From 51f14f51cd4f595205f7e54f8f499428b5148834 Mon Sep 17 00:00:00 2001 From: matentzn Date: Tue, 3 Dec 2019 10:41:34 +0000 Subject: [PATCH] Release 3 Dec 2019 --- pato-base.json | 458 +++---- pato-base.obo | 21 +- pato-base.owl | 77 +- pato-full.json | 3173 ++++----------------------------------------- pato-full.obo | 1770 +++++++------------------ pato-full.owl | 2760 ++------------------------------------- pato-simple.json | 637 ++++----- pato-simple.obo | 77 +- pato-simple.owl | 152 +-- pato.json | 3199 ++++------------------------------------------ pato.obo | 77 +- pato.owl | 2756 ++------------------------------------- 12 files changed, 1911 insertions(+), 13246 deletions(-) diff --git a/pato-base.json b/pato-base.json index b476ae9f..ae7e8865 100644 --- a/pato-base.json +++ b/pato-base.json @@ -7056,6 +7056,32 @@ }, "type" : "CLASS", "lbl" : "flared" + }, { + "id" : "http://purl.obolibrary.org/obo/PATO_0040027", + "meta" : { + "definition" : { + "val" : "A ploidy quality inhering in a bearer by virtue of the bearer's haploid cells undergo chromosome doubling.", + "xrefs" : [ "Wikipedia:https://en.wikipedia.org/wiki/Doubled_haploidy" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "double haploid", + "xrefs" : [ ] + }, { + "pred" : "hasExactSynonym", + "val" : "double-haploid", + "xrefs" : [ ] + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "quality" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "http://orcid.org/0000-0001-5208-3432" + } ] + }, + "type" : "CLASS", + "lbl" : "doubled haploid" }, { "id" : "http://purl.obolibrary.org/obo/PATO_0000808", "meta" : { @@ -34239,7 +34265,7 @@ "id" : "http://purl.obolibrary.org/obo/PATO_0045075", "meta" : { "definition" : { - "val" : "A variability which is relatively normal or average", + "val" : "A variability of color which is relatively normal or average", "xrefs" : [ ] }, "subsets" : [ "http://purl.obolibrary.org/obo/pato#value_slim" ], @@ -48361,7 +48387,7 @@ "id" : "http://purl.obolibrary.org/obo/PATO_0001384", "meta" : { "definition" : { - "val" : "A polyploidy quality inhering in a bearer by virtue of the bearer's containing four homologous sets of chromosomes.", + "val" : "A polyploidy quality inhering in a bearer by virtue of the bearer's containing six homologous sets of chromosomes.", "xrefs" : [ "Wikipedia:http://en.wikipedia.org/wiki/Hexaploid" ] }, "subsets" : [ "http://purl.obolibrary.org/obo/pato#cell_quality", "http://purl.obolibrary.org/obo/pato#value_slim" ], @@ -49921,14 +49947,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0001629", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000330" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0002178", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0000628" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001729", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001995" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0002178", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0000628" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0005004", "pred" : "is_a", @@ -50233,14 +50259,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0002189", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0002182" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0001632", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0000140" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001516", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001300" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0001632", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0000140" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001465", "pred" : "is_a", @@ -50250,17 +50276,17 @@ "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001590" }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0001659", + "sub" : "http://purl.obolibrary.org/obo/PATO_0000912", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0001599" + "obj" : "http://purl.obolibrary.org/obo/PATO_0002304" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0000941", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0002014" }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0000912", + "sub" : "http://purl.obolibrary.org/obo/PATO_0001659", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0002304" + "obj" : "http://purl.obolibrary.org/obo/PATO_0001599" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0045070", "pred" : "is_a", @@ -50593,14 +50619,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0015005", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000052" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0001777", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0002303" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001825", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001823" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0001777", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0002303" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001054", "pred" : "is_a", @@ -50785,14 +50811,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0001773", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000083" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0045047", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0001178" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001643", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000052" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0045047", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0001178" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001402", "pred" : "is_a", @@ -50925,14 +50951,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0001964", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000405" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0000998", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0000992" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002507", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000025" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0000998", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0000992" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0025001", "pred" : "is_a", @@ -51141,14 +51167,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0001965", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000405" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0002351", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0000025" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001877", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001419" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0002351", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0000025" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002140", "pred" : "is_a", @@ -51157,14 +51183,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0002541", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001995" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0002331", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0001431" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002460", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000141" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0002331", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0001431" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0000261", "pred" : "is_a", @@ -51557,14 +51583,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0000964", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000957" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0002091", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0001309" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001627", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001626" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0002091", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0001309" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001594", "pred" : "is_a", @@ -51641,14 +51667,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0001626", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001509" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0001963", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0000405" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001903", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000039" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0001963", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0000405" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002148", "pred" : "is_a", @@ -51697,14 +51723,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0002498", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000133" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0000944", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0000052" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002124", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000141" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0000944", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0000052" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002366", "pred" : "is_a", @@ -51797,14 +51823,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0002151", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001785" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0002018", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0002016" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002201", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000186" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0002018", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0002016" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002326", "pred" : "is_a", @@ -51845,6 +51871,10 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0002467", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000052" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0040027", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0001393" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002057", "pred" : "is_a", @@ -51941,14 +51971,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0001418", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0002265" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0001487", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0000011" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001372", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001294" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0001487", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0000011" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002322", "pred" : "is_a", @@ -52289,14 +52319,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0000015", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001301" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0001934", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0000411" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001961", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000141" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0001934", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0000411" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0045004", "pred" : "is_a", @@ -52449,14 +52479,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0001440", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001531" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0002376", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0002014" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001855", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000140" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0002376", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0002014" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001619", "pred" : "is_a", @@ -52529,14 +52559,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0002029", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0002027" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0040014", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0000052" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0045009", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000404" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0040014", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0000052" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002150", "pred" : "is_a", @@ -53021,14 +53051,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0045016", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0045001" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0000992", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0001548" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001997", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0002301" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0000992", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0001548" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002348", "pred" : "is_a", @@ -53289,14 +53319,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0000643", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001598" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0002050", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0000467" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002138", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001018" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0002050", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0000467" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0045013", "pred" : "is_a", @@ -53325,14 +53355,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0001873", "pred" : "http://purl.obolibrary.org/obo/pato#has_cross_section", "obj" : "http://purl.obolibrary.org/obo/PATO_0000411" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0000946", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0002006" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002132", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0002011" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0000946", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0002006" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001384", "pred" : "is_a", @@ -53441,14 +53471,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0000299", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000004" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0001923", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0000628" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001884", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001018" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0001923", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0000628" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001742", "pred" : "is_a", @@ -53593,22 +53623,22 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0002172", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001786" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0002279", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0002278" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002299", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0002078" }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0002306", + "sub" : "http://purl.obolibrary.org/obo/PATO_0002279", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0001875" + "obj" : "http://purl.obolibrary.org/obo/PATO_0002278" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002101", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001397" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0002306", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0001875" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002262", "pred" : "is_a", @@ -53753,14 +53783,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0001552", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001457" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0045073", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0001236" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0045051", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001323" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0045073", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0001236" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001739", "pred" : "is_a", @@ -53865,14 +53895,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0002283", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0002303" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0000634", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0000060" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0000626", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000140" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0000634", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0000060" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002370", "pred" : "is_a", @@ -54369,14 +54399,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0002304", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0002300" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0002328", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0002326" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0000757", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000185" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0002328", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0002326" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002111", "pred" : "is_a", @@ -54509,14 +54539,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0001333", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0002304" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0001675", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0001678" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0045013", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000406" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0001675", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0001678" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001229", "pred" : "is_a", @@ -54569,14 +54599,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0000375", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000040" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0045049", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0045001" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001193", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000140" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0045049", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0045001" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0045057", "pred" : "is_a", @@ -54621,14 +54651,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0000011", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000165" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0001861", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0002013" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001875", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0002006" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0001861", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0002013" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0000152", "pred" : "is_a", @@ -54869,14 +54899,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0000141", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000051" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0002052", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0002302" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0000021", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000186" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0002052", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0002302" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001876", "pred" : "is_a", @@ -54893,14 +54923,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0001833", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0002303" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0005008", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0002266" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001230", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001018" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0005008", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0002266" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0000276", "pred" : "is_a", @@ -55073,14 +55103,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0001951", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000060" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0001278", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0000953" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0000938", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0002264" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0001278", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0000953" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0000636", "pred" : "is_a", @@ -55161,14 +55191,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0001890", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000402" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0002075", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0002303" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0000633", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000060" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0002075", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0002303" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001843", "pred" : "is_a", @@ -55185,14 +55215,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0005007", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0002266" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0002430", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0000052" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0000638", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000141" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0002430", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0000052" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002062", "pred" : "is_a", @@ -55237,14 +55267,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0001830", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0002303" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0002135", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0000502" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002180", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000052" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0002135", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0000502" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002167", "pred" : "is_a", @@ -55465,14 +55495,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0001470", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001018" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0002000", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0001999" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002023", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001769" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0002000", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0001999" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002422", "pred" : "is_a", @@ -55821,14 +55851,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0001636", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001634" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0001528", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0001519" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001893", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001331" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0001528", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0001519" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0000018", "pred" : "is_a", @@ -56005,14 +56035,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0005015", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000117" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0001567", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0000060" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001990", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001309" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0001567", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0000060" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0005012", "pred" : "is_a", @@ -56069,14 +56099,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0001746", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001744" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0001748", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0001857" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001758", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001757" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0001748", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0001857" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002632", "pred" : "is_a", @@ -56285,14 +56315,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0005011", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000140" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0000574", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0000122" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0045062", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001537" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0000574", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0000122" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001275", "pred" : "is_a", @@ -56461,14 +56491,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0002214", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001979" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0001743", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0001741" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001776", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001544" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0001743", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0001741" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001606", "pred" : "is_a", @@ -56477,14 +56507,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0002106", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0002099" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0002078", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0002014" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002054", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0002254" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0002078", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0002014" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002403", "pred" : "is_a", @@ -56549,14 +56579,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0000462", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000070" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0001744", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0001739" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0000488", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000077" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0001744", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0001739" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0000330", "pred" : "is_a", @@ -56601,14 +56631,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0002034", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000052" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0001161", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0000033" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001306", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000146" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0001161", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0000033" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0005024", "pred" : "is_a", @@ -56713,14 +56743,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0040021", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000467" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0002503", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0000133" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001576", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001025" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0002503", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0000133" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001405", "pred" : "is_a", @@ -57069,26 +57099,26 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0015012", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001547" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0001874", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0001873" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002405", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000141" }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0001290", + "sub" : "http://purl.obolibrary.org/obo/PATO_0001874", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0000018" + "obj" : "http://purl.obolibrary.org/obo/PATO_0001873" }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0002534", + "sub" : "http://purl.obolibrary.org/obo/PATO_0001290", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0000052" + "obj" : "http://purl.obolibrary.org/obo/PATO_0000018" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001753", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001752" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0002534", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0000052" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002123", "pred" : "is_a", @@ -57261,14 +57291,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0001454", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000085" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0000632", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0000965" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002501", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000133" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0000632", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0000965" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002407", "pred" : "is_a", @@ -57653,14 +57683,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0002168", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000133" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0045092", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0045090" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002149", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001788" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0045092", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0045090" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001554", "pred" : "is_a", @@ -57697,14 +57727,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0001302", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000014" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0001321", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0002326" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0000761", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001707" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0001321", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0002326" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001826", "pred" : "is_a", @@ -57857,14 +57887,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0001194", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0002303" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0002155", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0001599" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002261", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000140" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0002155", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0001599" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001793", "pred" : "is_a", @@ -58003,22 +58033,22 @@ "subsets" : [ ], "xrefs" : [ ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#auto-generated-by", - "val" : "OBO-Edit 2.3.1" + "pred" : "http://purl.org/dc/elements/1.1/description", + "val" : "An ontology of phenotypic qualities (properties, attributes or characteristics)." + }, { + "pred" : "http://purl.org/dc/elements/1.1/title", + "val" : "PATO - the Phenotype And Trait Ontology" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#date", - "val" : "07:02:2018 10:27" + "pred" : "http://purl.org/dc/terms/license", + "val" : "https://creativecommons.org/licenses/by/3.0/" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#default-namespace", "val" : "quality" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBOFormatVersion", "val" : "1.2" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#saved-by", - "val" : "segerdel" } ], - "version" : "http://purl.obolibrary.org/obo/pato/releases/2019-11-05/pato-base.json" + "version" : "http://purl.obolibrary.org/obo/pato/releases/2019-12-03/pato-base.json" }, "equivalentNodesSets" : [ ], "logicalDefinitionAxioms" : [ { @@ -59906,17 +59936,17 @@ "fillerId" : "http://purl.obolibrary.org/obo/PATO_0000461" } ] }, { - "definedClassId" : "http://purl.obolibrary.org/obo/PATO_0045051", - "genusIds" : [ "http://purl.obolibrary.org/obo/PATO_0001323" ], + "definedClassId" : "http://purl.obolibrary.org/obo/PATO_0001664", + "genusIds" : [ "http://purl.obolibrary.org/obo/PATO_0001537" ], "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/pato#has_relative_magnitude", + "propertyId" : "http://purl.obolibrary.org/obo/pato#decreased_in_magnitude_relative_to", "fillerId" : "http://purl.obolibrary.org/obo/PATO_0000461" } ] }, { - "definedClassId" : "http://purl.obolibrary.org/obo/PATO_0001664", - "genusIds" : [ "http://purl.obolibrary.org/obo/PATO_0001537" ], + "definedClassId" : "http://purl.obolibrary.org/obo/PATO_0045051", + "genusIds" : [ "http://purl.obolibrary.org/obo/PATO_0001323" ], "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/pato#decreased_in_magnitude_relative_to", + "propertyId" : "http://purl.obolibrary.org/obo/pato#has_relative_magnitude", "fillerId" : "http://purl.obolibrary.org/obo/PATO_0000461" } ] }, { diff --git a/pato-base.obo b/pato-base.obo index 198d43c0..7074c48a 100644 --- a/pato-base.obo +++ b/pato-base.obo @@ -1,8 +1,5 @@ format-version: 1.2 -data-version: pato/releases/2019-11-05/pato-base.owl -date: 07:02:2018 10:27 -saved-by: segerdel -auto-generated-by: OBO-Edit 2.3.1 +data-version: pato/releases/2019-12-03/pato-base.owl subsetdef: abnormal_slim "Abnormal/normal slim" subsetdef: absent_slim "Absent/present slim" subsetdef: attribute_slim "Attribute slim" @@ -15,6 +12,9 @@ subsetdef: scalar_slim "Scalar slim" subsetdef: value_slim "Value slim" default-namespace: quality ontology: pato/pato-base +property_value: http://purl.org/dc/elements/1.1/description "An ontology of phenotypic qualities (properties, attributes or characteristics)." xsd:string +property_value: http://purl.org/dc/elements/1.1/title "PATO - the Phenotype And Trait Ontology" xsd:string +property_value: http://purl.org/dc/terms/license https://creativecommons.org/licenses/by/3.0/ xsd:string [Term] id: PATO:0000000 @@ -8768,7 +8768,7 @@ is_a: PATO:0001377 ! polyploid [Term] id: PATO:0001384 name: hexaploid -def: "A polyploidy quality inhering in a bearer by virtue of the bearer's containing four homologous sets of chromosomes." [Wikipedia:http\://en.wikipedia.org/wiki/Hexaploid] +def: "A polyploidy quality inhering in a bearer by virtue of the bearer's containing six homologous sets of chromosomes." [Wikipedia:http\://en.wikipedia.org/wiki/Hexaploid] subset: cell_quality subset: value_slim is_a: PATO:0001377 ! polyploid @@ -20420,6 +20420,15 @@ synonym: "structurally interrupted" EXACT [] is_a: PATO:0001241 ! physical object quality created_by: http://orcid.org/0000-0001-5208-3432 +[Term] +id: PATO:0040027 +name: doubled haploid +def: "A ploidy quality inhering in a bearer by virtue of the bearer's haploid cells undergo chromosome doubling." [Wikipedia:https\://en.wikipedia.org/wiki/Doubled_haploidy] +synonym: "double haploid" EXACT [] +synonym: "double-haploid" EXACT [] +is_a: PATO:0001393 ! euploid +created_by: http://orcid.org/0000-0001-5208-3432 + [Term] id: PATO:0045000 name: normal rate @@ -21351,7 +21360,7 @@ creation_date: 2017-12-22T14:16:43Z [Term] id: PATO:0045075 name: normal variability of color -def: "A variability which is relatively normal or average" [] +def: "A variability of color which is relatively normal or average" [] subset: value_slim intersection_of: PATO:0001615 ! variant color intersection_of: has_relative_magnitude PATO:0000461 ! normal diff --git a/pato-base.owl b/pato-base.owl index 2bc414ef..ce33a6e1 100644 --- a/pato-base.owl +++ b/pato-base.owl @@ -9,14 +9,15 @@ xmlns:xsd="http://www.w3.org/2001/XMLSchema#" xmlns:pato="http://purl.obolibrary.org/obo/pato#" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" + xmlns:terms="http://purl.org/dc/terms/" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - - OBO-Edit 2.3.1 - 07:02:2018 10:27 + + An ontology of phenotypic qualities (properties, attributes or characteristics). + PATO - the Phenotype And Trait Ontology + https://creativecommons.org/licenses/by/3.0/ quality 1.2 - segerdel @@ -172,12 +173,6 @@ - - - - - - @@ -198,12 +193,6 @@ - - - - - - @@ -300,12 +289,6 @@ - - - - - - @@ -21307,7 +21290,7 @@ Association is weaker than correlation or proportionality. These relations may b - A polyploidy quality inhering in a bearer by virtue of the bearer's containing four homologous sets of chromosomes. + A polyploidy quality inhering in a bearer by virtue of the bearer's containing six homologous sets of chromosomes. quality PATO:0001384 @@ -21317,7 +21300,7 @@ Association is weaker than correlation or proportionality. These relations may b - A polyploidy quality inhering in a bearer by virtue of the bearer's containing four homologous sets of chromosomes. + A polyploidy quality inhering in a bearer by virtue of the bearer's containing six homologous sets of chromosomes. Wikipedia:http://en.wikipedia.org/wiki/Hexaploid @@ -49547,6 +49530,27 @@ height'). + + + + + A ploidy quality inhering in a bearer by virtue of the bearer's haploid cells undergo chromosome doubling. + http://orcid.org/0000-0001-5208-3432 + double haploid + double-haploid + quality + PATO:0040027 + doubled haploid + + + + + A ploidy quality inhering in a bearer by virtue of the bearer's haploid cells undergo chromosome doubling. + Wikipedia:https://en.wikipedia.org/wiki/Doubled_haploidy + + + + @@ -51614,7 +51618,7 @@ height'). - A variability which is relatively normal or average + A variability of color which is relatively normal or average Luke Slater 2017-12-22T14:16:43Z quality @@ -52274,29 +52278,34 @@ height'). --> - + + - + - + - + - - - + + + + + + + - + - + diff --git a/pato-full.json b/pato-full.json index 53ca5621..fd9d263d 100644 --- a/pato-full.json +++ b/pato-full.json @@ -183,46 +183,6 @@ }, "type" : "CLASS", "lbl" : "obsolete mild response" - }, { - "id" : "http://purl.obolibrary.org/obo/PCO_0000004", - "meta" : { - "definition" : { - "val" : "A quality that inheres in a community.", - "xrefs" : [ ] - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000428" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "These may not belong under BFO:quality. May be better to call them community characteristics, and classify as specifically dependent continuants. Need to look at process profiles in BFO2." - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", - "val" : "Includes qualities like diversity, species richness, stability, resilience, community structure, number of trophic levels. A community quality may depend on the qualities of individual organism in the community, but cannot be measured or described for a single individual." - } ] - }, - "type" : "CLASS", - "lbl" : "quality of an ecological community" - }, { - "id" : "http://purl.obolibrary.org/obo/PCO_0000003", - "meta" : { - "definition" : { - "val" : "A quality that inheres in a biological population.", - "xrefs" : [ ] - }, - "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", - "val" : "Includes qualities like population size, population growth rate, carrying capacity, immigration rate, emigration rate, fecundity, and death rate. A population quality may depend on the qualities of individual organisms in the population, but cannot be measured or described for a single organism. This term may be replaced by a PATO term." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "See Chris's comments on population qualities at: http://code.google.com/p/popcomm-ontology/issues/detail?id=4. These may not belong under BFO:quality. May be better to call them population characteristics, and classify as specifically dependent continuants. Need to look at process profiles in BFO2." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000428" - } ] - }, - "type" : "CLASS", - "lbl" : "quality of a population" }, { "id" : "http://purl.obolibrary.org/obo/PATO_0000499", "meta" : { @@ -415,43 +375,6 @@ }, "type" : "CLASS", "lbl" : "obsolete phase value" - }, { - "id" : "http://purl.obolibrary.org/obo/PCO_0000017", - "meta" : { - "definition" : { - "val" : "A collection of organisms that has as parts every organism of given species and no organisms of any other species.", - "xrefs" : [ ] - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "At the moment there is no way to specify in an OWL axiom that the collection includes every individual of a species. This should be added, if possible." - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", - "val" : "This term is neutral with respect to which organisms are included in a species. Membership will depend on the species concept and the taxonomic assertions used to define the species. These criteria must be specified by the user." