO:0002343 property_value: IAO:0000112 "'pollen tube growth' results_in growth_of some 'pollen tube'" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string -is_a: has_participant +is_a: has_anatomical_participant ! has anatomical participant is_a: results_in_developmental_progression_of ! results in developmental progression of [Typedef] @@ -3485,7 +3492,7 @@ property_value: IAO:0000112 "bone maturation (GO:0070977) results_in_maturation_ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string -is_a: has_participant +is_a: has_anatomical_participant ! has anatomical participant is_a: results_in_developmental_progression_of ! results in developmental progression of [Typedef] @@ -3498,7 +3505,7 @@ property_value: IAO:0000112 "tongue morphogenesis (GO:0043587) results in morpho property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string -is_a: has_participant +is_a: has_anatomical_participant ! has anatomical participant is_a: results_in_developmental_progression_of ! results in developmental progression of [Typedef] @@ -3508,14 +3515,14 @@ def: "Holds between p and c when p is locomotion process and the outcome of this xref: RO:0002565 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000232 "" xsd:string -is_a: has_participant +is_a: has_anatomical_participant ! has anatomical participant [Typedef] id: results_in_organization_of name: results in organization of def: "p results in organization of c iff p results in the assembly, arrangement of constituent parts, or disassembly of c" [] xref: RO:0002592 -is_a: has_participant +is_a: has_anatomical_participant ! has anatomical participant [Typedef] id: results_in_remodeling_of @@ -3540,7 +3547,7 @@ name: results in structural organization of def: "A relationship between a process and an anatomical entity such that the process contributes to the act of creating the structural organization of the anatomical entity." [] xref: RO:0002355 property_value: IAO:0000117 "Chris Mungall" xsd:string -is_a: has_participant +is_a: has_anatomical_participant ! has anatomical participant is_a: results_in_developmental_progression_of ! results in developmental progression of [Typedef] @@ -3790,7 +3797,7 @@ def: "Holds between p and c when p is a localization process (localization cover xref: RO:0002313 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "regulates localization of" xsd:string -is_a: has_participant +is_a: has_anatomical_participant ! has anatomical participant is_a: related_via_localization_to ! related via localization to [Typedef] diff --git a/src/ontology/subsets/ro-causal.owl b/src/ontology/subsets/ro-causal.owl index 5b94e671..0a275674 100644 --- a/src/ontology/subsets/ro-causal.owl +++ b/src/ontology/subsets/ro-causal.owl @@ -381,6 +381,8 @@ + + David Osumi-Sutherland http://www.ncbi.nlm.nih.gov/pubmed/22402613 RO:0002005 @@ -787,6 +789,7 @@ Examples include: the relationship between two channels collected simultaneously + Relation between a neuron and an anatomical structure that its soma is part of. David Osumi-Sutherland @@ -931,6 +934,7 @@ Examples include: the relationship between two channels collected simultaneously + has neurotransmitter RO:0002111 @@ -1548,6 +1552,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.RO:0002216 capable_of_part_of capable of part of + @@ -1700,7 +1705,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - + x develops_in y if x is located in y whilst x is developing Chris Mungall @@ -1995,8 +2000,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - - + + Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong] x has developmental contribution from y iff x has some part z such that z develops from y @@ -2177,8 +2182,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - + every flower development (GO:0009908) results in development of some flower (PO:0009046) p 'results in development of' c if and only if p is a developmental process and p results in the state of c changing from its initial state as a primordium or anlage through its mature state and to its final state. @@ -2212,8 +2217,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - + an annotation of gene X to cell morphogenesis with results_in_morphogenesis_of CL:0000540 (neuron) means that at the end of the process an input neuron has attained its shape. tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723) @@ -2230,8 +2235,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - + an annotation of gene X to cell maturation with results_in_maturation_of CL:0000057 (fibroblast) means that the fibroblast is mature at the end of the process bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474) @@ -2362,8 +2367,8 @@ where - + Holds between p and c when p is a localization process (localization covers maintenance of localization as well as its establishment) and the outcome of this process is to regulate the localization of c. Chris Mungall regulates localization of @@ -2377,9 +2382,9 @@ where - - + + an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast. The relationship that links a specified entity with the process that results in an unspecified entity acquiring the features and characteristics of the specified entity Chris Mungall @@ -2720,8 +2725,8 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - + 'pollen tube growth' results_in growth_of some 'pollen tube' Chris Mungall RO:0002343 @@ -2834,8 +2839,8 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - + A relationship between a process and an anatomical entity such that the process contributes to the act of creating the structural organization of the anatomical entity. Chris Mungall RO:0002355 @@ -3126,6 +3131,8 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + + x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction). Chris Mungall @@ -3209,22 +3216,6 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - - - - - - Chris Mungall - RO:0002403 - obsolete_has_indirect_output - Likely to be obsoleted. See: -https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/edit - obsolete has indirect output - true - - - - @@ -3501,6 +3492,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p + OWL does not allow defining object properties via a Union Chris Mungall involved in or reguates RO:0002431 @@ -4675,8 +4667,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + p results in the end of s if p results in a change of state in s whereby s either ceases to exist, or s becomes functionally impaired or s has its fate committed such that it is put on a path to be degraded. Chris Mungall RO:0002552 @@ -4785,7 +4777,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c Chris Mungall @@ -4972,8 +4964,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + p 'results in closure of' c if and only if p is a developmental process and p results in a state of c changing from open to closed. RO:0002585 results_in_closure_of @@ -5056,7 +5048,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + p results in organization of c iff p results in the assembly, arrangement of constituent parts, or disassembly of c RO:0002592 results_in_organization_of @@ -6314,6 +6306,28 @@ Environmental exposures include those imposed by natural environments, experimen + + + + + + + + + + + + + p has anatomical participant c iff p has participant c, and c is an anatomical entity + cjm + 2018-09-26T01:08:58Z + RO:0040036 + has_anatomical_participant + has anatomical participant + + + + @@ -6385,6 +6399,12 @@ Environmental exposures include those imposed by natural environments, experimen + + + + + + diff --git a/src/ontology/subsets/ro-chado.obo b/src/ontology/subsets/ro-chado.obo index bdbb18e7..1acedc6d 100644 --- a/src/ontology/subsets/ro-chado.obo +++ b/src/ontology/subsets/ro-chado.obo @@ -5,14 +5,14 @@ remark: Includes Ontology(OntologyID(Anonymous-21)) [Axioms: 26 Logical Axioms: remark: Includes Ontology(OntologyID(Anonymous-21)) [Axioms: 32 Logical Axioms: 0] remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 61 Logical Axioms: 0] remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 18 Logical Axioms: 7] -remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 53 Logical Axioms: 12] +remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 56 Logical Axioms: 13] remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 9 Logical Axioms: 3] -remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 289 Logical Axioms: 60] +remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 291 Logical Axioms: 62] remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 6 Logical Axioms: 2] remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 42 Logical Axioms: 16] remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 49 Logical Axioms: 14] remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 29 Logical Axioms: 9] -remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 102 Logical Axioms: 24] +remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 110 Logical Axioms: 27] remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 20 Logical Axioms: 6] remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 731 Logical Axioms: 148] remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 146 Logical Axioms: 45] @@ -51,6 +51,7 @@ name: realizes id: BFO:0000060 name: obsolete_preceded_by is_transitive: true +is_obsolete: true [Typedef] id: BFO:0000062 @@ -1251,8 +1252,8 @@ is_a: RO:0002320 ! evolutionarily related to id: RO:0002313 name: transports_or_maintains_localization_of def: "Holds between p and c when p is a localization process (localization covers maintenance of localization as well as its establishment) and the outcome of this process is to regulate the localization of c." [] -is_a: RO:0000057 ! has participant is_a: RO:0002337 ! related via localization to +is_a: RO:0040036 ! has anatomical participant transitive_over: BFO:0000051 ! has part [Typedef] @@ -1408,7 +1409,7 @@ is_a: RO:0002344 ! results in transport to from or in id: RO:0002343 name: results_in_growth_of is_a: results_in_developmental_progression_of ! results in developmental progression of -is_a: RO:0000057 ! has participant +is_a: RO:0040036 ! has anatomical participant [Typedef] id: RO:0002344 @@ -1471,7 +1472,7 @@ id: RO:0002355 name: results_in_structural_organization_of def: "A relationship between a process and an anatomical entity such that the process contributes to the act of creating the structural organization of the anatomical entity." [] is_a: results_in_developmental_progression_of ! results in developmental progression of -is_a: RO:0000057 ! has participant +is_a: RO:0040036 ! has anatomical participant [Typedef] id: RO:0002356 @@ -1631,7 +1632,6 @@ is_obsolete: true id: RO:0002403 name: obsolete_has_indirect_output holds_over_chain: RO:0002411 RO:0002402 -is_a: RO:0002234 ! has output is_obsolete: true [Typedef] @@ -1981,7 +1981,7 @@ is_a: RO:0002461 ! partner in [Typedef] id: RO:0002464 -name: helper_property +name: helper_property_(not_for_use_in_curation) [Typedef] id: RO:0002465 @@ -2392,7 +2392,7 @@ id: RO:0002552 name: results_in_ending_of def: "p results in the end of s if p results in a change of state in s whereby s either ceases to exist, or s becomes functionally impaired or s has its fate committed such that it is put on a path to be degraded." [] is_a: results_in_developmental_progression_of ! results in developmental progression of -is_a: RO:0000057 ! has participant +is_a: RO:0040036 ! has anatomical participant [Typedef] id: RO:0002553 @@ -2445,7 +2445,7 @@ inverse_of: RO:0002566 ! causally influences [Typedef] id: RO:0002563 name: interaction_relation_helper_property -is_a: RO:0002464 ! helper property +is_a: RO:0002464 ! helper property (not for use in curation) [Typedef] id: RO:0002564 @@ -2456,7 +2456,7 @@ is_a: RO:0002563 ! interaction relation helper property id: RO:0002565 name: results_in_movement_of def: "Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c" [] -is_a: RO:0000057 ! has participant +is_a: RO:0040036 ! has anatomical participant [Typedef] id: RO:0002566 @@ -2541,7 +2541,7 @@ is_a: RO:0002595 ! causal relation between material entity and a process id: RO:0002585 name: results_in_closure_of is_a: results_in_developmental_progression_of ! results in developmental progression of -is_a: RO:0000057 ! has participant +is_a: RO:0040036 ! has anatomical participant [Typedef] id: RO:0002586 @@ -2582,7 +2582,7 @@ is_a: RO:0002592 ! results in organization of id: RO:0002592 name: results_in_organization_of def: "p results in organization of c iff p results in the assembly, arrangement of constituent parts, or disassembly of c" [] -is_a: RO:0000057 ! has participant +is_a: RO:0040036 ! has anatomical participant [Typedef] id: RO:0002593 @@ -3200,6 +3200,12 @@ id: RO:0040035 name: disease_relationship def: "This relation groups relations between diseases and any other kind of entity." [] +[Typedef] +id: RO:0040036 +name: has_anatomical_participant +def: "p has anatomical participant c iff p has participant c, and c is an anatomical entity" [] +is_a: RO:0000057 ! has participant + [Typedef] id: RO:HOM0000000 name: in_similarity_relationship_with @@ -3810,14 +3816,14 @@ id: results_in_acquisition_of_features_of name: results_in_acquisition_of_features_of def: "The relationship that links a specified entity with the process that results in an unspecified entity acquiring the features and characteristics of the specified entity" [] is_a: results_in_developmental_progression_of ! results in developmental progression of -is_a: RO:0000057 ! has participant +is_a: RO:0040036 ! has anatomical participant [Typedef] id: results_in_development_of name: results_in_development_of def: "p 'results in development of' c if and only if p is a developmental process and p results in the state of c changing from its initial state as a primordium or anlage through its mature state and to its final state." [] is_a: results_in_developmental_progression_of ! results in developmental progression of -is_a: RO:0000057 ! has participant +is_a: RO:0040036 ! has anatomical participant [Typedef] id: results_in_developmental_progression_of @@ -3841,12 +3847,12 @@ id: results_in_maturation_of name: results_in_maturation_of def: "The relationship that links an entity with a process that results in the progression of the entity over time that is independent of changes in it's shape and results in an end point state of that entity." [] is_a: results_in_developmental_progression_of ! results in developmental progression of -is_a: RO:0000057 ! has participant +is_a: RO:0040036 ! has anatomical participant [Typedef] id: results_in_morphogenesis_of name: results_in_morphogenesis_of def: "The relationship that links an entity with the process that results in the formation and shaping of that entity over time from an immature to a mature state." [] is_a: results_in_developmental_progression_of ! results in developmental progression of -is_a: RO:0000057 ! has participant +is_a: RO:0040036 ! has anatomical participant diff --git a/src/ontology/subsets/ro-chado.obo.tmp b/src/ontology/subsets/ro-chado.obo.tmp deleted file mode 100644 index 5330a29d..00000000 --- a/src/ontology/subsets/ro-chado.obo.tmp +++ /dev/null @@ -1,3852 +0,0 @@ -format-version: 1.2 -subsetdef: ro-eco "" -subsetdef: RO:0002259 "" -remark: Includes Ontology(OntologyID(Anonymous-21)) [Axioms: 26 Logical Axioms: 0] -remark: Includes Ontology(OntologyID(Anonymous-21)) [Axioms: 32 Logical Axioms: 0] -remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 61 Logical Axioms: 0] -remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 18 Logical Axioms: 7] -remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 53 Logical Axioms: 12] -remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 9 Logical Axioms: 3] -remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 289 Logical Axioms: 60] -remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 6 Logical Axioms: 2] -remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 42 Logical Axioms: 16] -remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 49 Logical Axioms: 14] -remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 29 Logical Axioms: 9] -remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 102 Logical Axioms: 24] -remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 20 Logical Axioms: 6] -remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 731 Logical Axioms: 148] -remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 146 Logical Axioms: 45] -ontology: ro/subsets/ro-chado.obo -property_value: http://purl.org/dc/elements/1.1/description "The OBO Relations Ontology (RO) is a collection of OWL relations (ObjectProperties) intended for use across a wide variety of biological ontologies." xsd:string -property_value: http://purl.org/dc/elements/1.1/source http://obofoundry.org/ro -property_value: http://purl.org/dc/elements/1.1/title "OBO Relations Ontology" xsd:string -property_value: http://xmlns.com/foaf/0.1/homepage " https://github.com/oborel/obo-relations/" xsd:anyURI -owl-axioms: Prefix(owl:=)\nPrefix(rdf:=)\nPrefix(xml:=)\nPrefix(xsd:=)\nPrefix(rdfs:=)\n\n\nOntology(\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(DataProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\n############################\n# Annotation Properties\n############################\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\nAnnotationPropertyRange( xsd:nonNegativeInteger)\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n\n############################\n# Object Properties\n############################\n\n# Object Property: (has member)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (anabranch of)\n\nSubObjectPropertyOf( ObjectInverseOf())\n\n# Object Property: (has substance added)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (has substance removed)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (immersed in)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (has primary substance added)\n\nIrreflexiveObjectProperty()\n\n\n############################\n# Data Properties\n############################\n\n# Data Property: ()\n\nDataPropertyRange( DatatypeRestriction(xsd:short xsd:minInclusive \"0\"^^xsd:short xsd:maxInclusive \"100\"^^xsd:short))\n\n\n\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain(ObjectInverseOf() ) )\nSubObjectPropertyOf(ObjectPropertyChain(ObjectInverseOf() ) )\nDLSafeRule(Annotation(rdfs:comment \"This rule is dubious: added as a quick fix for expected inference in GO-CAM. The problem is most acute for transmembrane proteins, such as receptors or cell adhesion molecules, which have some subfunctions inside the cell (e.g. kinase activity) and some subfunctions outside (e.g. ligand binding). Correct annotation of where these functions occurs leads to incorrect inference about the location of the whole protein. This should probably be weakened to \\\"... -> overlaps\\\"\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this.\") Annotation(rdfs:label \"inferring direct reg edge from input to regulatory subfunction\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"inferring direct neg reg edge from input to regulatory subfunction\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"inferring direct positive reg edge from input to regulatory subfunction\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"effector input is compound function input\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"Input of effector is input of its parent MF\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"if effector directly regulates X, its parent MF directly regulates X\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"if effector directly positively regulates X, its parent MF directly positively regulates X\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"if effector directly negatively regulates X, its parent MF directly negatively regulates X\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\n) - -[Typedef] -id: BFO:0000050 -name: part of -def: "a core relation that holds between a part and its whole" [] -is_transitive: true -is_a: RO:0002131 ! overlaps -inverse_of: BFO:0000051 ! has part - -[Typedef] -id: BFO:0000051 -name: has part -def: "a core relation that holds between a whole and its part" [] -is_transitive: true -is_a: RO:0002131 ! overlaps - -[Typedef] -id: BFO:0000054 -name: realized in -inverse_of: BFO:0000055 ! realizes - -[Typedef] -id: BFO:0000055 -name: realizes - -[Typedef] -id: BFO:0000060 -name: obsolete preceded by -is_transitive: true - -[Typedef] -id: BFO:0000062 -name: preceded by -def: "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." [] -holds_over_chain: BFO:0000050 BFO:0000062 -holds_over_chain: RO:0002091 BFO:0000062 -holds_over_chain: RO:0002092 BFO:0000062 -is_transitive: true -is_a: RO:0002086 ! ends after -inverse_of: BFO:0000063 ! precedes - -[Typedef] -id: BFO:0000063 -name: precedes -def: "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." [] -holds_over_chain: BFO:0000050 BFO:0000063 -holds_over_chain: RO:0002092 BFO:0000063 -is_transitive: true -is_a: RO:0002222 ! temporally related to - -[Typedef] -id: BFO:0000066 -name: occurs in -def: "b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" [] -holds_over_chain: BFO:0000050 BFO:0000066 -inverse_of: BFO:0000067 ! contains process -transitive_over: BFO:0000050 ! part of - -[Typedef] -id: BFO:0000067 -name: contains process -def: "[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" [] - -[Typedef] -id: R0:0009004 -name: has consumer -def: "'has consumer' is a relation between a material entity and an organism in which the former can normally be digested or otherwise absorbed by the latter without immediate or persistent ill effect." [] - -[Typedef] -id: RO:0000052 -name: inheres in -def: "a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence" [] -is_a: RO:0002314 ! inheres in part of -inverse_of: RO:0000053 ! bearer of - -[Typedef] -id: RO:0000053 -name: bearer of -def: "a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence" [] - -[Typedef] -id: RO:0000056 -name: participates in -def: "a relation between a continuant and a process, in which the continuant is somehow involved in the process" [] -inverse_of: RO:0000057 ! has participant - -[Typedef] -id: RO:0000057 -name: has participant -def: "a relation between a process and a continuant, in which the continuant is somehow involved in the process" [] -holds_over_chain: BFO:0000051 RO:0000057 - -[Typedef] -id: RO:0000058 -name: is concretized as -def: "A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants." [] -inverse_of: RO:0000059 ! concretizes - -[Typedef] -id: RO:0000059 -name: concretizes -def: "A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant." [] - -[Typedef] -id: RO:0000079 -name: function of -def: "a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence" [] -is_a: RO:0000052 ! inheres in -inverse_of: RO:0000085 ! has function - -[Typedef] -id: RO:0000080 -name: quality of -def: "a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence" [] -is_a: RO:0000052 ! inheres in -inverse_of: RO:0000086 ! has quality - -[Typedef] -id: RO:0000081 -name: role of -def: "a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence" [] -is_a: RO:0000052 ! inheres in -inverse_of: RO:0000087 ! has role - -[Typedef] -id: RO:0000085 -name: has function -def: "a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence" [] -is_a: RO:0000053 ! bearer of - -[Typedef] -id: RO:0000086 -name: has quality -def: "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence" [] -is_a: RO:0000053 ! bearer of - -[Typedef] -id: RO:0000087 -name: has role -def: "a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence" [] -is_a: RO:0000053 ! bearer of - -[Typedef] -id: RO:0000091 -name: has disposition -def: "a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence" [] -is_a: RO:0000053 ! bearer of -inverse_of: RO:0000092 ! disposition of - -[Typedef] -id: RO:0000092 -name: disposition of -def: "inverse of has disposition" [] -is_a: RO:0000052 ! inheres in - -[Typedef] -id: RO:0000300 -name: in neural circuit with -def: "A relation that holds between two neurons connected directly via a synapse, or indirectly via a series of synaptically connected neurons." [] -is_transitive: true - -[Typedef] -id: RO:0000301 -name: upstream in neural circuit with -def: "A relation that holds between a neuron that is synapsed_to another neuron or a neuron that is connected indirectly to another by a chain of neurons, each synapsed_to the next." [] -is_transitive: true -is_a: RO:0000300 ! in neural circuit with - -[Typedef] -id: RO:0000302 -name: downstream in neural circuit with -def: "A relation that holds between a neuron that is synapsed_to another neuron or a neuron that is connected indirectly to another by a chain of neurons, each synapsed_to the next." [] -is_transitive: true -is_a: RO:0000300 ! in neural circuit with - -[Typedef] -id: RO:0001000 -name: derives from -def: "a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity" [] -inverse_of: RO:0001001 ! derives into - -[Typedef] -id: RO:0001001 -name: derives into -def: "a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity" [] - -[Typedef] -id: RO:0001015 -name: location of -def: "a relation between two independent continuants, the location and the target, in which the target is entirely within the location" [] -is_transitive: true -inverse_of: RO:0001025 ! located in - -[Typedef] -id: RO:0001018 -name: contained in -holds_over_chain: RO:0001025 BFO:0000050 -inverse_of: RO:0001019 ! contains - -[Typedef] -id: RO:0001019 -name: contains - -[Typedef] -id: RO:0001020 -name: is allergic trigger for -def: "A relation between a material entity and a condition (a phenotype or disease) of a host, in which the material entity is not part of the host, and is considered harmless to non-allergic hosts, and the condition results in pathological processes that include an abnormally strong immune response against the material entity." [] -is_a: RO:0003302 ! causes or contributes to condition -inverse_of: RO:0001022 ! has allergic trigger - -[Typedef] -id: RO:0001021 -name: is autoimmune trigger for -def: "A relation between a material entity and a condition (a phenotype or disease) of a host, in which the material entity is part of the host itself, and the condition results in pathological processes that include an abnormally strong immune response against the material entity." [] -is_a: RO:0003302 ! causes or contributes to condition -inverse_of: RO:0001023 ! has autoimmune trigger - -[Typedef] -id: RO:0001022 -name: has allergic trigger -def: "A relation between a condition (a phenotype or disease) of a host and a material entity, in which the material entity is not part of the host, and is considered harmless to non-allergic hosts, and the condition results in pathological processes that include an abnormally strong immune response against the material entity." [] -is_a: RO:0003302 ! causes or contributes to condition - -[Typedef] -id: RO:0001023 -name: has autoimmune trigger -def: "A relation between a condition (a phenotype or disease) of a host and a material entity, in which the material entity is part of the host itself, and the condition results in pathological processes that include an abnormally strong immune response against the material entity." [] -is_a: RO:0003302 ! causes or contributes to condition - -[Typedef] -id: RO:0001025 -name: located in -def: "a relation between two independent continuants, the target and the location, in which the target is entirely within the location" [] -is_transitive: true - -[Typedef] -id: RO:0002000 -name: 2D boundary of -def: "a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity" [] -is_a: RO:0002323 ! mereotopologically related to -inverse_of: RO:0002002 ! has 2D boundary - -[Typedef] -id: RO:0002001 -name: aligned with -is_transitive: true - -[Typedef] -id: RO:0002002 -name: has 2D boundary -def: "a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity" [] -is_a: RO:0002323 ! mereotopologically related to - -[Typedef] -id: RO:0002003 -name: electrically_synapsed_to -def: "A relation that holds between two neurons that are electrically coupled via gap junctions." [] -is_a: RO:0000300 ! in neural circuit with - -[Typedef] -id: RO:0002004 -name: tracheates -def: "The relationship that holds between a trachea or tracheole and an antomical structure that is contained in (and so provides an oxygen supply to)." [] -is_a: RO:0001018 ! contained in - -[Typedef] -id: RO:0002005 -name: innervated_by -inverse_of: RO:0002134 ! innervates - -[Typedef] -id: RO:0002006 -name: has synaptic terminal of -is_a: RO:0002131 ! overlaps -inverse_of: RO:0002130 ! has synaptic terminal in - -[Typedef] -id: RO:0002007 -name: bounding layer of -def: "X outer_layer_of Y iff:\n. X :continuant that bearer_of some PATO:laminar\n. X part_of Y\n. exists Z :surface\n. X has_boundary Z\n. Z boundary_of Y\n\nhas_boundary: http://purl.obolibrary.org/obo/RO_0002002\nboundary_of: http://purl.obolibrary.org/obo/RO_0002000" [] -is_a: BFO:0000050 ! part of - -[Typedef] -id: RO:0002008 -name: coincident with -def: "A relation that holds between two linear structures that are approximately parallel to each other for their entire length and where either the two structures are adjacent to each other or one is part of the other." [] -is_a: RO:0002323 ! mereotopologically related to - -[Typedef] -id: RO:0002009 -name: cell expresses -def: "A relation that applies between a cell(c) and a gene(g) , where the process of 'transcription, DNA templated (GO_0006351)' is occuring in in cell c and that process has input gene g." [] -is_a: RO:0002292 ! expresses - -[Typedef] -id: RO:0002010 -name: regulates in other organism -def: "x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." [] -is_a: RO:0002418 ! causally upstream of or within - -[Typedef] -id: RO:0002011 -name: regulates transport of -def: "A relationship that holds between a process that regulates a transport process and the entity transported by that process." [] -holds_over_chain: RO:0002211 RO:0002313 - -[Typedef] -id: RO:0002012 -name: occurent part of -def: "A part of relation that applies only between occurents." [] -is_a: BFO:0000050 ! part of -is_a: RO:0002418 ! causally upstream of or within - -[Typedef] -id: RO:0002013 -name: has regulatory component activity -def: "A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B." [] -is_a: RO:0002017 ! has component activity -is_a: RO:0002334 ! regulated by - -[Typedef] -id: RO:0002014 -name: has negative regulatory component activity -def: "A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B." [] -is_a: RO:0002013 ! has regulatory component activity -is_a: RO:0002335 ! negatively regulated by - -[Typedef] -id: RO:0002015 -name: has positive regulatory component activity -def: "A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B." [] -is_a: RO:0002013 ! has regulatory component activity -is_a: RO:0002336 ! positively regulated by - -[Typedef] -id: RO:0002016 -name: has necessary component activity -is_a: RO:0002017 ! has component activity -is_a: RO:0002336 ! positively regulated by - -[Typedef] -id: RO:0002017 -name: has component activity -is_a: RO:0002018 ! has component process - -[Typedef] -id: RO:0002018 -name: has component process -def: "w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type." [] -is_a: RO:0002180 ! has component - -[Typedef] -id: RO:0002019 -name: has ligand -def: "A relationship that holds between between a receptor and an chemical entity, typically a small molecule or peptide, that carries information between cells or compartments of a cell and which binds the receptor and regulates its effector function." [] -is_a: RO:0002233 ! has input - -[Typedef] -id: RO:0002020 -name: transports -def: "Holds between p and c when p is a transport process or transporter activity and the outcome of this p is to move c from one location to another." [] -is_a: RO:0002313 ! transports or maintains localization of - -[Typedef] -id: RO:0002021 -name: occurs across -def: "A relationship between a process and a barrier, where the process occurs in a region spanning the barrier. For cellular processes the barrier is typically a membrane. Examples include transport across a membrane and membrane depolarization." [] -is_a: RO:0002479 ! has part that occurs in - -[Typedef] -id: RO:0002022 -name: directly regulated by -is_a: RO:0002334 ! regulated by -inverse_of: RO:0002578 ! directly regulates - -[Typedef] -id: RO:0002023 -name: directly negatively regulated by -def: "Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1." [GOC:dos] -is_a: RO:0002022 ! directly regulated by -inverse_of: RO:0002630 ! directly negatively regulates - -[Typedef] -id: RO:0002024 -name: directly positively regulated by -def: "Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1." [GOC:dos] -is_a: RO:0002022 ! directly regulated by -inverse_of: RO:0002629 ! directly positively regulates - -[Typedef] -id: RO:0002025 -name: has effector activity -def: "A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity." [GOC:dos] -is_functional: true -is_a: RO:0002017 ! has component activity -is_a: RO:0002211 ! regulates - -[Typedef] -id: RO:0002026 -name: in register with -def: "A relationship that holds between two images, A and B, where:\nA depicts X;\nB depicts Y;\nX and Y are both of type T'\nC is a 2 layer image consiting of layers A and B;\nA and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other.\nNote: A and B may be 2D or 3D.\nExamples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software." [GOC:dos] -is_a: RO:0002323 ! mereotopologically related to - -[Typedef] -id: RO:0002081 -name: before or simultaneous with -is_a: RO:0002222 ! temporally related to - -[Typedef] -id: RO:0002082 -name: simultaneous with -is_transitive: true -is_a: RO:0002081 ! before or simultaneous with - -[Typedef] -id: RO:0002083 -name: before -is_transitive: true -is_a: RO:0002081 ! before or simultaneous with - -[Typedef] -id: RO:0002084 -name: during which ends -is_a: RO:0002222 ! temporally related to -inverse_of: RO:0002093 ! ends during - -[Typedef] -id: RO:0002085 -name: encompasses -is_transitive: true -is_a: RO:0002088 ! during which starts -inverse_of: RO:0002092 ! happens during - -[Typedef] -id: RO:0002086 -name: ends after -holds_over_chain: RO:0002093 BFO:0000062 -is_transitive: true -is_a: RO:0002222 ! temporally related to - -[Typedef] -id: RO:0002087 -name: immediately preceded by -holds_over_chain: RO:0002224 RO:0002230 -is_a: BFO:0000062 ! preceded by -inverse_of: RO:0002090 ! immediately precedes - -[Typedef] -id: RO:0002088 -name: during which starts -is_a: RO:0002222 ! temporally related to -inverse_of: RO:0002091 ! starts during - -[Typedef] -id: RO:0002089 -name: starts before -holds_over_chain: RO:0002091 BFO:0000060 -is_transitive: true -is_a: RO:0002222 ! temporally related to - -[Typedef] -id: RO:0002090 -name: immediately precedes -holds_over_chain: RO:0002230 RO:0002224 -is_a: BFO:0000063 ! precedes - -[Typedef] -id: RO:0002091 -name: starts during -is_a: RO:0002222 ! temporally related to - -[Typedef] -id: RO:0002092 -name: happens during -is_transitive: true -is_a: RO:0002093 ! ends during - -[Typedef] -id: RO:0002093 -name: ends during -is_a: RO:0002222 ! temporally related to - -[Typedef] -id: RO:0002100 -name: has soma location -def: "Relation between a neuron and an anatomical structure that its soma is part of." [] -is_a: RO:0002131 ! overlaps -transitive_over: BFO:0000050 ! part of - -[Typedef] -id: RO:0002101 -name: fasciculates with -def: "relationship between a neuron and a neuron projection bundle (e.g.- tract or nerve bundle) that one or more of its projections travels through.\n" [] -is_a: RO:0002131 ! overlaps -inverse_of: RO:0002132 ! has fasciculating neuron projection - -[Typedef] -id: RO:0002102 -name: axon synapses in -def: "Relation between a neuron and some structure its axon forms (chemical) synapses in." [] -is_a: RO:0002113 ! has presynaptic terminal in -inverse_of: RO:0002110 ! has postsynaptic terminal in -transitive_over: BFO:0000050 ! part of - -[Typedef] -id: RO:0002103 -name: synapsed by -def: "Relation between an anatomical structure (including cells) and a neuron that chemically synapses to it. " [] -is_a: RO:0000301 ! upstream in neural circuit with -inverse_of: RO:0002120 ! synapsed to - -[Typedef] -id: RO:0002104 -name: has plasma membrane part -def: "Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part." [] -is_a: BFO:0000051 ! has part - -[Typedef] -id: RO:0002105 -name: synapsed_via_type_Ib_bouton_to -def: "A relation between a motor neuron and a muscle that it synapses to via a type Ib bouton." [] -is_a: RO:0002120 ! synapsed to -inverse_of: RO:0002109 ! synapsed_by_via_type_Ib_bouton - -[Typedef] -id: RO:0002106 -name: synapsed_via_type_Is_bouton_to -def: "A relation between a motor neuron and a muscle that it synapses to via a type Is bouton." [] -is_a: RO:0002120 ! synapsed to -inverse_of: RO:0002112 ! synapsed_by_via_type_Is_bouton - -[Typedef] -id: RO:0002107 -name: synapsed_via_type_II_bouton_to -def: "A relation between a motor neuron and a muscle that it synapses to via a type II bouton." [] -is_a: RO:0002120 ! synapsed to -inverse_of: RO:0002108 ! synapsed_by_via_type_II_bouton - -[Typedef] -id: RO:0002108 -name: synapsed_by_via_type_II_bouton -def: "Relation between a muscle and a motor neuron that synapses to it via a type II bouton." [] -is_a: RO:0002103 ! synapsed by - -[Typedef] -id: RO:0002109 -name: synapsed_by_via_type_Ib_bouton -def: "Relation between a muscle and a motor neuron that synapses to it via a type Ib bouton." [] -is_a: RO:0002103 ! synapsed by - -[Typedef] -id: RO:0002110 -name: has postsynaptic terminal in -def: "Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input. " [] -is_a: RO:0002130 ! has synaptic terminal in -transitive_over: BFO:0000050 ! part of - -[Typedef] -id: RO:0002111 -name: releases neurotransmitter - -[Typedef] -id: RO:0002112 -name: synapsed_by_via_type_Is_bouton -def: "Relation between a muscle and a motor neuron that synapses to it via a type Is bouton." [] -is_a: RO:0002103 ! synapsed by - -[Typedef] -id: RO:0002113 -name: has presynaptic terminal in -def: "Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input." [] -is_a: RO:0002130 ! has synaptic terminal in -transitive_over: BFO:0000050 ! part of - -[Typedef] -id: RO:0002114 -name: synapsed_via_type_III_bouton_to -def: "A relation between a motor neuron and a muscle that it synapses to via a type III bouton." [] -is_a: RO:0002120 ! synapsed to -inverse_of: RO:0002115 ! synapsed_by_via_type_III_bouton - -[Typedef] -id: RO:0002115 -name: synapsed_by_via_type_III_bouton -def: "Relation between a muscle and a motor neuron that synapses to it via a type III bouton.\n" [] -is_a: RO:0002103 ! synapsed by - -[Typedef] -id: RO:0002120 -name: synapsed to -def: " Relation between a neuron and an anatomical structure (including cells) that it chemically synapses to.\n " [] -is_a: RO:0000302 ! downstream in neural circuit with - -[Typedef] -id: RO:0002121 -name: dendrite synapsed in -def: "Relation between a neuron and some structure (e.g.- a brain region) in which its dendrite receives synaptic input.\n\n " [] -is_a: RO:0002110 ! has postsynaptic terminal in -transitive_over: BFO:0000050 ! part of - -[Typedef] -id: RO:0002130 -name: has synaptic terminal in -def: "A general relation between a neuron and some structure in which it either chemically synapses to some target or in which it receives (chemical) synaptic input." [] -is_a: RO:0002131 ! overlaps -transitive_over: BFO:0000050 ! part of - -[Typedef] -id: RO:0002131 -name: overlaps -def: "x overlaps y if and only if there exists some z such that x has part z and z part of y" [] -holds_over_chain: BFO:0000050 BFO:0000050 -holds_over_chain: BFO:0000051 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"} -holds_over_chain: BFO:0000051 RO:0002131 -is_a: RO:0002323 ! mereotopologically related to - -[Typedef] -id: RO:0002132 -name: has fasciculating neuron projection -def: "The relation between a neuron projection bundle and a neuron projection that is fasciculated with it." [] -is_a: RO:0002131 ! overlaps - -[Typedef] -id: RO:0002134 -name: innervates -def: "Relation between a 'neuron projection bundle' and a region in which one or more of its component neuron projections either synapses to targets or receives synaptic input.\nT innervates some R\nExpands_to: T has_fasciculating_neuron_projection that synapse_in some R." [] -transitive_over: BFO:0000050 ! part of - -[Typedef] -id: RO:0002150 -name: continuous with -def: "X continuous_with Y if and only if X and Y share a fiat boundary." [] -is_a: RO:0002323 ! mereotopologically related to - -[Typedef] -id: RO:0002151 -name: partially overlaps -def: "x partially overlaps y iff there exists some z such that z is part of x and z is part of y, and it is also the case that neither x is part of y or y is part of x" [] -is_a: RO:0002131 ! overlaps - -[Typedef] -id: RO:0002156 -name: derived by descent from -def: "d derived_by_descent_from a if d is specified by some genetic program that is sequence-inherited-from a genetic program that specifies a." [] -is_transitive: true -is_a: RO:0002320 ! evolutionarily related to -inverse_of: RO:0002157 ! has derived by descendant - -[Typedef] -id: RO:0002157 -name: has derived by descendant -def: "inverse of derived by descent from" [] -is_transitive: true -is_a: RO:0002320 ! evolutionarily related to - -[Typedef] -id: RO:0002158 -name: shares ancestor with -def: "two individual entities d1 and d2 stand in a shares_ancestor_with relation if and only if there exists some a such that d1 derived_by_descent_from a and d2 derived_by_descent_from a." [] -holds_over_chain: RO:0002156 RO:0002157 -is_symmetric: true -is_transitive: true -is_a: RO:0002320 ! evolutionarily related to - -[Typedef] -id: RO:0002159 -name: serially homologous to -is_symmetric: true -is_transitive: true -is_a: RO:0002320 ! evolutionarily related to - -[Typedef] -id: RO:0002160 -name: only in taxon -def: "x only in taxon y if and only if x is in taxon y, and there is no other organism z such that y!=z a and x is in taxon z." [] -is_a: RO:0002162 ! in taxon - -[Typedef] -id: RO:0002162 -name: in taxon -def: "x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed." [] -holds_over_chain: BFO:0000050 RO:0002162 -holds_over_chain: BFO:0000051 RO:0002162 -holds_over_chain: results_in_developmental_progression_of RO:0002162 -holds_over_chain: RO:0002202 RO:0002162 -holds_over_chain: RO:0002206 RO:0002162 -holds_over_chain: RO:0002214 RO:0002162 -holds_over_chain: RO:0002215 RO:0002162 -holds_over_chain: RO:0002217 RO:0002162 -holds_over_chain: RO:0002225 RO:0002162 -holds_over_chain: RO:0002254 RO:0002162 -is_a: RO:0002320 ! evolutionarily related to - -[Typedef] -id: RO:0002163 -name: spatially disjoint from -def: "A is spatially_disjoint_from B if and only if they have no parts in common" [] -is_a: RO:0002323 ! mereotopologically related to - -[Typedef] -id: RO:0002170 -name: connected to -def: "a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b" [] -is_a: RO:0002323 ! mereotopologically related to - -[Typedef] -id: RO:0002176 -name: connects -def: "c connects a if and only if there exist some b such that a and b are similar parts of the same system, and c connects b, specifically, c connects a with b. When one structure connects two others it unites some aspect of the function or role they play within the system." [] -is_a: RO:0002323 ! mereotopologically related to - -[Typedef] -id: RO:0002177 -name: attached to part of -def: "a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b." [] -holds_over_chain: RO:0002371 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"} -is_a: RO:0002323 ! mereotopologically related to -is_a: RO:0002567 ! biomechanically related to - -[Typedef] -id: RO:0002178 -name: supplies -def: "Relation between an arterial structure and another structure, where the arterial structure acts as a conduit channeling fluid, substance or energy." [] -is_a: RO:0002170 ! connected to - -[Typedef] -id: RO:0002179 -name: drains -def: "Relation between an collecting structure and another structure, where the collecting structure acts as a conduit channeling fluid, substance or energy away from the other structure." [] -is_a: RO:0002170 ! connected to - -[Typedef] -id: RO:0002180 -name: has component -def: "w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type." [] -is_a: BFO:0000051 ! has part - -[Typedef] -id: RO:0002200 -name: has phenotype -def: "A relationship that holds between a biological entity and a phenotype. Here a phenotype is construed broadly as any kind of quality of an organism part, a collection of these qualities, or a change in quality or qualities (e.g. abnormally increased temperature). The subject of this relationship can be an organism (where the organism has the phenotype, i.e. the qualities inhere in parts of this organism), a genomic entity such as a gene or genotype (if modifications of the gene or the genotype causes the phenotype), or a condition such as a disease (such that if the condition inheres in an organism, then the organism has the phenotype)." [] -inverse_of: RO:0002201 ! phenotype of - -[Typedef] -id: RO:0002201 -name: phenotype of -def: "inverse of has phenotype" [] -is_functional: true - -[Typedef] -id: RO:0002202 -name: develops from -def: "x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y" [] -is_transitive: true -is_a: RO:0002258 ! developmentally preceded by -inverse_of: RO:0002203 ! develops into - -[Typedef] -id: RO:0002203 -name: develops into -def: "inverse of develops from" [] -is_transitive: true -is_a: RO:0002286 ! developmentally succeeded by -is_a: RO:0002387 ! has potential to develop into -is_a: RO:0002388 ! has potential to directly develop into - -[Typedef] -id: RO:0002204 -name: gene product of -def: "definition \"x has gene product of y if and only if y is a gene (SO:0000704) that participates in some gene expression process (GO:0010467) where the output of that process is either y or something that is ribosomally translated from x\"" [] -holds_over_chain: RO:0002512 RO:0002510 -is_a: RO:0002330 ! genomically related to -inverse_of: RO:0002205 ! has gene product - -[Typedef] -id: RO:0002205 -name: has gene product -def: "x has gene product y if and only if x is a gene (SO:0000704) that participates in some gene expression process (GO:0010467) where the output of that process is either y or something that is ribosomally translated from y" [] -holds_over_chain: RO:0002511 RO:0002513 -is_a: RO:0002330 ! genomically related to - -[Typedef] -id: RO:0002206 -name: expressed in -def: "x expressed in y if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and the transcription of x is part of the gene expression process (iii) x is a mature gene product such as a protein, and x was translated or otherwise processes from a transcript that was transcribed as part of this gene expression process" [] -is_a: RO:0002330 ! genomically related to -inverse_of: RO:0002292 ! expresses -transitive_over: BFO:0000050 ! part of - -[Typedef] -id: RO:0002207 -name: directly develops from -def: "Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of y comes from x, and the start of x is coincident with or after the end of y" [] -is_a: RO:0002202 ! develops from -inverse_of: RO:0002210 ! directly develops into - -[Typedef] -id: RO:0002208 -name: parasitoid of -def: "A parasite that kills or sterilizes its host" [] -is_a: RO:0002444 ! parasite of -inverse_of: RO:0002209 ! has parasitoid - -[Typedef] -id: RO:0002209 -name: has parasitoid -def: "inverse of parasitoid of" [] -is_a: RO:0002445 ! parasitized by - -[Typedef] -id: RO:0002210 -name: directly develops into -def: "inverse of directly develops from" [] -is_a: RO:0002203 ! develops into - -[Typedef] -id: RO:0002211 -name: regulates -def: "process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2." [] -holds_over_chain: RO:0002230 RO:0002211 -holds_over_chain: RO:0002578 RO:0002578 -is_transitive: true -is_a: RO:0002411 ! causally upstream of -inverse_of: RO:0002334 ! regulated by - -[Typedef] -id: RO:0002212 -name: negatively regulates -def: "Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2." [] -holds_over_chain: RO:0002230 RO:0002212 -is_a: RO:0002211 ! regulates -is_a: RO:0002305 ! causally upstream of, negative effect -inverse_of: RO:0002335 ! negatively regulated by - -[Typedef] -id: RO:0002213 -name: positively regulates -def: "Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2." [] -holds_over_chain: RO:0002212 RO:0002212 -holds_over_chain: RO:0002230 RO:0002213 -is_transitive: true -is_a: RO:0002211 ! regulates -is_a: RO:0002304 ! causally upstream of, positive effect -inverse_of: RO:0002336 ! positively regulated by - -[Typedef] -id: RO:0002214 -name: has prototype -def: "x has prototype y if and only if x is an instance of C and y is a prototypical instance of C. For example, every instance of heart, both normal and abnormal is related by the has prototype relation to some instance of a \"canonical\" heart, which participates in blood circulation." [] - -[Typedef] -id: RO:0002215 -name: capable of -def: "A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. " [] -holds_over_chain: RO:0002214 RO:0002217 -is_a: RO:0002216 ! capable of part of - -[Typedef] -id: RO:0002216 -name: capable of part of -def: "c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p." [] -holds_over_chain: RO:0002215 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"} -is_a: RO:0002328 ! functionally related to -is_a: RO:0002500 ! causal agent in process - -[Typedef] -id: RO:0002217 -name: actively participates in -def: "x actively participates in y if and only if x participates in y and x realizes some active role" [] -is_a: RO:0000056 ! participates in -inverse_of: RO:0002218 ! has active participant - -[Typedef] -id: RO:0002218 -name: has active participant -def: "x has participant y if and only if x realizes some active role that inheres in y" [] -is_a: RO:0000057 ! has participant - -[Typedef] -id: RO:0002219 -name: surrounded by -def: "x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x" [] -is_a: RO:0002220 ! adjacent to -inverse_of: RO:0002221 ! surrounds - -[Typedef] -id: RO:0002220 -name: adjacent to -def: "x adjacent to y if and only if x and y share a boundary." [] -is_a: RO:0002163 ! spatially disjoint from - -[Typedef] -id: RO:0002221 -name: surrounds -def: "inverse of surrounded by" [] -is_a: RO:0002220 ! adjacent to - -[Typedef] -id: RO:0002222 -name: temporally related to - -[Typedef] -id: RO:0002223 -name: starts -def: "inverse of starts with" [] -is_a: BFO:0000050 ! part of -is_a: RO:0002222 ! temporally related to -inverse_of: RO:0002224 ! starts with - -[Typedef] -id: RO:0002224 -name: starts with -def: "x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(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." [] -is_transitive: true -is_a: BFO:0000051 ! has part -is_a: RO:0002222 ! temporally related to - -[Typedef] -id: RO:0002225 -name: develops from part of -def: "x develops from part of y if and only if there exists some z such that x develops from z and z is part of y" [] -holds_over_chain: RO:0002207 BFO:0000050 -is_a: RO:0002202 ! develops from - -[Typedef] -id: RO:0002226 -name: develops in -def: "x develops_in y if x is located in y whilst x is developing" [] -holds_over_chain: RO:0002207 RO:0001025 -is_a: RO:0002258 ! developmentally preceded by - -[Typedef] -id: RO:0002227 -name: obligate parasite of -def: "A sub-relation of parasite-of in which the parasite that cannot complete its life cycle without a host." [] -is_a: RO:0002444 ! parasite of - -[Typedef] -id: RO:0002228 -name: facultative parasite of -def: "A sub-relations of parasite-of in which the parasite that can complete its life cycle independent of a host." [] -is_a: RO:0002444 ! parasite of - -[Typedef] -id: RO:0002229 -name: ends -def: "inverse of ends with" [] -is_a: BFO:0000050 ! part of -is_a: RO:0002222 ! temporally related to -inverse_of: RO:0002230 ! ends with - -[Typedef] -id: RO:0002230 -name: ends with -def: "x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(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." [] -is_transitive: true -is_a: BFO:0000051 ! has part -is_a: RO:0002222 ! temporally related to - -[Typedef] -id: RO:0002231 -name: has start location -def: "x 'has starts location' y if and only if there exists some process z such that x 'starts with' z and z 'occurs in' y" [] -holds_over_chain: RO:0002224 BFO:0000066 -is_a: RO:0002479 ! has part that occurs in - -[Typedef] -id: RO:0002232 -name: has end location -def: "x 'has end location' y if and only if there exists some process z such that x 'ends with' z and z 'occurs in' y" [] -holds_over_chain: RO:0002230 BFO:0000066 -is_a: RO:0002479 ! has part that occurs in - -[Typedef] -id: RO:0002233 -name: has input -def: "p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p." [] -holds_over_chain: RO:0002224 RO:0002233 -is_a: RO:0000057 ! has participant -inverse_of: RO:0002352 ! input of - -[Typedef] -id: RO:0002234 -name: has output -def: "p has output c iff c is a participant in p, c is present at the end of p, and c is not present at the beginning of p." [] -holds_over_chain: RO:0002230 RO:0002234 -is_a: RO:0000057 ! has participant -inverse_of: RO:0002353 ! output of - -[Typedef] -id: RO:0002235 -name: stem parasite of -def: "A parasite-of relationship in which the host is a plant and the parasite that attaches to the host stem (PO:0009047)" [] -is_a: RO:0002444 ! parasite of - -[Typedef] -id: RO:0002236 -name: root parasite of -def: "A parasite-of relationship in which the host is a plant and the parasite that attaches to the host root (PO:0009005)" [] -is_a: RO:0002444 ! parasite of - -[Typedef] -id: RO:0002237 -name: hemiparasite of -def: "A sub-relation of parasite-of in which the parasite is a plant, and the parasite is parasitic under natural conditions and is also photosynthetic to some degree. Hemiparasites may just obtain water and mineral nutrients from the host plant. Many obtain at least part of their organic nutrients from the host as well." [] -is_a: RO:0002444 ! parasite of - -[Typedef] -id: RO:0002240 -name: has exposure receptor -def: "A broad relationship between an exposure event or process and any entity (e.g., an organism, organism population, or an organism part) that interacts with an exposure stimulus during the exposure event." [] -is_a: RO:0002244 ! related via exposure to - -[Typedef] -id: RO:0002241 -name: has exposure stressor -def: "A broad relationship between an exposure event or process and any agent, stimulus, activity, or event that causes stress or tension on an organism and interacts with an exposure receptor during an exposure event." [] -is_a: RO:0002309 ! has exposure stimulus - -[Typedef] -id: RO:0002242 -name: has exposure route -def: "A broad relationship between an exposure event or process and a process by which the exposure stressor comes into contact with the exposure receptor" [] -is_a: RO:0002244 ! related via exposure to - -[Typedef] -id: RO:0002243 -name: has exposure transport path -def: "A broad relationship between an exposure event or process and the course takes from the source to the target." [] -is_a: RO:0002244 ! related via exposure to - -[Typedef] -id: RO:0002244 -name: related via exposure to -def: "Any relationship between an exposure event or process and any other entity." [] -is_a: RO:0002410 ! causally related to - -[Typedef] -id: RO:0002245 -name: over-expressed in -def: "g is over-expressed in t iff g is expressed in t, and the expression level of g is increased relative to some background." [] -is_a: RO:0002206 ! expressed in - -[Typedef] -id: RO:0002246 -name: under-expressed in -def: "g is under-expressed in t iff g is expressed in t, and the expression level of g is decreased relative to some background." [] -is_a: RO:0002206 ! expressed in - -[Typedef] -id: RO:0002248 -name: has active ingredient -def: "A relationship that holds between a substance and a chemical entity, if the chemical entity is part of the substance, and the chemical entity forms the biologically active component of the substance." [] -synonym: "has active pharmaceutical ingredient" RELATED [] -synonym: "has active substance" EXACT [] -is_a: BFO:0000051 ! has part -inverse_of: RO:0002249 ! active ingredient in' - -[Typedef] -id: RO:0002249 -name: active ingredient in' -def: "inverse of has active ingredient" [] -is_a: BFO:0000050 ! part of - -[Typedef] -id: RO:0002252 -name: connecting branch of -def: "b connecting-branch-of s iff b is connected to s, and there exists some tree-like structure t such that the mereological sum of b plus s is either the same as t or a branching-part-of t." [] -is_a: RO:0002375 ! in branching relationship with -inverse_of: RO:0002253 ! has connecting branch - -[Typedef] -id: RO:0002253 -name: has connecting branch -def: "inverse of connecting branch of" [] -is_a: RO:0002375 ! in branching relationship with - -[Typedef] -id: RO:0002254 -name: has developmental contribution from -def: "x has developmental contribution from y iff x has some part z such that z develops from y" [] -holds_over_chain: BFO:0000051 RO:0002202 -is_a: RO:0002258 ! developmentally preceded by -inverse_of: RO:0002255 ! developmentally contributes to - -[Typedef] -id: RO:0002255 -name: developmentally contributes to -def: "inverse of has developmental contribution from" [] -holds_over_chain: RO:0002203 BFO:0000050 -is_a: RO:0002286 ! developmentally succeeded by -is_a: RO:0002385 ! has potential to developmentally contribute to - -[Typedef] -id: RO:0002256 -name: developmentally induced by -def: "t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor anatomical structure type T to T', where T' develops_from T" [] -is_a: RO:0002258 ! developmentally preceded by -inverse_of: RO:0002257 ! developmentally induces - -[Typedef] -id: RO:0002257 -name: developmentally induces -def: "Inverse of developmentally induced by" [] -is_a: RO:0002286 ! developmentally succeeded by -is_a: RO:0002386 ! has potential to developmentally induce - -[Typedef] -id: RO:0002258 -name: developmentally preceded by -def: "Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p" [] -is_a: RO:0002324 ! developmentally related to -inverse_of: RO:0002286 ! developmentally succeeded by - -[Typedef] -id: RO:0002260 -name: has biological role -def: "c has-biological-role r iff c has-role r and r is a biological role (CHEBI:24432)" [] -is_a: RO:0000087 ! has role - -[Typedef] -id: RO:0002261 -name: has application role -def: "c has-application-role r iff c has-role r and r is an application role (CHEBI:33232)" [] -is_a: RO:0000087 ! has role - -[Typedef] -id: RO:0002262 -name: has chemical role -def: "c has-chemical-role r iff c has-role r and r is a chemical role (CHEBI:51086)" [] -is_a: RO:0000087 ! has role - -[Typedef] -id: RO:0002263 -name: acts upstream of -def: "c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes." [] -holds_over_chain: RO:0002327 RO:0002411 -is_a: RO:0002264 ! acts upstream of or within - -[Typedef] -id: RO:0002264 -name: acts upstream of or within -def: "c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process." [] -synonym: "affects" RELATED [] -holds_over_chain: RO:0002327 RO:0002418 -is_a: RO:0002500 ! causal agent in process - -[Typedef] -id: RO:0002285 -name: developmentally replaces -def: "x developmentally replaces y if and only if there is some developmental process that causes x to move or to cease to exist, and for the site that was occupied by x to become occupied by y, where y either comes into existence in this site or moves to this site from somewhere else" [] -is_a: RO:0002258 ! developmentally preceded by - -[Typedef] -id: RO:0002286 -name: developmentally succeeded by -def: "Inverse of developmentally preceded by" [] -is_a: RO:0002384 ! has developmental potential involving - -[Typedef] -id: RO:0002287 -name: part of developmental precursor of -holds_over_chain: BFO:0000050 RO:0002210 -is_a: RO:0002286 ! developmentally succeeded by - -[Typedef] -id: RO:0002291 -name: ubiquitously expressed in -def: "x is ubiquitously expressed in y if and only if x is expressed in y, and the majority of cells in y express x" [] -is_a: RO:0002206 ! expressed in -inverse_of: RO:0002293 ! ubiquitously expresses - -[Typedef] -id: RO:0002292 -name: expresses -def: "Inverse of 'expressed in'" [] -is_a: RO:0002330 ! genomically related to - -[Typedef] -id: RO:0002293 -name: ubiquitously expresses -def: "inverse of ubiquiotously expressed in" [] -is_a: RO:0002292 ! expresses - -[Typedef] -id: RO:0002301 -name: results in developmental regression of -is_a: RO:0002552 ! results in ending of - -[Typedef] -id: RO:0002302 -name: is treated by substance -def: "Inverse of 'is substance that treats'" [] -is_a: RO:0002410 ! causally related to -inverse_of: RO:0002606 ! is substance that treats - -[Typedef] -id: RO:0002303 -name: has habitat -def: "x 'has habitat' y if and only if: x is an organism, y is a habitat, and y can sustain and allow the growth of a population of xs." [] -is_a: RO:0002321 ! ecologically related to - -[Typedef] -id: RO:0002304 -name: causally upstream of, positive effect -is_a: RO:0002411 ! causally upstream of -is_a: RO:0004047 ! causally upstream of or within, positive effect - -[Typedef] -id: RO:0002305 -name: causally upstream of, negative effect -is_a: RO:0002411 ! causally upstream of -is_a: RO:0004046 ! causally upstream of or within, negative effect - -[Typedef] -id: RO:0002309 -name: has exposure stimulus -def: "A relationship between an exposure event or process and any agent, stimulus, activity, or event that causally effects an organism and interacts with an exposure receptor during an exposure event." [] -is_a: RO:0002244 ! related via exposure to - -[Typedef] -id: RO:0002312 -name: evolutionary variant of -is_a: RO:0002320 ! evolutionarily related to - -[Typedef] -id: RO:0002313 -name: transports or maintains localization of -def: "Holds between p and c when p is a localization process (localization covers maintenance of localization as well as its establishment) and the outcome of this process is to regulate the localization of c." [] -is_a: RO:0000057 ! has participant -is_a: RO:0002337 ! related via localization to -transitive_over: BFO:0000051 ! has part - -[Typedef] -id: RO:0002314 -name: inheres in part of -def: "q inheres in part of w if and only if there exists some p such that q inheres in p and p part of w." [] -holds_over_chain: RO:0000052 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"} -is_a: RO:0002502 ! depends on -transitive_over: BFO:0000050 ! part of - -[Typedef] -id: RO:0002320 -name: evolutionarily related to -def: "A relationship that holds via some environmental process" [] - -[Typedef] -id: RO:0002321 -name: ecologically related to -def: "A relationship that is mediated in some way by the environment or environmental feature (ENVO:00002297)" [] - -[Typedef] -id: RO:0002322 -name: confers advantage in -is_a: RO:0002321 ! ecologically related to - -[Typedef] -id: RO:0002323 -name: mereotopologically related to -def: "A mereological relationship or a topological relationship" [] - -[Typedef] -id: RO:0002324 -name: developmentally related to -def: "A relationship that holds between entities participating in some developmental process (GO:0032502)" [] - -[Typedef] -id: RO:0002325 -name: colocalizes with -def: "a colocalizes_with b if and only if a is transiently or peripherally associated with b[GO]." [] -is_a: RO:0002323 ! mereotopologically related to - -[Typedef] -id: RO:0002326 -name: contributes to -is_a: RO:0002216 ! capable of part of -is_a: RO:0002329 ! part of structure that is capable of - -[Typedef] -id: RO:0002327 -name: enables -is_a: RO:0002215 ! capable of -inverse_of: RO:0002333 ! enabled by -transitive_over: BFO:0000051 ! has part -transitive_over: RO:0002017 ! has component activity - -[Typedef] -id: RO:0002328 -name: functionally related to -def: "A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities." [] - -[Typedef] -id: RO:0002329 -name: part of structure that is capable of -def: "this relation holds between c and p when c is part of some c', and c' is capable of p." [] -holds_over_chain: BFO:0000050 RO:0002215 {http://purl.obolibrary.org/obo/RO_0002581="true"} -is_a: RO:0002328 ! functionally related to - -[Typedef] -id: RO:0002330 -name: genomically related to -def: "holds between two entities when some genome-level process such as gene expression is involved. This includes transcriptional, spliceosomal events. These relations can be used between either macromolecule entities (such as regions of nucleic acid) or between their abstract informational counterparts." [] - -[Typedef] -id: RO:0002331 -name: involved in -def: "c involved_in p if and only if c enables some process p', and p' is part of p" [] -holds_over_chain: RO:0002327 BFO:0000050 -is_a: RO:0002217 ! actively participates in -is_a: RO:0002431 ! involved in or involved in regulation of -transitive_over: BFO:0000050 ! part of - -[Typedef] -id: RO:0002332 -name: regulates levels of -def: "p regulates levels of c if p regulates some amount (PATO:0000070) of c" [] -is_a: RO:0002328 ! functionally related to - -[Typedef] -id: RO:0002333 -name: enabled by -def: "inverse of enables" [] -is_a: RO:0002328 ! functionally related to - -[Typedef] -id: RO:0002334 -name: regulated by -def: "inverse of regulates" [] -is_transitive: true -is_a: RO:0002427 ! causally downstream of or within - -[Typedef] -id: RO:0002335 -name: negatively regulated by -def: "inverse of negatively regulates" [] -is_a: RO:0002334 ! regulated by - -[Typedef] -id: RO:0002336 -name: positively regulated by -def: "inverse of positively regulates" [] -is_a: RO:0002334 ! regulated by - -[Typedef] -id: RO:0002337 -name: related via localization to -def: "A relationship that holds via some process of localization" [] - -[Typedef] -id: RO:0002338 -name: has target start location -def: "This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from some initial location l to some destination." [] -is_a: RO:0002344 ! results in transport to from or in -transitive_over: BFO:0000050 ! part of - -[Typedef] -id: RO:0002339 -name: has target end location -def: "This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from a an initial location to some destination l." [] -is_a: RO:0002344 ! results in transport to from or in -transitive_over: BFO:0000050 ! part of - -[Typedef] -id: RO:0002340 -name: imports -def: "Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the start location of c is part of the region that surrounds s." [] -is_a: RO:0002020 ! transports -transitive_over: BFO:0000051 ! has part - -[Typedef] -id: RO:0002341 -name: results in transport along -def: "Holds between p and l when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that is aligned_with l " [] -is_a: RO:0002337 ! related via localization to - -[Typedef] -id: RO:0002342 -name: results in transport across -def: "Holds between p and m when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that crosses m." [] -is_a: RO:0002021 ! occurs across -is_a: RO:0002344 ! results in transport to from or in - -[Typedef] -id: RO:0002343 -name: results in growth of -is_a: results_in_developmental_progression_of ! results in developmental progression of -is_a: RO:0000057 ! has participant - -[Typedef] -id: RO:0002344 -name: results in transport to from or in -is_a: RO:0002337 ! related via localization to - -[Typedef] -id: RO:0002345 -name: exports -is_a: RO:0002020 ! transports -transitive_over: BFO:0000051 ! has part - -[Typedef] -id: RO:0002348 -name: results in commitment to -def: "p 'results in commitment to' c if and only if p is a developmental process and c is a cell and p results in the state of c changing such that is can only develop into a single cell type." [] -is_a: results_in_developmental_progression_of ! results in developmental progression of - -[Typedef] -id: RO:0002349 -name: results in determination of -def: "p 'results in determination of' c if and only if p is a developmental process and c is a cell and p results in the state of c changing to be determined. Once a cell becomes determined, it becomes committed to differentiate down a particular pathway regardless of its environment." [] -is_a: results_in_developmental_progression_of ! results in developmental progression of - -[Typedef] -id: