From 2d4b4300d6b0ef894c329f0dd110317c4a2ffdc7 Mon Sep 17 00:00:00 2001 From: Nico Matentzoglu Date: Mon, 8 Mar 2021 21:21:06 +0000 Subject: [PATCH] RO Release March 2021 --- ro-base.json | 247 ++++++++++++---------- ro-base.obo | 29 ++- ro-base.owl | 46 ++-- ro.json | 223 ++++++++++--------- ro.obo | 29 ++- ro.owl | 46 ++-- src/ontology/subsets/ro-causal.obo | 25 ++- src/ontology/subsets/ro-causal.owl | 35 ++- src/ontology/subsets/ro-chado.obo | 15 +- src/ontology/subsets/ro-chado.obo.tmp | 15 +- src/ontology/subsets/ro-developmental.obo | 25 ++- src/ontology/subsets/ro-developmental.owl | 35 ++- src/ontology/subsets/ro-eco.obo | 35 ++- src/ontology/subsets/ro-eco.owl | 69 ++++-- src/ontology/subsets/ro-interaction.obo | 25 ++- src/ontology/subsets/ro-interaction.owl | 35 ++- src/ontology/subsets/ro-mereotopology.obo | 25 ++- src/ontology/subsets/ro-mereotopology.owl | 35 ++- src/ontology/subsets/ro-sequence.obo | 25 ++- src/ontology/subsets/ro-sequence.owl | 35 ++- src/ontology/subsets/ro-time-interval.obo | 25 ++- src/ontology/subsets/ro-time-interval.owl | 35 ++- subsets/ro-causal.obo | 25 ++- subsets/ro-causal.owl | 35 ++- subsets/ro-chado.obo | 15 +- subsets/ro-chado.obo.tmp | 15 +- subsets/ro-developmental.obo | 25 ++- subsets/ro-developmental.owl | 35 ++- subsets/ro-eco.obo | 35 ++- subsets/ro-eco.owl | 69 ++++-- subsets/ro-interaction.obo | 25 ++- subsets/ro-interaction.owl | 35 ++- subsets/ro-mereotopology.obo | 25 ++- subsets/ro-mereotopology.owl | 35 ++- subsets/ro-sequence.obo | 25 ++- subsets/ro-sequence.owl | 35 ++- subsets/ro-time-interval.obo | 25 ++- subsets/ro-time-interval.owl | 35 ++- 38 files changed, 1228 insertions(+), 380 deletions(-) diff --git a/ro-base.json b/ro-base.json index a2b7aad8..726c52e4 100644 --- a/ro-base.json +++ b/ro-base.json @@ -2670,6 +2670,7 @@ "val" : "a relation between two independent continuants, the target and the location, in which the target is entirely within the location", "xrefs" : [ ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus" @@ -4594,7 +4595,7 @@ "val" : "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.", "xrefs" : [ ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_gocam", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_go_gp2term", "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension" ], + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_gocam", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" @@ -5172,7 +5173,7 @@ "val" : "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.", "xrefs" : [ ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam", "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "Regulation precludes parthood; the regulatory process may not be within the regulated process." @@ -5291,7 +5292,7 @@ "val" : "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.", "xrefs" : [ ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", "val" : "negatively regulates (process to process)" @@ -5865,6 +5866,7 @@ "val" : "a colocalizes_with b if and only if a is transiently or peripherally associated with b[GO].", "xrefs" : [ ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://www.geneontology.org/GO.annotation.conventions.shtml#colocalizes_with" @@ -5930,6 +5932,7 @@ }, { "id" : "http://purl.obolibrary.org/obo/RO_0002326", "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "We would like to say\n\nif and only if\n exists c', p'\n c part_of c' and c' capable_of p\n and\n c capable_of p' and p' part_of p\nthen\n c contributes_to p\n\nHowever, this is not possible in OWL. We instead make this relation a sub-relation of the two chains, which gives us the inference in the one direction." @@ -7843,6 +7846,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "https://en.wikipedia.org/wiki/Parasitism#Types" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "https://en.wikipedia.org/wiki/Communal_roosting" } ] }, "type" : "PROPERTY", @@ -10213,6 +10219,16 @@ }, "type" : "PROPERTY", "lbl" : "in regulogy relationship with" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002801", + "meta" : { + "definition" : { + "val" : "Two or more individuals sharing the same roost site (cave, mine, tree or tree hollow, animal burrow, leaf tent, rock crack, space in man-made structure, etc.). Individuals that are sharing a communal roost may be said to be co-roosting. The roost may be either a day roost where the individuals rest during daytime hours, or a night roost where individuals roost to feed, groom, or rest in between flights and/or foraging bouts. Communal roosting as thus defined is an umbrella term within which different specialized types -- which are not mutually exclusive -- may be recognized based on taxonomy and the temporal and spatial relationships of the individuals that are co-roosting.", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "co-roosts with" }, { "id" : "http://purl.obolibrary.org/obo/RO_HOM0000073", "meta" : { @@ -11121,6 +11137,20 @@ }, "type" : "PROPERTY", "lbl" : "results in adhesion of" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0012008", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_gocam", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension" ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "pg" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2021-02-26T07:28:29Z" + } ] + }, + "type" : "PROPERTY", + "lbl" : "results in fusion of" }, { "id" : "http://purl.obolibrary.org/obo/RO_HOM0000037", "meta" : { @@ -13096,14 +13126,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002002", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002323" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0011013", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0011004" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002083", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002081" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0011013", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0011004" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0004007", "pred" : "subPropertyOf", @@ -13236,14 +13266,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0004047", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002418" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0004005", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0004000" }, { "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_0004005", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0004000" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002016", "pred" : "subPropertyOf", @@ -13344,6 +13374,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000034", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_HOM0000017" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0012008", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002592" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002109", "pred" : "subPropertyOf", @@ -13452,6 +13486,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0011023", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0011022" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002801", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0008506" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002332", "pred" : "subPropertyOf", @@ -13556,14 +13594,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002291", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002206" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002225", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002202" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002223", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002222" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002225", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002202" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002492", "pred" : "subPropertyOf", @@ -13664,14 +13702,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0012006", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0012004" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000022", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_HOM0000011" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002230", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/BFO_0000051" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000022", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_HOM0000011" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002590", "pred" : "subPropertyOf", @@ -13708,14 +13746,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002339", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002344" - }, { - "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_0002012", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002418" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002209", "pred" : "subPropertyOf", @@ -13884,14 +13922,14 @@ "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_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_HOM0000007", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_HOM0000001" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0011014", "pred" : "subPropertyOf", @@ -14184,14 +14222,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002533", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/RO_0002532" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002022", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002334" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002260", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0000087" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002022", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002334" }, { "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000012", "pred" : "subPropertyOf", @@ -14624,10 +14662,6 @@ "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000062", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_HOM0000007" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002085", - "pred" : "inverseOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002092" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002084", "pred" : "inverseOf", @@ -14636,6 +14670,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002087", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002090" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002085", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002092" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0011004", "pred" : "subPropertyOf", @@ -14656,26 +14694,26 @@ "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_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_0002458", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002438" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002233", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0000057" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002006", - "pred" : "inverseOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002130" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0001020", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0001022" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002006", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002130" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002622", "pred" : "inverseOf", @@ -14704,14 +14742,14 @@ "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", @@ -14752,14 +14790,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002216", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002328" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002024", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002022" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002622", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002618" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002024", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002022" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002387", "pred" : "subPropertyOf", @@ -14820,14 +14858,14 @@ "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_0008501", - "pred" : "inverseOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0008502" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0000080", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0000086" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0008501", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0008502" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0012001", "pred" : "subPropertyOf", @@ -14876,14 +14914,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002203", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002286" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0004034", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002263" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002588", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002297" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0004034", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002263" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002219", "pred" : "inverseOf", @@ -15100,14 +15138,14 @@ "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_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_0002090", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000063" }, { "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000045", "pred" : "subPropertyOf", @@ -15308,14 +15346,14 @@ "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_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_0003305", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0003304" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002551", "pred" : "inverseOf", @@ -15424,14 +15462,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0013003", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0013001" - }, { - "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/RO_0002026", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002323" }, { "sub" : "http://purl.obolibrary.org/obo/BFO_0000050", "pred" : "inverseOf", @@ -15468,14 +15506,14 @@ "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", - "obj" : "http://purl.obolibrary.org/obo/RO_0004010" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002256", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002258" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0004015", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0004010" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002254", "pred" : "inverseOf", @@ -15496,14 +15534,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002237", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002444" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002014", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002013" }, { "sub" : "http://purl.obolibrary.org/obo/BFO_0000063", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002222" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002014", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002013" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002377", "pred" : "subPropertyOf", @@ -15784,10 +15822,6 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002462", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002461" - }, { - "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", @@ -15796,6 +15830,10 @@ "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_0002331", "pred" : "subPropertyOf", @@ -16054,7 +16092,7 @@ "pred" : "http://xmlns.com/foaf/0.1/homepage", "val" : " https://github.com/oborel/obo-relations/" } ], - "version" : "http://purl.obolibrary.org/obo/ro/releases/2020-12-18/ro-base.owl" + "version" : "http://purl.obolibrary.org/obo/ro/releases/2021-03-08/ro-base.owl" }, "equivalentNodesSets" : [ ], "logicalDefinitionAxioms" : [ ], @@ -16144,33 +16182,33 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/BFO_0000050", "allValuesFromEdges" : [ { - "sub" : "http://purl.obolibrary.org/obo/BFO_0000031", + "sub" : "http://purl.obolibrary.org/obo/BFO_0000004", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000031" + "obj" : "http://purl.obolibrary.org/obo/BFO_0000004" }, { - "sub" : "http://purl.obolibrary.org/obo/BFO_0000017", + "sub" : "http://purl.obolibrary.org/obo/BFO_0000019", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000017" + "obj" : "http://purl.obolibrary.org/obo/BFO_0000019" }, { - "sub" : "http://purl.obolibrary.org/obo/BFO_0000002", + "sub" : "http://purl.obolibrary.org/obo/BFO_0000031", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000002" + "obj" : "http://purl.obolibrary.org/obo/BFO_0000031" }, { "sub" : "http://purl.obolibrary.org/obo/BFO_0000020", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/BFO_0000020" }, { - "sub" : "http://purl.obolibrary.org/obo/BFO_0000019", + "sub" : "http://purl.obolibrary.org/obo/BFO_0000002", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000019" + "obj" : "http://purl.obolibrary.org/obo/BFO_0000002" }, { - "sub" : "http://purl.obolibrary.org/obo/BFO_0000003", + "sub" : "http://purl.obolibrary.org/obo/BFO_0000017", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000003" + "obj" : "http://purl.obolibrary.org/obo/BFO_0000017" }, { - "sub" : "http://purl.obolibrary.org/obo/BFO_0000004", + "sub" : "http://purl.obolibrary.org/obo/BFO_0000003", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000004" + "obj" : "http://purl.obolibrary.org/obo/BFO_0000003" } ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002202", @@ -16639,13 +16677,13 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002214", "allValuesFromEdges" : [ { - "sub" : "http://purl.obolibrary.org/obo/BFO_0000002", - "pred" : "http://purl.obolibrary.org/obo/RO_0002214", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000002" - }, { "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", @@ -16884,9 +16922,6 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002131", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/BFO_0000051", "http://purl.obolibrary.org/obo/RO_0002131" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002340", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002340", "http://purl.obolibrary.org/obo/BFO_0000051" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002131", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002131", "http://purl.obolibrary.org/obo/BFO_0000050" ] @@ -16989,9 +17024,6 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002496", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002496", "http://purl.obolibrary.org/obo/BFO_0000050" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002345", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002345", "http://purl.obolibrary.org/obo/BFO_0000051" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002428", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002331", "http://purl.obolibrary.org/obo/RO_0002211" ] @@ -17022,9 +17054,6 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002554", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002445", "http://purl.obolibrary.org/obo/RO_0002445" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002313", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002313", "http://purl.obolibrary.org/obo/BFO_0000051" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002492", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002593", "http://purl.obolibrary.org/obo/BFO_0000050" ] diff --git a/ro-base.obo b/ro-base.obo index 238d42cd..c659552d 100644 --- a/ro-base.obo +++ b/ro-base.obo @@ -1,5 +1,5 @@ format-version: 1.2 -data-version: ro/releases/2020-12-18/ro-base.owl +data-version: ro/releases/2021-03-08/ro-base.owl subsetdef: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension "" subsetdef: http://purl.obolibrary.org/obo/valid_for_go_gp2term "" subsetdef: http://purl.obolibrary.org/obo/valid_for_go_ontology "" @@ -625,6 +625,7 @@ is_a: RO:0003302 ! causes or contributes to condition 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" [] +subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term property_value: http://purl.org/dc/elements/1.1/source http://www.obofoundry.org/ro/#OBO_REL:located_in xsd:string property_value: IAO:0000111 "located in" xsd:string property_value: IAO:0000112 "my brain is located in my head" xsd:string @@ -1626,7 +1627,6 @@ 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." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension -subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: IAO:0000114 IAO:0000125 @@ -1653,7 +1653,6 @@ 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." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension -subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -1670,7 +1669,6 @@ 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." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension -subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -2271,7 +2269,6 @@ 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 -transitive_over: BFO:0000051 ! has part [Typedef] id: RO:0002314 @@ -2331,6 +2328,7 @@ property_value: IAO:0000232 "Do not use this relation directly. It is ended as a id: RO:0002325 name: colocalizes with def: "a colocalizes_with b if and only if a is transiently or peripherally associated with b[GO]." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term property_value: http://purl.org/dc/terms/creator "Gene Ontology Consortium" xsd:string property_value: IAO:0000112 "Clp1p relocalizes from the nucleolus to the spindle and site of cell division; i.e. it is associated transiently with the spindle pole body and the contractile ring (evidence from GFP fusion). Clp1p colocalizes_with spindle pole body (GO:0005816) and contractile ring (GO:0005826)" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -2343,6 +2341,7 @@ is_a: RO:0002323 ! mereotopologically related to [Typedef] id: RO:0002326 name: contributes to +subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term property_value: IAO:0000112 "ATP citrate lyase (ACL) in Arabidopsis: it is a heterooctamer, composed of two types of subunits, ACLA and ACLB in a A(4)B(4) stoichiometry. Neither of the subunits expressed alone give ACL activity, but co-expression results in ACL activity. Both subunits contribute_to the ATP citrate lyase activity." xsd:string property_value: IAO:0000112 "eIF2: has three subunits (alpha, beta, gamma); one binds GTP; one binds RNA; the whole complex binds the ribosome (all three subunits are required for ribosome binding). So one subunit is annotated to GTP binding and one to RNA binding without qualifiers, and all three stand in the contributes_to relationship to \"ribosome binding\". And all three are part_of an eIF2 complex" xsd:string property_value: IAO:0000112 "Subunits of nuclear RNA polymerases: none of the individual subunits have RNA polymerase activity, yet all of these subunits contribute_to DNA-dependent RNA polymerase activity." xsd:string @@ -2496,7 +2495,6 @@ def: "Holds between p and c when p is a transportation or localization process a subset: http://purl.obolibrary.org/obo/valid_for_go_ontology property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: RO:0002020 ! transports -transitive_over: BFO:0000051 ! has part [Typedef] id: RO:0002341 @@ -2536,7 +2534,6 @@ def: "Holds between p and c when p is a transportation or localization process a subset: http://purl.obolibrary.org/obo/valid_for_go_ontology property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: RO:0002020 ! transports -transitive_over: BFO:0000051 ! has part [Typedef] id: RO:0002348 @@ -4564,6 +4561,7 @@ is_a: RO:0002635 ! has endoparasite id: RO:0002640 name: intracellular endoparasite of def: "A sub-relation of endoparasite-of in which the parasite inhabits host cells." [] +property_value: IAO:0000119 Communal:roosting property_value: IAO:0000119 "Types" is_a: RO:0002634 ! endoparasite of inverse_of: RO:0002641 ! has intracellular endoparasite @@ -4575,6 +4573,13 @@ def: "inverse of intracellular endoparasite of" [] subset: RO:0002259 is_a: RO:0002635 ! has endoparasite +[Typedef] +id: RO:0002801 +name: co-roosts with +def: "Two or more individuals sharing the same roost site (cave, mine, tree or tree hollow, animal burrow, leaf tent, rock crack, space in man-made structure, etc.). Individuals that are sharing a communal roost may be said to be co-roosting. The roost may be either a day roost where the individuals rest during daytime hours, or a night roost where individuals roost to feed, groom, or rest in between flights and/or foraging bouts. Communal roosting as thus defined is an umbrella term within which different specialized types -- which are not mutually exclusive -- may be recognized based on taxonomy and the temporal and spatial relationships of the individuals that are co-roosting." [] +is_symmetric: true +is_a: RO:0008506 ! ecologically co-occurs with + [Typedef] id: RO:0003000 name: produces @@ -5408,6 +5413,16 @@ is_a: RO:0040036 ! has anatomical participant created_by: pg creation_date: 2020-08-27T08:13:59Z +[Typedef] +id: RO:0012008 +name: results in fusion of +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam +is_a: RO:0002592 ! results in organization of +created_by: pg +creation_date: 2021-02-26T07:28:29Z + [Typedef] id: RO:0013001 name: has synaptic IO in diff --git a/ro-base.owl b/ro-base.owl index f03a12e2..9e7693ac 100644 --- a/ro-base.owl +++ b/ro-base.owl @@ -17,7 +17,7 @@ xmlns:subsets="http://purl.obolibrary.org/obo/ro/subsets#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - + The OBO Relations Ontology (RO) is a collection of OWL relations (ObjectProperties) intended for use across a wide variety of biological ontologies. OBO Relations Ontology @@ -1642,6 +1642,7 @@ range: spatial region or site (immaterial continuant) located_in http://www.obofoundry.org/ro/#OBO_REL:located_in + located in @@ -3406,7 +3407,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.regulates (processual) false - regulates @@ -3430,7 +3430,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.negatively regulates (process to process) - negatively regulates @@ -3459,7 +3458,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.positively regulates (process to process) - positively regulates @@ -4451,10 +4449,6 @@ 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 @@ -4590,6 +4584,7 @@ where http://www.geneontology.org/GO.annotation.conventions.shtml#colocalizes_with In the context of the Gene Ontology, colocalizes_with may be used for annotating to cellular component terms[GO] Gene Ontology Consortium + colocalizes with @@ -4617,6 +4612,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati Chris Mungall http://www.geneontology.org/GO.annotation.conventions.shtml#contributes_to In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology. + contributes to @@ -4844,10 +4840,6 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - - - - 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. Chris Mungall @@ -4907,10 +4899,6 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - - - - 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 end location of c is part of the region that surrounds s. Chris Mungall @@ -8165,6 +8153,7 @@ the a supports either the existence of b, or the truth value of b. A sub-relation of endoparasite-of in which the parasite inhabits host cells. + intracellular endoparasite of @@ -8182,6 +8171,17 @@ the a supports either the existence of b, or the truth value of b. + + + + + Two or more individuals sharing the same roost site (cave, mine, tree or tree hollow, animal burrow, leaf tent, rock crack, space in man-made structure, etc.). Individuals that are sharing a communal roost may be said to be co-roosting. The roost may be either a day roost where the individuals rest during daytime hours, or a night roost where individuals roost to feed, groom, or rest in between flights and/or foraging bouts. Communal roosting as thus defined is an umbrella term within which different specialized types -- which are not mutually exclusive -- may be recognized based on taxonomy and the temporal and spatial relationships of the individuals that are co-roosting. + co-roosts with + + + + @@ -9507,6 +9507,20 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + pg + 2021-02-26T07:28:29Z + + + + results in fusion of + + + + diff --git a/ro.json b/ro.json index e8683fa6..77aa2e39 100644 --- a/ro.json +++ b/ro.json @@ -2487,7 +2487,7 @@ "val" : "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.", "xrefs" : [ ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_gocam", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_go_gp2term", "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension" ], + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_gocam", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" @@ -2788,7 +2788,7 @@ "val" : "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.", "xrefs" : [ ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam", "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "Regulation precludes parthood; the regulatory process may not be within the regulated process." @@ -2884,7 +2884,7 @@ "val" : "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.", "xrefs" : [ ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", "val" : "negatively regulates (process to process)" @@ -4176,6 +4176,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "https://en.wikipedia.org/wiki/Parasitism#Types" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "https://en.wikipedia.org/wiki/Communal_roosting" } ] }, "type" : "PROPERTY", @@ -6576,6 +6579,20 @@ }, "type" : "PROPERTY", "lbl" : "results in adhesion of" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0012008", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_gocam", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension" ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "pg" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2021-02-26T07:28:29Z" + } ] + }, + "type" : "PROPERTY", + "lbl" : "results in fusion of" }, { "id" : "http://purl.obolibrary.org/obo/RO_HOM0000037", "meta" : { @@ -9034,6 +9051,7 @@ "val" : "a relation between two independent continuants, the target and the location, in which the target is entirely within the location", "xrefs" : [ ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus" @@ -10696,6 +10714,7 @@ "val" : "a colocalizes_with b if and only if a is transiently or peripherally associated with b[GO].", "xrefs" : [ ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://www.geneontology.org/GO.annotation.conventions.shtml#colocalizes_with" @@ -10718,6 +10737,7 @@ }, { "id" : "http://purl.obolibrary.org/obo/RO_0002326", "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "We would like to say\n\nif and only if\n exists c', p'\n c part_of c' and c' capable_of p\n and\n c capable_of p' and p' part_of p\nthen\n c contributes_to p\n\nHowever, this is not possible in OWL. We instead make this relation a sub-relation of the two chains, which gives us the inference in the one direction." @@ -12625,6 +12645,16 @@ }, "type" : "PROPERTY", "lbl" : "decreases by repression quantity of" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002801", + "meta" : { + "definition" : { + "val" : "Two or more individuals sharing the same roost site (cave, mine, tree or tree hollow, animal burrow, leaf tent, rock crack, space in man-made structure, etc.). Individuals that are sharing a communal roost may be said to be co-roosting. The roost may be either a day roost where the individuals rest during daytime hours, or a night roost where individuals roost to feed, groom, or rest in between flights and/or foraging bouts. Communal roosting as thus defined is an umbrella term within which different specialized types -- which are not mutually exclusive -- may be recognized based on taxonomy and the temporal and spatial relationships of the individuals that are co-roosting.", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "co-roosts with" }, { "id" : "http://purl.obolibrary.org/obo/RO_0011010", "meta" : { @@ -13781,14 +13811,14 @@ "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_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_0002521", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002514" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002571", "pred" : "subPropertyOf", @@ -13817,6 +13847,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0004047", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002418" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0004005", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0004000" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002016", "pred" : "subPropertyOf", @@ -13825,10 +13859,6 @@ "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_0004005", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0004000" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0010001", "pred" : "inverseOf", @@ -13929,6 +13959,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000034", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_HOM0000017" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0012008", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002592" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002109", "pred" : "subPropertyOf", @@ -14057,6 +14091,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0011023", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0011022" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002801", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0008506" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002332", "pred" : "subPropertyOf", @@ -14297,14 +14335,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0012006", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0012004" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000022", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_HOM0000011" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002230", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/BFO_0000051" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000022", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_HOM0000011" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002590", "pred" : "subPropertyOf", @@ -14485,14 +14523,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002509", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002131" - }, { - "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/GO_0030425", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GO_0043005" + }, { + "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", @@ -14713,14 +14751,14 @@ "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", @@ -14877,14 +14915,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002533", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/RO_0002532" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002022", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002334" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002260", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0000087" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002022", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002334" }, { "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000012", "pred" : "subPropertyOf", @@ -15322,17 +15360,17 @@ "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002091" }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0004012", + "sub" : "http://purl.obolibrary.org/obo/RO_0004024", "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0004010" + "obj" : "http://purl.obolibrary.org/obo/RO_0004023" }, { "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", + "sub" : "http://purl.obolibrary.org/obo/RO_0004012", "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0004023" + "obj" : "http://purl.obolibrary.org/obo/RO_0004010" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002525", "pred" : "subPropertyOf", @@ -15369,14 +15407,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002085", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002092" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002087", - "pred" : "inverseOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002090" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002084", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002093" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002087", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002090" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0011004", "pred" : "subPropertyOf", @@ -15397,14 +15435,14 @@ "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", @@ -15445,14 +15483,14 @@ "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_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_0002495", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002494" }, { "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000044", "pred" : "subPropertyOf", @@ -15493,14 +15531,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002216", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002328" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002622", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002618" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002024", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002022" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002622", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002618" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002387", "pred" : "subPropertyOf", @@ -15569,14 +15607,14 @@ "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", - "obj" : "http://purl.obolibrary.org/obo/RO_0000086" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0008501", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0008502" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0000080", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0000086" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0012001", "pred" : "subPropertyOf", @@ -15801,14 +15839,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002444", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002454" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002461", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0000056" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002246", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002206" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002461", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0000056" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002232", "pred" : "subPropertyOf", @@ -16133,14 +16171,14 @@ "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", @@ -16641,14 +16679,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002641", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002635" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002091", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002222" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002326", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002329" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002091", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002222" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002512", "pred" : "inverseOf", @@ -16825,14 +16863,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002229", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002222" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0013002", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002110" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002020", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002313" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0013002", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002110" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002086", "pred" : "subPropertyOf", @@ -16909,7 +16947,7 @@ "pred" : "http://xmlns.com/foaf/0.1/homepage", "val" : " https://github.com/oborel/obo-relations/" } ], - "version" : "http://purl.obolibrary.org/obo/ro/releases/2020-12-18/ro.owl" + "version" : "http://purl.obolibrary.org/obo/ro/releases/2021-03-08/ro.owl" }, "equivalentNodesSets" : [ ], "logicalDefinitionAxioms" : [ ], @@ -16995,13 +17033,13 @@ }, { "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_0002449", @@ -17010,18 +17048,6 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/BFO_0000050", "allValuesFromEdges" : [ { - "sub" : "http://purl.obolibrary.org/obo/BFO_0000003", - "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000003" - }, { - "sub" : "http://purl.obolibrary.org/obo/BFO_0000017", - "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000017" - }, { - "sub" : "http://purl.obolibrary.org/obo/BFO_0000004", - "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000004" - }, { "sub" : "http://purl.obolibrary.org/obo/BFO_0000020", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/BFO_0000020" @@ -17033,6 +17059,18 @@ "sub" : "http://purl.obolibrary.org/obo/BFO_0000031", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/BFO_0000031" + }, { + "sub" : "http://purl.obolibrary.org/obo/BFO_0000004", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000004" + }, { + "sub" : "http://purl.obolibrary.org/obo/BFO_0000017", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000017" + }, { + "sub" : "http://purl.obolibrary.org/obo/BFO_0000003", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000003" }, { "sub" : "http://purl.obolibrary.org/obo/BFO_0000002", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -17169,13 +17207,13 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_HOM0000000", "allValuesFromEdges" : [ { - "sub" : "http://purl.obolibrary.org/obo/BFO_0000002", - "pred" : "http://purl.obolibrary.org/obo/RO_HOM0000000", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000002" - }, { "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", @@ -17750,9 +17788,6 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002131", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/BFO_0000051", "http://purl.obolibrary.org/obo/RO_0002131" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002340", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002340", "http://purl.obolibrary.org/obo/BFO_0000051" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002131", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002131", "http://purl.obolibrary.org/obo/BFO_0000050" ] @@ -17855,9 +17890,6 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002496", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002496", "http://purl.obolibrary.org/obo/BFO_0000050" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002345", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002345", "http://purl.obolibrary.org/obo/BFO_0000051" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002428", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002331", "http://purl.obolibrary.org/obo/RO_0002211" ] @@ -17888,9 +17920,6 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002554", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002445", "http://purl.obolibrary.org/obo/RO_0002445" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002313", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002313", "http://purl.obolibrary.org/obo/BFO_0000051" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002492", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002593", "http://purl.obolibrary.org/obo/BFO_0000050" ] diff --git a/ro.obo b/ro.obo index 158ec6b9..11815cfa 100644 --- a/ro.obo +++ b/ro.obo @@ -1,5 +1,5 @@ format-version: 1.2 -data-version: releases/2020-12-18 +data-version: releases/2021-03-08 subsetdef: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension "" subsetdef: http://purl.obolibrary.org/obo/valid_for_go_gp2term "" subsetdef: http://purl.obolibrary.org/obo/valid_for_go_ontology "" @@ -942,6 +942,7 @@ is_a: RO:0003302 ! causes or contributes to condition 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" [] +subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term property_value: http://purl.org/dc/elements/1.1/source http://www.obofoundry.org/ro/#OBO_REL:located_in xsd:string property_value: IAO:0000111 "located in" xsd:string property_value: IAO:0000112 "my brain is located in my head" xsd:string @@ -1943,7 +1944,6 @@ 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." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension -subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: IAO:0000114 IAO:0000125 @@ -1970,7 +1970,6 @@ 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." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension -subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -1987,7 +1986,6 @@ 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." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension -subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -2588,7 +2586,6 @@ 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 -transitive_over: BFO:0000051 ! has part [Typedef] id: RO:0002314 @@ -2648,6 +2645,7 @@ property_value: IAO:0000232 "Do not use this relation directly. It is ended as a id: RO:0002325 name: colocalizes with def: "a colocalizes_with b if and only if a is transiently or peripherally associated with b[GO]." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term property_value: http://purl.org/dc/terms/creator "Gene Ontology Consortium" xsd:string property_value: IAO:0000112 "Clp1p relocalizes from the nucleolus to the spindle and site of cell division; i.e. it is associated transiently with the spindle pole body and the contractile ring (evidence from GFP fusion). Clp1p colocalizes_with spindle pole body (GO:0005816) and contractile ring (GO:0005826)" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -2660,6 +2658,7 @@ is_a: RO:0002323 ! mereotopologically related to [Typedef] id: RO:0002326 name: contributes to +subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term property_value: IAO:0000112 "ATP citrate lyase (ACL) in Arabidopsis: it is a heterooctamer, composed of two types of subunits, ACLA and ACLB in a A(4)B(4) stoichiometry. Neither of the subunits expressed alone give ACL activity, but co-expression results in ACL activity. Both subunits contribute_to the ATP citrate lyase activity." xsd:string property_value: IAO:0000112 "eIF2: has three subunits (alpha, beta, gamma); one binds GTP; one binds RNA; the whole complex binds the ribosome (all three subunits are required for ribosome binding). So one subunit is annotated to GTP binding and one to RNA binding without qualifiers, and all three stand in the contributes_to relationship to \"ribosome binding\". And all three are part_of an eIF2 complex" xsd:string property_value: IAO:0000112 "Subunits of nuclear RNA polymerases: none of the individual subunits have RNA polymerase activity, yet all of these subunits contribute_to DNA-dependent RNA polymerase activity." xsd:string @@ -2813,7 +2812,6 @@ def: "Holds between p and c when p is a transportation or localization process a subset: http://purl.obolibrary.org/obo/valid_for_go_ontology property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: RO:0002020 ! transports -transitive_over: BFO:0000051 ! has part [Typedef] id: RO:0002341 @@ -2853,7 +2851,6 @@ def: "Holds between p and c when p is a transportation or localization process a subset: http://purl.obolibrary.org/obo/valid_for_go_ontology property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: RO:0002020 ! transports -transitive_over: BFO:0000051 ! has part [Typedef] id: RO:0002348 @@ -4881,6 +4878,7 @@ is_a: RO:0002635 ! has endoparasite id: RO:0002640 name: intracellular endoparasite of def: "A sub-relation of endoparasite-of in which the parasite inhabits host cells." [] +property_value: IAO:0000119 Communal:roosting property_value: IAO:0000119 "Types" is_a: RO:0002634 ! endoparasite of inverse_of: RO:0002641 ! has intracellular endoparasite @@ -4892,6 +4890,13 @@ def: "inverse of intracellular endoparasite of" [] subset: RO:0002259 is_a: RO:0002635 ! has endoparasite +[Typedef] +id: RO:0002801 +name: co-roosts with +def: "Two or more individuals sharing the same roost site (cave, mine, tree or tree hollow, animal burrow, leaf tent, rock crack, space in man-made structure, etc.). Individuals that are sharing a communal roost may be said to be co-roosting. The roost may be either a day roost where the individuals rest during daytime hours, or a night roost where individuals roost to feed, groom, or rest in between flights and/or foraging bouts. Communal roosting as thus defined is an umbrella term within which different specialized types -- which are not mutually exclusive -- may be recognized based on taxonomy and the temporal and spatial relationships of the individuals that are co-roosting." [] +is_symmetric: true +is_a: RO:0008506 ! ecologically co-occurs with + [Typedef] id: RO:0003000 name: produces @@ -5725,6 +5730,16 @@ is_a: RO:0040036 ! has anatomical participant created_by: pg creation_date: 2020-08-27T08:13:59Z +[Typedef] +id: RO:0012008 +name: results in fusion of +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam +is_a: RO:0002592 ! results in organization of +created_by: pg +creation_date: 2021-02-26T07:28:29Z + [Typedef] id: RO:0013001 name: has synaptic IO in diff --git a/ro.owl b/ro.owl index 2a91d4af..89f90cb0 100644 --- a/ro.owl +++ b/ro.owl @@ -17,7 +17,7 @@ xmlns:subsets="http://purl.obolibrary.org/obo/ro/subsets#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - + @@ -1076,6 +1076,7 @@ range: spatial region or site (immaterial continuant) + @@ -2686,7 +2687,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.regulates (processual) false - regulates @@ -2710,7 +2710,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.negatively regulates (process to process) - negatively regulates @@ -2739,7 +2738,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.positively regulates (process to process) - positively regulates @@ -3689,10 +3687,6 @@ 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 @@ -3828,6 +3822,7 @@ where http://www.geneontology.org/GO.annotation.conventions.shtml#colocalizes_with In the context of the Gene Ontology, colocalizes_with may be used for annotating to cellular component terms[GO] Gene Ontology Consortium + colocalizes with @@ -3855,6 +3850,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati Chris Mungall http://www.geneontology.org/GO.annotation.conventions.shtml#contributes_to In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology. + contributes to @@ -4082,10 +4078,6 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - - - - 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. Chris Mungall @@ -4145,10 +4137,6 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - - - - 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 end location of c is part of the region that surrounds s. Chris Mungall @@ -7374,6 +7362,7 @@ the a supports either the existence of b, or the truth value of b. A sub-relation of endoparasite-of in which the parasite inhabits host cells. + intracellular endoparasite of @@ -7391,6 +7380,17 @@ the a supports either the existence of b, or the truth value of b. + + + + + Two or more individuals sharing the same roost site (cave, mine, tree or tree hollow, animal burrow, leaf tent, rock crack, space in man-made structure, etc.). Individuals that are sharing a communal roost may be said to be co-roosting. The roost may be either a day roost where the individuals rest during daytime hours, or a night roost where individuals roost to feed, groom, or rest in between flights and/or foraging bouts. Communal roosting as thus defined is an umbrella term within which different specialized types -- which are not mutually exclusive -- may be recognized based on taxonomy and the temporal and spatial relationships of the individuals that are co-roosting. + co-roosts with + + + + @@ -8716,6 +8716,20 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + pg + 2021-02-26T07:28:29Z + + + + results in fusion of + + + + diff --git a/src/ontology/subsets/ro-causal.obo b/src/ontology/subsets/ro-causal.obo index 7b4ce749..9e36489f 100644 --- a/src/ontology/subsets/ro-causal.obo +++ b/src/ontology/subsets/ro-causal.obo @@ -560,6 +560,14 @@ xref: RO:0002478 property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: child_nucleus_of ! child nucleus of +[Typedef] +id: co-roosts_with +name: co-roosts with +def: "Two or more individuals sharing the same roost site (cave, mine, tree or tree hollow, animal burrow, leaf tent, rock crack, space in man-made structure, etc.). Individuals that are sharing a communal roost may be said to be co-roosting. The roost may be either a day roost where the individuals rest during daytime hours, or a night roost where individuals roost to feed, groom, or rest in between flights and/or foraging bouts. Communal roosting as thus defined is an umbrella term within which different specialized types -- which are not mutually exclusive -- may be recognized based on taxonomy and the temporal and spatial relationships of the individuals that are co-roosting." [] +xref: RO:0002801 +is_symmetric: true +is_a: ecologically_co-occurs_with ! ecologically co-occurs with + [Typedef] id: coincident_with name: coincident with @@ -575,6 +583,7 @@ is_a: mereotopologically_related_to ! mereotopologically related to id: colocalizes_with name: colocalizes with def: "a colocalizes_with b if and only if a is transiently or peripherally associated with b[GO]." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term xref: RO:0002325 property_value: http://purl.org/dc/terms/creator "Gene Ontology Consortium" xsd:string property_value: IAO:0000112 "Clp1p relocalizes from the nucleolus to the spindle and site of cell division; i.e. it is associated transiently with the spindle pole body and the contractile ring (evidence from GFP fusion). Clp1p colocalizes_with spindle pole body (GO:0005816) and contractile ring (GO:0005826)" xsd:string @@ -709,6 +718,7 @@ is_a: mereotopologically_related_to ! mereotopologically related to [Typedef] id: contributes_to name: contributes to +subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term xref: RO:0002326 property_value: IAO:0000112 "ATP citrate lyase (ACL) in Arabidopsis: it is a heterooctamer, composed of two types of subunits, ACLA and ACLB in a A(4)B(4) stoichiometry. Neither of the subunits expressed alone give ACL activity, but co-expression results in ACL activity. Both subunits contribute_to the ATP citrate lyase activity." xsd:string property_value: IAO:0000112 "eIF2: has three subunits (alpha, beta, gamma); one binds GTP; one binds RNA; the whole complex binds the ribosome (all three subunits are required for ribosome binding). So one subunit is annotated to GTP binding and one to RNA binding without qualifiers, and all three stand in the contributes_to relationship to \"ribosome binding\". And all three are part_of an eIF2 complex" xsd:string @@ -2685,6 +2695,7 @@ id: intracellular_endoparasite_of name: intracellular endoparasite of def: "A sub-relation of endoparasite-of in which the parasite inhabits host cells." [] xref: RO:0002640 +property_value: IAO:0000119 Communal:roosting property_value: IAO:0000119 "Types" is_a: endoparasite_of ! endoparasite of inverse_of: has_intracellular_endoparasite ! has intracellular endoparasite @@ -3167,7 +3178,6 @@ id: negatively_regulates 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." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension -subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002212 @@ -3427,7 +3437,6 @@ id: positively_regulates 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." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension -subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002213 @@ -3604,7 +3613,6 @@ id: regulates 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." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension -subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002211 @@ -3876,6 +3884,17 @@ is_a: has_output ! has output is_a: results_in_developmental_progression_of ! results in developmental progression of inverse_of: formed_as_result_of ! formed as result of +[Typedef] +id: results_in_fusion_of +name: results in fusion of +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam +xref: RO:0012008 +is_a: results_in_organization_of ! results in organization of +created_by: pg +creation_date: 2021-02-26T07:28:29Z + [Typedef] id: results_in_growth_of name: results in growth of diff --git a/src/ontology/subsets/ro-causal.owl b/src/ontology/subsets/ro-causal.owl index ecd37cb3..c957249e 100644 --- a/src/ontology/subsets/ro-causal.owl +++ b/src/ontology/subsets/ro-causal.owl @@ -1685,7 +1685,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.false RO:0002211 - regulates @@ -1707,7 +1706,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. RO:0002212 - negatively_regulates @@ -1730,7 +1728,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. RO:0002213 - positively_regulates @@ -2686,6 +2683,7 @@ where In the context of the Gene Ontology, colocalizes_with may be used for annotating to cellular component terms[GO] Gene Ontology Consortium RO:0002325 + colocalizes_with colocalizes with @@ -2715,6 +2713,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati http://www.geneontology.org/GO.annotation.conventions.shtml#contributes_to In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology. RO:0002326 + contributes_to contributes to @@ -5711,6 +5710,7 @@ For example, A and B may be gene products and binding of B by A positively regul A sub-relation of endoparasite-of in which the parasite inhabits host cells. + RO:0002640 intracellular_endoparasite_of @@ -5732,6 +5732,19 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + Two or more individuals sharing the same roost site (cave, mine, tree or tree hollow, animal burrow, leaf tent, rock crack, space in man-made structure, etc.). Individuals that are sharing a communal roost may be said to be co-roosting. The roost may be either a day roost where the individuals rest during daytime hours, or a night roost where individuals roost to feed, groom, or rest in between flights and/or foraging bouts. Communal roosting as thus defined is an umbrella term within which different specialized types -- which are not mutually exclusive -- may be recognized based on taxonomy and the temporal and spatial relationships of the individuals that are co-roosting. + RO:0002801 + co-roosts_with + co-roosts with + + + + @@ -7003,6 +7016,22 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + pg + 2021-02-26T07:28:29Z + RO:0012008 + + + + results_in_fusion_of + results in fusion of + + + + diff --git a/src/ontology/subsets/ro-chado.obo b/src/ontology/subsets/ro-chado.obo index 6bb25af8..84143aba 100644 --- a/src/ontology/subsets/ro-chado.obo +++ b/src/ontology/subsets/ro-chado.obo @@ -1253,7 +1253,6 @@ 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:0002337 ! related via localization to is_a: RO:0040036 ! has anatomical participant -transitive_over: BFO:0000051 ! has part [Typedef] id: RO:0002314 @@ -1390,7 +1389,6 @@ 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 @@ -1421,7 +1419,6 @@ id: RO:0002345 name: exports 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 end 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:0002348 @@ -2803,6 +2800,13 @@ name: has_intracellular_endoparasite def: "inverse of intracellular endoparasite of" [] is_a: RO:0002635 ! has endoparasite +[Typedef] +id: RO:0002801 +name: co-roosts_with +def: "Two or more individuals sharing the same roost site (cave, mine, tree or tree hollow, animal burrow, leaf tent, rock crack, space in man-made structure, etc.). Individuals that are sharing a communal roost may be said to be co-roosting. The roost may be either a day roost where the individuals rest during daytime hours, or a night roost where individuals roost to feed, groom, or rest in between flights and/or foraging bouts. Communal roosting as thus defined is an umbrella term within which different specialized types -- which are not mutually exclusive -- may be recognized based on taxonomy and the temporal and spatial relationships of the individuals that are co-roosting." [] +is_symmetric: true +is_a: RO:0008506 ! ecologically co-occurs with + [Typedef] id: RO:0003000 name: produces @@ -3365,6 +3369,11 @@ name: results_in_adhesion_of def: "The relationship that links anatomical entities with a process that results in the adhesion of two or more entities via the non-covalent interaction of molecules expressed in, located in, and/or adjacent to, those entities." [] is_a: RO:0040036 ! has anatomical participant +[Typedef] +id: RO:0012008 +name: results_in_fusion_of +is_a: RO:0002592 ! results in organization of + [Typedef] id: RO:0013001 name: has_synaptic_IO_in diff --git a/src/ontology/subsets/ro-chado.obo.tmp b/src/ontology/subsets/ro-chado.obo.tmp index d9623875..b94534b9 100644 --- a/src/ontology/subsets/ro-chado.obo.tmp +++ b/src/ontology/subsets/ro-chado.obo.tmp @@ -1253,7 +1253,6 @@ 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:0002337 ! related via localization to is_a: RO:0040036 ! has anatomical participant -transitive_over: BFO:0000051 ! has part [Typedef] id: RO:0002314 @@ -1390,7 +1389,6 @@ 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 @@ -1421,7 +1419,6 @@ id: RO:0002345 name: exports 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 end 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:0002348 @@ -2803,6 +2800,13 @@ name: has intracellular endoparasite def: "inverse of intracellular endoparasite of" [] is_a: RO:0002635 ! has endoparasite +[Typedef] +id: RO:0002801 +name: co-roosts with +def: "Two or more individuals sharing the same roost site (cave, mine, tree or tree hollow, animal burrow, leaf tent, rock crack, space in man-made structure, etc.). Individuals that are sharing a communal roost may be said to be co-roosting. The roost may be either a day roost where the individuals rest during daytime hours, or a night roost where individuals roost to feed, groom, or rest in between flights and/or foraging bouts. Communal roosting as thus defined is an umbrella term within which different specialized types -- which are not mutually exclusive -- may be recognized based on taxonomy and the temporal and spatial relationships of the individuals that are co-roosting." [] +is_symmetric: true +is_a: RO:0008506 ! ecologically co-occurs with + [Typedef] id: RO:0003000 name: produces @@ -3365,6 +3369,11 @@ name: results in adhesion of def: "The relationship that links anatomical entities with a process that results in the adhesion of two or more entities via the non-covalent interaction of molecules expressed in, located in, and/or adjacent to, those entities." [] is_a: RO:0040036 ! has anatomical participant +[Typedef] +id: RO:0012008 +name: results in fusion of +is_a: RO:0002592 ! results in organization of + [Typedef] id: RO:0013001 name: has synaptic IO in diff --git a/src/ontology/subsets/ro-developmental.obo b/src/ontology/subsets/ro-developmental.obo index 2ce63666..981fb37a 100644 --- a/src/ontology/subsets/ro-developmental.obo +++ b/src/ontology/subsets/ro-developmental.obo @@ -560,6 +560,14 @@ xref: RO:0002478 property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: child_nucleus_of ! child nucleus of +[Typedef] +id: co-roosts_with +name: co-roosts with +def: "Two or more individuals sharing the same roost site (cave, mine, tree or tree hollow, animal burrow, leaf tent, rock crack, space in man-made structure, etc.). Individuals that are sharing a communal roost may be said to be co-roosting. The roost may be either a day roost where the individuals rest during daytime hours, or a night roost where individuals roost to feed, groom, or rest in between flights and/or foraging bouts. Communal roosting as thus defined is an umbrella term within which different specialized types -- which are not mutually exclusive -- may be recognized based on taxonomy and the temporal and spatial relationships of the individuals that are co-roosting." [] +xref: RO:0002801 +is_symmetric: true +is_a: ecologically_co-occurs_with ! ecologically co-occurs with + [Typedef] id: coincident_with name: coincident with @@ -575,6 +583,7 @@ is_a: mereotopologically_related_to ! mereotopologically related to id: colocalizes_with name: colocalizes with def: "a colocalizes_with b if and only if a is transiently or peripherally associated with b[GO]." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term xref: RO:0002325 property_value: http://purl.org/dc/terms/creator "Gene Ontology Consortium" xsd:string property_value: IAO:0000112 "Clp1p relocalizes from the nucleolus to the spindle and site of cell division; i.e. it is associated transiently with the spindle pole body and the contractile ring (evidence from GFP fusion). Clp1p colocalizes_with spindle pole body (GO:0005816) and contractile ring (GO:0005826)" xsd:string @@ -709,6 +718,7 @@ is_a: mereotopologically_related_to ! mereotopologically related to [Typedef] id: contributes_to name: contributes to +subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term xref: RO:0002326 property_value: IAO:0000112 "ATP citrate lyase (ACL) in Arabidopsis: it is a heterooctamer, composed of two types of subunits, ACLA and ACLB in a A(4)B(4) stoichiometry. Neither of the subunits expressed alone give ACL activity, but co-expression results in ACL activity. Both subunits contribute_to the ATP citrate lyase activity." xsd:string property_value: IAO:0000112 "eIF2: has three subunits (alpha, beta, gamma); one binds GTP; one binds RNA; the whole complex binds the ribosome (all three subunits are required for ribosome binding). So one subunit is annotated to GTP binding and one to RNA binding without qualifiers, and all three stand in the contributes_to relationship to \"ribosome binding\". And all three are part_of an eIF2 complex" xsd:string @@ -2685,6 +2695,7 @@ id: intracellular_endoparasite_of name: intracellular endoparasite of def: "A sub-relation of endoparasite-of in which the parasite inhabits host cells." [] xref: RO:0002640 +property_value: IAO:0000119 Communal:roosting property_value: IAO:0000119 "Types" is_a: endoparasite_of ! endoparasite of inverse_of: has_intracellular_endoparasite ! has intracellular endoparasite @@ -3167,7 +3178,6 @@ id: negatively_regulates 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." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension -subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002212 @@ -3427,7 +3437,6 @@ id: positively_regulates 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." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension -subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002213 @@ -3604,7 +3613,6 @@ id: regulates 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." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension -subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002211 @@ -3876,6 +3884,17 @@ is_a: has_output ! has output is_a: results_in_developmental_progression_of ! results in developmental progression of inverse_of: formed_as_result_of ! formed as result of +[Typedef] +id: results_in_fusion_of +name: results in fusion of +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam +xref: RO:0012008 +is_a: results_in_organization_of ! results in organization of +created_by: pg +creation_date: 2021-02-26T07:28:29Z + [Typedef] id: results_in_growth_of name: results in growth of diff --git a/src/ontology/subsets/ro-developmental.owl b/src/ontology/subsets/ro-developmental.owl index ed3391ab..325845db 100644 --- a/src/ontology/subsets/ro-developmental.owl +++ b/src/ontology/subsets/ro-developmental.owl @@ -1685,7 +1685,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.false RO:0002211 - regulates @@ -1707,7 +1706,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. RO:0002212 - negatively_regulates @@ -1730,7 +1728,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. RO:0002213 - positively_regulates @@ -2686,6 +2683,7 @@ where In the context of the Gene Ontology, colocalizes_with may be used for annotating to cellular component terms[GO] Gene Ontology Consortium RO:0002325 + colocalizes_with colocalizes with @@ -2715,6 +2713,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati http://www.geneontology.org/GO.annotation.conventions.shtml#contributes_to In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology. RO:0002326 + contributes_to contributes to @@ -5711,6 +5710,7 @@ For example, A and B may be gene products and binding of B by A positively regul A sub-relation of endoparasite-of in which the parasite inhabits host cells. + RO:0002640 intracellular_endoparasite_of @@ -5732,6 +5732,19 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + Two or more individuals sharing the same roost site (cave, mine, tree or tree hollow, animal burrow, leaf tent, rock crack, space in man-made structure, etc.). Individuals that are sharing a communal roost may be said to be co-roosting. The roost may be either a day roost where the individuals rest during daytime hours, or a night roost where individuals roost to feed, groom, or rest in between flights and/or foraging bouts. Communal roosting as thus defined is an umbrella term within which different specialized types -- which are not mutually exclusive -- may be recognized based on taxonomy and the temporal and spatial relationships of the individuals that are co-roosting. + RO:0002801 + co-roosts_with + co-roosts with + + + + @@ -7003,6 +7016,22 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + pg + 2021-02-26T07:28:29Z + RO:0012008 + + + + results_in_fusion_of + results in fusion of + + + + diff --git a/src/ontology/subsets/ro-eco.obo b/src/ontology/subsets/ro-eco.obo index ed3d34b6..2065aac5 100644 --- a/src/ontology/subsets/ro-eco.obo +++ b/src/ontology/subsets/ro-eco.obo @@ -7,7 +7,7 @@ subsetdef: http://purl.obolibrary.org/obo/valid_for_gocam "" 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(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# Annotation Property: (is homeomorphic for)\n\nSubAnnotationPropertyOf( )\n\n\n############################\n# Object Properties\n############################\n\n# Object Property: (anabranch of)\n\nSubObjectPropertyOf( ObjectInverseOf())\n\n# Object Property: (has skeleton)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (has role in modeling)\n\nIrreflexiveObjectProperty()\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() ) )\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())))\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(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# Annotation Property: (is homeomorphic for)\n\nSubAnnotationPropertyOf( )\n\n\n############################\n# Object Properties\n############################\n\n# Object Property: (anabranch of)\n\nSubObjectPropertyOf( ObjectInverseOf())\n\n# Object Property: (has skeleton)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (has role in modeling)\n\nIrreflexiveObjectProperty()\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( 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())))\nAnnotationAssertion(rdfs:comment \"\")\n) [Typedef] id: BFO:0000050 @@ -97,6 +97,7 @@ property_value: IAO:0000116 "Containment obtains in each case between material a property_value: IAO:0000116 "Intended meaning:\ndomain: material entity\nrange: spatial region or site (immaterial continuant)\n " xsd:string property_value: IAO:0000118 "contained_in" xsd:string property_value: RO:0001900 RO:0001901 +holds_over_chain: RO:0001025 BFO:0000050 inverse_of: RO:0001019 ! contains [Typedef] @@ -134,6 +135,11 @@ 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 +subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term +transitive_over: BFO:0000050 + [Typedef] id: RO:0002001 name: aligned with @@ -959,7 +965,6 @@ 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." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension -subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: IAO:0000114 IAO:0000125 @@ -984,7 +989,6 @@ 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." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension -subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -1001,7 +1005,6 @@ 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." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension -subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -1146,6 +1149,7 @@ 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 +holds_over_chain: RO:0002207 RO:0001025 is_a: RO:0002258 ! developmentally preceded by [Typedef] @@ -1530,7 +1534,6 @@ 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 -transitive_over: BFO:0000051 [Typedef] id: RO:0002314 @@ -1588,6 +1591,7 @@ property_value: IAO:0000232 "Do not use this relation directly. It is ended as a id: RO:0002325 name: colocalizes with def: "a colocalizes_with b if and only if a is transiently or peripherally associated with b[GO]." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term property_value: http://purl.org/dc/terms/creator "Gene Ontology Consortium" xsd:string property_value: IAO:0000112 "Clp1p relocalizes from the nucleolus to the spindle and site of cell division; i.e. it is associated transiently with the spindle pole body and the contractile ring (evidence from GFP fusion). Clp1p colocalizes_with spindle pole body (GO:0005816) and contractile ring (GO:0005826)" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -1598,6 +1602,7 @@ is_a: RO:0002323 ! mereotopologically related to [Typedef] id: RO:0002326 name: contributes to +subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term property_value: IAO:0000112 "ATP citrate lyase (ACL) in Arabidopsis: it is a heterooctamer, composed of two types of subunits, ACLA and ACLB in a A(4)B(4) stoichiometry. Neither of the subunits expressed alone give ACL activity, but co-expression results in ACL activity. Both subunits contribute_to the ATP citrate lyase activity." xsd:string property_value: IAO:0000112 "eIF2: has three subunits (alpha, beta, gamma); one binds GTP; one binds RNA; the whole complex binds the ribosome (all three subunits are required for ribosome binding). So one subunit is annotated to GTP binding and one to RNA binding without qualifiers, and all three stand in the contributes_to relationship to \"ribosome binding\". And all three are part_of an eIF2 complex" xsd:string property_value: IAO:0000112 "Subunits of nuclear RNA polymerases: none of the individual subunits have RNA polymerase activity, yet all of these subunits contribute_to DNA-dependent RNA polymerase activity." xsd:string @@ -1741,7 +1746,6 @@ def: "Holds between p and c when p is a transportation or localization process a subset: http://purl.obolibrary.org/obo/valid_for_go_ontology property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: RO:0002020 ! transports -transitive_over: BFO:0000051 [Typedef] id: RO:0002341 @@ -1781,7 +1785,6 @@ def: "Holds between p and c when p is a transportation or localization process a subset: http://purl.obolibrary.org/obo/valid_for_go_ontology property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: RO:0002020 ! transports -transitive_over: BFO:0000051 [Typedef] id: RO:0002348 @@ -3725,6 +3728,7 @@ is_a: RO:0002635 ! has endoparasite id: RO:0002640 name: intracellular endoparasite of def: "A sub-relation of endoparasite-of in which the parasite inhabits host cells." [] +property_value: IAO:0000119 Communal:roosting property_value: IAO:0000119 "Types" is_a: RO:0002634 ! endoparasite of inverse_of: RO:0002641 ! has intracellular endoparasite @@ -3736,6 +3740,13 @@ def: "inverse of intracellular endoparasite of" [] subset: RO:0002259 is_a: RO:0002635 ! has endoparasite +[Typedef] +id: RO:0002801 +name: co-roosts with +def: "Two or more individuals sharing the same roost site (cave, mine, tree or tree hollow, animal burrow, leaf tent, rock crack, space in man-made structure, etc.). Individuals that are sharing a communal roost may be said to be co-roosting. The roost may be either a day roost where the individuals rest during daytime hours, or a night roost where individuals roost to feed, groom, or rest in between flights and/or foraging bouts. Communal roosting as thus defined is an umbrella term within which different specialized types -- which are not mutually exclusive -- may be recognized based on taxonomy and the temporal and spatial relationships of the individuals that are co-roosting." [] +is_symmetric: true +is_a: RO:0008506 ! ecologically co-occurs with + [Typedef] id: RO:0003000 name: produces @@ -4497,6 +4508,16 @@ is_a: RO:0040036 ! has anatomical participant created_by: pg creation_date: 2020-08-27T08:13:59Z +[Typedef] +id: RO:0012008 +name: results in fusion of +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam +is_a: RO:0002592 ! results in organization of +created_by: pg +creation_date: 2021-02-26T07:28:29Z + [Typedef] id: RO:0013001 name: has synaptic IO in diff --git a/src/ontology/subsets/ro-eco.owl b/src/ontology/subsets/ro-eco.owl index 8a74d87c..f8dbb544 100644 --- a/src/ontology/subsets/ro-eco.owl +++ b/src/ontology/subsets/ro-eco.owl @@ -1045,6 +1045,10 @@ Where we have an annotation assertion + + + + contained in Containment is location not involving parthood, and arises only where some immaterial continuant is involved. Containment obtains in each case between material and immaterial continuants, for instance: lung contained_in thoracic cavity; bladder contained_in pelvic cavity. Hence containment is not a transitive relation. If c part_of c1 at t then we have also, by our definition and by the axioms of mereology applied to spatial regions, c located_in c1 at t. Thus, many examples of instance-level location relations for continuants are in fact cases of instance-level parthood. For material continuants location and parthood coincide. Containment is location not involving parthood, and arises only where some immaterial continuant is involved. To understand this relation, we first define overlap for continuants as follows: c1 overlap c2 at t =def for some c, c part_of c1 at t and c part_of c2 at t. The containment relation on the instance level can then be defined (see definition): @@ -1115,6 +1119,18 @@ range: spatial region or site (immaterial continuant) + + + + + + + + + + + + @@ -2519,7 +2535,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.regulates (processual) false - regulates @@ -2543,7 +2558,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.negatively regulates (process to process) - negatively regulates @@ -2572,7 +2586,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.positively regulates (process to process) - positively regulates @@ -2776,6 +2789,10 @@ 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 @@ -3467,10 +3484,6 @@ 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 @@ -3589,6 +3602,7 @@ where http://www.geneontology.org/GO.annotation.conventions.shtml#colocalizes_with In the context of the Gene Ontology, colocalizes_with may be used for annotating to cellular component terms[GO] Gene Ontology Consortium + colocalizes with @@ -3616,6 +3630,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati Chris Mungall http://www.geneontology.org/GO.annotation.conventions.shtml#contributes_to In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology. + contributes to @@ -3833,10 +3848,6 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - - - - 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. Chris Mungall @@ -3896,10 +3907,6 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - - - - 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 end location of c is part of the region that surrounds s. Chris Mungall @@ -4167,6 +4174,12 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + + + + + + A lump of clay and a statue x spatially_coextensive_with y if and inly if x and y have the same location Chris Mungall @@ -6967,6 +6980,7 @@ the a supports either the existence of b, or the truth value of b. A sub-relation of endoparasite-of in which the parasite inhabits host cells. + intracellular endoparasite of @@ -6984,6 +6998,17 @@ the a supports either the existence of b, or the truth value of b. + + + + + Two or more individuals sharing the same roost site (cave, mine, tree or tree hollow, animal burrow, leaf tent, rock crack, space in man-made structure, etc.). Individuals that are sharing a communal roost may be said to be co-roosting. The roost may be either a day roost where the individuals rest during daytime hours, or a night roost where individuals roost to feed, groom, or rest in between flights and/or foraging bouts. Communal roosting as thus defined is an umbrella term within which different specialized types -- which are not mutually exclusive -- may be recognized based on taxonomy and the temporal and spatial relationships of the individuals that are co-roosting. + co-roosts with + + + + @@ -8187,6 +8212,20 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + pg + 2021-02-26T07:28:29Z + + + + results in fusion of + + + + diff --git a/src/ontology/subsets/ro-interaction.obo b/src/ontology/subsets/ro-interaction.obo index ce4681cb..8240e725 100644 --- a/src/ontology/subsets/ro-interaction.obo +++ b/src/ontology/subsets/ro-interaction.obo @@ -560,6 +560,14 @@ xref: RO:0002478 property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: child_nucleus_of ! child nucleus of +[Typedef] +id: co-roosts_with +name: co-roosts with +def: "Two or more individuals sharing the same roost site (cave, mine, tree or tree hollow, animal burrow, leaf tent, rock crack, space in man-made structure, etc.). Individuals that are sharing a communal roost may be said to be co-roosting. The roost may be either a day roost where the individuals rest during daytime hours, or a night roost where individuals roost to feed, groom, or rest in between flights and/or foraging bouts. Communal roosting as thus defined is an umbrella term within which different specialized types -- which are not mutually exclusive -- may be recognized based on taxonomy and the temporal and spatial relationships of the individuals that are co-roosting." [] +xref: RO:0002801 +is_symmetric: true +is_a: ecologically_co-occurs_with ! ecologically co-occurs with + [Typedef] id: coincident_with name: coincident with @@ -575,6 +583,7 @@ is_a: mereotopologically_related_to ! mereotopologically related to id: colocalizes_with name: colocalizes with def: "a colocalizes_with b if and only if a is transiently or peripherally associated with b[GO]." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term xref: RO:0002325 property_value: http://purl.org/dc/terms/creator "Gene Ontology Consortium" xsd:string property_value: IAO:0000112 "Clp1p relocalizes from the nucleolus to the spindle and site of cell division; i.e. it is associated transiently with the spindle pole body and the contractile ring (evidence from GFP fusion). Clp1p colocalizes_with spindle pole body (GO:0005816) and contractile ring (GO:0005826)" xsd:string @@ -709,6 +718,7 @@ is_a: mereotopologically_related_to ! mereotopologically related to [Typedef] id: contributes_to name: contributes to +subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term xref: RO:0002326 property_value: IAO:0000112 "ATP citrate lyase (ACL) in Arabidopsis: it is a heterooctamer, composed of two types of subunits, ACLA and ACLB in a A(4)B(4) stoichiometry. Neither of the subunits expressed alone give ACL activity, but co-expression results in ACL activity. Both subunits contribute_to the ATP citrate lyase activity." xsd:string property_value: IAO:0000112 "eIF2: has three subunits (alpha, beta, gamma); one binds GTP; one binds RNA; the whole complex binds the ribosome (all three subunits are required for ribosome binding). So one subunit is annotated to GTP binding and one to RNA binding without qualifiers, and all three stand in the contributes_to relationship to \"ribosome binding\". And all three are part_of an eIF2 complex" xsd:string @@ -2685,6 +2695,7 @@ id: intracellular_endoparasite_of name: intracellular endoparasite of def: "A sub-relation of endoparasite-of in which the parasite inhabits host cells." [] xref: RO:0002640 +property_value: IAO:0000119 Communal:roosting property_value: IAO:0000119 "Types" is_a: endoparasite_of ! endoparasite of inverse_of: has_intracellular_endoparasite ! has intracellular endoparasite @@ -3167,7 +3178,6 @@ id: negatively_regulates 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." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension -subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002212 @@ -3427,7 +3437,6 @@ id: positively_regulates 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." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension -subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002213 @@ -3604,7 +3613,6 @@ id: regulates 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." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension -subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002211 @@ -3876,6 +3884,17 @@ is_a: has_output ! has output is_a: results_in_developmental_progression_of ! results in developmental progression of inverse_of: formed_as_result_of ! formed as result of +[Typedef] +id: results_in_fusion_of +name: results in fusion of +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam +xref: RO:0012008 +is_a: results_in_organization_of ! results in organization of +created_by: pg +creation_date: 2021-02-26T07:28:29Z + [Typedef] id: results_in_growth_of name: results in growth of diff --git a/src/ontology/subsets/ro-interaction.owl b/src/ontology/subsets/ro-interaction.owl index 045c3fb2..f516fe1c 100644 --- a/src/ontology/subsets/ro-interaction.owl +++ b/src/ontology/subsets/ro-interaction.owl @@ -1685,7 +1685,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.false RO:0002211 - regulates @@ -1707,7 +1706,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. RO:0002212 - negatively_regulates @@ -1730,7 +1728,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. RO:0002213 - positively_regulates @@ -2686,6 +2683,7 @@ where In the context of the Gene Ontology, colocalizes_with may be used for annotating to cellular component terms[GO] Gene Ontology Consortium RO:0002325 + colocalizes_with colocalizes with @@ -2715,6 +2713,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati http://www.geneontology.org/GO.annotation.conventions.shtml#contributes_to In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology. RO:0002326 + contributes_to contributes to @@ -5711,6 +5710,7 @@ For example, A and B may be gene products and binding of B by A positively regul A sub-relation of endoparasite-of in which the parasite inhabits host cells. + RO:0002640 intracellular_endoparasite_of @@ -5732,6 +5732,19 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + Two or more individuals sharing the same roost site (cave, mine, tree or tree hollow, animal burrow, leaf tent, rock crack, space in man-made structure, etc.). Individuals that are sharing a communal roost may be said to be co-roosting. The roost may be either a day roost where the individuals rest during daytime hours, or a night roost where individuals roost to feed, groom, or rest in between flights and/or foraging bouts. Communal roosting as thus defined is an umbrella term within which different specialized types -- which are not mutually exclusive -- may be recognized based on taxonomy and the temporal and spatial relationships of the individuals that are co-roosting. + RO:0002801 + co-roosts_with + co-roosts with + + + + @@ -7003,6 +7016,22 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + pg + 2021-02-26T07:28:29Z + RO:0012008 + + + + results_in_fusion_of + results in fusion of + + + + diff --git a/src/ontology/subsets/ro-mereotopology.obo b/src/ontology/subsets/ro-mereotopology.obo index 741b97d3..575868e8 100644 --- a/src/ontology/subsets/ro-mereotopology.obo +++ b/src/ontology/subsets/ro-mereotopology.obo @@ -560,6 +560,14 @@ xref: RO:0002478 property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: child_nucleus_of ! child nucleus of +[Typedef] +id: co-roosts_with +name: co-roosts with +def: "Two or more individuals sharing the same roost site (cave, mine, tree or tree hollow, animal burrow, leaf tent, rock crack, space in man-made structure, etc.). Individuals that are sharing a communal roost may be said to be co-roosting. The roost may be either a day roost where the individuals rest during daytime hours, or a night roost where individuals roost to feed, groom, or rest in between flights and/or foraging bouts. Communal roosting as thus defined is an umbrella term within which different specialized types -- which are not mutually exclusive -- may be recognized based on taxonomy and the temporal and spatial relationships of the individuals that are co-roosting." [] +xref: RO:0002801 +is_symmetric: true +is_a: ecologically_co-occurs_with ! ecologically co-occurs with + [Typedef] id: coincident_with name: coincident with @@ -575,6 +583,7 @@ is_a: mereotopologically_related_to ! mereotopologically related to id: colocalizes_with name: colocalizes with def: "a colocalizes_with b if and only if a is transiently or peripherally associated with b[GO]." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term xref: RO:0002325 property_value: http://purl.org/dc/terms/creator "Gene Ontology Consortium" xsd:string property_value: IAO:0000112 "Clp1p relocalizes from the nucleolus to the spindle and site of cell division; i.e. it is associated transiently with the spindle pole body and the contractile ring (evidence from GFP fusion). Clp1p colocalizes_with spindle pole body (GO:0005816) and contractile ring (GO:0005826)" xsd:string @@ -709,6 +718,7 @@ is_a: mereotopologically_related_to ! mereotopologically related to [Typedef] id: contributes_to name: contributes to +subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term xref: RO:0002326 property_value: IAO:0000112 "ATP citrate lyase (ACL) in Arabidopsis: it is a heterooctamer, composed of two types of subunits, ACLA and ACLB in a A(4)B(4) stoichiometry. Neither of the subunits expressed alone give ACL activity, but co-expression results in ACL activity. Both subunits contribute_to the ATP citrate lyase activity." xsd:string property_value: IAO:0000112 "eIF2: has three subunits (alpha, beta, gamma); one binds GTP; one binds RNA; the whole complex binds the ribosome (all three subunits are required for ribosome binding). So one subunit is annotated to GTP binding and one to RNA binding without qualifiers, and all three stand in the contributes_to relationship to \"ribosome binding\". And all three are part_of an eIF2 complex" xsd:string @@ -2685,6 +2695,7 @@ id: intracellular_endoparasite_of name: intracellular endoparasite of def: "A sub-relation of endoparasite-of in which the parasite inhabits host cells." [] xref: RO:0002640 +property_value: IAO:0000119 Communal:roosting property_value: IAO:0000119 "Types" is_a: endoparasite_of ! endoparasite of inverse_of: has_intracellular_endoparasite ! has intracellular endoparasite @@ -3167,7 +3178,6 @@ id: negatively_regulates 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." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension -subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002212 @@ -3427,7 +3437,6 @@ id: positively_regulates 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." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension -subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002213 @@ -3604,7 +3613,6 @@ id: regulates 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." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension -subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002211 @@ -3876,6 +3884,17 @@ is_a: has_output ! has output is_a: results_in_developmental_progression_of ! results in developmental progression of inverse_of: formed_as_result_of ! formed as result of +[Typedef] +id: results_in_fusion_of +name: results in fusion of +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam +xref: RO:0012008 +is_a: results_in_organization_of ! results in organization of +created_by: pg +creation_date: 2021-02-26T07:28:29Z + [Typedef] id: results_in_growth_of name: results in growth of diff --git a/src/ontology/subsets/ro-mereotopology.owl b/src/ontology/subsets/ro-mereotopology.owl index 7cf84fdd..f49f5dfd 100644 --- a/src/ontology/subsets/ro-mereotopology.owl +++ b/src/ontology/subsets/ro-mereotopology.owl @@ -1685,7 +1685,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.false RO:0002211 - regulates @@ -1707,7 +1706,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. RO:0002212 - negatively_regulates @@ -1730,7 +1728,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. RO:0002213 - positively_regulates @@ -2686,6 +2683,7 @@ where In the context of the Gene Ontology, colocalizes_with may be used for annotating to cellular component terms[GO] Gene Ontology Consortium RO:0002325 + colocalizes_with colocalizes with @@ -2715,6 +2713,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati http://www.geneontology.org/GO.annotation.conventions.shtml#contributes_to In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology. RO:0002326 + contributes_to contributes to @@ -5711,6 +5710,7 @@ For example, A and B may be gene products and binding of B by A positively regul A sub-relation of endoparasite-of in which the parasite inhabits host cells. + RO:0002640 intracellular_endoparasite_of @@ -5732,6 +5732,19 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + Two or more individuals sharing the same roost site (cave, mine, tree or tree hollow, animal burrow, leaf tent, rock crack, space in man-made structure, etc.). Individuals that are sharing a communal roost may be said to be co-roosting. The roost may be either a day roost where the individuals rest during daytime hours, or a night roost where individuals roost to feed, groom, or rest in between flights and/or foraging bouts. Communal roosting as thus defined is an umbrella term within which different specialized types -- which are not mutually exclusive -- may be recognized based on taxonomy and the temporal and spatial relationships of the individuals that are co-roosting. + RO:0002801 + co-roosts_with + co-roosts with + + + + @@ -7003,6 +7016,22 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + pg + 2021-02-26T07:28:29Z + RO:0012008 + + + + results_in_fusion_of + results in fusion of + + + + diff --git a/src/ontology/subsets/ro-sequence.obo b/src/ontology/subsets/ro-sequence.obo index f4f16228..0fd6797c 100644 --- a/src/ontology/subsets/ro-sequence.obo +++ b/src/ontology/subsets/ro-sequence.obo @@ -560,6 +560,14 @@ xref: RO:0002478 property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: child_nucleus_of ! child nucleus of +[Typedef] +id: co-roosts_with +name: co-roosts with +def: "Two or more individuals sharing the same roost site (cave, mine, tree or tree hollow, animal burrow, leaf tent, rock crack, space in man-made structure, etc.). Individuals that are sharing a communal roost may be said to be co-roosting. The roost may be either a day roost where the individuals rest during daytime hours, or a night roost where individuals roost to feed, groom, or rest in between flights and/or foraging bouts. Communal roosting as thus defined is an umbrella term within which different specialized types -- which are not mutually exclusive -- may be recognized based on taxonomy and the temporal and spatial relationships of the individuals that are co-roosting." [] +xref: RO:0002801 +is_symmetric: true +is_a: ecologically_co-occurs_with ! ecologically co-occurs with + [Typedef] id: coincident_with name: coincident with @@ -575,6 +583,7 @@ is_a: mereotopologically_related_to ! mereotopologically related to id: colocalizes_with name: colocalizes with def: "a colocalizes_with b if and only if a is transiently or peripherally associated with b[GO]." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term xref: RO:0002325 property_value: http://purl.org/dc/terms/creator "Gene Ontology Consortium" xsd:string property_value: IAO:0000112 "Clp1p relocalizes from the nucleolus to the spindle and site of cell division; i.e. it is associated transiently with the spindle pole body and the contractile ring (evidence from GFP fusion). Clp1p colocalizes_with spindle pole body (GO:0005816) and contractile ring (GO:0005826)" xsd:string @@ -709,6 +718,7 @@ is_a: mereotopologically_related_to ! mereotopologically related to [Typedef] id: contributes_to name: contributes to +subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term xref: RO:0002326 property_value: IAO:0000112 "ATP citrate lyase (ACL) in Arabidopsis: it is a heterooctamer, composed of two types of subunits, ACLA and ACLB in a A(4)B(4) stoichiometry. Neither of the subunits expressed alone give ACL activity, but co-expression results in ACL activity. Both subunits contribute_to the ATP citrate lyase activity." xsd:string property_value: IAO:0000112 "eIF2: has three subunits (alpha, beta, gamma); one binds GTP; one binds RNA; the whole complex binds the ribosome (all three subunits are required for ribosome binding). So one subunit is annotated to GTP binding and one to RNA binding without qualifiers, and all three stand in the contributes_to relationship to \"ribosome binding\". And all three are part_of an eIF2 complex" xsd:string @@ -2685,6 +2695,7 @@ id: intracellular_endoparasite_of name: intracellular endoparasite of def: "A sub-relation of endoparasite-of in which the parasite inhabits host cells." [] xref: RO:0002640 +property_value: IAO:0000119 Communal:roosting property_value: IAO:0000119 "Types" is_a: endoparasite_of ! endoparasite of inverse_of: has_intracellular_endoparasite ! has intracellular endoparasite @@ -3167,7 +3178,6 @@ id: negatively_regulates 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." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension -subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002212 @@ -3427,7 +3437,6 @@ id: positively_regulates 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." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension -subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002213 @@ -3604,7 +3613,6 @@ id: regulates 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." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension -subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002211 @@ -3876,6 +3884,17 @@ is_a: has_output ! has output is_a: results_in_developmental_progression_of ! results in developmental progression of inverse_of: formed_as_result_of ! formed as result of +[Typedef] +id: results_in_fusion_of +name: results in fusion of +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam +xref: RO:0012008 +is_a: results_in_organization_of ! results in organization of +created_by: pg +creation_date: 2021-02-26T07:28:29Z + [Typedef] id: results_in_growth_of name: results in growth of diff --git a/src/ontology/subsets/ro-sequence.owl b/src/ontology/subsets/ro-sequence.owl index 5ec1445e..7cab64a1 100644 --- a/src/ontology/subsets/ro-sequence.owl +++ b/src/ontology/subsets/ro-sequence.owl @@ -1685,7 +1685,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.false RO:0002211 - regulates @@ -1707,7 +1706,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. RO:0002212 - negatively_regulates @@ -1730,7 +1728,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. RO:0002213 - positively_regulates @@ -2686,6 +2683,7 @@ where In the context of the Gene Ontology, colocalizes_with may be used for annotating to cellular component terms[GO] Gene Ontology Consortium RO:0002325 + colocalizes_with colocalizes with @@ -2715,6 +2713,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati http://www.geneontology.org/GO.annotation.conventions.shtml#contributes_to In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology. RO:0002326 + contributes_to contributes to @@ -5711,6 +5710,7 @@ For example, A and B may be gene products and binding of B by A positively regul A sub-relation of endoparasite-of in which the parasite inhabits host cells. + RO:0002640 intracellular_endoparasite_of @@ -5732,6 +5732,19 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + Two or more individuals sharing the same roost site (cave, mine, tree or tree hollow, animal burrow, leaf tent, rock crack, space in man-made structure, etc.). Individuals that are sharing a communal roost may be said to be co-roosting. The roost may be either a day roost where the individuals rest during daytime hours, or a night roost where individuals roost to feed, groom, or rest in between flights and/or foraging bouts. Communal roosting as thus defined is an umbrella term within which different specialized types -- which are not mutually exclusive -- may be recognized based on taxonomy and the temporal and spatial relationships of the individuals that are co-roosting. + RO:0002801 + co-roosts_with + co-roosts with + + + + @@ -7003,6 +7016,22 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + pg + 2021-02-26T07:28:29Z + RO:0012008 + + + + results_in_fusion_of + results in fusion of + + + + diff --git a/src/ontology/subsets/ro-time-interval.obo b/src/ontology/subsets/ro-time-interval.obo index 0ea762d0..6b9ab4bd 100644 --- a/src/ontology/subsets/ro-time-interval.obo +++ b/src/ontology/subsets/ro-time-interval.obo @@ -560,6 +560,14 @@ xref: RO:0002478 property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: child_nucleus_of ! child nucleus of +[Typedef] +id: co-roosts_with +name: co-roosts with +def: "Two or more individuals sharing the same roost site (cave, mine, tree or tree hollow, animal burrow, leaf tent, rock crack, space in man-made structure, etc.). Individuals that are sharing a communal roost may be said to be co-roosting. The roost may be either a day roost where the individuals rest during daytime hours, or a night roost where individuals roost to feed, groom, or rest in between flights and/or foraging bouts. Communal roosting as thus defined is an umbrella term within which different specialized types -- which are not mutually exclusive -- may be recognized based on taxonomy and the temporal and spatial relationships of the individuals that are co-roosting." [] +xref: RO:0002801 +is_symmetric: true +is_a: ecologically_co-occurs_with ! ecologically co-occurs with + [Typedef] id: coincident_with name: coincident with @@ -575,6 +583,7 @@ is_a: mereotopologically_related_to ! mereotopologically related to id: colocalizes_with name: colocalizes with def: "a colocalizes_with b if and only if a is transiently or peripherally associated with b[GO]." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term xref: RO:0002325 property_value: http://purl.org/dc/terms/creator "Gene Ontology Consortium" xsd:string property_value: IAO:0000112 "Clp1p relocalizes from the nucleolus to the spindle and site of cell division; i.e. it is associated transiently with the spindle pole body and the contractile ring (evidence from GFP fusion). Clp1p colocalizes_with spindle pole body (GO:0005816) and contractile ring (GO:0005826)" xsd:string @@ -709,6 +718,7 @@ is_a: mereotopologically_related_to ! mereotopologically related to [Typedef] id: contributes_to name: contributes to +subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term xref: RO:0002326 property_value: IAO:0000112 "ATP citrate lyase (ACL) in Arabidopsis: it is a heterooctamer, composed of two types of subunits, ACLA and ACLB in a A(4)B(4) stoichiometry. Neither of the subunits expressed alone give ACL activity, but co-expression results in ACL activity. Both subunits contribute_to the ATP citrate lyase activity." xsd:string property_value: IAO:0000112 "eIF2: has three subunits (alpha, beta, gamma); one binds GTP; one binds RNA; the whole complex binds the ribosome (all three subunits are required for ribosome binding). So one subunit is annotated to GTP binding and one to RNA binding without qualifiers, and all three stand in the contributes_to relationship to \"ribosome binding\". And all three are part_of an eIF2 complex" xsd:string @@ -2685,6 +2695,7 @@ id: intracellular_endoparasite_of name: intracellular endoparasite of def: "A sub-relation of endoparasite-of in which the parasite inhabits host cells." [] xref: RO:0002640 +property_value: IAO:0000119 Communal:roosting property_value: IAO:0000119 "Types" is_a: endoparasite_of ! endoparasite of inverse_of: has_intracellular_endoparasite ! has intracellular endoparasite @@ -3167,7 +3178,6 @@ id: negatively_regulates 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." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension -subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002212 @@ -3427,7 +3437,6 @@ id: positively_regulates 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." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension -subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002213 @@ -3604,7 +3613,6 @@ id: regulates 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." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension -subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002211 @@ -3876,6 +3884,17 @@ is_a: has_output ! has output is_a: results_in_developmental_progression_of ! results in developmental progression of inverse_of: formed_as_result_of ! formed as result of +[Typedef] +id: results_in_fusion_of +name: results in fusion of +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam +xref: RO:0012008 +is_a: results_in_organization_of ! results in organization of +created_by: pg +creation_date: 2021-02-26T07:28:29Z + [Typedef] id: results_in_growth_of name: results in growth of diff --git a/src/ontology/subsets/ro-time-interval.owl b/src/ontology/subsets/ro-time-interval.owl index 65991efd..a5404265 100644 --- a/src/ontology/subsets/ro-time-interval.owl +++ b/src/ontology/subsets/ro-time-interval.owl @@ -1685,7 +1685,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.false RO:0002211 - regulates @@ -1707,7 +1706,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. RO:0002212 - negatively_regulates @@ -1730,7 +1728,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. RO:0002213 - positively_regulates @@ -2686,6 +2683,7 @@ where In the context of the Gene Ontology, colocalizes_with may be used for annotating to cellular component terms[GO] Gene Ontology Consortium RO:0002325 + colocalizes_with colocalizes with @@ -2715,6 +2713,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati http://www.geneontology.org/GO.annotation.conventions.shtml#contributes_to In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology. RO:0002326 + contributes_to contributes to @@ -5711,6 +5710,7 @@ For example, A and B may be gene products and binding of B by A positively regul A sub-relation of endoparasite-of in which the parasite inhabits host cells. + RO:0002640 intracellular_endoparasite_of @@ -5732,6 +5732,19 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + Two or more individuals sharing the same roost site (cave, mine, tree or tree hollow, animal burrow, leaf tent, rock crack, space in man-made structure, etc.). Individuals that are sharing a communal roost may be said to be co-roosting. The roost may be either a day roost where the individuals rest during daytime hours, or a night roost where individuals roost to feed, groom, or rest in between flights and/or foraging bouts. Communal roosting as thus defined is an umbrella term within which different specialized types -- which are not mutually exclusive -- may be recognized based on taxonomy and the temporal and spatial relationships of the individuals that are co-roosting. + RO:0002801 + co-roosts_with + co-roosts with + + + + @@ -7003,6 +7016,22 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + pg + 2021-02-26T07:28:29Z + RO:0012008 + + + + results_in_fusion_of + results in fusion of + + + + diff --git a/subsets/ro-causal.obo b/subsets/ro-causal.obo index 7b4ce749..9e36489f 100644 --- a/subsets/ro-causal.obo +++ b/subsets/ro-causal.obo @@ -560,6 +560,14 @@ xref: RO:0002478 property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: child_nucleus_of ! child nucleus of +[Typedef] +id: co-roosts_with +name: co-roosts with +def: "Two or more individuals sharing the same roost site (cave, mine, tree or tree hollow, animal burrow, leaf tent, rock crack, space in man-made structure, etc.). Individuals that are sharing a communal roost may be said to be co-roosting. The roost may be either a day roost where the individuals rest during daytime hours, or a night roost where individuals roost to feed, groom, or rest in between flights and/or foraging bouts. Communal roosting as thus defined is an umbrella term within which different specialized types -- which are not mutually exclusive -- may be recognized based on taxonomy and the temporal and spatial relationships of the individuals that are co-roosting." [] +xref: RO:0002801 +is_symmetric: true +is_a: ecologically_co-occurs_with ! ecologically co-occurs with + [Typedef] id: coincident_with name: coincident with @@ -575,6 +583,7 @@ is_a: mereotopologically_related_to ! mereotopologically related to id: colocalizes_with name: colocalizes with def: "a colocalizes_with b if and only if a is transiently or peripherally associated with b[GO]." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term xref: RO:0002325 property_value: http://purl.org/dc/terms/creator "Gene Ontology Consortium" xsd:string property_value: IAO:0000112 "Clp1p relocalizes from the nucleolus to the spindle and site of cell division; i.e. it is associated transiently with the spindle pole body and the contractile ring (evidence from GFP fusion). Clp1p colocalizes_with spindle pole body (GO:0005816) and contractile ring (GO:0005826)" xsd:string @@ -709,6 +718,7 @@ is_a: mereotopologically_related_to ! mereotopologically related to [Typedef] id: contributes_to name: contributes to +subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term xref: RO:0002326 property_value: IAO:0000112 "ATP citrate lyase (ACL) in Arabidopsis: it is a heterooctamer, composed of two types of subunits, ACLA and ACLB in a A(4)B(4) stoichiometry. Neither of the subunits expressed alone give ACL activity, but co-expression results in ACL activity. Both subunits contribute_to the ATP citrate lyase activity." xsd:string property_value: IAO:0000112 "eIF2: has three subunits (alpha, beta, gamma); one binds GTP; one binds RNA; the whole complex binds the ribosome (all three subunits are required for ribosome binding). So one subunit is annotated to GTP binding and one to RNA binding without qualifiers, and all three stand in the contributes_to relationship to \"ribosome binding\". And all three are part_of an eIF2 complex" xsd:string @@ -2685,6 +2695,7 @@ id: intracellular_endoparasite_of name: intracellular endoparasite of def: "A sub-relation of endoparasite-of in which the parasite inhabits host cells." [] xref: RO:0002640 +property_value: IAO:0000119 Communal:roosting property_value: IAO:0000119 "Types" is_a: endoparasite_of ! endoparasite of inverse_of: has_intracellular_endoparasite ! has intracellular endoparasite @@ -3167,7 +3178,6 @@ id: negatively_regulates 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." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension -subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002212 @@ -3427,7 +3437,6 @@ id: positively_regulates 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." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension -subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002213 @@ -3604,7 +3613,6 @@ id: regulates 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." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension -subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002211 @@ -3876,6 +3884,17 @@ is_a: has_output ! has output is_a: results_in_developmental_progression_of ! results in developmental progression of inverse_of: formed_as_result_of ! formed as result of +[Typedef] +id: results_in_fusion_of +name: results in fusion of +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam +xref: RO:0012008 +is_a: results_in_organization_of ! results in organization of +created_by: pg +creation_date: 2021-02-26T07:28:29Z + [Typedef] id: results_in_growth_of name: results in growth of diff --git a/subsets/ro-causal.owl b/subsets/ro-causal.owl index ecd37cb3..c957249e 100644 --- a/subsets/ro-causal.owl +++ b/subsets/ro-causal.owl @@ -1685,7 +1685,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.false RO:0002211 - regulates @@ -1707,7 +1706,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. RO:0002212 - negatively_regulates @@ -1730,7 +1728,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. RO:0002213 - positively_regulates @@ -2686,6 +2683,7 @@ where In the context of the Gene Ontology, colocalizes_with may be used for annotating to cellular component terms[GO] Gene Ontology Consortium RO:0002325 + colocalizes_with colocalizes with @@ -2715,6 +2713,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati http://www.geneontology.org/GO.annotation.conventions.shtml#contributes_to In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology. RO:0002326 + contributes_to contributes to @@ -5711,6 +5710,7 @@ For example, A and B may be gene products and binding of B by A positively regul A sub-relation of endoparasite-of in which the parasite inhabits host cells. + RO:0002640 intracellular_endoparasite_of @@ -5732,6 +5732,19 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + Two or more individuals sharing the same roost site (cave, mine, tree or tree hollow, animal burrow, leaf tent, rock crack, space in man-made structure, etc.). Individuals that are sharing a communal roost may be said to be co-roosting. The roost may be either a day roost where the individuals rest during daytime hours, or a night roost where individuals roost to feed, groom, or rest in between flights and/or foraging bouts. Communal roosting as thus defined is an umbrella term within which different specialized types -- which are not mutually exclusive -- may be recognized based on taxonomy and the temporal and spatial relationships of the individuals that are co-roosting. + RO:0002801 + co-roosts_with + co-roosts with + + + + @@ -7003,6 +7016,22 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + pg + 2021-02-26T07:28:29Z + RO:0012008 + + + + results_in_fusion_of + results in fusion of + + + + diff --git a/subsets/ro-chado.obo b/subsets/ro-chado.obo index 6bb25af8..84143aba 100644 --- a/subsets/ro-chado.obo +++ b/subsets/ro-chado.obo @@ -1253,7 +1253,6 @@ 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:0002337 ! related via localization to is_a: RO:0040036 ! has anatomical participant -transitive_over: BFO:0000051 ! has part [Typedef] id: RO:0002314 @@ -1390,7 +1389,6 @@ 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 @@ -1421,7 +1419,6 @@ id: RO:0002345 name: exports 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 end 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:0002348 @@ -2803,6 +2800,13 @@ name: has_intracellular_endoparasite def: "inverse of intracellular endoparasite of" [] is_a: RO:0002635 ! has endoparasite +[Typedef] +id: RO:0002801 +name: co-roosts_with +def: "Two or more individuals sharing the same roost site (cave, mine, tree or tree hollow, animal burrow, leaf tent, rock crack, space in man-made structure, etc.). Individuals that are sharing a communal roost may be said to be co-roosting. The roost may be either a day roost where the individuals rest during daytime hours, or a night roost where individuals roost to feed, groom, or rest in between flights and/or foraging bouts. Communal roosting as thus defined is an umbrella term within which different specialized types -- which are not mutually exclusive -- may be recognized based on taxonomy and the temporal and spatial relationships of the individuals that are co-roosting." [] +is_symmetric: true +is_a: RO:0008506 ! ecologically co-occurs with + [Typedef] id: RO:0003000 name: produces @@ -3365,6 +3369,11 @@ name: results_in_adhesion_of def: "The relationship that links anatomical entities with a process that results in the adhesion of two or more entities via the non-covalent interaction of molecules expressed in, located in, and/or adjacent to, those entities." [] is_a: RO:0040036 ! has anatomical participant +[Typedef] +id: RO:0012008 +name: results_in_fusion_of +is_a: RO:0002592 ! results in organization of + [Typedef] id: RO:0013001 name: has_synaptic_IO_in diff --git a/subsets/ro-chado.obo.tmp b/subsets/ro-chado.obo.tmp index d9623875..b94534b9 100644 --- a/subsets/ro-chado.obo.tmp +++ b/subsets/ro-chado.obo.tmp @@ -1253,7 +1253,6 @@ 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:0002337 ! related via localization to is_a: RO:0040036 ! has anatomical participant -transitive_over: BFO:0000051 ! has part [Typedef] id: RO:0002314 @@ -1390,7 +1389,6 @@ 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 @@ -1421,7 +1419,6 @@ id: RO:0002345 name: exports 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 end 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:0002348 @@ -2803,6 +2800,13 @@ name: has intracellular endoparasite def: "inverse of intracellular endoparasite of" [] is_a: RO:0002635 ! has endoparasite +[Typedef] +id: RO:0002801 +name: co-roosts with +def: "Two or more individuals sharing the same roost site (cave, mine, tree or tree hollow, animal burrow, leaf tent, rock crack, space in man-made structure, etc.). Individuals that are sharing a communal roost may be said to be co-roosting. The roost may be either a day roost where the individuals rest during daytime hours, or a night roost where individuals roost to feed, groom, or rest in between flights and/or foraging bouts. Communal roosting as thus defined is an umbrella term within which different specialized types -- which are not mutually exclusive -- may be recognized based on taxonomy and the temporal and spatial relationships of the individuals that are co-roosting." [] +is_symmetric: true +is_a: RO:0008506 ! ecologically co-occurs with + [Typedef] id: RO:0003000 name: produces @@ -3365,6 +3369,11 @@ name: results in adhesion of def: "The relationship that links anatomical entities with a process that results in the adhesion of two or more entities via the non-covalent interaction of molecules expressed in, located in, and/or adjacent to, those entities." [] is_a: RO:0040036 ! has anatomical participant +[Typedef] +id: RO:0012008 +name: results in fusion of +is_a: RO:0002592 ! results in organization of + [Typedef] id: RO:0013001 name: has synaptic IO in diff --git a/subsets/ro-developmental.obo b/subsets/ro-developmental.obo index 2ce63666..981fb37a 100644 --- a/subsets/ro-developmental.obo +++ b/subsets/ro-developmental.obo @@ -560,6 +560,14 @@ xref: RO:0002478 property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: child_nucleus_of ! child nucleus of +[Typedef] +id: co-roosts_with +name: co-roosts with +def: "Two or more individuals sharing the same roost site (cave, mine, tree or tree hollow, animal burrow, leaf tent, rock crack, space in man-made structure, etc.). Individuals that are sharing a communal roost may be said to be co-roosting. The roost may be either a day roost where the individuals rest during daytime hours, or a night roost where individuals roost to feed, groom, or rest in between flights and/or foraging bouts. Communal roosting as thus defined is an umbrella term within which different specialized types -- which are not mutually exclusive -- may be recognized based on taxonomy and the temporal and spatial relationships of the individuals that are co-roosting." [] +xref: RO:0002801 +is_symmetric: true +is_a: ecologically_co-occurs_with ! ecologically co-occurs with + [Typedef] id: coincident_with name: coincident with @@ -575,6 +583,7 @@ is_a: mereotopologically_related_to ! mereotopologically related to id: colocalizes_with name: colocalizes with def: "a colocalizes_with b if and only if a is transiently or peripherally associated with b[GO]." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term xref: RO:0002325 property_value: http://purl.org/dc/terms/creator "Gene Ontology Consortium" xsd:string property_value: IAO:0000112 "Clp1p relocalizes from the nucleolus to the spindle and site of cell division; i.e. it is associated transiently with the spindle pole body and the contractile ring (evidence from GFP fusion). Clp1p colocalizes_with spindle pole body (GO:0005816) and contractile ring (GO:0005826)" xsd:string @@ -709,6 +718,7 @@ is_a: mereotopologically_related_to ! mereotopologically related to [Typedef] id: contributes_to name: contributes to +subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term xref: RO:0002326 property_value: IAO:0000112 "ATP citrate lyase (ACL) in Arabidopsis: it is a heterooctamer, composed of two types of subunits, ACLA and ACLB in a A(4)B(4) stoichiometry. Neither of the subunits expressed alone give ACL activity, but co-expression results in ACL activity. Both subunits contribute_to the ATP citrate lyase activity." xsd:string property_value: IAO:0000112 "eIF2: has three subunits (alpha, beta, gamma); one binds GTP; one binds RNA; the whole complex binds the ribosome (all three subunits are required for ribosome binding). So one subunit is annotated to GTP binding and one to RNA binding without qualifiers, and all three stand in the contributes_to relationship to \"ribosome binding\". And all three are part_of an eIF2 complex" xsd:string @@ -2685,6 +2695,7 @@ id: intracellular_endoparasite_of name: intracellular endoparasite of def: "A sub-relation of endoparasite-of in which the parasite inhabits host cells." [] xref: RO:0002640 +property_value: IAO:0000119 Communal:roosting property_value: IAO:0000119 "Types" is_a: endoparasite_of ! endoparasite of inverse_of: has_intracellular_endoparasite ! has intracellular endoparasite @@ -3167,7 +3178,6 @@ id: negatively_regulates 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." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension -subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002212 @@ -3427,7 +3437,6 @@ id: positively_regulates 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." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension -subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002213 @@ -3604,7 +3613,6 @@ id: regulates 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." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension -subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002211 @@ -3876,6 +3884,17 @@ is_a: has_output ! has output is_a: results_in_developmental_progression_of ! results in developmental progression of inverse_of: formed_as_result_of ! formed as result of +[Typedef] +id: results_in_fusion_of +name: results in fusion of +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam +xref: RO:0012008 +is_a: results_in_organization_of ! results in organization of +created_by: pg +creation_date: 2021-02-26T07:28:29Z + [Typedef] id: results_in_growth_of name: results in growth of diff --git a/subsets/ro-developmental.owl b/subsets/ro-developmental.owl index ed3391ab..325845db 100644 --- a/subsets/ro-developmental.owl +++ b/subsets/ro-developmental.owl @@ -1685,7 +1685,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.false RO:0002211 - regulates @@ -1707,7 +1706,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. RO:0002212 - negatively_regulates @@ -1730,7 +1728,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. RO:0002213 - positively_regulates @@ -2686,6 +2683,7 @@ where In the context of the Gene Ontology, colocalizes_with may be used for annotating to cellular component terms[GO] Gene Ontology Consortium RO:0002325 + colocalizes_with colocalizes with @@ -2715,6 +2713,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati http://www.geneontology.org/GO.annotation.conventions.shtml#contributes_to In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology. RO:0002326 + contributes_to contributes to @@ -5711,6 +5710,7 @@ For example, A and B may be gene products and binding of B by A positively regul A sub-relation of endoparasite-of in which the parasite inhabits host cells. + RO:0002640 intracellular_endoparasite_of @@ -5732,6 +5732,19 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + Two or more individuals sharing the same roost site (cave, mine, tree or tree hollow, animal burrow, leaf tent, rock crack, space in man-made structure, etc.). Individuals that are sharing a communal roost may be said to be co-roosting. The roost may be either a day roost where the individuals rest during daytime hours, or a night roost where individuals roost to feed, groom, or rest in between flights and/or foraging bouts. Communal roosting as thus defined is an umbrella term within which different specialized types -- which are not mutually exclusive -- may be recognized based on taxonomy and the temporal and spatial relationships of the individuals that are co-roosting. + RO:0002801 + co-roosts_with + co-roosts with + + + + @@ -7003,6 +7016,22 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + pg + 2021-02-26T07:28:29Z + RO:0012008 + + + + results_in_fusion_of + results in fusion of + + + + diff --git a/subsets/ro-eco.obo b/subsets/ro-eco.obo index ed3d34b6..2065aac5 100644 --- a/subsets/ro-eco.obo +++ b/subsets/ro-eco.obo @@ -7,7 +7,7 @@ subsetdef: http://purl.obolibrary.org/obo/valid_for_gocam "" 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(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# Annotation Property: (is homeomorphic for)\n\nSubAnnotationPropertyOf( )\n\n\n############################\n# Object Properties\n############################\n\n# Object Property: (anabranch of)\n\nSubObjectPropertyOf( ObjectInverseOf())\n\n# Object Property: (has skeleton)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (has role in modeling)\n\nIrreflexiveObjectProperty()\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() ) )\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())))\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(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# Annotation Property: (is homeomorphic for)\n\nSubAnnotationPropertyOf( )\n\n\n############################\n# Object Properties\n############################\n\n# Object Property: (anabranch of)\n\nSubObjectPropertyOf( ObjectInverseOf())\n\n# Object Property: (has skeleton)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (has role in modeling)\n\nIrreflexiveObjectProperty()\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( 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())))\nAnnotationAssertion(rdfs:comment \"\")\n) [Typedef] id: BFO:0000050 @@ -97,6 +97,7 @@ property_value: IAO:0000116 "Containment obtains in each case between material a property_value: IAO:0000116 "Intended meaning:\ndomain: material entity\nrange: spatial region or site (immaterial continuant)\n " xsd:string property_value: IAO:0000118 "contained_in" xsd:string property_value: RO:0001900 RO:0001901 +holds_over_chain: RO:0001025 BFO:0000050 inverse_of: RO:0001019 ! contains [Typedef] @@ -134,6 +135,11 @@ 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 +subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term +transitive_over: BFO:0000050 + [Typedef] id: RO:0002001 name: aligned with @@ -959,7 +965,6 @@ 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." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension -subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: IAO:0000114 IAO:0000125 @@ -984,7 +989,6 @@ 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." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension -subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -1001,7 +1005,6 @@ 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." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension -subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -1146,6 +1149,7 @@ 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 +holds_over_chain: RO:0002207 RO:0001025 is_a: RO:0002258 ! developmentally preceded by [Typedef] @@ -1530,7 +1534,6 @@ 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 -transitive_over: BFO:0000051 [Typedef] id: RO:0002314 @@ -1588,6 +1591,7 @@ property_value: IAO:0000232 "Do not use this relation directly. It is ended as a id: RO:0002325 name: colocalizes with def: "a colocalizes_with b if and only if a is transiently or peripherally associated with b[GO]." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term property_value: http://purl.org/dc/terms/creator "Gene Ontology Consortium" xsd:string property_value: IAO:0000112 "Clp1p relocalizes from the nucleolus to the spindle and site of cell division; i.e. it is associated transiently with the spindle pole body and the contractile ring (evidence from GFP fusion). Clp1p colocalizes_with spindle pole body (GO:0005816) and contractile ring (GO:0005826)" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -1598,6 +1602,7 @@ is_a: RO:0002323 ! mereotopologically related to [Typedef] id: RO:0002326 name: contributes to +subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term property_value: IAO:0000112 "ATP citrate lyase (ACL) in Arabidopsis: it is a heterooctamer, composed of two types of subunits, ACLA and ACLB in a A(4)B(4) stoichiometry. Neither of the subunits expressed alone give ACL activity, but co-expression results in ACL activity. Both subunits contribute_to the ATP citrate lyase activity." xsd:string property_value: IAO:0000112 "eIF2: has three subunits (alpha, beta, gamma); one binds GTP; one binds RNA; the whole complex binds the ribosome (all three subunits are required for ribosome binding). So one subunit is annotated to GTP binding and one to RNA binding without qualifiers, and all three stand in the contributes_to relationship to \"ribosome binding\". And all three are part_of an eIF2 complex" xsd:string property_value: IAO:0000112 "Subunits of nuclear RNA polymerases: none of the individual subunits have RNA polymerase activity, yet all of these subunits contribute_to DNA-dependent RNA polymerase activity." xsd:string @@ -1741,7 +1746,6 @@ def: "Holds between p and c when p is a transportation or localization process a subset: http://purl.obolibrary.org/obo/valid_for_go_ontology property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: RO:0002020 ! transports -transitive_over: BFO:0000051 [Typedef] id: RO:0002341 @@ -1781,7 +1785,6 @@ def: "Holds between p and c when p is a transportation or localization process a subset: http://purl.obolibrary.org/obo/valid_for_go_ontology property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: RO:0002020 ! transports -transitive_over: BFO:0000051 [Typedef] id: RO:0002348 @@ -3725,6 +3728,7 @@ is_a: RO:0002635 ! has endoparasite id: RO:0002640 name: intracellular endoparasite of def: "A sub-relation of endoparasite-of in which the parasite inhabits host cells." [] +property_value: IAO:0000119 Communal:roosting property_value: IAO:0000119 "Types" is_a: RO:0002634 ! endoparasite of inverse_of: RO:0002641 ! has intracellular endoparasite @@ -3736,6 +3740,13 @@ def: "inverse of intracellular endoparasite of" [] subset: RO:0002259 is_a: RO:0002635 ! has endoparasite +[Typedef] +id: RO:0002801 +name: co-roosts with +def: "Two or more individuals sharing the same roost site (cave, mine, tree or tree hollow, animal burrow, leaf tent, rock crack, space in man-made structure, etc.). Individuals that are sharing a communal roost may be said to be co-roosting. The roost may be either a day roost where the individuals rest during daytime hours, or a night roost where individuals roost to feed, groom, or rest in between flights and/or foraging bouts. Communal roosting as thus defined is an umbrella term within which different specialized types -- which are not mutually exclusive -- may be recognized based on taxonomy and the temporal and spatial relationships of the individuals that are co-roosting." [] +is_symmetric: true +is_a: RO:0008506 ! ecologically co-occurs with + [Typedef] id: RO:0003000 name: produces @@ -4497,6 +4508,16 @@ is_a: RO:0040036 ! has anatomical participant created_by: pg creation_date: 2020-08-27T08:13:59Z +[Typedef] +id: RO:0012008 +name: results in fusion of +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam +is_a: RO:0002592 ! results in organization of +created_by: pg +creation_date: 2021-02-26T07:28:29Z + [Typedef] id: RO:0013001 name: has synaptic IO in diff --git a/subsets/ro-eco.owl b/subsets/ro-eco.owl index 8a74d87c..f8dbb544 100644 --- a/subsets/ro-eco.owl +++ b/subsets/ro-eco.owl @@ -1045,6 +1045,10 @@ Where we have an annotation assertion + + + + contained in Containment is location not involving parthood, and arises only where some immaterial continuant is involved. Containment obtains in each case between material and immaterial continuants, for instance: lung contained_in thoracic cavity; bladder contained_in pelvic cavity. Hence containment is not a transitive relation. If c part_of c1 at t then we have also, by our definition and by the axioms of mereology applied to spatial regions, c located_in c1 at t. Thus, many examples of instance-level location relations for continuants are in fact cases of instance-level parthood. For material continuants location and parthood coincide. Containment is location not involving parthood, and arises only where some immaterial continuant is involved. To understand this relation, we first define overlap for continuants as follows: c1 overlap c2 at t =def for some c, c part_of c1 at t and c part_of c2 at t. The containment relation on the instance level can then be defined (see definition): @@ -1115,6 +1119,18 @@ range: spatial region or site (immaterial continuant) + + + + + + + + + + + + @@ -2519,7 +2535,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.regulates (processual) false - regulates @@ -2543,7 +2558,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.negatively regulates (process to process) - negatively regulates @@ -2572,7 +2586,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.positively regulates (process to process) - positively regulates @@ -2776,6 +2789,10 @@ 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 @@ -3467,10 +3484,6 @@ 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 @@ -3589,6 +3602,7 @@ where http://www.geneontology.org/GO.annotation.conventions.shtml#colocalizes_with In the context of the Gene Ontology, colocalizes_with may be used for annotating to cellular component terms[GO] Gene Ontology Consortium + colocalizes with @@ -3616,6 +3630,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati Chris Mungall http://www.geneontology.org/GO.annotation.conventions.shtml#contributes_to In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology. + contributes to @@ -3833,10 +3848,6 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - - - - 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. Chris Mungall @@ -3896,10 +3907,6 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - - - - 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 end location of c is part of the region that surrounds s. Chris Mungall @@ -4167,6 +4174,12 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + + + + + + A lump of clay and a statue x spatially_coextensive_with y if and inly if x and y have the same location Chris Mungall @@ -6967,6 +6980,7 @@ the a supports either the existence of b, or the truth value of b. A sub-relation of endoparasite-of in which the parasite inhabits host cells. + intracellular endoparasite of @@ -6984,6 +6998,17 @@ the a supports either the existence of b, or the truth value of b. + + + + + Two or more individuals sharing the same roost site (cave, mine, tree or tree hollow, animal burrow, leaf tent, rock crack, space in man-made structure, etc.). Individuals that are sharing a communal roost may be said to be co-roosting. The roost may be either a day roost where the individuals rest during daytime hours, or a night roost where individuals roost to feed, groom, or rest in between flights and/or foraging bouts. Communal roosting as thus defined is an umbrella term within which different specialized types -- which are not mutually exclusive -- may be recognized based on taxonomy and the temporal and spatial relationships of the individuals that are co-roosting. + co-roosts with + + + + @@ -8187,6 +8212,20 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + pg + 2021-02-26T07:28:29Z + + + + results in fusion of + + + + diff --git a/subsets/ro-interaction.obo b/subsets/ro-interaction.obo index ce4681cb..8240e725 100644 --- a/subsets/ro-interaction.obo +++ b/subsets/ro-interaction.obo @@ -560,6 +560,14 @@ xref: RO:0002478 property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: child_nucleus_of ! child nucleus of +[Typedef] +id: co-roosts_with +name: co-roosts with +def: "Two or more individuals sharing the same roost site (cave, mine, tree or tree hollow, animal burrow, leaf tent, rock crack, space in man-made structure, etc.). Individuals that are sharing a communal roost may be said to be co-roosting. The roost may be either a day roost where the individuals rest during daytime hours, or a night roost where individuals roost to feed, groom, or rest in between flights and/or foraging bouts. Communal roosting as thus defined is an umbrella term within which different specialized types -- which are not mutually exclusive -- may be recognized based on taxonomy and the temporal and spatial relationships of the individuals that are co-roosting." [] +xref: RO:0002801 +is_symmetric: true +is_a: ecologically_co-occurs_with ! ecologically co-occurs with + [Typedef] id: coincident_with name: coincident with @@ -575,6 +583,7 @@ is_a: mereotopologically_related_to ! mereotopologically related to id: colocalizes_with name: colocalizes with def: "a colocalizes_with b if and only if a is transiently or peripherally associated with b[GO]." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term xref: RO:0002325 property_value: http://purl.org/dc/terms/creator "Gene Ontology Consortium" xsd:string property_value: IAO:0000112 "Clp1p relocalizes from the nucleolus to the spindle and site of cell division; i.e. it is associated transiently with the spindle pole body and the contractile ring (evidence from GFP fusion). Clp1p colocalizes_with spindle pole body (GO:0005816) and contractile ring (GO:0005826)" xsd:string @@ -709,6 +718,7 @@ is_a: mereotopologically_related_to ! mereotopologically related to [Typedef] id: contributes_to name: contributes to +subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term xref: RO:0002326 property_value: IAO:0000112 "ATP citrate lyase (ACL) in Arabidopsis: it is a heterooctamer, composed of two types of subunits, ACLA and ACLB in a A(4)B(4) stoichiometry. Neither of the subunits expressed alone give ACL activity, but co-expression results in ACL activity. Both subunits contribute_to the ATP citrate lyase activity." xsd:string property_value: IAO:0000112 "eIF2: has three subunits (alpha, beta, gamma); one binds GTP; one binds RNA; the whole complex binds the ribosome (all three subunits are required for ribosome binding). So one subunit is annotated to GTP binding and one to RNA binding without qualifiers, and all three stand in the contributes_to relationship to \"ribosome binding\". And all three are part_of an eIF2 complex" xsd:string @@ -2685,6 +2695,7 @@ id: intracellular_endoparasite_of name: intracellular endoparasite of def: "A sub-relation of endoparasite-of in which the parasite inhabits host cells." [] xref: RO:0002640 +property_value: IAO:0000119 Communal:roosting property_value: IAO:0000119 "Types" is_a: endoparasite_of ! endoparasite of inverse_of: has_intracellular_endoparasite ! has intracellular endoparasite @@ -3167,7 +3178,6 @@ id: negatively_regulates 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." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension -subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002212 @@ -3427,7 +3437,6 @@ id: positively_regulates 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." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension -subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002213 @@ -3604,7 +3613,6 @@ id: regulates 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." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension -subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002211 @@ -3876,6 +3884,17 @@ is_a: has_output ! has output is_a: results_in_developmental_progression_of ! results in developmental progression of inverse_of: formed_as_result_of ! formed as result of +[Typedef] +id: results_in_fusion_of +name: results in fusion of +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam +xref: RO:0012008 +is_a: results_in_organization_of ! results in organization of +created_by: pg +creation_date: 2021-02-26T07:28:29Z + [Typedef] id: results_in_growth_of name: results in growth of diff --git a/subsets/ro-interaction.owl b/subsets/ro-interaction.owl index 045c3fb2..f516fe1c 100644 --- a/subsets/ro-interaction.owl +++ b/subsets/ro-interaction.owl @@ -1685,7 +1685,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.false RO:0002211 - regulates @@ -1707,7 +1706,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. RO:0002212 - negatively_regulates @@ -1730,7 +1728,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. RO:0002213 - positively_regulates @@ -2686,6 +2683,7 @@ where In the context of the Gene Ontology, colocalizes_with may be used for annotating to cellular component terms[GO] Gene Ontology Consortium RO:0002325 + colocalizes_with colocalizes with @@ -2715,6 +2713,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati http://www.geneontology.org/GO.annotation.conventions.shtml#contributes_to In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology. RO:0002326 + contributes_to contributes to @@ -5711,6 +5710,7 @@ For example, A and B may be gene products and binding of B by A positively regul A sub-relation of endoparasite-of in which the parasite inhabits host cells. + RO:0002640 intracellular_endoparasite_of @@ -5732,6 +5732,19 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + Two or more individuals sharing the same roost site (cave, mine, tree or tree hollow, animal burrow, leaf tent, rock crack, space in man-made structure, etc.). Individuals that are sharing a communal roost may be said to be co-roosting. The roost may be either a day roost where the individuals rest during daytime hours, or a night roost where individuals roost to feed, groom, or rest in between flights and/or foraging bouts. Communal roosting as thus defined is an umbrella term within which different specialized types -- which are not mutually exclusive -- may be recognized based on taxonomy and the temporal and spatial relationships of the individuals that are co-roosting. + RO:0002801 + co-roosts_with + co-roosts with + + + + @@ -7003,6 +7016,22 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + pg + 2021-02-26T07:28:29Z + RO:0012008 + + + + results_in_fusion_of + results in fusion of + + + + diff --git a/subsets/ro-mereotopology.obo b/subsets/ro-mereotopology.obo index 741b97d3..575868e8 100644 --- a/subsets/ro-mereotopology.obo +++ b/subsets/ro-mereotopology.obo @@ -560,6 +560,14 @@ xref: RO:0002478 property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: child_nucleus_of ! child nucleus of +[Typedef] +id: co-roosts_with +name: co-roosts with +def: "Two or more individuals sharing the same roost site (cave, mine, tree or tree hollow, animal burrow, leaf tent, rock crack, space in man-made structure, etc.). Individuals that are sharing a communal roost may be said to be co-roosting. The roost may be either a day roost where the individuals rest during daytime hours, or a night roost where individuals roost to feed, groom, or rest in between flights and/or foraging bouts. Communal roosting as thus defined is an umbrella term within which different specialized types -- which are not mutually exclusive -- may be recognized based on taxonomy and the temporal and spatial relationships of the individuals that are co-roosting." [] +xref: RO:0002801 +is_symmetric: true +is_a: ecologically_co-occurs_with ! ecologically co-occurs with + [Typedef] id: coincident_with name: coincident with @@ -575,6 +583,7 @@ is_a: mereotopologically_related_to ! mereotopologically related to id: colocalizes_with name: colocalizes with def: "a colocalizes_with b if and only if a is transiently or peripherally associated with b[GO]." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term xref: RO:0002325 property_value: http://purl.org/dc/terms/creator "Gene Ontology Consortium" xsd:string property_value: IAO:0000112 "Clp1p relocalizes from the nucleolus to the spindle and site of cell division; i.e. it is associated transiently with the spindle pole body and the contractile ring (evidence from GFP fusion). Clp1p colocalizes_with spindle pole body (GO:0005816) and contractile ring (GO:0005826)" xsd:string @@ -709,6 +718,7 @@ is_a: mereotopologically_related_to ! mereotopologically related to [Typedef] id: contributes_to name: contributes to +subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term xref: RO:0002326 property_value: IAO:0000112 "ATP citrate lyase (ACL) in Arabidopsis: it is a heterooctamer, composed of two types of subunits, ACLA and ACLB in a A(4)B(4) stoichiometry. Neither of the subunits expressed alone give ACL activity, but co-expression results in ACL activity. Both subunits contribute_to the ATP citrate lyase activity." xsd:string property_value: IAO:0000112 "eIF2: has three subunits (alpha, beta, gamma); one binds GTP; one binds RNA; the whole complex binds the ribosome (all three subunits are required for ribosome binding). So one subunit is annotated to GTP binding and one to RNA binding without qualifiers, and all three stand in the contributes_to relationship to \"ribosome binding\". And all three are part_of an eIF2 complex" xsd:string @@ -2685,6 +2695,7 @@ id: intracellular_endoparasite_of name: intracellular endoparasite of def: "A sub-relation of endoparasite-of in which the parasite inhabits host cells." [] xref: RO:0002640 +property_value: IAO:0000119 Communal:roosting property_value: IAO:0000119 "Types" is_a: endoparasite_of ! endoparasite of inverse_of: has_intracellular_endoparasite ! has intracellular endoparasite @@ -3167,7 +3178,6 @@ id: negatively_regulates 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." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension -subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002212 @@ -3427,7 +3437,6 @@ id: positively_regulates 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." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension -subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002213 @@ -3604,7 +3613,6 @@ id: regulates 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." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension -subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002211 @@ -3876,6 +3884,17 @@ is_a: has_output ! has output is_a: results_in_developmental_progression_of ! results in developmental progression of inverse_of: formed_as_result_of ! formed as result of +[Typedef] +id: results_in_fusion_of +name: results in fusion of +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam +xref: RO:0012008 +is_a: results_in_organization_of ! results in organization of +created_by: pg +creation_date: 2021-02-26T07:28:29Z + [Typedef] id: results_in_growth_of name: results in growth of diff --git a/subsets/ro-mereotopology.owl b/subsets/ro-mereotopology.owl index 7cf84fdd..f49f5dfd 100644 --- a/subsets/ro-mereotopology.owl +++ b/subsets/ro-mereotopology.owl @@ -1685,7 +1685,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.false RO:0002211 - regulates @@ -1707,7 +1706,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. RO:0002212 - negatively_regulates @@ -1730,7 +1728,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. RO:0002213 - positively_regulates @@ -2686,6 +2683,7 @@ where In the context of the Gene Ontology, colocalizes_with may be used for annotating to cellular component terms[GO] Gene Ontology Consortium RO:0002325 + colocalizes_with colocalizes with @@ -2715,6 +2713,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati http://www.geneontology.org/GO.annotation.conventions.shtml#contributes_to In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology. RO:0002326 + contributes_to contributes to @@ -5711,6 +5710,7 @@ For example, A and B may be gene products and binding of B by A positively regul A sub-relation of endoparasite-of in which the parasite inhabits host cells. + RO:0002640 intracellular_endoparasite_of @@ -5732,6 +5732,19 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + Two or more individuals sharing the same roost site (cave, mine, tree or tree hollow, animal burrow, leaf tent, rock crack, space in man-made structure, etc.). Individuals that are sharing a communal roost may be said to be co-roosting. The roost may be either a day roost where the individuals rest during daytime hours, or a night roost where individuals roost to feed, groom, or rest in between flights and/or foraging bouts. Communal roosting as thus defined is an umbrella term within which different specialized types -- which are not mutually exclusive -- may be recognized based on taxonomy and the temporal and spatial relationships of the individuals that are co-roosting. + RO:0002801 + co-roosts_with + co-roosts with + + + + @@ -7003,6 +7016,22 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + pg + 2021-02-26T07:28:29Z + RO:0012008 + + + + results_in_fusion_of + results in fusion of + + + + diff --git a/subsets/ro-sequence.obo b/subsets/ro-sequence.obo index f4f16228..0fd6797c 100644 --- a/subsets/ro-sequence.obo +++ b/subsets/ro-sequence.obo @@ -560,6 +560,14 @@ xref: RO:0002478 property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: child_nucleus_of ! child nucleus of +[Typedef] +id: co-roosts_with +name: co-roosts with +def: "Two or more individuals sharing the same roost site (cave, mine, tree or tree hollow, animal burrow, leaf tent, rock crack, space in man-made structure, etc.). Individuals that are sharing a communal roost may be said to be co-roosting. The roost may be either a day roost where the individuals rest during daytime hours, or a night roost where individuals roost to feed, groom, or rest in between flights and/or foraging bouts. Communal roosting as thus defined is an umbrella term within which different specialized types -- which are not mutually exclusive -- may be recognized based on taxonomy and the temporal and spatial relationships of the individuals that are co-roosting." [] +xref: RO:0002801 +is_symmetric: true +is_a: ecologically_co-occurs_with ! ecologically co-occurs with + [Typedef] id: coincident_with name: coincident with @@ -575,6 +583,7 @@ is_a: mereotopologically_related_to ! mereotopologically related to id: colocalizes_with name: colocalizes with def: "a colocalizes_with b if and only if a is transiently or peripherally associated with b[GO]." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term xref: RO:0002325 property_value: http://purl.org/dc/terms/creator "Gene Ontology Consortium" xsd:string property_value: IAO:0000112 "Clp1p relocalizes from the nucleolus to the spindle and site of cell division; i.e. it is associated transiently with the spindle pole body and the contractile ring (evidence from GFP fusion). Clp1p colocalizes_with spindle pole body (GO:0005816) and contractile ring (GO:0005826)" xsd:string @@ -709,6 +718,7 @@ is_a: mereotopologically_related_to ! mereotopologically related to [Typedef] id: contributes_to name: contributes to +subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term xref: RO:0002326 property_value: IAO:0000112 "ATP citrate lyase (ACL) in Arabidopsis: it is a heterooctamer, composed of two types of subunits, ACLA and ACLB in a A(4)B(4) stoichiometry. Neither of the subunits expressed alone give ACL activity, but co-expression results in ACL activity. Both subunits contribute_to the ATP citrate lyase activity." xsd:string property_value: IAO:0000112 "eIF2: has three subunits (alpha, beta, gamma); one binds GTP; one binds RNA; the whole complex binds the ribosome (all three subunits are required for ribosome binding). So one subunit is annotated to GTP binding and one to RNA binding without qualifiers, and all three stand in the contributes_to relationship to \"ribosome binding\". And all three are part_of an eIF2 complex" xsd:string @@ -2685,6 +2695,7 @@ id: intracellular_endoparasite_of name: intracellular endoparasite of def: "A sub-relation of endoparasite-of in which the parasite inhabits host cells." [] xref: RO:0002640 +property_value: IAO:0000119 Communal:roosting property_value: IAO:0000119 "Types" is_a: endoparasite_of ! endoparasite of inverse_of: has_intracellular_endoparasite ! has intracellular endoparasite @@ -3167,7 +3178,6 @@ id: negatively_regulates 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." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension -subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002212 @@ -3427,7 +3437,6 @@ id: positively_regulates 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." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension -subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002213 @@ -3604,7 +3613,6 @@ id: regulates 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." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension -subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002211 @@ -3876,6 +3884,17 @@ is_a: has_output ! has output is_a: results_in_developmental_progression_of ! results in developmental progression of inverse_of: formed_as_result_of ! formed as result of +[Typedef] +id: results_in_fusion_of +name: results in fusion of +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam +xref: RO:0012008 +is_a: results_in_organization_of ! results in organization of +created_by: pg +creation_date: 2021-02-26T07:28:29Z + [Typedef] id: results_in_growth_of name: results in growth of diff --git a/subsets/ro-sequence.owl b/subsets/ro-sequence.owl index 5ec1445e..7cab64a1 100644 --- a/subsets/ro-sequence.owl +++ b/subsets/ro-sequence.owl @@ -1685,7 +1685,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.false RO:0002211 - regulates @@ -1707,7 +1706,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. RO:0002212 - negatively_regulates @@ -1730,7 +1728,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. RO:0002213 - positively_regulates @@ -2686,6 +2683,7 @@ where In the context of the Gene Ontology, colocalizes_with may be used for annotating to cellular component terms[GO] Gene Ontology Consortium RO:0002325 + colocalizes_with colocalizes with @@ -2715,6 +2713,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati http://www.geneontology.org/GO.annotation.conventions.shtml#contributes_to In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology. RO:0002326 + contributes_to contributes to @@ -5711,6 +5710,7 @@ For example, A and B may be gene products and binding of B by A positively regul A sub-relation of endoparasite-of in which the parasite inhabits host cells. + RO:0002640 intracellular_endoparasite_of @@ -5732,6 +5732,19 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + Two or more individuals sharing the same roost site (cave, mine, tree or tree hollow, animal burrow, leaf tent, rock crack, space in man-made structure, etc.). Individuals that are sharing a communal roost may be said to be co-roosting. The roost may be either a day roost where the individuals rest during daytime hours, or a night roost where individuals roost to feed, groom, or rest in between flights and/or foraging bouts. Communal roosting as thus defined is an umbrella term within which different specialized types -- which are not mutually exclusive -- may be recognized based on taxonomy and the temporal and spatial relationships of the individuals that are co-roosting. + RO:0002801 + co-roosts_with + co-roosts with + + + + @@ -7003,6 +7016,22 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + pg + 2021-02-26T07:28:29Z + RO:0012008 + + + + results_in_fusion_of + results in fusion of + + + + diff --git a/subsets/ro-time-interval.obo b/subsets/ro-time-interval.obo index 0ea762d0..6b9ab4bd 100644 --- a/subsets/ro-time-interval.obo +++ b/subsets/ro-time-interval.obo @@ -560,6 +560,14 @@ xref: RO:0002478 property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: child_nucleus_of ! child nucleus of +[Typedef] +id: co-roosts_with +name: co-roosts with +def: "Two or more individuals sharing the same roost site (cave, mine, tree or tree hollow, animal burrow, leaf tent, rock crack, space in man-made structure, etc.). Individuals that are sharing a communal roost may be said to be co-roosting. The roost may be either a day roost where the individuals rest during daytime hours, or a night roost where individuals roost to feed, groom, or rest in between flights and/or foraging bouts. Communal roosting as thus defined is an umbrella term within which different specialized types -- which are not mutually exclusive -- may be recognized based on taxonomy and the temporal and spatial relationships of the individuals that are co-roosting." [] +xref: RO:0002801 +is_symmetric: true +is_a: ecologically_co-occurs_with ! ecologically co-occurs with + [Typedef] id: coincident_with name: coincident with @@ -575,6 +583,7 @@ is_a: mereotopologically_related_to ! mereotopologically related to id: colocalizes_with name: colocalizes with def: "a colocalizes_with b if and only if a is transiently or peripherally associated with b[GO]." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term xref: RO:0002325 property_value: http://purl.org/dc/terms/creator "Gene Ontology Consortium" xsd:string property_value: IAO:0000112 "Clp1p relocalizes from the nucleolus to the spindle and site of cell division; i.e. it is associated transiently with the spindle pole body and the contractile ring (evidence from GFP fusion). Clp1p colocalizes_with spindle pole body (GO:0005816) and contractile ring (GO:0005826)" xsd:string @@ -709,6 +718,7 @@ is_a: mereotopologically_related_to ! mereotopologically related to [Typedef] id: contributes_to name: contributes to +subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term xref: RO:0002326 property_value: IAO:0000112 "ATP citrate lyase (ACL) in Arabidopsis: it is a heterooctamer, composed of two types of subunits, ACLA and ACLB in a A(4)B(4) stoichiometry. Neither of the subunits expressed alone give ACL activity, but co-expression results in ACL activity. Both subunits contribute_to the ATP citrate lyase activity." xsd:string property_value: IAO:0000112 "eIF2: has three subunits (alpha, beta, gamma); one binds GTP; one binds RNA; the whole complex binds the ribosome (all three subunits are required for ribosome binding). So one subunit is annotated to GTP binding and one to RNA binding without qualifiers, and all three stand in the contributes_to relationship to \"ribosome binding\". And all three are part_of an eIF2 complex" xsd:string @@ -2685,6 +2695,7 @@ id: intracellular_endoparasite_of name: intracellular endoparasite of def: "A sub-relation of endoparasite-of in which the parasite inhabits host cells." [] xref: RO:0002640 +property_value: IAO:0000119 Communal:roosting property_value: IAO:0000119 "Types" is_a: endoparasite_of ! endoparasite of inverse_of: has_intracellular_endoparasite ! has intracellular endoparasite @@ -3167,7 +3178,6 @@ id: negatively_regulates 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." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension -subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002212 @@ -3427,7 +3437,6 @@ id: positively_regulates 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." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension -subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002213 @@ -3604,7 +3613,6 @@ id: regulates 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." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension -subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002211 @@ -3876,6 +3884,17 @@ is_a: has_output ! has output is_a: results_in_developmental_progression_of ! results in developmental progression of inverse_of: formed_as_result_of ! formed as result of +[Typedef] +id: results_in_fusion_of +name: results in fusion of +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam +xref: RO:0012008 +is_a: results_in_organization_of ! results in organization of +created_by: pg +creation_date: 2021-02-26T07:28:29Z + [Typedef] id: results_in_growth_of name: results in growth of diff --git a/subsets/ro-time-interval.owl b/subsets/ro-time-interval.owl index 65991efd..a5404265 100644 --- a/subsets/ro-time-interval.owl +++ b/subsets/ro-time-interval.owl @@ -1685,7 +1685,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.false RO:0002211 - regulates @@ -1707,7 +1706,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. RO:0002212 - negatively_regulates @@ -1730,7 +1728,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. RO:0002213 - positively_regulates @@ -2686,6 +2683,7 @@ where In the context of the Gene Ontology, colocalizes_with may be used for annotating to cellular component terms[GO] Gene Ontology Consortium RO:0002325 + colocalizes_with colocalizes with @@ -2715,6 +2713,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati http://www.geneontology.org/GO.annotation.conventions.shtml#contributes_to In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology. RO:0002326 + contributes_to contributes to @@ -5711,6 +5710,7 @@ For example, A and B may be gene products and binding of B by A positively regul A sub-relation of endoparasite-of in which the parasite inhabits host cells. + RO:0002640 intracellular_endoparasite_of @@ -5732,6 +5732,19 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + Two or more individuals sharing the same roost site (cave, mine, tree or tree hollow, animal burrow, leaf tent, rock crack, space in man-made structure, etc.). Individuals that are sharing a communal roost may be said to be co-roosting. The roost may be either a day roost where the individuals rest during daytime hours, or a night roost where individuals roost to feed, groom, or rest in between flights and/or foraging bouts. Communal roosting as thus defined is an umbrella term within which different specialized types -- which are not mutually exclusive -- may be recognized based on taxonomy and the temporal and spatial relationships of the individuals that are co-roosting. + RO:0002801 + co-roosts_with + co-roosts with + + + + @@ -7003,6 +7016,22 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + pg + 2021-02-26T07:28:29Z + RO:0012008 + + + + results_in_fusion_of + results in fusion of + + + +