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000120" - } ] - }, - "type" : "CLASS", - "lbl" : "species as a collection of organisms" - }, { - "id" : "http://purl.obolibrary.org/obo/PCO_0000018", - "meta" : { - "definition" : { - "val" : "A material entity that has as parts two or more organisms, viruses, or viroids of the same species and no members of any other species.", - "xrefs" : [ ] - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "collection of organisms of the same species" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000120" - } ] - }, - "type" : "CLASS", - "lbl" : "single-species collection of organisms" }, { "id" : "http://purl.obolibrary.org/obo/PATO_0002205", "meta" : { @@ -668,32 +591,6 @@ }, "type" : "CLASS", "lbl" : "vaporizability" - }, { - "id" : "http://purl.obolibrary.org/obo/PCO_0000000", - "meta" : { - "definition" : { - "val" : "A material entity that consists of two or more organisms, viruses, or viroids.", - "xrefs" : [ ] - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "group of organism" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", - "val" : "May be of the same or different species." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "Examples include: population, community, species (meaning the collection of organisms that makes up a species, not the taxonomic rank), and family." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "organism collection" - } ] - }, - "type" : "CLASS", - "lbl" : "collection of organisms" }, { "id" : "http://purl.obolibrary.org/obo/RO_0000080", "meta" : { @@ -717,58 +614,6 @@ }, "type" : "PROPERTY", "lbl" : "quality of" - }, { - "id" : "http://purl.obolibrary.org/obo/PCO_0000002", - "meta" : { - "definition" : { - "val" : "A community of at least two different species, living in a particular area. Must have at least two populations of different species as members.", - "xrefs" : [ ] - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "ISBN:0865423504" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000123" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "multispecies community" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", - "val" : "Ecological community is defined broadly here, but includes both ecological interactions (inherited from parent term community) and spatial co-existence. It may be used to describe every organisms living in an area, but is often used to refer only to organisms of a particular taxon or guild (e.g., the plant community, the insect community, the herbivore community). The word community, as it often used to describe a group of humans living together, is a type of single-species collection of organisms, not an ecological community." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Not sure if the equivalancy axiom specifies that both populations are located in the same site." - } ] - }, - "type" : "CLASS", - "lbl" : "ecological community" - }, { - "id" : "http://purl.obolibrary.org/obo/PCO_0000001", - "meta" : { - "definition" : { - "val" : "A collection of organisms, all of the same species, that live in the same place.", - "xrefs" : [ ] - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "This a general term that can include every organism of a species living in an area or any subset of them. Subclasses can be more specific as needed." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "ISBN:0878932739" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", - "val" : "It is sometimes difficult to define the physical boundaries of a population. In the case of sexually reproducing organisms, the individuals within a population have the potential to reproduce with one another during the course of their lifetimes. 'Community', as often used to describe a group of humans, is a type of population. \n\nClasses for population already exist in IDO ('organism population', IDO_0000509) and OBI ('population', OBI_0000181). The definitions should be standardized across OBO Foundry ontologies and only one term used." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - } ] - }, - "type" : "CLASS", - "lbl" : "population of organisms" }, { "id" : "http://purl.obolibrary.org/obo/PATO_0002216", "meta" : { @@ -940,21 +785,12 @@ "val" : "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence", "xrefs" : [ ] }, - "xrefs" : [ { - "val" : "RO:0000086" - } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "has_quality" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "this apple has quality this red color" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "has_quality" @@ -1845,20 +1681,6 @@ }, "type" : "CLASS", "lbl" : "increased intensity" - }, { - "id" : "http://purl.obolibrary.org/obo/PCO_0000031", - "meta" : { - "definition" : { - "val" : "A material entity that is one or more organisms, viruses or viroids.", - "xrefs" : [ ] - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - } ] - }, - "type" : "CLASS", - "lbl" : "organismal entity" }, { "id" : "http://purl.obolibrary.org/obo/PATO_0001798", "meta" : { @@ -2075,15 +1897,9 @@ "val" : "a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence", "xrefs" : [ ] }, - "xrefs" : [ { - "val" : "RO:0000053" - } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist." - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "this apple is bearer of this red color" @@ -2102,9 +1918,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "bearer of" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "bearer_of" } ] }, "type" : "PROPERTY", @@ -2357,66 +2170,6 @@ }, "type" : "CLASS", "lbl" : "right side of" - }, { - "id" : "http://purl.obolibrary.org/obo/PCO_0000028", - "meta" : { - "definition" : { - "val" : "A collection of organisms of the same species whose members are all either genealogically related to each other or have mated with each other.", - "xrefs" : [ ] - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Biological or social relations are covered by RO_0002437 (biotically interacts with), but that relations does provide an easy way to specify that two entities are interacting with each other (participating in the same interaction). Until that axiom is specified, the logical definition of this term is incomplete." - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", - "val" : "These relations can include shared values, occupying the same spatial regkion. A community be be a single species collection of organsisms (as in a human community, which is also a type of population) or a or multi-species collection of organisms (as in an ecological community)." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000123" - } ] - }, - "type" : "CLASS", - "lbl" : "community" - }, { - "id" : "http://purl.obolibrary.org/obo/PCO_0000027", - "meta" : { - "definition" : { - "val" : "A collection of organisms of the same species that has as members only humans.", - "xrefs" : [ ] - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "human population" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "human community" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - } ] - }, - "type" : "CLASS", - "lbl" : "collection of humans" - }, { - "id" : "http://purl.obolibrary.org/obo/PCO_0000029", - "meta" : { - "definition" : { - "val" : "A collection of organisms that consists of two or more organisms from at least two species.", - "xrefs" : [ ] - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Need to add axiom to specify that it has at a mimum members of two different species, but not sure how to specify that. Can't say \"('has member' only ('member of' min 2 'species as a collection of organisms'))\"." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000123" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", - "val" : "" - } ] - }, - "type" : "CLASS", - "lbl" : "multi-species collection of organisms" }, { "id" : "http://purl.obolibrary.org/obo/PATO_0000477", "meta" : { @@ -2606,26 +2359,6 @@ }, "type" : "CLASS", "lbl" : "obsolete shattering value" - }, { - "id" : "http://purl.obolibrary.org/obo/ENVO_01001055", - "meta" : { - "definition" : { - "val" : "An environmental system determined by part of a living or dead animal, or a whole small animal.", - "xrefs" : [ ] - } - }, - "type" : "CLASS", - "lbl" : "environment associated with an animal part or small animal" - }, { - "id" : "http://purl.obolibrary.org/obo/ENVO_01001057", - "meta" : { - "definition" : { - "val" : "An environmental system determined by part of a living or dead plant, or a whole small plant.", - "xrefs" : [ ] - } - }, - "type" : "CLASS", - "lbl" : "environment associated with a plant part or small plant" }, { "id" : "http://purl.obolibrary.org/obo/PATO_0000408", "meta" : { @@ -4729,17 +4462,6 @@ }, "type" : "CLASS", "lbl" : "cell" - }, { - "id" : "http://purl.obolibrary.org/obo/NCBITaxon_89593", - "meta" : { - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "Craniata", - "xrefs" : [ ] - } ] - }, - "type" : "CLASS", - "lbl" : "Craniata " }, { "id" : "http://purl.obolibrary.org/obo/PATO_0002186", "meta" : { @@ -5188,9 +4910,6 @@ } ] }, "type" : "PROPERTY" - }, { - "id" : "http://www.geneontology.org/formats/oboInOwl#Subset", - "type" : "CLASS" }, { "id" : "http://purl.obolibrary.org/obo/PATO_0002148", "meta" : { @@ -5413,40 +5132,6 @@ }, "type" : "CLASS", "lbl" : "decreased radiopacity" - }, { - "id" : "http://purl.obolibrary.org/obo/ENVO_01001000", - "meta" : { - "definition" : { - "val" : "An environmental system which is determined by a living organism.", - "xrefs" : [ ] - }, - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "host-associated environment", - "xrefs" : [ ] - } ] - }, - "type" : "CLASS", - "lbl" : "environmental system determined by an organism" - }, { - "id" : "http://purl.obolibrary.org/obo/ENVO_01001002", - "meta" : { - "definition" : { - "val" : "An environmental system determined by an animal.", - "xrefs" : [ ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "Metazoan-associated environment", - "xrefs" : [ ] - }, { - "pred" : "hasBroadSynonym", - "val" : "animal environment", - "xrefs" : [ ] - } ] - }, - "type" : "CLASS", - "lbl" : "animal-associated environment" }, { "id" : "http://purl.obolibrary.org/obo/PATO_0002159", "meta" : { @@ -6361,16 +6046,6 @@ }, "type" : "CLASS", "lbl" : "peripheral" - }, { - "id" : "http://purl.obolibrary.org/obo/ENVO_02500000", - "meta" : { - "definition" : { - "val" : "A process in which includes the components of an environmental system as participants.", - "xrefs" : [ ] - } - }, - "type" : "CLASS", - "lbl" : "environmental system process" }, { "id" : "http://purl.obolibrary.org/obo/PATO_0002104", "meta" : { @@ -6832,21 +6507,6 @@ }, "type" : "CLASS", "lbl" : "phosphorylation" - }, { - "id" : "http://purl.obolibrary.org/obo/NCBITaxon_33154", - "meta" : { - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "opisthokonts", - "xrefs" : [ ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "Fungi/Metazoa group", - "xrefs" : [ ] - } ] - }, - "type" : "CLASS", - "lbl" : "Opisthokonta" }, { "id" : "http://purl.obolibrary.org/obo/GO_0005634", "meta" : { @@ -6970,16 +6630,6 @@ }, "type" : "CLASS", "lbl" : "scirrhous" - }, { - "id" : "http://purl.obolibrary.org/obo/ENVO_02500027", - "meta" : { - "definition" : { - "val" : "An environmental process which is driven by the action of humans.", - "xrefs" : [ ] - } - }, - "type" : "CLASS", - "lbl" : "anthropogenic environmental process" }, { "id" : "http://purl.obolibrary.org/obo/PATO_0002120", "meta" : { @@ -7900,30 +7550,6 @@ }, "type" : "CLASS", "lbl" : "decreased distance" - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000409", - "meta" : { - "definition" : { - "val" : "A denotator type indicates how a term should be interpreted from an ontological perspective.", - "xrefs" : [ ] - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "Barry Smith, Werner Ceusters" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are \"natural kinds\" and the latter arbitrary collections of entities." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Alan Ruttenberg" - } ] - }, - "type" : "CLASS", - "lbl" : "denotator type" - }, { - "id" : "http://purl.obolibrary.org/obo/NCBITaxon_314146", - "type" : "CLASS", - "lbl" : "Euarchontoglires" }, { "id" : "http://purl.obolibrary.org/obo/PATO_0000389", "meta" : { @@ -8137,75 +7763,13 @@ }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000412", "meta" : { - "definition" : { - "val" : "For external terms/classes, the ontology from which the term was imported", - "xrefs" : [ ] - }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "imported from" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "PERSON:Melanie Courtot" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "GROUP:OBI:" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "PERSON:Alan Ruttenberg" } ] }, "type" : "PROPERTY", "lbl" : "imported from" - }, { - "id" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "meta" : { - "definition" : { - "val" : "An alternate textual definition for a class taken unmodified from an external source. This definition may have been used to derive a generalized definition for the new class.", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] - }, - "xrefs" : [ { - "val" : "UBPROP:0000001" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", - "val" : "This annotation property may be replaced with an annotation property from an external ontology such as IAO" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "external_definition" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", - "val" : "true" - } ] - }, - "type" : "PROPERTY", - "lbl" : "external_definition" - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000410", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Hard to give a definition for. Intuitively a \"natural kind\" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Alan Ruttenberg" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf" - } ] - }, - "type" : "INDIVIDUAL", - "lbl" : "universal" - }, { - "id" : "http://purl.obolibrary.org/obo/NCBITaxon_8287", - "type" : "CLASS", - "lbl" : "Sarcopterygii" }, { "id" : "http://purl.obolibrary.org/obo/pato#has_dividend_quality", "meta" : { @@ -8342,75 +7906,8 @@ "lbl" : "obsolete slight" }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000424", - "meta" : { - "definition" : { - "val" : "A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones", - "xrefs" : [ ] - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "ObjectProperty: RO_0002104\nLabel: has plasma membrane part\nAnnotations: IAO_0000424 \"http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.org/obo/owl/GO#GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)\"\n" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "expand expression to" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - } ] - }, "type" : "PROPERTY", "lbl" : "expand expression to" - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000423", - "meta" : { - "definition" : { - "val" : "Terms with this status should eventually replaced with a term from another ontology.", - "xrefs" : [ ] - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "group:OBI" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Alan Ruttenberg" - } ] - }, - "type" : "INDIVIDUAL", - "lbl" : "to be replaced with external ontology term" - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000420", - "meta" : { - "definition" : { - "val" : "A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal", - "xrefs" : [ ] - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "\"definitions\", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Alan Ruttenberg" - } ] - }, - "type" : "INDIVIDUAL", - "lbl" : "defined class" - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000421", - "meta" : { - "definition" : { - "val" : "A named class expression is a logical expression that is given a name. The name can be used in place of the expression.", - "xrefs" : [ ] - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Alan Ruttenberg" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions" - } ] - }, - "type" : "INDIVIDUAL", - "lbl" : "named class expression" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", "type" : "PROPERTY", @@ -10994,56 +10491,13 @@ }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000428", "meta" : { - "definition" : { - "val" : "A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues.", - "xrefs" : [ ] - }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Alan Ruttenberg" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "group:OBI" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" } ] }, "type" : "INDIVIDUAL", "lbl" : "requires discussion" - }, { - "id" : "http://purl.obolibrary.org/obo/NCBITaxon_32525", - "meta" : { - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "Theria", - "xrefs" : [ ] - } ] - }, - "type" : "CLASS", - "lbl" : "Theria " - }, { - "id" : "http://purl.obolibrary.org/obo/NCBITaxon_32524", - "meta" : { - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "amniotes", - "xrefs" : [ ] - } ] - }, - "type" : "CLASS", - "lbl" : "Amniota" - }, { - "id" : "http://purl.obolibrary.org/obo/NCBITaxon_32523", - "meta" : { - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "tetrapods", - "xrefs" : [ ] - } ] - }, - "type" : "CLASS", - "lbl" : "Tetrapoda" }, { "id" : "http://purl.obolibrary.org/obo/PATO_0001608", "meta" : { @@ -11806,51 +11260,6 @@ }, "type" : "CLASS", "lbl" : "increased affinity" - }, { - "id" : "http://purl.obolibrary.org/obo/NCBITaxon_9604", - "meta" : { - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "Pongidae", - "xrefs" : [ ] - }, { - "pred" : "hasExactSynonym", - "val" : "great apes", - "xrefs" : [ ] - } ] - }, - "type" : "CLASS", - "lbl" : "Hominidae" - }, { - "id" : "http://purl.obolibrary.org/obo/NCBITaxon_9605", - "meta" : { - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "humans", - "xrefs" : [ ] - } ] - }, - "type" : "CLASS", - "lbl" : "Homo" - }, { - "id" : "http://purl.obolibrary.org/obo/NCBITaxon_9606", - "meta" : { - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "man", - "xrefs" : [ ] - }, { - "pred" : "hasExactSynonym", - "val" : "human", - "xrefs" : [ ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "humans", - "xrefs" : [ ] - } ] - }, - "type" : "CLASS", - "lbl" : "Homo sapiens" }, { "id" : "http://purl.obolibrary.org/obo/PATO_0002087", "meta" : { @@ -12358,109 +11767,6 @@ }, "type" : "CLASS", "lbl" : "ballooning" - }, { - "id" : "http://purl.obolibrary.org/obo/PO_0000003", - "meta" : { - "definition" : { - "val" : "A plant structure (PO:0005679) which is a whole organism.", - "xrefs" : [ ] - }, - "synonyms" : [ { - "pred" : "hasNarrowSynonym", - "val" : "prothalli (narrow)", - "xrefs" : [ ] - }, { - "pred" : "hasExactSynonym", - "val" : "植物体全体 (Japanese, exact)", - "xrefs" : [ ] - }, { - "pred" : "hasNarrowSynonym", - "val" : "shrub (narrow)", - "xrefs" : [ ] - }, { - "pred" : "hasExactSynonym", - "val" : "planta entera (Spanish, exact)", - "xrefs" : [ ] - }, { - "pred" : "hasNarrowSynonym", - "val" : "gametophyte (narrow)", - "xrefs" : [ ] - }, { - "pred" : "hasNarrowSynonym", - "val" : "suffrutex (narrow)", - "xrefs" : [ ] - }, { - "pred" : "hasNarrowSynonym", - "val" : "herb (narrow)", - "xrefs" : [ ] - }, { - "pred" : "hasNarrowSynonym", - "val" : "suffrutices (narrow)", - "xrefs" : [ ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "clonal colony (related)", - "xrefs" : [ ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "colony (related)", - "xrefs" : [ ] - }, { - "pred" : "hasNarrowSynonym", - "val" : "frutices (narrow)", - "xrefs" : [ ] - }, { - "pred" : "hasBroadSynonym", - "val" : "ramet (broad)", - "xrefs" : [ ] - }, { - "pred" : "hasNarrowSynonym", - "val" : "prothallium (narrow)", - "xrefs" : [ ] - }, { - "pred" : "hasNarrowSynonym", - "val" : "woody clump (narrow)", - "xrefs" : [ ] - }, { - "pred" : "hasNarrowSynonym", - "val" : "vine (narrow)", - "xrefs" : [ ] - }, { - "pred" : "hasBroadSynonym", - "val" : "genet (broad)", - "xrefs" : [ ] - }, { - "pred" : "hasNarrowSynonym", - "val" : "prothallus (narrow)", - "xrefs" : [ ] - }, { - "pred" : "hasNarrowSynonym", - "val" : "tree (narrow)", - "xrefs" : [ ] - }, { - "pred" : "hasNarrowSynonym", - "val" : "sporophyte (narrow)", - "xrefs" : [ ] - }, { - "pred" : "hasNarrowSynonym", - "val" : "bush (narrow)", - "xrefs" : [ ] - }, { - "pred" : "hasNarrowSynonym", - "val" : "seedling (narrow)", - "xrefs" : [ ] - }, { - "pred" : "hasNarrowSynonym", - "val" : "liana (narrow)", - "xrefs" : [ ] - }, { - "pred" : "hasNarrowSynonym", - "val" : "frutex (narrow)", - "xrefs" : [ ] - } ] - }, - "type" : "CLASS", - "lbl" : "whole plant" }, { "id" : "http://purl.obolibrary.org/obo/PATO_0002029", "meta" : { @@ -13825,10 +13131,6 @@ }, "type" : "CLASS", "lbl" : "obsolete surface shape" - }, { - "id" : "http://purl.obolibrary.org/obo/NCBITaxon_1338369", - "type" : "CLASS", - "lbl" : "Dipnotetrapodomorpha" }, { "id" : "http://purl.obolibrary.org/obo/PATO_0002001", "meta" : { @@ -14080,22 +13382,6 @@ }, "type" : "CLASS", "lbl" : "fasciculation" - }, { - "id" : "http://xmlns.com/foaf/0.1/page", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "foaf-page" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", - "val" : "true" - } ] - }, - "type" : "PROPERTY", - "lbl" : "page" }, { "id" : "http://purl.obolibrary.org/obo/PATO_0002425", "meta" : { @@ -15359,7 +14645,7 @@ "meta" : { "definition" : { "val" : "A relationship that holds between between a receptor and an chemical entity, typically a small molecule or peptide, that carries information between cells or compartments of a cell and which binds the receptor and regulates its effector function.", - "xrefs" : [ "GOC:dos" ] + "xrefs" : [ ] }, "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", @@ -17757,10 +17043,6 @@ }, "type" : "CLASS", "lbl" : "obsolete solid substance value" - }, { - "id" : "http://purl.obolibrary.org/obo/NCBITaxon_376913", - "type" : "CLASS", - "lbl" : "Haplorrhini" }, { "id" : "http://purl.obolibrary.org/obo/PATO_0000675", "meta" : { @@ -19332,48 +18614,13 @@ }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000589", "meta" : { - "definition" : { - "val" : "An alternative name for a class or property which is unique across the OBO Foundry.", - "xrefs" : [ ] - }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "PERSON:Chris Mungall" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "GROUP:OBO Foundry " - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "OBO foundry unique label" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "PERSON:Bjoern Peters" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "The intended usage of that property is as follow: OBO foundry unique labels are automatically generated based on regular expressions provided by each ontology, so that SO could specify unique label = 'sequence ' + [label], etc. , MA could specify 'mouse + [label]' etc. Upon importing terms, ontology developers can choose to use the 'OBO foundry unique label' for an imported term or not. The same applies to tools ." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "PERSON:Alan Ruttenberg" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "PERSON:Melanie Courtot" } ] }, "type" : "PROPERTY", "lbl" : "OBO foundry unique label" - }, { - "id" : "http://purl.obolibrary.org/obo/ENVO_01000313", - "meta" : { - "definition" : { - "val" : "An anthropogenic environment is an environmental system which is the product of human activity.", - "xrefs" : [ ] - } - }, - "type" : "CLASS", - "lbl" : "anthropogenic environment" }, { "id" : "http://purl.obolibrary.org/obo/PATO_0001905", "meta" : { @@ -21540,51 +20787,15 @@ }, { "id" : "http://purl.obolibrary.org/obo/RO_0002087", "meta" : { - "definition" : { - "val" : "X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)", - "xrefs" : [ ] - }, - "xrefs" : [ { - "val" : "RO:0002087" - } ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "starts_at_end_of", - "xrefs" : [ ] - }, { - "pred" : "hasExactSynonym", - "val" : "directly preceded by", - "xrefs" : [ ] - }, { - "pred" : "hasExactSynonym", - "val" : "is directly preceded by", - "xrefs" : [ ] - }, { - "pred" : "hasExactSynonym", - "val" : "is immediately preceded by", - "xrefs" : [ "SIO:000251" ] - } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "David Osumi-Sutherland" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "immediately_preceded_by" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", "val" : "X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "A non-transitive temporal relation in which one process immediately precedes another process, such that there is no interval of time between the two processes[SIO:000251]." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "starts_at_end_of" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/SIO_000251" } ] }, "type" : "PROPERTY", @@ -22414,10 +21625,6 @@ }, "type" : "CLASS", "lbl" : "mediolateral polarity" - }, { - "id" : "http://purl.obolibrary.org/obo/NCBITaxon_6072", - "type" : "CLASS", - "lbl" : "Eumetazoa" }, { "id" : "http://purl.obolibrary.org/obo/PATO_0001043", "meta" : { @@ -23980,28 +23187,16 @@ "id" : "http://purl.obolibrary.org/obo/RO_0002131", "meta" : { "definition" : { - "val" : "A overlaps B if they share some part in common.", + "val" : "x overlaps y if and only if there exists some z such that x has part z and z part of y", "xrefs" : [ ] }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "RO:0002131" - } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", - "val" : "BFO_0000051 some (BFO_0000050 some ?Y)" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "overlaps" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", "val" : "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)" @@ -24265,25 +23460,6 @@ }, "type" : "CLASS", "lbl" : "increased height" - }, { - "id" : "http://purl.obolibrary.org/obo/PO_0009011", - "meta" : { - "definition" : { - "val" : "An anatomical structure that is or was part of a plant, or was derived from a part of a plant.", - "xrefs" : [ ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "estructura vegetal (Spanish, exact)", - "xrefs" : [ ] - }, { - "pred" : "hasExactSynonym", - "val" : "植物 構造 (Japanese, exact)", - "xrefs" : [ ] - } ] - }, - "type" : "CLASS", - "lbl" : "plant structure" }, { "id" : "http://purl.obolibrary.org/obo/PATO_0000572", "meta" : { @@ -24376,21 +23552,6 @@ "lbl" : "increased length" }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000600", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "elucidation" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", - "val" : "Primitive terms in a highest-level ontology such as BFO are terms which are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "Person:Barry Smith" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "person:Alan Ruttenberg" - } ] - }, "type" : "PROPERTY", "lbl" : "elucidation" }, { @@ -24634,26 +23795,6 @@ }, "type" : "CLASS", "lbl" : "hypertrophic" - }, { - "id" : "http://purl.obolibrary.org/obo/CHEBI_24431", - "meta" : { - "definition" : { - "val" : "A chemical entity is a physical entity of interest in chemistry including molecular entities, parts thereof, and chemical substances.", - "xrefs" : [ ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/chebi#3_STAR" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "chemical entity", - "xrefs" : [ "UniProt" ] - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "chebi_ontology" - } ] - }, - "type" : "CLASS", - "lbl" : "chemical entity" }, { "id" : "http://purl.obolibrary.org/obo/PATO_0000598", "meta" : { @@ -24862,26 +24003,6 @@ }, "type" : "CLASS", "lbl" : "increased volume" - }, { - "id" : "http://purl.obolibrary.org/obo/CHEBI_59999", - "meta" : { - "definition" : { - "val" : "A chemical substance is a portion of matter of constant composition, composed of molecular entities of the same type or of different types.", - "xrefs" : [ ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/chebi#3_STAR" ], - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "Chemische Substanz", - "xrefs" : [ "ChEBI" ] - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "chebi_ontology" - } ] - }, - "type" : "CLASS", - "lbl" : "chemical substance" }, { "id" : "http://purl.obolibrary.org/obo/GO_0038023", "meta" : { @@ -25243,15 +24364,6 @@ }, "type" : "CLASS", "lbl" : "scarred" - }, { - "id" : "http://purl.obolibrary.org/obo/chebi#3_STAR", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", - "val" : "Manually annotated by ChEBI Team" - } ] - }, - "type" : "PROPERTY" }, { "id" : "http://purl.obolibrary.org/obo/PATO_0000539", "meta" : { @@ -26085,17 +25197,6 @@ }, "type" : "CLASS", "lbl" : "obsolete thermoinsensitive" - }, { - "id" : "http://purl.obolibrary.org/obo/NCBITaxon_207598", - "meta" : { - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "Homo/Pan/Gorilla group", - "xrefs" : [ ] - } ] - }, - "type" : "CLASS", - "lbl" : "Homininae" }, { "id" : "http://purl.obolibrary.org/obo/PATO_0001885", "meta" : { @@ -26277,17 +25378,6 @@ }, "type" : "CLASS", "lbl" : "obsolete absolute temperature sensitivity value" - }, { - "id" : "http://purl.obolibrary.org/obo/NCBITaxon_117571", - "meta" : { - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "bony vertebrates", - "xrefs" : [ ] - } ] - }, - "type" : "CLASS", - "lbl" : "Euteleostomi" }, { "id" : "http://purl.obolibrary.org/obo/PATO_0001880", "meta" : { @@ -26348,10 +25438,6 @@ }, "type" : "CLASS", "lbl" : "obsolete u v light sensitivity value" - }, { - "id" : "http://purl.obolibrary.org/obo/NCBITaxon_117570", - "type" : "CLASS", - "lbl" : "Teleostomi" }, { "id" : "http://purl.obolibrary.org/obo/PATO_0001817", "meta" : { @@ -26718,25 +25804,6 @@ }, "type" : "CLASS", "lbl" : "increased wetness" - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0010000", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Person:Alan Ruttenberg" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "Person:Alan Ruttenberg" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "has axiom id" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", - "val" : "A URI that is intended to be unique label for an axiom used for tracking change to the ontology. For an axiom expressed in different languages, each expression is given the same URI" - } ] - }, - "type" : "PROPERTY", - "lbl" : "has axiom label" }, { "id" : "http://purl.obolibrary.org/obo/PATO_0001822", "meta" : { @@ -27514,25 +26581,6 @@ }, "type" : "CLASS", "lbl" : "tolerant to" - }, { - "id" : "http://purl.obolibrary.org/obo/PO_0025131", - "meta" : { - "definition" : { - "val" : "An anatomical entity that is or was part of a plant.", - "xrefs" : [ ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "entidad anatómica vegetal (Spanish, exact)", - "xrefs" : [ ] - }, { - "pred" : "hasExactSynonym", - "val" : "植物 解剖学（形態）的実体 (Japanese, exact)", - "xrefs" : [ ] - } ] - }, - "type" : "CLASS", - "lbl" : "plant anatomical entity" }, { "id" : "http://purl.obolibrary.org/obo/PATO_0001806", "meta" : { @@ -27722,33 +26770,6 @@ } ] }, "type" : "PROPERTY" - }, { - "id" : "http://purl.obolibrary.org/obo/NCBITaxon_33213", - "type" : "CLASS", - "lbl" : "Bilateria" - }, { - "id" : "http://purl.obolibrary.org/obo/NCBITaxon_33208", - "meta" : { - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "multicellular animals", - "xrefs" : [ ] - }, { - "pred" : "hasExactSynonym", - "val" : "metazoans", - "xrefs" : [ ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "Animalia", - "xrefs" : [ ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "animals", - "xrefs" : [ ] - } ] - }, - "type" : "CLASS", - "lbl" : "Metazoa" }, { "id" : "http://purl.obolibrary.org/obo/CARO_0030000", "type" : "CLASS", @@ -28045,42 +27066,6 @@ }, "type" : "CLASS", "lbl" : "semi erect" - }, { - "id" : "http://purl.obolibrary.org/obo/CHEBI_46662", - "meta" : { - "definition" : { - "val" : "In general, a mineral is a chemical substance that is normally crystalline formed and has been formed as a result of geological processes. The term also includes metamict substances (naturally occurring, formerly crystalline substances whose crystallinity has been destroyed by ionising radiation) and can include naturally occurring amorphous substances that have never been crystalline ('mineraloids') such as georgite and calciouranoite as well as substances formed by the action of geological processes on bigenic compounds ('biogenic minerals').", - "xrefs" : [ ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/chebi#3_STAR" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "mineral", - "xrefs" : [ "ChEBI" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "minerals", - "xrefs" : [ "ChEBI" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "mineraux", - "xrefs" : [ "ChEBI" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "Minerale", - "xrefs" : [ "ChEBI" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "minerales", - "xrefs" : [ "ChEBI" ] - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "chebi_ontology" - } ] - }, - "type" : "CLASS", - "lbl" : "mineral" }, { "id" : "http://purl.obolibrary.org/obo/GO_0005102", "meta" : { @@ -29638,17 +28623,6 @@ "lbl" : "increased_in_magnitude_relative_to" }, { "id" : "http://purl.obolibrary.org/obo/ENVO_01000254", - "meta" : { - "definition" : { - "val" : "A system which has the disposition to environ one or more material entities.", - "xrefs" : [ "DOI:10.1186/2041-1480-4-43" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "environment", - "xrefs" : [ ] - } ] - }, "type" : "CLASS", "lbl" : "environmental system" }, { @@ -29659,13 +28633,7 @@ "xrefs" : [ ] }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "RO:0002180" - } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "has_component" - }, { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" }, { @@ -29674,9 +28642,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit." - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity." @@ -30347,11 +29312,6 @@ "val" : "A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities", "xrefs" : [ "PATOC:GVG" ] }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "trait", - "xrefs" : [ ] - } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", "val" : "quality (PATO)" @@ -31104,7 +30064,7 @@ "id" : "http://purl.obolibrary.org/obo/RO_0002264", "meta" : { "definition" : { - "val" : "c acts upstream of or within p if c is enables 'p' and p' causally upstream of or within p", + "val" : "c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process.", "xrefs" : [ ] }, "synonyms" : [ { @@ -31349,18 +30309,9 @@ "val" : "Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p", "xrefs" : [ ] }, - "xrefs" : [ { - "val" : "RO:0002258" - } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Chris Mungall" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "developmentally_preceded_by" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", "val" : "This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from" @@ -31497,24 +30448,15 @@ "val" : "x has developmental contribution from y iff x has some part z such that z develops from y", "xrefs" : [ ] }, - "xrefs" : [ { - "val" : "RO:0002254" - } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Chris Mungall" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "has_developmental_contribution_from" } ] }, "type" : "PROPERTY", @@ -31536,25 +30478,16 @@ "xrefs" : [ ] }, "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], - "xrefs" : [ { - "val" : "RO:0002255" - } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "developmentally_contributes_to" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Chris Mungall" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" } ] }, "type" : "PROPERTY", - "lbl" : "developmentally_contributes_to" + "lbl" : "developmentally contributes to" }, { "id" : "http://purl.obolibrary.org/obo/PATO_0002628", "meta" : { @@ -31912,7 +30845,7 @@ "id" : "http://purl.obolibrary.org/obo/RO_0002233", "meta" : { "definition" : { - "val" : "p has direct input c iff c is a participant in p, c is present at the start of p, and the state of c is modified during p.", + "val" : "p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p.", "xrefs" : [ ] }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], @@ -32135,9 +31068,6 @@ }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", "val" : "A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations." - }, { - "pred" : "http://purl.org/dc/elements/1.1/source", - "val" : "https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1" }, { "pred" : "http://purl.org/dc/terms/source", "val" : "https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1" @@ -32225,9 +31155,6 @@ "xrefs" : [ ] }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Chris Mungall" }, { @@ -32266,7 +31193,7 @@ } ] }, "type" : "PROPERTY", - "lbl" : "has active participant" + "lbl" : "obsolete has active participant" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002213", "meta" : { @@ -32340,30 +31267,18 @@ "xrefs" : [ ] }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "RO:0002215" - } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "For compatibility with BFO, this relation has a shortcut definition in which the expression \"capable of some P\" expands to \"bearer_of (some realized_by only P)\"." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/21208450" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "has function realized in" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "capable_of" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "osteoclast SubClassOf 'capable of' some 'bone resorption'" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", "val" : "RO_0000053 some (RO_0000054 only ?Y)" @@ -32402,24 +31317,12 @@ "val" : "c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p.", "xrefs" : [ ] }, - "xrefs" : [ { - "val" : "RO:0002216" - } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "has function in" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "capable_of_part_of" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Chris Mungall" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", "val" : "RO_0000053 some (RO_0000054 only (BFO_0000050 some ?Y))" @@ -32541,9 +31444,6 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "negatively_regulates" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", "val" : "negatively regulates (process to process)" @@ -32618,18 +31518,12 @@ "val" : "x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y", "xrefs" : [ ] }, - "xrefs" : [ { - "val" : "RO:0002202" - } ], "basicPropertyValues" : [ { "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", "val" : "This is the transitive form of the develops from relation" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "David Osumi-Sutherland" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "develops_from" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Terry Meehan" @@ -32639,9 +31533,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Melissa Haendel" @@ -32670,21 +31561,12 @@ "xrefs" : [ ] }, "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], - "xrefs" : [ { - "val" : "RO:0002203" - } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "develops_into" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Chris Mungall" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "David Osumi-Sutherland" @@ -32897,21 +31779,6 @@ "id" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "type" : "PROPERTY", "lbl" : "has_obo_namespace" - }, { - "id" : "http://purl.obolibrary.org/obo/NCBITaxon_40674", - "meta" : { - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "mammals", - "xrefs" : [ ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "mammals", - "xrefs" : [ ] - } ] - }, - "type" : "CLASS", - "lbl" : "Mammalia" }, { "id" : "http://purl.obolibrary.org/obo/GO_0060089", "meta" : { @@ -33480,17 +32347,6 @@ }, "type" : "CLASS", "lbl" : "obsolete relative neurobehavioral function value" - }, { - "id" : "http://purl.obolibrary.org/obo/NCBITaxon_1437010", - "meta" : { - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "Boreotheria", - "xrefs" : [ ] - } ] - }, - "type" : "CLASS", - "lbl" : "Boreoeutheria" }, { "id" : "http://purl.obolibrary.org/obo/PATO_0000804", "meta" : { @@ -33644,6 +32500,32 @@ }, "type" : "CLASS", "lbl" : "obsolete reflex value" + }, { + "id" : "http://purl.obolibrary.org/obo/PATO_0040027", + "meta" : { + "definition" : { + "val" : "A ploidy quality inhering in a bearer by virtue of the bearer's haploid cells undergo chromosome doubling.", + "xrefs" : [ "Wikipedia:https://en.wikipedia.org/wiki/Doubled_haploidy" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "double-haploid", + "xrefs" : [ ] + }, { + "pred" : "hasExactSynonym", + "val" : "double haploid", + "xrefs" : [ ] + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "quality" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "http://orcid.org/0000-0001-5208-3432" + } ] + }, + "type" : "CLASS", + "lbl" : "doubled haploid" }, { "id" : "http://purl.obolibrary.org/obo/PATO_0000807", "meta" : { @@ -34270,17 +33152,6 @@ }, "type" : "CLASS", "lbl" : "obsolete quinine taste" - }, { - "id" : "http://purl.obolibrary.org/obo/NCBITaxon_33511", - "meta" : { - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "deuterostomes", - "xrefs" : [ ] - } ] - }, - "type" : "CLASS", - "lbl" : "Deuterostomia" }, { "id" : "http://purl.obolibrary.org/obo/PATO_0040012", "meta" : { @@ -34690,16 +33561,6 @@ }, "type" : "CLASS", "lbl" : "increased porosity" - }, { - "id" : "http://purl.obolibrary.org/obo/ENVO_01000997", - "meta" : { - "definition" : { - "val" : "An environmental system which is determined by materials bearing roughly homogeneous qualities.", - "xrefs" : [ ] - } - }, - "type" : "CLASS", - "lbl" : "environmental system determined by a quality" }, { "id" : "http://purl.obolibrary.org/obo/PATO_0015021", "meta" : { @@ -34715,16 +33576,6 @@ }, "type" : "CLASS", "lbl" : "combustibility" - }, { - "id" : "http://purl.obolibrary.org/obo/ENVO_01000998", - "meta" : { - "definition" : { - "val" : "An environmental system within which an environmental material strongly influences the system's composition and properties.", - "xrefs" : [ ] - } - }, - "type" : "CLASS", - "lbl" : "environmental system determined by a material" }, { "id" : "http://purl.obolibrary.org/obo/PATO_0015022", "meta" : { @@ -36395,33 +35246,6 @@ }, "type" : "CLASS", "lbl" : "desaturated yellow" - }, { - "id" : "http://purl.obolibrary.org/obo/NCBITaxon_9347", - "meta" : { - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "Placentalia", - "xrefs" : [ ] - }, { - "pred" : "hasExactSynonym", - "val" : "placentals", - "xrefs" : [ ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "placentals", - "xrefs" : [ ] - }, { - "pred" : "hasExactSynonym", - "val" : "placental mammals", - "xrefs" : [ ] - }, { - "pred" : "hasExactSynonym", - "val" : "eutherian mammals", - "xrefs" : [ ] - } ] - }, - "type" : "CLASS", - "lbl" : "Eutheria" }, { "id" : "http://purl.obolibrary.org/obo/PATO_0001287", "meta" : { @@ -37082,25 +35906,6 @@ "type" : "PROPERTY" }, { "id" : "http://purl.obolibrary.org/obo/IAO_0100001", - "meta" : { - "definition" : { - "val" : "Add as annotation triples in the granting ontology", - "xrefs" : [ ] - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Person:Alan Ruttenberg" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "Person:Alan Ruttenberg" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "term replaced by" - } ] - }, "type" : "PROPERTY", "lbl" : "term replaced by" }, { @@ -37110,21 +35915,12 @@ "val" : "x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y", "xrefs" : [ ] }, - "xrefs" : [ { - "val" : "RO:0002385" - } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000428" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Chris Mungall" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "has_potential_to_developmentally_contribute_to" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" } ] }, "type" : "PROPERTY", @@ -37159,6 +35955,21 @@ }, "type" : "CLASS", "lbl" : "dark green" + }, { + "id" : "http://purl.obolibrary.org/obo/PATO_0001246", + "meta" : { + "definition" : { + "val" : "A color consisting of brown hue and high brightness.", + "xrefs" : [ "PATOC:GVG" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/pato#mpath_slim", "http://purl.obolibrary.org/obo/pato#value_slim" ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "quality" + } ] + }, + "type" : "CLASS", + "lbl" : "light brown" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002387", "meta" : { @@ -37166,16 +35977,7 @@ "val" : "x has the potential to develop into y iff x develops into y or if x is capable of developing into y", "xrefs" : [ ] }, - "xrefs" : [ { - "val" : "RO:0002387" - } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "has_potential_to_develop_into" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Chris Mungall" }, { @@ -37185,21 +35987,6 @@ }, "type" : "PROPERTY", "lbl" : "has potential to develop into" - }, { - "id" : "http://purl.obolibrary.org/obo/PATO_0001246", - "meta" : { - "definition" : { - "val" : "A color consisting of brown hue and high brightness.", - "xrefs" : [ "PATOC:GVG" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/pato#mpath_slim", "http://purl.obolibrary.org/obo/pato#value_slim" ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "quality" - } ] - }, - "type" : "CLASS", - "lbl" : "light brown" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002388", "meta" : { @@ -37207,21 +35994,12 @@ "val" : "x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y", "xrefs" : [ ] }, - "xrefs" : [ { - "val" : "RO:0002388" - } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Chris Mungall" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000428" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "has_potential_to_directly_develop_into" } ] }, "type" : "PROPERTY", @@ -37962,27 +36740,18 @@ "val" : "a relation between two independent continuants, the target and the location, in which the target is entirely within the location", "xrefs" : [ ] }, - "xrefs" : [ { - "val" : "RO:0001025" - } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "located in" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "my brain is located in my head" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "located_in" }, { "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" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "this rat is located in this cage" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://purl.org/dc/elements/1.1/source", "val" : "http://www.obofoundry.org/ro/#OBO_REL:located_in" @@ -37998,7 +36767,7 @@ } ] }, "type" : "PROPERTY", - "lbl" : "located_in" + "lbl" : "located in" }, { "id" : "http://purl.obolibrary.org/obo/PATO_0002510", "meta" : { @@ -38028,18 +36797,9 @@ "xrefs" : [ ] }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco", "http://purl.obolibrary.org/obo/RO_0002259" ], - "xrefs" : [ { - "val" : "RO:0002352" - } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Chris Mungall" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "input_of" } ] }, "type" : "PROPERTY", @@ -38073,18 +36833,9 @@ "xrefs" : [ ] }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco", "http://purl.obolibrary.org/obo/RO_0002259" ], - "xrefs" : [ { - "val" : "RO:0002353" - } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "output_of" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Chris Mungall" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" } ] }, "type" : "PROPERTY", @@ -38207,18 +36958,9 @@ "val" : "is member of is a mereological relation between a item and a collection.", "xrefs" : [ ] }, - "xrefs" : [ { - "val" : "RO:0002350" - } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "is member of" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "member_of" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "An organism that is a member of a population of organisms" @@ -38270,21 +37012,12 @@ "val" : "has member is a mereological relation between a collection and an item.", "xrefs" : [ ] }, - "xrefs" : [ { - "val" : "RO:0002351" - } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "SIO" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "has_member" } ] }, "type" : "PROPERTY", @@ -38347,21 +37080,12 @@ "id" : "http://purl.obolibrary.org/obo/RO_0001019", "meta" : { "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "RO:0001019" - } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "contains" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "contains" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" } ] }, "type" : "PROPERTY", @@ -38419,24 +37143,15 @@ "val" : "a relation between two independent continuants, the location and the target, in which the target is entirely within the location", "xrefs" : [ ] }, - "xrefs" : [ { - "val" : "RO:0001015" - } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "this cage is the location of this rat" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "location_of" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "location_of" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "is location of" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Most location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime" @@ -38449,7 +37164,7 @@ } ] }, "type" : "PROPERTY", - "lbl" : "location_of" + "lbl" : "location of" }, { "id" : "http://purl.obolibrary.org/obo/pato#hpo_slim", "meta" : { @@ -38895,31 +37610,6 @@ }, "type" : "CLASS", "lbl" : "obsolete episodic" - }, { - "id" : "http://purl.obolibrary.org/obo/ENVO_01000952", - "meta" : { - "definition" : { - "val" : "A process during which a natural environmental system is altered by human action.", - "xrefs" : [ "https://en.wikipedia.org/wiki/Anthropization" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "anthropization", - "xrefs" : [ ] - } ] - }, - "type" : "CLASS", - "lbl" : "anthropisation" - }, { - "id" : "http://purl.obolibrary.org/obo/ENVO_01000951", - "meta" : { - "definition" : { - "val" : "An environmental system in which minimal to no anthropisation has occurred and non-human agents are the primary determinants of the system's dynamics and composition.", - "xrefs" : [ "https://en.wikipedia.org/wiki/Anthropization", "https://en.wikipedia.org/wiki/Natural_environment" ] - } - }, - "type" : "CLASS", - "lbl" : "natural environment" }, { "id" : "http://purl.obolibrary.org/obo/PATO_0000763", "meta" : { @@ -39198,21 +37888,12 @@ "val" : "A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities.", "xrefs" : [ ] }, - "xrefs" : [ { - "val" : "RO:0002328" - } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "This is a grouping relation that collects relations used for the purpose of connecting structure and function" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Chris Mungall" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "functionally_related_to" } ] }, "type" : "PROPERTY", @@ -39224,18 +37905,9 @@ "val" : "this relation holds between c and p when c is part of some c', and c' is capable of p.", "xrefs" : [ ] }, - "xrefs" : [ { - "val" : "RO:0002329" - } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Chris Mungall" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "part_of_structure_that_is_capable_of" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "false" @@ -39521,10 +38193,6 @@ }, "type" : "CLASS", "lbl" : "aversion" - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000002", - "type" : "INDIVIDUAL", - "lbl" : "example to be eventually removed" }, { "id" : "http://purl.obolibrary.org/obo/PATO_0000785", "meta" : { @@ -39612,9 +38280,6 @@ }, { "pred" : "http://purl.org/dc/terms/creator", "val" : "cjm" - }, { - "pred" : "http://purl.org/dc/elements/1.1/creator", - "val" : "cjm" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", "val" : "holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y" @@ -39686,9 +38351,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0004049", "val" : "http://purl.obolibrary.org/obo/RO_0002411" - }, { - "pred" : "http://purl.org/dc/elements/1.1/creator", - "val" : "cjm" } ] }, "type" : "PROPERTY", @@ -39852,10 +38514,6 @@ }, "type" : "CLASS", "lbl" : "obsolete immubocompetent value" - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000027", - "type" : "CLASS", - "lbl" : "data item" }, { "id" : "http://purl.obolibrary.org/obo/PATO_0000727", "meta" : { @@ -40529,21 +39187,6 @@ }, "type" : "CLASS", "lbl" : "obsolete learning and memory value" - }, { - "id" : "http://purl.obolibrary.org/obo/NCBITaxon_1", - "meta" : { - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "all", - "xrefs" : [ ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "all", - "xrefs" : [ ] - } ] - }, - "type" : "CLASS", - "lbl" : "root" }, { "id" : "http://purl.obolibrary.org/obo/GO_0050789", "meta" : { @@ -40944,8 +39587,7 @@ "val" : "http://purl.obolibrary.org/obo/GO_0038023" } ] }, - "type" : "CLASS", - "lbl" : "receptor activity" + "type" : "CLASS" }, { "id" : "http://purl.obolibrary.org/obo/PATO_0000719", "meta" : { @@ -41050,16 +39692,6 @@ }, "type" : "CLASS", "lbl" : "molecular function regulator" - }, { - "id" : "http://purl.obolibrary.org/obo/ENVO_00002297", - "meta" : { - "definition" : { - "val" : "A material entity which determines an environmental system.", - "xrefs" : [ "DOI:10.1186/2041-1480-4-43", "NM:nm", "ORCID:0000-0002-4366-3088" ] - } - }, - "type" : "CLASS", - "lbl" : "environmental feature" }, { "id" : "http://purl.obolibrary.org/obo/PATO_0001174", "meta" : { @@ -41551,22 +40183,6 @@ }, "type" : "CLASS", "lbl" : "medial to" - }, { - "id" : "http://purl.org/dc/elements/1.1/source", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "dc-source" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", - "val" : "true" - } ] - }, - "type" : "PROPERTY", - "lbl" : "derived from resource" }, { "id" : "http://purl.obolibrary.org/obo/PATO_0002469", "meta" : { @@ -41993,58 +40609,6 @@ }, "type" : "CLASS", "lbl" : "obsolete relative resistance value" - }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0001062", - "meta" : { - "definition" : { - "val" : "Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species.", - "xrefs" : [ "http://orcid.org/0000-0001-9114-8737", "FMA:62955" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], - "xrefs" : [ { - "val" : "NCIT:C12219" - }, { - "val" : "HAO:0000000" - }, { - "val" : "TAO:0100000" - }, { - "val" : "CARO:0000000" - }, { - "val" : "FBbt:10000000" - }, { - "val" : "AAO:0010841" - }, { - "val" : "EHDAA2:0002229" - }, { - "val" : "AEO:0000000" - }, { - "val" : "FMA:62955" - }, { - "val" : "WBbt:0000100" - }, { - "val" : "ZFA:0100000" - }, { - "val" : "XAO:0000000" - }, { - "val" : "TGMA:0001822" - }, { - "val" : "BIRNLEX:6" - }, { - "val" : "BILA:0000000" - }, { - "val" : "FBbt_root:00000000" - }, { - "val" : "UMLS:C1515976" - }, { - "val" : "MA:0000001" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] - }, - "type" : "CLASS", - "lbl" : "anatomical entity" }, { "id" : "http://purl.obolibrary.org/obo/PATO_0002472", "meta" : { @@ -44463,21 +43027,6 @@ }, "type" : "CLASS", "lbl" : "obsolete digestive function" - }, { - "id" : "http://purl.obolibrary.org/obo/NCBITaxon_131567", - "meta" : { - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "biota", - "xrefs" : [ ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "biota", - "xrefs" : [ ] - } ] - }, - "type" : "CLASS", - "lbl" : "cellular organisms" }, { "id" : "http://purl.obolibrary.org/obo/PATO_0001534", "meta" : { @@ -45219,9 +43768,6 @@ "xrefs" : [ ] }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "RO:0002473" - } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate'" @@ -45231,15 +43777,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Chris Mungall" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "composed_primarily_of" } ] }, "type" : "PROPERTY", @@ -45603,21 +44143,6 @@ }, "type" : "CLASS", "lbl" : "increased sensitivity of a process" - }, { - "id" : "http://purl.obolibrary.org/obo/NCBITaxon_314295", - "meta" : { - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "ape", - "xrefs" : [ ] - }, { - "pred" : "hasExactSynonym", - "val" : "apes", - "xrefs" : [ ] - } ] - }, - "type" : "CLASS", - "lbl" : "Hominoidea" }, { "id" : "http://purl.obolibrary.org/obo/GO_0005488", "meta" : { @@ -45712,9 +44237,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000428" } ] }, "type" : "PROPERTY", @@ -45831,17 +44353,6 @@ } ] }, "type" : "CLASS" - }, { - "id" : "http://purl.obolibrary.org/obo/NCBITaxon_314293", - "meta" : { - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "Anthropoidea", - "xrefs" : [ ] - } ] - }, - "type" : "CLASS", - "lbl" : "Simiiformes" }, { "id" : "http://purl.obolibrary.org/obo/PATO_0001560", "meta" : { @@ -46016,22 +44527,6 @@ "lbl" : "obsolete taste" }, { "id" : "http://purl.obolibrary.org/obo/CARO_0001010", - "meta" : { - "definition" : { - "val" : "Material anatomical entity that is a member of an individual species or is a viral or viroid particle.", - "xrefs" : [ ] - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_creation_date", - "val" : "9/18/11" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_created_by", - "val" : "Melissa Haendel" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "organism or virus" - } ] - }, "type" : "CLASS", "lbl" : "organism or virus or viroid" }, { @@ -46096,7 +44591,7 @@ } ] }, "type" : "PROPERTY", - "lbl" : "molecularly decreases activity of" + "lbl" : "activity directly negatively regulates activity of" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002447", "meta" : { @@ -46116,34 +44611,9 @@ }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000116", "meta" : { - "definition" : { - "val" : "An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology.", - "xrefs" : [ ] - }, - "xrefs" : [ { - "val" : "IAO:0000116" - } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "editor_note" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "editor note" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000122" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "GROUP:OBI:" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "PERSON:Daniel Schober" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", - "val" : "true" } ] }, "type" : "PROPERTY", @@ -46151,71 +44621,21 @@ }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000117", "meta" : { - "definition" : { - "val" : "Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people", - "xrefs" : [ ] - }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "term editor" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "20110707, MC: label update to term editor and definition modified accordingly. See http://code.google.com/p/information-artifact-ontology/issues/detail?id=115." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "PERSON:Daniel Schober" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000122" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "GROUP:OBI:" } ] }, "type" : "PROPERTY", "lbl" : "term editor" }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000114", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "PERSON:Melanie Courtot" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "PERSON:Bill Bug" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "has curation status" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "OBI_0000281" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "PERSON:Alan Ruttenberg" - } ] - }, "type" : "PROPERTY", "lbl" : "has curation status" }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000115", "meta" : { - "definition" : { - "val" : "The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.", - "xrefs" : [ ] - }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "definition" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "PERSON:Daniel Schober" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "GROUP:OBI:" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "2012-04-05: \nBarry Smith\n\nThe official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible.\n\nCan you fix to something like:\n\nA statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property.\n\nAlan Ruttenberg\n\nYour proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. \n\nOn the specifics of the proposed definition:\n\nWe don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. \n\nPersonally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. \n\nWe also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. " - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000122" } ] @@ -46225,59 +44645,15 @@ }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000112", "meta" : { - "definition" : { - "val" : "A phrase describing how a class name should be used. May also include other kinds of examples that facilitate immediate understanding of a class semantics, such as widely known prototypical subclasses or instances of the class. Although essential for high level terms, examples for low level terms (e.g., Affymetrix HU133 array) are not", - "xrefs" : [ ] - }, - "xrefs" : [ { - "val" : "IAO:0000112" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "GROUP:OBI:" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "example_of_usage" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "example" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", - "val" : "true" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000122" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "PERSON:Daniel Schober" } ] }, "type" : "PROPERTY", "lbl" : "example of usage" }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000111", - "meta" : { - "definition" : { - "val" : "The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English)", - "xrefs" : [ ] - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000122" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "PERSON:Daniel Schober" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "GROUP:OBI:" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "editor preferred term" - } ] - }, "type" : "PROPERTY", "lbl" : "editor preferred term" }, { @@ -46328,22 +44704,9 @@ }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000118", "meta" : { - "definition" : { - "val" : "An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent)", - "xrefs" : [ ] - }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "alternative term" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "GROUP:OBI:" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "PERSON:Daniel Schober" } ] }, "type" : "PROPERTY", @@ -46351,23 +44714,7 @@ }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000119", "meta" : { - "definition" : { - "val" : "formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007", - "xrefs" : [ ] - }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "PERSON:Daniel Schober" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "definition source" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "GROUP:OBI:" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000122" } ] @@ -46508,16 +44855,6 @@ }, "type" : "CLASS", "lbl" : "complex" - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000120", - "meta" : { - "definition" : { - "val" : "Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete.", - "xrefs" : [ ] - } - }, - "type" : "INDIVIDUAL", - "lbl" : "metadata complete" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002434", "meta" : { @@ -46582,10 +44919,6 @@ }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000125", "meta" : { - "definition" : { - "val" : "All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor.", - "xrefs" : [ ] - }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" @@ -46593,43 +44926,9 @@ }, "type" : "INDIVIDUAL", "lbl" : "pending final vetting" - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000123", - "meta" : { - "definition" : { - "val" : "Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors.", - "xrefs" : [ ] - } - }, - "type" : "INDIVIDUAL", - "lbl" : "metadata incomplete" - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000124", - "meta" : { - "definition" : { - "val" : "Nothing done yet beyond assigning a unique class ID and proposing a preferred term.", - "xrefs" : [ ] - } - }, - "type" : "INDIVIDUAL", - "lbl" : "uncurated" - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000121", - "meta" : { - "definition" : { - "val" : "term created to ease viewing/sort terms for development purpose, and will not be included in a release", - "xrefs" : [ ] - } - }, - "type" : "INDIVIDUAL", - "lbl" : "organizational term" }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000122", "meta" : { - "definition" : { - "val" : "Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking \"ready_for_release\" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed \"ready_for_release\" will also derived from a chain of ancestor classes that are also \"ready_for_release.\"", - "xrefs" : [ ] - }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" @@ -46667,15 +44966,6 @@ }, "type" : "CLASS", "lbl" : "sound quality" - }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#upper_level", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", - "val" : "abstract upper-level terms not directly useful for analysis" - } ] - }, - "type" : "PROPERTY" }, { "id" : "http://purl.obolibrary.org/obo/PATO_0001512", "meta" : { @@ -46927,7 +45217,7 @@ "id" : "http://purl.obolibrary.org/obo/RO_0002428", "meta" : { "definition" : { - "val" : "c involved in regulation of p if c is involved in some 'p' and p' regulates some p", + "val" : "c involved in regulation of p if c is involved in some p' and p' regulates some p", "xrefs" : [ ] }, "basicPropertyValues" : [ { @@ -46954,6 +45244,10 @@ }, "type" : "PROPERTY", "lbl" : "involved in positive regulation of" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002423", + "type" : "PROPERTY", + "lbl" : "logical macro assertion on an annotation property" }, { "id" : "http://purl.obolibrary.org/obo/PATO_0001529", "meta" : { @@ -47241,25 +45535,6 @@ }, "type" : "PROPERTY", "lbl" : "immediately causally downstream of" - }, { - "id" : "http://purl.obolibrary.org/obo/NCBITaxon_7742", - "meta" : { - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "Vertebrata", - "xrefs" : [ ] - }, { - "pred" : "hasExactSynonym", - "val" : "vertebrates", - "xrefs" : [ ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "vertebrates", - "xrefs" : [ ] - } ] - }, - "type" : "CLASS", - "lbl" : "Vertebrata " }, { "id" : "http://www.geneontology.org/formats/oboInOwl#hasDbXref", "type" : "PROPERTY", @@ -47409,49 +45684,6 @@ }, "type" : "CLASS", "lbl" : "ventralized" - }, { - "id" : "http://purl.obolibrary.org/obo/NCBITaxon_7711", - "meta" : { - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "chordates", - "xrefs" : [ ] - }, { - "pred" : "hasExactSynonym", - "val" : "chordates", - "xrefs" : [ ] - } ] - }, - "type" : "CLASS", - "lbl" : "Chordata" - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000103", - "meta" : { - "definition" : { - "val" : "The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job", - "xrefs" : [ ] - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Person:Alan Ruttenberg" - } ] - }, - "type" : "INDIVIDUAL", - "lbl" : "failed exploratory term" - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000102", - "meta" : { - "definition" : { - "val" : "data about an ontology part is a data item about a part of an ontology, for example a term", - "xrefs" : [ ] - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Person:Alan Ruttenberg" - } ] - }, - "type" : "CLASS", - "lbl" : "data about an ontology part" }, { "id" : "http://purl.obolibrary.org/obo/GO_0048585", "meta" : { @@ -47799,35 +46031,6 @@ }, "type" : "CLASS", "lbl" : "plumose" - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000078", - "meta" : { - "definition" : { - "val" : "The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value.", - "xrefs" : [ ] - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "GROUP:OBI:" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "curation status specification" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "PERSON:Bill Bug" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "OBI_0000266" - } ] - }, - "type" : "CLASS", - "lbl" : "curation status specification" }, { "id" : "http://purl.obolibrary.org/obo/pato#cell_quality", "meta" : { @@ -47837,21 +46040,6 @@ } ] }, "type" : "PROPERTY" - }, { - "id" : "http://purl.obolibrary.org/obo/NCBITaxon_7776", - "meta" : { - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "jawed vertebrates", - "xrefs" : [ ] - }, { - "pred" : "hasExactSynonym", - "val" : "Gnathostomata", - "xrefs" : [ ] - } ] - }, - "type" : "CLASS", - "lbl" : "Gnathostomata " }, { "id" : "http://www.geneontology.org/formats/oboInOwl#consider", "type" : "PROPERTY", @@ -47961,10 +46149,6 @@ }, "type" : "CLASS", "lbl" : "unicuspidate" - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000030", - "type" : "CLASS", - "lbl" : "information content entity" }, { "id" : "http://purl.obolibrary.org/obo/pato#value_slim", "meta" : { @@ -48437,10 +46621,6 @@ "id" : "http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym", "type" : "PROPERTY", "lbl" : "has_narrow_synonym" - }, { - "id" : "http://purl.obolibrary.org/obo/NCBITaxon_9526", - "type" : "CLASS", - "lbl" : "Catarrhini" }, { "id" : "http://purl.obolibrary.org/obo/GO_0048523", "meta" : { @@ -49134,7 +47314,7 @@ "id" : "http://purl.obolibrary.org/obo/PATO_0045075", "meta" : { "definition" : { - "val" : "A variability which is relatively normal or average", + "val" : "A variability of color which is relatively normal or average", "xrefs" : [ ] }, "subsets" : [ "http://purl.obolibrary.org/obo/pato#value_slim" ], @@ -50474,69 +48654,6 @@ }, "type" : "CLASS", "lbl" : "aerobic (for occurrence)" - }, { - "id" : "http://purl.obolibrary.org/obo/NCBITaxon_2759", - "meta" : { - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "eukaryotes", - "xrefs" : [ ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "Eucarya", - "xrefs" : [ ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "Eucaryotae", - "xrefs" : [ ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "eukaryotes", - "xrefs" : [ ] - }, { - "pred" : "hasExactSynonym", - "val" : "eucaryotes", - "xrefs" : [ ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "Eukarya", - "xrefs" : [ ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "Eukaryotae", - "xrefs" : [ ] - }, { - "pred" : "hasExactSynonym", - "val" : "eucaryotes", - "xrefs" : [ ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "Eucaryotae", - "xrefs" : [ ] - }, { - "pred" : "hasExactSynonym", - "val" : "eukaryotes", - "xrefs" : [ ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "Eukaryotae", - "xrefs" : [ ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "eukaryotes", - "xrefs" : [ ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "Eucarya", - "xrefs" : [ ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "Eukarya", - "xrefs" : [ ] - } ] - }, - "type" : "CLASS", - "lbl" : "Eukaryota" }, { "id" : "http://purl.obolibrary.org/obo/PATO_0001450", "meta" : { @@ -51556,25 +49673,16 @@ "xrefs" : [ ] }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "RO:0003001" - } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "produced_by" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Melissa Haendel" } ] }, "type" : "PROPERTY", - "lbl" : "produced_by" + "lbl" : "produced by" }, { "id" : "http://purl.obolibrary.org/obo/PATO_0000146", "meta" : { @@ -51663,18 +49771,9 @@ "xrefs" : [ ] }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "RO:0003000" - } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "produces" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Melissa Haendel" @@ -51730,21 +49829,6 @@ }, "type" : "CLASS", "lbl" : "decreased depth" - }, { - "id" : "http://purl.obolibrary.org/obo/ENVO_00010483", - "meta" : { - "definition" : { - "val" : "A portion of environmental material is a fiat object which forms the medium or part of the medium of an environmental system.", - "xrefs" : [ "DOI:10.1186/2041-1480-4-43", "MA:ma", "ORCID:0000-0002-4366-3088", "URL:http://ontology.buffalo.edu/smith/articles/niches.html" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "portion of environmental material", - "xrefs" : [ ] - } ] - }, - "type" : "CLASS", - "lbl" : "environmental material" }, { "id" : "http://purl.obolibrary.org/obo/PATO_0000141", "meta" : { @@ -54168,26 +52252,6 @@ }, "type" : "CLASS", "lbl" : "negative regulation of signal transduction" - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000228", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use." - } ] - }, - "type" : "INDIVIDUAL", - "lbl" : "term imported" - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000229", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created." - } ] - }, - "type" : "INDIVIDUAL", - "lbl" : "term split" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002575", "meta" : { @@ -54198,9 +52262,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "The general property hierarchy is:\n\n \"directly P\" SubPropertyOf \"P\"\n Transitive(P)\n\nWhere we have an annotation assertion\n\n \"directly P\" \"is direct form of\" \"P\"" - }, { - "pred" : "http://purl.org/dc/elements/1.1/creator", - "val" : "Chris Mungall" }, { "pred" : "http://purl.org/dc/terms/creator", "val" : "Chris Mungall" @@ -54257,58 +52318,16 @@ }, "type" : "PROPERTY", "lbl" : "causally influences" - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000231", - "meta" : { - "definition" : { - "val" : "Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification.", - "xrefs" : [ ] - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "PERSON:Melanie Courtot" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "has obsolescence reason" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "PERSON:Alan Ruttenberg" - } ] - }, - "type" : "PROPERTY", - "lbl" : "has obsolescence reason" }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000232", "meta" : { - "definition" : { - "val" : "An administrative note of use for a curator but of no use for a user", - "xrefs" : [ ] - }, - "xrefs" : [ { - "val" : "IAO:0000232" - } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "curator_notes" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "PERSON:Alan Ruttenberg" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "curator note" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", - "val" : "true" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000122" } ] }, "type" : "PROPERTY", - "lbl" : "curator notes" + "lbl" : "curator note" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002563", "meta" : { @@ -54492,22 +52511,6 @@ }, "type" : "CLASS", "lbl" : "nucleate quality" - }, { - "id" : "http://purl.org/dc/elements/1.1/creator", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", - "val" : "true" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "dc-creator" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] - }, - "type" : "PROPERTY", - "lbl" : "creator" }, { "id" : "http://purl.obolibrary.org/obo/PATO_0001405", "meta" : { @@ -55203,15 +53206,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "The label for this relation is probably too general for its restricted use, where the domain is a system. It may be relabeled in future" - }, { - "pred" : "http://purl.org/dc/elements/1.1/creator", - "val" : "Pier Buttigieg" }, { "pred" : "http://purl.org/dc/terms/creator", "val" : "Pier Buttigieg" - }, { - "pred" : "http://purl.org/dc/elements/1.1/creator", - "val" : "Chris Mungall" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", "val" : "determined by (system to material entity)" @@ -55397,63 +53394,6 @@ }, "type" : "CLASS", "lbl" : "obsolete inconsistent" - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000226", - "type" : "INDIVIDUAL", - "lbl" : "placeholder removed" - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000227", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "An editor note should explain what were the merged terms and the reason for the merge." - } ] - }, - "type" : "INDIVIDUAL", - "lbl" : "terms merged" - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000224", - "meta" : { - "definition" : { - "val" : "Core is an instance of a grouping of terms from an ontology or ontologies. It is used by the ontology to identify main classes.", - "xrefs" : [ ] - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "PERSON: Melanie Courtot" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "PERSON: Alan Ruttenberg" - } ] - }, - "type" : "INDIVIDUAL", - "lbl" : "core" - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000225", - "meta" : { - "definition" : { - "val" : "The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value.", - "xrefs" : [ ] - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "PERSON: Alan Ruttenberg" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "PERSON: Melanie Courtot" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "obsolescence reason specification" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - } ] - }, - "type" : "CLASS", - "lbl" : "obsolescence reason specification" }, { "id" : "http://purl.obolibrary.org/obo/PATO_0000925", "meta" : { @@ -56009,7 +53949,7 @@ "id" : "http://purl.obolibrary.org/obo/RO_0002608", "meta" : { "definition" : { - "val" : "Inverse of 'causal agent in'", + "val" : "Inverse of 'causal agent in process'", "xrefs" : [ ] }, "basicPropertyValues" : [ { @@ -56018,7 +53958,7 @@ } ] }, "type" : "PROPERTY", - "lbl" : "has causal agent" + "lbl" : "process has causal agent" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002609", "meta" : { @@ -56974,9 +54914,6 @@ }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "my brain is part of my body (continuant parthood, two material entities)" @@ -57089,9 +55026,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "this year has part this day (occurrent parthood)" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_cyclic", - "val" : "false" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" @@ -57104,9 +55038,6 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "chebi_ontology" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)\n\nA continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'." @@ -57128,9 +55059,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" } ] }, "type" : "PROPERTY", @@ -57219,25 +55147,6 @@ }, "type" : "CLASS", "lbl" : "obsolete herbicide sensitivity" - }, { - "id" : "http://purl.obolibrary.org/obo/NCBITaxon_9443", - "meta" : { - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "primate", - "xrefs" : [ ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "primates", - "xrefs" : [ ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "Primata", - "xrefs" : [ ] - } ] - }, - "type" : "CLASS", - "lbl" : "Primates" }, { "id" : "http://purl.obolibrary.org/obo/PATO_0000096", "meta" : { @@ -57277,16 +55186,6 @@ }, "type" : "CLASS", "lbl" : "obsolete insecticide sensitivity" - }, { - "id" : "http://purl.obolibrary.org/obo/ENVO_01001110", - "meta" : { - "definition" : { - "val" : "An environmental system which includes both living and non-living components.", - "xrefs" : [ "https://en.wikipedia.org/wiki/Ecosystem" ] - } - }, - "type" : "CLASS", - "lbl" : "ecosystem" }, { "id" : "http://purl.obolibrary.org/obo/PATO_0000091", "meta" : { @@ -57394,18 +55293,9 @@ "val" : "[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t", "xrefs" : [ ] }, - "xrefs" : [ { - "val" : "BFO:0000067" - } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "contains_process" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", "val" : "Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant" @@ -57420,34 +55310,16 @@ "id" : "http://purl.obolibrary.org/obo/BFO_0000062", "meta" : { "definition" : { - "val" : "X preceded_by Y iff: end(Y) before_or_simultaneous_with start(X)", + "val" : "x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.", "xrefs" : [ ] }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "BFO:0000062" - } ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "is preceded by", - "xrefs" : [ "SIO:000249" ] - }, { - "pred" : "hasExactSynonym", - "val" : "takes place after", - "xrefs" : [ "Allen:precedes" ] - } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "is preceded by" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "preceded by" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "preceded_by" }, { "pred" : "http://purl.org/dc/elements/1.1/source", "val" : "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" @@ -57460,7 +55332,7 @@ } ] }, "type" : "PROPERTY", - "lbl" : "preceded_by" + "lbl" : "preceded by" }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000063", "meta" : { @@ -57469,18 +55341,9 @@ "xrefs" : [ ] }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "BFO:0000063" - } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "precedes" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "precedes" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" } ] }, "type" : "PROPERTY", @@ -57493,7 +55356,7 @@ "id" : "http://purl.obolibrary.org/obo/BFO_0000015", "meta" : { "definition" : { - "val" : "p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])", + "val" : "An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t.", "xrefs" : [ ] } }, @@ -57841,7 +55704,7 @@ "id" : "http://purl.obolibrary.org/obo/BFO_0000004", "meta" : { "definition" : { - "val" : "b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])", + "val" : "A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything.", "xrefs" : [ ] } }, @@ -57938,7 +55801,7 @@ "id" : "http://purl.obolibrary.org/obo/PATO_0001384", "meta" : { "definition" : { - "val" : "A polyploidy quality inhering in a bearer by virtue of the bearer's containing four homologous sets of chromosomes.", + "val" : "A polyploidy quality inhering in a bearer by virtue of the bearer's containing six homologous sets of chromosomes.", "xrefs" : [ "Wikipedia:http://en.wikipedia.org/wiki/Hexaploid" ] }, "subsets" : [ "http://purl.obolibrary.org/obo/pato#cell_quality", "http://purl.obolibrary.org/obo/pato#value_slim" ], @@ -58174,10 +56037,6 @@ }, "type" : "CLASS", "lbl" : "monosomy" - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000001", - "type" : "CLASS", - "lbl" : "entity" }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000002", "meta" : { @@ -58563,22 +56422,10 @@ "definition" : { "val" : "A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time.", "xrefs" : [ ] - }, - "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", - "val" : "http://purl.obolibrary.org/obo/bfo.owl" - } ] + } }, "type" : "CLASS", "lbl" : "generically dependent continuant" - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000027", - "type" : "CLASS", - "lbl" : "object aggregate" - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000029", - "type" : "CLASS", - "lbl" : "site" }, { "id" : "http://purl.obolibrary.org/obo/PATO_0000073", "meta" : { @@ -58721,7 +56568,7 @@ "id" : "http://purl.obolibrary.org/obo/BFO_0000020", "meta" : { "definition" : { - "val" : "b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])", + "val" : "A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same.", "xrefs" : [ ] } }, @@ -58847,10 +56694,6 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0045936", "pred" : "http://purl.obolibrary.org/obo/RO_0002212", "obj" : "http://purl.obolibrary.org/obo/GO_0006796" - }, { - "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_33154", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_2759" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0015003", "pred" : "is_a", @@ -58895,10 +56738,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0002128", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000025" - }, { - "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_1", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000040" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001502", "pred" : "is_a", @@ -58971,10 +56810,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0000050", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000165" - }, { - "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_9526", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_314293" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0000599", "pred" : "is_a", @@ -58991,10 +56826,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0001890", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0002008" - }, { - "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_117570", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7776" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0008152", "pred" : "is_a", @@ -59003,6 +56834,10 