RO:0002350 -name: member of -def: "is member of is a mereological relation between a item and a collection." [] -is_a: BFO:0000050 ! part of -inverse_of: RO:0002351 ! has member - -[Typedef] -id: RO:0002351 -name: has member -def: "has member is a mereological relation between a collection and an item." [] -is_a: BFO:0000051 ! has part - -[Typedef] -id: RO:0002352 -name: input of -def: "inverse of has input" [] -is_a: RO:0000056 ! participates in -is_a: RO:0002328 ! functionally related to - -[Typedef] -id: RO:0002353 -name: output of -def: "inverse of has output" [] -is_a: RO:0000056 ! participates in -is_a: RO:0002328 ! functionally related to - -[Typedef] -id: RO:0002354 -name: formed as result of -is_a: RO:0002353 ! output of -inverse_of: results_in_formation_of ! results in formation of - -[Typedef] -id: RO:0002355 -name: results in structural organization of -def: "A relationship between a process and an anatomical entity such that the process contributes to the act of creating the structural organization of the anatomical entity." [] -is_a: results_in_developmental_progression_of ! results in developmental progression of -is_a: RO:0000057 ! has participant - -[Typedef] -id: RO:0002356 -name: results in specification of -def: "The relationship linking a cell and its participation in a process that results in the fate of the cell being specified. Once specification has taken place, a cell will be committed to differentiate down a specific pathway if left in its normal environment. " [] -is_a: results_in_developmental_progression_of ! results in developmental progression of - -[Typedef] -id: RO:0002357 -name: results in developmental induction of -def: "p results in developmental induction of c if and only if p is a collection of cell-cell signaling processes that signal to a neighbouring tissue that is the precursor of the mature c, where the signaling results in the commitment to cell types necessary for the formation of c." [] -is_a: results_in_developmental_progression_of ! results in developmental progression of - -[Typedef] -id: RO:0002360 -name: has dendrite location -is_a: RO:0002131 ! overlaps - -[Typedef] -id: RO:0002371 -name: attached to -def: "a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a" [] -is_symmetric: true -is_a: RO:0002170 ! connected to -is_a: RO:0002177 ! attached to part of - -[Typedef] -id: RO:0002372 -name: has muscle origin -def: "m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to." [] -is_a: RO:0002371 ! attached to -is_a: RO:0002567 ! biomechanically related to - -[Typedef] -id: RO:0002373 -name: has muscle insertion -def: "m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone." [] -is_a: RO:0002371 ! attached to -is_a: RO:0002567 ! biomechanically related to - -[Typedef] -id: RO:0002374 -name: derived from ancestral fusion of -def: "x has_fused_element y iff: there exists some z : x has_part z, z homologous_to y, and y is a distinct element, the boundary between x and z is largely fiat" [] -synonym: "has fused element" BROAD [] -is_a: RO:0002156 ! derived by descent from - -[Typedef] -id: RO:0002375 -name: in branching relationship with -def: "A relationship that holds between two material entities in a system of connected structures, where the branching relationship holds based on properties of the connecting network." [] -is_a: BFO:0000050 ! part of -is_a: RO:0002323 ! mereotopologically related to - -[Typedef] -id: RO:0002376 -name: tributary of -def: "x tributary_of y if and only if x a channel for the flow of a substance into y, where y is larger than x. If x and y are hydrographic features, then y is the main stem of a river, or a lake or bay, but not the sea or ocean. If x and y are anatomical, then y is a vein." [] -is_a: RO:0002375 ! in branching relationship with - -[Typedef] -id: RO:0002377 -name: distributary of -def: "x distributary_of y if and only if x is capable of channeling the flow of a substance to y, where y channels less of the substance than x" [] -is_a: RO:0002375 ! in branching relationship with - -[Typedef] -id: RO:0002378 -name: anabranch of -def: "x anabranch_of y if x is a distributary of y (i.e. it channels a from a larger flow from y) and x ultimately channels the flow back into y." [] -is_a: RO:0002377 ! distributary of -disjoint_from: RO:0002382 ! proper distributary of -disjoint_from: RO:0002383 ! proper tributary of - -[Typedef] -id: RO:0002379 -name: spatially coextensive with -def: "x spatially_coextensive_with y if and inly if x and y have the same location" [] -is_a: RO:0002131 ! overlaps - -[Typedef] -id: RO:0002380 -name: branching part of -def: "x is a branching part of y if and only if x is part of y and x is connected directly or indirectly to the main stem of y" [] -holds_over_chain: RO:0002377 RO:0002381 -is_a: BFO:0000050 ! part of -is_a: RO:0002375 ! in branching relationship with -inverse_of: RO:0002569 ! has branching part - -[Typedef] -id: RO:0002381 -name: main stem of -def: "x main_stem_of y if y is a branching structure and x is a channel that traces a linear path through y, such that x has higher capacity than any other such path." [] -is_a: RO:0002375 ! in branching relationship with - -[Typedef] -id: RO:0002382 -name: proper distributary of -def: "x proper_distributary_of y iff x distributary_of y and x does not flow back into y" [] -is_a: RO:0002377 ! distributary of - -[Typedef] -id: RO:0002383 -name: proper tributary of -def: "x proper_tributary_of y iff x tributary_of y and x does not originate from y" [] -is_a: RO:0002376 ! tributary of - -[Typedef] -id: RO:0002384 -name: has developmental potential involving -def: "x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction)." [] -is_a: RO:0002324 ! developmentally related to - -[Typedef] -id: RO:0002385 -name: has potential to developmentally contribute to -def: "x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y" [] -is_a: RO:0002384 ! has developmental potential involving - -[Typedef] -id: RO:0002386 -name: has potential to developmentally induce -def: "x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y" [] -is_a: RO:0002384 ! has developmental potential involving - -[Typedef] -id: RO:0002387 -name: has potential to develop into -def: "x has the potential to develop into y iff x develops into y or if x is capable of developing into y" [] -is_a: RO:0002384 ! has developmental potential involving - -[Typedef] -id: RO:0002388 -name: has potential to directly develop into -def: "x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y" [] -is_a: RO:0002387 ! has potential to develop into - -[Typedef] -id: RO:0002400 -name: has direct input -def: "p has direct input c iff c is a participant in p, c is present at the start of p, and the state of c is modified during p." [] -holds_over_chain: RO:0002224 RO:0002400 -is_a: RO:0002233 ! has input - -[Typedef] -id: RO:0002401 -name: obsolete has indirect input -is_obsolete: true - -[Typedef] -id: RO:0002402 -name: obsolete has direct output -def: "p has direct input c iff c is a participanti n p, c is present at the end of p, and c is not present at the beginning of c. " [] -is_obsolete: true - -[Typedef] -id: RO:0002403 -name: obsolete has indirect output -holds_over_chain: RO:0002411 RO:0002402 -is_a: RO:0002234 ! has output -is_obsolete: true - -[Typedef] -id: RO:0002404 -name: causally downstream of -def: "inverse of upstream of" [] -is_a: BFO:0000062 ! preceded by -is_a: RO:0002427 ! causally downstream of or within -inverse_of: RO:0002411 ! causally upstream of - -[Typedef] -id: RO:0002405 -name: immediately causally downstream of -is_a: RO:0002087 ! immediately preceded by -is_a: RO:0002404 ! causally downstream of -inverse_of: RO:0002412 ! immediately causally upstream of - -[Typedef] -id: RO:0002406 -name: directly activates -def: "p directly activates q if and only if p is immediately upstream of q and p is the realization of a function to increase the rate or activity of q" [] -is_a: RO:0002629 ! directly positively regulates - -[Typedef] -id: RO:0002407 -name: indirectly activates -def: "p directly activates q if and only if p is immediately upstream of q and p is the realization of a function to increase the rate or activity of q" [] -holds_over_chain: RO:0002406 RO:0002406 -holds_over_chain: RO:0002406 RO:0002407 -holds_over_chain: RO:0002409 RO:0002409 -is_transitive: true -is_a: RO:0002213 ! positively regulates -transitive_over: RO:0002406 ! directly activates - -[Typedef] -id: RO:0002408 -name: directly inhibits -is_a: RO:0002630 ! directly negatively regulates - -[Typedef] -id: RO:0002409 -name: indirectly inhibits -holds_over_chain: RO:0002408 RO:0002408 -holds_over_chain: RO:0002408 RO:0002409 -is_transitive: true -is_a: RO:0002212 ! negatively regulates -transitive_over: RO:0002408 ! directly inhibits - -[Typedef] -id: RO:0002410 -name: causally related to -def: "This relation groups causal relations between material entities and causal relations between processes" [] - -[Typedef] -id: RO:0002411 -name: causally upstream of -def: "p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain" [] -is_transitive: true -is_a: BFO:0000063 ! precedes -is_a: RO:0002418 ! causally upstream of or within - -[Typedef] -id: RO:0002412 -name: immediately causally upstream of -def: "p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q." [] -is_a: RO:0002090 ! immediately precedes -is_a: RO:0002411 ! causally upstream of - -[Typedef] -id: RO:0002413 -name: directly provides input for -def: "p1 directly provides input for p2 iff there exists some c such that p1 has_output c and p2 has_input c" [] -holds_over_chain: RO:0002402 RO:0002400 -is_a: RO:0002412 ! immediately causally upstream of -is_a: RO:0002414 ! transitively provides input for - -[Typedef] -id: RO:0002414 -name: transitively provides input for -def: "transitive form of directly_provides_input_for" [] -is_transitive: true -is_a: RO:0002411 ! causally upstream of - -[Typedef] -id: RO:0002418 -name: causally upstream of or within -def: "p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q." [] -synonym: "affects" RELATED [] -is_transitive: true -is_a: RO:0002501 ! causal relation between processes -inverse_of: RO:0002427 ! causally downstream of or within - -[Typedef] -id: RO:0002424 -name: differs in - -[Typedef] -id: RO:0002425 -name: differs in attribute of -is_a: RO:0002424 ! differs in - -[Typedef] -id: RO:0002426 -name: differs in attribute -is_a: RO:0002424 ! differs in - -[Typedef] -id: RO:0002427 -name: causally downstream of or within -def: "inverse of causally upstream of or within" [] -is_transitive: true -is_a: RO:0002501 ! causal relation between processes - -[Typedef] -id: RO:0002428 -name: involved in regulation of -def: "c involved in regulation of p if c is involved in some p' and p' regulates some p" [] -holds_over_chain: RO:0002327 RO:0002211 -holds_over_chain: RO:0002331 RO:0002211 -is_a: RO:0002263 ! acts upstream of -is_a: RO:0002431 ! involved in or involved in regulation of - -[Typedef] -id: RO:0002429 -name: involved in positive regulation of -def: "c involved in regulation of p if c is involved in some p' and p' positively regulates some p" [] -holds_over_chain: RO:0002327 RO:0002213 -holds_over_chain: RO:0002331 RO:0002213 -is_a: RO:0002428 ! involved in regulation of - -[Typedef] -id: RO:0002430 -name: involved in negative regulation of -def: "c involved in regulation of p if c is involved in some p' and p' negatively regulates some p" [] -holds_over_chain: RO:0002327 RO:0002212 -holds_over_chain: RO:0002331 RO:0002212 -is_a: RO:0002428 ! involved in regulation of - -[Typedef] -id: RO:0002431 -name: involved in or involved in regulation of -def: "c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p" [] -is_a: RO:0002264 ! acts upstream of or within -is_a: RO:0002328 ! functionally related to -is_a: RO:0002500 ! causal agent in process - -[Typedef] -id: RO:0002432 -name: is active in -def: "c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure." [GOC:cjm, GOC:dos] -synonym: "enables activity in" EXACT [] -holds_over_chain: RO:0002327 BFO:0000066 {http://purl.obolibrary.org/obo/RO_0002581="true"} -is_a: RO:0002131 ! overlaps -is_a: RO:0002328 ! functionally related to - -[Typedef] -id: RO:0002433 -name: contributes to morphology of -def: "p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm." [] -is_a: RO:0002131 ! overlaps - -[Typedef] -id: RO:0002434 -name: interacts with -def: "A relationship that holds between two entities in which the processes executed by the two entities are causally connected." [] -synonym: "in pairwise interaction with" EXACT [] -is_symmetric: true - -[Typedef] -id: RO:0002435 -name: genetically interacts with -is_symmetric: true -is_a: RO:0002434 ! interacts with - -[Typedef] -id: RO:0002436 -name: molecularly interacts with -def: "An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other." [] -is_symmetric: true -is_a: RO:0002434 ! interacts with - -[Typedef] -id: RO:0002437 -name: biotically interacts with -def: "An interaction relationship in which at least one of the partners is an organism and the other is either an organism or an abiotic entity with which the organism interacts." [] -is_symmetric: true -is_a: RO:0002321 ! ecologically related to -is_a: RO:0002434 ! interacts with - -[Typedef] -id: RO:0002438 -name: trophically interacts with -def: "An interaction relationship in which the partners are related via a feeding relationship." [] -is_a: RO:0002574 ! participates in a biotic-biotic interaction with - -[Typedef] -id: RO:0002439 -name: preys on -def: "An interaction relationship involving a predation process, where the subject kills the target in order to eat it or to feed to siblings, offspring or group members" [] -is_a: RO:0002438 ! trophically interacts with -inverse_of: RO:0002458 ! preyed upon by - -[Typedef] -id: RO:0002440 -name: symbiotically interacts with -def: "A biotic interaction in which the two organisms live together in more or less intimate association." [] -is_symmetric: true -is_a: RO:0002574 ! participates in a biotic-biotic interaction with - -[Typedef] -id: RO:0002441 -name: commensually interacts with -def: "An interaction relationship between two organisms living together in more or less intimate association in a relationship in which one benefits and the other is unaffected (GO)." [] -is_a: RO:0002440 ! symbiotically interacts with - -[Typedef] -id: RO:0002442 -name: mutualistically interacts with -def: "An interaction relationship between two organisms living together in more or less intimate association in a relationship in which both organisms benefit from each other (GO)." [] -is_a: RO:0002440 ! symbiotically interacts with - -[Typedef] -id: RO:0002443 -name: interacts with via parasite-host interaction -def: "An interaction relationship between two organisms living together in more or less intimate association in a relationship in which association is disadvantageous or destructive to one of the organisms (GO)." [] -is_a: RO:0002440 ! symbiotically interacts with - -[Typedef] -id: RO:0002444 -name: parasite of -synonym: "direct parasite of" EXACT [] -is_a: RO:0002443 ! interacts with via parasite-host interaction -is_a: RO:0002454 ! has host -inverse_of: RO:0002445 ! parasitized by - -[Typedef] -id: RO:0002445 -name: parasitized by -synonym: "directly parasitized by" EXACT [] -is_a: RO:0002443 ! interacts with via parasite-host interaction -is_a: RO:0002453 ! host of - -[Typedef] -id: RO:0002446 -name: participates in a abiotic-biotic interaction with -def: "A biotic interaction relationship in which one partner is an organism and the other partner is inorganic. For example, the relationship between a sponge and the substrate to which is it anchored." [] -synonym: "semibiotically interacts with" RELATED [] -is_a: RO:0002437 ! biotically interacts with - -[Typedef] -id: RO:0002447 -name: phosphorylates -is_a: RO:0002436 ! molecularly interacts with - -[Typedef] -id: RO:0002448 -name: activity directly regulates activity of -def: "Holds between molecular entities A and B where A can physically interact with B and in doing so regulates a process that B is capable of. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B." [] -synonym: "molecularly controls" EXACT [] -is_a: RO:0002436 ! molecularly interacts with -is_a: RO:0002566 ! causally influences - -[Typedef] -id: RO:0002449 -name: activity directly negatively regulates activity of -def: "Holds between molecular entities A and B where A can physically interact with B and in doing so negatively regulates a process that B is capable of. For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B." [] -synonym: "molecularly decreases activity of" EXACT [] -is_a: RO:0002448 ! activity directly regulates activity of - -[Typedef] -id: RO:0002450 -name: activity directly positively regulates activity of -def: "Holds between molecular entities A and B where A can physically interact with B and in doing so positively regulates a process that B is capable of. For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B." [] -synonym: "molecularly increases activity of" EXACT [] -is_a: RO:0002448 ! activity directly regulates activity of - -[Typedef] -id: RO:0002451 -name: transmitted by -def: "A relationship that holds between a disease and organism" [] -is_a: RO:0002321 ! ecologically related to - -[Typedef] -id: RO:0002452 -name: has symptom -def: "A relation that holds between a disease or an organism and a phenotype" [] -is_a: RO:0002200 ! has phenotype - -[Typedef] -id: RO:0002453 -name: host of -is_a: RO:0002440 ! symbiotically interacts with - -[Typedef] -id: RO:0002454 -name: has host -is_a: RO:0002440 ! symbiotically interacts with - -[Typedef] -id: RO:0002455 -name: pollinates -is_a: RO:0002442 ! mutualistically interacts with -inverse_of: RO:0002456 ! pollinated by - -[Typedef] -id: RO:0002456 -name: pollinated by -is_a: RO:0002442 ! mutualistically interacts with - -[Typedef] -id: RO:0002457 -name: acquires nutrients from -is_a: RO:0002438 ! trophically interacts with -inverse_of: RO:0002469 ! provides nutrients for - -[Typedef] -id: RO:0002458 -name: preyed upon by -def: "inverse of preys on" [] -is_a: RO:0002438 ! trophically interacts with - -[Typedef] -id: RO:0002459 -name: is vector for -is_a: RO:0002574 ! participates in a biotic-biotic interaction with -inverse_of: RO:0002460 ! has vector - -[Typedef] -id: RO:0002460 -name: has vector -is_a: RO:0002459 ! is vector for - -[Typedef] -id: RO:0002461 -name: partner in -is_a: RO:0000056 ! participates in - -[Typedef] -id: RO:0002462 -name: subject participant in -is_a: RO:0002461 ! partner in - -[Typedef] -id: RO:0002463 -name: target participant in -is_a: RO:0002461 ! partner in - -[Typedef] -id: RO:0002464 -name: helper property - -[Typedef] -id: RO:0002465 -name: is symbiosis -is_a: RO:0002563 ! interaction relation helper property - -[Typedef] -id: RO:0002466 -name: is commensalism -is_a: RO:0002465 ! is symbiosis - -[Typedef] -id: RO:0002467 -name: is mutualism -is_a: RO:0002465 ! is symbiosis - -[Typedef] -id: RO:0002468 -name: is parasitism -is_a: RO:0002465 ! is symbiosis - -[Typedef] -id: RO:0002469 -name: provides nutrients for -is_a: RO:0002438 ! trophically interacts with - -[Typedef] -id: RO:0002470 -name: eats -is_a: RO:0002438 ! trophically interacts with - -[Typedef] -id: RO:0002471 -name: is eaten by -is_a: RO:0002438 ! trophically interacts with - -[Typedef] -id: RO:0002472 -name: is evidence for -def: "A relationship between a piece of evidence a and some entity b, where b is an information content entity, material entity or process, and \nthe a supports either the existence of b, or the truth value of b." [] -is_a: RO:0002616 ! related via evidence or inference to -inverse_of: RO:0002558 ! has evidence - -[Typedef] -id: RO:0002473 -name: composed primarily of -def: "x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y." [] -is_a: BFO:0000051 ! has part - -[Typedef] -id: RO:0002476 -name: child nucleus of -def: "c is a child nucleus of d if and only if c and d are both nuclei and parts of cells c' and d', where c' is derived from d' by mitosis and the genetic material in c is a copy of the generic material in d" [] -is_a: RO:0002258 ! developmentally preceded by - -[Typedef] -id: RO:0002477 -name: child nucleus of in hermaphrodite -def: "A child nucleus relationship in which the cells are part of a hermaphroditic organism" [] -is_a: RO:0002476 ! child nucleus of - -[Typedef] -id: RO:0002478 -name: child nucleus of in male -def: "A child nucleus relationship in which the cells are part of a male organism" [] -is_a: RO:0002476 ! child nucleus of - -[Typedef] -id: RO:0002479 -name: has part that occurs in -def: "p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c." [] -holds_over_chain: BFO:0000051 BFO:0000066 {http://purl.obolibrary.org/obo/RO_0002581="true"} - -[Typedef] -id: RO:0002480 -name: ubiquitinates -def: "An interaction relation between x and y in which x catalyzes a reaction in which one or more ubiquitin groups are added to y" [] -is_a: RO:0002436 ! molecularly interacts with - -[Typedef] -id: RO:0002481 -name: is kinase activity -is_a: RO:0002564 ! molecular interaction relation helper property - -[Typedef] -id: RO:0002482 -name: is ubiquitination -is_a: RO:0002564 ! molecular interaction relation helper property - -[Typedef] -id: RO:0002485 -name: receives input from -is_a: RO:0002170 ! connected to -inverse_of: RO:0002486 ! sends output to - -[Typedef] -id: RO:0002486 -name: sends output to -is_a: RO:0002170 ! connected to - -[Typedef] -id: RO:0002487 -name: relation between structure and stage - -[Typedef] -id: RO:0002488 -name: existence starts during -def: "x existence starts during y if and only if the time point at which x starts is after or equivalent to the time point at which y starts and before or equivalent to the time point at which y ends. Formally: x existence starts during y iff α(x) >= α(y) & α(x) <= ω(y)." [] -holds_over_chain: RO:0002583 BFO:0000050 -is_a: RO:0002490 ! existence overlaps -is_a: RO:0002496 ! existence starts during or after -transitive_over: BFO:0000050 ! part of - -[Typedef] -id: RO:0002489 -name: existence starts with -def: "x starts ends with y if and only if the time point at which x starts is equivalent to the time point at which y starts. Formally: x existence starts with y iff α(x) = α(y)." [] -is_a: RO:0002488 ! existence starts during - -[Typedef] -id: RO:0002490 -name: existence overlaps -def: "x existence overlaps y if and only if either (a) the start of x is part of y or (b) the end of x is part of y. Formally: x existence starts and ends during y iff (α(x) >= α(y) & α(x) <= ω(y)) OR (ω(x) <= ω(y) & ω(x) >= α(y))" [] -is_a: RO:0002487 ! relation between structure and stage - -[Typedef] -id: RO:0002491 -name: existence starts and ends during -def: "x existence starts and ends during y if and only if the start of x is part of y and the end of x is part of y. Formally: x existence starts and ends during y iff α(x) >= α(y) & α(x) <= ω(y) & ω(x) <= ω(y) & ω(x) >= α(y)" [] -is_a: RO:0002488 ! existence starts during -is_a: RO:0002492 ! existence ends during - -[Typedef] -id: RO:0002492 -name: existence ends during -def: "x existence ends during y if and only if the time point at which x ends is before or equivalent to the time point at which y ends and after or equivalent to the point at which y starts. Formally: x existence ends during y iff ω(x) <= ω(y) and ω(x) >= α(y)." [] -holds_over_chain: RO:0002593 BFO:0000050 -is_a: RO:0002490 ! existence overlaps -is_a: RO:0002497 ! existence ends during or before -transitive_over: BFO:0000050 ! part of - -[Typedef] -id: RO:0002493 -name: existence ends with -def: "x existence ends with y if and only if the time point at which x ends is equivalent to the time point at which y ends. Formally: x existence ends with y iff ω(x) = ω(y)." [] -is_a: RO:0002492 ! existence ends during - -[Typedef] -id: RO:0002494 -name: transformation of -def: "x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships" [] -is_transitive: true -is_a: RO:0002202 ! develops from - -[Typedef] -id: RO:0002495 -name: immediate transformation of -def: "x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t" [] -is_a: RO:0002207 ! directly develops from -is_a: RO:0002494 ! transformation of - -[Typedef] -id: RO:0002496 -name: existence starts during or after -def: "x existence starts during or after y if and only if the time point at which x starts is after or equivalent to the time point at which y starts. Formally: x existence starts during or after y iff α (x) >= α (y)." [] -holds_over_chain: BFO:0000050 RO:0002496 -holds_over_chain: RO:0002258 RO:0002496 -is_a: RO:0002487 ! relation between structure and stage -transitive_over: BFO:0000050 ! part of -transitive_over: BFO:0000062 ! preceded by -transitive_over: RO:0002082 ! simultaneous with - -[Typedef] -id: RO:0002497 -name: existence ends during or before -def: "x existence ends during or before y if and only if the time point at which x ends is before or equivalent to the time point at which y ends." [] -holds_over_chain: BFO:0000050 RO:0002497 -holds_over_chain: RO:0002286 RO:0002497 -is_a: RO:0002487 ! relation between structure and stage -transitive_over: BFO:0000050 ! part of -transitive_over: BFO:0000063 ! precedes -transitive_over: RO:0002082 ! simultaneous with - -[Typedef] -id: RO:0002500 -name: causal agent in process -def: "A relationship between a material entity and a process where the material entity has some causal role that influences the process" [] -is_a: RO:0002595 ! causal relation between material entity and a process -inverse_of: RO:0002608 ! process has causal agent - -[Typedef] -id: RO:0002501 -name: causal relation between processes -def: "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." [] -is_a: RO:0002410 ! causally related to - -[Typedef] -id: RO:0002502 -name: depends on - -[Typedef] -id: RO:0002503 -name: towards -def: "q towards e2 if and only if q is a relational quality such that q inheres-in some e, and e != e2 and q is dependent on e2" [] -is_a: RO:0002502 ! depends on - -[Typedef] -id: RO:0002505 -name: has intermediate -def: "p has intermediate c if and only if p has parts p1, p2 and p1 has output c, and p2 has input c" [] -is_a: RO:0000057 ! has participant - -[Typedef] -id: RO:0002506 -name: causal relation between material entities -is_a: RO:0002410 ! causally related to - -[Typedef] -id: RO:0002507 -name: determined by -def: "s determined by f if and only if s is a type of system, and f is a material entity that is part of s, such that f exerts a strong causal influence on the functioning of s, and the removal of f would cause the collapse of s." [] -is_a: BFO:0000050 ! part of -is_a: RO:0002509 ! determined by part of -is_a: RO:0002559 ! causally influenced by -inverse_of: RO:0002508 ! determines - -[Typedef] -id: RO:0002508 -name: determines -def: "inverse of determined by" [] -is_a: RO:0002566 ! causally influences - -[Typedef] -id: RO:0002509 -name: determined by part of -def: "s 'determined by part of' w if and only if there exists some f such that (1) s 'determined by' f and (2) f part_of w, or f=w." [] -holds_over_chain: RO:0002507 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"} -is_a: RO:0002131 ! overlaps -is_a: RO:0002506 ! causal relation between material entities - -[Typedef] -id: RO:0002510 -name: transcribed from -def: "x is transcribed from y if and only if x is synthesized from template y" [] -is_a: RO:0002330 ! genomically related to -inverse_of: RO:0002511 ! transcribed to - -[Typedef] -id: RO:0002511 -name: transcribed to -def: "inverse of transcribed from" [] -is_a: RO:0002330 ! genomically related to - -[Typedef] -id: RO:0002512 -name: ribosomal translation of -def: "x is the ribosomal translation of y if and only if a ribosome reads x through a series of triplet codon-amino acid adaptor activities (GO:0030533) and produces y" [] -is_a: RO:0002330 ! genomically related to - -[Typedef] -id: RO:0002513 -name: ribosomally translates to -def: "inverse of ribosomal translation of" [] -is_a: RO:0002330 ! genomically related to - -[Typedef] -id: RO:0002514 -name: sequentially related to -def: "A relation that holds between two entities that have the property of being sequences or having sequences. " [] - -[Typedef] -id: RO:0002515 -name: sequentially adjacent to -def: "x is sequentially adjacent to y iff x and y do not overlap and if there are no base units intervening between x and y" [] -is_a: RO:0002527 ! does not overlap sequence of - -[Typedef] -id: RO:0002516 -name: has start sequence -def: "x has start sequence y if the start of x is identical to the start of y, and x has y as a subsequence" [] -is_transitive: true -is_a: RO:0002524 ! has subsequence -inverse_of: RO:0002517 ! is start sequence of - -[Typedef] -id: RO:0002517 -name: is start sequence of -def: "inverse of has start sequence" [] -is_transitive: true -is_a: RO:0002525 ! is subsequence of - -[Typedef] -id: RO:0002518 -name: has end sequence -def: "x has end sequence y if the end of x is identical to the end of y, and x has y as a subsequence" [] -is_transitive: true -is_a: RO:0002524 ! has subsequence -inverse_of: RO:0002519 ! is end sequence of - -[Typedef] -id: RO:0002519 -name: is end sequence of -def: "inverse of has end sequence" [] -is_transitive: true -is_a: RO:0002525 ! is subsequence of - -[Typedef] -id: RO:0002520 -name: is consecutive sequence of -def: "x is a consecutive sequence of y iff x has subsequence y, and all the parts of x are made of zero or more repetitions of y or sequences as the same type as y." [] -is_a: RO:0002524 ! has subsequence - -[Typedef] -id: RO:0002521 -name: is sequentially aligned with -def: "x is sequentially aligned with if a significant portion bases of x and y correspond in terms of their base type and their relative ordering" [] -is_symmetric: true -is_a: RO:0002514 ! sequentially related to - -[Typedef] -id: RO:0002522 -name: bounds sequence of -def: "x bounds the sequence of y iff the upstream-most part of x is upstream of or coincident with the upstream-most part of y, and the downstream-most part of x is downstream of or coincident with the downstream-most part of y" [] -is_transitive: true -is_a: RO:0002514 ! sequentially related to -inverse_of: RO:0002523 ! is bound by sequence of - -[Typedef] -id: RO:0002523 -name: is bound by sequence of -def: "inverse of bounds sequence of" [] -is_transitive: true -is_a: RO:0002514 ! sequentially related to - -[Typedef] -id: RO:0002524 -name: has subsequence -def: "x has subsequence y iff all of the sequence parts of x are sequence parts of y" [] -is_transitive: true -is_a: BFO:0000051 ! has part -is_a: RO:0002522 ! bounds sequence of -is_a: RO:0002526 ! overlaps sequence of -inverse_of: RO:0002525 ! is subsequence of - -[Typedef] -id: RO:0002525 -name: is subsequence of -def: "inverse of has subsequence" [] -is_transitive: true -is_a: BFO:0000050 ! part of -is_a: RO:0002523 ! is bound by sequence of -is_a: RO:0002526 ! overlaps sequence of - -[Typedef] -id: RO:0002526 -name: overlaps sequence of -def: "x overlaps the sequence of x if and only if x has a subsequence z and z is a subsequence of y." [] -holds_over_chain: RO:0002524 RO:0002525 -is_symmetric: true -is_a: RO:0002131 ! overlaps -is_a: RO:0002514 ! sequentially related to - -[Typedef] -id: RO:0002527 -name: does not overlap sequence of -def: "x does not overlaps the sequence of x if and only if there is no z such that x has a subsequence z and z is a subsequence of y." [] -is_symmetric: true -is_a: RO:0002514 ! sequentially related to - -[Typedef] -id: RO:0002528 -name: is upstream of sequence of -def: "inverse of downstream of sequence of" [] -is_transitive: true -is_a: RO:0002527 ! does not overlap sequence of - -[Typedef] -id: RO:0002529 -name: is downstream of sequence of -def: "x is downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, or (2) x and y are sequence units, and x is either immediately downstream of y, or transitively downstream of y." [] -is_transitive: true -is_a: RO:0002527 ! does not overlap sequence of -inverse_of: RO:0002529 ! is downstream of sequence of - -[Typedef] -id: RO:0002530 -name: is immediately downstream of sequence of -def: "x is immediately downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, and x is sequentially adjacent to y, or (2) x and y are sequence units, in which case the immediately downstream relation is primitive and defined by context: for DNA bases, y would be adjacent and 5' to y" [] -is_a: RO:0002515 ! sequentially adjacent to -is_a: RO:0002529 ! is downstream of sequence of - -[Typedef] -id: RO:0002531 -name: is immediately upstream of sequence of -def: "inverse of immediately downstream of" [] -is_a: RO:0002515 ! sequentially adjacent to -is_a: RO:0002528 ! is upstream of sequence of - -[Typedef] -id: RO:0002551 -name: has skeleton -def: "A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision." [] -is_a: BFO:0000051 ! has part -inverse_of: RO:0002576 ! skeleton of - -[Typedef] -id: RO:0002552 -name: results in ending of -def: "p results in the end of s if p results in a change of state in s whereby s either ceases to exist, or s becomes functionally impaired or s has its fate committed such that it is put on a path to be degraded." [] -is_a: results_in_developmental_progression_of ! results in developmental progression of -is_a: RO:0000057 ! has participant - -[Typedef] -id: RO:0002553 -name: hyperparasite of -def: "x is a hyperparasite of y iff x is a parasite of a parasite of the target organism y" [] -synonym: "epiparasite of" RELATED [] -synonym: "hyperparasitoid of" RELATED [] -holds_over_chain: RO:0002444 RO:0002444 -is_a: RO:0002454 ! has host -inverse_of: RO:0002554 ! hyperparasitized by - -[Typedef] -id: RO:0002554 -name: hyperparasitized by -def: "inverse of hyperparasite of" [] -synonym: "has epiparasite" RELATED [] -synonym: "has hyperparasite" RELATED [] -synonym: "hyperparasitoidized by" RELATED [] -holds_over_chain: RO:0002445 RO:0002445 -is_a: RO:0002453 ! host of - -[Typedef] -id: RO:0002555 -name: allelopath of -is_a: RO:0002574 ! participates in a biotic-biotic interaction with - -[Typedef] -id: RO:0002556 -name: pathogen of -is_a: RO:0002454 ! has host -inverse_of: RO:0002557 ! has pathogen - -[Typedef] -id: RO:0002557 -name: has pathogen -is_a: RO:0002453 ! host of - -[Typedef] -id: RO:0002558 -name: has evidence -def: "inverse of is evidence for" [] -is_a: RO:0002616 ! related via evidence or inference to - -[Typedef] -id: RO:0002559 -name: causally influenced by -is_a: RO:0002506 ! causal relation between material entities -inverse_of: RO:0002566 ! causally influences - -[Typedef] -id: RO:0002563 -name: interaction relation helper property -is_a: RO:0002464 ! helper property - -[Typedef] -id: RO:0002564 -name: molecular interaction relation helper property -is_a: RO:0002563 ! interaction relation helper property - -[Typedef] -id: RO:0002565 -name: results in movement of -def: "Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c" [] -is_a: RO:0000057 ! has participant - -[Typedef] -id: RO:0002566 -name: causally influences -def: "Holds between materal entities a and b if the activity of a is causally upstream of the activity of b, or causally upstream of a an activity that modifies b" [] -is_a: RO:0002506 ! causal relation between material entities - -[Typedef] -id: RO:0002567 -name: biomechanically related to -def: "A relation that holds between elements of a musculoskeletal system or its analogs." [] -is_a: RO:0002328 ! functionally related to - -[Typedef] -id: RO:0002568 -name: has muscle antagonist -def: "m1 has_muscle_antagonist m2 iff m1 has_muscle_insertion s, m2 has_muscle_insection s, m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position." [] -is_a: RO:0002567 ! biomechanically related to - -[Typedef] -id: RO:0002569 -name: has branching part -def: "inverse of branching part of" [] -is_a: RO:0002375 ! in branching relationship with - -[Typedef] -id: RO:0002570 -name: conduit for -def: "x is a conduit for y iff y overlaps through the lumen_of of x, and y has parts on either side of the lumen of x." [] -is_a: RO:0002131 ! overlaps - -[Typedef] -id: RO:0002571 -name: lumen of -def: "x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull." [] -is_a: BFO:0000050 ! part of - -[Typedef] -id: RO:0002572 -name: luminal space of -def: "s is luminal space of x iff s is lumen_of x and s is an immaterial entity" [] -is_a: RO:0002571 ! lumen of - -[Typedef] -id: RO:0002573 -name: has modifier -def: "A relation that holds between an attribute or a qualifier and another attribute." [] - -[Typedef] -id: RO:0002574 -name: participates in a biotic-biotic interaction with -is_a: RO:0002437 ! biotically interacts with - -[Typedef] -id: RO:0002576 -name: skeleton of -def: "inverse of has skeleton" [] -is_a: BFO:0000050 ! part of - -[Typedef] -id: RO:0002578 -name: directly regulates -def: "Process(P1) directly regulates process(P2) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2." [] -is_a: RO:0002211 ! regulates -is_a: RO:0002412 ! immediately causally upstream of - -[Typedef] -id: RO:0002583 -name: existence starts at point -def: "x existence starts at point y if and only if the time point at which x starts is equivalent to the time point at which y ends." [] -is_a: RO:0002487 ! relation between structure and stage - -[Typedef] -id: RO:0002584 -name: has part structure that is capable of -def: "s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p" [] -holds_over_chain: BFO:0000051 RO:0002215 -is_a: RO:0002328 ! functionally related to -is_a: RO:0002595 ! causal relation between material entity and a process - -[Typedef] -id: RO:0002585 -name: results in closure of -is_a: results_in_developmental_progression_of ! results in developmental progression of -is_a: RO:0000057 ! has participant - -[Typedef] -id: RO:0002586 -name: results in breakdown of -def: "p results in breakdown of c if and only if the execution of p leads to c no longer being present at the end of p" [] -is_a: RO:0002233 ! has input - -[Typedef] -id: RO:0002587 -name: results in synthesis of -is_a: results_in_formation_of ! results in formation of - -[Typedef] -id: RO:0002588 -name: results in assembly of -is_a: results_in_formation_of ! results in formation of -is_a: RO:0002592 ! results in organization of - -[Typedef] -id: RO:0002589 -name: results in catabolism of -def: "p results in catabolism of c if and only if p is a catabolic process, and the execution of p results in c being broken into smaller parts with energy being released." [] -is_a: RO:0002586 ! results in breakdown of - -[Typedef] -id: RO:0002590 -name: results in disassembly of -is_a: RO:0002586 ! results in breakdown of -is_a: RO:0002592 ! results in organization of - -[Typedef] -id: RO:0002591 -name: results in remodeling of -is_a: RO:0002233 ! has input -is_a: RO:0002592 ! results in organization of - -[Typedef] -id: RO:0002592 -name: results in organization of -def: "p results in organization of c iff p results in the assembly, arrangement of constituent parts, or disassembly of c" [] -is_a: RO:0000057 ! has participant - -[Typedef] -id: RO:0002593 -name: existence ends at point -def: "x existence starts at point y if and only if the time point at which x starts is equivalent to the time point at which y ends." [] -is_a: RO:0002487 ! relation between structure and stage - -[Typedef] -id: RO:0002595 -name: causal relation between material entity and a process -def: "A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity." [] -is_a: RO:0002410 ! causally related to - -[Typedef] -id: RO:0002596 -name: capable of regulating -def: "Holds between c and p if and only if c is capable of some activity a, and a regulates p." [] -holds_over_chain: RO:0002215 RO:0002211 -is_a: RO:0002500 ! causal agent in process - -[Typedef] -id: RO:0002597 -name: capable of negatively regulating -def: "Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p." [] -holds_over_chain: RO:0002215 RO:0002212 -is_a: RO:0002596 ! capable of regulating - -[Typedef] -id: RO:0002598 -name: capable of positively regulating -def: "Holds between c and p if and only if c is capable of some activity a, and a positively regulates p." [] -holds_over_chain: RO:0002215 RO:0002213 -is_a: RO:0002596 ! capable of regulating - -[Typedef] -id: RO:0002599 -name: capable of inhibiting or preventing pathological process -def: "Holds between a material entity c and a pathological process p if and only if c is capable of some activity a, where a inhibits p." [] -is_a: RO:0002597 ! capable of negatively regulating - -[Typedef] -id: RO:0002600 -name: capable of upregulating or causing pathological process -def: "Holds between a material entity c and a pathological process p if and only if c is capable of some activity a, where a negatively regulates p." [] -is_a: RO:0002598 ! capable of positively regulating - -[Typedef] -id: RO:0002606 -name: is substance that treats -def: "c is a substance that treats d if c is a material entity (such as a small molecule or compound) and d is a pathological process, phenotype or disease, and c is capable of some activity that negative regulates or decreases the magnitude of d." [] -is_a: RO:0002599 ! capable of inhibiting or preventing pathological process - -[Typedef] -id: RO:0002607 -name: is marker for -def: "c is marker for d iff the presence or occurrence of d is correlated with the presence of occurrence of c, and the observation of c is used to infer the presence or occurrence of d. Note that this does not imply that c and d are in a direct causal relationship, as it may be the case that there is a third entity e that stands in a direct causal relationship with c and d." [] -is_a: RO:0002610 ! correlated with - -[Typedef] -id: RO:0002608 -name: process has causal agent -def: "Inverse of 'causal agent in process'" [] -is_a: RO:0002410 ! causally related to - -[Typedef] -id: RO:0002609 -name: obsolete related via dependence to -def: "A relationship that holds between two entities, where the relationship holds based on the presence or absence of statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes." [] -is_obsolete: true - -[Typedef] -id: RO:0002610 -name: correlated with -def: "A relationship that holds between two entities, where the entities exhibit a statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes." [] - -[Typedef] -id: RO:0002614 -name: is evidence with support from -def: "A relationship between a piece of evidence and an entity that plays a role in supporting that evidence." [] -is_a: RO:0002616 ! related via evidence or inference to - -[Typedef] -id: RO:0002615 -name: has model -def: "Inverse of is-model-of" [] -inverse_of: RO:0003301 ! is model of - -[Typedef] -id: RO:0002616 -name: related via evidence or inference to - -[Typedef] -id: RO:0002618 -name: visits -is_a: RO:0002574 ! participates in a biotic-biotic interaction with -inverse_of: RO:0002619 ! visited by - -[Typedef] -id: RO:0002619 -name: visited by -is_a: RO:0002574 ! participates in a biotic-biotic interaction with - -[Typedef] -id: RO:0002622 -name: visits flowers of -is_a: RO:0002618 ! visits -inverse_of: RO:0002623 ! has flowers visited by - -[Typedef] -id: RO:0002623 -name: has flowers visited by -is_a: RO:0002619 ! visited by - -[Typedef] -id: RO:0002624 -name: lays eggs in -is_a: RO:0002444 ! parasite of -is_a: RO:0002618 ! visits -inverse_of: RO:0002625 ! has eggs laid in by - -[Typedef] -id: RO:0002625 -name: has eggs laid in by -is_a: RO:0002445 ! parasitized by -is_a: RO:0002619 ! visited by - -[Typedef] -id: RO:0002626 -name: kills -is_a: RO:0002574 ! participates in a biotic-biotic interaction with -inverse_of: RO:0002627 ! is killed by - -[Typedef] -id: RO:0002627 -name: is killed by -is_a: RO:0002574 ! participates in a biotic-biotic interaction with - -[Typedef] -id: RO:0002629 -name: directly positively regulates -def: "Process(P1) directly postively regulates process(P2) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P1 directly positively regulates P2." [] -is_a: RO:0002213 ! positively regulates -is_a: RO:0002578 ! directly regulates - -[Typedef] -id: RO:0002630 -name: directly negatively regulates -def: "Process(P1) directly negatively regulates process(P2) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P1 directly negatively regulates P2." [] -is_a: RO:0002212 ! negatively regulates -is_a: RO:0002578 ! directly regulates - -[Typedef] -id: RO:0002632 -name: ectoparasite of -def: "A sub-relation of parasite-of in which the parasite lives on or in the integumental system of the host" [] -is_a: RO:0002444 ! parasite of -inverse_of: RO:0002633 ! has ectoparasite - -[Typedef] -id: RO:0002633 -name: has ectoparasite -def: "inverse of ectoparasite of" [] -is_a: RO:0002445 ! parasitized by - -[Typedef] -id: RO:0002634 -name: endoparasite of -synonym: "lives inside of" RELATED [] -is_a: RO:0002444 ! parasite of -inverse_of: RO:0002635 ! has endoparasite - -[Typedef] -id: RO:0002635 -name: has endoparasite -is_a: RO:0002445 ! parasitized by - -[Typedef] -id: RO:0002636 -name: mesoparasite of -def: "A sub-relation of parasite-of in which the parasite is partially an endoparasite and partially an ectoparasite" [] -is_a: RO:0002444 ! parasite of -inverse_of: RO:0002637 ! has mesoparasite - -[Typedef] -id: RO:0002637 -name: has mesoparasite -def: "inverse of mesoparasite of" [] -is_a: RO:0002445 ! parasitized by - -[Typedef] -id: RO:0002638 -name: intercellular endoparasite of -def: "A sub-relation of endoparasite-of in which the parasite inhabits the spaces between host cells." [] -is_a: RO:0002634 ! endoparasite of -inverse_of: RO:0002639 ! has intercellular endoparasite - -[Typedef] -id: RO:0002639 -name: has intercellular endoparasite -def: "inverse of intercellular endoparasite of" [] -is_a: RO:0002635 ! has endoparasite - -[Typedef] -id: RO:0002640 -name: intracellular endoparasite of -def: "A sub-relation of endoparasite-of in which the parasite inhabits host cells." [] -is_a: RO:0002634 ! endoparasite of -inverse_of: RO:0002641 ! has intracellular endoparasite - -[Typedef] -id: RO:0002641 -name: has intracellular endoparasite -def: "inverse of intracellular endoparasite of" [] -is_a: RO:0002635 ! has endoparasite - -[Typedef] -id: RO:0003000 -name: produces -def: "a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix." [] -inverse_of: RO:0003001 ! produced by - -[Typedef] -id: RO:0003001 -name: produced by -def: "a produced_by b iff some process that occurs_in b has_output a." [] - -[Typedef] -id: RO:0003002 -name: represses expression of -def: "Holds between protein a (a transcription factor) and DNA element b if and only if a diminishes the process of transcription of b." [] -is_a: RO:0002449 ! activity directly negatively regulates activity of - -[Typedef] -id: RO:0003003 -name: increases expression of -def: "Holds between protein a (a transcription factor) and DNA element b if and only if a activates the process of transcription of b." [] -is_a: RO:0002450 ! activity directly positively regulates activity of - -[Typedef] -id: RO:0003301 -name: is model of -def: "Relation between a research artifact and an entity it is used to study, in virtue of its replicating or approximating features of the studied entity." [] - -[Typedef] -id: RO:0003302 -name: causes or contributes to condition -def: "A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some causal or contributing role that influences the condition." [] -is_a: RO:0002410 ! causally related to - -[Typedef] -id: RO:0003303 -name: causes condition -def: "A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some causal role for the condition." [] -is_a: RO:0003302 ! causes or contributes to condition - -[Typedef] -id: RO:0003304 -name: contributes to condition -def: "A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some contributing role that influences the condition." [] -is_a: RO:0003302 ! causes or contributes to condition - -[Typedef] -id: RO:0003305 -name: contributes to severity of condition -def: "A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity influences the severity with which a condition manifests in an individual." [] -is_a: RO:0003304 ! contributes to condition - -[Typedef] -id: RO:0003306 -name: contributes to frequency of condition -def: "A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity influences the frequency of the condition in a population." [] -is_a: RO:0003304 ! contributes to condition - -[Typedef] -id: RO:0003307 -name: ameliorates condition -def: "A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the presence of the entity reduces or eliminates some or all aspects of the condition." [] -is_a: RO:0003305 ! contributes to severity of condition - -[Typedef] -id: RO:0003308 -name: correlated with condition -def: "A relationship between an entity and a condition (phenotype or disease) with which it exhibits a statistical dependence relationship." [] -is_a: RO:0002610 ! correlated with - -[Typedef] -id: RO:0003309 -name: exacerbates condition -def: "A relationship between an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) and a condition (a phenotype or disease), where the presence of the entity worsens some or all aspects of the condition." [] -is_a: RO:0003305 ! contributes to severity of condition - -[Typedef] -id: RO:0003310 -name: condition ameliorated by -def: "A relationship between a condition (a phenotype or disease) and an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) where some or all aspects of the condition are reduced or eliminated by the presence of the entity." [] -is_a: RO:0002410 ! causally related to - -[Typedef] -id: RO:0003311 -name: condition exacerbated by -def: "A relationship between a condition (a phenotype or disease) and an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) where some or all aspects of the condition are worsened by the presence of the entity." [] -is_a: RO:0002410 ! causally related to - -[Typedef] -id: RO:0004000 -name: condition has genetic basis in -is_a: RO:0002410 ! causally related to -inverse_of: RO:0004010 ! is genetic basis for condition - -[Typedef] -id: RO:0004001 -name: has material basis in gain of function germline mutation in -is_a: RO:0004000 ! condition has genetic basis in -inverse_of: RO:0004011 ! is causal gain of function germline mutation of in - -[Typedef] -id: RO:0004002 -name: has material basis in loss of function germline mutation in -is_a: RO:0004000 ! condition has genetic basis in -inverse_of: RO:0004012 ! is causal loss of function germline mutation of in - -[Typedef] -id: RO:0004003 -name: has material basis in germline mutation in -is_a: RO:0004000 ! condition has genetic basis in -inverse_of: RO:0004013 ! is causal germline mutation in - -[Typedef] -id: RO:0004004 -name: has material basis in somatic mutation in -is_a: RO:0004000 ! condition has genetic basis in -inverse_of: RO:0004014 ! is causal somatic mutation in - -[Typedef] -id: RO:0004005 -name: has major susceptibility factor -is_a: RO:0004000 ! condition has genetic basis in -inverse_of: RO:0004015 ! is causal susceptibility factor for - -[Typedef] -id: RO:0004006 -name: has partial material basis in germline mutation in -is_a: RO:0004000 ! condition has genetic basis in -inverse_of: RO:0004016 ! is causal germline mutation partially giving rise to - -[Typedef] -id: RO:0004010 -name: is genetic basis for condition -is_a: RO:0004018 ! is basis for realizable - -[Typedef] -id: RO:0004011 -name: is causal gain of function germline mutation of in -def: "Relates a gene to condition, such that a mutation in this gene in a germ cell provides a new function of the corresponding product and that is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet]." [] -is_a: RO:0004010 ! is genetic basis for condition - -[Typedef] -id: RO:0004012 -name: is causal loss of function germline mutation of in -def: "Relates a gene to condition, such that a mutation in this gene in a germ cell impairs the function of the corresponding product and that is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet]." [] -is_a: RO:0004010 ! is genetic basis for condition - -[Typedef] -id: RO:0004013 -name: is causal germline mutation in -def: "Relates a gene to condition, such that a mutation in this gene is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet]." [] -is_a: RO:0004010 ! is genetic basis for condition - -[Typedef] -id: RO:0004014 -name: is causal somatic mutation in -def: "Relates a gene to condition, such that a mutation in this gene is sufficient to produce the condition but that cannot be passed on to offspring[modified from orphanet]." [] -is_a: RO:0004010 ! is genetic basis for condition - -[Typedef] -id: RO:0004015 -name: is causal susceptibility factor for -def: "Relates a gene to condition, such that a mutation in this gene predisposes to the development of a condition and that is necessary but not sufficient to develop the condition[modified from orphanet]." [] -is_a: RO:0004010 ! is genetic basis for condition - -[Typedef] -id: RO:0004016 -name: is causal germline mutation partially giving rise to -def: "Relates a gene to condition, such that a mutation in this gene partially contributes to the presentation of this condition[modified from orphanet]." [] -is_a: RO:0004010 ! is genetic basis for condition - -[Typedef] -id: RO:0004017 -name: realizable has basis in -is_a: RO:0002410 ! causally related to -inverse_of: RO:0004018 ! is basis for realizable - -[Typedef] -id: RO:0004018 -name: is basis for realizable -is_a: RO:0002410 ! causally related to - -[Typedef] -id: RO:0004019 -name: disease has basis in -is_a: RO:0004017 ! realizable has basis in -is_a: RO:0004023 ! causal relationship with disease as subject - -[Typedef] -id: RO:0004020 -name: disease has basis in dysfunction of -def: "A relation that holds between the disease and a material entity where the physical basis of the disease is a disorder of that material entity that affects its function." [] -is_a: RO:0004019 ! disease has basis in - -[Typedef] -id: RO:0004021 -name: disease has basis in disruption of -def: "A relation that holds between the disease and a process where the physical basis of the disease disrupts execution of a key biological process." [] -is_a: RO:0004019 ! disease has basis in - -[Typedef] -id: RO:0004022 -name: disease has basis in feature -def: "A relation that holds between the disease and a feature (a phenotype or other disease) where the physical basis of the disease is the feature." [] -is_a: RO:0002200 ! has phenotype -is_a: RO:0004019 ! disease has basis in - -[Typedef] -id: RO:0004023 -name: causal relationship with disease as subject -is_a: RO:0002410 ! causally related to -is_a: RO:0040035 ! disease relationship - -[Typedef] -id: RO:0004024 -name: disease causes disruption of -def: "A relationship between a disease and a process where the disease process disrupts the execution of the process." [] -is_a: RO:0004023 ! causal relationship with disease as subject -transitive_over: BFO:0000050 ! part of - -[Typedef] -id: RO:0004025 -name: disease causes dysfunction of -is_a: RO:0004023 ! causal relationship with disease as subject -transitive_over: BFO:0000050 ! part of - -[Typedef] -id: RO:0004026 -name: disease has location -def: "A relationship between a disease and an anatomical entity where the disease has one or more features that are located in that entity." [] -is_a: RO:0040035 ! disease relationship - -[Typedef] -id: RO:0004027 -name: disease has inflammation site -def: "A relationship between a disease and an anatomical entity where the disease is triggered by an inflammatory response to stimuli occurring in the anatomical entity" [] -is_a: RO:0004026 ! disease has location - -[Typedef] -id: RO:0004028 -name: realized in response to stimulus -def: "A relationship between a realizable entity R (e.g. function or disposition) and a material entity M where R is realized in response to a process that has an input stimulus of M." [] -holds_over_chain: RO:0009501 RO:0002233 -is_a: RO:0002410 ! causally related to - -[Typedef] -id: RO:0004029 -name: disease has feature -def: "A relationship between a disease and some feature of that disease, where the feature is either a phenotype or an isolated disease." [] -is_a: RO:0040035 ! disease relationship - -[Typedef] -id: RO:0004030 -name: disease arises from structure -def: "A relationship between a disease and an anatomical structure where the material basis of the disease is some pathological change in the structure." [] -is_a: RO:0004019 ! disease has basis in - -[Typedef] -id: RO:0004031 -name: enables subfunction -def: "Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P." [] -holds_over_chain: RO:0002327 BFO:0000051 -is_a: RO:0002328 ! functionally related to - -[Typedef] -id: RO:0004032 -name: acts upstream of or within, positive effect -holds_over_chain: RO:0002327 RO:0004047 -is_a: RO:0002264 ! acts upstream of or within - -[Typedef] -id: RO:0004033 -name: acts upstream of or within, negative effect -holds_over_chain: RO:0002327 RO:0004046 -is_a: RO:0002264 ! acts upstream of or within - -[Typedef] -id: RO:0004034 -name: acts upstream of, positive effect -def: "c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive" [] -holds_over_chain: RO:0002327 RO:0002304 -is_a: RO:0002263 ! acts upstream of -is_a: RO:0004032 ! acts upstream of or within, positive effect - -[Typedef] -id: RO:0004035 -name: acts upstream of, negative effect -def: "c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative" [] -holds_over_chain: RO:0002327 RO:0002305 -is_a: RO:0002263 ! acts upstream of -is_a: RO:0004033 ! acts upstream of or within, negative effect - -[Typedef] -id: RO:0004046 -name: causally upstream of or within, negative effect -is_a: RO:0002418 ! causally upstream of or within - -[Typedef] -id: RO:0004047 -name: causally upstream of or within, positive effect -is_a: RO:0002418 ! causally upstream of or within - -[Typedef] -id: RO:0008501 -name: epiphyte of -def: "An interaction relationship wherein a plant or algae is living on the outside surface of another plant." [] -is_a: RO:0002440 ! symbiotically interacts with -inverse_of: RO:0008502 ! has epiphyte - -[Typedef] -id: RO:0008502 -name: has epiphyte -def: "inverse of epiphyte of" [] -is_a: RO:0002440 ! symbiotically interacts with - -[Typedef] -id: RO:0008503 -name: kleptoparasite of -def: "A sub-relation of parasite of in which a parasite steals resources from another organism, usually food or nest material" [] -is_a: RO:0002444 ! parasite of -inverse_of: RO:0008504 ! kleptoparasitized by - -[Typedef] -id: RO:0008504 -name: kleptoparasitized by -def: "inverse of kleptoparasite of" [] -is_a: RO:0002445 ! parasitized by - -[Typedef] -id: RO:0008505 -name: creates habitat for -def: "An interaction relationship wherein one organism creates a structure or environment that is lived in by another organism." [] -is_a: RO:0002321 ! ecologically related to - -[Typedef] -id: RO:0008506 -name: ecologically co-occurs with -def: "An interaction relationship describing organisms that often occur together at the same time and space or in the same environment." [] -is_symmetric: true -is_a: RO:0002321 ! ecologically related to - -[Typedef] -id: RO:0008507 -name: lays eggs on -def: "An interaction relationship in which organism a lays eggs on the outside surface of organism b. Organism b is neither helped nor harmed in the process of egg laying or incubation." [] -is_a: RO:0002618 ! visits -inverse_of: RO:0008508 ! has eggs laid on by - -[Typedef] -id: RO:0008508 -name: has eggs laid on by -def: "An interaction relationship in which organism a lays eggs on the outside surface of organism b. Organism b is neither helped nor harmed in the process of egg laying or incubation." [] -is_a: RO:0002619 ! visited by - -[Typedef] -id: RO:0009001 -name: has substance added -def: "\"has substance added\" is a relation existing between a (physical) entity and a substance in which the entity has had the substance added to it at some point in time." [] - -[Typedef] -id: RO:0009002 -name: has substance removed -def: "\"has substance removed\" is a relation existing between two physical entities in which the first entity has had the second entity (a substance) removed from it at some point in time." [] - -[Typedef] -id: RO:0009003 -name: immersed in -def: "\"immersed in\" is a relation between a (physical) entity and a fluid substance in which the entity is wholely or substantially surrounded by the substance." [] - -[Typedef] -id: RO:0009005 -name: has primary substance added -def: "'has primary substance added' indicates that an entity has had the given substance added to it in a proportion greater than any other added substance." [] -is_a: RO:0009001 ! has substance added - -[Typedef] -id: RO:0009501 -name: realized in response to -def: "r 'realized in response to' s iff, r is a realizable (e.g. a plant trait such as responsivity to drought), s is an environmental stimulus (a process), and s directly causes the realization of r." [] -synonym: "triggered by process" EXACT [RO:cjm] -holds_over_chain: BFO:0000054 RO:0002404 -is_a: RO:0002410 ! causally related to - -[Typedef] -id: RO:0010001 -name: generically depends on -def: "A generically dependent continuant *b* generically depends on an independent continuant *c* at time *t* means: there inheres in *c* a specifically deendent continuant which concretizes *b* at *t*." [] -synonym: "g-depends on" EXACT [] -holds_over_chain: RO:0000052 RO:0000058 -inverse_of: RO:0010002 ! is carrier of - -[Typedef] -id: RO:0010002 -name: is carrier of -def: "*b* is carrier of *c* at time *t* if and only if *c* *g-depends on* *b* at *t*" [] -holds_over_chain: RO:0000059 RO:0000053 - -[Typedef] -id: RO:0040035 -name: disease relationship -def: "This relation groups relations between diseases and any other kind of entity." [] - -[Typedef] -id: RO:HOM0000000 -name: in similarity relationship with -def: "Relation between biological objects that resemble or are related to each other sufficiently to warrant a comparison." [BGEE:curator, http://purl.obolibrary.org/obo/HOM_0000000] -synonym: "correspondence" RELATED [http://dx.doi.org/10.1007/BF02814479] -synonym: "resemblance" RELATED [] -synonym: "sameness" EXACT [] -synonym: "similar to" EXACT [] -is_symmetric: true - -[Typedef] -id: RO:HOM0000001 -name: in homology relationship with -def: "Similarity that results from common evolutionary origin." [http://dx.doi.org/10.1002/bies.950180611, http://dx.doi.org/10.1002/jmor.1051730307, http://dx.doi.org/10.1007/BF02814480, http://purl.obolibrary.org/obo/HOM_0000001] -synonym: "homologous to" EXACT [] -is_symmetric: true -is_a: RO:0002158 ! shares ancestor with -is_a: RO:HOM0000000 ! in similarity relationship with -disjoint_from: RO:HOM0000002 ! in homoplasy relationship with - -[Typedef] -id: RO:HOM0000002 -name: in homoplasy relationship with -def: "Similarity that results from independent evolution." [http://dx.doi.org/10.1016/j.jhevol.2006.11.010, http://purl.obolibrary.org/obo/HOM_0000002] -synonym: "analogy" RELATED [] -synonym: "homoplasous to" EXACT [] -is_symmetric: true -is_a: RO:HOM0000000 ! in similarity relationship with - -[Typedef] -id: RO:HOM0000003 -name: in homocracy relationship with -def: "Similarity that is characterized by the organization of anatomical structures through the expression of homologous or identical patterning genes." [http://dx.doi.org/10.1007/BF02814484, http://dx.doi.org/10.1007/s00427-003-0301-4, http://dx.doi.org/10.1186/1742-9994-2-15, http://purl.obolibrary.org/obo/HOM_0000003] -synonym: "homocracous to" EXACT [] -is_symmetric: true -is_a: RO:0002320 ! evolutionarily related to -is_a: RO:HOM0000000 ! in similarity relationship with - -[Typedef] -id: RO:HOM0000004 -name: in convergence relationship with -def: "Homoplasy that involves different underlying mechanisms or structures." [http://dx.doi.org/10.1016/j.jhevol.2006.11.010, http://purl.obolibrary.org/obo/HOM_0000004] -synonym: "analogy" RELATED [] -is_symmetric: true -is_a: RO:HOM0000002 ! in homoplasy relationship with - -[Typedef] -id: RO:HOM0000005 -name: in parallelism relationship with -def: "Homoplasy that involves homologous underlying mechanisms or structures." [http://dx.doi.org/10.1016/j.jhevol.2006.11.010, http://purl.obolibrary.org/obo/HOM_0000005] -synonym: "parallel evolution" EXACT [] -is_symmetric: true -is_a: RO:HOM0000002 ! in homoplasy relationship with - -[Typedef] -id: RO:HOM0000006 -name: in structural homology relationship with -def: "Homology that is defined by similarity with regard to selected structural parameters." [http://dx.doi.org/10.1016/j.jhevol.2006.11.014, http://dx.doi.org/10.1146/annurev.es.20.110189.000411, http://purl.obolibrary.org/obo/HOM_0000006, ISBN:0123195837] -synonym: "idealistic homology" RELATED [] -synonym: "structural homologous to" EXACT [] -is_symmetric: true -is_a: RO:HOM0000001 ! in homology relationship with - -[Typedef] -id: RO:HOM0000007 -name: in historical homology relationship with -def: "Homology that is defined by common descent." [http://dx.doi.org/10.1016/S0169-5347(97)01125-7, http://purl.obolibrary.org/obo/HOM_0000007, ISBN:0123195837] -synonym: "cladistic homology" EXACT [] -synonym: "historical homologous to" EXACT [] -synonym: "homology" BROAD [] -synonym: "phylogenetic homology" EXACT [] -synonym: "taxic homology" EXACT [] -synonym: "true homology" RELATED [] -is_symmetric: true -is_a: RO:HOM0000001 ! in homology relationship with - -[Typedef] -id: RO:HOM0000008 -name: in biological homology relationship with -def: "Homology that is defined by sharing of a set of developmental constraints, caused by locally acting self-regulatory mechanisms of differentiation, between individualized parts of the phenotype." [http://dx.doi.org/10.1016/S0169-5347(97)01125-7, http://dx.doi.org/10.1146/annurev.es.20.110189.000411, http://purl.obolibrary.org/obo/HOM_0000008] -synonym: "biological homologous to" EXACT [] -synonym: "transformational homology" RELATED [] -is_symmetric: true -is_a: RO:HOM0000001 ! in homology relationship with - -[Typedef] -id: RO:HOM0000009 -name: in reversal relationship with -def: "Homoplasy that involves phenotypes similar to those seen in ancestors within the lineage." [http://dx.doi.org/10.1016/j.jhevol.2006.11.010, http://purl.obolibrary.org/obo/HOM_0000009] -synonym: "atavism" EXACT [] -synonym: "reversion" RELATED [] -synonym: "rudiment" EXACT [] -is_symmetric: true -is_a: RO:HOM0000002 ! in homoplasy relationship with - -[Typedef] -id: RO:HOM0000010 -name: in syntenic homology relationship with -def: "Structural homology that is detected by similarity in content and organization between chromosomes." [http://purl.obolibrary.org/obo/HOM_0000010, MeSH:Synteny] -synonym: "syntenic homologous to" EXACT [] -synonym: "synteny" RELATED [] -is_symmetric: true -is_a: RO:HOM0000006 ! in structural homology relationship with - -[Typedef] -id: RO:HOM0000011 -name: in paralogy relationship with -def: "Historical homology that involves genes that diverged after a duplication event." [http://dx.doi.org/10.1016/S0168-9525(00)02005-9, http://dx.doi.org/10.1146/annurev.genet.39.073003.114725, http://purl.obolibrary.org/obo/HOM_0000011, http://www.ncbi.nlm.nih.gov/pubmed/5449325] -synonym: "paralogous to" EXACT [] -is_symmetric: true -is_a: RO:HOM0000007 ! in historical homology relationship with -disjoint_from: RO:HOM0000017 ! in orthology relationship with - -[Typedef] -id: RO:HOM0000012 -name: in syntenic paralogy relationship with -def: "Paralogy that involves sets of syntenic blocks." [DOI:10.1002/1097-010X(20001215)288\:4<345\:\:AID-JEZ7>3.0.CO;2-Y, http://dx.doi.org/10.1186/1471-213X-7-100, http://purl.obolibrary.org/obo/HOM_0000012] -synonym: "duplicon" RELATED [] -synonym: "paralogon" RELATED [] -synonym: "syntenic paralogous to" EXACT [] -is_symmetric: true -is_a: RO:HOM0000010 ! in syntenic homology relationship with -is_a: RO:HOM0000011 ! in paralogy relationship with - -[Typedef] -id: RO:HOM0000013 -name: in syntenic orthology relationship with -def: "Syntenic homology that involves chromosomes of different species." [http://dx.doi.org/10.1101/gr.6380007, http://purl.obolibrary.org/obo/HOM_0000013] -synonym: "syntenic orthologous to" EXACT [] -is_symmetric: true -is_a: RO:HOM0000010 ! in syntenic homology relationship with - -[Typedef] -id: RO:HOM0000014 -name: in partial homology relationship with -def: "Structural homology that involves complex structures from which only a fraction of the elements that can be