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0015004", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0002304" + }, { + "sub" : "http://purl.obolibrary.org/obo/CARO_0001010", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000040" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001769", "pred" : "is_a", @@ -59111,10 +56946,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0001282", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000951" - }, { - "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_9606", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_9605" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002630", "pred" : "subPropertyOf", @@ -59155,14 +56986,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0000318", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000014" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_0009967", - "pred" : "http://purl.obolibrary.org/obo/RO_0002213", - "obj" : "http://purl.obolibrary.org/obo/GO_0007165" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0009968", "pred" : "http://purl.obolibrary.org/obo/RO_0002212", "obj" : "http://purl.obolibrary.org/obo/GO_0007165" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0009967", + "pred" : "http://purl.obolibrary.org/obo/RO_0002213", + "obj" : "http://purl.obolibrary.org/obo/GO_0007165" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001863", "pred" : "is_a", @@ -59187,10 +57018,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0000949", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000052" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0000409", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/IAO_0000102" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002126", "pred" : "is_a", @@ -59211,10 +57038,6 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0048519", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GO_0050789" - }, { - "sub" : "http://purl.obolibrary.org/obo/PCO_0000027", - "pred" : "http://purl.obolibrary.org/obo/RO_0002351", - "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001927", "pred" : "is_a", @@ -59263,14 +57086,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0001679", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000918" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_0005886", - "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", - "obj" : "http://purl.obolibrary.org/obo/GO_0071944" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001728", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001727" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0005886", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", + "obj" : "http://purl.obolibrary.org/obo/GO_0071944" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001678", "pred" : "is_a", @@ -59471,10 +57294,6 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0016740", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GO_0003824" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0000027", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/IAO_0000030" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001948", "pred" : "is_a", @@ -59491,10 +57310,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0001997", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000467" - }, { - "sub" : "http://www.geneontology.org/formats/oboInOwl#Subset", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/IAO_0000102" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0045070", "pred" : "is_a", @@ -59503,10 +57318,6 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0043393", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GO_0051098" - }, { - "sub" : "http://purl.obolibrary.org/obo/PCO_0000004", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0002003" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001904", "pred" : "is_a", @@ -59615,10 +57426,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0002259", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000140" - }, { - "sub" : "http://purl.obolibrary.org/obo/PO_0000003", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PO_0009011" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001645", "pred" : "is_a", @@ -59655,10 +57462,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0001877", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001419" - }, { - "sub" : "http://purl.obolibrary.org/obo/PCO_0000003", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0002003" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002482", "pred" : "is_a", @@ -59675,10 +57478,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0002043", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0002041" - }, { - "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_32525", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_40674" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0019220", "pred" : "http://purl.obolibrary.org/obo/RO_0002211", @@ -59727,10 +57526,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0001253", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000321" - }, { - "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_9605", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_207598" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001359", "pred" : "is_a", @@ -59791,10 +57586,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0000060", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000051" - }, { - "sub" : "http://purl.obolibrary.org/obo/ENVO_01001002", - "pred" : "http://purl.obolibrary.org/obo/RO_0002507", - "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001595", "pred" : "is_a", @@ -59839,10 +57630,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0000569", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000119" - }, { - "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_7776", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7742" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0000945", "pred" : "is_a", @@ -59899,14 +57686,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002013", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002334" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0001706", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0002265" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0055002", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0002304" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0001706", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0002265" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001724", "pred" : "is_a", @@ -59975,10 +57762,6 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002596", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002500" - }, { - "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_1437010", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_9347" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0015028", "pred" : "is_a", @@ -60003,10 +57786,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0000069", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000068" - }, { - "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_32524", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_32523" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002248", "pred" : "is_a", @@ -60019,10 +57798,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0000406", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001591" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0000421", - "pred" : "type", - "obj" : "http://purl.obolibrary.org/obo/IAO_0000409" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0005622", "pred" : "is_a", @@ -60043,6 +57818,10 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0002467", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000052" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0040027", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0001393" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0019220", "pred" : "is_a", @@ -60123,10 +57902,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0001487", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000011" - }, { - "sub" : "http://purl.obolibrary.org/obo/ENVO_01001110", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/ENVO_01000254" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001398", "pred" : "is_a", @@ -60139,10 +57914,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0000948", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0002008" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0000120", - "pred" : "type", - "obj" : "http://purl.obolibrary.org/obo/IAO_0000078" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002442", "pred" : "is_a", @@ -60251,10 +58022,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0001378", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001377" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0000226", - "pred" : "type", - "obj" : "http://purl.obolibrary.org/obo/IAO_0000225" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001287", "pred" : "is_a", @@ -60279,10 +58046,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0001555", "pred" : "http://purl.obolibrary.org/obo/pato#reciprocal_of", "obj" : "http://purl.obolibrary.org/obo/PATO_0000070" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0000121", - "pred" : "type", - "obj" : "http://purl.obolibrary.org/obo/IAO_0000078" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002508", "pred" : "subPropertyOf", @@ -60303,10 +58066,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0000761", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0002303" - }, { - "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_32523", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_1338369" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001907", "pred" : "is_a", @@ -60335,10 +58094,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0001460", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001458" - }, { - "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_33208", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_33154" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002028", "pred" : "is_a", @@ -60391,14 +58146,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0015010", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0015009" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0000381", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0000044" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0010004", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0010002" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0000381", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0000044" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0045083", "pred" : "is_a", @@ -60431,10 +58186,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0002342", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0002227" - }, { - "sub" : "http://purl.obolibrary.org/obo/ENVO_01001000", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/ENVO_01001110" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001989", "pred" : "is_a", @@ -60447,10 +58198,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0002334", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0002303" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0000103", - "pred" : "type", - "obj" : "http://purl.obolibrary.org/obo/IAO_0000225" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001716", "pred" : "is_a", @@ -60487,14 +58234,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0002113", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0002112" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0040005", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0000133" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002222", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0002220" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0040005", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0000133" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0048018", "pred" : "is_a", @@ -60527,10 +58274,6 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002352", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002328" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0000420", - "pred" : "type", - "obj" : "http://purl.obolibrary.org/obo/IAO_0000409" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0045015", "pred" : "is_a", @@ -60543,14 +58286,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0000014", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001300" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0002181", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0000140" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0010563", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GO_0031324" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0002181", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0000140" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002048", "pred" : "is_a", @@ -60664,9 +58407,9 @@ "pred" : "http://purl.obolibrary.org/obo/RO_0002212", "obj" : "http://purl.obolibrary.org/obo/GO_0009987" }, { - "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_314295", + "sub" : "http://purl.obolibrary.org/obo/GO_0016020", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_9526" + "obj" : "http://purl.obolibrary.org/obo/CARO_0000014" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002307", "pred" : "is_a", @@ -60731,10 +58474,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0002009", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000052" - }, { - "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_9347", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_32525" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0005515", "pred" : "is_a", @@ -60755,10 +58494,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0000410", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000052" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0000125", - "pred" : "type", - "obj" : "http://purl.obolibrary.org/obo/IAO_0000078" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001167", "pred" : "is_a", @@ -60767,10 +58502,6 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002216", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002500" - }, { - "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_33511", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_33213" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002024", "pred" : "subPropertyOf", @@ -60779,10 +58510,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0001397", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001396" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0000124", - "pred" : "type", - "obj" : "http://purl.obolibrary.org/obo/IAO_0000078" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0045080", "pred" : "is_a", @@ -60803,10 +58530,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0000304", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0002303" - }, { - "sub" : "http://purl.obolibrary.org/obo/PCO_0000000", - "pred" : "http://purl.obolibrary.org/obo/RO_0002351", - "obj" : "http://purl.obolibrary.org/obo/CARO_0001010" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002396", "pred" : "is_a", @@ -60875,10 +58598,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0045016", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0045001" - }, { - "sub" : "http://purl.obolibrary.org/obo/ENVO_01001055", - "pred" : "http://purl.obolibrary.org/obo/RO_0002507", - "obj" : "http://purl.obolibrary.org/obo/CARO_0000006" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0000078", "pred" : "is_a", @@ -60971,10 +58690,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0001983", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000141" - }, { - "sub" : "http://purl.obolibrary.org/obo/ENVO_00002297", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000040" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0045006", "pred" : "is_a", @@ -61043,10 +58758,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0002386", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0002008" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0000002", - "pred" : "type", - "obj" : "http://purl.obolibrary.org/obo/IAO_0000078" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0000642", "pred" : "is_a", @@ -61071,18 +58782,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002431", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002500" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0000227", - "pred" : "type", - "obj" : "http://purl.obolibrary.org/obo/IAO_0000225" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0000643", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001598" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0000122", - "pred" : "type", - "obj" : "http://purl.obolibrary.org/obo/IAO_0000078" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002050", "pred" : "is_a", @@ -61159,10 +58862,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0001940", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000586" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_0016020", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_0044464" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001817", "pred" : "is_a", @@ -61183,10 +58882,6 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0043227", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GO_0043226" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0000229", - "pred" : "type", - "obj" : "http://purl.obolibrary.org/obo/IAO_0000225" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001622", "pred" : "is_a", @@ -61215,10 +58910,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0001168", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001020" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0000123", - "pred" : "type", - "obj" : "http://purl.obolibrary.org/obo/IAO_0000078" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002354", "pred" : "subPropertyOf", @@ -61227,18 +58918,10 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0002395", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000628" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0000228", - "pred" : "type", - "obj" : "http://purl.obolibrary.org/obo/IAO_0000225" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002131", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0002168" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0000102", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/IAO_0000027" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001505", "pred" : "is_a", @@ -61275,10 +58958,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0002453", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000141" - }, { - "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_314146", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_1437010" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002306", "pred" : "is_a", @@ -61439,10 +59118,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0045028", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000891" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0000078", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/IAO_0000102" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0000584", "pred" : "is_a", @@ -61543,10 +59218,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0001553", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001459" - }, { - "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_9443", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_314146" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001838", "pred" : "is_a", @@ -61619,14 +59290,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0002303", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0002301" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0002373", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0001769" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002110", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0002099" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0002373", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0001769" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0004033", "pred" : "subPropertyOf", @@ -61727,10 +59398,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0001727", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001241" - }, { - "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_8287", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_117571" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0000077", "pred" : "is_a", @@ -61779,10 +59446,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0001259", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000951" - }, { - "sub" : "http://purl.obolibrary.org/obo/ENVO_00010483", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000040" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002413", "pred" : "is_a", @@ -61815,14 +59478,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0002304", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0002300" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0000757", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0000185" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002328", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0002326" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0000757", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0000185" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002111", "pred" : "is_a", @@ -61867,10 +59530,6 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0071944", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GO_0110165" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002215", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002328" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0000402", "pred" : "is_a", @@ -61959,10 +59618,6 @@ "sub" : "http://purl.obolibrary.org/obo/BFO_0000062", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002086" - }, { - "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_1338369", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_8287" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0000405", "pred" : "is_a", @@ -62003,10 +59658,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0001832", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0002305" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0000030", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000031" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0000396", "pred" : "is_a", @@ -62127,10 +59778,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0001859", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0002305" - }, { - "sub" : "http://purl.obolibrary.org/obo/PCO_0000000", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000027" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0004034", "pred" : "subPropertyOf", @@ -62151,14 +59798,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0001833", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0002303" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0001230", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0001018" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0005008", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0002266" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0001230", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0001018" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0000276", "pred" : "is_a", @@ -62319,10 +59966,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0045043", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0045040" - }, { - "sub" : "http://purl.obolibrary.org/obo/ENVO_01001057", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/ENVO_01000254" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002217", "pred" : "inverseOf", @@ -62583,14 +60226,14 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0043231", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GO_0043229" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0002292", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0000141" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002182", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001241" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0002292", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0000141" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001831", "pred" : "is_a", @@ -62643,10 +60286,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0001344", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001342" - }, { - "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_314293", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_376913" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0045045", "pred" : "is_a", @@ -62683,10 +60322,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0045089", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0045088" - }, { - "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_7742", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_89593" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001780", "pred" : "is_a", @@ -62715,14 +60350,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0045041", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0045040" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0015005", - "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", - "obj" : "http://purl.obolibrary.org/obo/PATO_0002212" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001430", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001428" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0015005", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", + "obj" : "http://purl.obolibrary.org/obo/PATO_0002212" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002324", "pred" : "is_a", @@ -62895,14 +60530,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0000983", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000970" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0001250", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0000320" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001900", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000039" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0001250", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0000320" }, { "sub" : "http://purl.obolibrary.org/obo/GO_1900122", "pred" : "is_a", @@ -62931,18 +60566,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002577", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/BFO_0000040" - }, { - "sub" : "http://purl.obolibrary.org/obo/ENVO_01000951", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/ENVO_01000254" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0000592", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000915" - }, { - "sub" : "http://purl.obolibrary.org/obo/PCO_0000003", - "pred" : "http://purl.obolibrary.org/obo/RO_0000052", - "obj" : "http://purl.obolibrary.org/obo/PCO_0000001" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002449", "pred" : "subPropertyOf", @@ -62963,10 +60590,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0002632", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000068" - }, { - "sub" : "http://purl.obolibrary.org/obo/PO_0009011", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PO_0025131" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002141", "pred" : "is_a", @@ -63043,34 +60666,30 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0030545", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GO_0098772" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0050001", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0000161" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002196", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0002193" }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0045088", + "sub" : "http://purl.obolibrary.org/obo/PATO_0050001", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0045073" + "obj" : "http://purl.obolibrary.org/obo/PATO_0000161" }, { - "sub" : "http://purl.obolibrary.org/obo/GO_0051174", + "sub" : "http://purl.obolibrary.org/obo/PATO_0045088", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_0031323" + "obj" : "http://purl.obolibrary.org/obo/PATO_0045073" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002197", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0002182" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0051174", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GO_0031323" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0045048", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001806" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002202", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002254" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0045069", "pred" : "is_a", @@ -63087,10 +60706,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0002630", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000057" - }, { - "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_207598", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_9604" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002418", "pred" : "subPropertyOf", @@ -63255,14 +60870,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0000985", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000973" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0001306", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0000146" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001161", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000033" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0001306", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0000146" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0005024", "pred" : "is_a", @@ -63471,10 +61086,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0045085", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0045084" - }, { - "sub" : "http://purl.obolibrary.org/obo/ENVO_01001055", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/ENVO_01000254" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002353", "pred" : "is_a", @@ -63575,14 +61186,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0015012", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001547" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0001874", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0001873" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002405", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000141" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0001874", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0001873" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002534", "pred" : "is_a", @@ -63879,10 +61490,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0000587", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000117" - }, { - "sub" : "http://purl.obolibrary.org/obo/ENVO_01000952", - "pred" : "http://purl.obolibrary.org/obo/RO_0002234", - "obj" : "http://purl.obolibrary.org/obo/ENVO_01000313" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0000591", "pred" : "is_a", @@ -63979,14 +61586,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0001672", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001476" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0000761", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0001707" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001321", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0002326" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0000761", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0001707" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001839", "pred" : "is_a", @@ -64027,10 +61634,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0000645", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0002290" - }, { - "sub" : "http://purl.obolibrary.org/obo/PCO_0000018", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PCO_0000000" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001186", "pred" : "is_a", @@ -64047,14 +61650,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0000586", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000117" - }, { - "sub" : "http://purl.obolibrary.org/obo/PCO_0000017", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PCO_0000018" - }, { - "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_89593", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7711" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002298", "pred" : "is_a", @@ -64063,10 +61658,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0001328", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001325" - }, { - "sub" : "http://purl.obolibrary.org/obo/BFO_0000029", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000141" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001437", "pred" : "is_a", @@ -64127,10 +61718,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0002035", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000140" - }, { - "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_9604", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_314295" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0000760", "pred" : "is_a", @@ -64147,14 +61734,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0001339", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000025" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0000627", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0000060" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0000619", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000140" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0000627", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0000060" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0009967", "pred" : "is_a", @@ -64163,14 +61750,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0010002", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0002062" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0001247", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0000319" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001163", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001159" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0001247", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0000319" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001381", "pred" : "is_a", @@ -64331,10 +61918,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0002339", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000454" - }, { - "sub" : "http://purl.obolibrary.org/obo/CHEBI_59999", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CHEBI_24431" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002507", "pred" : "inverseOf", @@ -64355,10 +61938,6 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0050794", "pred" : "http://purl.obolibrary.org/obo/RO_0002211", "obj" : "http://purl.obolibrary.org/obo/GO_0009987" - }, { - "sub" : "http://purl.obolibrary.org/obo/PCO_0000000", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PCO_0000031" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0005003", "pred" : "is_a", @@ -64367,10 +61946,6 @@ "sub" : "http://purl.obolibrary.org/obo/GO_1900120", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GO_0043393" - }, { - "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_33213", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0023057", "pred" : "http://purl.obolibrary.org/obo/RO_0002212", @@ -64391,10 +61966,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0002221", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0002305" - }, { - "sub" : "http://purl.obolibrary.org/obo/PCO_0000029", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PCO_0000000" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0000008", "pred" : "is_a", @@ -64419,10 +61990,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0002260", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000622" - }, { - "sub" : "http://purl.obolibrary.org/obo/PCO_0000027", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PCO_0000018" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0045091", "pred" : "is_a", @@ -64447,10 +62014,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0000708", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0002303" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0000428", - "pred" : "type", - "obj" : "http://purl.obolibrary.org/obo/IAO_0000078" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0000122", "pred" : "is_a", @@ -64499,10 +62062,6 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0007165", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/GO_0051716" - }, { - "sub" : "http://purl.obolibrary.org/obo/PCO_0000001", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PCO_0000018" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002189", "pred" : "is_a", @@ -64567,10 +62126,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0001824", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001822" - }, { - "sub" : "http://purl.obolibrary.org/obo/PCO_0000028", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PCO_0000000" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002250", "pred" : "is_a", @@ -64619,10 +62174,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0002383", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0002381" - }, { - "sub" : "http://purl.obolibrary.org/obo/PO_0025131", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000040" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0051348", "pred" : "is_a", @@ -64739,10 +62290,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0002251", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0002248" - }, { - "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_7711", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_33511" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002628", "pred" : "is_a", @@ -64907,14 +62454,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0001964", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000405" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0002507", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0000025" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0000998", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000992" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0002507", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0000025" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0025001", "pred" : "is_a", @@ -64983,10 +62530,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0002367", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000384" - }, { - "sub" : "http://purl.obolibrary.org/obo/ENVO_01001000", - "pred" : "http://purl.obolibrary.org/obo/RO_0002507", - "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_131567" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001786", "pred" : "is_a", @@ -65039,14 +62582,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0002541", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001995" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0002460", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0000141" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002331", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001431" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0002460", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0000141" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0000261", "pred" : "is_a", @@ -65063,10 +62606,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0002080", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001444" - }, { - "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_2759", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_131567" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001293", "pred" : "is_a", @@ -65103,10 +62642,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0025000", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001018" - }, { - "sub" : "http://purl.obolibrary.org/obo/ENVO_01000998", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/ENVO_01000254" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0045044", "pred" : "is_a", @@ -65123,10 +62658,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0002300", "pred" : "http://purl.obolibrary.org/obo/pato#increased_in_magnitude_relative_to", "obj" : "http://purl.obolibrary.org/obo/PATO_0000461" - }, { - "sub" : "http://purl.obolibrary.org/obo/PCO_0000004", - "pred" : "http://purl.obolibrary.org/obo/RO_0000052", - "obj" : "http://purl.obolibrary.org/obo/PCO_0000002" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002270", "pred" : "is_a", @@ -65191,10 +62722,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0002295", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001925" - }, { - "sub" : "http://purl.obolibrary.org/obo/ENVO_01001002", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/ENVO_01001000" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002428", "pred" : "subPropertyOf", @@ -65236,17 +62763,13 @@ "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000186" }, { - "sub" : "http://purl.obolibrary.org/obo/CHEBI_46662", + "sub" : "http://purl.obolibrary.org/obo/PATO_0002365", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CHEBI_59999" + "obj" : "http://purl.obolibrary.org/obo/PATO_0000383" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002185", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0002183" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0002365", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0000383" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0000646", "pred" : "is_a", @@ -65287,10 +62810,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0001319", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000189" - }, { - "sub" : "http://purl.obolibrary.org/obo/ENVO_01000997", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/ENVO_01000254" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0000694", "pred" : "is_a", @@ -65311,14 +62830,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0001518", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001516" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0002091", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0001309" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001627", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001626" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0002091", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0001309" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001594", "pred" : "is_a", @@ -65519,10 +63038,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0001702", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001424" - }, { - "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_117571", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_117570" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002057", "pred" : "is_a", @@ -65703,10 +63218,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0002058", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000587" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0000225", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/IAO_0000102" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001738", "pred" : "is_a", @@ -65911,14 +63422,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0001440", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001531" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0002376", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0002014" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001855", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000140" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0002376", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0002014" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002163", "pred" : "is_a", @@ -65999,10 +63510,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0002359", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000052" - }, { - "sub" : "http://purl.obolibrary.org/obo/ENVO_01000998", - "pred" : "http://purl.obolibrary.org/obo/RO_0002507", - "obj" : "http://purl.obolibrary.org/obo/ENVO_00010483" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002278", "pred" : "is_a", @@ -66079,10 +63586,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0001441", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001531" - }, { - "sub" : "http://purl.obolibrary.org/obo/ENVO_01000952", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/ENVO_02500027" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001291", "pred" : "is_a", @@ -66295,14 +63798,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0001807", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001806" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0001997", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0002301" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0000992", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001548" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0001997", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0002301" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002348", "pred" : "is_a", @@ -66331,10 +63834,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0000274", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001434" - }, { - "sub" : "http://purl.obolibrary.org/obo/ENVO_01000952", - "pred" : "http://purl.obolibrary.org/obo/RO_0002233", - "obj" : "http://purl.obolibrary.org/obo/ENVO_01000951" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0015025", "pred" : "is_a", @@ -66419,10 +63918,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0001850", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000141" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0000410", - "pred" : "type", - "obj" : "http://purl.obolibrary.org/obo/IAO_0000409" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0000309", "pred" : "is_a", @@ -66463,10 +63958,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0001922", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000628" - }, { - "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_40674", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_32524" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001929", "pred" : "http://purl.obolibrary.org/obo/pato#towards", @@ -66543,10 +64034,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0045019", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001720" - }, { - "sub" : "http://purl.obolibrary.org/obo/PCO_0000031", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000040" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0045027", "pred" : "is_a", @@ -66671,14 +64158,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0002172", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001786" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0002279", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0002278" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002299", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0002078" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0002279", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0002278" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002101", "pred" : "is_a", @@ -66751,10 +64238,6 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002405", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002087" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0000224", - "pred" : "type", - "obj" : "http://www.geneontology.org/formats/oboInOwl#Subset" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001688", "pred" : "is_a", @@ -66815,10 +64298,6 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002566", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002506" - }, { - "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_131567", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_1" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001917", "pred" : "is_a", @@ -66875,10 +64354,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0045011", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0045001" - }, { - "sub" : "http://purl.obolibrary.org/obo/BFO_0000003", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000001" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002282", "pred" : "is_a", @@ -66887,10 +64362,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0015004", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0015002" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002410", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002609" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0045059", "pred" : "is_a", @@ -66899,14 +64370,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0002283", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0002303" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0000626", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0000140" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0000634", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000060" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0000626", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0000140" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002370", "pred" : "is_a", @@ -67019,10 +64490,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0001695", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0002305" - }, { - "sub" : "http://purl.obolibrary.org/obo/BFO_0000002", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000001" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001751", "pred" : "is_a", @@ -67171,10 +64638,6 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0032091", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GO_0051100" - }, { - "sub" : "http://purl.obolibrary.org/obo/CARO_0001010", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PCO_0000031" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0045035", "pred" : "is_a", @@ -67379,10 +64842,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0002290", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001241" - }, { - "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_376913", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_9443" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0000595", "pred" : "is_a", @@ -67423,10 +64882,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0000380", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000912" - }, { - "sub" : "http://purl.obolibrary.org/obo/PCO_0000002", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/ENVO_01001110" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001478", "pred" : "is_a", @@ -67475,10 +64930,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0001476", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0002303" - }, { - "sub" : "http://purl.obolibrary.org/obo/ENVO_02500000", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000015" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0045054", "pred" : "is_a", @@ -67643,14 +65094,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002217", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0000056" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0002345", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0002007" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001814", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001439" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0002345", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0002007" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0045034", "pred" : "is_a", @@ -67699,10 +65150,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0002434", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000140" - }, { - "sub" : "http://purl.obolibrary.org/obo/ENVO_02500027", - "pred" : "http://purl.obolibrary.org/obo/RO_0002218", - "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002327", "pred" : "is_a", @@ -67763,10 +65210,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0045049", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000516" - }, { - "sub" : "http://purl.obolibrary.org/obo/ENVO_01000313", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/ENVO_01000254" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001547", "pred" : "is_a", @@ -68115,10 +65558,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0001975", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001976" - }, { - "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_6072", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001790", "pred" : "is_a", @@ -68199,10 +65638,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0001263", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000324" - }, { - "sub" : "http://purl.obolibrary.org/obo/ENVO_02500027", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/ENVO_02500000" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0000956", "pred" : "is_a", @@ -68215,14 +65650,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0005015", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000117" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0001567", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0000060" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001990", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001309" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0001567", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0000060" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0005012", "pred" : "is_a", @@ -68399,14 +65834,14 @@ "sub" : "http://purl.obolibrary.org/obo/GO_1902531", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GO_0009966" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0000574", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0000122" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0045062", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001537" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0000574", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0000122" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0005020", "pred" : "is_a", @@ -68811,10 +66246,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0000366", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000039" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0000423", - "pred" : "type", - "obj" : "http://purl.obolibrary.org/obo/IAO_0000078" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0045075", "pred" : "is_a", @@ -68911,10 +66342,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0002428", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000052" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0001062", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000004" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0044093", "pred" : "is_a", @@ -68931,10 +66358,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0000186", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001995" - }, { - "sub" : "http://purl.obolibrary.org/obo/ENVO_00002297", - "pred" : "http://purl.obolibrary.org/obo/RO_0002508", - "obj" : "http://purl.obolibrary.org/obo/ENVO_01000254" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0051174", "pred" : "http://purl.obolibrary.org/obo/RO_0002211", @@ -69187,10 +66610,6 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0045936", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GO_0019220" - }, { - "sub" : "http://purl.obolibrary.org/obo/BFO_0000027", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000040" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001448", "pred" : "is_a", @@ -69215,14 +66634,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0002168", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000133" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0045092", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0045090" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002149", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001788" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0045092", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0045090" }, { "sub" : "http://purl.obolibrary.org/obo/GO_1900122", "pred" : "http://purl.obolibrary.org/obo/RO_0002213", @@ -69375,14 +66794,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0001317", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001305" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0001885", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0001884" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002426", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000052" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0001885", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0001884" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001365", "pred" : "is_a", @@ -69407,18 +66826,10 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0045093", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0045090" - }, { - "sub" : "http://purl.obolibrary.org/obo/PCO_0000002", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PCO_0000029" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001577", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0002305" - }, { - "sub" : "http://purl.obolibrary.org/obo/PCO_0000002", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PCO_0000028" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001857", "pred" : "is_a", @@ -69453,22 +66864,22 @@ "subsets" : [ ], "xrefs" : [ ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#auto-generated-by", - "val" : "OBO-Edit 2.3.1" + "pred" : "http://purl.org/dc/elements/1.1/description", + "val" : "An ontology of phenotypic qualities (properties, attributes or characteristics)." }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#date", - "val" : "07:02:2018 10:27" + "pred" : "http://purl.org/dc/elements/1.1/title", + "val" : "PATO - the Phenotype And Trait Ontology" + }, { + "pred" : "http://purl.org/dc/terms/license", + "val" : "https://creativecommons.org/licenses/by/3.0/" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#default-namespace", "val" : "quality" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBOFormatVersion", "val" : "1.2" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#saved-by", - "val" : "segerdel" } ], - "version" : "http://purl.obolibrary.org/obo/pato/releases/2019-11-05/pato-full.json" + "version" : "http://purl.obolibrary.org/obo/pato/releases/2019-12-03/pato-full.json" }, "equivalentNodesSets" : [ ], "logicalDefinitionAxioms" : [ { @@ -69555,16 +66966,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/pato#decreased_in_magnitude_relative_to", "fillerId" : "http://purl.obolibrary.org/obo/PATO_0000461" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/ENVO_01000952", - "genusIds" : [ "http://purl.obolibrary.org/obo/ENVO_02500027" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002233", - "fillerId" : "http://purl.obolibrary.org/obo/ENVO_01000951" - }, { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002234", - "fillerId" : "http://purl.obolibrary.org/obo/ENVO_01000313" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/PATO_0002298", "genusIds" : [ "http://purl.obolibrary.org/obo/PATO_0001488" ], @@ -69586,13 +66987,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/pato#towards", "fillerId" : "http://purl.obolibrary.org/obo/PATO_0000146" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/ENVO_02500027", - "genusIds" : [ "http://purl.obolibrary.org/obo/ENVO_02500000" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002218", - "fillerId" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/PATO_0000595", "genusIds" : [ "http://purl.obolibrary.org/obo/PATO_0000918" ], @@ -69726,13 +67120,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/pato#has_relative_magnitude", "fillerId" : "http://purl.obolibrary.org/obo/PATO_0000461" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/ENVO_01001002", - "genusIds" : [ "http://purl.obolibrary.org/obo/ENVO_01000254" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002507", - "fillerId" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/PATO_0001163", "genusIds" : [ "http://purl.obolibrary.org/obo/PATO_0001159" ], @@ -69915,10 +67302,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/pato#has_relative_magnitude", "fillerId" : "http://purl.obolibrary.org/obo/PATO_0000461" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/ENVO_01001057", - "genusIds" : [ "http://purl.obolibrary.org/obo/ENVO_01000254" ], - "restrictions" : [ null ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/PATO_0000386", "genusIds" : [ "http://purl.obolibrary.org/obo/PATO_0000048" ], @@ -70165,17 +67548,17 @@ "fillerId" : "http://purl.obolibrary.org/obo/PATO_0000461" } ] }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0043086", + "definedClassId" : "http://purl.obolibrary.org/obo/GO_0043085", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0008150" ], "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002212", + "propertyId" : "http://purl.obolibrary.org/obo/RO_0002213", "fillerId" : "http://purl.obolibrary.org/obo/GO_0003824" } ] }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0043085", + "definedClassId" : "http://purl.obolibrary.org/obo/GO_0043086", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0008150" ], "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002213", + "propertyId" : "http://purl.obolibrary.org/obo/RO_0002212", "fillerId" : "http://purl.obolibrary.org/obo/GO_0003824" } ] }, { @@ -70193,15 +67576,15 @@ "fillerId" : "http://purl.obolibrary.org/obo/PATO_0000461" } ] }, { - "definedClassId" : "http://purl.obolibrary.org/obo/PATO_0001552", - "genusIds" : [ "http://purl.obolibrary.org/obo/PATO_0001457" ], + "definedClassId" : "http://purl.obolibrary.org/obo/PATO_0001779", + "genusIds" : [ "http://purl.obolibrary.org/obo/PATO_0001230" ], "restrictions" : [ { "propertyId" : "http://purl.obolibrary.org/obo/pato#decreased_in_magnitude_relative_to", "fillerId" : "http://purl.obolibrary.org/obo/PATO_0000461" } ] }, { - "definedClassId" : "http://purl.obolibrary.org/obo/PATO_0001779", - "genusIds" : [ "http://purl.obolibrary.org/obo/PATO_0001230" ], + "definedClassId" : "http://purl.obolibrary.org/obo/PATO_0001552", + "genusIds" : [ "http://purl.obolibrary.org/obo/PATO_0001457" ], "restrictions" : [ { "propertyId" : "http://purl.obolibrary.org/obo/pato#decreased_in_magnitude_relative_to", "fillerId" : "http://purl.obolibrary.org/obo/PATO_0000461" @@ -70290,13 +67673,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/pato#has_relative_magnitude", "fillerId" : "http://purl.obolibrary.org/obo/PATO_0000461" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/ENVO_01001055", - "genusIds" : [ "http://purl.obolibrary.org/obo/ENVO_01000254" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002507", - "fillerId" : "http://purl.obolibrary.org/obo/CARO_0000006" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/PATO_0000570", "genusIds" : [ "http://purl.obolibrary.org/obo/PATO_0000119" ], @@ -70304,10 +67680,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/pato#increased_in_magnitude_relative_to", "fillerId" : "http://purl.obolibrary.org/obo/PATO_0000461" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/ENVO_01000997", - "genusIds" : [ "http://purl.obolibrary.org/obo/ENVO_01000254" ], - "restrictions" : [ null ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/PATO_0045053", "genusIds" : [ "http://purl.obolibrary.org/obo/PATO_0000119" ], @@ -70435,17 +67807,17 @@ "fillerId" : "http://purl.obolibrary.org/obo/PATO_0000461" } ] }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0051347", + "definedClassId" : "http://purl.obolibrary.org/obo/GO_0051348", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0008150" ], "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002213", + "propertyId" : "http://purl.obolibrary.org/obo/RO_0002212", "fillerId" : "http://purl.obolibrary.org/obo/GO_0016740" } ] }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0051348", + "definedClassId" : "http://purl.obolibrary.org/obo/GO_0051347", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0008150" ], "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002212", + "propertyId" : "http://purl.obolibrary.org/obo/RO_0002213", "fillerId" : "http://purl.obolibrary.org/obo/GO_0016740" } ] }, { @@ -70813,17 +68185,17 @@ "fillerId" : "http://purl.obolibrary.org/obo/PATO_0000461" } ] }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0048585", + "definedClassId" : "http://purl.obolibrary.org/obo/GO_0048584", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0008150" ], "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002212", + "propertyId" : "http://purl.obolibrary.org/obo/RO_0002213", "fillerId" : "http://purl.obolibrary.org/obo/GO_0050896" } ] }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0048584", + "definedClassId" : "http://purl.obolibrary.org/obo/GO_0048585", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0008150" ], "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002213", + "propertyId" : "http://purl.obolibrary.org/obo/RO_0002212", "fillerId" : "http://purl.obolibrary.org/obo/GO_0050896" } ] }, { @@ -70966,10 +68338,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/pato#has_relative_magnitude", "fillerId" : "http://purl.obolibrary.org/obo/PATO_0000461" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/ENVO_01000313", - "genusIds" : [ "http://purl.obolibrary.org/obo/ENVO_01000254" ], - "restrictions" : [ null ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/PATO_0045067", "genusIds" : [ "http://purl.obolibrary.org/obo/PATO_0000146" ], @@ -71005,13 +68373,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/pato#decreased_in_magnitude_relative_to", "fillerId" : "http://purl.obolibrary.org/obo/PATO_0000461" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/PCO_0000004", - "genusIds" : [ "http://purl.obolibrary.org/obo/PATO_0002003" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0000052", - "fillerId" : "http://purl.obolibrary.org/obo/PCO_0000002" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/PATO_0001693", "genusIds" : [ "http://purl.obolibrary.org/obo/PATO_0000998" ], @@ -71040,13 +68401,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/pato#decreased_in_magnitude_relative_to", "fillerId" : "http://purl.obolibrary.org/obo/PATO_0000461" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/PCO_0000003", - "genusIds" : [ "http://purl.obolibrary.org/obo/PATO_0002003" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0000052", - "fillerId" : "http://purl.obolibrary.org/obo/PCO_0000001" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/PATO_0001714", "genusIds" : [ "http://purl.obolibrary.org/obo/PATO_0001334" ], @@ -71167,17 +68521,17 @@ "fillerId" : "http://purl.obolibrary.org/obo/PATO_0000461" } ] }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0048518", + "definedClassId" : "http://purl.obolibrary.org/obo/GO_0048519", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0008150" ], "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002213", + "propertyId" : "http://purl.obolibrary.org/obo/RO_0002212", "fillerId" : "http://purl.obolibrary.org/obo/GO_0008150" } ] }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0048519", + "definedClassId" : "http://purl.obolibrary.org/obo/GO_0048518", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0008150" ], "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002212", + "propertyId" : "http://purl.obolibrary.org/obo/RO_0002213", "fillerId" : "http://purl.obolibrary.org/obo/GO_0008150" } ] }, { @@ -71209,17 +68563,17 @@ "fillerId" : "http://purl.obolibrary.org/obo/PATO_0000461" } ] }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0023056", + "definedClassId" : "http://purl.obolibrary.org/obo/GO_0023057", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0008150" ], "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002213", + "propertyId" : "http://purl.obolibrary.org/obo/RO_0002212", "fillerId" : "http://purl.obolibrary.org/obo/GO_0023052" } ] }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0023057", + "definedClassId" : "http://purl.obolibrary.org/obo/GO_0023056", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0008150" ], "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002212", + "propertyId" : "http://purl.obolibrary.org/obo/RO_0002213", "fillerId" : "http://purl.obolibrary.org/obo/GO_0023052" } ] }, { @@ -71229,13 +68583,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002213", "fillerId" : "http://purl.obolibrary.org/obo/GO_0016301" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/ENVO_01001000", - "genusIds" : [ "http://purl.obolibrary.org/obo/ENVO_01000254" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002507", - "fillerId" : "http://purl.obolibrary.org/obo/NCBITaxon_131567" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/PATO_0001831", "genusIds" : [ "http://purl.obolibrary.org/obo/PATO_0000888" ], @@ -71304,17 +68651,17 @@ "fillerId" : "http://purl.obolibrary.org/obo/PATO_0000461" } ] }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0010563", + "definedClassId" : "http://purl.obolibrary.org/obo/GO_0010562", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0008150" ], "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002212", + "propertyId" : "http://purl.obolibrary.org/obo/RO_0002213", "fillerId" : "http://purl.obolibrary.org/obo/GO_0006793" } ] }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0010562", + "definedClassId" : "http://purl.obolibrary.org/obo/GO_0010563", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0008150" ], "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002213", + "propertyId" : "http://purl.obolibrary.org/obo/RO_0002212", "fillerId" : "http://purl.obolibrary.org/obo/GO_0006793" } ] }, { @@ -71331,13 +68678,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002213", "fillerId" : "http://purl.obolibrary.org/obo/GO_0016310" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/ENVO_01000998", - "genusIds" : [ "http://purl.obolibrary.org/obo/ENVO_01000254" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002507", - "fillerId" : "http://purl.obolibrary.org/obo/ENVO_00010483" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/PATO_0045027", "genusIds" : [ "http://purl.obolibrary.org/obo/PATO_0001685" ], @@ -71832,13 +69172,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/pato#increased_in_magnitude_relative_to", "fillerId" : "http://purl.obolibrary.org/obo/PATO_0000461" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0010648", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0008150" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002212", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0007154" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0010647", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0008150" ], @@ -71847,11 +69180,11 @@ "fillerId" : "http://purl.obolibrary.org/obo/GO_0007154" } ] }, { - "definedClassId" : "http://purl.obolibrary.org/obo/ENVO_00002297", - "genusIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ], + "definedClassId" : "http://purl.obolibrary.org/obo/GO_0010648", + "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0008150" ], "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002508", - "fillerId" : "http://purl.obolibrary.org/obo/ENVO_01000254" + "propertyId" : "http://purl.obolibrary.org/obo/RO_0002212", + "fillerId" : "http://purl.obolibrary.org/obo/GO_0007154" } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/PATO_0001723", @@ -72166,8 +69499,8 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002254", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000004", "http://purl.obolibrary.org/obo/CARO_0000000" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000000", "http://purl.obolibrary.org/obo/CARO_0000003" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000000" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000000" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002595", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ], @@ -72214,9 +69547,9 @@ "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/BFO_0000020" }, { - "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_0000003", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -72226,9 +69559,9 @@ "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/BFO_0000002" }, { - "sub" : "http://purl.obolibrary.org/obo/BFO_0000004", + "sub" : "http://purl.obolibrary.org/obo/BFO_0000031", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000004" + "obj" : "http://purl.obolibrary.org/obo/BFO_0000031" }, { "sub" : "http://purl.obolibrary.org/obo/BFO_0000017", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -72391,15 +69724,9 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002598", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002215", "http://purl.obolibrary.org/obo/RO_0002213" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002202", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002202", "http://purl.obolibrary.org/obo/BFO_0000050" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002314", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0000052", "http://purl.obolibrary.org/obo/BFO_0000050" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002202", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/BFO_0000050", "http://purl.obolibrary.org/obo/RO_0002202" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002211", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002578", "http://purl.obolibrary.org/obo/RO_0002578" ] diff --git a/pato-full.obo b/pato-full.obo index d70fd433..df1ebd06 100644 --- a/pato-full.obo +++ b/pato-full.obo @@ -1,9 +1,5 @@ format-version: 1.2 -data-version: pato/releases/2019-11-05/pato-full.owl -date: 07:02:2018 10:27 -saved-by: segerdel -auto-generated-by: OBO-Edit 2.3.1 -subsetdef: 3_STAR "Manually annotated by ChEBI Team" +data-version: pato/releases/2019-12-03/pato-full.owl subsetdef: abnormal_slim "Abnormal/normal slim" subsetdef: absent_slim "Absent/present slim" subsetdef: attribute_slim "Attribute slim" @@ -29,20 +25,17 @@ subsetdef: relational_slim "Relational slim: types of quality that require an ad subsetdef: ro-eco "" subsetdef: RO:0002259 "" subsetdef: scalar_slim "Scalar slim" -subsetdef: upper_level "abstract upper-level terms not directly useful for analysis" subsetdef: value_slim "Value slim" default-namespace: quality ontology: pato/pato-full - -[Term] -id: BFO:0000001 -name: entity +property_value: http://purl.org/dc/elements/1.1/description "An ontology of phenotypic qualities (properties, attributes or characteristics)." xsd:string +property_value: http://purl.org/dc/elements/1.1/title "PATO - the Phenotype And Trait Ontology" xsd:string +property_value: http://purl.org/dc/terms/license https://creativecommons.org/licenses/by/3.0/ xsd:string [Term] id: BFO:0000002 name: continuant def: "An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts." [] -is_a: BFO:0000001 ! entity disjoint_from: BFO:0000003 ! occurrent relationship: part_of BFO:0000002 ! continuant @@ -50,17 +43,14 @@ relationship: part_of BFO:0000002 ! continuant id: BFO:0000003 name: occurrent def: "An entity that has temporal parts and that happens, unfolds or develops through time." [] -is_a: BFO:0000001 ! entity relationship: part_of BFO:0000003 ! occurrent [Term] id: BFO:0000004 name: independent continuant def: "A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything." [] -def: "b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/017-002"} is_a: BFO:0000002 ! continuant disjoint_from: BFO:0000020 ! specifically dependent continuant -disjoint_from: BFO:0000020 ! specifically dependent continuant disjoint_from: BFO:0000031 ! generically dependent continuant relationship: part_of BFO:0000004 ! independent continuant @@ -73,7 +63,6 @@ is_a: BFO:0000141 ! immaterial entity id: BFO:0000015 name: process def: "An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t." [] -def: "p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/083-003"} is_a: BFO:0000003 ! occurrent [Term] @@ -94,30 +83,16 @@ relationship: part_of BFO:0000019 ! quality id: BFO:0000020 name: specifically dependent continuant def: "A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same." [] -def: "b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n > 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i < j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004])" [] -def: "b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/050-003"} is_a: BFO:0000002 ! continuant disjoint_from: BFO:0000031 ! generically dependent continuant relationship: part_of BFO:0000020 ! specifically dependent continuant -[Term] -id: BFO:0000027 -name: object aggregate -is_a: BFO:0000040 ! material entity - -[Term] -id: BFO:0000029 -name: site -is_a: BFO:0000141 ! immaterial entity - [Term] id: BFO:0000031 name: generically dependent continuant def: "A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time." [] -def: "b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])" [] is_a: BFO:0000002 ! continuant relationship: part_of BFO:0000031 ! generically dependent continuant -property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000040 @@ -139,7 +114,6 @@ property_value: IAO:0000412 http://purl.obolibrary.org/obo/caro.owl [Term] id: CARO:0000003 -name: anatomical structure name: connected anatomical structure is_a: CARO:0000006 ! material anatomical entity property_value: IAO:0000412 http://purl.obolibrary.org/obo/caro.owl @@ -154,179 +128,31 @@ property_value: IAO:0000412 http://purl.obolibrary.org/obo/caro.owl [Term] id: CARO:0000014 name: cell part -is_a: CARO:0000003 ! anatomical structure +is_a: CARO:0000003 ! connected anatomical structure property_value: IAO:0000412 http://purl.obolibrary.org/obo/caro.owl property_value: IAO:0000589 "cell part (CARO)" xsd:string [Term] id: CARO:0001010 name: organism or virus or viroid -def: "Material anatomical entity that is a member of an individual species or is a viral or viroid particle." [] -is_a: PCO:0000031 ! organismal entity -property_value: http://purl.obolibrary.org/obo/IAO_created_by "Melissa Haendel" xsd:string -property_value: http://purl.obolibrary.org/obo/IAO_creation_date "9/18/11" xsd:string -property_value: IAO:0000589 "organism or virus" xsd:string +is_a: BFO:0000040 ! material entity [Term] id: CARO:0030000 name: biological entity is_a: BFO:0000004 ! independent continuant -[Term] -id: CHEBI:24431 -name: chemical entity -namespace: chebi_ontology -def: "A chemical entity is a physical entity of interest in chemistry including molecular entities, parts thereof, and chemical substances." [] -subset: 3_STAR -synonym: "chemical entity" EXACT [UniProt] - -[Term] -id: CHEBI:46662 -name: mineral -namespace: chebi_ontology -def: "In general, a mineral is a chemical substance that is normally crystalline formed and has been formed as a result of geological processes. The term also includes metamict substances (naturally occurring, formerly crystalline substances whose crystallinity has been destroyed by ionising radiation) and can include naturally occurring amorphous substances that have never been crystalline ('mineraloids') such as georgite and calciouranoite as well as substances formed by the action of geological processes on bigenic compounds ('biogenic minerals')." [] -subset: 3_STAR -synonym: "mineral" EXACT [ChEBI] -synonym: "Minerale" RELATED [ChEBI] -synonym: "minerales" RELATED [ChEBI] -synonym: "minerals" RELATED [ChEBI] -synonym: "mineraux" RELATED [ChEBI] -is_a: CHEBI:59999 ! chemical substance - -[Term] -id: CHEBI:59999 -name: chemical substance -namespace: chebi_ontology -def: "A chemical substance is a portion of matter of constant composition, composed of molecular entities of the same type or of different types." [] -subset: 3_STAR -synonym: "Chemische Substanz" RELATED [ChEBI] -is_a: CHEBI:24431 ! chemical entity - [Term] id: CL:0000000 name: cell -is_a: CARO:0000003 ! anatomical structure +is_a: CARO:0000003 ! connected anatomical structure property_value: IAO:0000412 http://purl.obolibrary.org/obo/cl.owl -[Term] -id: ENVO:00002297 -name: environmental feature -def: "A material entity which determines an environmental system." [DOI:10.1186/2041-1480-4-43, NM:nm, ORCID:0000-0002-4366-3088] -is_a: BFO:0000040 ! material entity -intersection_of: BFO:0000040 ! material entity -intersection_of: RO:0002508 ENVO:01000254 ! determines environmental system -relationship: RO:0002508 ENVO:01000254 ! determines environmental system - -[Term] -id: ENVO:00010483 -name: environmental material -def: "A portion of environmental material is a fiat object which forms the medium or part of the medium of an environmental system." [DOI:10.1186/2041-1480-4-43, MA:ma, ORCID:0000-0002-4366-3088, URL:http\://ontology.buffalo.edu/smith/articles/niches.html] -synonym: "portion of environmental material" EXACT [] -is_a: BFO:0000040 ! material entity - [Term] id: ENVO:01000254 name: environmental system -def: "A system which has the disposition to environ one or more material entities." [DOI:10.1186/2041-1480-4-43] -synonym: "environment" EXACT [] is_a: RO:0002577 ! system -[Term] -id: ENVO:01000313 -name: anthropogenic environment -def: "An anthropogenic environment is an environmental system which is the product of human activity." [] -is_a: ENVO:01000254 ! environmental system - -[Term] -id: ENVO:01000951 -name: natural environment -def: "An environmental system in which minimal to no anthropisation has occurred and non-human agents are the primary determinants of the system's dynamics and composition." [https://en.wikipedia.org/wiki/Anthropization, https://en.wikipedia.org/wiki/Natural_environment] -is_a: ENVO:01000254 ! environmental system - -[Term] -id: ENVO:01000952 -name: anthropisation -def: "A process during which a natural environmental system is altered by human action." [https://en.wikipedia.org/wiki/Anthropization] -synonym: "anthropization" EXACT [] -is_a: ENVO:02500027 ! anthropogenic environmental process -intersection_of: ENVO:02500027 ! anthropogenic environmental process -intersection_of: RO:0002233 ENVO:01000951 ! has input natural environment -intersection_of: RO:0002234 ENVO:01000313 ! has output anthropogenic environment -relationship: RO:0002233 ENVO:01000951 ! has input natural environment -relationship: RO:0002234 ENVO:01000313 ! has output anthropogenic environment - -[Term] -id: ENVO:01000997 -name: environmental system determined by a quality -def: "An environmental system which is determined by materials bearing roughly homogeneous qualities." [] -is_a: ENVO:01000254 ! environmental system - -[Term] -id: ENVO:01000998 -name: environmental system determined by a material -def: "An environmental system within which an environmental material strongly influences the system's composition and properties." [] -is_a: ENVO:01000254 ! environmental system -intersection_of: ENVO:01000254 ! environmental system -intersection_of: RO:0002507 ENVO:00010483 ! determined by environmental material -relationship: RO:0002507 ENVO:00010483 ! determined by environmental material - -[Term] -id: ENVO:01001000 -name: environmental system determined by an organism -def: "An environmental system which is determined by a living organism." [] -synonym: "host-associated environment" RELATED [] -is_a: ENVO:01001110 ! ecosystem -intersection_of: ENVO:01000254 ! environmental system -intersection_of: RO:0002507 NCBITaxon:131567 ! determined by cellular organisms -relationship: RO:0002507 NCBITaxon:131567 ! determined by cellular organisms - -[Term] -id: ENVO:01001002 -name: animal-associated environment -def: "An environmental system determined by an animal." [] -synonym: "animal environment" BROAD [] -synonym: "Metazoan-associated environment" EXACT [] -is_a: ENVO:01001000 ! environmental system determined by an organism -intersection_of: ENVO:01000254 ! environmental system -intersection_of: RO:0002507 NCBITaxon:33208 ! determined by Metazoa -relationship: RO:0002507 NCBITaxon:33208 ! determined by Metazoa - -[Term] -id: ENVO:01001055 -name: environment associated with an animal part or small animal -def: "An environmental system determined by part of a living or dead animal, or a whole small animal." [] -is_a: ENVO:01000254 ! environmental system -intersection_of: ENVO:01000254 ! environmental system -intersection_of: RO:0002507 CARO:0000006 ! determined by material anatomical entity -relationship: RO:0002507 CARO:0000006 ! determined by material anatomical entity - -[Term] -id: ENVO:01001057 -name: environment associated with a plant part or small plant -def: "An environmental system determined by part of a living or dead plant, or a whole small plant." [] -is_a: ENVO:01000254 ! environmental system - -[Term] -id: ENVO:01001110 -name: ecosystem -def: "An environmental system which includes both living and non-living components." [https://en.wikipedia.org/wiki/Ecosystem] -is_a: ENVO:01000254 ! environmental system - -[Term] -id: ENVO:02500000 -name: environmental system process -def: "A process in which includes the components of an environmental system as participants." [] -is_a: BFO:0000015 ! process - -[Term] -id: ENVO:02500027 -name: anthropogenic environmental process -def: "An environmental process which is driven by the action of humans." [] -is_a: ENVO:02500000 ! environmental system process -intersection_of: ENVO:02500000 ! environmental system process -intersection_of: RO:0002218 NCBITaxon:9606 ! has active participant Homo sapiens -relationship: RO:0002218 NCBITaxon:9606 ! has active participant Homo sapiens - [Term] id: GO:0003674 name: molecular_function @@ -598,7 +424,6 @@ alt_id: GO:0000004 alt_id: GO:0007582 alt_id: GO:0044699 def: "A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence." [GOC:pdt] -def: "Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end." [GOC:go_curators, GOC:isa_complete] comment: Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code "no data" (ND), is used to indicate this. subset: goslim_aspergillus subset: goslim_candida @@ -837,7 +662,7 @@ subset: goslim_pir subset: goslim_plant subset: goslim_yeast xref: Wikipedia:Biological_membrane -is_a: GO:0044464 ! obsolete cell part +is_a: CARO:0000014 ! cell part is_a: GO:0110165 ! cellular anatomical entity property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl @@ -2061,264 +1886,6 @@ relationship: positively_regulates GO:0038023 ! signaling receptor activity created_by: rfoulger creation_date: 2010-12-02T09:28:50Z -[Term] -id: IAO:0000027 -name: data item -is_a: IAO:0000030 ! information content entity - -[Term] -id: IAO:0000030 -name: information content entity -is_a: BFO:0000031 ! generically dependent continuant - -[Term] -id: IAO:0000078 -name: curation status specification -def: "The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value." [] -is_a: IAO:0000102 ! data about an ontology part -property_value: editor_note "Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)" xsd:string -property_value: IAO:0000111 "curation status specification" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "PERSON:Bill Bug" xsd:string -property_value: IAO:0000119 GROUP:OBI: xsd:string -property_value: IAO:0000119 "OBI_0000266" xsd:string - -[Term] -id: IAO:0000102 -name: data about an ontology part -def: "data about an ontology part is a data item about a part of an ontology, for example a term" [] -is_a: IAO:0000027 ! data item -property_value: IAO:0000117 "Person:Alan Ruttenberg" xsd:string - -[Term] -id: IAO:0000225 -name: obsolescence reason specification -def: "The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value." [] -is_a: IAO:0000102 ! data about an ontology part -property_value: editor_note "The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology." xsd:string -property_value: IAO:0000111 "obsolescence reason specification" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string -property_value: IAO:0000117 "PERSON: Melanie Courtot" xsd:string - -[Term] -id: IAO:0000409 -name: denotator type -def: "A denotator type indicates how a term should be interpreted from an ontological perspective." [] -is_a: IAO:0000102 ! data about an ontology part -property_value: example_of_usage "The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are \"natural kinds\" and the latter arbitrary collections of entities." xsd:string -property_value: IAO:0000117 "Alan Ruttenberg" xsd:string -property_value: IAO:0000119 "Barry Smith, Werner Ceusters" xsd:string - -[Term] -id: NCBITaxon:1 -name: root -synonym: "all" RELATED synonym [] -is_a: BFO:0000040 ! material entity - -[Term] -id: NCBITaxon:117570 -name: Teleostomi -is_a: NCBITaxon:7776 ! Gnathostomata - -[Term] -id: NCBITaxon:117571 -name: Euteleostomi -synonym: "bony vertebrates" EXACT genbank_common_name [] -is_a: NCBITaxon:117570 ! Teleostomi - -[Term] -id: NCBITaxon:131567 -name: cellular organisms -synonym: "biota" RELATED synonym [] -is_a: NCBITaxon:1 ! root - -[Term] -id: NCBITaxon:1338369 -name: Dipnotetrapodomorpha -is_a: NCBITaxon:8287 ! Sarcopterygii - -[Term] -id: NCBITaxon:1437010 -name: Boreoeutheria -synonym: "Boreotheria" RELATED synonym [] -is_a: NCBITaxon:9347 ! Eutheria - -[Term] -id: NCBITaxon:207598 -name: Homininae -synonym: "Homo/Pan/Gorilla group" RELATED synonym [] -is_a: NCBITaxon:9604 ! Hominidae - -[Term] -id: NCBITaxon:2759 -name: Eukaryota -synonym: "Eucarya" RELATED synonym [] -synonym: "Eucaryotae" RELATED synonym [] -synonym: "eucaryotes" EXACT genbank_common_name [] -synonym: "Eukarya" RELATED synonym [] -synonym: "Eukaryotae" RELATED synonym [] -synonym: "eukaryotes" EXACT common_name [] -synonym: "eukaryotes" RELATED blast_name [] -is_a: NCBITaxon:131567 ! cellular organisms - -[Term] -id: NCBITaxon:314146 -name: Euarchontoglires -is_a: NCBITaxon:1437010 ! Boreoeutheria - -[Term] -id: NCBITaxon:314293 -name: Simiiformes -synonym: "Anthropoidea" RELATED synonym [] -is_a: NCBITaxon:376913 ! Haplorrhini - -[Term] -id: NCBITaxon:314295 -name: Hominoidea -synonym: "ape" EXACT common_name [] -synonym: "apes" EXACT genbank_common_name [] -is_a: NCBITaxon:9526 ! Catarrhini - -[Term] -id: NCBITaxon:32523 -name: Tetrapoda -synonym: "tetrapods" EXACT genbank_common_name [] -is_a: NCBITaxon:1338369 ! Dipnotetrapodomorpha - -[Term] -id: NCBITaxon:32524 -name: Amniota -synonym: "amniotes" EXACT genbank_common_name [] -is_a: NCBITaxon:32523 ! Tetrapoda - -[Term] -id: NCBITaxon:32525 -name: Theria -synonym: "Theria" EXACT scientific_name [] -is_a: NCBITaxon:40674 ! Mammalia - -[Term] -id: NCBITaxon:33154 -name: Opisthokonta -synonym: "Fungi/Metazoa group" RELATED synonym [] -synonym: "opisthokonts" RELATED synonym [] -is_a: NCBITaxon:2759 ! Eukaryota - -[Term] -id: NCBITaxon:33208 -name: Metazoa -synonym: "Animalia" RELATED synonym [] -synonym: "animals" RELATED blast_name [] -synonym: "metazoans" EXACT genbank_common_name [] -synonym: "multicellular animals" EXACT common_name [] -is_a: NCBITaxon:33154 ! Opisthokonta - -[Term] -id: NCBITaxon:33213 -name: Bilateria -is_a: NCBITaxon:6072 ! Eumetazoa - -[Term] -id: NCBITaxon:33511 -name: Deuterostomia -synonym: "deuterostomes" EXACT common_name [] -is_a: NCBITaxon:33213 ! Bilateria - -[Term] -id: NCBITaxon:376913 -name: Haplorrhini -is_a: NCBITaxon:9443 ! Primates - -[Term] -id: NCBITaxon:40674 -name: Mammalia -synonym: "mammals" EXACT genbank_common_name [] -synonym: "mammals" RELATED blast_name [] -is_a: NCBITaxon:32524 ! Amniota - -[Term] -id: NCBITaxon:6072 -name: Eumetazoa -is_a: NCBITaxon:33208 ! Metazoa - -[Term] -id: NCBITaxon:7711 -name: Chordata -synonym: "chordates" EXACT genbank_common_name [] -synonym: "chordates" RELATED blast_name [] -is_a: NCBITaxon:33511 ! Deuterostomia - -[Term] -id: NCBITaxon:7742 -name: Vertebrata -synonym: "Vertebrata" EXACT scientific_name [] -synonym: "vertebrates" EXACT genbank_common_name [] -synonym: "vertebrates" RELATED blast_name [] -is_a: NCBITaxon:89593 ! Craniata - -[Term] -id: NCBITaxon:7776 -name: Gnathostomata -synonym: "Gnathostomata" EXACT scientific_name [] -synonym: "jawed vertebrates" EXACT genbank_common_name [] -is_a: NCBITaxon:7742 ! Vertebrata - -[Term] -id: NCBITaxon:8287 -name: Sarcopterygii -is_a: NCBITaxon:117571 ! Euteleostomi - -[Term] -id: NCBITaxon:89593 -name: Craniata -synonym: "Craniata" EXACT scientific_name [] -is_a: NCBITaxon:7711 ! Chordata - -[Term] -id: NCBITaxon:9347 -name: Eutheria -synonym: "eutherian mammals" EXACT common_name [] -synonym: "placental mammals" EXACT common_name [] -synonym: "Placentalia" RELATED synonym [] -synonym: "placentals" EXACT genbank_common_name [] -synonym: "placentals" RELATED blast_name [] -is_a: NCBITaxon:32525 ! Theria - -[Term] -id: NCBITaxon:9443 -name: Primates -synonym: "Primata" RELATED synonym [] -synonym: "primate" EXACT equivalent_name [] -synonym: "primates" RELATED blast_name [] -is_a: NCBITaxon:314146 ! Euarchontoglires - -[Term] -id: NCBITaxon:9526 -name: Catarrhini -is_a: NCBITaxon:314293 ! Simiiformes - -[Term] -id: NCBITaxon:9604 -name: Hominidae -synonym: "great apes" EXACT genbank_common_name [] -synonym: "Pongidae" RELATED synonym [] -is_a: NCBITaxon:314295 ! Hominoidea - -[Term] -id: NCBITaxon:9605 -name: Homo -synonym: "humans" EXACT common_name [] -is_a: NCBITaxon:207598 ! Homininae - -[Term] -id: NCBITaxon:9606 -name: Homo sapiens -synonym: "human" EXACT genbank_common_name [] -synonym: "humans" RELATED [] -synonym: "man" EXACT common_name [] -is_a: NCBITaxon:9605 ! Homo - [Term] id: PATO:0000000 name: obsolete pato @@ -2329,7 +1896,6 @@ id: PATO:0000001 name: quality alt_id: PATO:0000072 def: "A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities" [PATOC:GVG] -synonym: "trait" EXACT [] is_a: BFO:0000020 ! specifically dependent continuant property_value: IAO:0000589 "quality (PATO)" xsd:string @@ -11079,7 +10645,7 @@ is_a: PATO:0001377 ! polyploid [Term] id: PATO:0001384 name: hexaploid -def: "A polyploidy quality inhering in a bearer by virtue of the bearer's containing four homologous sets of chromosomes." [Wikipedia:http\://en.wikipedia.org/wiki/Hexaploid] +def: "A polyploidy quality inhering in a bearer by virtue of the bearer's containing six homologous sets of chromosomes." [Wikipedia:http\://en.wikipedia.org/wiki/Hexaploid] subset: cell_quality subset: value_slim is_a: PATO:0001377 ! polyploid @@ -22774,6 +22340,15 @@ synonym: "structurally interrupted" EXACT [] is_a: PATO:0001241 ! physical object quality created_by: http://orcid.org/0000-0001-5208-3432 +[Term] +id: PATO:0040027 +name: doubled haploid +def: "A ploidy quality inhering in a bearer by virtue of the bearer's haploid cells undergo chromosome doubling." [Wikipedia:https\://en.wikipedia.org/wiki/Doubled_haploidy] +synonym: "double haploid" EXACT [] +synonym: "double-haploid" EXACT [] +is_a: PATO:0001393 ! euploid +created_by: http://orcid.org/0000-0001-5208-3432 + [Term] id: PATO:0045000 name: normal rate @@ -23710,7 +23285,7 @@ creation_date: 2017-12-22T14:16:43Z [Term] id: PATO:0045075 name: normal variability of color -def: "A variability which is relatively normal or average" [] +def: "A variability of color which is relatively normal or average" [] subset: value_slim is_a: PATO:0001615 ! variant color intersection_of: PATO:0001615 ! variant color @@ -23985,231 +23560,86 @@ is_a: PATO:0060001 ! sex-specific created_by: http://orcid.org/0000-0002-1373-1705 creation_date: 2019-08-23T08:51:22Z -[Term] -id: PCO:0000000 -name: collection of organisms -def: "A material entity that consists of two or more organisms, viruses, or viroids." [] -comment: May be of the same or different species. -is_a: BFO:0000027 ! object aggregate -is_a: PCO:0000031 ! organismal entity -intersection_of: has_member CARO:0001010 {all_only="true"} ! organism or virus or viroid -intersection_of: has_member CARO:0001010 {minCardinality="2"} ! organism or virus or viroid -relationship: has_member CARO:0001010 ! organism or virus or viroid -property_value: example_of_usage "Examples include: population, community, species (meaning the collection of organisms that makes up a species, not the taxonomic rank), and family." xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000118 "group of organism" xsd:string -property_value: IAO:0000118 "organism collection" xsd:string - -[Term] -id: PCO:0000001 -name: population of organisms -def: "A collection of organisms, all of the same species, that live in the same place." [] -comment: It is sometimes difficult to define the physical boundaries of a population. In the case of sexually reproducing organisms, the individuals within a population have the potential to reproduce with one another during the course of their lifetimes. 'Community', as often used to describe a group of humans, is a type of population. \n\nClasses for population already exist in IDO ('organism population', IDO_0000509) and OBI ('population', OBI_0000181). The definitions should be standardized across OBO Foundry ontologies and only one term used. -is_a: PCO:0000018 ! single-species collection of organisms -property_value: example_of_usage "" xsd:string -property_value: example_of_usage "This a general term that can include every organism of a species living in an area or any subset of them. Subclasses can be more specific as needed." xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000119 ISBN:0878932739 xsd:string - -[Term] -id: PCO:0000002 -name: ecological community -def: "A community of at least two different species, living in a particular area. Must have at least two populations of different species as members." [] -comment: Ecological community is defined broadly here, but includes both ecological interactions (inherited from parent term community) and spatial co-existence. It may be used to describe every organisms living in an area, but is often used to refer only to organisms of a particular taxon or guild (e.g., the plant community, the insect community, the herbivore community). The word community, as it often used to describe a group of humans living together, is a type of single-species collection of organisms, not an ecological community. -is_a: ENVO:01001110 ! ecosystem -is_a: PCO:0000028 ! community -is_a: PCO:0000029 ! multi-species collection of organisms -property_value: editor_note "Not sure if the equivalancy axiom specifies that both populations are located in the same site." xsd:string -property_value: IAO:0000114 IAO:0000123 -property_value: IAO:0000118 "multispecies community" xsd:string -property_value: IAO:0000119 ISBN:0865423504 xsd:string - -[Term] -id: PCO:0000003 -name: quality of a population -def: "A quality that inheres in a biological population." [] -comment: Includes qualities like population size, population growth rate, carrying capacity, immigration rate, emigration rate, fecundity, and death rate. A population quality may depend on the qualities of individual organisms in the population, but cannot be measured or described for a single organism. This term may be replaced by a PATO term. -is_a: PATO:0002003 ! population quality -intersection_of: PATO:0002003 ! population quality -intersection_of: RO:0000052 PCO:0000001 ! inheres in population of organisms -relationship: RO:0000052 PCO:0000001 ! inheres in population of organisms -property_value: editor_note "See Chris's comments on population qualities at: http://code.google.com/p/popcomm-ontology/issues/detail?id=4. These may not belong under BFO:quality. May be better to call them population characteristics, and classify as specifically dependent continuants. Need to look at process profiles in BFO2." xsd:string -property_value: IAO:0000114 IAO:0000428 - -[Term] -id: PCO:0000004 -name: quality of an ecological community -def: "A quality that inheres in a community." [] -comment: Includes qualities like diversity, species richness, stability, resilience, community structure, number of trophic levels. A community quality may depend on the qualities of individual organism in the community, but cannot be measured or described for a single individual. -is_a: PATO:0002003 ! population quality -intersection_of: PATO:0002003 ! population quality -intersection_of: RO:0000052 PCO:0000002 ! inheres in ecological community -relationship: RO:0000052 PCO:0000002 ! inheres in ecological community -property_value: editor_note "These may not belong under BFO:quality. May be better to call them community characteristics, and classify as specifically dependent continuants. Need to look at process profiles in BFO2." xsd:string -property_value: IAO:0000114 IAO:0000428 - -[Term] -id: PCO:0000017 -name: species as a collection of organisms -def: "A collection of organisms that has as parts every organism of given species and no organisms of any other species." [] -comment: This term is neutral with respect to which organisms are included in a species. Membership will depend on the species concept and the taxonomic assertions used to define the species. These criteria must be specified by the user. -is_a: PCO:0000018 ! single-species collection of organisms -property_value: editor_note "At the moment there is no way to specify in an OWL axiom that the collection includes every individual of a species. This should be added, if possible." xsd:string -property_value: IAO:0000114 IAO:0000120 - -[Term] -id: PCO:0000018 -name: single-species collection of organisms -def: "A material entity that has as parts two or more organisms, viruses, or viroids of the same species and no members of any other species." [] -is_a: PCO:0000000 ! collection of organisms -property_value: IAO:0000114 IAO:0000120 -property_value: IAO:0000118 "collection of organisms of the same species" xsd:string - -[Term] -id: PCO:0000027 -name: collection of humans -def: "A collection of organisms of the same species that has as members only humans." [] -is_a: PCO:0000018 ! single-species collection of organisms -intersection_of: PCO:0000018 ! single-species collection of organisms -intersection_of: has_member NCBITaxon:9606 {all_only="true"} ! Homo sapiens -intersection_of: has_member NCBITaxon:9606 {minCardinality="2"} ! Homo sapiens -relationship: has_member NCBITaxon:9606 ! Homo sapiens -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000118 "human community" xsd:string -property_value: IAO:0000118 "human population" xsd:string - -[Term] -id: PCO:0000028 -name: community -def: "A collection of organisms of the same species whose members are all either genealogically related to each other or have mated with each other." [] -comment: These relations can include shared values, occupying the same spatial regkion. A community be be a single species collection of organsisms (as in a human community, which is also a type of population) or a or multi-species collection of organisms (as in an ecological community). -is_a: PCO:0000000 ! collection of organisms -property_value: editor_note "Biological or social relations are covered by RO_0002437 (biotically interacts with), but that relations does provide an easy way to specify that two entities are interacting with each other (participating in the same interaction). Until that axiom is specified, the logical definition of this term is incomplete." xsd:string -property_value: IAO:0000114 IAO:0000123 - -[Term] -id: PCO:0000029 -name: multi-species collection of organisms -def: "A collection of organisms that consists of two or more organisms from at least two species." [] -is_a: PCO:0000000 ! collection of organisms -property_value: editor_note "Need to add axiom to specify that it has at a mimum members of two different species, but not sure how to specify that. Can't say \"('has member' only ('member of' min 2 'species as a collection of organisms'))\"." xsd:string -property_value: IAO:0000114 IAO:0000123 - -[Term] -id: PCO:0000031 -name: organismal entity -def: "A material entity that is one or more organisms, viruses or viroids." [] -is_a: BFO:0000040 ! material entity -union_of: CARO:0001010 ! organism or virus or viroid -union_of: PCO:0000000 ! collection of organisms -property_value: IAO:0000114 IAO:0000125 - -[Term] -id: PO:0000003 -name: whole plant -def: "A plant structure (PO:0005679) which is a whole organism." [] -synonym: "bush (narrow)" NARROW [] -synonym: "clonal colony (related)" RELATED [] -synonym: "colony (related)" RELATED [] -synonym: "frutex (narrow)" NARROW [] -synonym: "frutices (narrow)" NARROW [] -synonym: "gametophyte (narrow)" NARROW [] -synonym: "genet (broad)" BROAD [] -synonym: "herb (narrow)" NARROW [] -synonym: "liana (narrow)" NARROW [] -synonym: "planta entera (Spanish, exact)" EXACT [] -synonym: "prothalli (narrow)" NARROW [] -synonym: "prothallium (narrow)" NARROW [] -synonym: "prothallus (narrow)" NARROW [] -synonym: "ramet (broad)" BROAD [] -synonym: "seedling (narrow)" NARROW [] -synonym: "shrub (narrow)" NARROW [] -synonym: "sporophyte (narrow)" NARROW [] -synonym: "suffrutex (narrow)" NARROW [] -synonym: "suffrutices (narrow)" NARROW [] -synonym: "tree (narrow)" NARROW [] -synonym: "vine (narrow)" NARROW [] -synonym: "woody clump (narrow)" NARROW [] -synonym: "植物体全体 (Japanese, exact)" EXACT [] -is_a: PO:0009011 ! plant structure - -[Term] -id: PO:0009011 -name: plant structure -def: "An anatomical structure that is or was part of a plant, or was derived from a part of a plant." [] -synonym: "estructura vegetal (Spanish, exact)" EXACT [] -synonym: "植物 構造 (Japanese, exact)" EXACT [] -is_a: PO:0025131 ! plant anatomical entity - -[Term] -id: PO:0025131 -name: plant anatomical entity -def: "An anatomical entity that is or was part of a plant." [] -synonym: "entidad anatómica vegetal (Spanish, exact)" EXACT [] -synonym: "植物 解剖学（形態）的実体 (Japanese, exact)" EXACT [] -is_a: BFO:0000040 ! material entity - [Term] id: RO:0002577 name: system def: "A material entity consisting of multiple components that are causally integrated." [] is_a: BFO:0000040 ! material entity -property_value: editor_note "May be replaced by a BFO class, as discussed in http://www.jbiomedsem.com/content/4/1/43" xsd:string +property_value: IAO:0000116 "May be replaced by a BFO class, as discussed in http://www.jbiomedsem.com/content/4/1/43" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://www.jbiomedsem.com/content/4/1/43 xsd:string -[Term] -id: Subset -is_a: IAO:0000102 ! data about an ontology part +[Typedef] +id: BFO:0000062 +name: preceded by +def: "x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] +subset: ro-eco +property_value: http://purl.org/dc/elements/1.1/source http://www.obofoundry.org/ro/#OBO_REL:preceded_by xsd:string +property_value: IAO:0000111 "preceded by" xsd:string +property_value: IAO:0000116 "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." xsd:string +property_value: IAO:0000118 "is preceded by" xsd:string +property_value: IAO:0000118 "preceded_by" xsd:string +domain: BFO:0000003 ! occurrent +range: BFO:0000003 ! occurrent +holds_over_chain: part_of BFO:0000062 +is_transitive: true +is_a: RO:0002086 ! ends after +inverse_of: BFO:0000063 ! precedes -[Term] -id: UBERON:0001062 -name: anatomical entity -namespace: uberon -def: "Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species." [FMA:62955, http://orcid.org/0000-0001-9114-8737] -subset: upper_level -xref: AAO:0010841 -xref: AEO:0000000 -xref: BILA:0000000 -xref: BIRNLEX:6 -xref: CARO:0000000 -xref: EHDAA2:0002229 -xref: FBbt:10000000 -xref: FBbt_root:00000000 -xref: FMA:62955 -xref: HAO:0000000 -xref: http://linkedlifedata.com/resource/umls/id/C1515976 -xref: MA:0000001 -xref: NCIT:C12219 -xref: TAO:0100000 -xref: TGMA:0001822 -xref: UMLS:C1515976 {source="ncithesaurus:Anatomic_Structure_System_or_Substance"} -xref: WBbt:0000100 -xref: XAO:0000000 -xref: ZFA:0100000 -is_a: BFO:0000004 ! independent continuant +[Typedef] +id: BFO:0000063 +name: precedes +def: "x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] +subset: ro-eco +property_value: IAO:0000111 "precedes" xsd:string +domain: BFO:0000003 ! occurrent +range: BFO:0000003 ! occurrent +holds_over_chain: part_of BFO:0000063 +is_transitive: true +is_a: RO:0002222 ! temporally related to + +[Typedef] +id: BFO:0000067 +name: contains process +def: "[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" [] +comment: Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant +property_value: IAO:0000111 "site of" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Typedef] id: RO:0000052 name: inheres in def: "a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence" [] -property_value: editor_note "A dependent inheres in its bearer at all times for which the dependent exists." xsd:string -property_value: example_of_usage "this fragility inheres in this vase" xsd:string -property_value: example_of_usage "this red color inheres in this apple" xsd:string property_value: IAO:0000111 "inheres in" xsd:string +property_value: IAO:0000112 "this fragility inheres in this vase" xsd:string +property_value: IAO:0000112 "this red color inheres in this apple" xsd:string +property_value: IAO:0000116 "A dependent inheres in its bearer at all times for which the dependent exists." xsd:string property_value: IAO:0000118 "inheres_in" xsd:string property_value: RO:0001900 RO:0001901 is_a: RO:0002314 ! inheres in part of -inverse_of: bearer_of ! bearer of +inverse_of: RO:0000053 ! bearer of + +[Typedef] +id: RO:0000053 +name: bearer of +def: "a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence" [] +property_value: IAO:0000111 "bearer of" xsd:string +property_value: IAO:0000112 "this apple is bearer of this red color" xsd:string +property_value: IAO:0000112 "this vase is bearer of this fragility" xsd:string +property_value: IAO:0000116 "A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist." xsd:string +property_value: IAO:0000118 "bearer_of" xsd:string +property_value: IAO:0000118 "is bearer of" xsd:string +property_value: RO:0001900 RO:0001901 +range: BFO:0000020 ! specifically dependent continuant [Typedef] id: RO:0000056 name: participates in def: "a relation between a continuant and a process, in which the continuant is somehow involved in the process" [] -property_value: example_of_usage "this blood clot participates in this blood coagulation" xsd:string -property_value: example_of_usage "this input material (or this output material) participates in this process" xsd:string -property_value: example_of_usage "this investigator participates in this investigation" xsd:string property_value: IAO:0000111 "participates in" xsd:string +property_value: IAO:0000112 "this blood clot participates in this blood coagulation" xsd:string +property_value: IAO:0000112 "this input material (or this output material) participates in this process" xsd:string +property_value: IAO:0000112 "this investigator participates in this investigation" xsd:string property_value: IAO:0000118 "participates_in" xsd:string domain: BFO:0000002 ! continuant range: BFO:0000003 ! occurrent @@ -24219,12 +23649,12 @@ inverse_of: RO:0000057 ! has participant id: RO:0000057 name: has participant def: "a relation between a process and a continuant, in which the continuant is somehow involved in the process" [] -property_value: dc-source http://www.obofoundry.org/ro/#OBO_REL:has_participant xsd:string -property_value: editor_note "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time." xsd:string -property_value: example_of_usage "this blood coagulation has participant this blood clot" xsd:string -property_value: example_of_usage "this investigation has participant this investigator" xsd:string -property_value: example_of_usage "this process has participant this input material (or this output material)" xsd:string +property_value: http://purl.org/dc/elements/1.1/source http://www.obofoundry.org/ro/#OBO_REL:has_participant xsd:string property_value: IAO:0000111 "has participant" xsd:string +property_value: IAO:0000112 "this blood coagulation has participant this blood clot" xsd:string +property_value: IAO:0000112 "this investigation has participant this investigator" xsd:string +property_value: IAO:0000112 "this process has participant this input material (or this output material)" xsd:string +property_value: IAO:0000116 "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time." xsd:string property_value: IAO:0000118 "has_participant" xsd:string domain: BFO:0000003 ! occurrent range: BFO:0000002 ! continuant @@ -24234,27 +23664,73 @@ holds_over_chain: has_part RO:0000057 id: RO:0000080 name: quality of def: "a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence" [] -property_value: editor_note "A quality inheres in its bearer at all times for which the quality exists." xsd:string -property_value: example_of_usage "this red color is a quality of this apple" xsd:string +property_value: IAO:0000112 "this red color is a quality of this apple" xsd:string +property_value: IAO:0000116 "A quality inheres in its bearer at all times for which the quality exists." xsd:string property_value: IAO:0000118 "is quality of" xsd:string property_value: IAO:0000118 "quality_of" xsd:string is_a: RO:0000052 ! inheres in -inverse_of: has_quality ! has quality +inverse_of: RO:0000086 ! has quality + +[Typedef] +id: RO:0000086 +name: has quality +def: "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence" [] +property_value: IAO:0000112 "this apple has quality this red color" xsd:string +property_value: IAO:0000116 "A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist." xsd:string +property_value: IAO:0000118 "has_quality" xsd:string +range: BFO:0000019 ! quality +is_a: RO:0000053 ! bearer of + +[Typedef] +id: RO:0001015 +name: location of +def: "a relation between two independent continuants, the location and the target, in which the target is entirely within the location" [] +property_value: IAO:0000111 "is location of" xsd:string +property_value: IAO:0000112 "my head is the location of my brain" xsd:string +property_value: IAO:0000112 "this cage is the location of this rat" xsd:string +property_value: IAO:0000116 "Most location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime" xsd:string +property_value: IAO:0000118 "location_of" xsd:string +property_value: RO:0001900 RO:0001901 +is_transitive: true +inverse_of: RO:0001025 ! located in [Typedef] id: RO:0001018 name: contained in subset: ro-eco -property_value: editor_note "Containment is location not involving parthood, and arises only where some immaterial continuant is involved." xsd:string -property_value: editor_note "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):" xsd:string -property_value: editor_note "Intended meaning:\ndomain: material entity\nrange: spatial region or site (immaterial continuant)\n " xsd:string property_value: IAO:0000111 "contained in" xsd:string +property_value: IAO:0000116 "Containment is location not involving parthood, and arises only where some immaterial continuant is involved." xsd:string +property_value: IAO:0000116 "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):" xsd:string +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 domain: BFO:0000040 ! material entity range: BFO:0000004 ! independent continuant -holds_over_chain: located_in part_of -inverse_of: contains ! contains +holds_over_chain: RO:0001025 part_of +inverse_of: RO:0001019 ! contains + +[Typedef] +id: RO:0001019 +name: contains +subset: ro-eco +property_value: IAO:0000111 "contains" xsd:string +property_value: RO:0001900 RO:0001901 + +[Typedef] +id: RO:0001025 +name: located in +def: "a relation between two independent continuants, the target and the location, in which the target is entirely within the location" [] +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 +property_value: IAO:0000112 "this rat is located in this cage" xsd:string +property_value: IAO:0000116 "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" xsd:string +property_value: IAO:0000116 "Most location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime" xsd:string +property_value: IAO:0000118 "located_in" xsd:string +property_value: RO:0001900 RO:0001901 +domain: BFO:0000004 {http://purl.obolibrary.org/obo/IAO_0000116="This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation."} ! independent continuant +range: BFO:0000004 {http://purl.obolibrary.org/obo/IAO_0000116="This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation."} ! independent continuant +is_transitive: true [Typedef] id: RO:0002013 @@ -24299,14 +23775,14 @@ name: has component process def: "w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type." [] domain: BFO:0000015 ! process range: BFO:0000015 ! process -is_a: has_component ! has component +is_a: RO:0002180 ! has component created_by: dos creation_date: 2017-05-24T09:49:21Z [Typedef] id: RO:0002019 name: has ligand -def: "A relationship that holds between between a receptor and an chemical entity, typically a small molecule or peptide, that carries information between cells or compartments of a cell and which binds the receptor and regulates its effector function." [GOC:dos] +def: "A relationship that holds between between a receptor and an chemical entity, typically a small molecule or peptide, that carries information between cells or compartments of a cell and which binds the receptor and regulates its effector function." [] domain: GO:0004872 is_a: RO:0002233 ! has input created_by: dos @@ -24359,6 +23835,15 @@ property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string is_transitive: true is_a: RO:0002222 ! temporally related to +[Typedef] +id: RO:0002087 +name: immediately preceded by +comment: X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000118 "starts_at_end_of" xsd:string +is_a: BFO:0000062 ! preceded by +inverse_of: RO:0002090 ! immediately precedes + [Typedef] id: RO:0002090 name: immediately precedes @@ -24368,27 +23853,110 @@ property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string property_value: IAO:0000118 "ends_at_start_of" xsd:string property_value: IAO:0000118 "meets" xsd:string property_value: RO:0002575 BFO:0000063 -is_a: precedes ! precedes +is_a: BFO:0000063 ! precedes [Typedef] -id: RO:0002217 -name: actively participates in -def: "x actively participates in y if and only if x participates in y and x realizes some active role" [] +id: RO:0002131 +name: overlaps +def: "x overlaps y if and only if there exists some z such that x has part z and z part of y" [] +subset: ro-eco property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000118 "agent in" xsd:string -is_a: RO:0000056 ! participates in -inverse_of: RO:0002218 ! has active participant +property_value: RO:0001900 RO:0001901 +holds_over_chain: has_part part_of {http://purl.obolibrary.org/obo/RO_0002582="true"} +holds_over_chain: has_part RO:0002131 +holds_over_chain: part_of part_of +is_a: RO:0002323 ! mereotopologically related to +transitive_over: part_of ! part_of +expand_expression_to: "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)" [] + +[Typedef] +id: RO:0002180 +name: has component +def: "w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type." [] +subset: ro-eco +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000116 "The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity." xsd:string +property_value: IAO:0000232 "For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit." xsd:string +property_value: RO:0001900 RO:0001901 +property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:Componency +is_a: has_part ! has part + +[Typedef] +id: RO:0002202 +name: develops from +def: "x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y" [] +comment: This is the transitive form of the develops from relation +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 "Melissa Haendel" xsd:string +property_value: IAO:0000117 "Terry Meehan" xsd:string +domain: BFO:0000004 ! independent continuant +range: BFO:0000004 ! independent continuant +is_transitive: true +is_a: RO:0002258 ! developmentally preceded by +inverse_of: RO:0002203 ! develops into + +[Typedef] +id: RO:0002203 +name: develops into +def: "inverse of develops from" [] +subset: RO:0002259 +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 "Terry Meehan" xsd:string +is_transitive: true +is_a: RO:0002286 ! developmentally succeeded by +is_a: RO:0002387 ! has potential to develop into +is_a: RO:0002388 ! has potential to directly develop into + +[Typedef] +id: RO:0002215 +name: capable of +def: "A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. " [] +subset: ro-eco +property_value: IAO:0000112 "mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)" xsd:string +property_value: IAO:0000112 "osteoclast SubClassOf 'capable of' some 'bone resorption'" xsd:string +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "has function realized in" xsd:string +property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20123131 +property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/21208450 +property_value: IAO:0000232 "For compatibility with BFO, this relation has a shortcut definition in which the expression \"capable of some P\" expands to \"bearer_of (some realized_by only P)\"." xsd:string +domain: BFO:0000004 ! independent continuant +range: BFO:0000015 ! process +is_a: RO:0002216 ! capable of part of +expand_expression_to: "RO_0000053 some (RO_0000054 only ?Y)" [] + +[Typedef] +id: RO:0002216 +name: capable of part of +def: "c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p." [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "has function in" xsd:string +property_value: seeAlso "defining-property-chains-involving-reflexivity" +holds_over_chain: RO:0002215 part_of {http://purl.obolibrary.org/obo/RO_0002582="true"} +is_a: RO:0002328 ! functionally related to +is_a: RO:0002500 ! causal agent in process +expand_expression_to: "RO_0000053 some (RO_0000054 only (BFO_0000050 some ?Y))" [] + +[Typedef] +id: RO:0002217 +name: actively participates in +def: "x actively participates in y if and only if x participates in y and x realizes some active role" [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "agent in" xsd:string +is_a: RO:0000056 ! participates in +inverse_of: RO:0002218 ! obsolete has active participant [Typedef] id: RO:0002218 -name: has active participant name: obsolete has active participant def: "x has participant y if and only if x realizes some active role that inheres in y" [] subset: ro-eco -property_value: editor_note "This may be obsoleted and replaced by the original 'has agent' relation" xsd:string -property_value: example_of_usage "'heart development' has active participant some Shh protein" xsd:string +property_value: IAO:0000112 "'heart development' has active participant some Shh protein" xsd:string property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000116 "This may be obsoleted and replaced by the original 'has agent' relation" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "has agent" xsd:string is_a: RO:0000057 ! has participant @@ -24399,19 +23967,17 @@ id: RO:0002222 name: temporally related to comment: A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. subset: ro-eco -property_value: curator_notes "Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends." xsd:string -property_value: dc-source https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 xsd:anyURI property_value: http://purl.org/dc/terms/source https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 xsd:anyURI property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 https://en.wikipedia.org/wiki/Allen%27s_interval_algebra +property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends." xsd:string domain: BFO:0000003 ! occurrent range: BFO:0000003 ! occurrent [Typedef] id: RO:0002233 name: has input -def: "p has direct input c iff c is a participant in p, c is present at the start of p, and the state of c is modified during p." [] def: "p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p." [] subset: ro-eco property_value: IAO:0000114 IAO:0000125 @@ -24420,7 +23986,7 @@ property_value: IAO:0000118 "consumes" xsd:string domain: BFO:0000015 ! process range: BFO:0000040 ! material entity is_a: RO:0000057 ! has participant -inverse_of: input_of ! input of +inverse_of: RO:0002352 ! input of [Typedef] id: RO:0002234 @@ -24431,14 +23997,51 @@ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "produces" xsd:string is_a: RO:0000057 ! has participant -inverse_of: output_of ! output of +inverse_of: RO:0002353 ! output of + +[Typedef] +id: RO:0002254 +name: has developmental contribution from +def: "x has developmental contribution from y iff x has some part z such that z develops from y" [] +property_value: IAO:0000112 "Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]" xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 "Chris Mungall" xsd:string +domain: CARO:0000000 ! anatomical entity +range: CARO:0000000 ! anatomical entity +holds_over_chain: has_part RO:0002202 +is_a: RO:0002258 ! developmentally preceded by +inverse_of: RO:0002255 ! developmentally contributes to + +[Typedef] +id: RO:0002255 +name: developmentally contributes to +def: "inverse of has developmental contribution from" [] +subset: RO:0002259 +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 "Chris Mungall" xsd:string +holds_over_chain: RO:0002203 part_of +is_a: RO:0002286 ! developmentally succeeded by +is_a: RO:0002385 ! has potential to developmentally contribute to + +[Typedef] +id: RO:0002258 +name: developmentally preceded by +def: "Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p" [] +comment: This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000116 "false" xsd:boolean +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000232 "In general you should not use this relation to make assertions - use one of the more specific relations below this one" xsd:string +domain: BFO:0000002 ! continuant +range: BFO:0000002 ! continuant +is_a: RO:0002324 ! developmentally related to +inverse_of: RO:0002286 ! developmentally succeeded by [Typedef] id: RO:0002263 name: acts upstream of def: "c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes." [] -def: "c involved in regulation of p if c enables 'p' and p' causally upstream of p" [] -property_value: example_of_usage "A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision." xsd:string +property_value: IAO:0000112 "A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision." xsd:string property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of holds_over_chain: RO:0002327 RO:0002411 is_a: RO:0002264 ! acts upstream of or within @@ -24446,13 +24049,12 @@ is_a: RO:0002264 ! acts upstream of or within [Typedef] id: RO:0002264 name: acts