isolated are separately homologous." [http://purl.obolibrary.org/obo/HOM_0000014, ISBN:0123195837, ISBN:978-0471984931] -synonym: "fractional homology" EXACT [] -synonym: "mixed homology" RELATED [] -synonym: "modular homology" RELATED [] -synonym: "partial correspondence" RELATED [] -synonym: "partial homologous to" EXACT [] -synonym: "percent homology" RELATED [] -synonym: "segmental homology" EXACT [] -is_symmetric: true -is_a: RO:HOM0000006 ! in structural homology relationship with - -[Typedef] -id: RO:HOM0000015 -name: in protein structural homology relationship with -def: "Structural homology that is detected at the level of the 3D protein structure, but maybe not at the level of the amino acid sequence." [http://dx.doi.org/10.1016/0022-2836(76)90195-9, http://purl.obolibrary.org/obo/HOM_0000015] -synonym: "protein structural homologous to" EXACT [] -is_symmetric: true -is_a: RO:HOM0000006 ! in structural homology relationship with - -[Typedef] -id: RO:HOM0000016 -name: in non functional homology relationship with -def: "Structural homology that involves a pseudogenic feature and its functional ancestor." [http://purl.obolibrary.org/obo/HOM_0000016, SO:non_functional_homolog_of] -synonym: "non functional homologous to" EXACT [] -synonym: "pseudogene" BROAD [] -is_symmetric: true -is_a: RO:HOM0000006 ! in structural homology relationship with -disjoint_from: RO:HOM0000062 ! in equivalogy relationship with - -[Typedef] -id: RO:HOM0000017 -name: in orthology relationship with -def: "Historical homology that involves genes that diverged after a speciation event." [http://dx.doi.org/10.1007/BF02814484, http://dx.doi.org/10.1016/S0168-9525(00)02005-9, http://dx.doi.org/10.1146/annurev.genet.39.073003.114725, http://purl.obolibrary.org/obo/HOM_0000017, http://www.ncbi.nlm.nih.gov/pubmed/5449325] -synonym: "orthologous to" EXACT [] -is_symmetric: true -is_a: RO:HOM0000007 ! in historical homology relationship with - -[Typedef] -id: RO:HOM0000018 -name: in xenology relationship with -def: "Historical homology that is characterized by an interspecies (horizontal) transfer since the common ancestor." [http://dx.doi.org/10.1016/S0168-9525(00)02005-9, http://dx.doi.org/10.1146/annurev.genet.39.073003.114725, http://purl.obolibrary.org/obo/HOM_0000018] -synonym: "xenologous to" EXACT [] -is_symmetric: true -is_a: RO:HOM0000007 ! in historical homology relationship with - -[Typedef] -id: RO:HOM0000019 -name: in 1 to 1 homology relationship with -def: "Historical homology that involves two members sharing no other homologs in the lineages considered." [BGEE:curator, http://purl.obolibrary.org/obo/HOM_0000019] -synonym: "1 to 1 homologous to" EXACT [] -synonym: "1:1 homology" EXACT [] -synonym: "one-to-one homology" EXACT [] -is_symmetric: true -is_a: RO:HOM0000007 ! in historical homology relationship with - -[Typedef] -id: RO:HOM0000020 -name: in 1 to 1 orthology relationship with -def: "Orthology that involves two genes that did not experience any duplication after the speciation event that created them." [http://dx.doi.org/10.1007/BF02814484, http://purl.obolibrary.org/obo/HOM_0000020, http://www.ensembl.org/info/docs/compara/homology_method.html] -synonym: "1 to 1 orthologous to" EXACT [] -synonym: "1:1 orthology" EXACT [] -synonym: "one-to-one orthology" EXACT [] -is_symmetric: true -is_a: RO:HOM0000017 ! in orthology relationship with -is_a: RO:HOM0000019 ! in 1 to 1 homology relationship with - -[Typedef] -id: RO:HOM0000022 -name: in ohnology relationship with -def: "Paralogy that results from a whole genome duplication event." [http://dx.doi.org/10.1038/75560, http://purl.obolibrary.org/obo/HOM_0000022] -synonym: "homoeology" RELATED [] -synonym: "ohnologous to" EXACT [] -is_symmetric: true -is_a: RO:HOM0000011 ! in paralogy relationship with - -[Typedef] -id: RO:HOM0000023 -name: in in-paralogy relationship with -def: "Paralogy that results from a lineage-specific duplication subsequent to a given speciation event." [http://dx.doi.org/10.1146/annurev.genet.39.073003.114725, http://purl.obolibrary.org/obo/HOM_0000023] -synonym: "in-paralogous to" EXACT [] -synonym: "inparalogy" EXACT [] -synonym: "symparalogy" EXACT [] -is_symmetric: true -is_a: RO:HOM0000011 ! in paralogy relationship with -disjoint_from: RO:HOM0000024 ! in out-paralogy relationship with - -[Typedef] -id: RO:HOM0000024 -name: in out-paralogy relationship with -def: "Paralogy that results from a duplication preceding a given speciation event." [http://dx.doi.org/10.1146/annurev.genet.39.073003.114725, http://purl.obolibrary.org/obo/HOM_0000024] -synonym: "alloparalogy" EXACT [] -synonym: "out-paralogous to" EXACT [] -synonym: "outparalogy" EXACT [] -is_symmetric: true -is_a: RO:HOM0000011 ! in paralogy relationship with - -[Typedef] -id: RO:HOM0000025 -name: in pro-orthology relationship with -def: "1:many orthology that involves a gene in species A and one of its ortholog in species B, when duplications more recent than the species split have occurred in species B but not in species A." [http://dx.doi.org/10.1006/scdb.1999.0338, http://dx.doi.org/10.1038/nrg2099, http://purl.obolibrary.org/obo/HOM_0000025] -synonym: "pro-orthologous to" EXACT [] -is_symmetric: true -is_a: RO:HOM0000034 ! in 1 to many orthology relationship with - -[Typedef] -id: RO:HOM0000026 -name: in semi-orthology relationship with -def: "1:many orthology that involves a gene in species A and its ortholog in species B, when duplications more recent than the species split have occurred in species A but not in species B." [http://dx.doi.org/10.1006/scdb.1999.0338, http://dx.doi.org/10.1038/nrg2099, http://purl.obolibrary.org/obo/HOM_0000026] -synonym: "semi-orthologous to" EXACT [] -is_symmetric: true -is_a: RO:HOM0000034 ! in 1 to many orthology relationship with - -[Typedef] -id: RO:HOM0000027 -name: in serial homology relationship with -def: "Iterative homology that involves structures arranged along the main body axis." [http://dx.doi.org/10.1146/annurev.es.20.110189.000411, http://purl.obolibrary.org/obo/HOM_0000027] -synonym: "homonomy" RELATED [] -synonym: "serial homologous to" EXACT [] -is_symmetric: true -is_a: RO:HOM0000066 ! in iterative homology relationship with - -[Typedef] -id: RO:HOM0000028 -name: in heterochronous homology relationship with -def: "Biological homology that is characterized by changes, over evolutionary time, in the rate or timing of developmental events of homologous structures." [http://purl.obolibrary.org/obo/HOM_0000028, ISBN:978-0674639416] -synonym: "heterochronous homologous to" EXACT [] -synonym: "heterochrony" EXACT [] -is_symmetric: true -is_a: RO:HOM0000008 ! in biological homology relationship with - -[Typedef] -id: RO:HOM0000029 -name: in paedomorphorsis relationship with -def: "Heterochronous homology that is produced by a retention in adults of a species of traits previously seen only in juveniles." [http://en.wikipedia.org/wiki/Pedomorphosis, http://purl.obolibrary.org/obo/HOM_0000029, ISBN:978-0674639416] -synonym: "juvenification" EXACT [] -synonym: "pedomorphosis" EXACT [] -is_symmetric: true -is_a: RO:HOM0000028 ! in heterochronous homology relationship with -disjoint_from: RO:HOM0000030 ! in peramorphosis relationship with - -[Typedef] -id: RO:HOM0000030 -name: in peramorphosis relationship with -def: "Heterochronous homology that is produced by a maturation of individuals of a species past adulthood, which take on hitherto unseen traits." [http://en.wikipedia.org/wiki/Peramorphosis, http://purl.obolibrary.org/obo/HOM_0000030] -is_symmetric: true -is_a: RO:HOM0000028 ! in heterochronous homology relationship with - -[Typedef] -id: RO:HOM0000031 -name: in progenesis relationship with -def: "Paedomorphosis that is produced by precocious sexual maturation of an organism still in a morphologically juvenile stage." [http://en.wikipedia.org/wiki/Progenesis, http://purl.obolibrary.org/obo/HOM_0000031, ISBN:978-0674639416] -is_symmetric: true -is_a: RO:HOM0000029 ! in paedomorphorsis relationship with - -[Typedef] -id: RO:HOM0000032 -name: in neoteny relationship with -def: "Paedomorphosis that is produced by a retardation of somatic development." [http://en.wikipedia.org/wiki/Neoteny, http://purl.obolibrary.org/obo/HOM_0000032, ISBN:978-0674639416] -synonym: "juvenilization" EXACT [] -synonym: "neotenous to" EXACT [] -is_symmetric: true -is_a: RO:HOM0000029 ! in paedomorphorsis relationship with - -[Typedef] -id: RO:HOM0000033 -name: in mimicry relationship with -def: "Convergence that results from co-evolution usually involving an evolutionary arms race." [http://purl.obolibrary.org/obo/HOM_0000033, http:\://en.wikipedia.org/wiki/Mimicry] -synonym: "mimicrous to" EXACT [] -is_symmetric: true -is_a: RO:HOM0000004 ! in convergence relationship with - -[Typedef] -id: RO:HOM0000034 -name: in 1 to many orthology relationship with -def: "Orthology that involves two genes when duplications more recent than the species split have occurred in one species but not the other." [http://dx.doi.org/10.1038/415741a, http://purl.obolibrary.org/obo/HOM_0000034, http://www.ensembl.org/info/docs/compara/homology_method.html] -synonym: "1 to many orthologous to" EXACT [] -synonym: "1:many orthology" EXACT [] -synonym: "co-orthology" RELATED [] -synonym: "many to 1 orthology" RELATED [] -synonym: "one-to-many orthology" EXACT [] -is_symmetric: true -is_a: RO:HOM0000017 ! in orthology relationship with -is_a: RO:HOM0000037 ! in 1 to many homology relationship with - -[Typedef] -id: RO:HOM0000036 -name: in many to many homology relationship with -def: "Historical homology that involves two members of a larger set of homologs." [http://dx.doi.org/10.1093/molbev/msp002, http://purl.obolibrary.org/obo/HOM_0000036] -synonym: "many to many homologous to" EXACT [] -synonym: "many-to-many homology" EXACT [] -synonym: "many:many homology " EXACT [] -is_symmetric: true -is_a: RO:HOM0000007 ! in historical homology relationship with - -[Typedef] -id: RO:HOM0000037 -name: in 1 to many homology relationship with -def: "Historical homology that involves a structure that has no other homologs in the species in which it is defined, and several homologous structures in another species." [BGEE:curator, http://purl.obolibrary.org/obo/HOM_0000037] -synonym: "1 to many homologous to" EXACT [] -synonym: "1:many homology" RELATED [] -synonym: "one-to-many homology" EXACT [] -is_symmetric: true -is_a: RO:HOM0000007 ! in historical homology relationship with - -[Typedef] -id: RO:HOM0000042 -name: in apomorphy relationship with -def: "Historical homology that is based on recent shared ancestry, characterizing a monophyletic group." [http://purl.obolibrary.org/obo/HOM_0000042, ISBN:978-0252068140] -synonym: "apomorphous to" EXACT [] -synonym: "synapomorphy" RELATED [] -is_symmetric: true -is_a: RO:HOM0000007 ! in historical homology relationship with -disjoint_from: RO:HOM0000043 ! in plesiomorphy relationship with - -[Typedef] -id: RO:HOM0000043 -name: in plesiomorphy relationship with -def: "Historical homology that is based on distant shared ancestry." [http://purl.obolibrary.org/obo/HOM_0000043, ISBN:978-0252068140] -synonym: "plesiomorphous to" EXACT [] -synonym: "symplesiomorphy" RELATED [] -is_symmetric: true -is_a: RO:HOM0000007 ! in historical homology relationship with - -[Typedef] -id: RO:HOM0000044 -name: in deep homology relationship with -def: "Homocracy that involves morphologically and phylogenetically disparate structures that are the result of parallel evolution." [http://dx.doi.org/10.1007/BF02814485, http://dx.doi.org/10.1038/nature07891, http://purl.obolibrary.org/obo/HOM_0000044] -synonym: "deep genetic homology" EXACT [] -synonym: "deep homologous to" EXACT [] -synonym: "generative homology" RELATED [] -synonym: "homoiology" RELATED [] -is_symmetric: true -is_a: RO:HOM0000003 ! in homocracy relationship with -is_a: RO:HOM0000005 ! in parallelism relationship with - -[Typedef] -id: RO:HOM0000045 -name: in hemiplasy relationship with -def: "Historical homology that is characterized by topological discordance between a gene tree and a species tree attributable to the phylogenetic sorting of genetic polymorphisms across successive nodes in a species tree." [http://dx.doi.org/10.1073/pnas.0807433105, http://purl.obolibrary.org/obo/HOM_0000045] -synonym: "hemiplasous to" EXACT [] -is_symmetric: true -is_a: RO:HOM0000007 ! in historical homology relationship with - -[Typedef] -id: RO:HOM0000046 -name: in gametology relationship with -def: "Historical homology that involves not recombining and subsequently differentiated sex chromosomes." [http://purl.obolibrary.org/obo/HOM_0000046, http://www.ncbi.nlm.nih.gov/pubmed/11110898] -synonym: "gametologous to" EXACT [] -is_symmetric: true -is_a: RO:HOM0000047 ! in chromosomal homology relationship with - -[Typedef] -id: RO:HOM0000047 -name: in chromosomal homology relationship with -def: "Historical homology that involves the chromosomes able to pair (synapse) during meiosis." [http://purl.obolibrary.org/obo/HOM_0000047, ISBN:0195307615] -synonym: "chromosomal homologous to" EXACT [] -is_symmetric: true -is_a: RO:HOM0000007 ! in historical homology relationship with - -[Typedef] -id: RO:HOM0000048 -name: in many to many orthology relationship with -def: "Orthology that involves two genes that experienced duplications more recent than the species split that created them." [http://dx.doi.org/10.1038/415741a, http://purl.obolibrary.org/obo/HOM_0000048, http://www.ensembl.org/info/docs/compara/homology_method.html] -synonym: "co-orthology" RELATED [] -synonym: "many to many orthologous to" EXACT [] -synonym: "many-to-many orthology" EXACT [] -synonym: "many:many orthology" EXACT [] -synonym: "trans-homology" RELATED [] -synonym: "trans-orthology" EXACT [] -is_symmetric: true -is_a: RO:HOM0000017 ! in orthology relationship with -is_a: RO:HOM0000036 ! in many to many homology relationship with - -[Typedef] -id: RO:HOM0000049 -name: in within-species paralogy relationship with -def: "Paralogy that involves genes from the same species." [http://purl.obolibrary.org/obo/HOM_0000049, http://www.ensembl.org/info/docs/compara/homology_method.html] -synonym: "within-species paralogous to" EXACT [] -is_symmetric: true -is_a: RO:HOM0000011 ! in paralogy relationship with -disjoint_from: RO:HOM0000050 ! in between-species paralogy relationship with - -[Typedef] -id: RO:HOM0000050 -name: in between-species paralogy relationship with -def: "Paralogy that involves genes from different species." [http://purl.obolibrary.org/obo/HOM_0000050, http://www.ensembl.org/info/docs/compara/homology_method.html] -synonym: "between-species paralogous to" EXACT [] -is_symmetric: true -is_a: RO:HOM0000011 ! in paralogy relationship with - -[Typedef] -id: RO:HOM0000051 -name: in postdisplacement relationship with -def: "Paedomorphosis that is produced by delayed growth of immature structures into the adult form." [http://en.wikipedia.org/wiki/Pedomorphosis, http://purl.obolibrary.org/obo/HOM_0000051] -synonym: "post-displacement" EXACT [] -is_symmetric: true -is_a: RO:HOM0000029 ! in paedomorphorsis relationship with - -[Typedef] -id: RO:HOM0000052 -name: in hypermorphosis relationship with -def: "Peramorphosis that is produced by a delay in the offset of development." [http://en.wikipedia.org/wiki/Peramorphosis, http://purl.obolibrary.org/obo/HOM_0000052, ISBN:978-0674639416] -is_symmetric: true -is_a: RO:HOM0000030 ! in peramorphosis relationship with - -[Typedef] -id: RO:HOM0000053 -name: in synology relationship with -def: "Xenology that results, not from the transfer of a gene between two species, but from a hybridization of two species." [http://dx.doi.org/10.1007/BF00173425, http://dx.doi.org/10.1016/S0168-9525(00)02005-9, http://purl.obolibrary.org/obo/HOM_0000053] -synonym: "synologous to" EXACT [] -is_symmetric: true -is_a: RO:HOM0000018 ! in xenology relationship with - -[Typedef] -id: RO:HOM0000054 -name: in isoorthology relationship with -def: "Orthology that involves functional equivalent genes with retention of the ancestral function." [http://dx.doi.org/10.1016/S0168-9525(00)02005-9, http://purl.obolibrary.org/obo/HOM_0000054] -synonym: "isoorthologous to" EXACT [] -is_symmetric: true -is_a: RO:HOM0000017 ! in orthology relationship with -is_a: RO:HOM0000062 ! in equivalogy relationship with - -[Typedef] -id: RO:HOM0000055 -name: in tandem paralogy relationship with -def: "Paralogy that is characterized by duplication of adjacent sequences on a chromosome segment." [http://dx.doi.org/10.1016/S0168-9525(00)02005-9, http://purl.obolibrary.org/obo/HOM_0000055, ISBN:978-0878932665] -synonym: "iterative paralogy" RELATED [] -synonym: "serial paralogy" RELATED [] -synonym: "tandem paralogous to" EXACT [] -is_symmetric: true -is_a: RO:HOM0000011 ! in paralogy relationship with - -[Typedef] -id: RO:HOM0000057 -name: in latent homology relationship with -def: "Parallelism that involves morphologically very similar structures, occurring only within some members of a taxon and absent in the common ancestor (which possessed the developmental basis to develop this character)." [http://dx.doi.org/10.1007/BF02814485, http://dx.doi.org/10.1016/j.jhevol.2006.11.010, http://dx.doi.org/10.1186/1742-9994-2-15, http://purl.obolibrary.org/obo/HOM_0000057, ISBN:0199141118] -synonym: "apomorphic tendency" EXACT [] -synonym: "cryptic homology" EXACT [] -synonym: "homoiology" RELATED [] -synonym: "homoplastic tendency" RELATED [] -synonym: "latent homologous to" EXACT [] -synonym: "re-awakening" RELATED [] -synonym: "underlying synapomorphy" EXACT [] -is_symmetric: true -is_a: RO:HOM0000005 ! in parallelism relationship with -is_a: RO:HOM0000058 ! in syngeny relationship with - -[Typedef] -id: RO:HOM0000058 -name: in syngeny relationship with -def: "Homocracy that involves recognizably corresponding characters that occurs in two or more taxa, or as a repeated unit within an individual." [DOI:10.1002/1521-1878(200009)22\:9<846\:\:AID-BIES10>3.0.CO;2-R, http://dx.doi.org/10.1186/1742-9994-2-15, http://purl.obolibrary.org/obo/HOM_0000058] -synonym: "generative homology" EXACT [] -synonym: "syngenous to" EXACT [] -is_symmetric: true -is_a: RO:HOM0000003 ! in homocracy relationship with - -[Typedef] -id: RO:HOM0000060 -name: in apparent orthology relationship with -def: "Between-species paralogy that involves single copy paralogs resulting from reciprocal gene loss." [http://dx.doi.org/10.1146/annurev.genet.39.073003.114725, http://purl.obolibrary.org/obo/HOM_0000060, http://www.ensembl.org/info/docs/compara/homology_method.html] -synonym: "1:1 paralogy" EXACT [] -synonym: "apparent 1:1 orthology" EXACT [] -synonym: "apparent orthologous to" EXACT [] -synonym: "pseudoorthology" EXACT [] -is_symmetric: true -is_a: RO:HOM0000019 ! in 1 to 1 homology relationship with -is_a: RO:HOM0000050 ! in between-species paralogy relationship with - -[Typedef] -id: RO:HOM0000061 -name: in pseudoparalogy relationship with -def: "Xenology that involves genes that ended up in a given genome as a result of a combination of vertical inheritance and horizontal gene transfer." [http://dx.doi.org/10.1146/annurev.genet.39.073003.114725, http://purl.obolibrary.org/obo/HOM_0000061] -synonym: "pseudoparalogous to" EXACT [] -is_symmetric: true -is_a: RO:HOM0000018 ! in xenology relationship with - -[Typedef] -id: RO:HOM0000062 -name: in equivalogy relationship with -def: "Historical homology that involves functional equivalent genes with retention of the ancestral function." [http://dx.doi.org/10.1093/nar/gkl1043, http://purl.obolibrary.org/obo/HOM_0000062] -synonym: "equivalogous to" EXACT [] -is_symmetric: true -is_a: RO:HOM0000007 ! in historical homology relationship with -is_a: RO:HOM0000065 ! in functional equivalence relationship with - -[Typedef] -id: RO:HOM0000063 -name: in interology relationship with -def: "Historical homology that involves orthologous pairs of interacting molecules in different organisms." [http://dx.doi.org/10.1101/gr.1774904, http://dx.doi.org/10.1126/science.287.5450.116, http://purl.obolibrary.org/obo/HOM_0000063] -synonym: "interologous to" EXACT [] -is_symmetric: true -is_a: RO:HOM0000007 ! in historical homology relationship with - -[Typedef] -id: RO:HOM0000065 -name: in functional equivalence relationship with -def: "Similarity that is characterized by interchangeability in function." [http://dx.doi.org/10.1007/BF02814484, http://dx.doi.org/10.1038/415741a, http://purl.obolibrary.org/obo/HOM_0000065] -synonym: "functional similarity" RELATED [] -is_symmetric: true -is_a: RO:HOM0000000 ! in similarity relationship with - -[Typedef] -id: RO:HOM0000066 -name: in iterative homology relationship with -def: "Biological homology that involves parts of the same organism." [http://dx.doi.org/10.1146/annurev.es.20.110189.000411, http://purl.obolibrary.org/obo/HOM_0000066] -synonym: "iterative homologous to" EXACT [] -is_symmetric: true -is_a: RO:HOM0000008 ! in biological homology relationship with - -[Typedef] -id: RO:HOM0000068 -name: in paraxenology relationship with -def: "Xenology that is characterized by multiple horizontal transfer events, resulting in the presence of two or more copies of the foreign gene in the host genome." [http://purl.obolibrary.org/obo/HOM_0000068, http://www.ncbi.nlm.nih.gov/pubmed/3065587] -synonym: "duplicate xenology" EXACT [] -synonym: "multiple xenology" EXACT [] -synonym: "paraxenologous to" EXACT [] -is_symmetric: true -is_a: RO:HOM0000018 ! in xenology relationship with - -[Typedef] -id: RO:HOM0000069 -name: in plerology relationship with -def: "Paralogy that is characterized by extra similarity between paralogous sequences resulting from concerted evolution." [http://purl.obolibrary.org/obo/HOM_0000069, http://www.ncbi.nlm.nih.gov/pubmed/3065587] -synonym: "plerologous to" EXACT [] -is_symmetric: true -is_a: RO:HOM0000011 ! in paralogy relationship with - -[Typedef] -id: RO:HOM0000071 -name: in homotopy relationship with -def: "Structural homology that involves structures with the same or similar relative positions." [http://dx.doi.org/10.1007/BF02814484, http://dx.doi.org/10.1007/BF02814485, http://purl.obolibrary.org/obo/HOM_0000071, ISBN:0123195837] -synonym: "homotopous to" EXACT [] -is_symmetric: true -is_a: RO:HOM0000006 ! in structural homology relationship with -disjoint_from: RO:HOM0000072 ! in homeosis relationship with - -[Typedef] -id: RO:HOM0000072 -name: in homeosis relationship with -def: "Biological homology that involves an ectopic structure and the normally positioned structure." [http://dx.doi.org/10.1007/BF02814485, http://dx.doi.org/10.1016/j.cell.2008.06.030, http://purl.obolibrary.org/obo/HOM_0000072] -synonym: "heterotopy" RELATED [] -is_symmetric: true -is_a: RO:HOM0000008 ! in biological homology relationship with - -[Typedef] -id: RO:HOM0000073 -name: in homoeology relationship with -def: "Synology that results from allopolyploidy." [http://dx.doi.org/10.1073/pnas.0505156102, http://purl.obolibrary.org/obo/HOM_0000073] -synonym: "homoeologous to" EXACT [] -is_symmetric: true -is_a: RO:HOM0000022 ! in ohnology relationship with -is_a: RO:HOM0000053 ! in synology relationship with - -[Typedef] -id: RO:HOM0000074 -name: in paramorphism relationship with -def: "Iterative homology that involves two structures, one of which originated as a duplicate of the other and co-opted the expression of patterning genes of the ancestral structure." [http://dx.doi.org/10.1007/s10441-007-9023-8, http://dx.doi.org/10.1046/j.1525-142x.2000.00054.x, http://purl.obolibrary.org/obo/HOM_0000074] -synonym: "axis paramorphism" RELATED [] -is_symmetric: true -is_a: RO:HOM0000003 ! in homocracy relationship with -is_a: RO:HOM0000066 ! in iterative homology relationship with - -[Typedef] -id: RO:HOM0000075 -name: in regulogy relationship with -def: "Historical homology that involves orthologous pairs of transcription factors and downstream regulated genes in different organisms." [http://dx.doi.org/10.1101/gr.1774904, http://purl.obolibrary.org/obo/HOM_0000075] -synonym: "regulogous to" EXACT [] -is_symmetric: true -is_a: RO:HOM0000007 ! in historical homology relationship with - -[Typedef] -id: results_in_acquisition_of_features_of -name: results in acquisition of features of -def: "The relationship that links a specified entity with the process that results in an unspecified entity acquiring the features and characteristics of the specified entity" [] -is_a: results_in_developmental_progression_of ! results in developmental progression of -is_a: RO:0000057 ! has participant - -[Typedef] -id: results_in_development_of -name: results in development of -def: "p 'results in development of' c if and only if p is a developmental process and p results in the state of c changing from its initial state as a primordium or anlage through its mature state and to its final state." [] -is_a: results_in_developmental_progression_of ! results in developmental progression of -is_a: RO:0000057 ! has participant - -[Typedef] -id: results_in_developmental_progression_of -name: results in developmental progression of -def: "p results in the developmental progression of s iff p is a developmental process and s is an anatomical structure and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss)." [] -is_a: RO:0002324 ! developmentally related to - -[Typedef] -id: results_in_disappearance_of -name: results in disappearance of -is_a: RO:0002552 ! results in ending of - -[Typedef] -id: results_in_formation_of -name: results in formation of -is_a: results_in_developmental_progression_of ! results in developmental progression of -is_a: RO:0002234 ! has output - -[Typedef] -id: results_in_maturation_of -name: results in maturation of -def: "The relationship that links an entity with a process that results in the progression of the entity over time that is independent of changes in it's shape and results in an end point state of that entity." [] -is_a: results_in_developmental_progression_of ! results in developmental progression of -is_a: RO:0000057 ! has participant - -[Typedef] -id: results_in_morphogenesis_of -name: results in morphogenesis of -def: "The relationship that links an entity with the process that results in the formation and shaping of that entity over time from an immature to a mature state." [] -is_a: results_in_developmental_progression_of ! results in developmental progression of -is_a: RO:0000057 ! has participant - diff --git a/src/ontology/subsets/ro-developmental.obo b/src/ontology/subsets/ro-developmental.obo index 2dc49ef5..76d738aa 100644 --- a/src/ontology/subsets/ro-developmental.obo +++ b/src/ontology/subsets/ro-developmental.obo @@ -1,6 +1,6 @@ format-version: 1.2 ontology: ro/subsets/ro-developmental -owl-axioms: Prefix(owl:=)\nPrefix(rdf:=)\nPrefix(xml:=)\nPrefix(xsd:=)\nPrefix(rdfs:=)\n\n\nOntology(\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\n\n############################\n# Object Properties\n############################\n\n# Object Property: (coincident with)\n\nObjectPropertyRange( ObjectIntersectionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (has fasciculating neuron projection)\n\nObjectPropertyRange( ObjectUnionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (connected to)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (connects)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (directly develops from)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (anabranch of)\n\nSubObjectPropertyOf( ObjectInverseOf())\n\n# Object Property: (branching part of)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (condition has genetic basis in)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has basis in feature)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has location)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has feature)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n\n\n\nAnnotationAssertion(rdfs:comment \"\")\n) +owl-axioms: Prefix(owl:=)\nPrefix(rdf:=)\nPrefix(xml:=)\nPrefix(xsd:=)\nPrefix(rdfs:=)\n\n\nOntology(\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\n\n############################\n# Object Properties\n############################\n\n# Object Property: (coincident with)\n\nObjectPropertyRange( ObjectIntersectionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (has fasciculating neuron projection)\n\nObjectPropertyRange( ObjectUnionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (connected to)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (connects)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (directly develops from)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (anabranch of)\n\nSubObjectPropertyOf( ObjectInverseOf())\n\n# Object Property: (branching part of)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (condition has genetic basis in)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has basis in feature)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has location)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has feature)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (has anatomical participant)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n\n\n\nAnnotationAssertion(rdfs:comment \"\")\n) [Typedef] id: 2D_boundary_of @@ -327,6 +327,7 @@ def: "c stands in this relationship to p if and only if there exists some p' suc xref: RO:0002216 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "has function in" xsd:string +property_value: seeAlso "defining-property-chains-involving-reflexivity" is_a: causal_agent_in_process ! causal agent in process is_a: functionally_related_to ! functionally related to expand_expression_to: "RO_0000053 some (RO_0000054 only (BFO_0000050 some ?Y))" [] @@ -948,7 +949,7 @@ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 "EHDAA2" xsd:string property_value: IAO:0000119 "Jonathan Bard, EHDAA2" xsd:string -domain: CARO:0000003 +domain: CARO:0000000 is_a: developmentally_preceded_by ! developmentally preceded by [Typedef] @@ -1449,6 +1450,15 @@ property_value: IAO:0000112 "penicillin allergy (DOID:0060520) has allergic trig range: BFO:0000040 is_a: causes_or_contributes_to_condition ! causes or contributes to condition +[Typedef] +id: has_anatomical_participant +name: has anatomical participant +def: "p has anatomical participant c iff p has participant c, and c is an anatomical entity" [] +xref: RO:0040036 +is_a: has_participant +created_by: cjm +creation_date: 2018-09-26T01:08:58Z + [Typedef] id: has_autoimmune_trigger name: has autoimmune trigger @@ -1522,8 +1532,8 @@ xref: RO:0002254 property_value: IAO:0000112 "Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string -domain: BFO:0000004 -range: CARO:0000003 +domain: CARO:0000000 +range: CARO:0000000 is_a: developmentally_preceded_by ! developmentally preceded by inverse_of: developmentally_contributes_to ! developmentally contributes to @@ -1534,6 +1544,8 @@ def: "x has developmental potential involving y iff x is capable of a developmen xref: RO:0002384 property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Chris Mungall" xsd:string +domain: CARO:0000000 +range: CARO:0000000 is_a: developmentally_related_to ! developmentally related to [Typedef] @@ -2069,6 +2081,7 @@ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string property_value: RO:0001900 RO:0001901 domain: CL:0000540 +range: CARO:0000003 is_a: overlaps ! overlaps expand_expression_to: "BFO_0000051 some (\n GO_0043025 and BFO_0000050 some ?Y)" [] @@ -2324,6 +2337,8 @@ name: innervated_by xref: RO:0002005 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 xsd:anyURI property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +domain: CARO:0000003 +range: CARO:0001001 inverse_of: innervates ! innervates [Typedef] @@ -2422,6 +2437,7 @@ id: involved_in_or_involved_in_regulation_of name: involved in or involved in regulation of def: "c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p" [] xref: RO:0002431 +property_value: IAO:0000116 "OWL does not allow defining object properties via a Union" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "involved in or reguates" xsd:string is_a: acts_upstream_of_or_within ! acts upstream of or within @@ -2861,16 +2877,6 @@ def: "A sub-relation of parasite-of in which the parasite that cannot complete i xref: RO:0002227 is_a: parasite_of ! parasite of -[Typedef] -id: obsolete_has_indirect_output -name: obsolete has indirect output -comment: Likely to be obsoleted. See:\nhttps://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/edit -xref: RO:0002403 -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string -is_a: has_output ! has output -is_obsolete: true - [Typedef] id: occurent_part_of name: occurent part of @@ -3313,6 +3319,7 @@ name: releases neurotransmitter xref: RO:0002111 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000118 "has neurotransmitter" xsd:string +domain: CARO:0000003 [Typedef] id: represses_expression_of @@ -3330,8 +3337,8 @@ xref: RO:0002315 property_value: IAO:0000112 "an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast." xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string -range: CL:0000000 -is_a: has_participant +range: CARO:0000003 +is_a: has_anatomical_participant ! has anatomical participant is_a: results_in_developmental_progression_of ! results in developmental progression of [Typedef] @@ -3360,7 +3367,7 @@ id: results_in_closure_of name: results in closure of xref: RO:0002585 property_value: IAO:0000116 "p 'results in closure of' c if and only if p is a developmental process and p results in a state of c changing from open to closed." xsd:string -is_a: has_participant +is_a: has_anatomical_participant ! has anatomical participant is_a: results_in_developmental_progression_of ! results in developmental progression of [Typedef] @@ -3393,7 +3400,7 @@ property_value: IAO:0000112 "every flower development (GO:0009908) results in de property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://www.geneontology.org/GO.doc.development.shtml xsd:anyURI -is_a: has_participant +is_a: has_anatomical_participant ! has anatomical participant is_a: results_in_developmental_progression_of ! results in developmental progression of [Typedef] @@ -3450,7 +3457,7 @@ name: results in ending of def: "p results in the end of s if p results in a change of state in s whereby s either ceases to exist, or s becomes functionally impaired or s has its fate committed such that it is put on a path to be degraded." [] xref: RO:0002552 property_value: IAO:0000117 "Chris Mungall" xsd:string -is_a: has_participant +is_a: has_anatomical_participant ! has anatomical participant is_a: results_in_developmental_progression_of ! results in developmental progression of [Typedef] @@ -3472,7 +3479,7 @@ name: results in growth of xref: RO:0002343 property_value: IAO:0000112 "'pollen tube growth' results_in growth_of some 'pollen tube'" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string -is_a: has_participant +is_a: has_anatomical_participant ! has anatomical participant is_a: results_in_developmental_progression_of ! results in developmental progression of [Typedef] @@ -3485,7 +3492,7 @@ property_value: IAO:0000112 "bone maturation (GO:0070977) results_in_maturation_ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string -is_a: has_participant +is_a: has_anatomical_participant ! has anatomical participant is_a: results_in_developmental_progression_of ! results in developmental progression of [Typedef] @@ -3498,7 +3505,7 @@ property_value: IAO:0000112 "tongue morphogenesis (GO:0043587) results in morpho property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string -is_a: has_participant +is_a: has_anatomical_participant ! has anatomical participant is_a: results_in_developmental_progression_of ! results in developmental progression of [Typedef] @@ -3508,14 +3515,14 @@ def: "Holds between p and c when p is locomotion process and the outcome of this xref: RO:0002565 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000232 "" xsd:string -is_a: has_participant +is_a: has_anatomical_participant ! has anatomical participant [Typedef] id: results_in_organization_of name: results in organization of def: "p results in organization of c iff p results in the assembly, arrangement of constituent parts, or disassembly of c" [] xref: RO:0002592 -is_a: has_participant +is_a: has_anatomical_participant ! has anatomical participant [Typedef] id: results_in_remodeling_of @@ -3540,7 +3547,7 @@ name: results in structural organization of def: "A relationship between a process and an anatomical entity such that the process contributes to the act of creating the structural organization of the anatomical entity." [] xref: RO:0002355 property_value: IAO:0000117 "Chris Mungall" xsd:string -is_a: has_participant +is_a: has_anatomical_participant ! has anatomical participant is_a: results_in_developmental_progression_of ! results in developmental progression of [Typedef] @@ -3790,7 +3797,7 @@ def: "Holds between p and c when p is a localization process (localization cover xref: RO:0002313 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "regulates localization of" xsd:string -is_a: has_participant +is_a: has_anatomical_participant ! has anatomical participant is_a: related_via_localization_to ! related via localization to [Typedef] diff --git a/src/ontology/subsets/ro-developmental.owl b/src/ontology/subsets/ro-developmental.owl index d8362155..19e36944 100644 --- a/src/ontology/subsets/ro-developmental.owl +++ b/src/ontology/subsets/ro-developmental.owl @@ -381,6 +381,8 @@ + + David Osumi-Sutherland http://www.ncbi.nlm.nih.gov/pubmed/22402613 RO:0002005 @@ -787,6 +789,7 @@ Examples include: the relationship between two channels collected simultaneously + Relation between a neuron and an anatomical structure that its soma is part of. David Osumi-Sutherland @@ -931,6 +934,7 @@ Examples include: the relationship between two channels collected simultaneously + has neurotransmitter RO:0002111 @@ -1548,6 +1552,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.RO:0002216 capable_of_part_of capable of part of + @@ -1700,7 +1705,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - + x develops_in y if x is located in y whilst x is developing Chris Mungall @@ -1995,8 +2000,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - - + + Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong] x has developmental contribution from y iff x has some part z such that z develops from y @@ -2177,8 +2182,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - + every flower development (GO:0009908) results in development of some flower (PO:0009046) p 'results in development of' c if and only if p is a developmental process and p results in the state of c changing from its initial state as a primordium or anlage through its mature state and to its final state. @@ -2212,8 +2217,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - + an annotation of gene X to cell morphogenesis with results_in_morphogenesis_of CL:0000540 (neuron) means that at the end of the process an input neuron has attained its shape. tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723) @@ -2230,8 +2235,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - + an annotation of gene X to cell maturation with results_in_maturation_of CL:0000057 (fibroblast) means that the fibroblast is mature at the end of the process bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474) @@ -2362,8 +2367,8 @@ where - + Holds between p and c when p is a localization process (localization covers maintenance of localization as well as its establishment) and the outcome of this process is to regulate the localization of c. Chris Mungall regulates localization of @@ -2377,9 +2382,9 @@ where - - + + an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast. The relationship that links a specified entity with the process that results in an unspecified entity acquiring the features and characteristics of the specified entity Chris Mungall @@ -2720,8 +2725,8 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - + 'pollen tube growth' results_in growth_of some 'pollen tube' Chris Mungall RO:0002343 @@ -2834,8 +2839,8 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - + A relationship between a process and an anatomical entity such that the process contributes to the act of creating the structural organization of the anatomical entity. Chris Mungall RO:0002355 @@ -3126,6 +3131,8 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + + x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction). Chris Mungall @@ -3209,22 +3216,6 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - - - - - - Chris Mungall - RO:0002403 - obsolete_has_indirect_output - Likely to be obsoleted. See: -https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/edit - obsolete has indirect output - true - - - - @@ -3501,6 +3492,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p + OWL does not allow defining object properties via a Union Chris Mungall involved in or reguates RO:0002431 @@ -4675,8 +4667,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + p results in the end of s if p results in a change of state in s whereby s either ceases to exist, or s becomes functionally impaired or s has its fate committed such that it is put on a path to be degraded. Chris Mungall RO:0002552 @@ -4785,7 +4777,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c Chris Mungall @@ -4972,8 +4964,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + p 'results in closure of' c if and only if p is a developmental process and p results in a state of c changing from open to closed. RO:0002585 results_in_closure_of @@ -5056,7 +5048,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + p results in organization of c iff p results in the assembly, arrangement of constituent parts, or disassembly of c RO:0002592 results_in_organization_of @@ -6314,6 +6306,28 @@ Environmental exposures include those imposed by natural environments, experimen + + + + + + + + + + + + + p has anatomical participant c iff p has participant c, and c is an anatomical entity + cjm + 2018-09-26T01:08:58Z + RO:0040036 + has_anatomical_participant + has anatomical participant + + + + @@ -6385,6 +6399,12 @@ Environmental exposures include those imposed by natural environments, experimen + + + + + + diff --git a/src/ontology/subsets/ro-eco.obo b/src/ontology/subsets/ro-eco.obo index 477804ba..8d0712cc 100644 --- a/src/ontology/subsets/ro-eco.obo +++ b/src/ontology/subsets/ro-eco.obo @@ -1000,6 +1000,7 @@ name: capable of part of def: "c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p." [] property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "has function in" xsd:string +property_value: seeAlso "defining-property-chains-involving-reflexivity" holds_over_chain: RO:0002215 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"} is_a: RO:0002328 ! functionally related to is_a: RO:0002500 ! causal agent in process @@ -1458,6 +1459,7 @@ def: "Holds between p and c when p is a localization process (localization cover property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "regulates localization of" xsd:string is_a: RO:0002337 ! related via localization to +is_a: RO:0040036 ! has anatomical participant [Typedef] id: RO:0002314 @@ -1467,6 +1469,7 @@ property_value: IAO:0000116 "Because part_of is transitive, inheres in is a sub- property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 property_value: RO:0001900 RO:0001901 +property_value: seeAlso "defining-property-chains-involving-reflexivity" is_a: RO:0002502 ! depends on transitive_over: BFO:0000050 @@ -1679,6 +1682,7 @@ name: results in growth of property_value: IAO:0000112 "'pollen tube growth' results_in growth_of some 'pollen tube'" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: results_in_developmental_progression_of ! results in developmental progression of +is_a: RO:0040036 ! has anatomical participant [Typedef] id: RO:0002344 @@ -1740,6 +1744,7 @@ name: results in structural organization of def: "A relationship between a process and an anatomical entity such that the process contributes to the act of creating the structural organization of the anatomical entity." [] property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: results_in_developmental_progression_of ! results in developmental progression of +is_a: RO:0040036 ! has anatomical participant [Typedef] id: RO:0002356 @@ -1991,7 +1996,6 @@ comment: Likely to be obsoleted. See:\nhttps://docs.google.com/document/d/1QMhs9 property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Chris Mungall" xsd:string holds_over_chain: RO:0002411 RO:0002402 -is_a: RO:0002234 ! has output is_obsolete: true [Typedef] @@ -2188,6 +2192,7 @@ is_a: RO:0002428 ! involved in regulation of id: RO:0002431 name: involved in or involved in regulation of def: "c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p" [] +property_value: IAO:0000116 "OWL does not allow defining object properties via a Union" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "involved in or reguates" xsd:string is_a: RO:0002264 ! acts upstream of or within @@ -2517,7 +2522,7 @@ is_a: RO:0002461 ! partner in [Typedef] id: RO:0002464 -name: helper property +name: helper property (not for use in curation) property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000232 "This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning." xsd:string @@ -3093,6 +3098,7 @@ name: results in ending of def: "p results in the end of s if p results in a change of state in s whereby s either ceases to exist, or s becomes functionally impaired or s has its fate committed such that it is put on a path to be degraded." [] property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: results_in_developmental_progression_of ! results in developmental progression of +is_a: RO:0040036 ! has anatomical participant [Typedef] id: RO:0002553 @@ -3173,7 +3179,7 @@ name: interaction relation helper property property_value: http://xmlns.com/foaf/0.1/page https://github.com/oborel/obo-relations/wiki/InteractionRelations xsd:anyURI property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:N-Ary_Relation_Pattern_%28OWL_2%29 -is_a: RO:0002464 ! helper property +is_a: RO:0002464 ! helper property (not for use in curation) [Typedef] id: RO:0002564 @@ -3187,6 +3193,7 @@ name: results in movement of def: "Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c" [] property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000232 "" xsd:string +is_a: RO:0040036 ! has anatomical participant [Typedef] id: RO:0002566 @@ -3305,6 +3312,7 @@ id: RO:0002585 name: results in closure of property_value: IAO:0000116 "p 'results in closure of' c if and only if p is a developmental process and p results in a state of c changing from open to closed." xsd:string is_a: results_in_developmental_progression_of ! results in developmental progression of +is_a: RO:0040036 ! has anatomical participant [Typedef] id: RO:0002586 @@ -3345,6 +3353,7 @@ is_a: RO:0002592 ! results in organization of id: RO:0002592 name: results in organization of def: "p results in organization of c iff p results in the assembly, arrangement of constituent parts, or disassembly of c" [] +is_a: RO:0040036 ! has anatomical participant [Typedef] id: RO:0002593 @@ -4155,6 +4164,13 @@ property_value: IAO:0000232 "Do not use this relation directly. It is intended a created_by: cjm creation_date: 2018-09-26T00:00:32Z +[Typedef] +id: RO:0040036 +name: has anatomical participant +def: "p has anatomical participant c iff p has participant c, and c is an anatomical entity" [] +created_by: cjm +creation_date: 2018-09-26T01:08:58Z + [Typedef] id: results_in_acquisition_of_features_of name: results in acquisition of features of @@ -4163,6 +4179,7 @@ property_value: IAO:0000112 "an annotation of gene X to cell differentiation wit property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string is_a: results_in_developmental_progression_of ! results in developmental progression of +is_a: RO:0040036 ! has anatomical participant [Typedef] id: results_in_development_of @@ -4173,6 +4190,7 @@ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://www.geneontology.org/GO.doc.development.shtml xsd:anyURI is_a: results_in_developmental_progression_of ! results in developmental progression of +is_a: RO:0040036 ! has anatomical participant [Typedef] id: results_in_developmental_progression_of @@ -4215,6 +4233,7 @@ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string is_a: results_in_developmental_progression_of ! results in developmental progression of +is_a: RO:0040036 ! has anatomical participant [Typedef] id: results_in_morphogenesis_of @@ -4226,4 +4245,5 @@ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string is_a: results_in_developmental_progression_of ! results in developmental progression of +is_a: RO:0040036 ! has anatomical participant diff --git a/src/ontology/subsets/ro-eco.owl b/src/ontology/subsets/ro-eco.owl index 5d321e09..b3724f2b 100644 --- a/src/ontology/subsets/ro-eco.owl +++ b/src/ontology/subsets/ro-eco.owl @@ -2555,6 +2555,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.has function in RO_0000053 some (RO_0000054 only (BFO_0000050 some ?Y)) capable of part of + @@ -3175,6 +3176,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. + every flower development (GO:0009908) results in development of some flower (PO:0009046) p 'results in development of' c if and only if p is a developmental process and p results in the state of c changing from its initial state as a primordium or anlage through its mature state and to its final state. @@ -3207,6 +3209,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. + an annotation of gene X to cell morphogenesis with results_in_morphogenesis_of CL:0000540 (neuron) means that at the end of the process an input neuron has attained its shape. tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723) @@ -3223,6 +3226,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. + an annotation of gene X to cell maturation with results_in_maturation_of CL:0000057 (fibroblast) means that the fibroblast is mature at the end of the process bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474) @@ -3348,6 +3352,7 @@ where + Holds between p and c when p is a localization process (localization covers maintenance of localization as well as its establishment) and the outcome of this process is to regulate the localization of c. Chris Mungall regulates localization of @@ -3370,6 +3375,7 @@ where inheres in part of + @@ -3378,6 +3384,7 @@ where + an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast. The relationship that links a specified entity with the process that results in an unspecified entity acquiring the features and characteristics of the specified entity Chris Mungall @@ -3724,6 +3731,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + 'pollen tube growth' results_in growth_of some 'pollen tube' Chris Mungall results in growth of @@ -3817,6 +3825,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + A relationship between a process and an anatomical entity such that the process contributes to the act of creating the structural organization of the anatomical entity. Chris Mungall results in structural organization of @@ -4178,7 +4187,6 @@ https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/ - @@ -4522,6 +4530,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p + OWL does not allow defining object properties via a Union Chris Mungall involved in or reguates involved in or involved in regulation of @@ -5047,7 +5056,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different Chris Mungall This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning. - helper property + helper property (not for use in curation) @@ -5942,6 +5951,7 @@ the a supports either the existence of b, or the truth value of b. + p results in the end of s if p results in a change of state in s whereby s either ceases to exist, or s becomes functionally impaired or s has its fate committed such that it is put on a path to be degraded. Chris Mungall results in ending of @@ -6081,6 +6091,7 @@ the a supports either the existence of b, or the truth value of b. + Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c Chris Mungall @@ -6267,6 +6278,7 @@ the a supports either the existence of b, or the truth value of b. + p 'results in closure of' c if and only if p is a developmental process and p results in a state of c changing from open to closed. results in closure of @@ -6335,6 +6347,7 @@ the a supports either the existence of b, or the truth value of b. + p results in organization of c iff p results in the assembly, arrangement of constituent parts, or disassembly of c results in organization of @@ -7606,6 +7619,17 @@ Environmental exposures include those imposed by natural environments, experimen + + + + p has anatomical participant c iff p has participant c, and c is an anatomical entity + cjm + 2018-09-26T01:08:58Z + has anatomical participant + + + + + + true + inverse of has disposition diff --git a/src/ontology/subsets/ro-interaction.obo b/src/ontology/subsets/ro-interaction.obo index 083be570..3e27e98a 100644 --- a/src/ontology/subsets/ro-interaction.obo +++ b/src/ontology/subsets/ro-interaction.obo @@ -1,6 +1,6 @@ format-version: 1.2 ontology: ro/subsets/ro-interaction -owl-axioms: Prefix(owl:=)\nPrefix(rdf:=)\nPrefix(xml:=)\nPrefix(xsd:=)\nPrefix(rdfs:=)\n\n\nOntology(\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\n\n############################\n# Object Properties\n############################\n\n# Object Property: (coincident with)\n\nObjectPropertyRange( ObjectIntersectionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (has fasciculating neuron projection)\n\nObjectPropertyRange( ObjectUnionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (connected to)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (connects)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (directly develops from)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (anabranch of)\n\nSubObjectPropertyOf( ObjectInverseOf())\n\n# Object Property: (branching part of)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (condition has genetic basis in)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has basis in feature)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has location)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has feature)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n\n\n\nAnnotationAssertion(rdfs:comment \"\")\n) +owl-axioms: Prefix(owl:=)\nPrefix(rdf:=)\nPrefix(xml:=)\nPrefix(xsd:=)\nPrefix(rdfs:=)\n\n\nOntology(\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\n\n############################\n# Object Properties\n############################\n\n# Object Property: (coincident with)\n\nObjectPropertyRange( ObjectIntersectionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (has fasciculating neuron projection)\n\nObjectPropertyRange( ObjectUnionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (connected to)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (connects)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (directly develops from)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (anabranch of)\n\nSubObjectPropertyOf( ObjectInverseOf())\n\n# Object Property: (branching part of)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (condition has genetic basis in)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has basis in feature)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has location)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has feature)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (has anatomical participant)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n\n\n\nAnnotationAssertion(rdfs:comment \"\")\n) [Typedef] id: 2D_boundary_of @@ -327,6 +327,7 @@ def: "c stands in this relationship to p if and only if there exists some p' suc xref: RO:0002216 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "has function in" xsd:string +property_value: seeAlso "defining-property-chains-involving-reflexivity" is_a: causal_agent_in_process ! causal agent in process is_a: functionally_related_to ! functionally related to expand_expression_to: "RO_0000053 some (RO_0000054 only (BFO_0000050 some ?Y))" [] @@ -948,7 +949,7 @@ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 "EHDAA2" xsd:string property_value: IAO:0000119 "Jonathan Bard, EHDAA2" xsd:string -domain: CARO:0000003 +domain: CARO:0000000 is_a: developmentally_preceded_by ! developmentally preceded by [Typedef] @@ -1449,6 +1450,15 @@ property_value: IAO:0000112 "penicillin allergy (DOID:0060520) has allergic trig range: BFO:0000040 is_a: causes_or_contributes_to_condition ! causes or contributes to condition +[Typedef] +id: has_anatomical_participant +name: has anatomical participant +def: "p has anatomical participant c iff p has participant c, and c is an anatomical entity" [] +xref: RO:0040036 +is_a: has_participant +created_by: cjm +creation_date: 2018-09-26T01:08:58Z + [Typedef] id: has_autoimmune_trigger name: has autoimmune trigger @@ -1522,8 +1532,8 @@ xref: RO:0002254 property_value: IAO:0000112 "Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string -domain: BFO:0000004 -range: CARO:0000003 +domain: CARO:0000000 +range: CARO:0000000 is_a: developmentally_preceded_by ! developmentally preceded by inverse_of: developmentally_contributes_to ! developmentally contributes to @@ -1534,6 +1544,8 @@ def: "x has developmental potential involving y iff x is capable of a developmen xref: RO:0002384 property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Chris Mungall" xsd:string +domain: CARO:0000000 +range: CARO:0000000 is_a: developmentally_related_to ! developmentally related to [Typedef] @@ -2069,6 +2081,7 @@ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string property_value: RO:0001900 RO:0001901 domain: CL:0000540 +range: CARO:0000003 is_a: overlaps ! overlaps expand_expression_to: "BFO_0000051 some (\n GO_0043025 and BFO_0000050 some ?Y)" [] @@ -2324,6 +2337,8 @@ name: innervated_by xref: RO:0002005 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 xsd:anyURI property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +domain: CARO:0000003 +range: CARO:0001001 inverse_of: innervates ! innervates [Typedef] @@ -2422,6 +2437,7 @@ id: involved_in_or_involved_in_regulation_of name: involved in or involved in regulation of def: "c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p" [] xref: RO:0002431 +property_value: IAO:0000116 "OWL does not allow defining object properties via a Union" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "involved in or reguates" xsd:string is_a: acts_upstream_of_or_within ! acts upstream of or within @@ -2861,16 +2877,6 @@ def: "A sub-relation of parasite-of in which the parasite that cannot complete i xref: RO:0002227 is_a: parasite_of ! parasite of -[Typedef] -id: obsolete_has_indirect_output -name: obsolete has indirect output -comment: Likely to be obsoleted. See:\nhttps://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/edit -xref: RO:0002403 -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string -is_a: has_output ! has output -is_obsolete: true - [Typedef] id: occurent_part_of name: occurent part of @@ -3313,6 +3319,7 @@ name: releases neurotransmitter xref: RO:0002111 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000118 "has neurotransmitter" xsd:string +domain: CARO:0000003 [Typedef] id: represses_expression_of @@ -3330,8 +3337,8 @@ xref: RO:0002315 property_value: IAO:0000112 "an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast." xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string -range: CL:0000000 -is_a: has_participant +range: CARO:0000003 +is_a: has_anatomical_participant ! has anatomical participant is_a: results_in_developmental_progression_of ! results in developmental progression of [Typedef] @@ -3360,7 +3367,7 @@ id: results_in_closure_of name: results in closure of xref: RO:0002585 property_value: IAO:0000116 "p 'results in closure of' c if and only if p is a developmental process and p results in a state of c changing from open to closed." xsd:string -is_a: has_participant +is_a: has_anatomical_participant ! has anatomical participant is_a: results_in_developmental_progression_of ! results in developmental progression of [Typedef] @@ -3393,7 +3400,7 @@ property_value: IAO:0000112 "every flower development (GO:0009908) results in de property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://www.geneontology.org/GO.doc.development.shtml xsd:anyURI -is_a: has_participant +is_a: has_anatomical_participant ! has anatomical participant is_a: results_in_developmental_progression_of ! results in developmental progression of [Typedef] @@ -3450,7 +3457,7 @@ name: results in ending of def: "p results in the end of s if p results in a change of state in s whereby s either ceases to exist, or s becomes functionally impaired or s has its fate committed such that it is put on a path to be degraded." [] xref: RO:0002552 property_value: IAO:0000117 "Chris Mungall" xsd:string -is_a: has_participant +is_a: has_anatomical_participant ! has anatomical participant is_a: results_in_developmental_progression_of ! results in developmental progression of [Typedef] @@ -3472,7 +3479,7 @@ name: results in growth of xref: RO:0002343 property_value: IAO:0000112 "'pollen tube growth' results_in growth_of some 'pollen tube'" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string -is_a: has_participant +is_a: has_anatomical_participant ! has anatomical participant is_a: results_in_developmental_progression_of ! results in developmental progression of [Typedef] @@ -3485,7 +3492,7 @@ property_value: IAO:0000112 "bone maturation (GO:0070977) results_in_maturation_ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string -is_a: has_participant +is_a: has_anatomical_participant ! has anatomical participant is_a: results_in_developmental_progression_of ! results in developmental progression of [Typedef] @@ -3498,7 +3505,7 @@ property_value: IAO:0000112 "tongue morphogenesis (GO:0043587) results in morpho property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string -is_a: has_participant +is_a: has_anatomical_participant ! has anatomical participant is_a: results_in_developmental_progression_of ! results in developmental progression of [Typedef] @@ -3508,14 +3515,14 @@ def: "Holds between p and c when p is locomotion process and the outcome of this xref: RO:0002565 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000232 "" xsd:string -is_a: has_participant +is_a: has_anatomical_participant ! has anatomical participant [Typedef] id: results_in_organization_of name: results in organization of def: "p results in organization of c iff p results in the assembly, arrangement of constituent parts, or disassembly of c" [] xref: RO:0002592 -is_a: has_participant +is_a: has_anatomical_participant ! has anatomical participant [Typedef] id: results_in_remodeling_of @@ -3540,7 +3547,7 @@ name: results in structural organization of def: "A relationship between a process and an anatomical entity such that the process contributes to the act of creating the structural organization of the anatomical entity." [] xref: RO:0002355 property_value: IAO:0000117 "Chris Mungall" xsd:string -is_a: has_participant +is_a: has_anatomical_participant ! has anatomical participant is_a: results_in_developmental_progression_of ! results in developmental progression of [Typedef] @@ -3790,7 +3797,7 @@ def: "Holds between p and c when p is a localization process (localization cover xref: RO:0002313 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "regulates localization of" xsd:string -is_a: has_participant +is_a: has_anatomical_participant ! has anatomical participant is_a: related_via_localization_to ! related via localization to [Typedef] diff --git a/src/ontology/subsets/ro-interaction.owl b/src/ontology/subsets/ro-interaction.owl index 980a4b83..118e3ab1 100644 --- a/src/ontology/subsets/ro-interaction.owl +++ b/src/ontology/subsets/ro-interaction.owl @@ -381,6 +381,8 @@ + + David Osumi-Sutherland http://www.ncbi.nlm.nih.gov/pubmed/22402613 RO:0002005 @@ -787,6 +789,7 @@ Examples include: the relationship between two channels collected simultaneously + Relation between a neuron and an anatomical structure that its soma is part of. David Osumi-Sutherland @@ -931,6 +934,7 @@ Examples include: the relationship between two channels collected simultaneously + has neurotransmitter RO:0002111 @@ -1548,6 +1552,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.RO:0002216 capable_of_part_of capable of part of + @@ -1700,7 +1705,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - + x develops_in y if x is located in y whilst x is developing Chris Mungall @@ -1995,8 +2000,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - - + + Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong] x has developmental contribution from y iff x has some part z such that z develops from y @@ -2177,8 +2182,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - + every flower development (GO:0009908) results in development of some flower (PO:0009046) p 'results in development of' c if and only if p is a developmental process and p results in the state of c changing from its initial state as a primordium or anlage through its mature state and to its final state. @@ -2212,8 +2217,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - + an annotation of gene X to cell morphogenesis with results_in_morphogenesis_of CL:0000540 (neuron) means that at the end of the process an input neuron has attained its shape. tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723) @@ -2230,8 +2235,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - + an annotation of gene X to cell maturation with results_in_maturation_of CL:0000057 (fibroblast) means that the fibroblast is mature at the end of the process bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474) @@ -2362,8 +2367,8 @@ where - + Holds between p and c when p is a localization process (localization covers maintenance of localization as well as its establishment) and the outcome of this process is to regulate the localization of c. Chris Mungall regulates localization of @@ -2377,9 +2382,9 @@ where - - + + an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast. The relationship that links a specified entity with the process that results in an unspecified entity acquiring the features and characteristics of the specified entity Chris Mungall @@ -2720,8 +2725,8 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - + 'pollen tube growth' results_in growth_of some 'pollen tube' Chris Mungall RO:0002343 @@ -2834,8 +2839,8 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - + A relationship between a process and an anatomical entity such that the process contributes to the act of creating the structural organization of the anatomical entity. Chris Mungall RO:0002355 @@ -3126,6 +3131,8 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + + x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction). Chris Mungall @@ -3209,22 +3216,6 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - - - - - - Chris Mungall - RO:0002403 - obsolete_has_indirect_output - Likely to be obsoleted. See: -https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/edit - obsolete has indirect output - true - - - - @@ -3501,6 +3492,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p + OWL does not allow defining object properties via a Union Chris Mungall involved in or reguates RO:0002431 @@ -4675,8 +4667,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + p results in the end of s if p results in a change of state in s whereby s either ceases to exist, or s becomes functionally impaired or s has its fate committed such that it is put on a path to be degraded. Chris Mungall RO:0002552 @@ -4785,7 +4777,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c Chris Mungall @@ -4972,8 +4964,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + p 'results in closure of' c if and only if p is a developmental process and p results in a state of c changing from open to closed. RO:0002585 results_in_closure_of @@ -5056,7 +5048,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + p results in organization of c iff p results in the assembly, arrangement of constituent parts, or disassembly of c RO:0002592 results_in_organization_of @@ -6314,6 +6306,28 @@ Environmental exposures include those imposed by natural environments, experimen + + + + + + + + + + + + + p has anatomical participant c iff p has participant c, and c is an anatomical entity + cjm + 2018-09-26T01:08:58Z + RO:0040036 + has_anatomical_participant + has anatomical participant + + + + @@ -6385,6 +6399,12 @@ Environmental exposures include those imposed by natural environments, experimen + + + + + + diff --git a/src/ontology/subsets/ro-mereotopology.obo b/src/ontology/subsets/ro-mereotopology.obo index 9b6e6850..96aa8f24 100644 --- a/src/ontology/subsets/ro-mereotopology.obo +++ b/src/ontology/subsets/ro-mereotopology.obo @@ -1,6 +1,6 @@ format-version: 1.2 ontology: ro/subsets/ro-mereotopology -owl-axioms: Prefix(owl:=)\nPrefix(rdf:=)\nPrefix(xml:=)\nPrefix(xsd:=)\nPrefix(rdfs:=)\n\n\nOntology(\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\n\n############################\n# Object Properties\n############################\n\n# Object Property: (coincident with)\n\nObjectPropertyRange( ObjectIntersectionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (has fasciculating neuron projection)\n\nObjectPropertyRange( ObjectUnionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (connected to)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (connects)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (directly develops from)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (anabranch of)\n\nSubObjectPropertyOf( ObjectInverseOf())\n\n# Object Property: (branching part of)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (condition has genetic basis in)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has basis in feature)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has location)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has feature)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n\n\n\nAnnotationAssertion(rdfs:comment \"\")\n) +owl-axioms: Prefix(owl:=)\nPrefix(rdf:=)\nPrefix(xml:=)\nPrefix(xsd:=)\nPrefix(rdfs:=)\n\n\nOntology(\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\n\n############################\n# Object Properties\n############################\n\n# Object Property: (coincident with)\n\nObjectPropertyRange( ObjectIntersectionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (has fasciculating neuron projection)\n\nObjectPropertyRange( ObjectUnionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (connected to)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (connects)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (directly develops from)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (anabranch of)\n\nSubObjectPropertyOf( ObjectInverseOf())\n\n# Object Property: (branching part of)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (condition has genetic basis in)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has basis in feature)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has location)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has feature)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (has anatomical participant)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n\n\n\nAnnotationAssertion(rdfs:comment \"\")\n) [Typedef] id: 2D_boundary_of @@ -327,6 +327,7 @@ def: "c stands in this relationship to p if and only if there exists some p' suc xref: RO:0002216 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "has function in" xsd:string +property_value: seeAlso "defining-property-chains-involving-reflexivity" is_a: causal_agent_in_process ! causal agent in process is_a: functionally_related_to ! functionally related to expand_expression_to: "RO_0000053 some (RO_0000054 only (BFO_0000050 some ?Y))" [] @@ -948,7 +949,7 @@ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 "EHDAA2" xsd:string property_value: IAO:0000119 "Jonathan Bard, EHDAA2" xsd:string -domain: CARO:0000003 +domain: CARO:0000000 is_a: developmentally_preceded_by ! developmentally preceded by [Typedef] @@ -1449,6 +1450,15 @@ property_value: IAO:0000112 "penicillin allergy (DOID:0060520) has allergic trig range: BFO:0000040 is_a: causes_or_contributes_to_condition ! causes or contributes to condition +[Typedef] +id: has_anatomical_participant +name: has anatomical participant +def: "p has anatomical participant c iff p has participant c, and c is an anatomical entity" [] +xref: RO:0040036 +is_a: has_participant +created_by: cjm +creation_date: 2018-09-26T01:08:58Z + [Typedef] id: has_autoimmune_trigger name: has autoimmune trigger @@ -1522,8 +1532,8 @@ xref: RO:0002254 property_value: IAO:0000112 "Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string -domain: BFO:0000004 -range: CARO:0000003 +domain: CARO:0000000 +range: CARO:0000000 is_a: developmentally_preceded_by ! developmentally preceded by inverse_of: developmentally_contributes_to ! developmentally contributes to @@ -1534,6 +1544,8 @@ def: "x has developmental potential involving y iff x is capable of a developmen xref: RO:0002384 property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Chris Mungall" xsd:string +domain: CARO:0000000 +range: CARO:0000000 is_a: developmentally_related_to ! developmentally related to [Typedef] @@ -2069,6 +2081,7 @@ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string property_value: RO:0001900 RO:0001901 domain: CL:0000540 +range: CARO:0000003 is_a: overlaps ! overlaps expand_expression_to: "BFO_0000051 some (\n GO_0043025 and BFO_0000050 some ?Y)" [] @@ -2324,6 +2337,8 @@ name: innervated_by xref: RO:0002005 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 xsd:anyURI property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +domain: CARO:0000003 +range: CARO:0001001 inverse_of: innervates ! innervates [Typedef] @@ -2422,6 +2437,7 @@ id: involved_in_or_involved_in_regulation_of name: involved in or involved in regulation of def: "c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p" [] xref: RO:0002431 +property_value: IAO:0000116 "OWL does not allow defining object properties via a Union" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "involved in or reguates" xsd:string is_a: acts_upstream_of_or_within ! acts upstream of or within @@ -2861,16 +2877,6 @@ def: "A sub-relation of parasite-of in which the parasite that cannot complete i xref: RO:0002227 is_a: parasite_of ! parasite of -[Typedef] -id: obsolete_has_indirect_output -name: obsolete has indirect output -comment: Likely to be obsoleted. See:\nhttps://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/edit -xref: RO:0002403 -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string -is_a: has_output ! has output -is_obsolete: true - [Typedef] id: occurent_part_of name: occurent part of @@ -3313,6 +3319,7 @@ name: releases neurotransmitter xref: RO:0002111 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000118 "has neurotransmitter" xsd:string +domain: CARO:0000003 [Typedef] id: represses_expression_of @@ -3330,8 +3337,8 @@ xref: RO:0002315 property_value: IAO:0000112 "an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast." xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string -range: CL:0000000 -is_a: has_participant +range: CARO:0000003 +is_a: has_anatomical_participant ! has anatomical participant is_a: results_in_developmental_progression_of ! results in developmental progression of [Typedef] @@ -3360,7 +3367,7 @@ id: results_in_closure_of name: results in closure of xref: RO:0002585 property_value: IAO:0000116 "p 'results in closure of' c if and only if p is a developmental process and p results in a state of c changing from open to closed." xsd:string -is_a: has_participant +is_a: has_anatomical_participant ! has anatomical participant is_a: results_in_developmental_progression_of ! results in developmental progression of [Typedef] @@ -3393,7 +3400,7 @@ property_value: IAO:0000112 "every flower development (GO:0009908) results in de property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://www.geneontology.org/GO.doc.development.shtml xsd:anyURI -is_a: has_participant +is_a: has_anatomical_participant ! has anatomical participant is_a: results_in_developmental_progression_of ! results in developmental progression of [Typedef] @@ -3450,7 +3457,7 @@ name: results in ending of def: "p results in the end of s if p results in a change of state in s whereby s either ceases to exist, or s becomes functionally impaired or s has its fate committed such that it is put on a path to be degraded." [] xref: RO:0002552 property_value: IAO:0000117 "Chris Mungall" xsd:string -is_a: has_participant +is_a: has_anatomical_participant ! has anatomical participant is_a: results_in_developmental_progression_of ! results in developmental progression of [Typedef] @@ -3472,7 +3479,7 @@ name: results in growth of xref: RO:0002343 property_value: IAO:0000112 "'pollen tube growth' results_in growth_of some 'pollen tube'" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string -is_a: has_participant +is_a: has_anatomical_participant ! has anatomical participant is_a: results_in_developmental_progression_of ! results in developmental progression of [Typedef] @@ -3485,7 +3492,7 @@ property_value: IAO:0000112 "bone maturation (GO:0070977) results_in_maturation_ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string -is_a: has_participant +is_a: has_anatomical_participant ! has anatomical participant is_a: results_in_developmental_progression_of ! results in developmental progression of [Typedef] @@ -3498,7 +3505,7 @@ property_value: IAO:0000112 "tongue morphogenesis (GO:0043587) results in morpho property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string -is_a: has_participant +is_a: has_anatomical_participant ! has anatomical participant is_a: results_in_developmental_progression_of ! results in developmental progression of [Typedef] @@ -3508,14 +3515,14 @@ def: "Holds between p and c when p is locomotion process and the outcome of this xref: RO:0002565 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000232 "" xsd:string -is_a: has_participant +is_a: has_anatomical_participant ! has anatomical participant [Typedef] id: results_in_organization_of name: results in organization of def: "p results in organization of c iff p results in the assembly, arrangement of constituent parts, or disassembly of c" [] xref: RO:0002592 -is_a: has_participant +is_a: has_anatomical_participant ! has anatomical participant [Typedef] id: results_in_remodeling_of @@ -3540,7 +3547,7 @@ name: results in structural organization of def: "A relationship between a process and an anatomical entity such that the process contributes to the act of creating the structural organization of the anatomical entity." [] xref: RO:0002355 property_value: IAO:0000117 "Chris Mungall" xsd:string -is_a: has_participant +is_a: has_anatomical_participant ! has anatomical participant is_a: results_in_developmental_progression_of ! results in developmental progression of [Typedef] @@ -3790,7 +3797,7 @@ def: "Holds between p and c when p is a localization process (localization cover xref: RO:0002313 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "regulates localization of" xsd:string -is_a: has_participant +is_a: has_anatomical_participant ! has anatomical participant is_a: related_via_localization_to ! related via localization to [Typedef] diff --git a/src/ontology/subsets/ro-mereotopology.owl b/src/ontology/subsets/ro-mereotopology.owl index 410f398d..6d1d6757 100644 --- a/src/ontology/subsets/ro-mereotopology.owl +++ b/src/ontology/subsets/ro-mereotopology.owl @@ -381,6 +381,8 @@ + + David Osumi-Sutherland http://www.ncbi.nlm.nih.gov/pubmed/22402613 RO:0002005 @@ -787,6 +789,7 @@ Examples include: the relationship between two channels collected simultaneously + Relation between a neuron and an anatomical structure that its soma is part of. David Osumi-Sutherland @@ -931,6 +934,7 @@ Examples include: the relationship between two channels collected simultaneously + has neurotransmitter RO:0002111 @@ -1548,6 +1552,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.RO:0002216 capable_of_part_of capable of part of + @@ -1700,7 +1705,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - + x develops_in y if x is located in y whilst x is developing Chris Mungall @@ -1995,8 +2000,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - - + + Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong] x has developmental contribution from y iff x has some part z such that z develops from y @@ -2177,8 +2182,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - + every flower development (GO:0009908) results in development of some flower (PO:0009046) p 'results in development of' c if and only if p is a developmental process and p results in the state of c changing from its initial state as a primordium or anlage through its mature state and to its final state. @@ -2212,8 +2217,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - + an annotation of gene X to cell morphogenesis with results_in_morphogenesis_of CL:0000540 (neuron) means that at the end of the process an input neuron has attained its shape. tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723) @@ -2230,8 +2235,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - + an annotation of gene X to cell maturation with results_in_maturation_of CL:0000057 (fibroblast) means that the fibroblast is mature at the end of the process bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474) @@ -2362,8 +2367,8 @@ where - + Holds between p and c when p is a localization process (localization covers maintenance of localization as well as its establishment) and the outcome of this process is to regulate the localization of c. Chris Mungall regulates localization of @@ -2377,9 +2382,9 @@ where - - + + an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast. The relationship that links a specified entity with the process that results in an unspecified entity acquiring the features and characteristics of the specified entity Chris Mungall @@ -2720,8 +2725,8 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - + 'pollen tube growth' results_in growth_of some 'pollen tube' Chris Mungall RO:0002343 @@ -2834,8 +2839,8 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - + A relationship between a process and an anatomical entity such that the process contributes to the act of creating the structural organization of the anatomical entity. Chris Mungall RO:0002355 @@ -3126,6 +3131,8 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + + x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction). Chris Mungall @@ -3209,22 +3216,6 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - - - - - - Chris Mungall - RO:0002403 - obsolete_has_indirect_output - Likely to be obsoleted. See: -https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/edit - obsolete has indirect output - true - - - - @@ -3501,6 +3492,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p + OWL does not allow defining object properties via a Union Chris Mungall involved in or reguates RO:0002431 @@ -4675,8 +4667,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + p results in the end of s if p results in a change of state in s whereby s either ceases to exist, or s becomes functionally impaired or s has its fate committed such that it is put on a path to be degraded. Chris Mungall RO:0002552 @@ -4785,7 +4777,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c Chris Mungall @@ -4972,8 +4964,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + p 'results in closure of' c if and only if p is a developmental process and p results in a state of c changing from open to closed. RO:0002585 results_in_closure_of @@ -5056,7 +5048,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + p results in organization of c iff p results in the assembly, arrangement of constituent parts, or disassembly of c RO:0002592 results_in_organization_of @@ -6314,6 +6306,28 @@ Environmental exposures include those imposed by natural environments, experimen + + + + + + + + + + + + + p has anatomical participant c iff p has participant c, and c is an anatomical entity + cjm + 2018-09-26T01:08:58Z + RO:0040036 + has_anatomical_participant + has anatomical participant + + + + @@ -6385,6 +6399,12 @@ Environmental exposures include those imposed by natural environments, experimen + + + + + + diff --git a/src/ontology/subsets/ro-sequence.obo b/src/ontology/subsets/ro-sequence.obo index db9bdacf..3bd07400 100644 --- a/src/ontology/subsets/ro-sequence.obo +++ b/src/ontology/subsets/ro-sequence.obo @@ -1,6 +1,6 @@ format-version: 1.2 ontology: ro/subsets/ro-sequence -owl-axioms: Prefix(owl:=)\nPrefix(rdf:=)\nPrefix(xml:=)\nPrefix(xsd:=)\nPrefix(rdfs:=)\n\n\nOntology(\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\n\n############################\n# Object Properties\n############################\n\n# Object Property: (coincident with)\n\nObjectPropertyRange( ObjectIntersectionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (has fasciculating neuron projection)\n\nObjectPropertyRange( ObjectUnionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (connected to)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (connects)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (directly develops from)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (anabranch of)\n\nSubObjectPropertyOf( ObjectInverseOf())\n\n# Object Property: (branching part of)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (condition has genetic basis in)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has basis in feature)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has location)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has feature)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n\n\n\nAnnotationAssertion(rdfs:comment \"\")\n) +owl-axioms: Prefix(owl:=)\nPrefix(rdf:=)\nPrefix(xml:=)\nPrefix(xsd:=)\nPrefix(rdfs:=)\n\n\nOntology(\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\n\n############################\n# Object Properties\n############################\n\n# Object Property: (coincident with)\n\nObjectPropertyRange( ObjectIntersectionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (has fasciculating neuron projection)\n\nObjectPropertyRange( ObjectUnionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (connected to)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (connects)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (directly develops from)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (anabranch of)\n\nSubObjectPropertyOf( ObjectInverseOf())\n\n# Object Property: (branching part of)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (condition has genetic basis in)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has basis in feature)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has location)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has feature)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (has anatomical participant)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n\n\n\nAnnotationAssertion(rdfs:comment \"\")\n) [Typedef] id: 2D_boundary_of @@ -327,6 +327,7 @@ def: "c stands in this relationship to p if and only if there exists some p' suc xref: RO:0002216 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "has function in" xsd:string +property_value: seeAlso "defining-property-chains-involving-reflexivity" is_a: causal_agent_in_process ! causal agent in process is_a: functionally_related_to ! functionally related to expand_expression_to: "RO_0000053 some (RO_0000054 only (BFO_0000050 some ?Y))" [] @@ -948,7 +949,7 @@ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 "EHDAA2" xsd:string property_value: IAO:0000119 "Jonathan Bard, EHDAA2" xsd:string -domain: CARO:0000003 +domain: CARO:0000000 is_a: developmentally_preceded_by ! developmentally preceded by [Typedef] @@ -1449,6 +1450,15 @@ property_value: IAO:0000112 "penicillin allergy (DOID:0060520) has allergic trig range: BFO:0000040 is_a: causes_or_contributes_to_condition ! causes or contributes to condition +[Typedef] +id: has_anatomical_participant +name: has anatomical participant +def: "p has anatomical participant c iff p has participant c, and c is an anatomical entity" [] +xref: RO:0040036 +is_a: has_participant +created_by: cjm +creation_date: 2018-09-26T01:08:58Z + [Typedef] id: has_autoimmune_trigger name: has autoimmune trigger @@ -1522,8 +1532,8 @@ xref: RO:0002254 property_value: IAO:0000112 "Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string -domain: BFO:0000004 -range: CARO:0000003 +domain: CARO:0000000 +range: CARO:0000000 is_a: developmentally_preceded_by ! developmentally preceded by inverse_of: developmentally_contributes_to ! developmentally contributes to @@ -1534,6 +1544,8 @@ def: "x has developmental potential involving y iff x is capable of a developmen xref: RO:0002384 property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Chris Mungall" xsd:string +domain: CARO:0000000 +range: CARO:0000000 is_a: developmentally_related_to ! developmentally related to [Typedef] @@ -2069,6 +2081,7 @@ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string property_value: RO:0001900 RO:0001901 domain: CL:0000540 +range: CARO:0000003 is_a: overlaps ! overlaps expand_expression_to: "BFO_0000051 some (\n GO_0043025 and BFO_0000050 some ?Y)" [] @@ -2324,6 +2337,8 @@ name: innervated_by xref: RO:0002005 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 xsd:anyURI property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +domain: CARO:0000003 +range: CARO:0001001 inverse_of: innervates ! innervates [Typedef] @@ -2422,6 +2437,7 @@ id: involved_in_or_involved_in_regulation_of name: involved in or involved in regulation of def: "c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p" [] xref: RO:0002431 +property_value: IAO:0000116 "OWL does not allow defining object properties via a Union" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "involved in or reguates" xsd:string is_a: acts_upstream_of_or_within ! acts upstream of or within @@ -2861,16 +2877,6 @@ def: "A sub-relation of parasite-of in which the parasite that cannot complete i xref: RO:0002227 is_a: parasite_of ! parasite of -[Typedef] -id: obsolete_has_indirect_output -name: obsolete has indirect output -comment: Likely to be obsoleted. See:\nhttps://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/edit -xref: RO:0002403 -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string -is_a: has_output ! has output -is_obsolete: true - [Typedef] id: occurent_part_of name: occurent part of @@ -3313,6 +3319,7 @@ name: releases neurotransmitter xref: RO:0002111 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000118 "has neurotransmitter" xsd:string +domain: CARO:0000003 [Typedef] id: represses_expression_of @@ -3330,8 +3337,8 @@ xref: RO:0002315 property_value: IAO:0000112 "an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast." xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string -range: CL:0000000 -is_a: has_participant +range: CARO:0000003 +is_a: has_anatomical_participant ! has anatomical participant is_a: results_in_developmental_progression_of ! results in developmental progression of [Typedef] @@ -3360,7 +3367,7 @@ id: results_in_closure_of name: results in closure of xref: RO:0002585 property_value: IAO:0000116 "p 'results in closure of' c if and only if p is a developmental process and p results in a state of c changing from open to closed." xsd:string -is_a: has_participant +is_a: has_anatomical_participant ! has anatomical participant is_a: results_in_developmental_progression_of ! results in developmental progression of [Typedef] @@ -3393,7 +3400,7 @@ property_value: IAO:0000112 "every flower development (GO:0009908) results in de property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://www.geneontology.org/GO.doc.development.shtml xsd:anyURI -is_a: has_participant +is_a: has_anatomical_participant ! has anatomical participant is_a: results_in_developmental_progression_of ! results in developmental progression of [Typedef] @@ -3450,7 +3457,7 @@ name: results in ending of def: "p results in the end of s if p results in a change of state in s whereby s either ceases to exist, or s becomes functionally impaired or s has its fate committed such that it is put on a path to be degraded." [] xref: RO:0002552 property_value: IAO:0000117 "Chris Mungall" xsd:string -is_a: has_participant +is_a: has_anatomical_participant ! has anatomical participant is_a: results_in_developmental_progression_of ! results in developmental progression of [Typedef] @@ -3472,7 +3479,7 @@ name: results in growth of xref: RO:0002343 property_value: IAO:0000112 "'pollen tube growth' results_in growth_of some 'pollen tube'" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string -is_a: has_participant +is_a: has_anatomical_participant ! has anatomical participant is_a: results_in_developmental_progression_of ! results in developmental progression of [Typedef] @@ -3485,7 +3492,7 @@ property_value: IAO:0000112 "bone maturation (GO:0070977) results_in_maturation_ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string -is_a: has_participant +is_a: has_anatomical_participant ! has anatomical participant is_a: results_in_developmental_progression_of ! results in developmental progression of [Typedef] @@ -3498,7 +3505,7 @@ property_value: IAO:0000112 "tongue morphogenesis (GO:0043587) results in morpho property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string -is_a: has_participant +is_a: has_anatomical_participant ! has anatomical participant is_a: results_in_developmental_progression_of ! results in developmental progression of [Typedef] @@ -3508,14 +3515,14 @@ def: "Holds between p and c when p is locomotion process and the outcome of this xref: RO:0002565 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000232 "" xsd:string -is_a: has_participant +is_a: has_anatomical_participant ! has anatomical participant [Typedef] id: results_in_organization_of name: results in organization of def: "p results in organization of c iff p results in the assembly, arrangement of constituent parts, or disassembly of c" [] xref: RO:0002592 -is_a: has_participant +is_a: has_anatomical_participant ! has anatomical participant [Typedef] id: results_in_remodeling_of @@ -3540,7 +3547,7 @@ name: results in structural organization of def: "A relationship between a process and an anatomical entity such that the process contributes to the act of creating the structural organization of the anatomical entity." [] xref: RO:0002355 property_value: IAO:0000117 "Chris Mungall" xsd:string -is_a: has_participant +is_a: has_anatomical_participant ! has anatomical participant is_a: results_in_developmental_progression_of ! results in developmental progression of [Typedef] @@ -3790,7 +3797,7 @@ def: "Holds between p and c when p is a localization process (localization cover xref: RO:0002313 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "regulates localization of" xsd:string -is_a: has_participant +is_a: has_anatomical_participant ! has anatomical participant is_a: related_via_localization_to ! related via localization to [Typedef] diff --git a/src/ontology/subsets/ro-sequence.owl b/src/ontology/subsets/ro-sequence.owl index 5ecb1bf7..2224004b 100644 --- a/src/ontology/subsets/ro-sequence.owl +++ b/src/ontology/subsets/ro-sequence.owl @@ -381,6 +381,8 @@ + + David Osumi-Sutherland http://www.ncbi.nlm.nih.gov/pubmed/22402613 RO:0002005 @@ -787,6 +789,7 @@ Examples include: the relationship between two channels collected simultaneously + Relation between a neuron and an anatomical structure that its soma is part of. David Osumi-Sutherland @@ -931,6 +934,7 @@ Examples include: the relationship between two channels collected simultaneously + has neurotransmitter RO:0002111 @@ -1548,6 +1552,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.RO:0002216 capable_of_part_of capable of part of + @@ -1700,7 +1705,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - + x develops_in y if x is located in y whilst x is developing Chris Mungall @@ -1995,8 +2000,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - - + + Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong] x has developmental contribution from y iff x has some part z such that z develops from y @@ -2177,8 +2182,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - + every flower development (GO:0009908) results in development of some flower (PO:0009046) p 'results in development of' c if and only if p is a developmental process and p results in the state of c changing from its initial state as a primordium or anlage through its mature state and to its final state. @@ -2212,8 +2217,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - + an annotation of gene X to cell morphogenesis with results_in_morphogenesis_of CL:0000540 (neuron) means that at the end of the process an input neuron has attained its shape. tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723) @@ -2230,8 +2235,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - + an annotation of gene X to cell maturation with results_in_maturation_of CL:0000057 (fibroblast) means that the fibroblast is mature at the end of the process bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474) @@ -2362,8 +2367,8 @@ where - + Holds between p and c when p is a localization process (localization covers maintenance of localization as well as its establishment) and the outcome of this process is to regulate the localization of c. Chris Mungall regulates localization of @@ -2377,9 +2382,9 @@ where - - + + an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast. The relationship that links a specified entity with the process that results in an unspecified entity acquiring the features and characteristics of the specified entity Chris Mungall @@ -2720,8 +2725,8 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - + 'pollen tube growth' results_in growth_of some 'pollen tube' Chris Mungall RO:0002343 @@ -2834,8 +2839,8 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - + A relationship between a process and an anatomical entity such that the process contributes to the act of creating the structural organization of the anatomical entity. Chris Mungall RO:0002355 @@ -3126,6 +3131,8 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + + x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction). Chris Mungall @@ -3209,22 +3216,6 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - - - - - - Chris Mungall - RO:0002403 - obsolete_has_indirect_output - Likely to be obsoleted. See: -https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/edit - obsolete has indirect output - true - - - - @@ -3501,6 +3492,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p + OWL does not allow defining object properties via a Union Chris Mungall involved in or reguates RO:0002431 @@ -4675,8 +4667,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + p results in the end of s if p results in a change of state in s whereby s either ceases to exist, or s becomes functionally impaired or s has its fate committed such that it is put on a path to be degraded. Chris Mungall RO:0002552 @@ -4785,7 +4777,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c Chris Mungall @@ -4972,8 +4964,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + p 'results in closure of' c if and only if p is a developmental process and p results in a state of c changing from open to closed. RO:0002585 results_in_closure_of @@ -5056,7 +5048,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + p results in organization of c iff p results in the assembly, arrangement of constituent parts, or disassembly of c RO:0002592 results_in_organization_of @@ -6314,6 +6306,28 @@ Environmental exposures include those imposed by natural environments, experimen + + + + + + + + + + + + + p has anatomical participant c iff p has participant c, and c is an anatomical entity + cjm + 2018-09-26T01:08:58Z + RO:0040036 + has_anatomical_participant + has anatomical participant + + + + @@ -6385,6 +6399,12 @@ Environmental exposures include those imposed by natural environments, experimen + + + + + + diff --git a/src/ontology/subsets/ro-time-interval.obo b/src/ontology/subsets/ro-time-interval.obo index 50c2e1ca..d63edc70 100644 --- a/src/ontology/subsets/ro-time-interval.obo +++ b/src/ontology/subsets/ro-time-interval.obo @@ -1,6 +1,6 @@ format-version: 1.2 ontology: ro/subsets/ro-time-interval -owl-axioms: Prefix(owl:=)\nPrefix(rdf:=)\nPrefix(xml:=)\nPrefix(xsd:=)\nPrefix(rdfs:=)\n\n\nOntology(\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\n\n############################\n# Object Properties\n############################\n\n# Object Property: (coincident with)\n\nObjectPropertyRange( ObjectIntersectionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (has fasciculating neuron projection)\n\nObjectPropertyRange( ObjectUnionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (connected to)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (connects)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (directly develops from)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (anabranch of)\n\nSubObjectPropertyOf( ObjectInverseOf())\n\n# Object Property: (branching part of)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (condition has genetic basis in)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has basis in feature)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has location)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has feature)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n\n\n\nAnnotationAssertion(rdfs:comment \"\")\n) +owl-axioms: Prefix(owl:=)\nPrefix(rdf:=)\nPrefix(xml:=)\nPrefix(xsd:=)\nPrefix(rdfs:=)\n\n\nOntology(\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\n\n############################\n# Object Properties\n############################\n\n# Object Property: (coincident with)\n\nObjectPropertyRange( ObjectIntersectionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (has fasciculating neuron projection)\n\nObjectPropertyRange( ObjectUnionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (connected to)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (connects)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (directly develops from)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (anabranch of)\n\nSubObjectPropertyOf( ObjectInverseOf())\n\n# Object Property: (branching part of)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (condition has genetic basis in)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has basis in feature)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has location)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has feature)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (has anatomical participant)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n\n\n\nAnnotationAssertion(rdfs:comment \"\")\n) [Typedef] id: 2D_boundary_of @@ -327,6 +327,7 @@ def: "c stands in this relationship to p if and only if there exists some p' suc xref: RO:0002216 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "has function in" xsd:string +property_value: seeAlso "defining-property-chains-involving-reflexivity" is_a: causal_agent_in_process ! causal agent in process is_a: functionally_related_to ! functionally related to expand_expression_to: "RO_0000053 some (RO_0000054 only (BFO_0000050 some ?Y))" [] @@ -948,7 +949,7 @@ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 "EHDAA2" xsd:string property_value: IAO:0000119 "Jonathan Bard, EHDAA2" xsd:string -domain: CARO:0000003 +domain: CARO:0000000 is_a: developmentally_preceded_by ! developmentally preceded by [Typedef] @@ -1449,6 +1450,15 @@ property_value: IAO:0000112 "penicillin allergy (DOID:0060520) has allergic trig range: BFO:0000040 is_a: causes_or_contributes_to_condition ! causes or contributes to condition +[Typedef] +id: has_anatomical_participant +name: has anatomical participant +def: "p has anatomical participant c iff p has participant c, and c is an anatomical entity" [] +xref: RO:0040036 +is_a: has_participant +created_by: cjm +creation_date: 2018-09-26T01:08:58Z + [Typedef] id: has_autoimmune_trigger name: has autoimmune trigger @@ -1522,8 +1532,8 @@ xref: RO:0002254 property_value: IAO:0000112 "Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string -domain: BFO:0000004 -range: CARO:0000003 +domain: CARO:0000000 +range: CARO:0000000 is_a: developmentally_preceded_by ! developmentally preceded by inverse_of: developmentally_contributes_to ! developmentally contributes to @@ -1534,6 +1544,8 @@ def: "x has developmental potential involving y iff x is capable of a developmen xref: RO:0002384 property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Chris Mungall" xsd:string +domain: CARO:0000000 +range: CARO:0000000 is_a: developmentally_related_to ! developmentally related to [Typedef] @@ -2069,6 +2081,7 @@ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string property_value: RO:0001900 RO:0001901 domain: CL:0000540 +range: CARO:0000003 is_a: overlaps ! overlaps expand_expression_to: "BFO_0000051 some (\n GO_0043025 and BFO_0000050 some ?Y)" [] @@ -2324,6 +2337,8 @@ name: innervated_by xref: RO:0002005 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 xsd:anyURI property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +domain: CARO:0000003 +range: CARO:0001001 inverse_of: innervates ! innervates [Typedef] @@ -2422,6 +2437,7 @@ id: involved_in_or_involved_in_regulation_of name: involved in or involved in regulation of def: "c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p" [] xref: RO:0002431 +property_value: IAO:0000116 "OWL does not allow defining object properties via a Union" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "involved in or reguates" xsd:string is_a: acts_upstream_of_or_within ! acts upstream of or within @@ -2861,16 +2877,6 @@ def: "A sub-relation of parasite-of in which the parasite that cannot complete i xref: RO:0002227 is_a: parasite_of ! parasite of -[Typedef] -id: obsolete_has_indirect_output -name: obsolete has indirect output -comment: Likely to be obsoleted. See:\nhttps://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/edit -xref: RO:0002403 -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string -is_a: has_output ! has output -is_obsolete: true - [Typedef] id: occurent_part_of name: occurent part of @@ -3313,6 +3319,7 @@ name: releases neurotransmitter xref: RO:0002111 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000118 "has neurotransmitter" xsd:string +domain: CARO:0000003 [Typedef] id: represses_expression_of @@ -3330,8 +3337,8 @@ xref: RO:0002315 property_value: IAO:0000112 "an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast." xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string -range: CL:0000000 -is_a: has_participant +range: CARO:0000003 +is_a: has_anatomical_participant ! has anatomical participant is_a: results_in_developmental_progression_of ! results in developmental progression of [Typedef] @@ -3360,7 +3367,7 @@ id: results_in_closure_of name: results in closure of xref: RO:0002585 property_value: IAO:0000116 "p 'results in closure of' c if and only if p is a developmental process and p results in a state of c changing from open to closed." xsd:string -is_a: has_participant +is_a: has_anatomical_participant ! has anatomical participant is_a: results_in_developmental_progression_of ! results in developmental progression of [Typedef] @@ -3393,7 +3400,7 @@ property_value: IAO:0000112 "every flower development (GO:0009908) results in de property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://www.geneontology.org/GO.doc.development.shtml xsd:anyURI -is_a: has_participant +is_a: has_anatomical_participant ! has anatomical participant is_a: results_in_developmental_progression_of ! results in developmental progression of [Typedef] @@ -3450,7 +3457,7 @@ name: results in ending of def: "p results in the end of s if p results in a change of state in s whereby s either ceases to exist, or s becomes functionally impaired or s has its fate committed such that it is put on a path to be degraded." [] xref: RO:0002552 property_value: IAO:0000117 "Chris Mungall" xsd:string -is_a: has_participant +is_a: has_anatomical_participant ! has anatomical participant is_a: results_in_developmental_progression_of ! results in developmental progression of [Typedef] @@ -3472,7 +3479,7 @@ name: results in growth of xref: RO:0002343 property_value: IAO:0000112 "'pollen tube growth' results_in growth_of some 'pollen tube'" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string -is_a: has_participant +is_a: has_anatomical_participant ! has anatomical participant is_a: results_in_developmental_progression_of ! results in developmental progression of [Typedef] @@ -3485,7 +3492,7 @@ property_value: IAO:0000112 "bone maturation (GO:0070977) results_in_maturation_ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string -is_a: has_participant +is_a: has_anatomical_participant ! has anatomical participant is_a: results_in_developmental_progression_of ! results in developmental progression of [Typedef] @@ -3498,7 +3505,7 @@ property_value: IAO:0000112 "tongue morphogenesis (GO:0043587) results in morpho property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string -is_a: has_participant +is_a: has_anatomical_participant ! has anatomical participant is_a: results_in_developmental_progression_of ! results in developmental progression of [Typedef] @@ -3508,14 +3515,14 @@ def: "Holds between p and c when p is locomotion process and the outcome of this xref: RO:0002565 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000232 "" xsd:string -is_a: has_participant +is_a: has_anatomical_participant ! has anatomical participant [Typedef] id: results_in_organization_of name: results in organization of def: "p results in organization of c iff p results in the assembly, arrangement of constituent parts, or disassembly of c" [] xref: RO:0002592 -is_a: has_participant +is_a: has_anatomical_participant ! has anatomical participant [Typedef] id: results_in_remodeling_of @@ -3540,7 +3547,7 @@ name: results in structural organization of def: "A relationship between a process and an anatomical entity such that the process contributes to the act of creating the structural organization of the anatomical entity." [] xref: RO:0002355 property_value: IAO:0000117 "Chris Mungall" xsd:string -is_a: has_participant +is_a: has_anatomical_participant ! has anatomical participant is_a: results_in_developmental_progression_of ! results in developmental progression of [Typedef] @@ -3790,7 +3797,7 @@ def: "Holds between p and c when p is a localization process (localization cover xref: RO:0002313 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "regulates localization of" xsd:string -is_a: has_participant +is_a: has_anatomical_participant ! has anatomical participant is_a: related_via_localization_to ! related via localization to [Typedef] diff --git a/src/ontology/subsets/ro-time-interval.owl b/src/ontology/subsets/ro-time-interval.owl index 5e33cb7a..8c61af62 100644 --- a/src/ontology/subsets/ro-time-interval.owl +++ b/src/ontology/subsets/ro-time-interval.owl @@ -381,6 +381,8 @@ + + David Osumi-Sutherland http://www.ncbi.nlm.nih.gov/pubmed/22402613 RO:0002005 @@ -787,6 +789,7 @@ Examples include: the relationship between two channels collected simultaneously + Relation between a neuron and an anatomical structure that its soma is part of. David Osumi-Sutherland @@ -931,6 +934,7 @@ Examples include: the relationship between two channels collected simultaneously + has neurotransmitter RO:0002111 @@ -1548,6 +1552,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.RO:0002216 capable_of_part_of capable of part of + @@ -1700,7 +1705,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - + x develops_in y if x is located in y whilst x is developing Chris Mungall @@ -1995,8 +2000,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - - + + Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong] x has developmental contribution from y iff x has some part z such that z develops from y @@ -2177,8 +2182,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - + every flower development (GO:0009908) results in development of some flower (PO:0009046) p 'results in development of' c if and only if p is a developmental process and p results in the state of c changing from its initial state as a primordium or anlage through its mature state and to its final state. @@ -2212,8 +2217,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - + an annotation of gene X to cell morphogenesis with results_in_morphogenesis_of CL:0000540 (neuron) means that at the end of the process an input neuron has attained its shape. tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723) @@ -2230,8 +2235,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - + an annotation of gene X to cell maturation with results_in_maturation_of CL:0000057 (fibroblast) means that the fibroblast is mature at the end of the process bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474) @@ -2362,8 +2367,8 @@ where - + Holds between p and c when p is a localization process (localization covers maintenance of localization as well as its establishment) and the outcome of this process is to regulate the localization of c. Chris Mungall regulates localization of @@ -2377,9 +2382,9 @@ where - - + + an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast. The relationship that links a specified entity with the process that results in an unspecified entity acquiring the features and characteristics of the specified entity Chris Mungall @@ -2720,8 +2725,8 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - + 'pollen tube growth' results_in growth_of some 'pollen tube' Chris Mungall RO:0002343 @@ -2834,8 +2839,8 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - + A relationship between a process and an anatomical entity such that the process contributes to the act of creating the structural organization of the anatomical entity. Chris Mungall RO:0002355 @@ -3126,6 +3131,8 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + + x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction). Chris Mungall @@ -3209,22 +3216,6 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - - - - - - Chris Mungall - RO:0002403 - obsolete_has_indirect_output - Likely to be obsoleted. See: -https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/edit - obsolete has indirect output - true - - - - @@ -3501,6 +3492,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p + OWL does not allow defining object properties via a Union Chris Mungall involved in or reguates RO:0002431 @@ -4675,8 +4667,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + p results in the end of s if p results in a change of state in s whereby s either ceases to exist, or s becomes functionally impaired or s has its fate committed such that it is put on a path to be degraded. Chris Mungall RO:0002552 @@ -4785,7 +4777,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c Chris Mungall @@ -4972,8 +4964,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + p 'results in closure of' c if and only if p is a developmental process and p results in a state of c changing from open to closed. RO:0002585 results_in_closure_of @@ -5056,7 +5048,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + p results in organization of c iff p results in the assembly, arrangement of constituent parts, or disassembly of c RO:0002592 results_in_organization_of @@ -6314,6 +6306,28 @@ Environmental exposures include those imposed by natural environments, experimen + + + + + + + + + + + + + p has anatomical participant c iff p has participant c, and c is an anatomical entity + cjm + 2018-09-26T01:08:58Z + RO:0040036 + has_anatomical_participant + has anatomical participant + + + + @@ -6385,6 +6399,12 @@ Environmental exposures include those imposed by natural environments, experimen + + + + + + diff --git a/subsets/ro-causal.obo b/subsets/ro-causal.obo index 4f469366..c69c7a3b 100644 --- a/subsets/ro-causal.obo +++ b/subsets/ro-causal.obo @@ -1,6 +1,6 @@ format-version: 1.2 ontology: ro/subsets/ro-causal -owl-axioms: Prefix(owl:=)\nPrefix(rdf:=)\nPrefix(xml:=)\nPrefix(xsd:=)\nPrefix(rdfs:=)\n\n\nOntology(\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\n\n############################\n# Object Properties\n############################\n\n# Object Property: (coincident with)\n\nObjectPropertyRange( ObjectIntersectionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (has fasciculating neuron projection)\n\nObjectPropertyRange( ObjectUnionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (connected to)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (connects)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (directly develops from)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (enabled by)\n\nSubObjectPropertyOf( ObjectInverseOf())\n\n# Object Property: (anabranch of)\n\nSubObjectPropertyOf( ObjectInverseOf())\n\n# Object Property: (branching part of)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (condition has genetic basis in)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has feature)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n\n\n\nAnnotationAssertion(rdfs:comment \"\")\n) +owl-axioms: Prefix(owl:=)\nPrefix(rdf:=)\nPrefix(xml:=)\nPrefix(xsd:=)\nPrefix(rdfs:=)\n\n\nOntology(\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\n\n############################\n# Object Properties\n############################\n\n# Object Property: (coincident with)\n\nObjectPropertyRange( ObjectIntersectionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (has fasciculating neuron projection)\n\nObjectPropertyRange( ObjectUnionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (connected to)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (connects)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (directly develops from)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (anabranch of)\n\nSubObjectPropertyOf( ObjectInverseOf())\n\n# Object Property: (branching part of)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (condition has genetic basis in)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has basis in feature)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has location)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has feature)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (has anatomical participant)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n\n\n\nAnnotationAssertion(rdfs:comment \"\")\n) [Typedef] id: 2D_boundary_of @@ -184,6 +184,7 @@ def: "a is attached to b if and only if a and b are discrete objects or object p subset: ro-eco xref: RO:0002371 property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000589 "attached to (anatomical structure to anatomical structure)" xsd:string is_symmetric: true is_a: attached_to_part_of ! attached to part of is_a: connected_to ! connected to @@ -193,8 +194,9 @@ id: attached_to_part_of name: attached to part of def: "a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b." [] xref: RO:0002177 -domain: BFO:0000040 -range: BFO:0000040 +property_value: IAO:0000589 "attached to part of (anatomical structure to anatomical structure)" xsd:string +domain: CARO:0000003 +range: CARO:0000003 is_a: biomechanically_related_to ! biomechanically related to is_a: mereotopologically_related_to ! mereotopologically related to @@ -225,6 +227,8 @@ def: "A relation that holds between elements of a musculoskeletal system or its xref: RO:0002567 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes." xsd:string +domain: CARO:0000003 +range: CARO:0000003 is_a: functionally_related_to ! functionally related to [Typedef] @@ -323,6 +327,7 @@ def: "c stands in this relationship to p if and only if there exists some p' suc xref: RO:0002216 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "has function in" xsd:string +property_value: seeAlso "defining-property-chains-involving-reflexivity" is_a: causal_agent_in_process ! causal agent in process is_a: functionally_related_to ! functionally related to expand_expression_to: "RO_0000053 some (RO_0000054 only (BFO_0000050 some ?Y))" [] @@ -406,8 +411,9 @@ name: causal relationship with disease as subject xref: RO:0004023 property_value: IAO:0000116 "After import upper level from OGMS, make domain more specific." xsd:string property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all of which have a disease as the subject." xsd:string -domain: BFO:0000016 +domain: OGMS:0000031 is_a: causally_related_to ! causally related to +is_a: disease_relationship ! disease relationship created_by: cjm creation_date: 2017-11-05T03:50:54Z @@ -462,7 +468,6 @@ property_value: IAO:0000114 IAO:0000428 property_value: 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." xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: 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." xsd:string -is_a: related_via_dependence_to ! related via dependence to [Typedef] id: causally_upstream_of @@ -571,14 +576,6 @@ xref: RO:0002478 property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: child_nucleus_of ! child nucleus of -[Typedef] -id: co-occurs -name: co-occurs -def: "An interaction relationship describing organisms that often occur together at the same time and space or in the same environment." [] -xref: RO:0008506 -is_symmetric: true -is_a: ecologically_related_to ! ecologically related to - [Typedef] id: coincident_with name: coincident with @@ -673,6 +670,7 @@ xref: RO:0002322 property_value: IAO:0000116 "An experimental relation currently used to connect a feature possessed by an organism (e.g. anatomical structure, biological process, phenotype or quality) to a habitat or environment in which that feature is well suited, adapted or provides a reproductive advantage for the organism. For example, fins to an aquatic environment. Usually this will mean that the structure is adapted for this environment, but we avoid saying this directly - primitive forms of the structure may not have evolved specifically for that environment (for example, early wings were not necessarily adapted for an aerial environment). Note also that this is a statement about the general class of structures - not every instance of a limb need confer an advantage for a terrestrial environment, e.g. if the limb is vestigial." xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "adapted for" xsd:string +range: ENVO:01000254 is_a: ecologically_related_to ! ecologically related to [Typedef] @@ -767,26 +765,13 @@ xref: RO:0003305 property_value: IAO:0000118 "contributes to expressivity of condition" xsd:string is_a: contributes_to_condition ! contributes to condition -[Typedef] -id: correlated_with -name: correlated with -def: "A relationship that holds between two entities, where the entities exhibit a statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes." [] -xref: RO:0002610 -property_value: IAO:0000232 "Groups both positive and negative correlation" xsd:string -is_a: related_via_dependence_to ! related via dependence to - -[Typedef] -id: correlated_with_condition -name: correlated with condition -def: "A relationship between an entity and a condition (phenotype or disease) with which it exhibits a statistical dependence relationship." [] -xref: RO:0003308 -is_a: correlated_with ! correlated with - [Typedef] id: creates_habitat_for name: creates habitat for def: "An interaction relationship wherein one organism creates a structure or environment that is lived in by another organism." [] xref: RO:0008505 +domain: CARO:0001010 +range: CARO:0001010 is_a: ecologically_related_to ! ecologically related to [Typedef] @@ -964,7 +949,7 @@ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 "EHDAA2" xsd:string property_value: IAO:0000119 "Jonathan Bard, EHDAA2" xsd:string -domain: CARO:0000003 +domain: CARO:0000000 is_a: developmentally_preceded_by ! developmentally preceded by [Typedef] @@ -1121,6 +1106,8 @@ id: disease_causes_disruption_of name: disease causes disruption of def: "A relationship between a disease and a process where the disease process disrupts the execution of the process." [] xref: RO:0004024 +property_value: IAO:0000589 "disease causes disruption of (disease to process)" xsd:string +domain: OGMS:0000031 range: BFO:0000015 is_a: causal_relationship_with_disease_as_subject ! causal relationship with disease as subject created_by: cjm @@ -1130,7 +1117,9 @@ creation_date: 2017-11-05T03:51:09Z id: disease_causes_dysfunction_of name: disease causes dysfunction of xref: RO:0004025 -range: BFO:0000004 +property_value: IAO:0000589 "disease causes dysfunction of (disease to anatomical entity)" xsd:string +domain: OGMS:0000031 +range: CARO:0000006 is_a: causal_relationship_with_disease_as_subject ! causal relationship with disease as subject created_by: cjm creation_date: 2017-11-05T03:58:20Z @@ -1139,7 +1128,7 @@ creation_date: 2017-11-05T03:58:20Z id: disease_has_basis_in name: disease has basis in xref: RO:0004019 -domain: BFO:0000016 +domain: OGMS:0000031 is_a: causal_relationship_with_disease_as_subject ! causal relationship with disease as subject is_a: realizable_has_basis_in ! realizable has basis in created_by: cjm @@ -1150,6 +1139,7 @@ id: disease_has_basis_in_disruption_of name: disease has basis in disruption of def: "A relation that holds between the disease and a process where the physical basis of the disease disrupts execution of a key biological process." [] xref: RO:0004021 +property_value: IAO:0000589 "disease has basis in disruption of (disease to process)" xsd:string range: BFO:0000015 is_a: disease_has_basis_in ! disease has basis in created_by: cjm @@ -1160,7 +1150,8 @@ id: disease_has_basis_in_dysfunction_of name: disease has basis in dysfunction of def: "A relation that holds between the disease and a material entity where the physical basis of the disease is a disorder of that material entity that affects its function." [] xref: RO:0004020 -range: BFO:0000040 +property_value: IAO:0000589 "disease has basis in dysfunction of (disease to anatomical structure)" xsd:string +range: CARO:0000006 is_a: disease_has_basis_in ! disease has basis in created_by: cjm creation_date: 2017-11-05T03:29:32Z @@ -1170,6 +1161,7 @@ id: disease_has_basis_in_feature name: disease has basis in feature def: "A relation that holds between the disease and a feature (a phenotype or other disease) where the physical basis of the disease is the feature." [] xref: RO:0004022 +domain: OGMS:0000031 is_a: disease_has_basis_in ! disease has basis in is_a: has_phenotype ! has phenotype created_by: cjm @@ -1180,7 +1172,8 @@ id: disease_has_feature name: disease has feature def: "A relationship between a disease and some feature of that disease, where the feature is either a phenotype or an isolated disease." [] xref: RO:0004029 -is_a: causal_relationship_with_disease_as_subject ! causal relationship with disease as subject +domain: OGMS:0000031 +is_a: disease_relationship ! disease relationship created_by: cjm creation_date: 2017-12-26T19:50:53Z @@ -1189,6 +1182,8 @@ id: disease_has_inflammation_site name: disease has inflammation site def: "A relationship between a disease and an anatomical entity where the disease is triggered by an inflammatory response to stimuli occurring in the anatomical entity" [] xref: RO:0004027 +domain: OGMS:0000031 +range: CARO:0000003 is_a: disease_has_location ! disease has location created_by: cjm creation_date: 2017-12-26T19:37:31Z @@ -1200,11 +1195,21 @@ def: "A relationship between a disease and an anatomical entity where the diseas xref: RO:0004026 property_value: IAO:0000116 "TODO: complete range axiom once more of CARO has been mireoted in to this ontology" xsd:string property_value: IAO:0000232 "This relation is intentionally very general, and covers isolated diseases, where the disease is realized as a process occurring in the location, and syndromic diseases, where one or more of the features may be present in that location. Thus any given disease can have multiple locations in the sense defined here." xsd:string +domain: OGMS:0000031 range: BFO:0000004 -is_a: causal_relationship_with_disease_as_subject ! causal relationship with disease as subject +is_a: disease_relationship ! disease relationship created_by: cjm creation_date: 2017-11-05T04:06:02Z +[Typedef] +id: disease_relationship +name: disease relationship +def: "This relation groups relations between diseases and any other kind of entity." [] +xref: RO:0040035 +property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, in which the subject or object is a disease." xsd:string +created_by: cjm +creation_date: 2018-09-26T00:00:32Z + [Typedef] id: distributary_of name: distributary of @@ -1249,12 +1254,23 @@ property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "is subject of eating interaction with" xsd:string is_a: trophically_interacts_with ! trophically interacts with +[Typedef] +id: ecologically_co-occurs_with +name: ecologically co-occurs with +def: "An interaction relationship describing organisms that often occur together at the same time and space or in the same environment." [] +xref: RO:0008506 +domain: CARO:0001010 +range: CARO:0001010 +is_symmetric: true +is_a: ecologically_related_to ! ecologically related to + [Typedef] id: ecologically_related_to name: ecologically related to def: "A relationship that is mediated in some way by the environment or environmental feature (ENVO:00002297)" [] subset: ro-eco xref: RO:0002321 +property_value: IAO:0000116 "Awaiting class for domain/range constraint, see: https://github.com/OBOFoundry/Experimental-OBO-Core/issues/6" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving ecological interactions" xsd:string @@ -1379,6 +1395,7 @@ is_a: output_of ! output of [Typedef] id: functionally_related_to name: functionally related to +def: "A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities." [] xref: RO:0002328 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000232 "This is a grouping relation that collects relations used for the purpose of connecting structure and function" xsd:string @@ -1433,6 +1450,15 @@ property_value: IAO:0000112 "penicillin allergy (DOID:0060520) has allergic trig range: BFO:0000040 is_a: causes_or_contributes_to_condition ! causes or contributes to condition +[Typedef] +id: has_anatomical_participant +name: has anatomical participant +def: "p has anatomical participant c iff p has participant c, and c is an anatomical entity" [] +xref: RO:0040036 +is_a: has_participant +created_by: cjm +creation_date: 2018-09-26T01:08:58Z + [Typedef] id: has_autoimmune_trigger name: has autoimmune trigger @@ -1506,8 +1532,8 @@ xref: RO:0002254 property_value: IAO:0000112 "Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string -domain: BFO:0000004 -range: CARO:0000003 +domain: CARO:0000000 +range: CARO:0000000 is_a: developmentally_preceded_by ! developmentally preceded by inverse_of: developmentally_contributes_to ! developmentally contributes to @@ -1518,6 +1544,8 @@ def: "x has developmental potential involving y iff x is capable of a developmen xref: RO:0002384 property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Chris Mungall" xsd:string +domain: CARO:0000000 +range: CARO:0000000 is_a: developmentally_related_to ! developmentally related to [Typedef] @@ -1682,7 +1710,7 @@ property_value: IAO:0000112 "Hydrozoa (NCBITaxon_6074) SubClassOf 'has habitat' property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Pier Buttigieg" xsd:string property_value: IAO:0000118 "adapted for living in" xsd:string -domain: CARO:0000006 +domain: CARO:0001010 range: ENVO:01000254 is_a: ecologically_related_to ! ecologically related to @@ -1820,6 +1848,7 @@ xref: RO:0002373 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 Wikipedia:Insertion_(anatomy) xsd:string property_value: seeAlso http://dbpedia.org/property/insertion +domain: CARO:0000003 {http://purl.obolibrary.org/obo/IAO_0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} is_a: attached_to ! attached to is_a: biomechanically_related_to ! biomechanically related to @@ -1831,6 +1860,7 @@ xref: RO:0002372 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 Wikipedia:Insertion_(anatomy) xsd:string property_value: seeAlso http://dbpedia.org/property/origin +domain: CARO:0000003 {comment="We need to import uberon muscle to create a stricter domain constraint"} is_a: attached_to ! attached to is_a: biomechanically_related_to ! biomechanically related to @@ -1929,7 +1959,7 @@ subset: ro-eco xref: RO:0002200 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string -domain: BFO:0000002 +range: UPHENO:0001001 inverse_of: phenotype_of ! phenotype of [Typedef] @@ -2051,6 +2081,7 @@ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string property_value: RO:0001900 RO:0001901 domain: CL:0000540 +range: CARO:0000003 is_a: overlaps ! overlaps expand_expression_to: "BFO_0000051 some (\n GO_0043025 and BFO_0000050 some ?Y)" [] @@ -2306,6 +2337,8 @@ name: innervated_by xref: RO:0002005 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 xsd:anyURI property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +domain: CARO:0000003 +range: CARO:0001001 inverse_of: innervates ! innervates [Typedef] @@ -2404,6 +2437,7 @@ id: involved_in_or_involved_in_regulation_of name: involved in or involved in regulation of def: "c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p" [] xref: RO:0002431 +property_value: IAO:0000116 "OWL does not allow defining object properties via a Union" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "involved in or reguates" xsd:string is_a: acts_upstream_of_or_within ! acts upstream of or within @@ -2622,14 +2656,6 @@ name: is killed by xref: RO:0002627 is_a: participates_in_a_biotic-biotic_interaction_with ! participates in a biotic-biotic interaction with -[Typedef] -id: is_marker_for -name: is marker for -def: "c is marker for d iff the presence or occurrence of d is correlated with the presence of occurrence of c, and the observation of c is used to infer the presence or occurrence of d. Note that this does not imply that c and d are in a direct causal relationship, as it may be the case that there is a third entity e that stands in a direct causal relationship with c and d." [] -xref: RO:0002607 -property_value: IAO:0000116 "May be ceded to OBI" xsd:string -is_a: correlated_with ! correlated with - [Typedef] id: is_sequentially_aligned_with name: is sequentially aligned with @@ -2851,16 +2877,6 @@ def: "A sub-relation of parasite-of in which the parasite that cannot complete i xref: RO:0002227 is_a: parasite_of ! parasite of -[Typedef] -id: obsolete_has_indirect_output -name: obsolete has indirect output -comment: Likely to be obsoleted. See:\nhttps://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/edit -xref: RO:0002403 -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string -is_a: has_output ! has output -is_obsolete: true - [Typedef] id: occurent_part_of name: occurent part of @@ -3010,6 +3026,8 @@ subset: ro-eco xref: RO:0002574 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: seeAlso http://dx.doi.org/10.1016/j.ecoinf.2014.08.005 +domain: CARO:0001010 +range: CARO:0001010 is_a: biotically_interacts_with ! biotically interacts with [Typedef] @@ -3277,13 +3295,6 @@ property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relati property_value: IAO:0000589 "regulates levels of (process to entity)" xsd:string is_a: functionally_related_to ! functionally related to -[Typedef] -id: related_via_dependence_to -name: related via dependence to -def: "A relationship that holds between two entities, where the relationship holds based on the presence or absence of statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes." [] -xref: RO:0002609 -property_value: 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." xsd:string - [Typedef] id: related_via_exposure_to name: related via exposure to @@ -3308,6 +3319,7 @@ name: releases neurotransmitter xref: RO:0002111 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000118 "has neurotransmitter" xsd:string +domain: CARO:0000003 [Typedef] id: represses_expression_of @@ -3325,8 +3337,8 @@ xref: RO:0002315 property_value: IAO:0000112 "an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast." xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string -range: CL:0000000 -is_a: has_participant +range: CARO:0000003 +is_a: has_anatomical_participant ! has anatomical participant is_a: results_in_developmental_progression_of ! results in developmental progression of [Typedef] @@ -3355,7 +3367,7 @@ id: results_in_closure_of name: results in closure of xref: RO:0002585 property_value: IAO:0000116 "p 'results in closure of' c if and only if p is a developmental process and p results in a state of c changing from open to closed." xsd:string -is_a: has_participant +is_a: has_anatomical_participant ! has anatomical participant is_a: results_in_developmental_progression_of ! results in developmental progression of [Typedef] @@ -3388,7 +3400,7 @@ property_value: IAO:0000112 "every flower development (GO:0009908) results in de property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://www.geneontology.org/GO.doc.development.shtml xsd:anyURI -is_a: has_participant +is_a: has_anatomical_participant ! has anatomical participant is_a: results_in_developmental_progression_of ! results in developmental progression of [Typedef] @@ -3445,7 +3457,7 @@ name: results in ending of def: "p results in the end of s if p results in a change of state in s whereby s either ceases to exist, or s becomes functionally impaired or s has its fate committed such that it is put on a path to be degraded." [] xref: RO:0002552 property_value: IAO:0000117 "Chris Mungall" xsd:string -is_a: has_participant +is_a: has_anatomical_participant ! has anatomical participant is_a: results_in_developmental_progression_of ! results in developmental progression of [Typedef] @@ -3467,7 +3479,7 @@ name: results in growth of xref: RO:0002343 property_value: IAO:0000112 "'pollen tube growth' results_in growth_of some 'pollen tube'" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string -is_a: has_participant +is_a: has_anatomical_participant ! has anatomical participant is_a: results_in_developmental_progression_of ! results in developmental progression of [Typedef] @@ -3480,7 +3492,7 @@ property_value: IAO:0000112 "bone maturation (GO:0070977) results_in_maturation_ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string -is_a: has_participant +is_a: has_anatomical_participant ! has anatomical participant is_a: results_in_developmental_progression_of ! results in developmental progression of [Typedef] @@ -3493,7 +3505,7 @@ property_value: IAO:0000112 "tongue morphogenesis (GO:0043587) results in morpho property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string -is_a: has_participant +is_a: has_anatomical_participant ! has anatomical participant is_a: results_in_developmental_progression_of ! results in developmental progression of [Typedef] @@ -3503,14 +3515,14 @@ def: "Holds between p and c when p is locomotion process and the outcome of this xref: RO:0002565 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000232 "" xsd:string -is_a: has_participant +is_a: has_anatomical_participant ! has anatomical participant [Typedef] id: results_in_organization_of name: results in organization of def: "p results in organization of c iff p results in the assembly, arrangement of constituent parts, or disassembly of c" [] xref: RO:0002592 -is_a: has_participant +is_a: has_anatomical_participant ! has anatomical participant [Typedef] id: results_in_remodeling_of @@ -3535,7 +3547,7 @@ name: results in structural organization of def: "A relationship between a process and an anatomical entity such that the process contributes to the act of creating the structural organization of the anatomical entity." [] xref: RO:0002355 property_value: IAO:0000117 "Chris Mungall" xsd:string -is_a: has_participant +is_a: has_anatomical_participant ! has anatomical participant is_a: results_in_developmental_progression_of ! results in developmental progression of [Typedef] @@ -3785,7 +3797,7 @@ def: "Holds between p and c when p is a localization process (localization cover xref: RO:0002313 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "regulates localization of" xsd:string -is_a: has_participant +is_a: has_anatomical_participant ! has anatomical participant is_a: related_via_localization_to ! related via localization to [Typedef] diff --git a/subsets/ro-causal.owl b/subsets/ro-causal.owl index 5dba616d..0a275674 100644 --- a/subsets/ro-causal.owl +++ b/subsets/ro-causal.owl @@ -381,6 +381,8 @@ + + David Osumi-Sutherland http://www.ncbi.nlm.nih.gov/pubmed/22402613 RO:0002005 @@ -787,6 +789,7 @@ Examples include: the relationship between two channels collected simultaneously + Relation between a neuron and an anatomical structure that its soma is part of. David Osumi-Sutherland @@ -931,6 +934,7 @@ Examples include: the relationship between two channels collected simultaneously + has neurotransmitter RO:0002111 @@ -1231,9 +1235,10 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - - + + a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b. + attached to part of (anatomical structure to anatomical structure) RO:0002177 attached_to_part_of attached to part of @@ -1292,7 +1297,16 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - + + + + + + + + + + A relationship that holds between a biological entity and a phenotype. Here a phenotype is construed broadly as any kind of quality of an organism part, a collection of these qualities, or a change in quality or qualities (e.g. abnormally increased temperature). The subject of this relationship can be an organism (where the organism has the phenotype, i.e. the qualities inhere in parts of this organism), a genomic entity such as a gene or genotype (if modifications of the gene or the genotype causes the phenotype), or a condition such as a disease (such that if the condition inheres in an organism, then the organism has the phenotype). Chris Mungall @@ -1538,6 +1552,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.RO:0002216 capable_of_part_of capable of part of + @@ -1690,7 +1705,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - + x develops_in y if x is located in y whilst x is developing Chris Mungall @@ -1985,8 +2000,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - - + + Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong] x has developmental contribution from y iff x has some part z such that z develops from y @@ -2167,8 +2182,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - + every flower development (GO:0009908) results in development of some flower (PO:0009046) p 'results in development of' c if and only if p is a developmental process and p results in the state of c changing from its initial state as a primordium or anlage through its mature state and to its final state. @@ -2202,8 +2217,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - + an annotation of gene X to cell morphogenesis with results_in_morphogenesis_of CL:0000540 (neuron) means that at the end of the process an input neuron has attained its shape. tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723) @@ -2220,8 +2235,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - + an annotation of gene X to cell maturation with results_in_maturation_of CL:0000057 (fibroblast) means that the fibroblast is mature at the end of the process bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474) @@ -2284,7 +2299,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - + Hydrozoa (NCBITaxon_6074) SubClassOf 'has habitat' some 'Hydrozoa habitat' where @@ -2352,8 +2367,8 @@ where - + Holds between p and c when p is a localization process (localization covers maintenance of localization as well as its establishment) and the outcome of this process is to regulate the localization of c. Chris Mungall regulates localization of @@ -2367,9 +2382,9 @@ where - - + + an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast. The relationship that links a specified entity with the process that results in an unspecified entity acquiring the features and characteristics of the specified entity Chris Mungall @@ -2385,6 +2400,7 @@ where A relationship that is mediated in some way by the environment or environmental feature (ENVO:00002297) + Awaiting class for domain/range constraint, see: https://github.com/OBOFoundry/Experimental-OBO-Core/issues/6 Chris Mungall Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving ecological interactions RO:0002321 @@ -2399,6 +2415,7 @@ where + An experimental relation currently used to connect a feature possessed by an organism (e.g. anatomical structure, biological process, phenotype or quality) to a habitat or environment in which that feature is well suited, adapted or provides a reproductive advantage for the organism. For example, fins to an aquatic environment. Usually this will mean that the structure is adapted for this environment, but we avoid saying this directly - primitive forms of the structure may not have evolved specifically for that environment (for example, early wings were not necessarily adapted for an aerial environment). Note also that this is a statement about the general class of structures - not every instance of a limb need confer an advantage for a terrestrial environment, e.g. if the limb is vestigial. Chris Mungall adapted for @@ -2509,6 +2526,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities. Chris Mungall This is a grouping relation that collects relations used for the purpose of connecting structure and function RO:0002328 @@ -2569,11 +2587,6 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - - - - - inverse of enables Chris Mungall RO:0002333 @@ -2712,8 +2725,8 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - + 'pollen tube growth' results_in growth_of some 'pollen tube' Chris Mungall RO:0002343 @@ -2826,8 +2839,8 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - + A relationship between a process and an anatomical entity such that the process contributes to the act of creating the structural organization of the anatomical entity. Chris Mungall RO:0002355 @@ -2886,6 +2899,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a Chris Mungall + attached to (anatomical structure to anatomical structure) RO:0002371 attached_to @@ -2899,6 +2913,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to. Chris Mungall Wikipedia:Insertion_(anatomy) @@ -2907,6 +2922,12 @@ However, this is not possible in OWL. We instead make this relation a sub-relati has muscle origin + + + + + We need to import uberon muscle to create a stricter domain constraint + @@ -2915,6 +2936,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone. Chris Mungall Wikipedia:Insertion_(anatomy) @@ -2923,6 +2945,12 @@ However, this is not possible in OWL. We instead make this relation a sub-relati has muscle insertion + + + + + We need to import uberon muscle into RO to use as a stricter domain constraint + @@ -3103,6 +3131,8 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + + x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction). Chris Mungall @@ -3186,22 +3216,6 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - - - - - - Chris Mungall - RO:0002403 - obsolete_has_indirect_output - Likely to be obsoleted. See: -https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/edit - obsolete has indirect output - true - - - - @@ -3300,7 +3314,6 @@ https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/ - This relation groups causal relations between material entities and causal relations between processes 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. @@ -3479,6 +3492,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p + OWL does not allow defining object properties via a Union Chris Mungall involved in or reguates RO:0002431 @@ -4653,8 +4667,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + p results in the end of s if p results in a change of state in s whereby s either ceases to exist, or s becomes functionally impaired or s has its fate committed such that it is put on a path to be degraded. Chris Mungall RO:0002552 @@ -4763,7 +4777,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c Chris Mungall @@ -4793,6 +4807,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + A relation that holds between elements of a musculoskeletal system or its analogs. Chris Mungall Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes. @@ -4885,6 +4901,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + Chris Mungall RO:0002574 @@ -4946,8 +4964,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + p 'results in closure of' c if and only if p is a developmental process and p results in a state of c changing from open to closed. RO:0002585 results_in_closure_of @@ -5030,7 +5048,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + p results in organization of c iff p results in the assembly, arrangement of constituent parts, or disassembly of c RO:0002592 results_in_organization_of @@ -5149,19 +5167,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - c is marker for d iff the presence or occurrence of d is correlated with the presence of occurrence of c, and the observation of c is used to infer the presence or occurrence of d. Note that this does not imply that c and d are in a direct causal relationship, as it may be the case that there is a third entity e that stands in a direct causal relationship with c and d. - May be ceded to OBI - RO:0002607 - is_marker_for - is marker for - - - - @@ -5175,31 +5180,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - A relationship that holds between two entities, where the relationship holds based on the presence or absence of statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes. - Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. - RO:0002609 - related_via_dependence_to - related via dependence to - - - - - - - - - A relationship that holds between two entities, where the entities exhibit a statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes. - Groups both positive and negative correlation - RO:0002610 - correlated_with - correlated with - - - - @@ -5572,18 +5552,6 @@ Environmental exposures include those imposed by natural environments, experimen - - - - - A relationship between an entity and a condition (phenotype or disease) with which it exhibits a statistical dependence relationship. - RO:0003308 - correlated_with_condition - correlated with condition - - - - @@ -5870,7 +5838,7 @@ Environmental exposures include those imposed by natural environments, experimen - + cjm 2017-11-05T03:26:47Z RO:0004019 @@ -5884,8 +5852,9 @@ Environmental exposures include those imposed by natural environments, experimen - + A relation that holds between the disease and a material entity where the physical basis of the disease is a disorder of that material entity that affects its function. + disease has basis in dysfunction of (disease to anatomical structure) cjm 2017-11-05T03:29:32Z RO:0004020 @@ -5901,6 +5870,7 @@ Environmental exposures include those imposed by natural environments, experimen A relation that holds between the disease and a process where the physical basis of the disease disrupts execution of a key biological process. + disease has basis in disruption of (disease to process) cjm 2017-11-05T03:37:52Z RO:0004021 @@ -5915,6 +5885,15 @@ Environmental exposures include those imposed by natural environments, experimen + + + + + + + + + A relation that holds between the disease and a feature (a phenotype or other disease) where the physical basis of the disease is the feature. cjm 2017-11-05T03:46:07Z @@ -5929,7 +5908,8 @@ Environmental exposures include those imposed by natural environments, experimen - + + After import upper level from OGMS, make domain more specific. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all of which have a disease as the subject. cjm @@ -5945,8 +5925,10 @@ Environmental exposures include those imposed by natural environments, experimen + A relationship between a disease and a process where the disease process disrupts the execution of the process. + disease causes disruption of (disease to process) cjm 2017-11-05T03:51:09Z RO:0004024 @@ -5960,7 +5942,9 @@ Environmental exposures include those imposed by natural environments, experimen - + + + disease causes dysfunction of (disease to anatomical entity) cjm 2017-11-05T03:58:20Z RO:0004025 @@ -5973,8 +5957,17 @@ Environmental exposures include those imposed by natural environments, experimen - + + + + + + + + + + A relationship between a disease and an anatomical entity where the disease has one or more features that are located in that entity. TODO: complete range axiom once more of CARO has been mireoted in to this ontology This relation is intentionally very general, and covers isolated diseases, where the disease is realized as a process occurring in the location, and syndromic diseases, where one or more of the features may be present in that location. Thus any given disease can have multiple locations in the sense defined here. @@ -5991,6 +5984,8 @@ Environmental exposures include those imposed by natural environments, experimen + + A relationship between a disease and an anatomical entity where the disease is triggered by an inflammatory response to stimuli occurring in the anatomical entity cjm 2017-12-26T19:37:31Z @@ -6020,12 +6015,13 @@ Environmental exposures include those imposed by natural environments, experimen - + + - - + + @@ -6217,6 +6213,8 @@ Environmental exposures include those imposed by natural environments, experimen + + An interaction relationship wherein one organism creates a structure or environment that is lived in by another organism. RO:0008505 creates_habitat_for @@ -6230,10 +6228,12 @@ Environmental exposures include those imposed by natural environments, experimen + + An interaction relationship describing organisms that often occur together at the same time and space or in the same environment. RO:0008506 - co-occurs - co-occurs + ecologically_co-occurs_with + ecologically co-occurs with @@ -6292,6 +6292,42 @@ Environmental exposures include those imposed by natural environments, experimen + + + + This relation groups relations between diseases and any other kind of entity. + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, in which the subject or object is a disease. + cjm + 2018-09-26T00:00:32Z + RO:0040035 + disease_relationship + disease relationship + + + + + + + + + + + + + + + + + p has anatomical participant c iff p has participant c, and c is an anatomical entity + cjm + 2018-09-26T01:08:58Z + RO:0040036 + has_anatomical_participant + has anatomical participant + + + + @@ -6333,12 +6369,6 @@ Environmental exposures include those imposed by natural environments, experimen - - - - - - @@ -6351,6 +6381,12 @@ Environmental exposures include those imposed by natural environments, experimen + + + + + + @@ -6363,6 +6399,12 @@ Environmental exposures include those imposed by natural environments, experimen + + + + + + @@ -6375,12 +6417,24 @@ Environmental exposures include those imposed by natural environments, experimen + + + + + + + + + + + + @@ -6423,6 +6477,12 @@ Environmental exposures include those imposed by natural environments, experimen + + + + + + @@ -6459,6 +6519,12 @@ Environmental exposures include those imposed by natural environments, experimen + + + + + + diff --git a/subsets/ro-chado.obo b/subsets/ro-chado.obo index d22c3acb..1acedc6d 100644 --- a/subsets/ro-chado.obo +++ b/subsets/ro-chado.obo @@ -5,12 +5,14 @@ remark: Includes Ontology(OntologyID(Anonymous-21)) [Axioms: 26 Logical Axioms: remark: Includes Ontology(OntologyID(Anonymous-21)) [Axioms: 32 Logical Axioms: 0] remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 61 Logical Axioms: 0] remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 18 Logical Axioms: 7] -remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 53 Logical Axioms: 12] -remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 278 Logical Axioms: 58] +remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 56 Logical Axioms: 13] +remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 9 Logical Axioms: 3] +remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 291 Logical Axioms: 62] remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 6 Logical Axioms: 2] remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 42 Logical Axioms: 16] remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 49 Logical Axioms: 14] remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 29 Logical Axioms: 9] +remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 110 Logical Axioms: 27] remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 20 Logical Axioms: 6] remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 731 Logical Axioms: 148] remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 146 Logical Axioms: 45] @@ -49,6 +51,7 @@ name: realizes id: BFO:0000060 name: obsolete_preceded_by is_transitive: true +is_obsolete: true [Typedef] id: BFO:0000062 @@ -1249,8 +1252,8 @@ is_a: RO:0002320 ! evolutionarily related to id: RO:0002313 name: transports_or_maintains_localization_of def: "Holds between p and c when p is a localization process (localization covers maintenance of localization as well as its establishment) and the outcome of this process is to regulate the localization of c." [] -is_a: RO:0000057 ! has participant is_a: RO:0002337 ! related via localization to +is_a: RO:0040036 ! has anatomical participant transitive_over: BFO:0000051 ! has part [Typedef] @@ -1309,6 +1312,7 @@ transitive_over: RO:0002017 ! has component activity [Typedef] id: RO:0002328 name: functionally_related_to +def: "A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities." [] [Typedef] id: RO:0002329 @@ -1405,7 +1409,7 @@ is_a: RO:0002344 ! results in transport to from or in id: RO:0002343 name: results_in_growth_of is_a: results_in_developmental_progression_of ! results in developmental progression of -is_a: RO:0000057 ! has participant +is_a: RO:0040036 ! has anatomical participant [Typedef] id: RO:0002344 @@ -1468,7 +1472,7 @@ id: RO:0002355 name: results_in_structural_organization_of def: "A relationship between a process and an anatomical entity such that the process contributes to the act of creating the structural organization of the anatomical entity." [] is_a: results_in_developmental_progression_of ! results in developmental progression of -is_a: RO:0000057 ! has participant +is_a: RO:0040036 ! has anatomical participant [Typedef] id: RO:0002356 @@ -1511,9 +1515,10 @@ is_a: RO:0002567 ! biomechanically related to [Typedef] id: RO:0002374 -name: has_fused_element +name: derived_from_ancestral_fusion_of def: "x has_fused_element y iff: there exists some z : x has_part z, z homologous_to y, and y is a distinct element, the boundary between x and z is largely fiat" [] -is_a: RO:0002320 ! evolutionarily related to +synonym: "has fused element" BROAD [] +is_a: RO:0002156 ! derived by descent from [Typedef] id: RO:0002375 @@ -1627,7 +1632,6 @@ is_obsolete: true id: RO:0002403 name: obsolete_has_indirect_output holds_over_chain: RO:0002411 RO:0002402 -is_a: RO:0002234 ! has output is_obsolete: true [Typedef] @@ -1680,7 +1684,6 @@ transitive_over: RO:0002408 ! directly inhibits id: RO:0002410 name: causally_related_to def: "This relation groups causal relations between material entities and causal relations between processes" [] -is_a: RO:0002609 ! related via dependence to [Typedef] id: RO:0002411 @@ -1978,7 +1981,7 @@ is_a: RO:0002461 ! partner in [Typedef] id: RO:0002464 -name: helper_property +name: helper_property_(not_for_use_in_curation) [Typedef] id: RO:0002465 @@ -2389,7 +2392,7 @@ id: RO:0002552 name: results_in_ending_of def: "p results in the end of s if p results in a change of state in s whereby s either ceases to exist, or s becomes functionally impaired or s has its fate committed such that it is put on a path to be degraded." [] is_a: results_in_developmental_progression_of ! results in developmental progression of -is_a: RO:0000057 ! has participant +is_a: RO:0040036 ! has anatomical participant [Typedef] id: RO:0002553 @@ -2442,7 +2445,7 @@ inverse_of: RO:0002566 ! causally influences [Typedef] id: RO:0002563 name: interaction_relation_helper_property -is_a: RO:0002464 ! helper property +is_a: RO:0002464 ! helper property (not for use in curation) [Typedef] id: RO:0002564 @@ -2453,7 +2456,7 @@ is_a: RO:0002563 ! interaction relation helper property id: RO:0002565 name: results_in_movement_of def: "Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c" [] -is_a: RO:0000057 ! has participant +is_a: RO:0040036 ! has anatomical participant [Typedef] id: RO:0002566 @@ -2538,7 +2541,7 @@ is_a: RO:0002595 ! causal relation between material entity and a process id: RO:0002585 name: results_in_closure_of is_a: results_in_developmental_progression_of ! results in developmental progression of -is_a: RO:0000057 ! has participant +is_a: RO:0040036 ! has anatomical participant [Typedef] id: RO:0002586 @@ -2579,7 +2582,7 @@ is_a: RO:0002592 ! results in organization of id: RO:0002592 name: results_in_organization_of def: "p results in organization of c iff p results in the assembly, arrangement of constituent parts, or disassembly of c" [] -is_a: RO:0000057 ! has participant +is_a: RO:0040036 ! has anatomical participant [Typedef] id: RO:0002593 @@ -2646,14 +2649,14 @@ is_a: RO:0002410 ! causally related to [Typedef] id: RO:0002609 -name: related_via_dependence_to +name: obsolete_related_via_dependence_to def: "A relationship that holds between two entities, where the relationship holds based on the presence or absence of statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes." [] +is_obsolete: true [Typedef] id: RO:0002610 name: correlated_with def: "A relationship that holds between two entities, where the entities exhibit a statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes." [] -is_a: RO:0002609 ! related via dependence to [Typedef] id: RO:0002614 @@ -3006,6 +3009,7 @@ is_a: RO:0004019 ! disease has basis in id: RO:0004023 name: causal_relationship_with_disease_as_subject is_a: RO:0002410 ! causally related to +is_a: RO:0040035 ! disease relationship [Typedef] id: RO:0004024 @@ -3024,7 +3028,7 @@ transitive_over: BFO:0000050 ! part of id: RO:0004026 name: disease_has_location def: "A relationship between a disease and an anatomical entity where the disease has one or more features that are located in that entity." [] -is_a: RO:0004023 ! causal relationship with disease as subject +is_a: RO:0040035 ! disease relationship [Typedef] id: RO:0004027 @@ -3043,7 +3047,7 @@ is_a: RO:0002410 ! causally related to id: RO:0004029 name: disease_has_feature def: "A relationship between a disease and some feature of that disease, where the feature is either a phenotype or an isolated disease." [] -is_a: RO:0004023 ! causal relationship with disease as subject +is_a: RO:0040035 ! disease relationship [Typedef] id: RO:0004030 @@ -3130,7 +3134,7 @@ is_a: RO:0002321 ! ecologically related to [Typedef] id: RO:0008506 -name: co-occurs +name: ecologically_co-occurs_with def: "An interaction relationship describing organisms that often occur together at the same time and space or in the same environment." [] is_symmetric: true is_a: RO:0002321 ! ecologically related to @@ -3177,6 +3181,31 @@ synonym: "triggered by process" EXACT [RO:cjm] holds_over_chain: BFO:0000054 RO:0002404 is_a: RO:0002410 ! causally related to +[Typedef] +id: RO:0010001 +name: generically_depends_on +def: "A generically dependent continuant *b* generically depends on an independent continuant *c* at time *t* means: there inheres in *c* a specifically deendent continuant which concretizes *b* at *t*." [] +synonym: "g-depends on" EXACT [] +holds_over_chain: RO:0000052 RO:0000058 +inverse_of: RO:0010002 ! is carrier of + +[Typedef] +id: RO:0010002 +name: is_carrier_of +def: "*b* is carrier of *c* at time *t* if and only if *c* *g-depends on* *b* at *t*" [] +holds_over_chain: RO:0000059 RO:0000053 + +[Typedef] +id: RO:0040035 +name: disease_relationship +def: "This relation groups relations between diseases and any other kind of entity." [] + +[Typedef] +id: RO:0040036 +name: has_anatomical_participant +def: "p has anatomical participant c iff p has participant c, and c is an anatomical entity" [] +is_a: RO:0000057 ! has participant + [Typedef] id: RO:HOM0000000 name: in_similarity_relationship_with @@ -3787,14 +3816,14 @@ id: results_in_acquisition_of_features_of name: results_in_acquisition_of_features_of def: "The relationship that links a specified entity with the process that results in an unspecified entity acquiring the features and characteristics of the specified entity" [] is_a: results_in_developmental_progression_of ! results in developmental progression of -is_a: RO:0000057 ! has participant +is_a: RO:0040036 ! has anatomical participant [Typedef] id: results_in_development_of name: results_in_development_of def: "p 'results in development of' c if and only if p is a developmental process and p results in the state of c changing from its initial state as a primordium or anlage through its mature state and to its final state." [] is_a: results_in_developmental_progression_of ! results in developmental progression of -is_a: RO:0000057 ! has participant +is_a: RO:0040036 ! has anatomical participant [Typedef] id: results_in_developmental_progression_of @@ -3818,12 +3847,12 @@ id: results_in_maturation_of name: results_in_maturation_of def: "The relationship that links an entity with a process that results in the progression of the entity over time that is independent of changes in it's shape and results in an end point state of that entity." [] is_a: results_in_developmental_progression_of ! results in developmental progression of -is_a: RO:0000057 ! has participant +is_a: RO:0040036 ! has anatomical participant [Typedef] id: results_in_morphogenesis_of name: results_in_morphogenesis_of def: "The relationship that links an entity with the process that results in the formation and shaping of that entity over time from an immature to a mature state." [] is_a: results_in_developmental_progression_of ! results in developmental progression of -is_a: RO:0000057 ! has participant +is_a: RO:0040036 ! has anatomical participant diff --git a/subsets/ro-developmental.obo b/subsets/ro-developmental.obo index 46570d9b..76d738aa 100644 --- a/subsets/ro-developmental.obo +++ b/subsets/ro-developmental.obo @@ -1,6 +1,6 @@ format-version: 1.2 ontology: ro/subsets/ro-developmental -owl-axioms: Prefix(owl:=)\nPrefix(rdf:=)\nPrefix(xml:=)\nPrefix(xsd:=)\nPrefix(rdfs:=)\n\n\nOntology(\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\n\n############################\n# Object Properties\n############################\n\n# Object Property: (coincident with)\n\nObjectPropertyRange( ObjectIntersectionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (has fasciculating neuron projection)\n\nObjectPropertyRange( ObjectUnionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (connected to)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (connects)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (directly develops from)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (enabled by)\n\nSubObjectPropertyOf( ObjectInverseOf())\n\n# Object Property: (anabranch of)\n\nSubObjectPropertyOf( ObjectInverseOf())\n\n# Object Property: (branching part of)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (condition has genetic basis in)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has feature)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n\n\n\nAnnotationAssertion(rdfs:comment \"\")\n) +owl-axioms: Prefix(owl:=)\nPrefix(rdf:=)\nPrefix(xml:=)\nPrefix(xsd:=)\nPrefix(rdfs:=)\n\n\nOntology(\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\n\n############################\n# Object Properties\n############################\n\n# Object Property: (coincident with)\n\nObjectPropertyRange( ObjectIntersectionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (has fasciculating neuron projection)\n\nObjectPropertyRange( ObjectUnionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (connected to)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (connects)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (directly develops from)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (anabranch of)\n\nSubObjectPropertyOf( ObjectInverseOf())\n\n# Object Property: (branching part of)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (condition has genetic basis in)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has basis in feature)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has location)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has feature)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (has anatomical participant)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n\n\n\nAnnotationAssertion(rdfs:comment \"\")\n) [Typedef] id: 2D_boundary_of @@ -184,6 +184,7 @@ def: "a is attached to b if and only if a and b are discrete objects or object p subset: ro-eco xref: RO:0002371 property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000589 "attached to (anatomical structure to anatomical structure)" xsd:string is_symmetric: true is_a: attached_to_part_of ! attached to part of is_a: connected_to ! connected to @@ -193,8 +194,9 @@ id: attached_to_part_of name: attached to part of def: "a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b." [] xref: RO:0002177 -domain: BFO:0000040 -range: BFO:0000040 +property_value: IAO:0000589 "attached to part of (anatomical structure to anatomical structure)" xsd:string +domain: CARO:0000003 +range: CARO:0000003 is_a: biomechanically_related_to ! biomechanically related to is_a: mereotopologically_related_to ! mereotopologically related to @@ -225,6 +227,8 @@ def: "A relation that holds between elements of a musculoskeletal system or its xref: RO:0002567 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes." xsd:string +domain: CARO:0000003 +range: CARO:0000003 is_a: functionally_related_to ! functionally related to [Typedef] @@ -323,6 +327,7 @@ def: "c stands in this relationship to p if and only if there exists some p' suc xref: RO:0002216 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "has function in" xsd:string +property_value: seeAlso "defining-property-chains-involving-reflexivity" is_a: causal_agent_in_process ! causal agent in process is_a: functionally_related_to ! functionally related to expand_expression_to: "RO_0000053 some (RO_0000054 only (BFO_0000050 some ?Y))" [] @@ -406,8 +411,9 @@ name: causal relationship with disease as subject xref: RO:0004023 property_value: IAO:0000116 "After import upper level from OGMS, make domain more specific." xsd:string property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all of which have a disease as the subject." xsd:string -domain: BFO:0000016 +domain: OGMS:0000031 is_a: causally_related_to ! causally related to +is_a: disease_relationship ! disease relationship created_by: cjm creation_date: 2017-11-05T03:50:54Z @@ -462,7 +468,6 @@ property_value: IAO:0000114 IAO:0000428 property_value: 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." xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: 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." xsd:string -is_a: related_via_dependence_to ! related via dependence to [Typedef] id: causally_upstream_of @@ -571,14 +576,6 @@ xref: RO:0002478 property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: child_nucleus_of ! child nucleus of -[Typedef] -id: co-occurs -name: co-occurs -def: "An interaction relationship describing organisms that often occur together at the same time and space or in the same environment." [] -xref: RO:0008506 -is_symmetric: true -is_a: ecologically_related_to ! ecologically related to - [Typedef] id: coincident_with name: coincident with @@ -673,6 +670,7 @@ xref: RO:0002322 property_value: IAO:0000116 "An experimental relation currently used to connect a feature possessed by an organism (e.g. anatomical structure, biological process, phenotype or quality) to a habitat or environment in which that feature is well suited, adapted or provides a reproductive advantage for the organism. For example, fins to an aquatic environment. Usually this will mean that the structure is adapted for this environment, but we avoid saying this directly - primitive forms of the structure may not have evolved specifically for that environment (for example, early wings were not necessarily adapted for an aerial environment). Note also that this is a statement about the general class of structures - not every instance of a limb need confer an advantage for a terrestrial environment, e.g. if the limb is vestigial." xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "adapted for" xsd:string +range: ENVO:01000254 is_a: ecologically_related_to ! ecologically related to [Typedef] @@ -767,26 +765,13 @@ xref: RO:0003305 property_value: IAO:0000118 "contributes to expressivity of condition" xsd:string is_a: contributes_to_condition ! contributes to condition -[Typedef] -id: correlated_with -name: correlated with -def: "A relationship that holds between two entities, where the entities exhibit a statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes." [] -xref: RO:0002610 -property_value: IAO:0000232 "Groups both positive and negative correlation" xsd:string -is_a: related_via_dependence_to ! related via dependence to - -[Typedef] -id: correlated_with_condition -name: correlated with condition -def: "A relationship between an entity and a condition (phenotype or disease) with which it exhibits a statistical dependence relationship." [] -xref: RO:0003308 -is_a: correlated_with ! correlated with - [Typedef] id: creates_habitat_for name: creates habitat for def: "An interaction relationship wherein one organism creates a structure or environment that is lived in by another organism." [] xref: RO:0008505 +domain: CARO:0001010 +range: CARO:0001010 is_a: ecologically_related_to ! ecologically related to [Typedef] @@ -964,7 +949,7 @@ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 "EHDAA2" xsd:string property_value: IAO:0000119 "Jonathan Bard, EHDAA2" xsd:string -domain: CARO:0000003 +domain: CARO:0000000 is_a: developmentally_preceded_by ! developmentally preceded by [Typedef] @@ -1121,6 +1106,8 @@ id: disease_causes_disruption_of name: disease causes disruption of def: "A relationship between a disease and a process where the disease process disrupts the execution of the process." [] xref: RO:0004024 +property_value: IAO:0000589 "disease causes disruption of (disease to process)" xsd:string +domain: OGMS:0000031 range: BFO:0000015 is_a: causal_relationship_with_disease_as_subject ! causal relationship with disease as subject created_by: cjm @@ -1130,7 +1117,9 @@ creation_date: 2017-11-05T03:51:09Z id: disease_causes_dysfunction_of name: disease causes dysfunction of xref: RO:0004025 -range: BFO:0000004 +property_value: IAO:0000589 "disease causes dysfunction of (disease to anatomical entity)" xsd:string +domain: OGMS:0000031 +range: CARO:0000006 is_a: causal_relationship_with_disease_as_subject ! causal relationship with disease as subject created_by: cjm creation_date: 2017-11-05T03:58:20Z @@ -1139,7 +1128,7 @@ creation_date: 2017-11-05T03:58:20Z id: disease_has_basis_in name: disease has basis in xref: RO:0004019 -domain: BFO:0000016 +domain: OGMS:0000031 is_a: causal_relationship_with_disease_as_subject ! causal relationship with disease as subject is_a: realizable_has_basis_in ! realizable has basis in created_by: cjm @@ -1150,6 +1139,7 @@ id: disease_has_basis_in_disruption_of name: disease has basis in disruption of def: "A relation that holds between the disease and a process where the physical basis of the disease disrupts execution of a key biological process." [] xref: RO:0004021 +property_value: IAO:0000589 "disease has basis in disruption of (disease to process)" xsd:string range: BFO:0000015 is_a: disease_has_basis_in ! disease has basis in created_by: cjm @@ -1160,7 +1150,8 @@ id: disease_has_basis_in_dysfunction_of name: disease has basis in dysfunction of def: "A relation that holds between the disease and a material entity where the physical basis of the disease is a disorder of that material entity that affects its function." [] xref: RO:0004020 -range: BFO:0000040 +property_value: IAO:0000589 "disease has basis in dysfunction of (disease to anatomical structure)" xsd:string +range: CARO:0000006 is_a: disease_has_basis_in ! disease has basis in created_by: cjm creation_date: 2017-11-05T03:29:32Z @@ -1170,6 +1161,7 @@ id: disease_has_basis_in_feature name: disease has basis in feature def: "A relation that holds between the disease and a feature (a phenotype or other disease) where the physical basis of the disease is the feature." [] xref: RO:0004022 +domain: OGMS:0000031 is_a: disease_has_basis_in ! disease has basis in is_a: has_phenotype ! has phenotype created_by: cjm @@ -1180,7 +1172,8 @@ id: disease_has_feature name: disease has feature def: "A relationship between a disease and some feature of that disease, where the feature is either a phenotype or an isolated disease." [] xref: RO:0004029 -is_a: causal_relationship_with_disease_as_subject ! causal relationship with disease as subject +domain: OGMS:0000031 +is_a: disease_relationship ! disease relationship created_by: cjm creation_date: 2017-12-26T19:50:53Z @@ -1189,6 +1182,8 @@ id: disease_has_inflammation_site name: disease has inflammation site def: "A relationship between a disease and an anatomical entity where the disease is triggered by an inflammatory response to stimuli occurring in the anatomical entity" [] xref: RO:0004027 +domain: OGMS:0000031 +range: CARO:0000003 is_a: disease_has_location ! disease has location created_by: cjm creation_date: 2017-12-26T19:37:31Z @@ -1200,11 +1195,21 @@ def: "A relationship between a disease and an anatomical entity where the diseas xref: RO:0004026 property_value: IAO:0000116 "TODO: complete range axiom once more of CARO has been mireoted in to this ontology" xsd:string property_value: IAO:0000232 "This relation is intentionally very general, and covers isolated diseases, where the disease is realized as a process occurring in the location, and syndromic diseases, where one or more of the features may be present in that location. Thus any given disease can have multiple locations in the sense defined here." xsd:string +domain: OGMS:0000031 range: BFO:0000004 -is_a: causal_relationship_with_disease_as_subject ! causal relationship with disease as subject +is_a: disease_relationship ! disease relationship created_by: cjm creation_date: 2017-11-05T04:06:02Z +[Typedef] +id: disease_relationship +name: disease relationship +def: "This relation groups relations between diseases and any other kind of entity." [] +xref: RO:0040035 +property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, in which the subject or object is a disease." xsd:string +created_by: cjm +creation_date: 2018-09-26T00:00:32Z + [Typedef] id: distributary_of name: distributary of @@ -1249,12 +1254,23 @@ property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "is subject of eating interaction with" xsd:string is_a: trophically_interacts_with ! trophically interacts with +[Typedef] +id: ecologically_co-occurs_with +name: ecologically co-occurs with +def: "An interaction relationship describing organisms that often occur together at the same time and space or in the same environment." [] +xref: RO:0008506 +domain: CARO:0001010 +range: CARO:0001010 +is_symmetric: true +is_a: ecologically_related_to ! ecologically related to + [Typedef] id: ecologically_related_to name: ecologically related to def: "A relationship that is mediated in some way by the environment or environmental feature (ENVO:00002297)" [] subset: ro-eco xref: RO:0002321 +property_value: IAO:0000116 "Awaiting class for domain/range constraint, see: https://github.com/OBOFoundry/Experimental-OBO-Core/issues/6" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving ecological interactions" xsd:string @@ -1379,6 +1395,7 @@ is_a: output_of ! output of [Typedef] id: functionally_related_to name: functionally related to +def: "A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities." [] xref: RO:0002328 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000232 "This is a grouping relation that collects relations used for the purpose of connecting structure and function" xsd:string @@ -1433,6 +1450,15 @@ property_value: IAO:0000112 "penicillin allergy (DOID:0060520) has allergic trig range: BFO:0000040 is_a: causes_or_contributes_to_condition ! causes or contributes to condition +[Typedef] +id: has_anatomical_participant +name: has anatomical participant +def: "p has anatomical participant c iff p has participant c, and c is an anatomical entity" [] +xref: RO:0040036 +is_a: has_participant +created_by: cjm +creation_date: 2018-09-26T01:08:58Z + [Typedef] id: has_autoimmune_trigger name: has autoimmune trigger @@ -1506,8 +1532,8 @@ xref: RO:0002254 property_value: IAO:0000112 "Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string -domain: BFO:0000004 -range: CARO:0000003 +domain: CARO:0000000 +range: CARO:0000000 is_a: developmentally_preceded_by ! developmentally preceded by inverse_of: developmentally_contributes_to ! developmentally contributes to @@ -1518,6 +1544,8 @@ def: "x has developmental potential involving y iff x is capable of a developmen xref: RO:0002384 property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Chris Mungall" xsd:string +domain: CARO:0000000 +range: CARO:0000000 is_a: developmentally_related_to ! developmentally related to [Typedef] @@ -1682,7 +1710,7 @@ property_value: IAO:0000112 "Hydrozoa (NCBITaxon_6074) SubClassOf 'has habitat' property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Pier Buttigieg" xsd:string property_value: IAO:0000118 "adapted for living in" xsd:string -domain: CARO:0000006 +domain: CARO:0001010 range: ENVO:01000254 is_a: ecologically_related_to ! ecologically related to @@ -1820,6 +1848,7 @@ xref: RO:0002373 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 Wikipedia:Insertion_(anatomy) xsd:string property_value: seeAlso http://dbpedia.org/property/insertion +domain: CARO:0000003 {http://purl.obolibrary.org/obo/IAO_0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} is_a: attached_to ! attached to is_a: biomechanically_related_to ! biomechanically related to @@ -1831,6 +1860,7 @@ xref: RO:0002372 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 Wikipedia:Insertion_(anatomy) xsd:string property_value: seeAlso http://dbpedia.org/property/origin +domain: CARO:0000003 {comment="We need to import uberon muscle to create a stricter domain constraint"} is_a: attached_to ! attached to is_a: biomechanically_related_to ! biomechanically related to @@ -1929,7 +1959,7 @@ subset: ro-eco xref: RO:0002200 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string -domain: BFO:0000002 +range: UPHENO:0001001 inverse_of: phenotype_of ! phenotype of [Typedef] @@ -2051,6 +2081,7 @@ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string property_value: RO:0001900 RO:0001901 domain: CL:0000540 +range: CARO:0000003 is_a: overlaps ! overlaps expand_expression_to: "BFO_0000051 some (\n GO_0043025 and BFO_0000050 some ?Y)" [] @@ -2306,6 +2337,8 @@ name: innervated_by xref: RO:0002005 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 xsd:anyURI property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +domain: CARO:0000003 +range: CARO:0001001 inverse_of: innervates ! innervates [Typedef] @@ -2404,6 +2437,7 @@ id: involved_in_or_involved_in_regulation_of name: involved in or involved in regulation of def: "c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p" [] xref: RO:0002431 +property_value: IAO:0000116 "OWL does not allow defining object properties via a Union" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "involved in or reguates" xsd:string is_a: acts_upstream_of_or_within ! acts upstream of or within @@ -2622,14 +2656,6 @@ name: is killed by xref: RO:0002627 is_a: participates_in_a_biotic-biotic_interaction_with ! participates in a biotic-biotic interaction with -[Typedef] -id: is_marker_for -name: is marker for -def: "c is marker for d iff the presence or occurrence of d is correlated with the presence of occurrence of c, and the observation of c is used to infer the presence or occurrence of d. Note that this does not imply that c and d are in a direct causal relationship, as it may be the case that there is a third entity e that stands in a direct causal relationship with c and d." [] -xref: RO:0002607 -property_value: IAO:0000116 "May be ceded to OBI" xsd:string -is_a: correlated_with ! correlated with - [Typedef] id: is_sequentially_aligned_with name: is sequentially aligned with @@ -2851,16 +2877,6 @@ def: "A sub-relation of parasite-of in which the parasite that cannot complete i xref: RO:0002227 is_a: parasite_of ! parasite of -[Typedef] -id: obsolete_has_indirect_output -name: obsolete has indirect output -comment: Likely to be obsoleted. See:\nhttps://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/edit -xref: RO:0002403 -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string -is_a: has_output ! has output -is_obsolete: true - [Typedef] id: occurent_part_of name: occurent part of @@ -3010,6 +3026,8 @@ subset: ro-eco xref: RO:0002574 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: seeAlso http://dx.doi.org/10.1016/j.ecoinf.2014.08.005 +domain: CARO:0001010 +range: CARO:0001010 is_a: biotically_interacts_with ! biotically interacts with [Typedef] @@ -3277,13 +3295,6 @@ property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relati property_value: IAO:0000589 "regulates levels of (process to entity)" xsd:string is_a: functionally_related_to ! functionally related to -[Typedef] -id: related_via_dependence_to -name: related via dependence to -def: "A relationship that holds between two entities, where the relationship holds based on the presence or absence of statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes." [] -xref: RO:0002609 -property_value: 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." xsd:string - [Typedef] id: related_via_exposure_to name: related via exposure to @@ -3308,6 +3319,7 @@ name: releases neurotransmitter xref: RO:0002111 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000118 "has neurotransmitter" xsd:string +domain: CARO:0000003 [Typedef] id: represses_expression_of @@ -3325,8 +3337,8 @@ xref: RO:0002315 property_value: IAO:0000112 "an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast." xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string -range: CL:0000000 -is_a: has_participant +range: CARO:0000003 +is_a: has_anatomical_participant ! has anatomical participant is_a: results_in_developmental_progression_of ! results in developmental progression of [Typedef] @@ -3355,7 +3367,7 @@ id: results_in_closure_of name: results in closure of xref: RO:0002585 property_value: IAO:0000116 "p 'results in closure of' c if and only if p is a developmental process and p results in a state of c changing from open to closed." xsd:string -is_a: has_participant +is_a: has_anatomical_participant ! has anatomical participant is_a: results_in_developmental_progression_of ! results in developmental progression of [Typedef] @@ -3388,7 +3400,7 @@ property_value: IAO:0000112 "every flower development (GO:0009908) results in de property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://www.geneontology.org/GO.doc.development.shtml xsd:anyURI -is_a: has_participant +is_a: has_anatomical_participant ! has anatomical participant is_a: results_in_developmental_progression_of ! results in developmental progression of [Typedef] @@ -3445,7 +3457,7 @@ name: results in ending of def: "p results in the end of s if p results in a change of state in s whereby s either ceases to exist, or s becomes functionally impaired or s has its fate committed such that it is put on a path to be degraded." [] xref: RO:0002552 property_value: IAO:0000117 "Chris Mungall" xsd:string -is_a: has_participant +is_a: has_anatomical_participant ! has anatomical participant is_a: results_in_developmental_progression_of ! results in developmental progression of [Typedef] @@ -3467,7 +3479,7 @@ name: results in growth of xref: RO:0002343 property_value: IAO:0000112 "'pollen tube growth' results_in growth_of some 'pollen tube'" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string -is_a: has_participant +is_a: has_anatomical_participant ! has anatomical participant is_a: results_in_developmental_progression_of ! results in developmental progression of [Typedef] @@ -3480,7 +3492,7 @@ property_value: IAO:0000112 "bone maturation (GO:0070977) results_in_maturation_ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string -is_a: has_participant +is_a: has_anatomical_participant ! has anatomical participant is_a: results_in_developmental_progression_of ! results in developmental progression of [Typedef] @@ -3493,7 +3505,7 @@ property_value: IAO:0000112 "tongue morphogenesis (GO:0043587) results in morpho property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string -is_a: has_participant +is_a: has_anatomical_participant ! has anatomical participant is_a: results_in_developmental_progression_of ! results in developmental progression of [Typedef] @@ -3503,14 +3515,14 @@ def: "Holds between p and c when p is locomotion process and the outcome of this xref: RO:0002565 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000232 "" xsd:string -is_a: has_participant +is_a: has_anatomical_participant ! has anatomical participant [Typedef] id: results_in_organization_of name: results in organization of def: "p results in organization of c iff p results in the assembly, arrangement of constituent parts, or disassembly of c" [] xref: RO:0002592 -is_a: has_participant +is_a: has_anatomical_participant ! has anatomical participant [Typedef] id: results_in_remodeling_of @@ -3535,7 +3547,7 @@ name: results in structural organization of def: "A relationship between a process and an anatomical entity such that the process contributes to the act of creating the structural organization of the anatomical entity." [] xref: RO:0002355 property_value: IAO:0000117 "Chris Mungall" xsd:string -is_a: has_participant +is_a: has_anatomical_participant ! has anatomical participant is_a: results_in_developmental_progression_of ! results in developmental progression of [Typedef] @@ -3785,7 +3797,7 @@ def: "Holds between p and c when p is a localization process (localization cover xref: RO:0002313 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "regulates localization of" xsd:string -is_a: has_participant +is_a: has_anatomical_participant ! has anatomical participant is_a: related_via_localization_to ! related via localization to [Typedef] diff --git a/subsets/ro-developmental.owl b/subsets/ro-developmental.owl index 9b7f5a9c..19e36944 100644 --- a/subsets/ro-developmental.owl +++ b/subsets/ro-developmental.owl @@ -381,6 +381,8 @@ + + David Osumi-Sutherland http://www.ncbi.nlm.nih.gov/pubmed/22402613 RO:0002005 @@ -787,6 +789,7 @@ Examples include: the relationship between two channels collected simultaneously + Relation between a neuron and an anatomical structure that its soma is part of. David Osumi-Sutherland @@ -931,6 +934,7 @@ Examples include: the relationship between two channels collected simultaneously + has neurotransmitter RO:0002111 @@ -1231,9 +1235,10 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - - + + a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b. + attached to part of (anatomical structure to anatomical structure) RO:0002177 attached_to_part_of attached to part of @@ -1292,7 +1297,16 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - + + + + + + + + + + A relationship that holds between a biological entity and a phenotype. Here a phenotype is construed broadly as any kind of quality of an organism part, a collection of these qualities, or a change in quality or qualities (e.g. abnormally increased temperature). The subject of this relationship can be an organism (where the organism has the phenotype, i.e. the qualities inhere in parts of this organism), a genomic entity such as a gene or genotype (if modifications of the gene or the genotype causes the phenotype), or a condition such as a disease (such that if the condition inheres in an organism, then the organism has the phenotype). Chris Mungall @@ -1538,6 +1552,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.RO:0002216 capable_of_part_of capable of part of + @@ -1690,7 +1705,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - + x develops_in y if x is located in y whilst x is developing Chris Mungall @@ -1985,8 +2000,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - - + + Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong] x has developmental contribution from y iff x has some part z such that z develops from y @@ -2167,8 +2182,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - + every flower development (GO:0009908) results in development of some flower (PO:0009046) p 'results in development of' c if and only if p is a developmental process and p results in the state of c changing from its initial state as a primordium or anlage through its mature state and to its final state. @@ -2202,8 +2217,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - + an annotation of gene X to cell morphogenesis with results_in_morphogenesis_of CL:0000540 (neuron) means that at the end of the process an input neuron has attained its shape. tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723) @@ -2220,8 +2235,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - + an annotation of gene X to cell maturation with results_in_maturation_of CL:0000057 (fibroblast) means that the fibroblast is mature at the end of the process bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474) @@ -2284,7 +2299,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - + Hydrozoa (NCBITaxon_6074) SubClassOf 'has habitat' some 'Hydrozoa habitat' where @@ -2352,8 +2367,8 @@ where - + Holds between p and c when p is a localization process (localization covers maintenance of localization as well as its establishment) and the outcome of this process is to regulate the localization of c. Chris Mungall regulates localization of @@ -2367,9 +2382,9 @@ where - - + + an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast. The relationship that links a specified entity with the process that results in an unspecified entity acquiring the features and characteristics of the specified entity Chris Mungall @@ -2385,6 +2400,7 @@ where A relationship that is mediated in some way by the environment or environmental feature (ENVO:00002297) + Awaiting class for domain/range constraint, see: https://github.com/OBOFoundry/Experimental-OBO-Core/issues/6 Chris Mungall Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving ecological interactions RO:0002321 @@ -2399,6 +2415,7 @@ where + An experimental relation currently used to connect a feature possessed by an organism (e.g. anatomical structure, biological process, phenotype or quality) to a habitat or environment in which that feature is well suited, adapted or provides a reproductive advantage for the organism. For example, fins to an aquatic environment. Usually this will mean that the structure is adapted for this environment, but we avoid saying this directly - primitive forms of the structure may not have evolved specifically for that environment (for example, early wings were not necessarily adapted for an aerial environment). Note also that this is a statement about the general class of structures - not every instance of a limb need confer an advantage for a terrestrial environment, e.g. if the limb is vestigial. Chris Mungall adapted for @@ -2509,6 +2526,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities. Chris Mungall This is a grouping relation that collects relations used for the purpose of connecting structure and function RO:0002328 @@ -2569,11 +2587,6 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - - - - - inverse of enables Chris Mungall RO:0002333 @@ -2712,8 +2725,8 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - + 'pollen tube growth' results_in growth_of some 'pollen tube' Chris Mungall RO:0002343 @@ -2826,8 +2839,8 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - + A relationship between a process and an anatomical entity such that the process contributes to the act of creating the structural organization of the anatomical entity. Chris Mungall RO:0002355 @@ -2886,6 +2899,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a Chris Mungall + attached to (anatomical structure to anatomical structure) RO:0002371 attached_to @@ -2899,6 +2913,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to. Chris Mungall Wikipedia:Insertion_(anatomy) @@ -2907,6 +2922,12 @@ However, this is not possible in OWL. We instead make this relation a sub-relati has muscle origin + + + + + We need to import uberon muscle to create a stricter domain constraint + @@ -2915,6 +2936,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone. Chris Mungall Wikipedia:Insertion_(anatomy) @@ -2923,6 +2945,12 @@ However, this is not possible in OWL. We instead make this relation a sub-relati has muscle insertion + + + + + We need to import uberon muscle into RO to use as a stricter domain constraint + @@ -3103,6 +3131,8 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + + x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction). Chris Mungall @@ -3186,22 +3216,6 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - - - - - - Chris Mungall - RO:0002403 - obsolete_has_indirect_output - Likely to be obsoleted. See: -https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/edit - obsolete has indirect output - true - - - - @@ -3300,7 +3314,6 @@ https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/ - This relation groups causal relations between material entities and causal relations between processes 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. @@ -3479,6 +3492,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p + OWL does not allow defining object properties via a Union Chris Mungall involved in or reguates RO:0002431 @@ -4653,8 +4667,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + p results in the end of s if p results in a change of state in s whereby s either ceases to exist, or s becomes functionally impaired or s has its fate committed such that it is put on a path to be degraded. Chris Mungall RO:0002552 @@ -4763,7 +4777,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c Chris Mungall @@ -4793,6 +4807,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + A relation that holds between elements of a musculoskeletal system or its analogs. Chris Mungall Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes. @@ -4885,6 +4901,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + Chris Mungall RO:0002574 @@ -4946,8 +4964,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + p 'results in closure of' c if and only if p is a developmental process and p results in a state of c changing from open to closed. RO:0002585 results_in_closure_of @@ -5030,7 +5048,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + p results in organization of c iff p results in the assembly, arrangement of constituent parts, or disassembly of c RO:0002592 results_in_organization_of @@ -5149,19 +5167,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - c is marker for d iff the presence or occurrence of d is correlated with the presence of occurrence of c, and the observation of c is used to infer the presence or occurrence of d. Note that this does not imply that c and d are in a direct causal relationship, as it may be the case that there is a third entity e that stands in a direct causal relationship with c and d. - May be ceded to OBI - RO:0002607 - is_marker_for - is marker for - - - - @@ -5175,31 +5180,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - A relationship that holds between two entities, where the relationship holds based on the presence or absence of statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes. - Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. - RO:0002609 - related_via_dependence_to - related via dependence to - - - - - - - - - A relationship that holds between two entities, where the entities exhibit a statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes. - Groups both positive and negative correlation - RO:0002610 - correlated_with - correlated with - - - - @@ -5572,18 +5552,6 @@ Environmental exposures include those imposed by natural environments, experimen - - - - - A relationship between an entity and a condition (phenotype or disease) with which it exhibits a statistical dependence relationship. - RO:0003308 - correlated_with_condition - correlated with condition - - - - @@ -5870,7 +5838,7 @@ Environmental exposures include those imposed by natural environments, experimen - + cjm 2017-11-05T03:26:47Z RO:0004019 @@ -5884,8 +5852,9 @@ Environmental exposures include those imposed by natural environments, experimen - + A relation that holds between the disease and a material entity where the physical basis of the disease is a disorder of that material entity that affects its function. + disease has basis in dysfunction of (disease to anatomical structure) cjm 2017-11-05T03:29:32Z RO:0004020 @@ -5901,6 +5870,7 @@ Environmental exposures include those imposed by natural environments, experimen A relation that holds between the disease and a process where the physical basis of the disease disrupts execution of a key biological process. + disease has basis in disruption of (disease to process) cjm 2017-11-05T03:37:52Z RO:0004021 @@ -5915,6 +5885,15 @@ Environmental exposures include those imposed by natural environments, experimen + + + + + + + + + A relation that holds between the disease and a feature (a phenotype or other disease) where the physical basis of the disease is the feature. cjm 2017-11-05T03:46:07Z @@ -5929,7 +5908,8 @@ Environmental exposures include those imposed by natural environments, experimen - + + After import upper level from OGMS, make domain more specific. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all of which have a disease as the subject. cjm @@ -5945,8 +5925,10 @@ Environmental exposures include those imposed by natural environments, experimen + A relationship between a disease and a process where the disease process disrupts the execution of the process. + disease causes disruption of (disease to process) cjm 2017-11-05T03:51:09Z RO:0004024 @@ -5960,7 +5942,9 @@ Environmental exposures include those imposed by natural environments, experimen - + + + disease causes dysfunction of (disease to anatomical entity) cjm 2017-11-05T03:58:20Z RO:0004025 @@ -5973,8 +5957,17 @@ Environmental exposures include those imposed by natural environments, experimen - + + + + + + + + + + A relationship between a disease and an anatomical entity where the disease has one or more features that are located in that entity. TODO: complete range axiom once more of CARO has been mireoted in to this ontology This relation is intentionally very general, and covers isolated diseases, where the disease is realized as a process occurring in the location, and syndromic diseases, where one or more of the features may be present in that location. Thus any given disease can have multiple locations in the sense defined here. @@ -5991,6 +5984,8 @@ Environmental exposures include those imposed by natural environments, experimen + + A relationship between a disease and an anatomical entity where the disease is triggered by an inflammatory response to stimuli occurring in the anatomical entity cjm 2017-12-26T19:37:31Z @@ -6020,12 +6015,13 @@ Environmental exposures include those imposed by natural environments, experimen - + + - - + + @@ -6217,6 +6213,8 @@ Environmental exposures include those imposed by natural environments, experimen + + An interaction relationship wherein one organism creates a structure or environment that is lived in by another organism. RO:0008505 creates_habitat_for @@ -6230,10 +6228,12 @@ Environmental exposures include those imposed by natural environments, experimen + + An interaction relationship describing organisms that often occur together at the same time and space or in the same environment. RO:0008506 - co-occurs - co-occurs + ecologically_co-occurs_with + ecologically co-occurs with @@ -6292,6 +6292,42 @@ Environmental exposures include those imposed by natural environments, experimen + + + + This relation groups relations between diseases and any other kind of entity. + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, in which the subject or object is a disease. + cjm + 2018-09-26T00:00:32Z + RO:0040035 + disease_relationship + disease relationship + + + + + + + + + + + + + + + + + p has anatomical participant c iff p has participant c, and c is an anatomical entity + cjm + 2018-09-26T01:08:58Z + RO:0040036 + has_anatomical_participant + has anatomical participant + + + + @@ -6333,12 +6369,6 @@ Environmental exposures include those imposed by natural environments, experimen - - - - - - @@ -6351,6 +6381,12 @@ Environmental exposures include those imposed by natural environments, experimen + + + + + + @@ -6363,6 +6399,12 @@ Environmental exposures include those imposed by natural environments, experimen + + + + + + @@ -6375,12 +6417,24 @@ Environmental exposures include those imposed by natural environments, experimen + + + + + + + + + + + + @@ -6423,6 +6477,12 @@ Environmental exposures include those imposed by natural environments, experimen + + + + + + @@ -6459,6 +6519,12 @@ Environmental exposures include those imposed by natural environments, experimen + + + + + + diff --git a/subsets/ro-eco.obo b/subsets/ro-eco.obo index ddb7a338..8d0712cc 100644 --- a/subsets/ro-eco.obo +++ b/subsets/ro-eco.obo @@ -3,7 +3,7 @@ data-version: ro/ro-edit.owl/subsets/ro-eco.owl subsetdef: ro-eco "" subsetdef: RO:0002259 "" ontology: ro/subsets/ro-eco -owl-axioms: Prefix(owl:=)\nPrefix(rdf:=)\nPrefix(xml:=)\nPrefix(xsd:=)\nPrefix(rdfs:=)\n\n\nOntology(\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\n############################\n# Annotation Properties\n############################\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (never in taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (mutually spatially disjoint with)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (taxonomic class assertion)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (ambiguous for taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (dubious for taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (present in taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (annotation property cardinality)\n\nSubAnnotationPropertyOf( )\nAnnotationPropertyRange( xsd:nonNegativeInteger)\n\n# Annotation Property: (logical macro assertion on a class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on a property)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on an object property)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on an annotation property)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (dispositional interpretation)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has no connections with)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (curator guidance link)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (always present in taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (temporal logical macro assertion on a class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (measurement property has unit)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has start time value)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has end time value)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, days post fertilization)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, days post fertilization)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, years post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, years post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, months post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, months post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (month of gestation)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has developmental stage marker)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, days post coitum)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, days post coitum)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, weeks post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, weeks post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is asymmetric relational form of process class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is symmetric relational form of process class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is relational form of process class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is direct form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is indirect form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on an axiom)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is a defining property chain axiom)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is a defining property chain axiom where second argument is reflexive)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is relational form of a class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion involving identity)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (in approximate one to one relationship with)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is approximately equivalent to)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is opposite of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is indistinguishable from)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (evidential logical macro assertion on an axiom)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (axiom has evidence)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (axiom contradicted by evidence)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is representative IRI for equivalence set)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is directional form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is positive form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is negative form of)\n\nSubAnnotationPropertyOf( )\n\n\n############################\n# Object Properties\n############################\n\n# Object Property: (enabled by)\n\nSubObjectPropertyOf( ObjectInverseOf())\n\n# Object Property: (anabranch of)\n\nSubObjectPropertyOf( ObjectInverseOf())\n\n# Object Property: (has substance added)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (has substance removed)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (immersed in)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (has primary substance added)\n\nIrreflexiveObjectProperty()\n\n\n\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain(ObjectInverseOf() ) )\nDLSafeRule(Annotation(rdfs:comment \"If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this.\") Annotation(rdfs:label \"inferring direct reg edge from input to regulatory subfunction\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"inferring direct neg reg edge from input to regulatory subfunction\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"inferring direct positive reg edge from input to regulatory subfunction\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"effector input is compound function input\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"Input of effector is input of its parent MF\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"if effector directly regulates X, its parent MF directly regulates X\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"if effector directly positively regulates X, its parent MF directly positively regulates X\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"if effector directly negatively regulates X, its parent MF directly negatively regulates X\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nAnnotationAssertion(rdfs:comment \"\")\n) +owl-axioms: Prefix(owl:=)\nPrefix(rdf:=)\nPrefix(xml:=)\nPrefix(xsd:=)\nPrefix(rdfs:=)\n\n\nOntology(\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(DataProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\n############################\n# Annotation Properties\n############################\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (never in taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (mutually spatially disjoint with)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (taxonomic class assertion)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (ambiguous for taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (dubious for taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (present in taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (annotation property cardinality)\n\nSubAnnotationPropertyOf( )\nAnnotationPropertyRange( xsd:nonNegativeInteger)\n\n# Annotation Property: (logical macro assertion on a class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on a property)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on an object property)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on an annotation property)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (dispositional interpretation)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has no connections with)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (curator guidance link)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (always present in taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (temporal logical macro assertion on a class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (measurement property has unit)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has start time value)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has end time value)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, days post fertilization)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, days post fertilization)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, years post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, years post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, months post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, months post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (month of gestation)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has developmental stage marker)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, days post coitum)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, days post coitum)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, weeks post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, weeks post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is asymmetric relational form of process class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is symmetric relational form of process class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is relational form of process class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is direct form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is indirect form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on an axiom)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is a defining property chain axiom)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is a defining property chain axiom where second argument is reflexive)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is relational form of a class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion involving identity)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (in approximate one to one relationship with)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is approximately equivalent to)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is opposite of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is indistinguishable from)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (evidential logical macro assertion on an axiom)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (axiom has evidence)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (axiom contradicted by evidence)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is representative IRI for equivalence set)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is directional form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is positive form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is negative form of)\n\nSubAnnotationPropertyOf( )\n\n\n############################\n# Object Properties\n############################\n\n# Object Property: (anabranch of)\n\nSubObjectPropertyOf( ObjectInverseOf())\n\n# Object Property: (has substance added)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (has substance removed)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (immersed in)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (has primary substance added)\n\nIrreflexiveObjectProperty()\n\n\n############################\n# Data Properties\n############################\n\n# Data Property: (has increased age-specific mortality rate)\n\nDataPropertyRange( DatatypeRestriction(xsd:short xsd:minInclusive \"0\"^^xsd:short xsd:maxInclusive \"100\"^^xsd:short))\n\n\n\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain(ObjectInverseOf() ) )\nDLSafeRule(Annotation(rdfs:comment \"If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this.\") Annotation(rdfs:label \"inferring direct reg edge from input to regulatory subfunction\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"inferring direct neg reg edge from input to regulatory subfunction\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"inferring direct positive reg edge from input to regulatory subfunction\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"effector input is compound function input\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"Input of effector is input of its parent MF\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"if effector directly regulates X, its parent MF directly regulates X\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"if effector directly positively regulates X, its parent MF directly positively regulates X\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"if effector directly negatively regulates X, its parent MF directly negatively regulates X\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nAnnotationAssertion(rdfs:comment \"\")\n) [Typedef] id: BFO:0000050 @@ -117,6 +117,7 @@ is_a: RO:0003302 ! causes or contributes to condition id: RO:0002001 name: aligned with property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000116 "May be obsoleted, see https://github.com/oborel/obo-relations/issues/260" xsd:string property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string property_value: RO:0001900 RO:0001901 is_transitive: true @@ -769,6 +770,7 @@ is_a: RO:0002323 ! mereotopologically related to id: RO:0002177 name: attached to part of def: "a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b." [] +property_value: IAO:0000589 "attached to part of (anatomical structure to anatomical structure)" xsd:string holds_over_chain: RO:0002371 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"} is_a: RO:0002323 ! mereotopologically related to is_a: RO:0002567 ! biomechanically related to @@ -998,6 +1000,7 @@ name: capable of part of def: "c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p." [] property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "has function in" xsd:string +property_value: seeAlso "defining-property-chains-involving-reflexivity" holds_over_chain: RO:0002215 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"} is_a: RO:0002328 ! functionally related to is_a: RO:0002500 ! causal agent in process @@ -1311,21 +1314,6 @@ property_value: IAO:0000232 "In general you should not use this relation to make is_a: RO:0002324 ! developmentally related to inverse_of: RO:0002286 ! developmentally succeeded by -[Typedef] -id: RO:0002260 -name: has biological role -def: "c has-biological-role r iff c has-role r and r is a biological role (CHEBI:24432)" [] - -[Typedef] -id: RO:0002261 -name: has application role -def: "c has-application-role r iff c has-role r and r is an application role (CHEBI:33232)" [] - -[Typedef] -id: RO:0002262 -name: has chemical role -def: "c has-chemical-role r iff c has-role r and r is a chemical role (CHEBI:51086)" [] - [Typedef] id: RO:0002263 name: acts upstream of @@ -1471,6 +1459,7 @@ def: "Holds between p and c when p is a localization process (localization cover property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "regulates localization of" xsd:string is_a: RO:0002337 ! related via localization to +is_a: RO:0040036 ! has anatomical participant [Typedef] id: RO:0002314 @@ -1480,6 +1469,7 @@ property_value: IAO:0000116 "Because part_of is transitive, inheres in is a sub- property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 property_value: RO:0001900 RO:0001901 +property_value: seeAlso "defining-property-chains-involving-reflexivity" is_a: RO:0002502 ! depends on transitive_over: BFO:0000050 @@ -1495,6 +1485,7 @@ id: RO:0002321 name: ecologically related to def: "A relationship that is mediated in some way by the environment or environmental feature (ENVO:00002297)" [] subset: ro-eco +property_value: IAO:0000116 "Awaiting class for domain/range constraint, see: https://github.com/OBOFoundry/Experimental-OBO-Core/issues/6" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving ecological interactions" xsd:string @@ -1565,6 +1556,7 @@ transitive_over: RO:0002017 ! has component activity [Typedef] id: RO:0002328 name: functionally related to +def: "A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities." [] property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000232 "This is a grouping relation that collects relations used for the purpose of connecting structure and function" xsd:string @@ -1690,6 +1682,7 @@ name: results in growth of property_value: IAO:0000112 "'pollen tube growth' results_in growth_of some 'pollen tube'" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: results_in_developmental_progression_of ! results in developmental progression of +is_a: RO:0040036 ! has anatomical participant [Typedef] id: RO:0002344 @@ -1751,6 +1744,7 @@ name: results in structural organization of def: "A relationship between a process and an anatomical entity such that the process contributes to the act of creating the structural organization of the anatomical entity." [] property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: results_in_developmental_progression_of ! results in developmental progression of +is_a: RO:0040036 ! has anatomical participant [Typedef] id: RO:0002356 @@ -1780,6 +1774,7 @@ name: attached to def: "a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a" [] subset: ro-eco property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000589 "attached to (anatomical structure to anatomical structure)" xsd:string is_symmetric: true is_a: RO:0002170 ! connected to is_a: RO:0002177 ! attached to part of @@ -1806,15 +1801,16 @@ is_a: RO:0002567 ! biomechanically related to [Typedef] id: RO:0002374 -name: has fused element +name: derived from ancestral fusion of def: "x has_fused_element y iff: there exists some z : x has_part z, z homologous_to y, and y is a distinct element, the boundary between x and z is largely fiat" [] comment: A has_fused_element B does not imply that A has_part some B: rather than A has_part some B', where B' that has some evolutionary relationship to B. +synonym: "has fused element" BROAD [] property_value: IAO:0000112 "false" xsd:boolean property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 -is_a: RO:0002320 ! evolutionarily related to +is_a: RO:0002156 ! derived by descent from [Typedef] id: RO:0002375 @@ -2000,7 +1996,6 @@ comment: Likely to be obsoleted. See:\nhttps://docs.google.com/document/d/1QMhs9 property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Chris Mungall" xsd:string holds_over_chain: RO:0002411 RO:0002402 -is_a: RO:0002234 ! has output is_obsolete: true [Typedef] @@ -2076,7 +2071,6 @@ property_value: IAO:0000114 IAO:0000428 property_value: 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." xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: 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." xsd:string -is_a: RO:0002609 ! related via dependence to [Typedef] id: RO:0002411 @@ -2198,6 +2192,7 @@ is_a: RO:0002428 ! involved in regulation of id: RO:0002431 name: involved in or involved in regulation of def: "c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p" [] +property_value: IAO:0000116 "OWL does not allow defining object properties via a Union" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "involved in or reguates" xsd:string is_a: RO:0002264 ! acts upstream of or within @@ -2527,7 +2522,7 @@ is_a: RO:0002461 ! partner in [Typedef] id: RO:0002464 -name: helper property +name: helper property (not for use in curation) property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000232 "This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning." xsd:string @@ -3103,6 +3098,7 @@ name: results in ending of def: "p results in the end of s if p results in a change of state in s whereby s either ceases to exist, or s becomes functionally impaired or s has its fate committed such that it is put on a path to be degraded." [] property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: results_in_developmental_progression_of ! results in developmental progression of +is_a: RO:0040036 ! has anatomical participant [Typedef] id: RO:0002553 @@ -3183,7 +3179,7 @@ name: interaction relation helper property property_value: http://xmlns.com/foaf/0.1/page https://github.com/oborel/obo-relations/wiki/InteractionRelations xsd:anyURI property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:N-Ary_Relation_Pattern_%28OWL_2%29 -is_a: RO:0002464 ! helper property +is_a: RO:0002464 ! helper property (not for use in curation) [Typedef] id: RO:0002564 @@ -3197,6 +3193,7 @@ name: results in movement of def: "Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c" [] property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000232 "" xsd:string +is_a: RO:0040036 ! has anatomical participant [Typedef] id: RO:0002566 @@ -3315,6 +3312,7 @@ id: RO:0002585 name: results in closure of property_value: IAO:0000116 "p 'results in closure of' c if and only if p is a developmental process and p results in a state of c changing from open to closed." xsd:string is_a: results_in_developmental_progression_of ! results in developmental progression of +is_a: RO:0040036 ! has anatomical participant [Typedef] id: RO:0002586 @@ -3355,6 +3353,7 @@ is_a: RO:0002592 ! results in organization of id: RO:0002592 name: results in organization of def: "p results in organization of c iff p results in the assembly, arrangement of constituent parts, or disassembly of c" [] +is_a: RO:0040036 ! has anatomical participant [Typedef] id: RO:0002593 @@ -3441,16 +3440,16 @@ is_a: RO:0002410 ! causally related to [Typedef] id: RO:0002609 -name: related via dependence to +name: obsolete related via dependence to def: "A relationship that holds between two entities, where the relationship holds based on the presence or absence of statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes." [] property_value: 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." xsd:string +is_obsolete: true [Typedef] id: RO:0002610 name: correlated with def: "A relationship that holds between two entities, where the entities exhibit a statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes." [] property_value: IAO:0000232 "Groups both positive and negative correlation" xsd:string -is_a: RO:0002609 ! related via dependence to [Typedef] id: RO:0002614 @@ -3868,6 +3867,7 @@ creation_date: 2017-11-05T03:26:47Z id: RO:0004020 name: disease has basis in dysfunction of def: "A relation that holds between the disease and a material entity where the physical basis of the disease is a disorder of that material entity that affects its function." [] +property_value: IAO:0000589 "disease has basis in dysfunction of (disease to anatomical structure)" xsd:string is_a: RO:0004019 ! disease has basis in created_by: cjm creation_date: 2017-11-05T03:29:32Z @@ -3876,6 +3876,7 @@ creation_date: 2017-11-05T03:29:32Z id: RO:0004021 name: disease has basis in disruption of def: "A relation that holds between the disease and a process where the physical basis of the disease disrupts execution of a key biological process." [] +property_value: IAO:0000589 "disease has basis in disruption of (disease to process)" xsd:string is_a: RO:0004019 ! disease has basis in created_by: cjm creation_date: 2017-11-05T03:37:52Z @@ -3895,6 +3896,7 @@ name: causal relationship with disease as subject property_value: IAO:0000116 "After import upper level from OGMS, make domain more specific." xsd:string property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all of which have a disease as the subject." xsd:string is_a: RO:0002410 ! causally related to +is_a: RO:0040035 ! disease relationship created_by: cjm creation_date: 2017-11-05T03:50:54Z @@ -3902,6 +3904,7 @@ creation_date: 2017-11-05T03:50:54Z id: RO:0004024 name: disease causes disruption of def: "A relationship between a disease and a process where the disease process disrupts the execution of the process." [] +property_value: IAO:0000589 "disease causes disruption of (disease to process)" xsd:string is_a: RO:0004023 ! causal relationship with disease as subject transitive_over: BFO:0000050 created_by: cjm @@ -3910,6 +3913,7 @@ creation_date: 2017-11-05T03:51:09Z [Typedef] id: RO:0004025 name: disease causes dysfunction of +property_value: IAO:0000589 "disease causes dysfunction of (disease to anatomical entity)" xsd:string is_a: RO:0004023 ! causal relationship with disease as subject transitive_over: BFO:0000050 created_by: cjm @@ -3921,7 +3925,7 @@ name: disease has location def: "A relationship between a disease and an anatomical entity where the disease has one or more features that are located in that entity." [] property_value: IAO:0000116 "TODO: complete range axiom once more of CARO has been mireoted in to this ontology" xsd:string property_value: IAO:0000232 "This relation is intentionally very general, and covers isolated diseases, where the disease is realized as a process occurring in the location, and syndromic diseases, where one or more of the features may be present in that location. Thus any given disease can have multiple locations in the sense defined here." xsd:string -is_a: RO:0004023 ! causal relationship with disease as subject +is_a: RO:0040035 ! disease relationship created_by: cjm creation_date: 2017-11-05T04:06:02Z @@ -3946,7 +3950,7 @@ creation_date: 2017-12-26T19:45:49Z id: RO:0004029 name: disease has feature def: "A relationship between a disease and some feature of that disease, where the feature is either a phenotype or an isolated disease." [] -is_a: RO:0004023 ! causal relationship with disease as subject +is_a: RO:0040035 ! disease relationship created_by: cjm creation_date: 2017-12-26T19:50:53Z @@ -4063,7 +4067,7 @@ is_a: RO:0002321 ! ecologically related to [Typedef] id: RO:0008506 -name: co-occurs +name: ecologically co-occurs with def: "An interaction relationship describing organisms that often occur together at the same time and space or in the same environment." [] is_symmetric: true is_a: RO:0002321 ! ecologically related to @@ -4130,6 +4134,43 @@ property_value: IAO:0000112 "Environmental polymorphism in butterflies: These bu property_value: seeAlso https://docs.google.com/document/d/1KWhZxVBhIPkV6_daHta0h6UyHbjY2eIrnON1WIRGgdY/edit xsd:anyURI is_a: RO:0002410 ! causally related to +[Typedef] +id: RO:0010001 +name: generically depends on +def: "A generically dependent continuant *b* generically depends on an independent continuant *c* at time *t* means: there inheres in *c* a specifically deendent continuant which concretizes *b* at *t*." [] +synonym: "g-depends on" EXACT [] +property_value: IAO:0000112 "Genetic information generically depend on molecules of DNA." xsd:string +property_value: IAO:0000112 "The novel *War and Peace* generically depends on this copy of the novel." xsd:string +property_value: IAO:0000112 "The pattern shared by chess boards generically depends on any chess board." xsd:string +property_value: IAO:0000112 "The score of a symphony g-depends on a copy of the score." xsd:string +property_value: IAO:0000112 "This pdf file generically depends on this server." xsd:string +property_value: IAO:0000119 "[072-ISO]" xsd:string +inverse_of: RO:0010002 ! is carrier of + +[Typedef] +id: RO:0010002 +name: is carrier of +def: "*b* is carrier of *c* at time *t* if and only if *c* *g-depends on* *b* at *t*" [] +property_value: IAO:0000112 "Molecules of DNA are carriers of genetic information." xsd:string +property_value: IAO:0000112 "This copy of *War and Peace* is carrier of the novel written by Tolstoy." xsd:string +property_value: IAO:0000112 "This hard drive is carrier of these data items." xsd:string +property_value: IAO:0000119 "[072-ISO]" xsd:string + +[Typedef] +id: RO:0040035 +name: disease relationship +def: "This relation groups relations between diseases and any other kind of entity." [] +property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, in which the subject or object is a disease." xsd:string +created_by: cjm +creation_date: 2018-09-26T00:00:32Z + +[Typedef] +id: RO:0040036 +name: has anatomical participant +def: "p has anatomical participant c iff p has participant c, and c is an anatomical entity" [] +created_by: cjm +creation_date: 2018-09-26T01:08:58Z + [Typedef] id: results_in_acquisition_of_features_of name: results in acquisition of features of @@ -4138,6 +4179,7 @@ property_value: IAO:0000112 "an annotation of gene X to cell differentiation wit property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string is_a: results_in_developmental_progression_of ! results in developmental progression of +is_a: RO:0040036 ! has anatomical participant [Typedef] id: results_in_development_of @@ -4148,6 +4190,7 @@ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://www.geneontology.org/GO.doc.development.shtml xsd:anyURI is_a: results_in_developmental_progression_of ! results in developmental progression of +is_a: RO:0040036 ! has anatomical participant [Typedef] id: results_in_developmental_progression_of @@ -4190,6 +4233,7 @@ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string is_a: results_in_developmental_progression_of ! results in developmental progression of +is_a: RO:0040036 ! has anatomical participant [Typedef] id: results_in_morphogenesis_of @@ -4201,4 +4245,5 @@ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string is_a: results_in_developmental_progression_of ! results in developmental progression of +is_a: RO:0040036 ! has anatomical participant diff --git a/subsets/ro-eco.owl b/subsets/ro-eco.owl index 54356c2d..b3724f2b 100644 --- a/subsets/ro-eco.owl +++ b/subsets/ro-eco.owl @@ -110,10 +110,7 @@ - - - OBO foundry unique label - + @@ -793,6 +790,12 @@ Where we have an annotation assertion + + + + + + @@ -1092,6 +1095,7 @@ range: spatial region or site (immaterial continuant) + May be obsoleted, see https://github.com/oborel/obo-relations/issues/260 David Osumi-Sutherland aligned with @@ -2200,6 +2204,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b. + attached to part of (anatomical structure to anatomical structure) attached to part of @@ -2550,6 +2555,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.has function in RO_0000053 some (RO_0000054 only (BFO_0000050 some ?Y)) capable of part of + @@ -3037,33 +3043,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - - - c has-biological-role r iff c has-role r and r is a biological role (CHEBI:24432) - has biological role - - - - - - - - c has-application-role r iff c has-role r and r is an application role (CHEBI:33232) - has application role - - - - - - - - c has-chemical-role r iff c has-role r and r is a chemical role (CHEBI:51086) - has chemical role - - - - @@ -3197,6 +3176,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. + every flower development (GO:0009908) results in development of some flower (PO:0009046) p 'results in development of' c if and only if p is a developmental process and p results in the state of c changing from its initial state as a primordium or anlage through its mature state and to its final state. @@ -3229,6 +3209,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. + an annotation of gene X to cell morphogenesis with results_in_morphogenesis_of CL:0000540 (neuron) means that at the end of the process an input neuron has attained its shape. tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723) @@ -3245,6 +3226,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. + an annotation of gene X to cell maturation with results_in_maturation_of CL:0000057 (fibroblast) means that the fibroblast is mature at the end of the process bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474) @@ -3370,6 +3352,7 @@ where + Holds between p and c when p is a localization process (localization covers maintenance of localization as well as its establishment) and the outcome of this process is to regulate the localization of c. Chris Mungall regulates localization of @@ -3392,6 +3375,7 @@ where inheres in part of + @@ -3400,6 +3384,7 @@ where + an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast. The relationship that links a specified entity with the process that results in an unspecified entity acquiring the features and characteristics of the specified entity Chris Mungall @@ -3425,6 +3410,7 @@ where A relationship that is mediated in some way by the environment or environmental feature (ENVO:00002297) + Awaiting class for domain/range constraint, see: https://github.com/OBOFoundry/Experimental-OBO-Core/issues/6 Chris Mungall Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving ecological interactions @@ -3537,6 +3523,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities. Chris Mungall This is a grouping relation that collects relations used for the purpose of connecting structure and function functionally related to @@ -3621,11 +3608,6 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - - - - - inverse of enables Chris Mungall enabled by @@ -3749,6 +3731,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + 'pollen tube growth' results_in growth_of some 'pollen tube' Chris Mungall results in growth of @@ -3842,6 +3825,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + A relationship between a process and an anatomical entity such that the process contributes to the act of creating the structural organization of the anatomical entity. Chris Mungall results in structural organization of @@ -3891,6 +3875,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a Chris Mungall + attached to (anatomical structure to anatomical structure) attached to @@ -3928,15 +3913,16 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - + false x has_fused_element y iff: there exists some z : x has_part z, z homologous_to y, and y is a distinct element, the boundary between x and z is largely fiat Chris Mungall Chris Mungall + has fused element A has_fused_element B does not imply that A has_part some B: rather than A has_part some B', where B' that has some evolutionary relationship to B. - has fused element + derived from ancestral fusion of @@ -4201,7 +4187,6 @@ https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/ - @@ -4329,7 +4314,6 @@ https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/ - This relation groups causal relations between material entities and causal relations between processes 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. @@ -4546,6 +4530,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p + OWL does not allow defining object properties via a Union Chris Mungall involved in or reguates involved in or involved in regulation of @@ -5071,7 +5056,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different Chris Mungall This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning. - helper property + helper property (not for use in curation) @@ -5966,6 +5951,7 @@ the a supports either the existence of b, or the truth value of b. + p results in the end of s if p results in a change of state in s whereby s either ceases to exist, or s becomes functionally impaired or s has its fate committed such that it is put on a path to be degraded. Chris Mungall results in ending of @@ -6105,6 +6091,7 @@ the a supports either the existence of b, or the truth value of b. + Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c Chris Mungall @@ -6291,6 +6278,7 @@ the a supports either the existence of b, or the truth value of b. + p 'results in closure of' c if and only if p is a developmental process and p results in a state of c changing from open to closed. results in closure of @@ -6359,6 +6347,7 @@ the a supports either the existence of b, or the truth value of b. + p results in organization of c iff p results in the assembly, arrangement of constituent parts, or disassembly of c results in organization of @@ -6508,7 +6497,8 @@ the a supports either the existence of b, or the truth value of b. A relationship that holds between two entities, where the relationship holds based on the presence or absence of statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. - related via dependence to + obsolete related via dependence to + true @@ -6516,7 +6506,6 @@ the a supports either the existence of b, or the truth value of b. - A relationship that holds between two entities, where the entities exhibit a statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes. Groups both positive and negative correlation correlated with @@ -7167,6 +7156,7 @@ Environmental exposures include those imposed by natural environments, experimen A relation that holds between the disease and a material entity where the physical basis of the disease is a disorder of that material entity that affects its function. + disease has basis in dysfunction of (disease to anatomical structure) cjm 2017-11-05T03:29:32Z disease has basis in dysfunction of @@ -7179,6 +7169,7 @@ Environmental exposures include those imposed by natural environments, experimen A relation that holds between the disease and a process where the physical basis of the disease disrupts execution of a key biological process. + disease has basis in disruption of (disease to process) cjm 2017-11-05T03:37:52Z disease has basis in disruption of @@ -7203,6 +7194,7 @@ Environmental exposures include those imposed by natural environments, experimen + After import upper level from OGMS, make domain more specific. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all of which have a disease as the subject. cjm @@ -7221,6 +7213,7 @@ Environmental exposures include those imposed by natural environments, experimen A relationship between a disease and a process where the disease process disrupts the execution of the process. + disease causes disruption of (disease to process) cjm 2017-11-05T03:51:09Z disease causes disruption of @@ -7236,6 +7229,7 @@ Environmental exposures include those imposed by natural environments, experimen + disease causes dysfunction of (disease to anatomical entity) cjm 2017-11-05T03:58:20Z disease causes dysfunction of @@ -7246,7 +7240,7 @@ Environmental exposures include those imposed by natural environments, experimen - + A relationship between a disease and an anatomical entity where the disease has one or more features that are located in that entity. TODO: complete range axiom once more of CARO has been mireoted in to this ontology This relation is intentionally very general, and covers isolated diseases, where the disease is realized as a process occurring in the location, and syndromic diseases, where one or more of the features may be present in that location. Thus any given disease can have multiple locations in the sense defined here. @@ -7288,7 +7282,7 @@ Environmental exposures include those imposed by natural environments, experimen - + A relationship between a disease and some feature of that disease, where the feature is either a phenotype or an isolated disease. cjm 2017-12-26T19:50:53Z @@ -7478,7 +7472,7 @@ Environmental exposures include those imposed by natural environments, experimen An interaction relationship describing organisms that often occur together at the same time and space or in the same environment. - co-occurs + ecologically co-occurs with @@ -7583,6 +7577,102 @@ Environmental exposures include those imposed by natural environments, experimen + + + + + Genetic information generically depend on molecules of DNA. + The novel *War and Peace* generically depends on this copy of the novel. + The pattern shared by chess boards generically depends on any chess board. + The score of a symphony g-depends on a copy of the score. + This pdf file generically depends on this server. + A generically dependent continuant *b* generically depends on an independent continuant *c* at time *t* means: there inheres in *c* a specifically deendent continuant which concretizes *b* at *t*. + [072-ISO] + g-depends on + generically depends on + + + + + + + + Molecules of DNA are carriers of genetic information. + This copy of *War and Peace* is carrier of the novel written by Tolstoy. + This hard drive is carrier of these data items. + *b* is carrier of *c* at time *t* if and only if *c* *g-depends on* *b* at *t* + [072-ISO] + is carrier of + + + + + + + + This relation groups relations between diseases and any other kind of entity. + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, in which the subject or object is a disease. + cjm + 2018-09-26T00:00:32Z + disease relationship + + + + + + + + p has anatomical participant c iff p has participant c, and c is an anatomical entity + cjm + 2018-09-26T01:08:58Z + has anatomical participant + + + + + + + + + + + + + + + + + + 0 + + + 100 + + + + + Then percentage of organisms in a population that die during some specified age range (age-specific mortality rate), minus the percentage that die in during the same age range in a wild-type population. + 2018-05-22T16:43:28Z + This could be used to record the increased infant morality rate in some population compared to wild-type. For examples of usage see http://purl.obolibrary.org/obo/FBcv_0000351 and subclasses. + has increased age-specific mortality rate + dos + + + + + Then percentage of organisms in a population that die during some specified age range (age-specific mortality rate), minus the percentage that die in during the same age range in a wild-type population. + PMID:24138933 + Wikipedia:Infant_mortality + + + + - - - curation status specification - - - ready for release - - - - - pending final vetting - - - - obsolescence reason specification - - - requires discussion - - - - - term replaced by + + true inverse of has disposition diff --git a/subsets/ro-interaction.obo b/subsets/ro-interaction.obo index b8de82d2..3e27e98a 100644 --- a/subsets/ro-interaction.obo +++ b/subsets/ro-interaction.obo @@ -1,6 +1,6 @@ format-version: 1.2 ontology: ro/subsets/ro-interaction -owl-axioms: Prefix(owl:=)\nPrefix(rdf:=)\nPrefix(xml:=)\nPrefix(xsd:=)\nPrefix(rdfs:=)\n\n\nOntology(\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\n\n############################\n# Object Properties\n############################\n\n# Object Property: (coincident with)\n\nObjectPropertyRange( ObjectIntersectionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (has fasciculating neuron projection)\n\nObjectPropertyRange( ObjectUnionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (connected to)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (connects)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (directly develops from)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (enabled by)\n\nSubObjectPropertyOf( ObjectInverseOf())\n\n# Object Property: (anabranch of)\n\nSubObjectPropertyOf( ObjectInverseOf())\n\n# Object Property: (branching part of)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (condition has genetic basis in)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has feature)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n\n\n\nAnnotationAssertion(rdfs:comment \"\")\n) +owl-axioms: Prefix(owl:=)\nPrefix(rdf:=)\nPrefix(xml:=)\nPrefix(xsd:=)\nPrefix(rdfs:=)\n\n\nOntology(\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\n\n############################\n# Object Properties\n############################\n\n# Object Property: (coincident with)\n\nObjectPropertyRange( ObjectIntersectionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (has fasciculating neuron projection)\n\nObjectPropertyRange( ObjectUnionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (connected to)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (connects)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (directly develops from)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (anabranch of)\n\nSubObjectPropertyOf( ObjectInverseOf())\n\n# Object Property: (branching part of)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (condition has genetic basis in)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has basis in feature)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has location)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has feature)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (has anatomical participant)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n\n\n\nAnnotationAssertion(rdfs:comment \"\")\n) [Typedef] id: 2D_boundary_of @@ -184,6 +184,7 @@ def: "a is attached to b if and only if a and b are discrete objects or object p subset: ro-eco xref: RO:0002371 property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000589 "attached to (anatomical structure to anatomical structure)" xsd:string is_symmetric: true is_a: attached_to_part_of ! attached to part of is_a: connected_to ! connected to @@ -193,8 +194,9 @@ id: attached_to_part_of name: attached to part of def: "a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b." [] xref: RO:0002177 -domain: BFO:0000040 -range: BFO:0000040 +property_value: IAO:0000589 "attached to part of (anatomical structure to anatomical structure)" xsd:string +domain: CARO:0000003 +range: CARO:0000003 is_a: biomechanically_related_to ! biomechanically related to is_a: mereotopologically_related_to ! mereotopologically related to @@ -225,6 +227,8 @@ def: "A relation that holds between elements of a musculoskeletal system or its xref: RO:0002567 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes." xsd:string +domain: CARO:0000003 +range: CARO:0000003 is_a: functionally_related_to ! functionally related to [Typedef] @@ -323,6 +327,7 @@ def: "c stands in this relationship to p if and only if there exists some p' suc xref: RO:0002216 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "has function in" xsd:string +property_value: seeAlso "defining-property-chains-involving-reflexivity" is_a: causal_agent_in_process ! causal agent in process is_a: functionally_related_to ! functionally related to expand_expression_to: "RO_0000053 some (RO_0000054 only (BFO_0000050 some ?Y))" [] @@ -406,8 +411,9 @@ name: causal relationship with disease as subject xref: RO:0004023 property_value: IAO:0000116 "After import upper level from OGMS, make domain more specific." xsd:string property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all of which have a disease as the subject." xsd:string -domain: BFO:0000016 +domain: OGMS:0000031 is_a: causally_related_to ! causally related to +is_a: disease_relationship ! disease relationship created_by: cjm creation_date: 2017-11-05T03:50:54Z @@ -462,7 +468,6 @@ property_value: IAO:0000114 IAO:0000428 property_value: 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." xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: 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." xsd:string -is_a: related_via_dependence_to ! related via dependence to [Typedef] id: causally_upstream_of @@ -571,14 +576,6 @@ xref: RO:0002478 property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: child_nucleus_of ! child nucleus of -[Typedef] -id: co-occurs -name: co-occurs -def: "An interaction relationship describing organisms that often occur together at the same time and space or in the same environment." [] -xref: RO:0008506 -is_symmetric: true -is_a: ecologically_related_to ! ecologically related to - [Typedef] id: coincident_with name: coincident with @@ -673,6 +670,7 @@ xref: RO:0002322 property_value: IAO:0000116 "An experimental relation currently used to connect a feature possessed by an organism (e.g. anatomical structure, biological process, phenotype or quality) to a habitat or environment in which that feature is well suited, adapted or provides a reproductive advantage for the organism. For example, fins to an aquatic environment. Usually this will mean that the structure is adapted for this environment, but we avoid saying this directly - primitive forms of the structure may not have evolved specifically for that environment (for example, early wings were not necessarily adapted for an aerial environment). Note also that this is a statement about the general class of structures - not every instance of a limb need confer an advantage for a terrestrial environment, e.g. if the limb is vestigial." xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "adapted for" xsd:string +range: ENVO:01000254 is_a: ecologically_related_to ! ecologically related to [Typedef] @@ -767,26 +765,13 @@ xref: RO:0003305 property_value: IAO:0000118 "contributes to expressivity of condition" xsd:string is_a: contributes_to_condition ! contributes to condition -[Typedef] -id: correlated_with -name: correlated with -def: "A relationship that holds between two entities, where the entities exhibit a statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes." [] -xref: RO:0002610 -property_value: IAO:0000232 "Groups both positive and negative correlation" xsd:string -is_a: related_via_dependence_to ! related via dependence to - -[Typedef] -id: correlated_with_condition -name: correlated with condition -def: "A relationship between an entity and a condition (phenotype or disease) with which it exhibits a statistical dependence relationship." [] -xref: RO:0003308 -is_a: correlated_with ! correlated with - [Typedef] id: creates_habitat_for name: creates habitat for def: "An interaction relationship wherein one organism creates a structure or environment that is lived in by another organism." [] xref: RO:0008505 +domain: CARO:0001010 +range: CARO:0001010 is_a: ecologically_related_to ! ecologically related to [Typedef] @@ -964,7 +949,7 @@ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 "EHDAA2" xsd:string property_value: IAO:0000119 "Jonathan Bard, EHDAA2" xsd:string -domain: CARO:0000003 +domain: CARO:0000000 is_a: developmentally_preceded_by ! developmentally preceded by [Typedef] @@ -1121,6 +1106,8 @@ id: disease_causes_disruption_of name: disease causes disruption of def: "A relationship between a disease and a process where the disease process disrupts the execution of the process." [] xref: RO:0004024 +property_value: IAO:0000589 "disease causes disruption of (disease to process)" xsd:string +domain: OGMS:0000031 range: BFO:0000015 is_a: causal_relationship_with_disease_as_subject ! causal relationship with disease as subject created_by: cjm @@ -1130,7 +1117,9 @@ creation_date: 2017-11-05T03:51:09Z id: disease_causes_dysfunction_of name: disease causes dysfunction of xref: RO:0004025 -range: BFO:0000004 +property_value: IAO:0000589 "disease causes dysfunction of (disease to anatomical entity)" xsd:string +domain: OGMS:0000031 +range: CARO:0000006 is_a: causal_relationship_with_disease_as_subject ! causal relationship with disease as subject created_by: cjm creation_date: 2017-11-05T03:58:20Z @@ -1139,7 +1128,7 @@ creation_date: 2017-11-05T03:58:20Z id: disease_has_basis_in name: disease has basis in xref: RO:0004019 -domain: BFO:0000016 +domain: OGMS:0000031 is_a: causal_relationship_with_disease_as_subject ! causal relationship with disease as subject is_a: realizable_has_basis_in ! realizable has basis in created_by: cjm @@ -1150,6 +1139,7 @@ id: disease_has_basis_in_disruption_of name: disease has basis in disruption of def: "A relation that holds between the disease and a process where the physical basis of the disease disrupts execution of a key biological process." [] xref: RO:0004021 +property_value: IAO:0000589 "disease has basis in disruption of (disease to process)" xsd:string range: BFO:0000015 is_a: disease_has_basis_in ! disease has basis in created_by: cjm @@ -1160,7 +1150,8 @@ id: disease_has_basis_in_dysfunction_of name: disease has basis in dysfunction of def: "A relation that holds between the disease and a material entity where the physical basis of the disease is a disorder of that material entity that affects its function." [] xref: RO:0004020 -range: BFO:0000040 +property_value: IAO:0000589 "disease has basis in dysfunction of (disease to anatomical structure)" xsd:string +range: CARO:0000006 is_a: disease_has_basis_in ! disease has basis in created_by: cjm creation_date: 2017-11-05T03:29:32Z @@ -1170,6 +1161,7 @@ id: disease_has_basis_in_feature name: disease has basis in feature def: "A relation that holds between the disease and a feature (a phenotype or other disease) where the physical basis of the disease is the feature." [] xref: RO:0004022 +domain: OGMS:0000031 is_a: disease_has_basis_in ! disease has basis in is_a: has_phenotype ! has phenotype created_by: cjm @@ -1180,7 +1172,8 @@ id: disease_has_feature name: disease has feature def: "A relationship between a disease and some feature of that disease, where the feature is either a phenotype or an isolated disease." [] xref: RO:0004029 -is_a: causal_relationship_with_disease_as_subject ! causal relationship with disease as subject +domain: OGMS:0000031 +is_a: disease_relationship ! disease relationship created_by: cjm creation_date: 2017-12-26T19:50:53Z @@ -1189,6 +1182,8 @@ id: disease_has_inflammation_site name: disease has inflammation site def: "A relationship between a disease and an anatomical entity where the disease is triggered by an inflammatory response to stimuli occurring in the anatomical entity" [] xref: RO:0004027 +domain: OGMS:0000031 +range: CARO:0000003 is_a: disease_has_location ! disease has location created_by: cjm creation_date: 2017-12-26T19:37:31Z @@ -1200,11 +1195,21 @@ def: "A relationship between a disease and an anatomical entity where the diseas xref: RO:0004026 property_value: IAO:0000116 "TODO: complete range axiom once more of CARO has been mireoted in to this ontology" xsd:string property_value: IAO:0000232 "This relation is intentionally very general, and covers isolated diseases, where the disease is realized as a process occurring in the location, and syndromic diseases, where one or more of the features may be present in that location. Thus any given disease can have multiple locations in the sense defined here." xsd:string +domain: OGMS:0000031 range: BFO:0000004 -is_a: causal_relationship_with_disease_as_subject ! causal relationship with disease as subject +is_a: disease_relationship ! disease relationship created_by: cjm creation_date: 2017-11-05T04:06:02Z +[Typedef] +id: disease_relationship +name: disease relationship +def: "This relation groups relations between diseases and any other kind of entity." [] +xref: RO:0040035 +property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, in which the subject or object is a disease." xsd:string +created_by: cjm +creation_date: 2018-09-26T00:00:32Z + [Typedef] id: distributary_of name: distributary of @@ -1249,12 +1254,23 @@ property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "is subject of eating interaction with" xsd:string is_a: trophically_interacts_with ! trophically interacts with +[Typedef] +id: ecologically_co-occurs_with +name: ecologically co-occurs with +def: "An interaction relationship describing organisms that often occur together at the same time and space or in the same environment." [] +xref: RO:0008506 +domain: CARO:0001010 +range: CARO:0001010 +is_symmetric: true +is_a: ecologically_related_to ! ecologically related to + [Typedef] id: ecologically_related_to name: ecologically related to def: "A relationship that is mediated in some way by the environment or environmental feature (ENVO:00002297)" [] subset: ro-eco xref: RO:0002321 +property_value: IAO:0000116 "Awaiting class for domain/range constraint, see: https://github.com/OBOFoundry/Experimental-OBO-Core/issues/6" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving ecological interactions" xsd:string @@ -1379,6 +1395,7 @@ is_a: output_of ! output of [Typedef] id: functionally_related_to name: functionally related to +def: "A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities." [] xref: RO:0002328 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000232 "This is a grouping relation that collects relations used for the purpose of connecting structure and function" xsd:string @@ -1433,6 +1450,15 @@ property_value: IAO:0000112 "penicillin allergy (DOID:0060520) has allergic trig range: BFO:0000040 is_a: causes_or_contributes_to_condition ! causes or contributes to condition +[Typedef] +id: has_anatomical_participant +name: has anatomical participant +def: "p has anatomical participant c iff p has participant c, and c is an anatomical entity" [] +xref: RO:0040036 +is_a: has_participant +created_by: cjm +creation_date: 2018-09-26T01:08:58Z + [Typedef] id: has_autoimmune_trigger name: has autoimmune trigger @@ -1506,8 +1532,8 @@ xref: RO:0002254 property_value: IAO:0000112 "Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string -domain: BFO:0000004 -range: CARO:0000003 +domain: CARO:0000000 +range: CARO:0000000 is_a: developmentally_preceded_by ! developmentally preceded by inverse_of: developmentally_contributes_to ! developmentally contributes to @@ -1518,6 +1544,8 @@ def: "x has developmental potential involving y iff x is capable of a developmen xref: RO:0002384 property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Chris Mungall" xsd:string +domain: CARO:0000000 +range: CARO:0000000 is_a: developmentally_related_to ! developmentally related to [Typedef] @@ -1682,7 +1710,7 @@ property_value: IAO:0000112 "Hydrozoa (NCBITaxon_6074) SubClassOf 'has habitat' property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Pier Buttigieg" xsd:string property_value: IAO:0000118 "adapted for living in" xsd:string -domain: CARO:0000006 +domain: CARO:0001010 range: ENVO:01000254 is_a: ecologically_related_to ! ecologically related to @@ -1820,6 +1848,7 @@ xref: RO:0002373 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 Wikipedia:Insertion_(anatomy) xsd:string property_value: seeAlso http://dbpedia.org/property/insertion +domain: CARO:0000003 {http://purl.obolibrary.org/obo/IAO_0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} is_a: attached_to ! attached to is_a: biomechanically_related_to ! biomechanically related to @@ -1831,6 +1860,7 @@ xref: RO:0002372 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 Wikipedia:Insertion_(anatomy) xsd:string property_value: seeAlso http://dbpedia.org/property/origin +domain: CARO:0000003 {comment="We need to import uberon muscle to create a stricter domain constraint"} is_a: attached_to ! attached to is_a: biomechanically_related_to ! biomechanically related to @@ -1929,7 +1959,7 @@ subset: ro-eco xref: RO:0002200 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string -domain: BFO:0000002 +range: UPHENO:0001001 inverse_of: phenotype_of ! phenotype of [Typedef] @@ -2051,6 +2081,7 @@ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string property_value: RO:0001900 RO:0001901 domain: CL:0000540 +range: CARO:0000003 is_a: overlaps ! overlaps expand_expression_to: "BFO_0000051 some (\n GO_0043025 and BFO_0000050 some ?Y)" [] @@ -2306,6 +2337,8 @@ name: innervated_by xref: RO:0002005 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 xsd:anyURI property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +domain: CARO:0000003 +range: CARO:0001001 inverse_of: innervates ! innervates [Typedef] @@ -2404,6 +2437,7 @@ id: involved_in_or_involved_in_regulation_of name: involved in or involved in regulation of def: "c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p" [] xref: RO:0002431 +property_value: IAO:0000116 "OWL does not allow defining object properties via a Union" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "involved in or reguates" xsd:string is_a: acts_upstream_of_or_within ! acts upstream of or within @@ -2622,14 +2656,6 @@ name: is killed by xref: RO:0002627 is_a: participates_in_a_biotic-biotic_interaction_with ! participates in a biotic-biotic interaction with -[Typedef] -id: is_marker_for -name: is marker for -def: "c is marker for d iff the presence or occurrence of d is correlated with the presence of occurrence of c, and the observation of c is used to infer the presence or occurrence of d. Note that this does not imply that c and d are in a direct causal relationship, as it may be the case that there is a third entity e that stands in a direct causal relationship with c and d." [] -xref: RO:0002607 -property_value: IAO:0000116 "May be ceded to OBI" xsd:string -is_a: correlated_with ! correlated with - [Typedef] id: is_sequentially_aligned_with name: is sequentially aligned with @@ -2851,16 +2877,6 @@ def: "A sub-relation of parasite-of in which the parasite that cannot complete i xref: RO:0002227 is_a: parasite_of ! parasite of -[Typedef] -id: obsolete_has_indirect_output -name: obsolete has indirect output -comment: Likely to be obsoleted. See:\nhttps://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/edit -xref: RO:0002403 -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string -is_a: has_output ! has output -is_obsolete: true - [Typedef] id: occurent_part_of name: occurent part of @@ -3010,6 +3026,8 @@ subset: ro-eco xref: RO:0002574 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: seeAlso http://dx.doi.org/10.1016/j.ecoinf.2014.08.005 +domain: CARO:0001010 +range: CARO:0001010 is_a: biotically_interacts_with ! biotically interacts with [Typedef] @@ -3277,13 +3295,6 @@ property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relati property_value: IAO:0000589 "regulates levels of (process to entity)" xsd:string is_a: functionally_related_to ! functionally related to -[Typedef] -id: related_via_dependence_to -name: related via dependence to -def: "A relationship that holds between two entities, where the relationship holds based on the presence or absence of statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes." [] -xref: RO:0002609 -property_value: 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." xsd:string - [Typedef] id: related_via_exposure_to name: related via exposure to @@ -3308,6 +3319,7 @@ name: releases neurotransmitter xref: RO:0002111 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000118 "has neurotransmitter" xsd:string +domain: CARO:0000003 [Typedef] id: represses_expression_of @@ -3325,8 +3337,8 @@ xref: RO:0002315 property_value: IAO:0000112 "an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast." xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string -range: CL:0000000 -is_a: has_participant +range: CARO:0000003 +is_a: has_anatomical_participant ! has anatomical participant is_a: results_in_developmental_progression_of ! results in developmental progression of [Typedef] @@ -3355,7 +3367,7 @@ id: results_in_closure_of name: results in closure of xref: RO:0002585 property_value: IAO:0000116 "p 'results in closure of' c if and only if p is a developmental process and p results in a state of c changing from open to closed." xsd:string -is_a: has_participant +is_a: has_anatomical_participant ! has anatomical participant is_a: results_in_developmental_progression_of ! results in developmental progression of [Typedef] @@ -3388,7 +3400,7 @@ property_value: IAO:0000112 "every flower development (GO:0009908) results in de property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://www.geneontology.org/GO.doc.development.shtml xsd:anyURI -is_a: has_participant +is_a: has_anatomical_participant ! has anatomical participant is_a: results_in_developmental_progression_of ! results in developmental progression of [Typedef] @@ -3445,7 +3457,7 @@ name: results in ending of def: "p results in the end of s if p results in a change of state in s whereby s either ceases to exist, or s becomes functionally impaired or s has its fate committed such that it is put on a path to be degraded." [] xref: RO:0002552 property_value: IAO:0000117 "Chris Mungall" xsd:string -is_a: has_participant +is_a: has_anatomical_participant ! has anatomical participant is_a: results_in_developmental_progression_of ! results in developmental progression of [Typedef] @@ -3467,7 +3479,7 @@ name: results in growth of xref: RO:0002343 property_value: IAO:0000112 "'pollen tube growth' results_in growth_of some 'pollen tube'" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string -is_a: has_participant +is_a: has_anatomical_participant ! has anatomical participant is_a: results_in_developmental_progression_of ! results in developmental progression of [Typedef] @@ -3480,7 +3492,7 @@ property_value: IAO:0000112 "bone maturation (GO:0070977) results_in_maturation_ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string -is_a: has_participant +is_a: has_anatomical_participant ! has anatomical participant is_a: results_in_developmental_progression_of ! results in developmental progression of [Typedef] @@ -3493,7 +3505,7 @@ property_value: IAO:0000112 "tongue morphogenesis (GO:0043587) results in morpho property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string -is_a: has_participant +is_a: has_anatomical_participant ! has anatomical participant is_a: results_in_developmental_progression_of ! results in developmental progression of [Typedef] @@ -3503,14 +3515,14 @@ def: "Holds between p and c when p is locomotion process and the outcome of this xref: RO:0002565 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000232 "" xsd:string -is_a: has_participant +is_a: has_anatomical_participant ! has anatomical participant [Typedef] id: results_in_organization_of name: results in organization of def: "p results in organization of c iff p results in the assembly, arrangement of constituent parts, or disassembly of c" [] xref: RO:0002592 -is_a: has_participant +is_a: has_anatomical_participant ! has anatomical participant [Typedef] id: results_in_remodeling_of @@ -3535,7 +3547,7 @@ name: results in structural organization of def: "A relationship between a process and an anatomical entity such that the process contributes to the act of creating the structural organization of the anatomical entity." [] xref: RO:0002355 property_value: IAO:0000117 "Chris Mungall" xsd:string -is_a: has_participant +is_a: has_anatomical_participant ! has anatomical participant is_a: results_in_developmental_progression_of ! results in developmental progression of [Typedef] @@ -3785,7 +3797,7 @@ def: "Holds between p and c when p is a localization process (localization cover xref: RO:0002313 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "regulates localization of" xsd:string -is_a: has_participant +is_a: has_anatomical_participant ! has anatomical participant is_a: related_via_localization_to ! related via localization to [Typedef] diff --git a/subsets/ro-interaction.owl b/subsets/ro-interaction.owl index 114ca066..118e3ab1 100644 --- a/subsets/ro-interaction.owl +++ b/subsets/ro-interaction.owl @@ -381,6 +381,8 @@ + + David Osumi-Sutherland http://www.ncbi.nlm.nih.gov/pubmed/22402613 RO:0002005 @@ -787,6 +789,7 @@ Examples include: the relationship between two channels collected simultaneously + Relation between a neuron and an anatomical structure that its soma is part of. David Osumi-Sutherland @@ -931,6 +934,7 @@ Examples include: the relationship between two channels collected simultaneously + has neurotransmitter RO:0002111 @@ -1231,9 +1235,10 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - - + + a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b. + attached to part of (anatomical structure to anatomical structure) RO:0002177 attached_to_part_of attached to part of @@ -1292,7 +1297,16 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - + + + + + + + + + + A relationship that holds between a biological entity and a phenotype. Here a phenotype is construed broadly as any kind of quality of an organism part, a collection of these qualities, or a change in quality or qualities (e.g. abnormally increased temperature). The subject of this relationship can be an organism (where the organism has the phenotype, i.e. the qualities inhere in parts of this organism), a genomic entity such as a gene or genotype (if modifications of the gene or the genotype causes the phenotype), or a condition such as a disease (such that if the condition inheres in an organism, then the organism has the phenotype). Chris Mungall @@ -1538,6 +1552,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.RO:0002216 capable_of_part_of capable of part of + @@ -1690,7 +1705,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - + x develops_in y if x is located in y whilst x is developing Chris Mungall @@ -1985,8 +2000,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - - + + Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong] x has developmental contribution from y iff x has some part z such that z develops from y @@ -2167,8 +2182,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - + every flower development (GO:0009908) results in development of some flower (PO:0009046) p 'results in development of' c if and only if p is a developmental process and p results in the state of c changing from its initial state as a primordium or anlage through its mature state and to its final state. @@ -2202,8 +2217,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - + an annotation of gene X to cell morphogenesis with results_in_morphogenesis_of CL:0000540 (neuron) means that at the end of the process an input neuron has attained its shape. tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723) @@ -2220,8 +2235,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - + an annotation of gene X to cell maturation with results_in_maturation_of CL:0000057 (fibroblast) means that the fibroblast is mature at the end of the process bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474) @@ -2284,7 +2299,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - + Hydrozoa (NCBITaxon_6074) SubClassOf 'has habitat' some 'Hydrozoa habitat' where @@ -2352,8 +2367,8 @@ where - + Holds between p and c when p is a localization process (localization covers maintenance of localization as well as its establishment) and the outcome of this process is to regulate the localization of c. Chris Mungall regulates localization of @@ -2367,9 +2382,9 @@ where - - + + an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast. The relationship that links a specified entity with the process that results in an unspecified entity acquiring the features and characteristics of the specified entity Chris Mungall @@ -2385,6 +2400,7 @@ where A relationship that is mediated in some way by the environment or environmental feature (ENVO:00002297) + Awaiting class for domain/range constraint, see: https://github.com/OBOFoundry/Experimental-OBO-Core/issues/6 Chris Mungall Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving ecological interactions RO:0002321 @@ -2399,6 +2415,7 @@ where + An experimental relation currently used to connect a feature possessed by an organism (e.g. anatomical structure, biological process, phenotype or quality) to a habitat or environment in which that feature is well suited, adapted or provides a reproductive advantage for the organism. For example, fins to an aquatic environment. Usually this will mean that the structure is adapted for this environment, but we avoid saying this directly - primitive forms of the structure may not have evolved specifically for that environment (for example, early wings were not necessarily adapted for an aerial environment). Note also that this is a statement about the general class of structures - not every instance of a limb need confer an advantage for a terrestrial environment, e.g. if the limb is vestigial. Chris Mungall adapted for @@ -2509,6 +2526,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities. Chris Mungall This is a grouping relation that collects relations used for the purpose of connecting structure and function RO:0002328 @@ -2569,11 +2587,6 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - - - - - inverse of enables Chris Mungall RO:0002333 @@ -2712,8 +2725,8 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - + 'pollen tube growth' results_in growth_of some 'pollen tube' Chris Mungall RO:0002343 @@ -2826,8 +2839,8 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - + A relationship between a process and an anatomical entity such that the process contributes to the act of creating the structural organization of the anatomical entity. Chris Mungall RO:0002355 @@ -2886,6 +2899,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a Chris Mungall + attached to (anatomical structure to anatomical structure) RO:0002371 attached_to @@ -2899,6 +2913,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to. Chris Mungall Wikipedia:Insertion_(anatomy) @@ -2907,6 +2922,12 @@ However, this is not possible in OWL. We instead make this relation a sub-relati has muscle origin + + + + + We need to import uberon muscle to create a stricter domain constraint + @@ -2915,6 +2936,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone. Chris Mungall Wikipedia:Insertion_(anatomy) @@ -2923,6 +2945,12 @@ However, this is not possible in OWL. We instead make this relation a sub-relati has muscle insertion + + + + + We need to import uberon muscle into RO to use as a stricter domain constraint + @@ -3103,6 +3131,8 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + + x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction). Chris Mungall @@ -3186,22 +3216,6 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - - - - - - Chris Mungall - RO:0002403 - obsolete_has_indirect_output - Likely to be obsoleted. See: -https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/edit - obsolete has indirect output - true - - - - @@ -3300,7 +3314,6 @@ https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/ - This relation groups causal relations between material entities and causal relations between processes 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. @@ -3479,6 +3492,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p + OWL does not allow defining object properties via a Union Chris Mungall involved in or reguates RO:0002431 @@ -4653,8 +4667,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + p results in the end of s if p results in a change of state in s whereby s either ceases to exist, or s becomes functionally impaired or s has its fate committed such that it is put on a path to be degraded. Chris Mungall RO:0002552 @@ -4763,7 +4777,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c Chris Mungall @@ -4793,6 +4807,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + A relation that holds between elements of a musculoskeletal system or its analogs. Chris Mungall Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes. @@ -4885,6 +4901,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + Chris Mungall RO:0002574 @@ -4946,8 +4964,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + p 'results in closure of' c if and only if p is a developmental process and p results in a state of c changing from open to closed. RO:0002585 results_in_closure_of @@ -5030,7 +5048,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + p results in organization of c iff p results in the assembly, arrangement of constituent parts, or disassembly of c RO:0002592 results_in_organization_of @@ -5149,19 +5167,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - c is marker for d iff the presence or occurrence of d is correlated with the presence of occurrence of c, and the observation of c is used to infer the presence or occurrence of d. Note that this does not imply that c and d are in a direct causal relationship, as it may be the case that there is a third entity e that stands in a direct causal relationship with c and d. - May be ceded to OBI - RO:0002607 - is_marker_for - is marker for - - - - @@ -5175,31 +5180,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - A relationship that holds between two entities, where the relationship holds based on the presence or absence of statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes. - Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. - RO:0002609 - related_via_dependence_to - related via dependence to - - - - - - - - - A relationship that holds between two entities, where the entities exhibit a statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes. - Groups both positive and negative correlation - RO:0002610 - correlated_with - correlated with - - - - @@ -5572,18 +5552,6 @@ Environmental exposures include those imposed by natural environments, experimen - - - - - A relationship between an entity and a condition (phenotype or disease) with which it exhibits a statistical dependence relationship. - RO:0003308 - correlated_with_condition - correlated with condition - - - - @@ -5870,7 +5838,7 @@ Environmental exposures include those imposed by natural environments, experimen - + cjm 2017-11-05T03:26:47Z RO:0004019 @@ -5884,8 +5852,9 @@ Environmental exposures include those imposed by natural environments, experimen - + A relation that holds between the disease and a material entity where the physical basis of the disease is a disorder of that material entity that affects its function. + disease has basis in dysfunction of (disease to anatomical structure) cjm 2017-11-05T03:29:32Z RO:0004020 @@ -5901,6 +5870,7 @@ Environmental exposures include those imposed by natural environments, experimen A relation that holds between the disease and a process where the physical basis of the disease disrupts execution of a key biological process. + disease has basis in disruption of (disease to process) cjm 2017-11-05T03:37:52Z RO:0004021 @@ -5915,6 +5885,15 @@ Environmental exposures include those imposed by natural environments, experimen + + + + + + + + + A relation that holds between the disease and a feature (a phenotype or other disease) where the physical basis of the disease is the feature. cjm 2017-11-05T03:46:07Z @@ -5929,7 +5908,8 @@ Environmental exposures include those imposed by natural environments, experimen - + + After import upper level from OGMS, make domain more specific. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all of which have a disease as the subject. cjm @@ -5945,8 +5925,10 @@ Environmental exposures include those imposed by natural environments, experimen + A relationship between a disease and a process where the disease process disrupts the execution of the process. + disease causes disruption of (disease to process) cjm 2017-11-05T03:51:09Z RO:0004024 @@ -5960,7 +5942,9 @@ Environmental exposures include those imposed by natural environments, experimen - + + + disease causes dysfunction of (disease to anatomical entity) cjm 2017-11-05T03:58:20Z RO:0004025 @@ -5973,8 +5957,17 @@ Environmental exposures include those imposed by natural environments, experimen - + + + + + + + + + + A relationship between a disease and an anatomical entity where the disease has one or more features that are located in that entity. TODO: complete range axiom once more of CARO has been mireoted in to this ontology This relation is intentionally very general, and covers isolated diseases, where the disease is realized as a process occurring in the location, and syndromic diseases, where one or more of the features may be present in that location. Thus any given disease can have multiple locations in the sense defined here. @@ -5991,6 +5984,8 @@ Environmental exposures include those imposed by natural environments, experimen + + A relationship between a disease and an anatomical entity where the disease is triggered by an inflammatory response to stimuli occurring in the anatomical entity cjm 2017-12-26T19:37:31Z @@ -6020,12 +6015,13 @@ Environmental exposures include those imposed by natural environments, experimen - + + - - + + @@ -6217,6 +6213,8 @@ Environmental exposures include those imposed by natural environments, experimen + + An interaction relationship wherein one organism creates a structure or environment that is lived in by another organism. RO:0008505 creates_habitat_for @@ -6230,10 +6228,12 @@ Environmental exposures include those imposed by natural environments, experimen + + An interaction relationship describing organisms that often occur together at the same time and space or in the same environment. RO:0008506 - co-occurs - co-occurs + ecologically_co-occurs_with + ecologically co-occurs with @@ -6292,6 +6292,42 @@ Environmental exposures include those imposed by natural environments, experimen + + + + This relation groups relations between diseases and any other kind of entity. + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, in which the subject or object is a disease. + cjm + 2018-09-26T00:00:32Z + RO:0040035 + disease_relationship + disease relationship + + + + + + + + + + + + + + + + + p has anatomical participant c iff p has participant c, and c is an anatomical entity + cjm + 2018-09-26T01:08:58Z + RO:0040036 + has_anatomical_participant + has anatomical participant + + + + @@ -6333,12 +6369,6 @@ Environmental exposures include those imposed by natural environments, experimen - - - - - - @@ -6351,6 +6381,12 @@ Environmental exposures include those imposed by natural environments, experimen + + + + + + @@ -6363,6 +6399,12 @@ Environmental exposures include those imposed by natural environments, experimen + + + + + + @@ -6375,12 +6417,24 @@ Environmental exposures include those imposed by natural environments, experimen + + + + + + + + + + + + @@ -6423,6 +6477,12 @@ Environmental exposures include those imposed by natural environments, experimen + + + + + + @@ -6459,6 +6519,12 @@ Environmental exposures include those imposed by natural environments, experimen + + + + + + diff --git a/subsets/ro-mereotopology.obo b/subsets/ro-mereotopology.obo index fcb92a2a..96aa8f24 100644 --- a/subsets/ro-mereotopology.obo +++ b/subsets/ro-mereotopology.obo @@ -1,6 +1,6 @@ format-version: 1.2 ontology: ro/subsets/ro-mereotopology -owl-axioms: Prefix(owl:=)\nPrefix(rdf:=)\nPrefix(xml:=)\nPrefix(xsd:=)\nPrefix(rdfs:=)\n\n\nOntology(\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\n\n############################\n# Object Properties\n############################\n\n# Object Property: (coincident with)\n\nObjectPropertyRange( ObjectIntersectionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (has fasciculating neuron projection)\n\nObjectPropertyRange( ObjectUnionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (connected to)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (connects)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (directly develops from)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (enabled by)\n\nSubObjectPropertyOf( ObjectInverseOf())\n\n# Object Property: (anabranch of)\n\nSubObjectPropertyOf( ObjectInverseOf())\n\n# Object Property: (branching part of)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (condition has genetic basis in)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has feature)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n\n\n\nAnnotationAssertion(rdfs:comment \"\")\n) +owl-axioms: Prefix(owl:=)\nPrefix(rdf:=)\nPrefix(xml:=)\nPrefix(xsd:=)\nPrefix(rdfs:=)\n\n\nOntology(\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\n\n############################\n# Object Properties\n############################\n\n# Object Property: (coincident with)\n\nObjectPropertyRange( ObjectIntersectionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (has fasciculating neuron projection)\n\nObjectPropertyRange( ObjectUnionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (connected to)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (connects)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (directly develops from)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (anabranch of)\n\nSubObjectPropertyOf( ObjectInverseOf())\n\n# Object Property: (branching part of)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (condition has genetic basis in)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has basis in feature)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has location)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has feature)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (has anatomical participant)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n\n\n\nAnnotationAssertion(rdfs:comment \"\")\n) [Typedef] id: 2D_boundary_of @@ -184,6 +184,7 @@ def: "a is attached to b if and only if a and b are discrete objects or object p subset: ro-eco xref: RO:0002371 property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000589 "attached to (anatomical structure to anatomical structure)" xsd:string is_symmetric: true is_a: attached_to_part_of ! attached to part of is_a: connected_to ! connected to @@ -193,8 +194,9 @@ id: attached_to_part_of name: attached to part of def: "a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b." [] xref: RO:0002177 -domain: BFO:0000040 -range: BFO:0000040 +property_value: IAO:0000589 "attached to part of (anatomical structure to anatomical structure)" xsd:string +domain: CARO:0000003 +range: CARO:0000003 is_a: biomechanically_related_to ! biomechanically related to is_a: mereotopologically_related_to ! mereotopologically related to @@ -225,6 +227,8 @@ def: "A relation that holds between elements of a musculoskeletal system or its xref: RO:0002567 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes." xsd:string +domain: CARO:0000003 +range: CARO:0000003 is_a: functionally_related_to ! functionally related to [Typedef] @@ -323,6 +327,7 @@ def: "c stands in this relationship to p if and only if there exists some p' suc xref: RO:0002216 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "has function in" xsd:string +property_value: seeAlso "defining-property-chains-involving-reflexivity" is_a: causal_agent_in_process ! causal agent in process is_a: functionally_related_to ! functionally related to expand_expression_to: "RO_0000053 some (RO_0000054 only (BFO_0000050 some ?Y))" [] @@ -406,8 +411,9 @@ name: causal relationship with disease as subject xref: RO:0004023 property_value: IAO:0000116 "After import upper level from OGMS, make domain more specific." xsd:string property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all of which have a disease as the subject." xsd:string -domain: BFO:0000016 +domain: OGMS:0000031 is_a: causally_related_to ! causally related to +is_a: disease_relationship ! disease relationship created_by: cjm creation_date: 2017-11-05T03:50:54Z @@ -462,7 +468,6 @@ property_value: IAO:0000114 IAO:0000428 property_value: 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." xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: 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." xsd:string -is_a: related_via_dependence_to ! related via dependence to [Typedef] id: causally_upstream_of @@ -571,14 +576,6 @@ xref: RO:0002478 property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: child_nucleus_of ! child nucleus of -[Typedef] -id: co-occurs -name: co-occurs -def: "An interaction relationship describing organisms that often occur together at the same time and space or in the same environment." [] -xref: RO:0008506 -is_symmetric: true -is_a: ecologically_related_to ! ecologically related to - [Typedef] id: coincident_with name: coincident with @@ -673,6 +670,7 @@ xref: RO:0002322 property_value: IAO:0000116 "An experimental relation currently used to connect a feature possessed by an organism (e.g. anatomical structure, biological process, phenotype or quality) to a habitat or environment in which that feature is well suited, adapted or provides a reproductive advantage for the organism. For example, fins to an aquatic environment. Usually this will mean that the structure is adapted for this environment, but we avoid saying this directly - primitive forms of the structure may not have evolved specifically for that environment (for example, early wings were not necessarily adapted for an aerial environment). Note also that this is a statement about the general class of structures - not every instance of a limb need confer an advantage for a terrestrial environment, e.g. if the limb is vestigial." xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "adapted for" xsd:string +range: ENVO:01000254 is_a: ecologically_related_to ! ecologically related to [Typedef] @@ -767,26 +765,13 @@ xref: RO:0003305 property_value: IAO:0000118 "contributes to expressivity of condition" xsd:string is_a: contributes_to_condition ! contributes to condition -[Typedef] -id: correlated_with -name: correlated with -def: "A relationship that holds between two entities, where the entities exhibit a statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes." [] -xref: RO:0002610 -property_value: IAO:0000232 "Groups both positive and negative correlation" xsd:string -is_a: related_via_dependence_to ! related via dependence to - -[Typedef] -id: correlated_with_condition -name: correlated with condition -def: "A relationship between an entity and a condition (phenotype or disease) with which it exhibits a statistical dependence relationship." [] -xref: RO:0003308 -is_a: correlated_with ! correlated with - [Typedef] id: creates_habitat_for name: creates habitat for def: "An interaction relationship wherein one organism creates a structure or environment that is lived in by another organism." [] xref: RO:0008505 +domain: CARO:0001010 +range: CARO:0001010 is_a: ecologically_related_to ! ecologically related to [Typedef] @@ -964,7 +949,7 @@ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 "EHDAA2" xsd:string property_value: IAO:0000119 "Jonathan Bard, EHDAA2" xsd:string -domain: CARO:0000003 +domain: CARO:0000000 is_a: developmentally_preceded_by ! developmentally preceded by [Typedef] @@ -1121,6 +1106,8 @@ id: disease_causes_disruption_of name: disease causes disruption of def: "A relationship between a disease and a process where the disease process disrupts the execution of the process." [] xref: RO:0004024 +property_value: IAO:0000589 "disease causes disruption of (disease to process)" xsd:string +domain: OGMS:0000031 range: BFO:0000015 is_a: causal_relationship_with_disease_as_subject ! causal relationship with disease as subject created_by: cjm @@ -1130,7 +1117,9 @@ creation_date: 2017-11-05T03:51:09Z id: disease_causes_dysfunction_of name: disease causes dysfunction of xref: RO:0004025 -range: BFO:0000004 +property_value: IAO:0000589 "disease causes dysfunction of (disease to anatomical entity)" xsd:string +domain: OGMS:0000031 +range: CARO:0000006 is_a: causal_relationship_with_disease_as_subject ! causal relationship with disease as subject created_by: cjm creation_date: 2017-11-05T03:58:20Z @@ -1139,7 +1128,7 @@ creation_date: 2017-11-05T03:58:20Z id: disease_has_basis_in name: disease has basis in xref: RO:0004019 -domain: BFO:0000016 +domain: OGMS:0000031 is_a: causal_relationship_with_disease_as_subject ! causal relationship with disease as subject is_a: realizable_has_basis_in ! realizable has basis in created_by: cjm @@ -1150,6 +1139,7 @@ id: disease_has_basis_in_disruption_of name: disease has basis in disruption of def: "A relation that holds between the disease and a process where the physical basis of the disease disrupts execution of a key biological process." [] xref: RO:0004021 +property_value: IAO:0000589 "disease has basis in disruption of (disease to process)" xsd:string range: BFO:0000015 is_a: disease_has_basis_in ! disease has basis in created_by: cjm @@ -1160,7 +1150,8 @@ id: disease_has_basis_in_dysfunction_of name: disease has basis in dysfunction of def: "A relation that holds between the disease and a material entity where the physical basis of the disease is a disorder of that material entity that affects its function." [] xref: RO:0004020 -range: BFO:0000040 +property_value: IAO:0000589 "disease has basis in dysfunction of (disease to anatomical structure)" xsd:string +range: CARO:0000006 is_a: disease_has_basis_in ! disease has basis in created_by: cjm creation_date: 2017-11-05T03:29:32Z @@ -1170,6 +1161,7 @@ id: disease_has_basis_in_feature name: disease has basis in feature def: "A relation that holds between the disease and a feature (a phenotype or other disease) where the physical basis of the disease is the feature." [] xref: RO:0004022 +domain: OGMS:0000031 is_a: disease_has_basis_in ! disease has basis in is_a: has_phenotype ! has phenotype created_by: cjm @@ -1180,7 +1172,8 @@ id: disease_has_feature name: disease has feature def: "A relationship between a disease and some feature of that disease, where the feature is either a phenotype or an isolated disease." [] xref: RO:0004029 -is_a: causal_relationship_with_disease_as_subject ! causal relationship with disease as subject +domain: OGMS:0000031 +is_a: disease_relationship ! disease relationship created_by: cjm creation_date: 2017-12-26T19:50:53Z @@ -1189,6 +1182,8 @@ id: disease_has_inflammation_site name: disease has inflammation site def: "A relationship between a disease and an anatomical entity where the disease is triggered by an inflammatory response to stimuli occurring in the anatomical entity" [] xref: RO:0004027 +domain: OGMS:0000031 +range: CARO:0000003 is_a: disease_has_location ! disease has location created_by: cjm creation_date: 2017-12-26T19:37:31Z @@ -1200,11 +1195,21 @@ def: "A relationship between a disease and an anatomical entity where the diseas xref: RO:0004026 property_value: IAO:0000116 "TODO: complete range axiom once more of CARO has been mireoted in to this ontology" xsd:string property_value: IAO:0000232 "This relation is intentionally very general, and covers isolated diseases, where the disease is realized as a process occurring in the location, and syndromic diseases, where one or more of the features may be present in that location. Thus any given disease can have multiple locations in the sense defined here." xsd:string +domain: OGMS:0000031 range: BFO:0000004 -is_a: causal_relationship_with_disease_as_subject ! causal relationship with disease as subject +is_a: disease_relationship ! disease relationship created_by: cjm creation_date: 2017-11-05T04:06:02Z +[Typedef] +id: disease_relationship +name: disease relationship +def: "This relation groups relations between diseases and any other kind of entity." [] +xref: RO:0040035 +property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, in which the subject or object is a disease." xsd:string +created_by: cjm +creation_date: 2018-09-26T00:00:32Z + [Typedef] id: distributary_of name: distributary of @@ -1249,12 +1254,23 @@ property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "is subject of eating interaction with" xsd:string is_a: trophically_interacts_with ! trophically interacts with +[Typedef] +id: ecologically_co-occurs_with +name: ecologically co-occurs with +def: "An interaction relationship describing organisms that often occur together at the same time and space or in the same environment." [] +xref: RO:0008506 +domain: CARO:0001010 +range: CARO:0001010 +is_symmetric: true +is_a: ecologically_related_to ! ecologically related to + [Typedef] id: ecologically_related_to name: ecologically related to def: "A relationship that is mediated in some way by the environment or environmental feature (ENVO:00002297)" [] subset: ro-eco xref: RO:0002321 +property_value: IAO:0000116 "Awaiting class for domain/range constraint, see: https://github.com/OBOFoundry/Experimental-OBO-Core/issues/6" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving ecological interactions" xsd:string @@ -1379,6 +1395,7 @@ is_a: output_of ! output of [Typedef] id: functionally_related_to name: functionally related to +def: "A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities." [] xref: RO:0002328 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000232 "This is a grouping relation that collects relations used for the purpose of connecting structure and function" xsd:string @@ -1433,6 +1450,15 @@ property_value: IAO:0000112 "penicillin allergy (DOID:0060520) has allergic trig range: BFO:0000040 is_a: causes_or_contributes_to_condition ! causes or contributes to condition +[Typedef] +id: has_anatomical_participant +name: has anatomical participant +def: "p has anatomical participant c iff p has participant c, and c is an anatomical entity" [] +xref: RO:0040036 +is_a: has_participant +created_by: cjm +creation_date: 2018-09-26T01:08:58Z + [Typedef] id: has_autoimmune_trigger name: has autoimmune trigger @@ -1506,8 +1532,8 @@ xref: RO:0002254 property_value: IAO:0000112 "Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string -domain: BFO:0000004 -range: CARO:0000003 +domain: CARO:0000000 +range: CARO:0000000 is_a: developmentally_preceded_by ! developmentally preceded by inverse_of: developmentally_contributes_to ! developmentally contributes to @@ -1518,6 +1544,8 @@ def: "x has developmental potential involving y iff x is capable of a developmen xref: RO:0002384 property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Chris Mungall" xsd:string +domain: CARO:0000000 +range: CARO:0000000 is_a: developmentally_related_to ! developmentally related to [Typedef] @@ -1682,7 +1710,7 @@ property_value: IAO:0000112 "Hydrozoa (NCBITaxon_6074) SubClassOf 'has habitat' property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Pier Buttigieg" xsd:string property_value: IAO:0000118 "adapted for living in" xsd:string -domain: CARO:0000006 +domain: CARO:0001010 range: ENVO:01000254 is_a: ecologically_related_to ! ecologically related to @@ -1820,6 +1848,7 @@ xref: RO:0002373 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 Wikipedia:Insertion_(anatomy) xsd:string property_value: seeAlso http://dbpedia.org/property/insertion +domain: CARO:0000003 {http://purl.obolibrary.org/obo/IAO_0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} is_a: attached_to ! attached to is_a: biomechanically_related_to ! biomechanically related to @@ -1831,6 +1860,7 @@ xref: RO:0002372 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 Wikipedia:Insertion_(anatomy) xsd:string property_value: seeAlso http://dbpedia.org/property/origin +domain: CARO:0000003 {comment="We need to import uberon muscle to create a stricter domain constraint"} is_a: attached_to ! attached to is_a: biomechanically_related_to ! biomechanically related to @@ -1929,7 +1959,7 @@ subset: ro-eco xref: RO:0002200 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string -domain: BFO:0000002 +range: UPHENO:0001001 inverse_of: phenotype_of ! phenotype of [Typedef] @@ -2051,6 +2081,7 @@ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string property_value: RO:0001900 RO:0001901 domain: CL:0000540 +range: CARO:0000003 is_a: overlaps ! overlaps expand_expression_to: "BFO_0000051 some (\n GO_0043025 and BFO_0000050 some ?Y)" [] @@ -2306,6 +2337,8 @@ name: innervated_by xref: RO:0002005 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 xsd:anyURI property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +domain: CARO:0000003 +range: CARO:0001001 inverse_of: innervates ! innervates [Typedef] @@ -2404,6 +2437,7 @@ id: involved_in_or_involved_in_regulation_of name: involved in or involved in regulation of def: "c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p" [] xref: RO:0002431 +property_value: IAO:0000116 "OWL does not allow defining object properties via a Union" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "involved in or reguates" xsd:string is_a: acts_upstream_of_or_within ! acts upstream of or within @@ -2622,14 +2656,6 @@ name: is killed by xref: RO:0002627 is_a: participates_in_a_biotic-biotic_interaction_with ! participates in a biotic-biotic interaction with -[Typedef] -id: is_marker_for -name: is marker for -def: "c is marker for d iff the presence or occurrence of d is correlated with the presence of occurrence of c, and the observation of c is used to infer the presence or occurrence of d. Note that this does not imply that c and d are in a direct causal relationship, as it may be the case that there is a third entity e that stands in a direct causal relationship with c and d." [] -xref: RO:0002607 -property_value: IAO:0000116 "May be ceded to OBI" xsd:string -is_a: correlated_with ! correlated with - [Typedef] id: is_sequentially_aligned_with name: is sequentially aligned with @@ -2851,16 +2877,6 @@ def: "A sub-relation of parasite-of in which the parasite that cannot complete i xref: RO:0002227 is_a: parasite_of ! parasite of -[Typedef] -id: obsolete_has_indirect_output -name: obsolete has indirect output -comment: Likely to be obsoleted. See:\nhttps://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/edit -xref: RO:0002403 -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string -is_a: has_output ! has output -is_obsolete: true - [Typedef] id: occurent_part_of name: occurent part of @@ -3010,6 +3026,8 @@ subset: ro-eco xref: RO:0002574 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: seeAlso http://dx.doi.org/10.1016/j.ecoinf.2014.08.005 +domain: CARO:0001010 +range: CARO:0001010 is_a: biotically_interacts_with ! biotically interacts with [Typedef] @@ -3277,13 +3295,6 @@ property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relati property_value: IAO:0000589 "regulates levels of (process to entity)" xsd:string is_a: functionally_related_to ! functionally related to -[Typedef] -id: related_via_dependence_to -name: related via dependence to -def: "A relationship that holds between two entities, where the relationship holds based on the presence or absence of statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes." [] -xref: RO:0002609 -property_value: 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." xsd:string - [Typedef] id: related_via_exposure_to name: related via exposure to @@ -3308,6 +3319,7 @@ name: releases neurotransmitter xref: RO:0002111 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000118 "has neurotransmitter" xsd:string +domain: CARO:0000003 [Typedef] id: represses_expression_of @@ -3325,8 +3337,8 @@ xref: RO:0002315 property_value: IAO:0000112 "an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast." xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string -range: CL:0000000 -is_a: has_participant +range: CARO:0000003 +is_a: has_anatomical_participant ! has anatomical participant is_a: results_in_developmental_progression_of ! results in developmental progression of [Typedef] @@ -3355,7 +3367,7 @@ id: results_in_closure_of name: results in closure of xref: RO:0002585 property_value: IAO:0000116 "p 'results in closure of' c if and only if p is a developmental process and p results in a state of c changing from open to closed." xsd:string -is_a: has_participant +is_a: has_anatomical_participant ! has anatomical participant is_a: results_in_developmental_progression_of ! results in developmental progression of [Typedef] @@ -3388,7 +3400,7 @@ property_value: IAO:0000112 "every flower development (GO:0009908) results in de property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://www.geneontology.org/GO.doc.development.shtml xsd:anyURI -is_a: has_participant +is_a: has_anatomical_participant ! has anatomical participant is_a: results_in_developmental_progression_of ! results in developmental progression of [Typedef] @@ -3445,7 +3457,7 @@ name: results in ending of def: "p results in the end of s if p results in a change of state in s whereby s either ceases to exist, or s becomes functionally impaired or s has its fate committed such that it is put on a path to be degraded." [] xref: RO:0002552 property_value: IAO:0000117 "Chris Mungall" xsd:string -is_a: has_participant +is_a: has_anatomical_participant ! has anatomical participant is_a: results_in_developmental_progression_of ! results in developmental progression of [Typedef] @@ -3467,7 +3479,7 @@ name: results in growth of xref: RO:0002343 property_value: IAO:0000112 "'pollen tube growth' results_in growth_of some 'pollen tube'" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string -is_a: has_participant +is_a: has_anatomical_participant ! has anatomical participant is_a: results_in_developmental_progression_of ! results in developmental progression of [Typedef] @@ -3480,7 +3492,7 @@ property_value: IAO:0000112 "bone maturation (GO:0070977) results_in_maturation_ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string -is_a: has_participant +is_a: has_anatomical_participant ! has anatomical participant is_a: results_in_developmental_progression_of ! results in developmental progression of [Typedef] @@ -3493,7 +3505,7 @@ property_value: IAO:0000112 "tongue morphogenesis (GO:0043587) results in morpho property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string -is_a: has_participant +is_a: has_anatomical_participant ! has anatomical participant is_a: results_in_developmental_progression_of ! results in developmental progression of [Typedef] @@ -3503,14 +3515,14 @@ def: "Holds between p and c when p is locomotion process and the outcome of this xref: RO:0002565 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000232 "" xsd:string -is_a: has_participant +is_a: has_anatomical_participant ! has anatomical participant [Typedef] id: results_in_organization_of name: results in organization of def: "p results in organization of c iff p results in the assembly, arrangement of constituent parts, or disassembly of c" [] xref: RO:0002592 -is_a: has_participant +is_a: has_anatomical_participant ! has anatomical participant [Typedef] id: results_in_remodeling_of @@ -3535,7 +3547,7 @@ name: results in structural organization of def: "A relationship between a process and an anatomical entity such that the process contributes to the act of creating the structural organization of the anatomical entity." [] xref: RO:0002355 property_value: IAO:0000117 "Chris Mungall" xsd:string -is_a: has_participant +is_a: has_anatomical_participant ! has anatomical participant is_a: results_in_developmental_progression_of ! results in developmental progression of [Typedef] @@ -3785,7 +3797,7 @@ def: "Holds between p and c when p is a localization process (localization cover xref: RO:0002313 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "regulates localization of" xsd:string -is_a: has_participant +is_a: has_anatomical_participant ! has anatomical participant is_a: related_via_localization_to ! related via localization to [Typedef] diff --git a/subsets/ro-mereotopology.owl b/subsets/ro-mereotopology.owl index 8bcb6d5d..6d1d6757 100644 --- a/subsets/ro-mereotopology.owl +++ b/subsets/ro-mereotopology.owl @@ -381,6 +381,8 @@ + + David Osumi-Sutherland http://www.ncbi.nlm.nih.gov/pubmed/22402613 RO:0002005 @@ -787,6 +789,7 @@ Examples include: the relationship between two channels collected simultaneously + Relation between a neuron and an anatomical structure that its soma is part of. David Osumi-Sutherland @@ -931,6 +934,7 @@ Examples include: the relationship between two channels collected simultaneously + has neurotransmitter RO:0002111 @@ -1231,9 +1235,10 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - - + + a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b. + attached to part of (anatomical structure to anatomical structure) RO:0002177 attached_to_part_of attached to part of @@ -1292,7 +1297,16 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - + + + + + + + + + + A relationship that holds between a biological entity and a phenotype. Here a phenotype is construed broadly as any kind of quality of an organism part, a collection of these qualities, or a change in quality or qualities (e.g. abnormally increased temperature). The subject of this relationship can be an organism (where the organism has the phenotype, i.e. the qualities inhere in parts of this organism), a genomic entity such as a gene or genotype (if modifications of the gene or the genotype causes the phenotype), or a condition such as a disease (such that if the condition inheres in an organism, then the organism has the phenotype). Chris Mungall @@ -1538,6 +1552,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.RO:0002216 capable_of_part_of capable of part of + @@ -1690,7 +1705,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - + x develops_in y if x is located in y whilst x is developing Chris Mungall @@ -1985,8 +2000,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - - + + Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong] x has developmental contribution from y iff x has some part z such that z develops from y @@ -2167,8 +2182,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - + every flower development (GO:0009908) results in development of some flower (PO:0009046) p 'results in development of' c if and only if p is a developmental process and p results in the state of c changing from its initial state as a primordium or anlage through its mature state and to its final state. @@ -2202,8 +2217,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - + an annotation of gene X to cell morphogenesis with results_in_morphogenesis_of CL:0000540 (neuron) means that at the end of the process an input neuron has attained its shape. tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723) @@ -2220,8 +2235,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - + an annotation of gene X to cell maturation with results_in_maturation_of CL:0000057 (fibroblast) means that the fibroblast is mature at the end of the process bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474) @@ -2284,7 +2299,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - + Hydrozoa (NCBITaxon_6074) SubClassOf 'has habitat' some 'Hydrozoa habitat' where @@ -2352,8 +2367,8 @@ where - + Holds between p and c when p is a localization process (localization covers maintenance of localization as well as its establishment) and the outcome of this process is to regulate the localization of c. Chris Mungall regulates localization of @@ -2367,9 +2382,9 @@ where - - + + an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast. The relationship that links a specified entity with the process that results in an unspecified entity acquiring the features and characteristics of the specified entity Chris Mungall @@ -2385,6 +2400,7 @@ where A relationship that is mediated in some way by the environment or environmental feature (ENVO:00002297) + Awaiting class for domain/range constraint, see: https://github.com/OBOFoundry/Experimental-OBO-Core/issues/6 Chris Mungall Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving ecological interactions RO:0002321 @@ -2399,6 +2415,7 @@ where + An experimental relation currently used to connect a feature possessed by an organism (e.g. anatomical structure, biological process, phenotype or quality) to a habitat or environment in which that feature is well suited, adapted or provides a reproductive advantage for the organism. For example, fins to an aquatic environment. Usually this will mean that the structure is adapted for this environment, but we avoid saying this directly - primitive forms of the structure may not have evolved specifically for that environment (for example, early wings were not necessarily adapted for an aerial environment). Note also that this is a statement about the general class of structures - not every instance of a limb need confer an advantage for a terrestrial environment, e.g. if the limb is vestigial. Chris Mungall adapted for @@ -2509,6 +2526,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities. Chris Mungall This is a grouping relation that collects relations used for the purpose of connecting structure and function RO:0002328 @@ -2569,11 +2587,6 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - - - - - inverse of enables Chris Mungall RO:0002333 @@ -2712,8 +2725,8 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - + 'pollen tube growth' results_in growth_of some 'pollen tube' Chris Mungall RO:0002343 @@ -2826,8 +2839,8 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - + A relationship between a process and an anatomical entity such that the process contributes to the act of creating the structural organization of the anatomical entity. Chris Mungall RO:0002355 @@ -2886,6 +2899,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a Chris Mungall + attached to (anatomical structure to anatomical structure) RO:0002371 attached_to @@ -2899,6 +2913,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to. Chris Mungall Wikipedia:Insertion_(anatomy) @@ -2907,6 +2922,12 @@ However, this is not possible in OWL. We instead make this relation a sub-relati has muscle origin + + + + + We need to import uberon muscle to create a stricter domain constraint + @@ -2915,6 +2936,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone. Chris Mungall Wikipedia:Insertion_(anatomy) @@ -2923,6 +2945,12 @@ However, this is not possible in OWL. We instead make this relation a sub-relati has muscle insertion + + + + + We need to import uberon muscle into RO to use as a stricter domain constraint + @@ -3103,6 +3131,8 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + + x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction). Chris Mungall @@ -3186,22 +3216,6 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - - - - - - Chris Mungall - RO:0002403 - obsolete_has_indirect_output - Likely to be obsoleted. See: -https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/edit - obsolete has indirect output - true - - - - @@ -3300,7 +3314,6 @@ https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/ - This relation groups causal relations between material entities and causal relations between processes 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. @@ -3479,6 +3492,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p + OWL does not allow defining object properties via a Union Chris Mungall involved in or reguates RO:0002431 @@ -4653,8 +4667,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + p results in the end of s if p results in a change of state in s whereby s either ceases to exist, or s becomes functionally impaired or s has its fate committed such that it is put on a path to be degraded. Chris Mungall RO:0002552 @@ -4763,7 +4777,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c Chris Mungall @@ -4793,6 +4807,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + A relation that holds between elements of a musculoskeletal system or its analogs. Chris Mungall Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes. @@ -4885,6 +4901,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + Chris Mungall RO:0002574 @@ -4946,8 +4964,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + p 'results in closure of' c if and only if p is a developmental process and p results in a state of c changing from open to closed. RO:0002585 results_in_closure_of @@ -5030,7 +5048,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + p results in organization of c iff p results in the assembly, arrangement of constituent parts, or disassembly of c RO:0002592 results_in_organization_of @@ -5149,19 +5167,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - c is marker for d iff the presence or occurrence of d is correlated with the presence of occurrence of c, and the observation of c is used to infer the presence or occurrence of d. Note that this does not imply that c and d are in a direct causal relationship, as it may be the case that there is a third entity e that stands in a direct causal relationship with c and d. - May be ceded to OBI - RO:0002607 - is_marker_for - is marker for - - - - @@ -5175,31 +5180,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - A relationship that holds between two entities, where the relationship holds based on the presence or absence of statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes. - Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. - RO:0002609 - related_via_dependence_to - related via dependence to - - - - - - - - - A relationship that holds between two entities, where the entities exhibit a statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes. - Groups both positive and negative correlation - RO:0002610 - correlated_with - correlated with - - - - @@ -5572,18 +5552,6 @@ Environmental exposures include those imposed by natural environments, experimen - - - - - A relationship between an entity and a condition (phenotype or disease) with which it exhibits a statistical dependence relationship. - RO:0003308 - correlated_with_condition - correlated with condition - - - - @@ -5870,7 +5838,7 @@ Environmental exposures include those imposed by natural environments, experimen - + cjm 2017-11-05T03:26:47Z RO:0004019 @@ -5884,8 +5852,9 @@ Environmental exposures include those imposed by natural environments, experimen - + A relation that holds between the disease and a material entity where the physical basis of the disease is a disorder of that material entity that affects its function. + disease has basis in dysfunction of (disease to anatomical structure) cjm 2017-11-05T03:29:32Z RO:0004020 @@ -5901,6 +5870,7 @@ Environmental exposures include those imposed by natural environments, experimen A relation that holds between the disease and a process where the physical basis of the disease disrupts execution of a key biological process. + disease has basis in disruption of (disease to process) cjm 2017-11-05T03:37:52Z RO:0004021 @@ -5915,6 +5885,15 @@ Environmental exposures include those imposed by natural environments, experimen + + + + + + + + + A relation that holds between the disease and a feature (a phenotype or other disease) where the physical basis of the disease is the feature. cjm 2017-11-05T03:46:07Z @@ -5929,7 +5908,8 @@ Environmental exposures include those imposed by natural environments, experimen - + + After import upper level from OGMS, make domain more specific. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all of which have a disease as the subject. cjm @@ -5945,8 +5925,10 @@ Environmental exposures include those imposed by natural environments, experimen + A relationship between a disease and a process where the disease process disrupts the execution of the process. + disease causes disruption of (disease to process) cjm 2017-11-05T03:51:09Z RO:0004024 @@ -5960,7 +5942,9 @@ Environmental exposures include those imposed by natural environments, experimen - + + + disease causes dysfunction of (disease to anatomical entity) cjm 2017-11-05T03:58:20Z RO:0004025 @@ -5973,8 +5957,17 @@ Environmental exposures include those imposed by natural environments, experimen - + + + + + + + + + + A relationship between a disease and an anatomical entity where the disease has one or more features that are located in that entity. TODO: complete range axiom once more of CARO has been mireoted in to this ontology This relation is intentionally very general, and covers isolated diseases, where the disease is realized as a process occurring in the location, and syndromic diseases, where one or more of the features may be present in that location. Thus any given disease can have multiple locations in the sense defined here. @@ -5991,6 +5984,8 @@ Environmental exposures include those imposed by natural environments, experimen + + A relationship between a disease and an anatomical entity where the disease is triggered by an inflammatory response to stimuli occurring in the anatomical entity cjm 2017-12-26T19:37:31Z @@ -6020,12 +6015,13 @@ Environmental exposures include those imposed by natural environments, experimen - + + - - + + @@ -6217,6 +6213,8 @@ Environmental exposures include those imposed by natural environments, experimen + + An interaction relationship wherein one organism creates a structure or environment that is lived in by another organism. RO:0008505 creates_habitat_for @@ -6230,10 +6228,12 @@ Environmental exposures include those imposed by natural environments, experimen + + An interaction relationship describing organisms that often occur together at the same time and space or in the same environment. RO:0008506 - co-occurs - co-occurs + ecologically_co-occurs_with + ecologically co-occurs with @@ -6292,6 +6292,42 @@ Environmental exposures include those imposed by natural environments, experimen + + + + This relation groups relations between diseases and any other kind of entity. + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, in which the subject or object is a disease. + cjm + 2018-09-26T00:00:32Z + RO:0040035 + disease_relationship + disease relationship + + + + + + + + + + + + + + + + + p has anatomical participant c iff p has participant c, and c is an anatomical entity + cjm + 2018-09-26T01:08:58Z + RO:0040036 + has_anatomical_participant + has anatomical participant + + + + @@ -6333,12 +6369,6 @@ Environmental exposures include those imposed by natural environments, experimen - - - - - - @@ -6351,6 +6381,12 @@ Environmental exposures include those imposed by natural environments, experimen + + + + + + @@ -6363,6 +6399,12 @@ Environmental exposures include those imposed by natural environments, experimen + + + + + + @@ -6375,12 +6417,24 @@ Environmental exposures include those imposed by natural environments, experimen + + + + + + + + + + + + @@ -6423,6 +6477,12 @@ Environmental exposures include those imposed by natural environments, experimen + + + + + + @@ -6459,6 +6519,12 @@ Environmental exposures include those imposed by natural environments, experimen + + + + + + diff --git a/subsets/ro-sequence.obo b/subsets/ro-sequence.obo index 0442a521..3bd07400 100644 --- a/subsets/ro-sequence.obo +++ b/subsets/ro-sequence.obo @@ -1,6 +1,6 @@ format-version: 1.2 ontology: ro/subsets/ro-sequence -owl-axioms: Prefix(owl:=)\nPrefix(rdf:=)\nPrefix(xml:=)\nPrefix(xsd:=)\nPrefix(rdfs:=)\n\n\nOntology(\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\n\n############################\n# Object Properties\n############################\n\n# Object Property: (coincident with)\n\nObjectPropertyRange( ObjectIntersectionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (has fasciculating neuron projection)\n\nObjectPropertyRange( ObjectUnionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (connected to)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (connects)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (directly develops from)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (enabled by)\n\nSubObjectPropertyOf( ObjectInverseOf())\n\n# Object Property: (anabranch of)\n\nSubObjectPropertyOf( ObjectInverseOf())\n\n# Object Property: (branching part of)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (condition has genetic basis in)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has feature)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n\n\n\nAnnotationAssertion(rdfs:comment \"\")\n) +owl-axioms: Prefix(owl:=)\nPrefix(rdf:=)\nPrefix(xml:=)\nPrefix(xsd:=)\nPrefix(rdfs:=)\n\n\nOntology(\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\n\n############################\n# Object Properties\n############################\n\n# Object Property: (coincident with)\n\nObjectPropertyRange( ObjectIntersectionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (has fasciculating neuron projection)\n\nObjectPropertyRange( ObjectUnionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (connected to)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (connects)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (directly develops from)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (anabranch of)\n\nSubObjectPropertyOf( ObjectInverseOf())\n\n# Object Property: (branching part of)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (condition has genetic basis in)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has basis in feature)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has location)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has feature)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (has anatomical participant)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n\n\n\nAnnotationAssertion(rdfs:comment \"\")\n) [Typedef] id: 2D_boundary_of @@ -184,6 +184,7 @@ def: "a is attached to b if and only if a and b are discrete objects or object p subset: ro-eco xref: RO:0002371 property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000589 "attached to (anatomical structure to anatomical structure)" xsd:string is_symmetric: true is_a: attached_to_part_of ! attached to part of is_a: connected_to ! connected to @@ -193,8 +194,9 @@ id: attached_to_part_of name: attached to part of def: "a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b." [] xref: RO:0002177 -domain: BFO:0000040 -range: BFO:0000040 +property_value: IAO:0000589 "attached to part of (anatomical structure to anatomical structure)" xsd:string +domain: CARO:0000003 +range: CARO:0000003 is_a: biomechanically_related_to ! biomechanically related to is_a: mereotopologically_related_to ! mereotopologically related to @@ -225,6 +227,8 @@ def: "A relation that holds between elements of a musculoskeletal system or its xref: RO:0002567 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes." xsd:string +domain: CARO:0000003 +range: CARO:0000003 is_a: functionally_related_to ! functionally related to [Typedef] @@ -323,6 +327,7 @@ def: "c stands in this relationship to p if and only if there exists some p' suc xref: RO:0002216 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "has function in" xsd:string +property_value: seeAlso "defining-property-chains-involving-reflexivity" is_a: causal_agent_in_process ! causal agent in process is_a: functionally_related_to ! functionally related to expand_expression_to: "RO_0000053 some (RO_0000054 only (BFO_0000050 some ?Y))" [] @@ -406,8 +411,9 @@ name: causal relationship with disease as subject xref: RO:0004023 property_value: IAO:0000116 "After import upper level from OGMS, make domain more specific." xsd:string property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all of which have a disease as the subject." xsd:string -domain: BFO:0000016 +domain: OGMS:0000031 is_a: causally_related_to ! causally related to +is_a: disease_relationship ! disease relationship created_by: cjm creation_date: 2017-11-05T03:50:54Z @@ -462,7 +468,6 @@ property_value: IAO:0000114 IAO:0000428 property_value: 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." xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: 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." xsd:string -is_a: related_via_dependence_to ! related via dependence to [Typedef] id: causally_upstream_of @@ -571,14 +576,6 @@ xref: RO:0002478 property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: child_nucleus_of ! child nucleus of -[Typedef] -id: co-occurs -name: co-occurs -def: "An interaction relationship describing organisms that often occur together at the same time and space or in the same environment." [] -xref: RO:0008506 -is_symmetric: true -is_a: ecologically_related_to ! ecologically related to - [Typedef] id: coincident_with name: coincident with @@ -673,6 +670,7 @@ xref: RO:0002322 property_value: IAO:0000116 "An experimental relation currently used to connect a feature possessed by an organism (e.g. anatomical structure, biological process, phenotype or quality) to a habitat or environment in which that feature is well suited, adapted or provides a reproductive advantage for the organism. For example, fins to an aquatic environment. Usually this will mean that the structure is adapted for this environment, but we avoid saying this directly - primitive forms of the structure may not have evolved specifically for that environment (for example, early wings were not necessarily adapted for an aerial environment). Note also that this is a statement about the general class of structures - not every instance of a limb need confer an advantage for a terrestrial environment, e.g. if the limb is vestigial." xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "adapted for" xsd:string +range: ENVO:01000254 is_a: ecologically_related_to ! ecologically related to [Typedef] @@ -767,26 +765,13 @@ xref: RO:0003305 property_value: IAO:0000118 "contributes to expressivity of condition" xsd:string is_a: contributes_to_condition ! contributes to condition -[Typedef] -id: correlated_with -name: correlated with -def: "A relationship that holds between two entities, where the entities exhibit a statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes." [] -xref: RO:0002610 -property_value: IAO:0000232 "Groups both positive and negative correlation" xsd:string -is_a: related_via_dependence_to ! related via dependence to - -[Typedef] -id: correlated_with_condition -name: correlated with condition -def: "A relationship between an entity and a condition (phenotype or disease) with which it exhibits a statistical dependence relationship." [] -xref: RO:0003308 -is_a: correlated_with ! correlated with - [Typedef] id: creates_habitat_for name: creates habitat for def: "An interaction relationship wherein one organism creates a structure or environment that is lived in by another organism." [] xref: RO:0008505 +domain: CARO:0001010 +range: CARO:0001010 is_a: ecologically_related_to ! ecologically related to [Typedef] @@ -964,7 +949,7 @@ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 "EHDAA2" xsd:string property_value: IAO:0000119 "Jonathan Bard, EHDAA2" xsd:string -domain: CARO:0000003 +domain: CARO:0000000 is_a: developmentally_preceded_by ! developmentally preceded by [Typedef] @@ -1121,6 +1106,8 @@ id: disease_causes_disruption_of name: disease causes disruption of def: "A relationship between a disease and a process where the disease process disrupts the execution of the process." [] xref: RO:0004024 +property_value: IAO:0000589 "disease causes disruption of (disease to process)" xsd:string +domain: OGMS:0000031 range: BFO:0000015 is_a: causal_relationship_with_disease_as_subject ! causal relationship with disease as subject created_by: cjm @@ -1130,7 +1117,9 @@ creation_date: 2017-11-05T03:51:09Z id: disease_causes_dysfunction_of name: disease causes dysfunction of xref: RO:0004025 -range: BFO:0000004 +property_value: IAO:0000589 "disease causes dysfunction of (disease to anatomical entity)" xsd:string +domain: OGMS:0000031 +range: CARO:0000006 is_a: causal_relationship_with_disease_as_subject ! causal relationship with disease as subject created_by: cjm creation_date: 2017-11-05T03:58:20Z @@ -1139,7 +1128,7 @@ creation_date: 2017-11-05T03:58:20Z id: disease_has_basis_in name: disease has basis in xref: RO:0004019 -domain: BFO:0000016 +domain: OGMS:0000031 is_a: causal_relationship_with_disease_as_subject ! causal relationship with disease as subject is_a: realizable_has_basis_in ! realizable has basis in created_by: cjm @@ -1150,6 +1139,7 @@ id: disease_has_basis_in_disruption_of name: disease has basis in disruption of def: "A relation that holds between the disease and a process where the physical basis of the disease disrupts execution of a key biological process." [] xref: RO:0004021 +property_value: IAO:0000589 "disease has basis in disruption of (disease to process)" xsd:string range: BFO:0000015 is_a: disease_has_basis_in ! disease has basis in created_by: cjm @@ -1160,7 +1150,8 @@ id: disease_has_basis_in_dysfunction_of name: disease has basis in dysfunction of def: "A relation that holds between the disease and a material entity where the physical basis of the disease is a disorder of that material entity that affects its function." [] xref: RO:0004020 -range: BFO:0000040 +property_value: IAO:0000589 "disease has basis in dysfunction of (disease to anatomical structure)" xsd:string +range: CARO:0000006 is_a: disease_has_basis_in ! disease has basis in created_by: cjm creation_date: 2017-11-05T03:29:32Z @@ -1170,6 +1161,7 @@ id: disease_has_basis_in_feature name: disease has basis in feature def: "A relation that holds between the disease and a feature (a phenotype or other disease) where the physical basis of the disease is the feature." [] xref: RO:0004022 +domain: OGMS:0000031 is_a: disease_has_basis_in ! disease has basis in is_a: has_phenotype ! has phenotype created_by: cjm @@ -1180,7 +1172,8 @@ id: disease_has_feature name: disease has feature def: "A relationship between a disease and some feature of that disease, where the feature is either a phenotype or an isolated disease." [] xref: RO:0004029 -is_a: causal_relationship_with_disease_as_subject ! causal relationship with disease as subject +domain: OGMS:0000031 +is_a: disease_relationship ! disease relationship created_by: cjm creation_date: 2017-12-26T19:50:53Z @@ -1189,6 +1182,8 @@ id: disease_has_inflammation_site name: disease has inflammation site def: "A relationship between a disease and an anatomical entity where the disease is triggered by an inflammatory response to stimuli occurring in the anatomical entity" [] xref: RO:0004027 +domain: OGMS:0000031 +range: CARO:0000003 is_a: disease_has_location ! disease has location created_by: cjm creation_date: 2017-12-26T19:37:31Z @@ -1200,11 +1195,21 @@ def: "A relationship between a disease and an anatomical entity where the diseas xref: RO:0004026 property_value: IAO:0000116 "TODO: complete range axiom once more of CARO has been mireoted in to this ontology" xsd:string property_value: IAO:0000232 "This relation is intentionally very general, and covers isolated diseases, where the disease is realized as a process occurring in the location, and syndromic diseases, where one or more of the features may be present in that location. Thus any given disease can have multiple locations in the sense defined here." xsd:string +domain: OGMS:0000031 range: BFO:0000004 -is_a: causal_relationship_with_disease_as_subject ! causal relationship with disease as subject +is_a: disease_relationship ! disease relationship created_by: cjm creation_date: 2017-11-05T04:06:02Z +[Typedef] +id: disease_relationship +name: disease relationship +def: "This relation groups relations between diseases and any other kind of entity." [] +xref: RO:0040035 +property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, in which the subject or object is a disease." xsd:string +created_by: cjm +creation_date: 2018-09-26T00:00:32Z + [Typedef] id: distributary_of name: distributary of @@ -1249,12 +1254,23 @@ property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "is subject of eating interaction with" xsd:string is_a: trophically_interacts_with ! trophically interacts with +[Typedef] +id: ecologically_co-occurs_with +name: ecologically co-occurs with +def: "An interaction relationship describing organisms that often occur together at the same time and space or in the same environment." [] +xref: RO:0008506 +domain: CARO:0001010 +range: CARO:0001010 +is_symmetric: true +is_a: ecologically_related_to ! ecologically related to + [Typedef] id: ecologically_related_to name: ecologically related to def: "A relationship that is mediated in some way by the environment or environmental feature (ENVO:00002297)" [] subset: ro-eco xref: RO:0002321 +property_value: IAO:0000116 "Awaiting class for domain/range constraint, see: https://github.com/OBOFoundry/Experimental-OBO-Core/issues/6" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving ecological interactions" xsd:string @@ -1379,6 +1395,7 @@ is_a: output_of ! output of [Typedef] id: functionally_related_to name: functionally related to +def: "A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities." [] xref: RO:0002328 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000232 "This is a grouping relation that collects relations used for the purpose of connecting structure and function" xsd:string @@ -1433,6 +1450,15 @@ property_value: IAO:0000112 "penicillin allergy (DOID:0060520) has allergic trig range: BFO:0000040 is_a: causes_or_contributes_to_condition ! causes or contributes to condition +[Typedef] +id: has_anatomical_participant +name: has anatomical participant +def: "p has anatomical participant c iff p has participant c, and c is an anatomical entity" [] +xref: RO:0040036 +is_a: has_participant +created_by: cjm +creation_date: 2018-09-26T01:08:58Z + [Typedef] id: has_autoimmune_trigger name: has autoimmune trigger @@ -1506,8 +1532,8 @@ xref: RO:0002254 property_value: IAO:0000112 "Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string -domain: BFO:0000004 -range: CARO:0000003 +domain: CARO:0000000 +range: CARO:0000000 is_a: developmentally_preceded_by ! developmentally preceded by inverse_of: developmentally_contributes_to ! developmentally contributes to @@ -1518,6 +1544,8 @@ def: "x has developmental potential involving y iff x is capable of a developmen xref: RO:0002384 property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Chris Mungall" xsd:string +domain: CARO:0000000 +range: CARO:0000000 is_a: developmentally_related_to ! developmentally related to [Typedef] @@ -1682,7 +1710,7 @@ property_value: IAO:0000112 "Hydrozoa (NCBITaxon_6074) SubClassOf 'has habitat' property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Pier Buttigieg" xsd:string property_value: IAO:0000118 "adapted for living in" xsd:string -domain: CARO:0000006 +domain: CARO:0001010 range: ENVO:01000254 is_a: ecologically_related_to ! ecologically related to @@ -1820,6 +1848,7 @@ xref: RO:0002373 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 Wikipedia:Insertion_(anatomy) xsd:string property_value: seeAlso http://dbpedia.org/property/insertion +domain: CARO:0000003 {http://purl.obolibrary.org/obo/IAO_0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} is_a: attached_to ! attached to is_a: biomechanically_related_to ! biomechanically related to @@ -1831,6 +1860,7 @@ xref: RO:0002372 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 Wikipedia:Insertion_(anatomy) xsd:string property_value: seeAlso http://dbpedia.org/property/origin +domain: CARO:0000003 {comment="We need to import uberon muscle to create a stricter domain constraint"} is_a: attached_to ! attached to is_a: biomechanically_related_to ! biomechanically related to @@ -1929,7 +1959,7 @@ subset: ro-eco xref: RO:0002200 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string -domain: BFO:0000002 +range: UPHENO:0001001 inverse_of: phenotype_of ! phenotype of [Typedef] @@ -2051,6 +2081,7 @@ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string property_value: RO:0001900 RO:0001901 domain: CL:0000540 +range: CARO:0000003 is_a: overlaps ! overlaps expand_expression_to: "BFO_0000051 some (\n GO_0043025 and BFO_0000050 some ?Y)" [] @@ -2306,6 +2337,8 @@ name: innervated_by xref: RO:0002005 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 xsd:anyURI property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +domain: CARO:0000003 +range: CARO:0001001 inverse_of: innervates ! innervates [Typedef] @@ -2404,6 +2437,7 @@ id: involved_in_or_involved_in_regulation_of name: involved in or involved in regulation of def: "c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p" [] xref: RO:0002431 +property_value: IAO:0000116 "OWL does not allow defining object properties via a Union" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "involved in or reguates" xsd:string is_a: acts_upstream_of_or_within ! acts upstream of or within @@ -2622,14 +2656,6 @@ name: is killed by xref: RO:0002627 is_a: participates_in_a_biotic-biotic_interaction_with ! participates in a biotic-biotic interaction with -[Typedef] -id: is_marker_for -name: is marker for -def: "c is marker for d iff the presence or occurrence of d is correlated with the presence of occurrence of c, and the observation of c is used to infer the presence or occurrence of d. Note that this does not imply that c and d are in a direct causal relationship, as it may be the case that there is a third entity e that stands in a direct causal relationship with c and d." [] -xref: RO:0002607 -property_value: IAO:0000116 "May be ceded to OBI" xsd:string -is_a: correlated_with ! correlated with - [Typedef] id: is_sequentially_aligned_with name: is sequentially aligned with @@ -2851,16 +2877,6 @@ def: "A sub-relation of parasite-of in which the parasite that cannot complete i xref: RO:0002227 is_a: parasite_of ! parasite of -[Typedef] -id: obsolete_has_indirect_output -name: obsolete has indirect output -comment: Likely to be obsoleted. See:\nhttps://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/edit -xref: RO:0002403 -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string -is_a: has_output ! has output -is_obsolete: true - [Typedef] id: occurent_part_of name: occurent part of @@ -3010,6 +3026,8 @@ subset: ro-eco xref: RO:0002574 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: seeAlso http://dx.doi.org/10.1016/j.ecoinf.2014.08.005 +domain: CARO:0001010 +range: CARO:0001010 is_a: biotically_interacts_with ! biotically interacts with [Typedef] @@ -3277,13 +3295,6 @@ property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relati property_value: IAO:0000589 "regulates levels of (process to entity)" xsd:string is_a: functionally_related_to ! functionally related to -[Typedef] -id: related_via_dependence_to -name: related via dependence to -def: "A relationship that holds between two entities, where the relationship holds based on the presence or absence of statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes." [] -xref: RO:0002609 -property_value: 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." xsd:string - [Typedef] id: related_via_exposure_to name: related via exposure to @@ -3308,6 +3319,7 @@ name: releases neurotransmitter xref: RO:0002111 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000118 "has neurotransmitter" xsd:string +domain: CARO:0000003 [Typedef] id: represses_expression_of @@ -3325,8 +3337,8 @@ xref: RO:0002315 property_value: IAO:0000112 "an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast." xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string -range: CL:0000000 -is_a: has_participant +range: CARO:0000003 +is_a: has_anatomical_participant ! has anatomical participant is_a: results_in_developmental_progression_of ! results in developmental progression of [Typedef] @@ -3355,7 +3367,7 @@ id: results_in_closure_of name: results in closure of xref: RO:0002585 property_value: IAO:0000116 "p 'results in closure of' c if and only if p is a developmental process and p results in a state of c changing from open to closed." xsd:string -is_a: has_participant +is_a: has_anatomical_participant ! has anatomical participant is_a: results_in_developmental_progression_of ! results in developmental progression of [Typedef] @@ -3388,7 +3400,7 @@ property_value: IAO:0000112 "every flower development (GO:0009908) results in de property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://www.geneontology.org/GO.doc.development.shtml xsd:anyURI -is_a: has_participant +is_a: has_anatomical_participant ! has anatomical participant is_a: results_in_developmental_progression_of ! results in developmental progression of [Typedef] @@ -3445,7 +3457,7 @@ name: results in ending of def: "p results in the end of s if p results in a change of state in s whereby s either ceases to exist, or s becomes functionally impaired or s has its fate committed such that it is put on a path to be degraded." [] xref: RO:0002552 property_value: IAO:0000117 "Chris Mungall" xsd:string -is_a: has_participant +is_a: has_anatomical_participant ! has anatomical participant is_a: results_in_developmental_progression_of ! results in developmental progression of [Typedef] @@ -3467,7 +3479,7 @@ name: results in growth of xref: RO:0002343 property_value: IAO:0000112 "'pollen tube growth' results_in growth_of some 'pollen tube'" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string -is_a: has_participant +is_a: has_anatomical_participant ! has anatomical participant is_a: results_in_developmental_progression_of ! results in developmental progression of [Typedef] @@ -3480,7 +3492,7 @@ property_value: IAO:0000112 "bone maturation (GO:0070977) results_in_maturation_ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string -is_a: has_participant +is_a: has_anatomical_participant ! has anatomical participant is_a: results_in_developmental_progression_of ! results in developmental progression of [Typedef] @@ -3493,7 +3505,7 @@ property_value: IAO:0000112 "tongue morphogenesis (GO:0043587) results in morpho property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string -is_a: has_participant +is_a: has_anatomical_participant ! has anatomical participant is_a: results_in_developmental_progression_of ! results in developmental progression of [Typedef] @@ -3503,14 +3515,14 @@ def: "Holds between p and c when p is locomotion process and the outcome of this xref: RO:0002565 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000232 "" xsd:string -is_a: has_participant +is_a: has_anatomical_participant ! has anatomical participant [Typedef] id: results_in_organization_of name: results in organization of def: "p results in organization of c iff p results in the assembly, arrangement of constituent parts, or disassembly of c" [] xref: RO:0002592 -is_a: has_participant +is_a: has_anatomical_participant ! has anatomical participant [Typedef] id: results_in_remodeling_of @@ -3535,7 +3547,7 @@ name: results in structural organization of def: "A relationship between a process and an anatomical entity such that the process contributes to the act of creating the structural organization of the anatomical entity." [] xref: RO:0002355 property_value: IAO:0000117 "Chris Mungall" xsd:string -is_a: has_participant +is_a: has_anatomical_participant ! has anatomical participant is_a: results_in_developmental_progression_of ! results in developmental progression of [Typedef] @@ -3785,7 +3797,7 @@ def: "Holds between p and c when p is a localization process (localization cover xref: RO:0002313 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "regulates localization of" xsd:string -is_a: has_participant +is_a: has_anatomical_participant ! has anatomical participant is_a: related_via_localization_to ! related via localization to [Typedef] diff --git a/subsets/ro-sequence.owl b/subsets/ro-sequence.owl index 37d8c63a..2224004b 100644 --- a/subsets/ro-sequence.owl +++ b/subsets/ro-sequence.owl @@ -381,6 +381,8 @@ + + David Osumi-Sutherland http://www.ncbi.nlm.nih.gov/pubmed/22402613 RO:0002005 @@ -787,6 +789,7 @@ Examples include: the relationship between two channels collected simultaneously + Relation between a neuron and an anatomical structure that its soma is part of. David Osumi-Sutherland @@ -931,6 +934,7 @@ Examples include: the relationship between two channels collected simultaneously + has neurotransmitter RO:0002111 @@ -1231,9 +1235,10 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - - + + a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b. + attached to part of (anatomical structure to anatomical structure) RO:0002177 attached_to_part_of attached to part of @@ -1292,7 +1297,16 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - + + + + + + + + + + A relationship that holds between a biological entity and a phenotype. Here a phenotype is construed broadly as any kind of quality of an organism part, a collection of these qualities, or a change in quality or qualities (e.g. abnormally increased temperature). The subject of this relationship can be an organism (where the organism has the phenotype, i.e. the qualities inhere in parts of this organism), a genomic entity such as a gene or genotype (if modifications of the gene or the genotype causes the phenotype), or a condition such as a disease (such that if the condition inheres in an organism, then the organism has the phenotype). Chris Mungall @@ -1538,6 +1552,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.RO:0002216 capable_of_part_of capable of part of + @@ -1690,7 +1705,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - + x develops_in y if x is located in y whilst x is developing Chris Mungall @@ -1985,8 +2000,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - - + + Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong] x has developmental contribution from y iff x has some part z such that z develops from y @@ -2167,8 +2182,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - + every flower development (GO:0009908) results in development of some flower (PO:0009046) p 'results in development of' c if and only if p is a developmental process and p results in the state of c changing from its initial state as a primordium or anlage through its mature state and to its final state. @@ -2202,8 +2217,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - + an annotation of gene X to cell morphogenesis with results_in_morphogenesis_of CL:0000540 (neuron) means that at the end of the process an input neuron has attained its shape. tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723) @@ -2220,8 +2235,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - + an annotation of gene X to cell maturation with results_in_maturation_of CL:0000057 (fibroblast) means that the fibroblast is mature at the end of the process bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474) @@ -2284,7 +2299,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - + Hydrozoa (NCBITaxon_6074) SubClassOf 'has habitat' some 'Hydrozoa habitat' where @@ -2352,8 +2367,8 @@ where - + Holds between p and c when p is a localization process (localization covers maintenance of localization as well as its establishment) and the outcome of this process is to regulate the localization of c. Chris Mungall regulates localization of @@ -2367,9 +2382,9 @@ where - - + + an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast. The relationship that links a specified entity with the process that results in an unspecified entity acquiring the features and characteristics of the specified entity Chris Mungall @@ -2385,6 +2400,7 @@ where A relationship that is mediated in some way by the environment or environmental feature (ENVO:00002297) + Awaiting class for domain/range constraint, see: https://github.com/OBOFoundry/Experimental-OBO-Core/issues/6 Chris Mungall Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving ecological interactions RO:0002321 @@ -2399,6 +2415,7 @@ where + An experimental relation currently used to connect a feature possessed by an organism (e.g. anatomical structure, biological process, phenotype or quality) to a habitat or environment in which that feature is well suited, adapted or provides a reproductive advantage for the organism. For example, fins to an aquatic environment. Usually this will mean that the structure is adapted for this environment, but we avoid saying this directly - primitive forms of the structure may not have evolved specifically for that environment (for example, early wings were not necessarily adapted for an aerial environment). Note also that this is a statement about the general class of structures - not every instance of a limb need confer an advantage for a terrestrial environment, e.g. if the limb is vestigial. Chris Mungall adapted for @@ -2509,6 +2526,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities. Chris Mungall This is a grouping relation that collects relations used for the purpose of connecting structure and function RO:0002328 @@ -2569,11 +2587,6 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - - - - - inverse of enables Chris Mungall RO:0002333 @@ -2712,8 +2725,8 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - + 'pollen tube growth' results_in growth_of some 'pollen tube' Chris Mungall RO:0002343 @@ -2826,8 +2839,8 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - + A relationship between a process and an anatomical entity such that the process contributes to the act of creating the structural organization of the anatomical entity. Chris Mungall RO:0002355 @@ -2886,6 +2899,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a Chris Mungall + attached to (anatomical structure to anatomical structure) RO:0002371 attached_to @@ -2899,6 +2913,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to. Chris Mungall Wikipedia:Insertion_(anatomy) @@ -2907,6 +2922,12 @@ However, this is not possible in OWL. We instead make this relation a sub-relati has muscle origin + + + + + We need to import uberon muscle to create a stricter domain constraint + @@ -2915,6 +2936,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone. Chris Mungall Wikipedia:Insertion_(anatomy) @@ -2923,6 +2945,12 @@ However, this is not possible in OWL. We instead make this relation a sub-relati has muscle insertion + + + + + We need to import uberon muscle into RO to use as a stricter domain constraint + @@ -3103,6 +3131,8 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + + x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction). Chris Mungall @@ -3186,22 +3216,6 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - - - - - - Chris Mungall - RO:0002403 - obsolete_has_indirect_output - Likely to be obsoleted. See: -https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/edit - obsolete has indirect output - true - - - - @@ -3300,7 +3314,6 @@ https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/ - This relation groups causal relations between material entities and causal relations between processes 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. @@ -3479,6 +3492,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p + OWL does not allow defining object properties via a Union Chris Mungall involved in or reguates RO:0002431 @@ -4653,8 +4667,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + p results in the end of s if p results in a change of state in s whereby s either ceases to exist, or s becomes functionally impaired or s has its fate committed such that it is put on a path to be degraded. Chris Mungall RO:0002552 @@ -4763,7 +4777,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c Chris Mungall @@ -4793,6 +4807,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + A relation that holds between elements of a musculoskeletal system or its analogs. Chris Mungall Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes. @@ -4885,6 +4901,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + Chris Mungall RO:0002574 @@ -4946,8 +4964,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + p 'results in closure of' c if and only if p is a developmental process and p results in a state of c changing from open to closed. RO:0002585 results_in_closure_of @@ -5030,7 +5048,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + p results in organization of c iff p results in the assembly, arrangement of constituent parts, or disassembly of c RO:0002592 results_in_organization_of @@ -5149,19 +5167,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - c is marker for d iff the presence or occurrence of d is correlated with the presence of occurrence of c, and the observation of c is used to infer the presence or occurrence of d. Note that this does not imply that c and d are in a direct causal relationship, as it may be the case that there is a third entity e that stands in a direct causal relationship with c and d. - May be ceded to OBI - RO:0002607 - is_marker_for - is marker for - - - - @@ -5175,31 +5180,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - A relationship that holds between two entities, where the relationship holds based on the presence or absence of statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes. - Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. - RO:0002609 - related_via_dependence_to - related via dependence to - - - - - - - - - A relationship that holds between two entities, where the entities exhibit a statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes. - Groups both positive and negative correlation - RO:0002610 - correlated_with - correlated with - - - - @@ -5572,18 +5552,6 @@ Environmental exposures include those imposed by natural environments, experimen - - - - - A relationship between an entity and a condition (phenotype or disease) with which it exhibits a statistical dependence relationship. - RO:0003308 - correlated_with_condition - correlated with condition - - - - @@ -5870,7 +5838,7 @@ Environmental exposures include those imposed by natural environments, experimen - + cjm 2017-11-05T03:26:47Z RO:0004019 @@ -5884,8 +5852,9 @@ Environmental exposures include those imposed by natural environments, experimen - + A relation that holds between the disease and a material entity where the physical basis of the disease is a disorder of that material entity that affects its function. + disease has basis in dysfunction of (disease to anatomical structure) cjm 2017-11-05T03:29:32Z RO:0004020 @@ -5901,6 +5870,7 @@ Environmental exposures include those imposed by natural environments, experimen A relation that holds between the disease and a process where the physical basis of the disease disrupts execution of a key biological process. + disease has basis in disruption of (disease to process) cjm 2017-11-05T03:37:52Z RO:0004021 @@ -5915,6 +5885,15 @@ Environmental exposures include those imposed by natural environments, experimen + + + + + + + + + A relation that holds between the disease and a feature (a phenotype or other disease) where the physical basis of the disease is the feature. cjm 2017-11-05T03:46:07Z @@ -5929,7 +5908,8 @@ Environmental exposures include those imposed by natural environments, experimen - + + After import upper level from OGMS, make domain more specific. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all of which have a disease as the subject. cjm @@ -5945,8 +5925,10 @@ Environmental exposures include those imposed by natural environments, experimen + A relationship between a disease and a process where the disease process disrupts the execution of the process. + disease causes disruption of (disease to process) cjm 2017-11-05T03:51:09Z RO:0004024 @@ -5960,7 +5942,9 @@ Environmental exposures include those imposed by natural environments, experimen - + + + disease causes dysfunction of (disease to anatomical entity) cjm 2017-11-05T03:58:20Z RO:0004025 @@ -5973,8 +5957,17 @@ Environmental exposures include those imposed by natural environments, experimen - + + + + + + + + + + A relationship between a disease and an anatomical entity where the disease has one or more features that are located in that entity. TODO: complete range axiom once more of CARO has been mireoted in to this ontology This relation is intentionally very general, and covers isolated diseases, where the disease is realized as a process occurring in the location, and syndromic diseases, where one or more of the features may be present in that location. Thus any given disease can have multiple locations in the sense defined here. @@ -5991,6 +5984,8 @@ Environmental exposures include those imposed by natural environments, experimen + + A relationship between a disease and an anatomical entity where the disease is triggered by an inflammatory response to stimuli occurring in the anatomical entity cjm 2017-12-26T19:37:31Z @@ -6020,12 +6015,13 @@ Environmental exposures include those imposed by natural environments, experimen - + + - - + + @@ -6217,6 +6213,8 @@ Environmental exposures include those imposed by natural environments, experimen + + An interaction relationship wherein one organism creates a structure or environment that is lived in by another organism. RO:0008505 creates_habitat_for @@ -6230,10 +6228,12 @@ Environmental exposures include those imposed by natural environments, experimen + + An interaction relationship describing organisms that often occur together at the same time and space or in the same environment. RO:0008506 - co-occurs - co-occurs + ecologically_co-occurs_with + ecologically co-occurs with @@ -6292,6 +6292,42 @@ Environmental exposures include those imposed by natural environments, experimen + + + + This relation groups relations between diseases and any other kind of entity. + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, in which the subject or object is a disease. + cjm + 2018-09-26T00:00:32Z + RO:0040035 + disease_relationship + disease relationship + + + + + + + + + + + + + + + + + p has anatomical participant c iff p has participant c, and c is an anatomical entity + cjm + 2018-09-26T01:08:58Z + RO:0040036 + has_anatomical_participant + has anatomical participant + + + + @@ -6333,12 +6369,6 @@ Environmental exposures include those imposed by natural environments, experimen - - - - - - @@ -6351,6 +6381,12 @@ Environmental exposures include those imposed by natural environments, experimen + + + + + + @@ -6363,6 +6399,12 @@ Environmental exposures include those imposed by natural environments, experimen + + + + + + @@ -6375,12 +6417,24 @@ Environmental exposures include those imposed by natural environments, experimen + + + + + + + + + + + + @@ -6423,6 +6477,12 @@ Environmental exposures include those imposed by natural environments, experimen + + + + + + @@ -6459,6 +6519,12 @@ Environmental exposures include those imposed by natural environments, experimen + + + + + + diff --git a/subsets/ro-time-interval.obo b/subsets/ro-time-interval.obo index d70a263a..d63edc70 100644 --- a/subsets/ro-time-interval.obo +++ b/subsets/ro-time-interval.obo @@ -1,6 +1,6 @@ format-version: 1.2 ontology: ro/subsets/ro-time-interval -owl-axioms: Prefix(owl:=)\nPrefix(rdf:=)\nPrefix(xml:=)\nPrefix(xsd:=)\nPrefix(rdfs:=)\n\n\nOntology(\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\n\n############################\n# Object Properties\n############################\n\n# Object Property: (coincident with)\n\nObjectPropertyRange( ObjectIntersectionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (has fasciculating neuron projection)\n\nObjectPropertyRange( ObjectUnionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (connected to)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (connects)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (directly develops from)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (enabled by)\n\nSubObjectPropertyOf( ObjectInverseOf())\n\n# Object Property: (anabranch of)\n\nSubObjectPropertyOf( ObjectInverseOf())\n\n# Object Property: (branching part of)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (condition has genetic basis in)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has feature)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n\n\n\nAnnotationAssertion(rdfs:comment \"\")\n) +owl-axioms: Prefix(owl:=)\nPrefix(rdf:=)\nPrefix(xml:=)\nPrefix(xsd:=)\nPrefix(rdfs:=)\n\n\nOntology(\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\n\n############################\n# Object Properties\n############################\n\n# Object Property: (coincident with)\n\nObjectPropertyRange( ObjectIntersectionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (has fasciculating neuron projection)\n\nObjectPropertyRange( ObjectUnionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (connected to)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (connects)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (directly develops from)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (anabranch of)\n\nSubObjectPropertyOf( ObjectInverseOf())\n\n# Object Property: (branching part of)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (condition has genetic basis in)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has basis in feature)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has location)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has feature)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (has anatomical participant)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n\n\n\nAnnotationAssertion(rdfs:comment \"\")\n) [Typedef] id: 2D_boundary_of @@ -184,6 +184,7 @@ def: "a is attached to b if and only if a and b are discrete objects or object p subset: ro-eco xref: RO:0002371 property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000589 "attached to (anatomical structure to anatomical structure)" xsd:string is_symmetric: true is_a: attached_to_part_of ! attached to part of is_a: connected_to ! connected to @@ -193,8 +194,9 @@ id: attached_to_part_of name: attached to part of def: "a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b." [] xref: RO:0002177 -domain: BFO:0000040 -range: BFO:0000040 +property_value: IAO:0000589 "attached to part of (anatomical structure to anatomical structure)" xsd:string +domain: CARO:0000003 +range: CARO:0000003 is_a: biomechanically_related_to ! biomechanically related to is_a: mereotopologically_related_to ! mereotopologically related to @@ -225,6 +227,8 @@ def: "A relation that holds between elements of a musculoskeletal system or its xref: RO:0002567 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes." xsd:string +domain: CARO:0000003 +range: CARO:0000003 is_a: functionally_related_to ! functionally related to [Typedef] @@ -323,6 +327,7 @@ def: "c stands in this relationship to p if and only if there exists some p' suc xref: RO:0002216 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "has function in" xsd:string +property_value: seeAlso "defining-property-chains-involving-reflexivity" is_a: causal_agent_in_process ! causal agent in process is_a: functionally_related_to ! functionally related to expand_expression_to: "RO_0000053 some (RO_0000054 only (BFO_0000050 some ?Y))" [] @@ -406,8 +411,9 @@ name: causal relationship with disease as subject xref: RO:0004023 property_value: IAO:0000116 "After import upper level from OGMS, make domain more specific." xsd:string property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all of which have a disease as the subject." xsd:string -domain: BFO:0000016 +domain: OGMS:0000031 is_a: causally_related_to ! causally related to +is_a: disease_relationship ! disease relationship created_by: cjm creation_date: 2017-11-05T03:50:54Z @@ -462,7 +468,6 @@ property_value: IAO:0000114 IAO:0000428 property_value: 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." xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: 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." xsd:string -is_a: related_via_dependence_to ! related via dependence to [Typedef] id: causally_upstream_of @@ -571,14 +576,6 @@ xref: RO:0002478 property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: child_nucleus_of ! child nucleus of -[Typedef] -id: co-occurs -name: co-occurs -def: "An interaction relationship describing organisms that often occur together at the same time and space or in the same environment." [] -xref: RO:0008506 -is_symmetric: true -is_a: ecologically_related_to ! ecologically related to - [Typedef] id: coincident_with name: coincident with @@ -673,6 +670,7 @@ xref: RO:0002322 property_value: IAO:0000116 "An experimental relation currently used to connect a feature possessed by an organism (e.g. anatomical structure, biological process, phenotype or quality) to a habitat or environment in which that feature is well suited, adapted or provides a reproductive advantage for the organism. For example, fins to an aquatic environment. Usually this will mean that the structure is adapted for this environment, but we avoid saying this directly - primitive forms of the structure may not have evolved specifically for that environment (for example, early wings were not necessarily adapted for an aerial environment). Note also that this is a statement about the general class of structures - not every instance of a limb need confer an advantage for a terrestrial environment, e.g. if the limb is vestigial." xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "adapted for" xsd:string +range: ENVO:01000254 is_a: ecologically_related_to ! ecologically related to [Typedef] @@ -767,26 +765,13 @@ xref: RO:0003305 property_value: IAO:0000118 "contributes to expressivity of condition" xsd:string is_a: contributes_to_condition ! contributes to condition -[Typedef] -id: correlated_with -name: correlated with -def: "A relationship that holds between two entities, where the entities exhibit a statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes." [] -xref: RO:0002610 -property_value: IAO:0000232 "Groups both positive and negative correlation" xsd:string -is_a: related_via_dependence_to ! related via dependence to - -[Typedef] -id: correlated_with_condition -name: correlated with condition -def: "A relationship between an entity and a condition (phenotype or disease) with which it exhibits a statistical dependence relationship." [] -xref: RO:0003308 -is_a: correlated_with ! correlated with - [Typedef] id: creates_habitat_for name: creates habitat for def: "An interaction relationship wherein one organism creates a structure or environment that is lived in by another organism." [] xref: RO:0008505 +domain: CARO:0001010 +range: CARO:0001010 is_a: ecologically_related_to ! ecologically related to [Typedef] @@ -964,7 +949,7 @@ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 "EHDAA2" xsd:string property_value: IAO:0000119 "Jonathan Bard, EHDAA2" xsd:string -domain: CARO:0000003 +domain: CARO:0000000 is_a: developmentally_preceded_by ! developmentally preceded by [Typedef] @@ -1121,6 +1106,8 @@ id: disease_causes_disruption_of name: disease causes disruption of def: "A relationship between a disease and a process where the disease process disrupts the execution of the process." [] xref: RO:0004024 +property_value: IAO:0000589 "disease causes disruption of (disease to process)" xsd:string +domain: OGMS:0000031 range: BFO:0000015 is_a: causal_relationship_with_disease_as_subject ! causal relationship with disease as subject created_by: cjm @@ -1130,7 +1117,9 @@ creation_date: 2017-11-05T03:51:09Z id: disease_causes_dysfunction_of name: disease causes dysfunction of xref: RO:0004025 -range: BFO:0000004 +property_value: IAO:0000589 "disease causes dysfunction of (disease to anatomical entity)" xsd:string +domain: OGMS:0000031 +range: CARO:0000006 is_a: causal_relationship_with_disease_as_subject ! causal relationship with disease as subject created_by: cjm creation_date: 2017-11-05T03:58:20Z @@ -1139,7 +1128,7 @@ creation_date: 2017-11-05T03:58:20Z id: disease_has_basis_in name: disease has basis in xref: RO:0004019 -domain: BFO:0000016 +domain: OGMS:0000031 is_a: causal_relationship_with_disease_as_subject ! causal relationship with disease as subject is_a: realizable_has_basis_in ! realizable has basis in created_by: cjm @@ -1150,6 +1139,7 @@ id: disease_has_basis_in_disruption_of name: disease has basis in disruption of def: "A relation that holds between the disease and a process where the physical basis of the disease disrupts execution of a key biological process." [] xref: RO:0004021 +property_value: IAO:0000589 "disease has basis in disruption of (disease to process)" xsd:string range: BFO:0000015 is_a: disease_has_basis_in ! disease has basis in created_by: cjm @@ -1160,7 +1150,8 @@ id: disease_has_basis_in_dysfunction_of name: disease has basis in dysfunction of def: "A relation that holds between the disease and a material entity where the physical basis of the disease is a disorder of that material entity that affects its function." [] xref: RO:0004020 -range: BFO:0000040 +property_value: IAO:0000589 "disease has basis in dysfunction of (disease to anatomical structure)" xsd:string +range: CARO:0000006 is_a: disease_has_basis_in ! disease has basis in created_by: cjm creation_date: 2017-11-05T03:29:32Z @@ -1170,6 +1161,7 @@ id: disease_has_basis_in_feature name: disease has basis in feature def: "A relation that holds between the disease and a feature (a phenotype or other disease) where the physical basis of the disease is the feature." [] xref: RO:0004022 +domain: OGMS:0000031 is_a: disease_has_basis_in ! disease has basis in is_a: has_phenotype ! has phenotype created_by: cjm @@ -1180,7 +1172,8 @@ id: disease_has_feature name: disease has feature def: "A relationship between a disease and some feature of that disease, where the feature is either a phenotype or an isolated disease." [] xref: RO:0004029 -is_a: causal_relationship_with_disease_as_subject ! causal relationship with disease as subject +domain: OGMS:0000031 +is_a: disease_relationship ! disease relationship created_by: cjm creation_date: 2017-12-26T19:50:53Z @@ -1189,6 +1182,8 @@ id: disease_has_inflammation_site name: disease has inflammation site def: "A relationship between a disease and an anatomical entity where the disease is triggered by an inflammatory response to stimuli occurring in the anatomical entity" [] xref: RO:0004027 +domain: OGMS:0000031 +range: CARO:0000003 is_a: disease_has_location ! disease has location created_by: cjm creation_date: 2017-12-26T19:37:31Z @@ -1200,11 +1195,21 @@ def: "A relationship between a disease and an anatomical entity where the diseas xref: RO:0004026 property_value: IAO:0000116 "TODO: complete range axiom once more of CARO has been mireoted in to this ontology" xsd:string property_value: IAO:0000232 "This relation is intentionally very general, and covers isolated diseases, where the disease is realized as a process occurring in the location, and syndromic diseases, where one or more of the features may be present in that location. Thus any given disease can have multiple locations in the sense defined here." xsd:string +domain: OGMS:0000031 range: BFO:0000004 -is_a: causal_relationship_with_disease_as_subject ! causal relationship with disease as subject +is_a: disease_relationship ! disease relationship created_by: cjm creation_date: 2017-11-05T04:06:02Z +[Typedef] +id: disease_relationship +name: disease relationship +def: "This relation groups relations between diseases and any other kind of entity." [] +xref: RO:0040035 +property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, in which the subject or object is a disease." xsd:string +created_by: cjm +creation_date: 2018-09-26T00:00:32Z + [Typedef] id: distributary_of name: distributary of @@ -1249,12 +1254,23 @@ property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "is subject of eating interaction with" xsd:string is_a: trophically_interacts_with ! trophically interacts with +[Typedef] +id: ecologically_co-occurs_with +name: ecologically co-occurs with +def: "An interaction relationship describing organisms that often occur together at the same time and space or in the same environment." [] +xref: RO:0008506 +domain: CARO:0001010 +range: CARO:0001010 +is_symmetric: true +is_a: ecologically_related_to ! ecologically related to + [Typedef] id: ecologically_related_to name: ecologically related to def: "A relationship that is mediated in some way by the environment or environmental feature (ENVO:00002297)" [] subset: ro-eco xref: RO:0002321 +property_value: IAO:0000116 "Awaiting class for domain/range constraint, see: https://github.com/OBOFoundry/Experimental-OBO-Core/issues/6" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving ecological interactions" xsd:string @@ -1379,6 +1395,7 @@ is_a: output_of ! output of [Typedef] id: functionally_related_to name: functionally related to +def: "A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities." [] xref: RO:0002328 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000232 "This is a grouping relation that collects relations used for the purpose of connecting structure and function" xsd:string @@ -1433,6 +1450,15 @@ property_value: IAO:0000112 "penicillin allergy (DOID:0060520) has allergic trig range: BFO:0000040 is_a: causes_or_contributes_to_condition ! causes or contributes to condition +[Typedef] +id: has_anatomical_participant +name: has anatomical participant +def: "p has anatomical participant c iff p has participant c, and c is an anatomical entity" [] +xref: RO:0040036 +is_a: has_participant +created_by: cjm +creation_date: 2018-09-26T01:08:58Z + [Typedef] id: has_autoimmune_trigger name: has autoimmune trigger @@ -1506,8 +1532,8 @@ xref: RO:0002254 property_value: IAO:0000112 "Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string -domain: BFO:0000004 -range: CARO:0000003 +domain: CARO:0000000 +range: CARO:0000000 is_a: developmentally_preceded_by ! developmentally preceded by inverse_of: developmentally_contributes_to ! developmentally contributes to @@ -1518,6 +1544,8 @@ def: "x has developmental potential involving y iff x is capable of a developmen xref: RO:0002384 property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Chris Mungall" xsd:string +domain: CARO:0000000 +range: CARO:0000000 is_a: developmentally_related_to ! developmentally related to [Typedef] @@ -1682,7 +1710,7 @@ property_value: IAO:0000112 "Hydrozoa (NCBITaxon_6074) SubClassOf 'has habitat' property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Pier Buttigieg" xsd:string property_value: IAO:0000118 "adapted for living in" xsd:string -domain: CARO:0000006 +domain: CARO:0001010 range: ENVO:01000254 is_a: ecologically_related_to ! ecologically related to @@ -1820,6 +1848,7 @@ xref: RO:0002373 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 Wikipedia:Insertion_(anatomy) xsd:string property_value: seeAlso http://dbpedia.org/property/insertion +domain: CARO:0000003 {http://purl.obolibrary.org/obo/IAO_0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} is_a: attached_to ! attached to is_a: biomechanically_related_to ! biomechanically related to @@ -1831,6 +1860,7 @@ xref: RO:0002372 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 Wikipedia:Insertion_(anatomy) xsd:string property_value: seeAlso http://dbpedia.org/property/origin +domain: CARO:0000003 {comment="We need to import uberon muscle to create a stricter domain constraint"} is_a: attached_to ! attached to is_a: biomechanically_related_to ! biomechanically related to @@ -1929,7 +1959,7 @@ subset: ro-eco xref: RO:0002200 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string -domain: BFO:0000002 +range: UPHENO:0001001 inverse_of: phenotype_of ! phenotype of [Typedef] @@ -2051,6 +2081,7 @@ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string property_value: RO:0001900 RO:0001901 domain: CL:0000540 +range: CARO:0000003 is_a: overlaps ! overlaps expand_expression_to: "BFO_0000051 some (\n GO_0043025 and BFO_0000050 some ?Y)" [] @@ -2306,6 +2337,8 @@ name: innervated_by xref: RO:0002005 property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 xsd:anyURI property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +domain: CARO:0000003 +range: CARO:0001001 inverse_of: innervates ! innervates [Typedef] @@ -2404,6 +2437,7 @@ id: involved_in_or_involved_in_regulation_of name: involved in or involved in regulation of def: "c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p" [] xref: RO:0002431 +property_value: IAO:0000116 "OWL does not allow defining object properties via a Union" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "involved in or reguates" xsd:string is_a: acts_upstream_of_or_within ! acts upstream of or within @@ -2622,14 +2656,6 @@ name: is killed by xref: RO:0002627 is_a: participates_in_a_biotic-biotic_interaction_with ! participates in a biotic-biotic interaction with -[Typedef] -id: is_marker_for -name: is marker for -def: "c is marker for d iff the presence or occurrence of d is correlated with the presence of occurrence of c, and the observation of c is used to infer the presence or occurrence of d. Note that this does not imply that c and d are in a direct causal relationship, as it may be the case that there is a third entity e that stands in a direct causal relationship with c and d." [] -xref: RO:0002607 -property_value: IAO:0000116 "May be ceded to OBI" xsd:string -is_a: correlated_with ! correlated with - [Typedef] id: is_sequentially_aligned_with name: is sequentially aligned with @@ -2851,16 +2877,6 @@ def: "A sub-relation of parasite-of in which the parasite that cannot complete i xref: RO:0002227 is_a: parasite_of ! parasite of -[Typedef] -id: obsolete_has_indirect_output -name: obsolete has indirect output -comment: Likely to be obsoleted. See:\nhttps://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/edit -xref: RO:0002403 -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string -is_a: has_output ! has output -is_obsolete: true - [Typedef] id: occurent_part_of name: occurent part of @@ -3010,6 +3026,8 @@ subset: ro-eco xref: RO:0002574 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: seeAlso http://dx.doi.org/10.1016/j.ecoinf.2014.08.005 +domain: CARO:0001010 +range: CARO:0001010 is_a: biotically_interacts_with ! biotically interacts with [Typedef] @@ -3277,13 +3295,6 @@ property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relati property_value: IAO:0000589 "regulates levels of (process to entity)" xsd:string is_a: functionally_related_to ! functionally related to -[Typedef] -id: related_via_dependence_to -name: related via dependence to -def: "A relationship that holds between two entities, where the relationship holds based on the presence or absence of statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes." [] -xref: RO:0002609 -property_value: 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." xsd:string - [Typedef] id: related_via_exposure_to name: related via exposure to @@ -3308,6 +3319,7 @@ name: releases neurotransmitter xref: RO:0002111 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000118 "has neurotransmitter" xsd:string +domain: CARO:0000003 [Typedef] id: represses_expression_of @@ -3325,8 +3337,8 @@ xref: RO:0002315 property_value: IAO:0000112 "an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast." xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string -range: CL:0000000 -is_a: has_participant +range: CARO:0000003 +is_a: has_anatomical_participant ! has anatomical participant is_a: results_in_developmental_progression_of ! results in developmental progression of [Typedef] @@ -3355,7 +3367,7 @@ id: results_in_closure_of name: results in closure of xref: RO:0002585 property_value: IAO:0000116 "p 'results in closure of' c if and only if p is a developmental process and p results in a state of c changing from open to closed." xsd:string -is_a: has_participant +is_a: has_anatomical_participant ! has anatomical participant is_a: results_in_developmental_progression_of ! results in developmental progression of [Typedef] @@ -3388,7 +3400,7 @@ property_value: IAO:0000112 "every flower development (GO:0009908) results in de property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://www.geneontology.org/GO.doc.development.shtml xsd:anyURI -is_a: has_participant +is_a: has_anatomical_participant ! has anatomical participant is_a: results_in_developmental_progression_of ! results in developmental progression of [Typedef] @@ -3445,7 +3457,7 @@ name: results in ending of def: "p results in the end of s if p results in a change of state in s whereby s either ceases to exist, or s becomes functionally impaired or s has its fate committed such that it is put on a path to be degraded." [] xref: RO:0002552 property_value: IAO:0000117 "Chris Mungall" xsd:string -is_a: has_participant +is_a: has_anatomical_participant ! has anatomical participant is_a: results_in_developmental_progression_of ! results in developmental progression of [Typedef] @@ -3467,7 +3479,7 @@ name: results in growth of xref: RO:0002343 property_value: IAO:0000112 "'pollen tube growth' results_in growth_of some 'pollen tube'" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string -is_a: has_participant +is_a: has_anatomical_participant ! has anatomical participant is_a: results_in_developmental_progression_of ! results in developmental progression of [Typedef] @@ -3480,7 +3492,7 @@ property_value: IAO:0000112 "bone maturation (GO:0070977) results_in_maturation_ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string -is_a: has_participant +is_a: has_anatomical_participant ! has anatomical participant is_a: results_in_developmental_progression_of ! results in developmental progression of [Typedef] @@ -3493,7 +3505,7 @@ property_value: IAO:0000112 "tongue morphogenesis (GO:0043587) results in morpho property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string -is_a: has_participant +is_a: has_anatomical_participant ! has anatomical participant is_a: results_in_developmental_progression_of ! results in developmental progression of [Typedef] @@ -3503,14 +3515,14 @@ def: "Holds between p and c when p is locomotion process and the outcome of this xref: RO:0002565 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000232 "" xsd:string -is_a: has_participant +is_a: has_anatomical_participant ! has anatomical participant [Typedef] id: results_in_organization_of name: results in organization of def: "p results in organization of c iff p results in the assembly, arrangement of constituent parts, or disassembly of c" [] xref: RO:0002592 -is_a: has_participant +is_a: has_anatomical_participant ! has anatomical participant [Typedef] id: results_in_remodeling_of @@ -3535,7 +3547,7 @@ name: results in structural organization of def: "A relationship between a process and an anatomical entity such that the process contributes to the act of creating the structural organization of the anatomical entity." [] xref: RO:0002355 property_value: IAO:0000117 "Chris Mungall" xsd:string -is_a: has_participant +is_a: has_anatomical_participant ! has anatomical participant is_a: results_in_developmental_progression_of ! results in developmental progression of [Typedef] @@ -3785,7 +3797,7 @@ def: "Holds between p and c when p is a localization process (localization cover xref: RO:0002313 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "regulates localization of" xsd:string -is_a: has_participant +is_a: has_anatomical_participant ! has anatomical participant is_a: related_via_localization_to ! related via localization to [Typedef] diff --git a/subsets/ro-time-interval.owl b/subsets/ro-time-interval.owl index d15dff26..8c61af62 100644 --- a/subsets/ro-time-interval.owl +++ b/subsets/ro-time-interval.owl @@ -381,6 +381,8 @@ + + David Osumi-Sutherland http://www.ncbi.nlm.nih.gov/pubmed/22402613 RO:0002005 @@ -787,6 +789,7 @@ Examples include: the relationship between two channels collected simultaneously + Relation between a neuron and an anatomical structure that its soma is part of. David Osumi-Sutherland @@ -931,6 +934,7 @@ Examples include: the relationship between two channels collected simultaneously + has neurotransmitter RO:0002111 @@ -1231,9 +1235,10 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - - + + a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b. + attached to part of (anatomical structure to anatomical structure) RO:0002177 attached_to_part_of attached to part of @@ -1292,7 +1297,16 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - + + + + + + + + + + A relationship that holds between a biological entity and a phenotype. Here a phenotype is construed broadly as any kind of quality of an organism part, a collection of these qualities, or a change in quality or qualities (e.g. abnormally increased temperature). The subject of this relationship can be an organism (where the organism has the phenotype, i.e. the qualities inhere in parts of this organism), a genomic entity such as a gene or genotype (if modifications of the gene or the genotype causes the phenotype), or a condition such as a disease (such that if the condition inheres in an organism, then the organism has the phenotype). Chris Mungall @@ -1538,6 +1552,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.RO:0002216 capable_of_part_of capable of part of + @@ -1690,7 +1705,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - + x develops_in y if x is located in y whilst x is developing Chris Mungall @@ -1985,8 +2000,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - - + + Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong] x has developmental contribution from y iff x has some part z such that z develops from y @@ -2167,8 +2182,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - + every flower development (GO:0009908) results in development of some flower (PO:0009046) p 'results in development of' c if and only if p is a developmental process and p results in the state of c changing from its initial state as a primordium or anlage through its mature state and to its final state. @@ -2202,8 +2217,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - + an annotation of gene X to cell morphogenesis with results_in_morphogenesis_of CL:0000540 (neuron) means that at the end of the process an input neuron has attained its shape. tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723) @@ -2220,8 +2235,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - + an annotation of gene X to cell maturation with results_in_maturation_of CL:0000057 (fibroblast) means that the fibroblast is mature at the end of the process bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474) @@ -2284,7 +2299,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - + Hydrozoa (NCBITaxon_6074) SubClassOf 'has habitat' some 'Hydrozoa habitat' where @@ -2352,8 +2367,8 @@ where - + Holds between p and c when p is a localization process (localization covers maintenance of localization as well as its establishment) and the outcome of this process is to regulate the localization of c. Chris Mungall regulates localization of @@ -2367,9 +2382,9 @@ where - - + + an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast. The relationship that links a specified entity with the process that results in an unspecified entity acquiring the features and characteristics of the specified entity Chris Mungall @@ -2385,6 +2400,7 @@ where A relationship that is mediated in some way by the environment or environmental feature (ENVO:00002297) + Awaiting class for domain/range constraint, see: https://github.com/OBOFoundry/Experimental-OBO-Core/issues/6 Chris Mungall Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving ecological interactions RO:0002321 @@ -2399,6 +2415,7 @@ where + An experimental relation currently used to connect a feature possessed by an organism (e.g. anatomical structure, biological process, phenotype or quality) to a habitat or environment in which that feature is well suited, adapted or provides a reproductive advantage for the organism. For example, fins to an aquatic environment. Usually this will mean that the structure is adapted for this environment, but we avoid saying this directly - primitive forms of the structure may not have evolved specifically for that environment (for example, early wings were not necessarily adapted for an aerial environment). Note also that this is a statement about the general class of structures - not every instance of a limb need confer an advantage for a terrestrial environment, e.g. if the limb is vestigial. Chris Mungall adapted for @@ -2509,6 +2526,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities. Chris Mungall This is a grouping relation that collects relations used for the purpose of connecting structure and function RO:0002328 @@ -2569,11 +2587,6 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - - - - - inverse of enables Chris Mungall RO:0002333 @@ -2712,8 +2725,8 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - + 'pollen tube growth' results_in growth_of some 'pollen tube' Chris Mungall RO:0002343 @@ -2826,8 +2839,8 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - + A relationship between a process and an anatomical entity such that the process contributes to the act of creating the structural organization of the anatomical entity. Chris Mungall RO:0002355 @@ -2886,6 +2899,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a Chris Mungall + attached to (anatomical structure to anatomical structure) RO:0002371 attached_to @@ -2899,6 +2913,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to. Chris Mungall Wikipedia:Insertion_(anatomy) @@ -2907,6 +2922,12 @@ However, this is not possible in OWL. We instead make this relation a sub-relati has muscle origin + + + + + We need to import uberon muscle to create a stricter domain constraint + @@ -2915,6 +2936,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone. Chris Mungall Wikipedia:Insertion_(anatomy) @@ -2923,6 +2945,12 @@ However, this is not possible in OWL. We instead make this relation a sub-relati has muscle insertion + + + + + We need to import uberon muscle into RO to use as a stricter domain constraint + @@ -3103,6 +3131,8 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + + x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction). Chris Mungall @@ -3186,22 +3216,6 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - - - - - - Chris Mungall - RO:0002403 - obsolete_has_indirect_output - Likely to be obsoleted. See: -https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/edit - obsolete has indirect output - true - - - - @@ -3300,7 +3314,6 @@ https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/ - This relation groups causal relations between material entities and causal relations between processes 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. @@ -3479,6 +3492,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p + OWL does not allow defining object properties via a Union Chris Mungall involved in or reguates RO:0002431 @@ -4653,8 +4667,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + p results in the end of s if p results in a change of state in s whereby s either ceases to exist, or s becomes functionally impaired or s has its fate committed such that it is put on a path to be degraded. Chris Mungall RO:0002552 @@ -4763,7 +4777,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c Chris Mungall @@ -4793,6 +4807,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + A relation that holds between elements of a musculoskeletal system or its analogs. Chris Mungall Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes. @@ -4885,6 +4901,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + Chris Mungall RO:0002574 @@ -4946,8 +4964,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + p 'results in closure of' c if and only if p is a developmental process and p results in a state of c changing from open to closed. RO:0002585 results_in_closure_of @@ -5030,7 +5048,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + p results in organization of c iff p results in the assembly, arrangement of constituent parts, or disassembly of c RO:0002592 results_in_organization_of @@ -5149,19 +5167,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - c is marker for d iff the presence or occurrence of d is correlated with the presence of occurrence of c, and the observation of c is used to infer the presence or occurrence of d. Note that this does not imply that c and d are in a direct causal relationship, as it may be the case that there is a third entity e that stands in a direct causal relationship with c and d. - May be ceded to OBI - RO:0002607 - is_marker_for - is marker for - - - - @@ -5175,31 +5180,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - A relationship that holds between two entities, where the relationship holds based on the presence or absence of statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes. - Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. - RO:0002609 - related_via_dependence_to - related via dependence to - - - - - - - - - A relationship that holds between two entities, where the entities exhibit a statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes. - Groups both positive and negative correlation - RO:0002610 - correlated_with - correlated with - - - - @@ -5572,18 +5552,6 @@ Environmental exposures include those imposed by natural environments, experimen - - - - - A relationship between an entity and a condition (phenotype or disease) with which it exhibits a statistical dependence relationship. - RO:0003308 - correlated_with_condition - correlated with condition - - - - @@ -5870,7 +5838,7 @@ Environmental exposures include those imposed by natural environments, experimen - + cjm 2017-11-05T03:26:47Z RO:0004019 @@ -5884,8 +5852,9 @@ Environmental exposures include those imposed by natural environments, experimen - + A relation that holds between the disease and a material entity where the physical basis of the disease is a disorder of that material entity that affects its function. + disease has basis in dysfunction of (disease to anatomical structure) cjm 2017-11-05T03:29:32Z RO:0004020 @@ -5901,6 +5870,7 @@ Environmental exposures include those imposed by natural environments, experimen A relation that holds between the disease and a process where the physical basis of the disease disrupts execution of a key biological process. + disease has basis in disruption of (disease to process) cjm 2017-11-05T03:37:52Z RO:0004021 @@ -5915,6 +5885,15 @@ Environmental exposures include those imposed by natural environments, experimen + + + + + + + + + A relation that holds between the disease and a feature (a phenotype or other disease) where the physical basis of the disease is the feature. cjm 2017-11-05T03:46:07Z @@ -5929,7 +5908,8 @@ Environmental exposures include those imposed by natural environments, experimen - + + After import upper level from OGMS, make domain more specific. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all of which have a disease as the subject. cjm @@ -5945,8 +5925,10 @@ Environmental exposures include those imposed by natural environments, experimen + A relationship between a disease and a process where the disease process disrupts the execution of the process. + disease causes disruption of (disease to process) cjm 2017-11-05T03:51:09Z RO:0004024 @@ -5960,7 +5942,9 @@ Environmental exposures include those imposed by natural environments, experimen - + + + disease causes dysfunction of (disease to anatomical entity) cjm 2017-11-05T03:58:20Z RO:0004025 @@ -5973,8 +5957,17 @@ Environmental exposures include those imposed by natural environments, experimen - + + + + + + + + + + A relationship between a disease and an anatomical entity where the disease has one or more features that are located in that entity. TODO: complete range axiom once more of CARO has been mireoted in to this ontology This relation is intentionally very general, and covers isolated diseases, where the disease is realized as a process occurring in the location, and syndromic diseases, where one or more of the features may be present in that location. Thus any given disease can have multiple locations in the sense defined here. @@ -5991,6 +5984,8 @@ Environmental exposures include those imposed by natural environments, experimen + + A relationship between a disease and an anatomical entity where the disease is triggered by an inflammatory response to stimuli occurring in the anatomical entity cjm 2017-12-26T19:37:31Z @@ -6020,12 +6015,13 @@ Environmental exposures include those imposed by natural environments, experimen - + + - - + + @@ -6217,6 +6213,8 @@ Environmental exposures include those imposed by natural environments, experimen + + An interaction relationship wherein one organism creates a structure or environment that is lived in by another organism. RO:0008505 creates_habitat_for @@ -6230,10 +6228,12 @@ Environmental exposures include those imposed by natural environments, experimen + + An interaction relationship describing organisms that often occur together at the same time and space or in the same environment. RO:0008506 - co-occurs - co-occurs + ecologically_co-occurs_with + ecologically co-occurs with @@ -6292,6 +6292,42 @@ Environmental exposures include those imposed by natural environments, experimen + + + + This relation groups relations between diseases and any other kind of entity. + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, in which the subject or object is a disease. + cjm + 2018-09-26T00:00:32Z + RO:0040035 + disease_relationship + disease relationship + + + + + + + + + + + + + + + + + p has anatomical participant c iff p has participant c, and c is an anatomical entity + cjm + 2018-09-26T01:08:58Z + RO:0040036 + has_anatomical_participant + has anatomical participant + + + + @@ -6333,12 +6369,6 @@ Environmental exposures include those imposed by natural environments, experimen - - - - - - @@ -6351,6 +6381,12 @@ Environmental exposures include those imposed by natural environments, experimen + + + + + + @@ -6363,6 +6399,12 @@ Environmental exposures include those imposed by natural environments, experimen + + + + + + @@ -6375,12 +6417,24 @@ Environmental exposures include those imposed by natural environments, experimen + + + + + + + + + + + + @@ -6423,6 +6477,12 @@ Environmental exposures include those imposed by natural environments, experimen + + + + + + @@ -6459,6 +6519,12 @@ Environmental exposures include those imposed by natural environments, experimen + + + + + + diff --git a/temporal-intervals.owl b/temporal-intervals.owl index 312aa81c..bb7ee22f 100644 --- a/temporal-intervals.owl +++ b/temporal-intervals.owl @@ -1,27 +1,34 @@ + + + + + - - - - - - -]> + + - - - - + + + + @@ -38,284 +45,282 @@ - - - obsolete preceded by + + accidentally included in BFO 1.2 proposal - should have been BFO_0000062 + obsolete preceded by - - - preceded by - http://www.obofoundry.org/ro/#OBO_REL:preceded_by - is preceded by - preceded by - preceded_by - 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. - 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. - - - - + + + + + + - - + + - - + + + preceded by + 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. + 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. + is preceded by + preceded_by + http://www.obofoundry.org/ro/#OBO_REL:preceded_by + preceded by - - - precedes + + + + precedes 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. - - + precedes - - before or simultaneous with - Primitive instance level timing relation between events - <= - + + David Osumi-Sutherland + <= + Primitive instance level timing relation between events + before or simultaneous with - - - simultaneous with - t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2) - + + + David Osumi-Sutherland + t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2) + simultaneous with - - - before - t1 before t2 iff:= t1 before_or_simulataneous_with t2 and not (t1 simultaeous_with t2) - + + + David Osumi-Sutherland + t1 before t2 iff:= t1 before_or_simulataneous_with t2 and not (t1 simultaeous_with t2) + before - - during which ends - Previously had ID http://purl.obolibrary.org/obo/RO_0002122 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. - - + + + David Osumi-Sutherland + Previously had ID http://purl.obolibrary.org/obo/RO_0002122 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. + during which ends - - - ends after - X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) - + + + - - + + David Osumi-Sutherland + X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) + ends after - - immediately preceded by + + + + David Osumi-Sutherland starts_at_end_of X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) - - - David Osumi-Sutherland + immediately preceded by - - during which starts - Previously had ID http://purl.obolibrary.org/obo/RO_0002123 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. - - + + + David Osumi-Sutherland + Previously had ID http://purl.obolibrary.org/obo/RO_0002123 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. + during which starts - - - starts before - + + + - - + + David Osumi-Sutherland + starts before - - immediately precedes + + + David Osumi-Sutherland ends_at_start_of - X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) meets - - David Osumi-Sutherland + X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) + immediately precedes - - starts during + + + + + David Osumi-Sutherland io X starts_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (start(X) before_or_simultaneous_with end(Y)) - - - - David Osumi-Sutherland + starts during - - - happens during + + + + David Osumi-Sutherland d during X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y)) - - David Osumi-Sutherland + happens during - - ends during + + + David Osumi-Sutherland o overlaps X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y). - - David Osumi-Sutherland + ends during - - temporally related to - A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. - - - + + + + - Chris Mungall + A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. + temporally related to - - starts + + + + inverse of starts with Chris Mungall Allen - - - Chris Mungall + starts - - - starts with - started by - x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(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. + + + Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor - - - + + x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(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. Chris Mungall + started by + starts with - - ends + + + + inverse of ends with - - - Chris Mungall + ends - - - ends with + + + + x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(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. - finished by - - Chris Mungall + finished by + ends with - +