upstream of or within -def: "c acts upstream of or within p if c is enables 'p' and p' causally upstream of or within p" [] def: "c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process." [] synonym: "affects" RELATED [] -property_value: example_of_usage "A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway." xsd:string +property_value: IAO:0000112 "A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway." xsd:string property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within holds_over_chain: RO:0002327 RO:0002418 -is_a: RO:0002500 ! causal agent in +is_a: RO:0002500 ! causal agent in process [Typedef] id: RO:0002286 @@ -24466,7 +24068,6 @@ is_a: RO:0002384 ! has developmental potential involving id: RO:0002304 name: causally upstream of, positive effect comment: holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y -property_value: dc-creator "cjm" xsd:string property_value: http://purl.org/dc/terms/creator "cjm" xsd:string property_value: RO:0004049 RO:0002411 is_a: RO:0002411 ! causally upstream of @@ -24476,7 +24077,6 @@ is_a: RO:0004047 ! causally upstream of or within, positive effect id: RO:0002305 name: causally upstream of, negative effect comment: holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y -property_value: dc-creator "cjm" xsd:string property_value: http://purl.org/dc/terms/creator "cjm" xsd:string property_value: RO:0004050 RO:0002411 is_a: RO:0002411 ! causally upstream of @@ -24486,7 +24086,7 @@ is_a: RO:0004046 ! causally upstream of or within, negative effect id: RO:0002314 name: inheres in part of def: "q inheres in part of w if and only if there exists some p such that q inheres in p and p part of w." [] -property_value: editor_note "Because part_of is transitive, inheres in is a sub-relation of inheres in part of" xsd:string +property_value: IAO:0000116 "Because part_of is transitive, inheres in is a sub-relation of inheres in part of" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 property_value: RO:0001900 RO:0001901 @@ -24499,47 +24099,63 @@ transitive_over: part_of ! part_of id: RO:0002323 name: mereotopologically related to def: "A mereological relationship or a topological relationship" [] -property_value: curator_notes "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships" xsd:string property_value: RO:0001900 RO:0001901 [Typedef] id: RO:0002324 name: developmentally related to def: "A relationship that holds between entities participating in some developmental process (GO:0032502)" [] -property_value: curator_notes "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development" xsd:string [Typedef] id: RO:0002326 name: contributes to -property_value: curator_notes "In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology. " xsd:string -property_value: editor_note "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." xsd:string -property_value: example_of_usage "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: example_of_usage "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: example_of_usage "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 +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 +property_value: IAO:0000116 "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." xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://www.geneontology.org/GO.annotation.conventions.shtml#contributes_to xsd:string -is_a: capable_of_part_of ! capable of part of -is_a: part_of_structure_that_is_capable_of ! part of structure that is capable of +property_value: IAO:0000232 "In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology. " xsd:string +is_a: RO:0002216 ! capable of part of +is_a: RO:0002329 ! part of structure that is capable of [Typedef] id: RO:0002327 name: enables -property_value: curator_notes "This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized." xsd:string -property_value: curator_notes "This relation is currently used experimentally by the Gene Ontology Consortium. It may not be stable and may be obsoleted at some future time." xsd:string -property_value: example_of_usage "a particular instances of akt-2 enables some instance of protein kinase activity" xsd:string +property_value: IAO:0000112 "a particular instances of akt-2 enables some instance of protein kinase activity" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "catalyzes" xsd:string property_value: IAO:0000118 "executes" xsd:string property_value: IAO:0000118 "has" xsd:string property_value: IAO:0000118 "is catalyzing" xsd:string property_value: IAO:0000118 "is executing" xsd:string -is_a: capable_of ! capable of +property_value: IAO:0000232 "This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized." xsd:string +property_value: IAO:0000232 "This relation is currently used experimentally by the Gene Ontology Consortium. It may not be stable and may be obsoleted at some future time." xsd:string +is_a: RO:0002215 ! capable of inverse_of: RO:0002333 ! enabled by transitive_over: has_part ! has part transitive_over: RO:0002017 ! has component activity +[Typedef] +id: RO:0002328 +name: functionally related to +def: "A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities." [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000232 "This is a grouping relation that collects relations used for the purpose of connecting structure and function" xsd:string + +[Typedef] +id: RO:0002329 +name: part of structure that is capable of +def: "this relation holds between c and p when c is part of some c', and c' is capable of p." [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "false" xsd:boolean +holds_over_chain: part_of RO:0002215 {http://purl.obolibrary.org/obo/RO_0002581="true"} +is_a: RO:0002328 ! functionally related to + [Typedef] id: RO:0002331 name: involved in @@ -24558,8 +24174,8 @@ id: RO:0002333 name: enabled by def: "inverse of enables" [] property_value: IAO:0000117 "Chris Mungall" xsd:string -is_a: functionally_related_to ! functionally related to is_a: RO:0000057 ! has participant +is_a: RO:0002328 ! functionally related to [Typedef] id: RO:0002334 @@ -24589,20 +24205,60 @@ subset: RO:0002259 property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: RO:0002334 ! regulated by +[Typedef] +id: RO:0002350 +name: member of +def: "is member of is a mereological relation between a item and a collection." [] +property_value: IAO:0000112 "An organism that is a member of a population of organisms" xsd:string +property_value: IAO:0000118 "is member of" xsd:string +property_value: IAO:0000118 "member part of" xsd:string +property_value: IAO:0000119 "SIO" xsd:string +property_value: RO:0001900 RO:0001901 +is_a: part_of ! part_of +inverse_of: RO:0002351 ! has member + +[Typedef] +id: RO:0002351 +name: has member +def: "has member is a mereological relation between a collection and an item." [] +property_value: IAO:0000119 "SIO" xsd:string +property_value: RO:0001900 RO:0001901 +is_a: has_part ! has part + +[Typedef] +id: RO:0002352 +name: input of +def: "inverse of has input" [] +subset: ro-eco +subset: RO:0002259 +property_value: IAO:0000117 "Chris Mungall" xsd:string +is_a: RO:0000056 ! participates in +is_a: RO:0002328 ! functionally related to + +[Typedef] +id: RO:0002353 +name: output of +def: "inverse of has output" [] +subset: ro-eco +subset: RO:0002259 +property_value: IAO:0000117 "Chris Mungall" xsd:string +is_a: RO:0000056 ! participates in +is_a: RO:0002328 ! functionally related to + [Typedef] id: RO:0002354 name: formed as result of property_value: IAO:0000117 "Chris Mungall" xsd:string -is_a: output_of ! output of +is_a: RO:0002353 ! output of [Typedef] id: RO:0002379 name: spatially coextensive with def: "x spatially_coextensive_with y if and inly if x and y have the same location" [] -property_value: curator_notes "This relation is added for formal completeness. It is unlikely to be used in many practical scenarios" xsd:string -property_value: example_of_usage "A lump of clay and a statue" xsd:string +property_value: IAO:0000112 "A lump of clay and a statue" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string -is_a: overlaps ! overlaps +property_value: IAO:0000232 "This relation is added for formal completeness. It is unlikely to be used in many practical scenarios" xsd:string +is_a: RO:0002131 ! overlaps [Typedef] id: RO:0002384 @@ -24614,13 +24270,37 @@ domain: CARO:0000000 ! anatomical entity range: CARO:0000000 ! anatomical entity is_a: RO:0002324 ! developmentally related to +[Typedef] +id: RO:0002385 +name: has potential to developmentally contribute to +def: "x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y" [] +property_value: IAO:0000114 IAO:0000428 +property_value: IAO:0000117 "Chris Mungall" xsd:string +is_a: RO:0002384 ! has developmental potential involving + +[Typedef] +id: RO:0002387 +name: has potential to develop into +def: "x has the potential to develop into y iff x develops into y or if x is capable of developing into y" [] +property_value: IAO:0000114 IAO:0000428 +property_value: IAO:0000117 "Chris Mungall" xsd:string +is_a: RO:0002384 ! has developmental potential involving + +[Typedef] +id: RO:0002388 +name: has potential to directly develop into +def: "x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y" [] +property_value: IAO:0000114 IAO:0000428 +property_value: IAO:0000117 "Chris Mungall" xsd:string +is_a: RO:0002387 ! has potential to develop into + [Typedef] id: RO:0002404 name: causally downstream of def: "inverse of upstream of" [] property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Chris Mungall" xsd:string -is_a: preceded_by ! preceded_by +is_a: BFO:0000062 ! preceded by is_a: RO:0002427 ! causally downstream of or within inverse_of: RO:0002411 ! causally upstream of @@ -24629,7 +24309,7 @@ id: RO:0002405 name: immediately causally downstream of property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Chris Mungall" xsd:string -is_a: immediately_preceded_by ! immediately preceded by +is_a: RO:0002087 ! immediately preceded by is_a: RO:0002404 ! causally downstream of inverse_of: RO:0002412 ! immediately causally upstream of @@ -24637,11 +24317,10 @@ inverse_of: RO:0002412 ! immediately causally upstream of id: RO:0002410 name: causally related to def: "This relation groups causal relations between material entities and causal relations between processes" [] -property_value: curator_notes "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string -property_value: editor_note "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative\n\nThe first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.\n\nFor the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.\n\nFor the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." xsd:string property_value: IAO:0000114 IAO:0000428 +property_value: IAO:0000116 "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative\n\nThe first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.\n\nFor the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.\n\nFor the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string -is_a: RO:0002609 ! related via dependence to +property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string [Typedef] id: RO:0002411 @@ -24650,7 +24329,7 @@ def: "p is causally upstream of q if and only if p precedes q and p and q are li property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Chris Mungall" xsd:string is_transitive: true -is_a: precedes ! precedes +is_a: BFO:0000063 ! precedes is_a: RO:0002418 ! causally upstream of or within [Typedef] @@ -24668,7 +24347,7 @@ id: RO:0002418 name: causally upstream of or within def: "p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q." [] synonym: "affects" RELATED [] -property_value: editor_note "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2" xsd:string +property_value: IAO:0000116 "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "influences (processual)" xsd:string is_transitive: true @@ -24688,7 +24367,6 @@ is_a: RO:0002501 ! causal relation between processes [Typedef] id: RO:0002428 name: involved in regulation of -def: "c involved in regulation of p if c is involved in some 'p' and p' regulates some p" [] def: "c involved in regulation of p if c is involved in some p' and p' regulates some p" [] property_value: IAO:0000117 "Chris Mungall" xsd:string holds_over_chain: RO:0002327 regulates @@ -24720,26 +24398,24 @@ is_a: RO:0002428 ! involved in regulation of id: RO:0002431 name: involved in or involved in regulation of def: "c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p" [] -property_value: editor_note "OWL does not allow defining object properties via a Union" xsd:string +property_value: IAO:0000116 "OWL does not allow defining object properties via a Union" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "involved in or reguates" xsd:string -is_a: functionally_related_to ! functionally related to is_a: RO:0002264 ! acts upstream of or within -is_a: RO:0002500 ! causal agent in +is_a: RO:0002328 ! functionally related to +is_a: RO:0002500 ! causal agent in process [Typedef] id: RO:0002432 -name: enables activity in name: is active in -def: "c executes activity in d if and only if c enables p and p occurs_in d" [] def: "c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure." [GOC:cjm, GOC:dos] synonym: "enables activity in" EXACT [] -property_value: example_of_usage "A protein that enables activity in a cytosol." xsd:string +property_value: IAO:0000112 "A protein that enables activity in a cytosol." xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "executes activity in" xsd:string holds_over_chain: RO:0002327 occurs_in {http://purl.obolibrary.org/obo/RO_0002581="true"} -is_a: functionally_related_to ! functionally related to -is_a: overlaps ! overlaps +is_a: RO:0002131 ! overlaps +is_a: RO:0002328 ! functionally related to [Typedef] id: RO:0002434 @@ -24747,11 +24423,11 @@ name: interacts with def: "A relationship that holds between two entities in which the processes executed by the two entities are causally connected." [] subset: ro-eco synonym: "in pairwise interaction with" EXACT [] -property_value: curator_notes "Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules." xsd:string -property_value: editor_note "Considering relabeling as 'pairwise interacts with'" xsd:anyURI -property_value: editor_note "This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact." xsd:string -property_value: foaf-page https://github.com/oborel/obo-relations/wiki/InteractionRelations xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/page https://github.com/oborel/obo-relations/wiki/InteractionRelations xsd:anyURI +property_value: IAO:0000116 "Considering relabeling as 'pairwise interacts with'" xsd:anyURI +property_value: IAO:0000116 "This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact." xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000232 "Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules." xsd:string property_value: seeAlso http://purl.obolibrary.org/obo/MI_0914 xsd:anyURI domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity @@ -24760,7 +24436,6 @@ is_symmetric: true [Typedef] id: RO:0002436 name: molecularly interacts with -def: "An interaction relationship in which the two partners are molecular entities and are executing molecular processes that are directly causally connected." [] def: "An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other." [] property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "binds" xsd:string @@ -24773,7 +24448,7 @@ is_a: RO:0002434 ! interacts with [Typedef] id: RO:0002447 name: phosphorylates -property_value: editor_note "Axiomatization to GO to be added later" xsd:string +property_value: IAO:0000116 "Axiomatization to GO to be added later" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y." xsd:string is_a: RO:0002436 ! molecularly interacts with @@ -24781,8 +24456,6 @@ is_a: RO:0002436 ! molecularly interacts with [Typedef] id: RO:0002448 name: activity directly regulates activity of -name: molecularly controls -def: "Holds between molecular entities a and b when the execution of a activates or inhibits the activity of b" [] def: "Holds between molecular entities A and B where A can physically interact with B and in doing so regulates a process that B is capable of. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B." [] synonym: "molecularly controls" EXACT [] property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -24792,32 +24465,39 @@ is_a: RO:0002566 ! causally influences [Typedef] id: RO:0002449 name: activity directly negatively regulates activity of -name: molecularly decreases activity of def: "Holds between molecular entities A and B where A can physically interact with B and in doing so negatively regulates a process that B is capable of. For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B." [] -def: "Holds between molecules a and b if and only if a executes a process that directly diminishes a process executed by b." [] synonym: "molecularly decreases activity of" EXACT [] property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "inhibits" xsd:string -is_a: RO:0002448 ! molecularly controls +is_a: RO:0002448 ! activity directly regulates activity of [Typedef] id: RO:0002450 name: activity directly positively regulates activity of -name: molecularly increases activity of def: "Holds between molecular entities A and B where A can physically interact with B and in doing so positively regulates a process that B is capable of. For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B." [] -def: "Holds between molecules a and b if and only if a executes a process that directly activates a process executed by b." [] synonym: "molecularly increases activity of" EXACT [] property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "activates" xsd:string -is_a: RO:0002448 ! molecularly controls +is_a: RO:0002448 ! activity directly regulates activity of [Typedef] id: RO:0002464 -name: helper property name: helper property (not for use in curation) -property_value: curator_notes "This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning." xsd:string -property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000232 "This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning." xsd:string + +[Typedef] +id: RO:0002473 +name: composed primarily of +def: "x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y." [] +subset: ro-eco +property_value: IAO:0000112 "'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate'" xsd:string +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 +property_value: RO:0001900 RO:0001901 +domain: BFO:0000040 ! material entity +range: BFO:0000040 ! material entity +is_a: has_part ! has part [Typedef] id: RO:0002479 @@ -24837,20 +24517,19 @@ is_a: RO:0002564 ! molecular interaction relation helper property [Typedef] id: RO:0002500 -name: causal agent in name: causal agent in process def: "A relationship between a material entity and a process where the material entity has some causal role that influences the process" [] property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations is_a: RO:0002595 ! causal relation between material entity and a process -inverse_of: RO:0002608 ! has causal agent +inverse_of: RO:0002608 ! process has causal agent [Typedef] id: RO:0002501 name: causal relation between processes def: "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q." [] -property_value: curator_notes "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string domain: BFO:0000003 ! occurrent range: BFO:0000003 ! occurrent is_a: RO:0002410 ! causally related to @@ -24864,10 +24543,10 @@ property_value: seeAlso BFO:0000169 [Typedef] id: RO:0002506 name: causal relation between material entities -property_value: curator_notes "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string -property_value: editor_note "The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch" xsd:string +property_value: IAO:0000116 "The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity is_a: RO:0002410 ! causally related to @@ -24877,12 +24556,10 @@ id: RO:0002507 name: determined by def: "s determined by f if and only if s is a type of system, and f is a material entity that is part of s, such that f exerts a strong causal influence on the functioning of s, and the removal of f would cause the collapse of s." [] subset: ro-eco -property_value: dc-creator "Chris Mungall" xsd:string -property_value: dc-creator "Pier Buttigieg" xsd:string -property_value: editor_note "The label for this relation is probably too general for its restricted use, where the domain is a system. It may be relabeled in future" xsd:string -property_value: example_of_usage "A coral reef environment is determined by a particular coral reef" xsd:string property_value: http://purl.org/dc/terms/creator "Chris Mungall" xsd:string property_value: http://purl.org/dc/terms/creator "Pier Buttigieg" xsd:string +property_value: IAO:0000112 "A coral reef environment is determined by a particular coral reef" xsd:string +property_value: IAO:0000116 "The label for this relation is probably too general for its restricted use, where the domain is a system. It may be relabeled in future" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/24330602 property_value: IAO:0000589 "determined by (system to material entity)" xsd:string @@ -24912,7 +24589,7 @@ property_value: IAO:0000117 "Chris Mungall" xsd:string domain: RO:0002577 ! system range: BFO:0000040 ! material entity holds_over_chain: RO:0002507 part_of {http://purl.obolibrary.org/obo/RO_0002582="true"} -is_a: overlaps ! overlaps +is_a: RO:0002131 ! overlaps is_a: RO:0002506 ! causal relation between material entities [Typedef] @@ -24927,7 +24604,7 @@ inverse_of: RO:0002566 ! causally influences [Typedef] id: RO:0002563 name: interaction relation helper property -property_value: foaf-page https://github.com/oborel/obo-relations/wiki/InteractionRelations xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/page https://github.com/oborel/obo-relations/wiki/InteractionRelations xsd:anyURI property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:N-Ary_Relation_Pattern_%28OWL_2%29 is_a: RO:0002464 ! helper property (not for use in curation) @@ -24962,17 +24639,17 @@ is_a: RO:0002412 ! immediately causally upstream of id: RO:0002584 name: has part structure that is capable of def: "s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p" [] -property_value: example_of_usage "gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'" xsd:string +property_value: IAO:0000112 "gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string -holds_over_chain: has_part capable_of -is_a: functionally_related_to ! functionally related to +holds_over_chain: has_part RO:0002215 +is_a: RO:0002328 ! functionally related to is_a: RO:0002595 ! causal relation between material entity and a process [Typedef] id: RO:0002595 name: causal relation between material entity and a process def: "A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity." [] -property_value: editor_note "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string +property_value: IAO:0000116 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations domain: BFO:0000040 ! material entity @@ -24983,50 +24660,46 @@ is_a: RO:0002410 ! causally related to id: RO:0002596 name: capable of regulating def: "Holds between c and p if and only if c is capable of some activity a, and a regulates p." [] -property_value: example_of_usage "pyrethroid -> growth" xsd:string +property_value: IAO:0000112 "pyrethroid -> growth" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -holds_over_chain: capable_of regulates -is_a: RO:0002500 ! causal agent in +holds_over_chain: RO:0002215 regulates +is_a: RO:0002500 ! causal agent in process [Typedef] id: RO:0002597 name: capable of negatively regulating def: "Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p." [] property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -holds_over_chain: capable_of negatively_regulates +holds_over_chain: RO:0002215 negatively_regulates is_a: RO:0002596 ! capable of regulating [Typedef] id: RO:0002598 name: capable of positively regulating def: "Holds between c and p if and only if c is capable of some activity a, and a positively regulates p." [] -property_value: example_of_usage "renin -> arteriolar smooth muscle contraction" xsd:string +property_value: IAO:0000112 "renin -> arteriolar smooth muscle contraction" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -holds_over_chain: capable_of positively_regulates +holds_over_chain: RO:0002215 positively_regulates is_a: RO:0002596 ! capable of regulating [Typedef] id: RO:0002608 -name: has causal agent name: process has causal agent def: "Inverse of 'causal agent in process'" [] -def: "Inverse of 'causal agent in'" [] property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations is_a: RO:0002410 ! causally related to [Typedef] id: RO:0002609 name: obsolete related via dependence to -name: related via dependence to def: "A relationship that holds between two entities, where the relationship holds based on the presence or absence of statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes." [] -property_value: curator_notes "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string +property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string is_obsolete: true [Typedef] id: RO:0002629 name: directly positively regulates def: "Process(P1) directly postively regulates process(P2) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P1 directly positively regulates P2." [] -def: "Process(P1) directly regulates process(P2) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P1 directly positively regulates P2." [] property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly positively regulates (process to process)" xsd:string property_value: RO:0004049 RO:0002578 @@ -25037,19 +24710,40 @@ is_a: RO:0002578 ! directly regulates id: RO:0002630 name: directly negatively regulates def: "Process(P1) directly negatively regulates process(P2) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P1 directly negatively regulates P2." [] -def: "Process(P1) directly regulates process(P2) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P1 directly negatively regulates P2." [] property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly negatively regulates (process to process)" xsd:string property_value: RO:0004050 RO:0002578 is_a: negatively_regulates ! negatively regulates is_a: RO:0002578 ! directly regulates +[Typedef] +id: RO:0003000 +name: produces +def: "a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix." [] +comment: Note that this definition doesn't quite distinguish the output of a transformation process from a production process, which is related to the identity/granularity issue. +subset: ro-eco +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 "Melissa Haendel" xsd:string +domain: BFO:0000040 ! material entity +range: BFO:0000040 ! material entity +inverse_of: RO:0003001 ! produced by + +[Typedef] +id: RO:0003001 +name: produced by +def: "a produced_by b iff some process that occurs_in b has_output a." [] +subset: ro-eco +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 "Melissa Haendel" xsd:string +domain: BFO:0000040 ! material entity +range: BFO:0000040 ! material entity + [Typedef] id: RO:0004031 name: enables subfunction def: "Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P." [] holds_over_chain: RO:0002327 has_part -is_a: functionally_related_to ! functionally related to +is_a: RO:0002328 ! functionally related to created_by: cjm creation_date: 2018-01-25T23:20:13Z @@ -25112,122 +24806,10 @@ is_a: RO:0002418 ! causally upstream of or within created_by: cjm creation_date: 2018-03-13T23:55:19Z -[Typedef] -id: bearer_of -name: bearer of -namespace: uberon -def: "a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence" [] -xref: RO:0000053 -property_value: editor_note "A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist." xsd:string -property_value: example_of_usage "this apple is bearer of this red color" xsd:string -property_value: example_of_usage "this vase is bearer of this fragility" xsd:string -property_value: IAO:0000111 "bearer of" xsd:string -property_value: IAO:0000118 "bearer_of" xsd:string -property_value: IAO:0000118 "is bearer of" xsd:string -property_value: RO:0001900 RO:0001901 -range: BFO:0000020 ! specifically dependent continuant - -[Typedef] -id: capable_of -name: capable of -namespace: uberon -def: "A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. " [] -subset: ro-eco -xref: RO:0002215 -property_value: curator_notes "For compatibility with BFO, this relation has a shortcut definition in which the expression \"capable of some P\" expands to \"bearer_of (some realized_by only P)\"." xsd:string -property_value: example_of_usage "mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)" xsd:string -property_value: example_of_usage "osteoclast SubClassOf 'capable of' some 'bone resorption'" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000118 "has function realized in" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20123131 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/21208450 -domain: BFO:0000004 ! independent continuant -range: BFO:0000015 ! process -is_a: capable_of_part_of ! capable of part of -is_a: functionally_related_to ! functionally related to -expand_expression_to: "RO_0000053 some (RO_0000054 only ?Y)" [] - -[Typedef] -id: capable_of_part_of -name: capable of part of -namespace: uberon -def: "c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p." [] -xref: RO:0002216 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000118 "has function in" xsd:string -property_value: seeAlso "defining-property-chains-involving-reflexivity" -holds_over_chain: capable_of part_of {http://purl.obolibrary.org/obo/RO_0002582="true"} -is_a: functionally_related_to ! functionally related to -is_a: RO:0002500 ! causal agent in -expand_expression_to: "RO_0000053 some (RO_0000054 only (BFO_0000050 some ?Y))" [] - -[Typedef] -id: composed_primarily_of -name: composed primarily of -namespace: uberon -def: "x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y." [] -def: "x composed_primarily_of y iff: more than half of the mass of x is made from parts of y" [] -subset: ro-eco -xref: RO:0002473 -property_value: example_of_usage "'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate'" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 -property_value: RO:0001900 RO:0001901 -domain: BFO:0000040 ! material entity -range: BFO:0000040 ! material entity -is_a: has_part ! has part - -[Typedef] -id: contains -name: contains -namespace: uberon -subset: ro-eco -xref: RO:0001019 -property_value: IAO:0000111 "contains" xsd:string -property_value: RO:0001900 RO:0001901 - -[Typedef] -id: contains_process -name: contains process -namespace: uberon -def: "[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" [] -comment: Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant -xref: BFO:0000067 -property_value: IAO:0000111 "site of" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl - [Typedef] id: correlates_with name: correlates_with -[Typedef] -id: curator_notes -name: curator note -name: curator notes -namespace: uberon -def: "An administrative note of use for a curator but of no use for a user" [] -xref: IAO:0000232 -property_value: IAO:0000111 "curator note" xsd:string -property_value: IAO:0000114 IAO:0000122 -property_value: IAO:0000117 "PERSON:Alan Ruttenberg" xsd:string -is_metadata_tag: true - -[Typedef] -id: dc-creator -name: creator -namespace: uberon -xref: http://purl.org/dc/elements/1.1/creator -is_metadata_tag: true - -[Typedef] -id: dc-source -name: derived from resource -namespace: uberon -xref: http://purl.org/dc/elements/1.1/source -is_metadata_tag: true - [Typedef] id: decreased_in_magnitude_relative_to name: decreased_in_magnitude_relative_to @@ -25238,75 +24820,6 @@ range: PATO:0000001 ! quality is_transitive: true is_a: different_in_magnitude_relative_to ! different_in_magnitude_relative_to -[Typedef] -id: developmentally_contributes_to -name: developmentally contributes to -name: developmentally_contributes_to -namespace: uberon -def: "inverse of has developmental contribution from" [] -subset: RO:0002259 -xref: RO:0002255 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -holds_over_chain: develops_into part_of -is_a: has_potential_to_developmentally_contribute_to ! has potential to developmentally contribute to -is_a: RO:0002286 ! developmentally succeeded by - -[Typedef] -id: developmentally_preceded_by -name: developmentally preceded by -namespace: uberon -def: "Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p" [] -comment: This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from -xref: RO:0002258 -property_value: curator_notes "In general you should not use this relation to make assertions - use one of the more specific relations below this one" xsd:string -property_value: editor_note "false" xsd:boolean -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -domain: BFO:0000002 ! continuant -range: BFO:0000002 ! continuant -is_a: RO:0002324 ! developmentally related to -inverse_of: RO:0002286 ! developmentally succeeded by - -[Typedef] -id: develops_from -name: develops from -name: develops_from -namespace: uberon -def: "x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y" [] -comment: This is the transitive form of the develops from relation -xref: RO:0002202 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Melissa Haendel" xsd:string -property_value: IAO:0000117 "Terry Meehan" xsd:string -domain: BFO:0000004 ! independent continuant -range: BFO:0000004 ! independent continuant -holds_over_chain: part_of develops_from -is_transitive: true -is_a: developmentally_preceded_by ! developmentally preceded by -is_a: has_developmental_contribution_from ! has developmental contribution from -inverse_of: develops_into ! develops_into -transitive_over: part_of ! part_of - -[Typedef] -id: develops_into -name: develops into -name: develops_into -namespace: uberon -def: "inverse of develops from" [] -subset: RO:0002259 -xref: RO:0002203 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Terry Meehan" xsd:string -is_transitive: true -is_a: has_potential_to_develop_into ! has potential to develop into -is_a: has_potential_to_directly_develop_into ! has potential to directly develop into -is_a: RO:0002286 ! developmentally succeeded by - [Typedef] id: different_in_magnitude_relative_to name: different_in_magnitude_relative_to @@ -25324,93 +24837,12 @@ range: PATO:0000001 ! quality created_by: cjm creation_date: 2009-08-26T02:50:08Z -[Typedef] -id: editor_note -name: editor note -namespace: uberon -def: "An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology." [] -xref: IAO:0000116 -property_value: IAO:0000111 "editor note" xsd:string -property_value: IAO:0000114 IAO:0000122 -property_value: IAO:0000117 "PERSON:Daniel Schober" xsd:string -property_value: IAO:0000119 GROUP:OBI: xsd:string -is_metadata_tag: true - -[Typedef] -id: example_of_usage -name: example of usage -namespace: uberon -def: "A phrase describing how a class name should be used. May also include other kinds of examples that facilitate immediate understanding of a class semantics, such as widely known prototypical subclasses or instances of the class. Although essential for high level terms, examples for low level terms (e.g., Affymetrix HU133 array) are not" [] -xref: IAO:0000112 -property_value: IAO:0000111 "example" xsd:string -property_value: IAO:0000114 IAO:0000122 -property_value: IAO:0000117 "PERSON:Daniel Schober" xsd:string -property_value: IAO:0000119 GROUP:OBI: xsd:string -is_metadata_tag: true - -[Typedef] -id: external_definition -name: external_definition -namespace: uberon -def: "An alternate textual definition for a class taken unmodified from an external source. This definition may have been used to derive a generalized definition for the new class." [https://orcid.org/0000-0002-6601-2165] -comment: This annotation property may be replaced with an annotation property from an external ontology such as IAO -xref: UBPROP:0000001 -is_metadata_tag: true - -[Typedef] -id: foaf-page -name: page -namespace: uberon -xref: http://xmlns.com/foaf/0.1/page -is_metadata_tag: true - -[Typedef] -id: functionally_related_to -name: functionally related to -namespace: uberon -def: "A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities." [] -xref: RO:0002328 -property_value: curator_notes "This is a grouping relation that collects relations used for the purpose of connecting structure and function" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string - -[Typedef] -id: has_component -name: has component -namespace: uberon -def: "w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type." [] -subset: ro-eco -xref: RO:0002180 -property_value: curator_notes "For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit." xsd:string -property_value: editor_note "The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity." xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: RO:0001900 RO:0001901 -property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:Componency -is_a: has_part ! has part - [Typedef] id: has_cross_section name: has_cross_section def: "s3 has_cross_section s3 if and only if : there exists some 2d plane that intersects the bearer of s3, and the impression of s3 upon that plane has shape quality s2." [PATOC:CJM] comment: Example: a spherical object has the quality of being spherical, and the spherical quality has_cross_section round. -[Typedef] -id: has_developmental_contribution_from -name: has developmental contribution from -namespace: uberon -def: "x has developmental contribution from y iff x has some part z such that z develops from y" [] -xref: RO:0002254 -property_value: example_of_usage "Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -domain: BFO:0000004 ! independent continuant -domain: CARO:0000000 ! anatomical entity -range: CARO:0000000 ! anatomical entity -range: CARO:0000003 ! anatomical structure -holds_over_chain: has_part develops_from -is_transitive: true -is_a: developmentally_preceded_by ! developmentally preceded by -inverse_of: developmentally_contributes_to ! developmentally contributes to - [Typedef] id: has_dividend_entity name: has_dividend_entity @@ -25435,81 +24867,26 @@ domain: PATO:0001470 ! proportionality to range: PATO:0000001 ! quality is_a: has_ratio_quality ! has_ratio_quality -[Typedef] -id: has_member -name: has member -namespace: uberon -def: "has member is a mereological relation between a collection and an item." [] -xref: RO:0002351 -property_value: IAO:0000119 "SIO" xsd:string -property_value: RO:0001900 RO:0001901 -is_a: has_part ! has part - [Typedef] id: has_part name: has part name: has_part -namespace: chebi_ontology namespace: external -namespace: uberon def: "a core relation that holds between a whole and its part" [] def: "Q1 has_part Q2 if and only if: every instance of Q1 is a quality_of an entity that has_quality some Q2." [PATOC:CJM] comment: We use the has_part relation to relate complex qualities to more primitive ones. A complex quality is a collection of qualities. The complex quality cannot exist without the sub-qualities. For example, the quality 'swollen' necessarily comes with the qualities of 'protruding' and 'increased size'. xref: BFO:0000051 -property_value: editor_note "Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part." xsd:string -property_value: editor_note "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime" xsd:string -property_value: editor_note "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)\n\nA continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'." xsd:string -property_value: example_of_usage "my body has part my brain (continuant parthood, two material entities)" xsd:string -property_value: example_of_usage "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)" xsd:string -property_value: example_of_usage "this year has part this day (occurrent parthood)" xsd:string property_value: IAO:0000111 "has part" xsd:string +property_value: IAO:0000112 "my body has part my brain (continuant parthood, two material entities)" xsd:string +property_value: IAO:0000112 "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)" xsd:string +property_value: IAO:0000112 "this year has part this day (occurrent parthood)" xsd:string +property_value: IAO:0000116 "Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part." xsd:string +property_value: IAO:0000116 "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime" xsd:string +property_value: IAO:0000116 "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)\n\nA continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'." xsd:string property_value: IAO:0000118 "has_part" xsd:string property_value: RO:0001900 RO:0001901 -is_cyclic: false is_transitive: true -is_a: overlaps ! overlaps - -[Typedef] -id: has_potential_to_develop_into -name: has potential to develop into -namespace: uberon -def: "x has the potential to develop into y iff x develops into y or if x is capable of developing into y" [] -xref: RO:0002387 -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string -is_a: RO:0002384 ! has developmental potential involving - -[Typedef] -id: has_potential_to_developmentally_contribute_to -name: has potential to developmentally contribute to -namespace: uberon -def: "x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y" [] -xref: RO:0002385 -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string -is_a: RO:0002384 ! has developmental potential involving - -[Typedef] -id: has_potential_to_directly_develop_into -name: has potential to directly develop into -namespace: uberon -def: "x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y" [] -xref: RO:0002388 -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string -is_a: has_potential_to_develop_into ! has potential to develop into - -[Typedef] -id: has_quality -name: has quality -namespace: uberon -def: "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence" [] -xref: RO:0000086 -property_value: editor_note "A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist." xsd:string -property_value: example_of_usage "this apple has quality this red color" xsd:string -property_value: IAO:0000118 "has_quality" xsd:string -range: BFO:0000019 ! quality -is_a: bearer_of ! bearer of +is_a: RO:0002131 ! overlaps [Typedef] id: has_ratio_quality @@ -25521,25 +24898,6 @@ range: PATO:0000001 ! quality id: has_relative_magnitude name: has_relative_magnitude -[Typedef] -id: immediately_preceded_by -name: immediately preceded by -name: immediately_preceded_by -namespace: uberon -def: "X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)" [] -comment: X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) -synonym: "directly preceded by" EXACT [] -synonym: "is directly preceded by" EXACT [] -synonym: "is immediately preceded by" EXACT [SIO:000251] -synonym: "starts_at_end_of" EXACT [] -xref: RO:0002087 -property_value: external_definition "A non-transitive temporal relation in which one process immediately precedes another process, such that there is no interval of time between the two processes[SIO:000251]." xsd:string {source="SIO:000251"} -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000118 "starts_at_end_of" xsd:string -property_value: seeAlso SIO:000251 -is_a: preceded_by ! preceded_by -inverse_of: RO:0002090 ! immediately precedes - [Typedef] id: increased_in_magnitude_relative_to name: increased_in_magnitude_relative_to @@ -25550,18 +24908,6 @@ range: PATO:0000001 ! quality is_transitive: true is_a: different_in_magnitude_relative_to ! different_in_magnitude_relative_to -[Typedef] -id: input_of -name: input of -namespace: uberon -def: "inverse of has input" [] -subset: ro-eco -subset: RO:0002259 -xref: RO:0002352 -property_value: IAO:0000117 "Chris Mungall" xsd:string -is_a: functionally_related_to ! functionally related to -is_a: RO:0000056 ! participates in - [Typedef] id: inversely_associated_with name: inversely_associated_with @@ -25588,8 +24934,8 @@ name: is opposite of name: is_opposite_of def: "x is the opposite of y if there exists some distance metric M, and there exists no z such as M(x,z) <= M(x,y) or M(y,z) <= M(y,x)." [] xref: RO:0002604 -property_value: example_of_usage "'anterior end of organism' is-opposite-of 'posterior end of organism'" xsd:string -property_value: example_of_usage "'increase in temperature' is-opposite-of 'decrease in temperature'" xsd:string +property_value: IAO:0000112 "'anterior end of organism' is-opposite-of 'posterior end of organism'" xsd:string +property_value: IAO:0000112 "'increase in temperature' is-opposite-of 'decrease in temperature'" xsd:string is_metadata_tag: true is_class_level: true @@ -25598,62 +24944,12 @@ id: is_unit_of name: is_unit_of namespace: pato.ontology -[Typedef] -id: located_in -name: located in -name: located_in -namespace: uberon -def: "a relation between two independent continuants, the target and the location, in which the target is entirely within the location" [] -xref: RO:0001025 -property_value: dc-source http://www.obofoundry.org/ro/#OBO_REL:located_in xsd:string -property_value: editor_note "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" xsd:string -property_value: editor_note "Most location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime" xsd:string -property_value: example_of_usage "my brain is located in my head" xsd:string -property_value: example_of_usage "this rat is located in this cage" xsd:string -property_value: IAO:0000111 "located in" xsd:string -property_value: IAO:0000118 "located_in" xsd:string -property_value: RO:0001900 RO:0001901 -domain: BFO:0000004 {http://purl.obolibrary.org/obo/IAO_0000116="This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation."} ! independent continuant -range: BFO:0000004 {http://purl.obolibrary.org/obo/IAO_0000116="This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation."} ! independent continuant -is_transitive: true - -[Typedef] -id: location_of -name: location of -name: location_of -namespace: uberon -def: "a relation between two independent continuants, the location and the target, in which the target is entirely within the location" [] -xref: RO:0001015 -property_value: editor_note "Most location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime" xsd:string -property_value: example_of_usage "my head is the location of my brain" xsd:string -property_value: example_of_usage "this cage is the location of this rat" xsd:string -property_value: IAO:0000111 "is location of" xsd:string -property_value: IAO:0000118 "location_of" xsd:string -property_value: RO:0001900 RO:0001901 -is_transitive: true -inverse_of: located_in ! located in - -[Typedef] -id: member_of -name: member of -namespace: uberon -def: "is member of is a mereological relation between a item and a collection." [] -xref: RO:0002350 -property_value: example_of_usage "An organism that is a member of a population of organisms" xsd:string -property_value: IAO:0000118 "is member of" xsd:string -property_value: IAO:0000118 "member part of" xsd:string -property_value: IAO:0000119 "SIO" xsd:string -property_value: RO:0001900 RO:0001901 -is_a: part_of ! part_of -inverse_of: has_member ! has member - [Typedef] id: negatively_regulates name: negatively regulates namespace: external 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." [] xref: RO:0002212 -property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "negatively regulates (process to process)" xsd:string @@ -25677,54 +24973,23 @@ property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl domain: BFO:0000003 ! occurrent range: BFO:0000004 ! independent continuant holds_over_chain: part_of occurs_in -inverse_of: contains_process ! contains process +inverse_of: BFO:0000067 ! contains process transitive_over: part_of ! part_of -[Typedef] -id: output_of -name: output of -namespace: uberon -def: "inverse of has output" [] -subset: ro-eco -subset: RO:0002259 -xref: RO:0002353 -property_value: IAO:0000117 "Chris Mungall" xsd:string -is_a: functionally_related_to ! functionally related to -is_a: RO:0000056 ! participates in - -[Typedef] -id: overlaps -name: overlaps -namespace: uberon -def: "A overlaps B if they share some part in common." [] -def: "x overlaps y if and only if there exists some z such that x has part z and z part of y" [] -subset: ro-eco -xref: RO:0002131 -property_value: IAO:0000114 IAO:0000125 -property_value: RO:0001900 RO:0001901 -holds_over_chain: has_part overlaps -holds_over_chain: has_part part_of {http://purl.obolibrary.org/obo/RO_0002582="true"} -holds_over_chain: part_of part_of -is_a: RO:0002323 ! mereotopologically related to -transitive_over: part_of ! part_of -expand_expression_to: "BFO_0000051 some (BFO_0000050 some ?Y)" [] -expand_expression_to: "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)" [] - [Typedef] id: part_of name: part of name: part_of namespace: external -namespace: uberon def: "a core relation that holds between a part and its whole" [] xref: BFO:0000050 -property_value: editor_note "Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other." xsd:string -property_value: editor_note "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime" xsd:string -property_value: editor_note "Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)\n\nA continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'." xsd:string -property_value: example_of_usage "my brain is part of my body (continuant parthood, two material entities)" xsd:string -property_value: example_of_usage "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)" xsd:string -property_value: example_of_usage "this day is part of this year (occurrent parthood)" xsd:string property_value: IAO:0000111 "is part of" xsd:string +property_value: IAO:0000112 "my brain is part of my body (continuant parthood, two material entities)" xsd:string +property_value: IAO:0000112 "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)" xsd:string +property_value: IAO:0000112 "this day is part of this year (occurrent parthood)" xsd:string +property_value: IAO:0000116 "Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other." xsd:string +property_value: IAO:0000116 "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime" xsd:string +property_value: IAO:0000116 "Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)\n\nA continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'." xsd:string property_value: IAO:0000118 "part_of" xsd:string property_value: RO:0001900 RO:0001901 property_value: RO:0040042 BFO:0000002 @@ -25738,20 +25003,9 @@ property_value: seeAlso http://ontologydesignpatterns.org/wiki/Community:Parts_a property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:PartOf property_value: seeAlso http://www.obofoundry.org/ro/#OBO_REL:part_of xsd:string is_transitive: true -is_a: overlaps ! overlaps +is_a: RO:0002131 ! overlaps inverse_of: has_part ! has part -[Typedef] -id: part_of_structure_that_is_capable_of -name: part of structure that is capable of -namespace: uberon -def: "this relation holds between c and p when c is part of some c', and c' is capable of p." [] -xref: RO:0002329 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000118 "false" xsd:boolean -holds_over_chain: part_of capable_of {http://purl.obolibrary.org/obo/RO_0002581="true"} -is_a: functionally_related_to ! functionally related to - [Typedef] id: positively_regulates name: positively regulates @@ -25768,70 +25022,6 @@ is_a: regulates ! regulates is_a: RO:0002304 ! causally upstream of, positive effect inverse_of: RO:0002336 ! positively regulated by -[Typedef] -id: preceded_by -name: preceded by -name: preceded_by -namespace: uberon -def: "x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] -def: "X preceded_by Y iff: end(Y) before_or_simultaneous_with start(X)" [] -subset: ro-eco -synonym: "is preceded by" EXACT [SIO:000249] -synonym: "takes place after" EXACT [Allen:precedes] -xref: BFO:0000062 -property_value: dc-source http://www.obofoundry.org/ro/#OBO_REL:preceded_by xsd:string -property_value: editor_note "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." xsd:string -property_value: IAO:0000111 "preceded by" xsd:string -property_value: IAO:0000118 "is preceded by" xsd:string -property_value: IAO:0000118 "preceded_by" xsd:string -domain: BFO:0000003 ! occurrent -range: BFO:0000003 ! occurrent -holds_over_chain: part_of preceded_by -is_transitive: true -is_a: RO:0002086 ! ends after -inverse_of: precedes ! precedes - -[Typedef] -id: precedes -name: precedes -namespace: uberon -def: "x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] -subset: ro-eco -xref: BFO:0000063 -property_value: IAO:0000111 "precedes" xsd:string -domain: BFO:0000003 ! occurrent -range: BFO:0000003 ! occurrent -holds_over_chain: part_of precedes -is_transitive: true -is_a: RO:0002222 ! temporally related to - -[Typedef] -id: produced_by -name: produced by -name: produced_by -namespace: uberon -def: "a produced_by b iff some process that occurs_in b has_output a." [] -subset: ro-eco -xref: RO:0003001 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Melissa Haendel" xsd:string -domain: BFO:0000040 ! material entity -range: BFO:0000040 ! material entity - -[Typedef] -id: produces -name: produces -namespace: uberon -def: "a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix." [] -comment: Note that this definition doesn't quite distinguish the output of a transformation process from a production process, which is related to the identity/granularity issue. -subset: ro-eco -xref: RO:0003000 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Melissa Haendel" xsd:string -domain: BFO:0000040 ! material entity -range: BFO:0000040 ! material entity -inverse_of: produced_by ! produced_by - [Typedef] id: realized_by name: realized_by @@ -25848,14 +25038,14 @@ name: regulates namespace: external 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." [] xref: RO:0002211 -property_value: curator_notes "Regulation precludes parthood; the regulatory process may not be within the regulated process." xsd:string -property_value: editor_note "We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit" xsd:string property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000116 "We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 "David Hill" xsd:string property_value: IAO:0000117 "Tanya Berardini" xsd:string property_value: IAO:0000119 "GO" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: IAO:0000232 "Regulation precludes parthood; the regulatory process may not be within the regulated process." xsd:string property_value: IAO:0000589 "regulates (processual)" xsd:string property_value: IAO:0000600 "false" xsd:boolean domain: BFO:0000015 ! process @@ -25869,19 +25059,19 @@ inverse_of: RO:0002334 ! regulated by id: results_in_developmental_progression_of name: results in developmental progression of def: "p results in the developmental progression of s iff p is a developmental process and s is an anatomical structure and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss)." [] -property_value: editor_note "This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint." xsd:string property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000116 "This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint." xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: seeAlso Ontology:extensions domain: GO:0008150 ! biological_process -range: CARO:0000003 ! anatomical structure +range: CARO:0000003 ! connected anatomical structure is_a: RO:0002324 ! developmentally related to [Typedef] id: results_in_formation_of name: results in formation of -property_value: example_of_usage "an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists." xsd:string -property_value: example_of_usage "every \"endocardial cushion formation\" (GO:0003272) results_in_formation_of some \"endocardial cushion\" (UBERON:0002062)" xsd:string +property_value: IAO:0000112 "an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists." xsd:string +property_value: IAO:0000112 "every \"endocardial cushion formation\" (GO:0003272) results_in_formation_of some \"endocardial cushion\" (UBERON:0002062)" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string diff --git a/pato-full.owl b/pato-full.owl index bef1a297..245ccdc2 100644 --- a/pato-full.owl +++ b/pato-full.owl @@ -8,24 +8,22 @@ xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:xml="http://www.w3.org/XML/1998/namespace" xmlns:xsd="http://www.w3.org/2001/XMLSchema#" - xmlns:core="http://purl.obolibrary.org/obo/uberon/core#" xmlns:foaf="http://xmlns.com/foaf/0.1/" xmlns:pato="http://purl.obolibrary.org/obo/pato#" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" xmlns:swrl="http://www.w3.org/2003/11/swrl#" - xmlns:chebi="http://purl.obolibrary.org/obo/chebi#3" xmlns:swrla="http://swrl.stanford.edu/ontologies/3.3/swrla.owl#" xmlns:swrlb="http://www.w3.org/2003/11/swrlb#" xmlns:terms="http://purl.org/dc/terms/" xmlns:subsets="http://purl.obolibrary.org/obo/ro/subsets#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - - OBO-Edit 2.3.1 - 07:02:2018 10:27 + + An ontology of phenotypic qualities (properties, attributes or characteristics). + PATO - the Phenotype And Trait Ontology + https://creativecommons.org/licenses/by/3.0/ quality 1.2 - segerdel @@ -44,11 +42,6 @@ - editor preferred term - - The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English) - PERSON:Daniel Schober - GROUP:OBI:<http://purl.obolibrary.org/obo/obi> editor preferred term @@ -57,17 +50,7 @@ - example - A phrase describing how a class name should be used. May also include other kinds of examples that facilitate immediate understanding of a class semantics, such as widely known prototypical subclasses or instances of the class. Although essential for high level terms, examples for low level terms (e.g., Affymetrix HU133 array) are not - PERSON:Daniel Schober - GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - IAO:0000112 - uberon - example_of_usage - true - example_of_usage - example of usage example of usage @@ -76,11 +59,6 @@ - has curation status - PERSON:Alan Ruttenberg - PERSON:Bill Bug - PERSON:Melanie Courtot - OBI_0000281 has curation status @@ -89,31 +67,7 @@ - definition - The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. - 2012-04-05: -Barry Smith - -The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. - -Can you fix to something like: - -A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. - -Alan Ruttenberg - -Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. - -On the specifics of the proposed definition: - -We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. - -Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. - -We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. - PERSON:Daniel Schober - GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition definition @@ -123,17 +77,7 @@ We also have the outstanding issue of how to aim different definitions to differ - editor note - An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology. - PERSON:Daniel Schober - GROUP:OBI:<http://purl.obfoundry.org/obo/obi> - IAO:0000116 - uberon - editor_note - true - editor_note - editor note editor note @@ -142,12 +86,7 @@ We also have the outstanding issue of how to aim different definitions to differ - term editor - Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people - 20110707, MC: label update to term editor and definition modified accordingly. See http://code.google.com/p/information-artifact-ontology/issues/detail?id=115. - PERSON:Daniel Schober - GROUP:OBI:<http://purl.obolibrary.org/obo/obi> term editor @@ -156,11 +95,7 @@ We also have the outstanding issue of how to aim different definitions to differ - alternative term - An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent) - PERSON:Daniel Schober - GROUP:OBI:<http://purl.obolibrary.org/obo/obi> alternative term @@ -169,12 +104,7 @@ We also have the outstanding issue of how to aim different definitions to differ - definition source - formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007 - PERSON:Daniel Schober - Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w - GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition source @@ -182,30 +112,15 @@ We also have the outstanding issue of how to aim different definitions to differ - - has obsolescence reason - Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification. - PERSON:Alan Ruttenberg - PERSON:Melanie Courtot - has obsolescence reason - + - curator note - An administrative note of use for a curator but of no use for a user - PERSON:Alan Ruttenberg - IAO:0000232 - uberon - curator_notes - true - curator_notes curator note - curator notes @@ -213,12 +128,7 @@ We also have the outstanding issue of how to aim different definitions to differ - imported from - For external terms/classes, the ontology from which the term was imported - PERSON:Alan Ruttenberg - PERSON:Melanie Courtot - GROUP:OBI:<http://purl.obolibrary.org/obo/obi> imported from @@ -227,14 +137,6 @@ We also have the outstanding issue of how to aim different definitions to differ - expand expression to - ObjectProperty: RO_0002104 -Label: has plasma membrane part -Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.org/obo/owl/GO#GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)" - - A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones - Chris Mungall - expand expression to expand expression to @@ -243,15 +145,7 @@ Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some ( - OBO foundry unique label - An alternative name for a class or property which is unique across the OBO Foundry. - The intended usage of that property is as follow: OBO foundry unique labels are automatically generated based on regular expressions provided by each ontology, so that SO could specify unique label = 'sequence ' + [label], etc. , MA could specify 'mouse + [label]' etc. Upon importing terms, ontology developers can choose to use the 'OBO foundry unique label' for an imported term or not. The same applies to tools . - PERSON:Alan Ruttenberg - PERSON:Bjoern Peters - PERSON:Chris Mungall - PERSON:Melanie Courtot - GROUP:OBO Foundry <http://obofoundry.org/> OBO foundry unique label @@ -260,54 +154,19 @@ Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some ( - elucidation - person:Alan Ruttenberg - Person:Barry Smith - Primitive terms in a highest-level ontology such as BFO are terms which are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms elucidation - - - - has axiom id - Person:Alan Ruttenberg - Person:Alan Ruttenberg - A URI that is intended to be unique label for an axiom used for tracking change to the ontology. For an axiom expressed in different languages, each expression is given the same URI - has axiom label - - - - - term replaced by - - Add as annotation triples in the granting ontology - Use on obsolete terms, relating the term to another term that can be used as a substitute - Person:Alan Ruttenberg - Person:Alan Ruttenberg - term replaced by term replaced by - - - - - - - - - - - - @@ -329,7 +188,9 @@ Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some ( - + + logical macro assertion on an annotation property + @@ -346,7 +207,6 @@ Where we have an annotation assertion "directly P" "is direct form of" "P" If we have the annotation P is-direct-form-of Q, and we have inverses P' and Q', then it follows that P' is-direct-form-of Q' - Chris Mungall Chris Mungall is direct form of @@ -423,36 +283,6 @@ Where we have an annotation assertion - - - - An alternate textual definition for a class taken unmodified from an external source. This definition may have been used to derive a generalized definition for the new class. - UBPROP:0000001 - uberon - external_definition - true - external_definition - This annotation property may be replaced with an annotation property from an external ontology such as IAO - external_definition - - - - - An alternate textual definition for a class taken unmodified from an external source. This definition may have been used to derive a generalized definition for the new class. - - - - - - - - - Manually annotated by ChEBI Team - - - - - @@ -678,25 +508,9 @@ Where we have an annotation assertion - - - - abstract upper-level terms not directly useful for analysis - - - - - - - - uberon - dc-creator - true - dc-creator - creator - + @@ -708,14 +522,7 @@ Where we have an annotation assertion - - - uberon - dc-source - true - dc-source - derived from resource - + @@ -745,12 +552,6 @@ Where we have an annotation assertion - - - - - - @@ -771,12 +572,6 @@ Where we have an annotation assertion - - - - - - @@ -875,24 +670,12 @@ Where we have an annotation assertion - - - - - - - - - - - - @@ -901,12 +684,6 @@ Where we have an annotation assertion - - - - - - @@ -927,14 +704,7 @@ Where we have an annotation assertion - - - uberon - foaf-page - true - foaf-page - page - + @@ -977,7 +747,6 @@ A continuant cannot be part of an occurrent: use 'participates in'. An BFO:0000050 external quality - uberon part_of part_of part of @@ -1009,12 +778,9 @@ A continuant cannot have an occurrent as part: use 'participates in'. has_part BFO:0000051 - chebi_ontology external quality - uberon has_part - false has_part We use the has_part relation to relate complex qualities to more primitive ones. A complex quality is a collection of qualities. The complex quality cannot exist without the sub-qualities. For example, the quality 'swollen' necessarily comes with the qualities of 'protruding' and 'increased size'. has part @@ -1043,34 +809,14 @@ A continuant cannot have an occurrent as part: use 'participates in'. preceded by - X preceded_by Y iff: end(Y) before_or_simultaneous_with start(X) x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other. is preceded by preceded_by http://www.obofoundry.org/ro/#OBO_REL:preceded_by - BFO:0000062 - is preceded by - takes place after - uberon - preceded_by - preceded_by preceded by - preceded_by - - - - is preceded by - SIO:000249 - - - - - takes place after - Allen:precedes - @@ -1087,12 +833,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. precedes x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. - BFO:0000063 - uberon - precedes - precedes - precedes precedes @@ -1134,13 +875,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. site of [copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t - BFO:0000067 - uberon - contains_process - contains_process Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant - contains process contains process @@ -1175,11 +911,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. bearer_of is bearer of - RO:0000053 - uberon - bearer_of - bearer_of - bearer of bearer of @@ -1248,11 +979,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist. has_quality - RO:0000086 - uberon - has_quality - has_quality - has quality has quality @@ -1270,12 +996,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. Most location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime location_of - RO:0001015 - uberon - location_of - location_of location of - location_of @@ -1310,12 +1031,7 @@ range: spatial region or site (immaterial continuant) contains - RO:0001019 - uberon - contains - contains - contains contains @@ -1356,12 +1072,7 @@ range: spatial region or site (immaterial continuant) located_in http://www.obofoundry.org/ro/#OBO_REL:located_in - RO:0001025 - uberon - located_in - located_in located in - located_in @@ -1455,12 +1166,6 @@ range: spatial region or site (immaterial continuant) 2017-07-19T17:30:36Z has ligand - - - - A relationship that holds between between a receptor and an chemical entity, typically a small molecule or peptide, that carries information between cells or compartments of a cell and which binds the receptor and regulates its effector function. - GOC:dos - @@ -1560,35 +1265,11 @@ range: spatial region or site (immaterial continuant) - X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) David Osumi-Sutherland starts_at_end_of - A non-transitive temporal relation in which one process immediately precedes another process, such that there is no interval of time between the two processes[SIO:000251]. - RO:0002087 - directly preceded by - is directly preceded by - is immediately preceded by - starts_at_end_of - uberon - immediately_preceded_by - immediately_preceded_by X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) immediately preceded by - immediately_preceded_by - - - - - A non-transitive temporal relation in which one process immediately precedes another process, such that there is no interval of time between the two processes[SIO:000251]. - SIO:000251 - - - - - is immediately preceded by - SIO:000251 - @@ -1628,17 +1309,10 @@ range: spatial region or site (immaterial continuant) - A overlaps B if they share some part in common. x overlaps y if and only if there exists some z such that x has part z and z part of y - BFO_0000051 some (BFO_0000050 some ?Y) http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y) - RO:0002131 - uberon - overlaps - overlaps - overlaps overlaps @@ -1662,12 +1336,7 @@ range: spatial region or site (immaterial continuant) The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity. For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit. - RO:0002180 - uberon - has_component - has_component - has component has component @@ -1677,33 +1346,19 @@ range: spatial region or site (immaterial continuant) - - - - - - - - - x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y Chris Mungall David Osumi-Sutherland Melissa Haendel Terry Meehan - RO:0002202 - uberon - develops_from - develops_from This is the transitive form of the develops from relation develops from - develops_from @@ -1720,13 +1375,8 @@ range: spatial region or site (immaterial continuant) Chris Mungall David Osumi-Sutherland Terry Meehan - RO:0002203 - uberon - develops_into - develops_into develops into - develops_into @@ -1770,7 +1420,6 @@ range: spatial region or site (immaterial continuant) - 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. Chris Mungall @@ -1816,12 +1465,10 @@ range: spatial region or site (immaterial continuant) - mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974) osteoclast SubClassOf 'capable of' some 'bone resorption' - A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. Chris Mungall has function realized in @@ -1829,12 +1476,7 @@ range: spatial region or site (immaterial continuant) For compatibility with BFO, this relation has a shortcut definition in which the expression "capable of some P" expands to "bearer_of (some realized_by only P)". RO_0000053 some (RO_0000054 only ?Y) - RO:0002215 - uberon - capable_of - capable_of - capable of capable of @@ -1849,16 +1491,10 @@ range: spatial region or site (immaterial continuant) - c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p. Chris Mungall has function in RO_0000053 some (RO_0000054 only (BFO_0000050 some ?Y)) - RO:0002216 - uberon - capable_of_part_of - capable_of_part_of - capable of part of capable of part of @@ -1879,7 +1515,6 @@ range: spatial region or site (immaterial continuant) - x actively participates in y if and only if x participates in y and x realizes some active role Chris Mungall agent in @@ -1899,7 +1534,6 @@ range: spatial region or site (immaterial continuant) Chris Mungall has agent - has active participant obsolete has active participant true @@ -1915,7 +1549,6 @@ range: spatial region or site (immaterial continuant) Chris Mungall Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends. - https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. @@ -1932,7 +1565,6 @@ range: spatial region or site (immaterial continuant) - p has direct input c iff c is a participant in p, c is present at the start of p, and the state of c is modified during p. p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p. Chris Mungall consumes @@ -1962,11 +1594,8 @@ range: spatial region or site (immaterial continuant) - - - @@ -1975,11 +1604,6 @@ range: spatial region or site (immaterial continuant) x has developmental contribution from y iff x has some part z such that z develops from y Chris Mungall - RO:0002254 - uberon - has_developmental_contribution_from - has_developmental_contribution_from - has developmental contribution from has developmental contribution from @@ -1997,13 +1621,8 @@ range: spatial region or site (immaterial continuant) inverse of has developmental contribution from Chris Mungall - RO:0002255 - uberon - developmentally_contributes_to - developmentally_contributes_to developmentally contributes to - developmentally_contributes_to @@ -2020,12 +1639,7 @@ range: spatial region or site (immaterial continuant) false Chris Mungall In general you should not use this relation to make assertions - use one of the more specific relations below this one - RO:0002258 - uberon - developmentally_preceded_by - developmentally_preceded_by This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from - developmentally preceded by developmentally preceded by @@ -2041,7 +1655,6 @@ range: spatial region or site (immaterial continuant) A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision. c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes. - c involved in regulation of p if c enables 'p' and p' causally upstream of p acts upstream of @@ -2057,7 +1670,6 @@ range: spatial region or site (immaterial continuant) A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway. - c acts upstream of or within p if c is enables 'p' and p' causally upstream of or within p c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process. affects acts upstream of or within @@ -2118,7 +1730,6 @@ range: spatial region or site (immaterial continuant) - cjm cjm holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y causally upstream of, positive effect @@ -2132,7 +1743,6 @@ range: spatial region or site (immaterial continuant) - cjm cjm holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y causally upstream of, negative effect @@ -2255,11 +1865,6 @@ However, this is not possible in OWL. We instead make this relation a sub-relati A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities. Chris Mungall This is a grouping relation that collects relations used for the purpose of connecting structure and function - RO:0002328 - uberon - functionally_related_to - functionally_related_to - functionally related to functionally related to @@ -2273,18 +1878,9 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - - - - this relation holds between c and p when c is part of some c', and c' is capable of p. Chris Mungall false - RO:0002329 - uberon - part_of_structure_that_is_capable_of - part_of_structure_that_is_capable_of - part of structure that is capable of part of structure that is capable of @@ -2327,11 +1923,6 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - - - - - inverse of enables Chris Mungall enabled by @@ -2390,11 +1981,6 @@ However, this is not possible in OWL. We instead make this relation a sub-relati member part of SIO - RO:0002350 - uberon - member_of - member_of - member of member of @@ -2408,11 +1994,6 @@ However, this is not possible in OWL. We instead make this relation a sub-relati has member is a mereological relation between a collection and an item. SIO - RO:0002351 - uberon - has_member - has_member - has member has member @@ -2425,13 +2006,8 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inverse of has input Chris Mungall - RO:0002352 - uberon - input_of - input_of - input of input of @@ -2444,13 +2020,8 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inverse of has output Chris Mungall - RO:0002353 - uberon - output_of - output_of - output of output of @@ -2504,14 +2075,8 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y Chris Mungall - RO:0002385 - uberon - has_potential_to_developmentally_contribute_to - has_potential_to_developmentally_contribute_to - has potential to developmentally contribute to has potential to developmentally contribute to @@ -2522,14 +2087,8 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - x has the potential to develop into y iff x develops into y or if x is capable of developing into y x has the potential to develop into y iff x develops into y or if x is capable of developing into y Chris Mungall - RO:0002387 - uberon - has_potential_to_develop_into - has_potential_to_develop_into - has potential to develop into has potential to develop into @@ -2540,14 +2099,8 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y Chris Mungall - RO:0002388 - uberon - has_potential_to_directly_develop_into - has_potential_to_directly_develop_into - has potential to directly develop into has potential to directly develop into @@ -2583,7 +2136,6 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - This relation groups causal relations between material entities and causal relations between processes This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents. @@ -2679,7 +2231,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - c involved in regulation of p if c is involved in some 'p' and p' regulates some p c involved in regulation of p if c is involved in some p' and p' regulates some p Chris Mungall involved in regulation of @@ -2752,13 +2303,11 @@ Each of these 3 primitives can be composed to yield a cross-product of different A protein that enables activity in a cytosol. - c executes activity in d if and only if c enables p and p occurs_in d c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. Chris Mungall executes activity in enables activity in - enables activity in is active in @@ -2805,7 +2354,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - An interaction relationship in which the two partners are molecular entities and are executing molecular processes that are directly causally connected. An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other. Chris Mungall binds @@ -2840,11 +2388,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different Holds between molecular entities A and B where A can physically interact with B and in doing so regulates a process that B is capable of. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B. - Holds between molecular entities a and b when the execution of a activates or inhibits the activity of b Chris Mungall molecularly controls activity directly regulates activity of - molecularly controls @@ -2859,12 +2405,10 @@ Each of these 3 primitives can be composed to yield a cross-product of different Holds between molecular entities A and B where A can physically interact with B and in doing so negatively regulates a process that B is capable of. For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B. - Holds between molecules a and b if and only if a executes a process that directly diminishes a process executed by b. Chris Mungall inhibits molecularly decreases activity of activity directly negatively regulates activity of - molecularly decreases activity of @@ -2879,12 +2423,10 @@ Each of these 3 primitives can be composed to yield a cross-product of different Holds between molecular entities A and B where A can physically interact with B and in doing so positively regulates a process that B is capable of. For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B. - Holds between molecules a and b if and only if a executes a process that directly activates a process executed by b. Chris Mungall activates molecularly increases activity of activity directly positively regulates activity of - molecularly increases activity of @@ -2892,10 +2434,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - Chris Mungall This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning. - helper property helper property (not for use in curation) @@ -2909,16 +2449,10 @@ Each of these 3 primitives can be composed to yield a cross-product of different 'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate' x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y. - x composed_primarily_of y iff: more than half of the mass of x is made from parts of y Chris Mungall - RO:0002473 - uberon - RO:0002473 - composed_primarily_of - composed_primarily_of composed primarily of @@ -2967,7 +2501,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different A relationship between a material entity and a process where the material entity has some causal role that influences the process - causal agent in causal agent in process @@ -3028,8 +2561,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different Chris Mungall determined by (system to material entity) - Chris Mungall - Pier Buttigieg Chris Mungall Pier Buttigieg @@ -3237,9 +2768,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different Inverse of 'causal agent in process' - Inverse of 'causal agent in' - has causal agent process has causal agent @@ -3251,7 +2780,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different A relationship that holds between two entities, where the relationship holds based on the presence or absence of statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. obsolete related via dependence to - related via dependence to true @@ -3263,7 +2791,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different Process(P1) directly postively regulates process(P2) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P1 directly positively regulates P2. - Process(P1) directly regulates process(P2) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P1 directly positively regulates P2. directly positively regulates (process to process) @@ -3278,7 +2805,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different Process(P1) directly negatively regulates process(P2) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P1 directly negatively regulates P2. - Process(P1) directly regulates process(P2) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P1 directly negatively regulates P2. directly negatively regulates (process to process) @@ -3302,13 +2828,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix. Melissa Haendel - RO:0003000 - uberon - produces - produces Note that this definition doesn't quite distinguish the output of a transformation process from a production process, which is related to the identity/granularity issue. - produces produces @@ -3322,13 +2843,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different a produced_by b iff some process that occurs_in b has_output a. Melissa Haendel - RO:0003001 - uberon - produced_by - produced_by produced by - produced_by @@ -3763,18 +3279,9 @@ Association is weaker than correlation or proportionality. These relations may b - - - - entity - - - - - @@ -3797,7 +3304,6 @@ Association is weaker than correlation or proportionality. These relations may b - @@ -3829,15 +3335,8 @@ Association is weaker than correlation or proportionality. These relations may b A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. - b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) independent continuant - - - - b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) - - @@ -3855,15 +3354,8 @@ Association is weaker than correlation or proportionality. These relations may b An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. - p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) process - - - - p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) - - @@ -3911,34 +3403,8 @@ Association is weaker than correlation or proportionality. These relations may b A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. - b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n &gt; 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i &lt; j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004]) - b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) specifically dependent continuant - - - - b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) - - - - - - - - - - object aggregate - - - - - - - - - site - @@ -3953,8 +3419,6 @@ Association is weaker than correlation or proportionality. These relations may b A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time. - b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) - generically dependent continuant @@ -4007,7 +3471,6 @@ Association is weaker than correlation or proportionality. These relations may b - anatomical structure connected anatomical structure @@ -4038,11 +3501,7 @@ Association is weaker than correlation or proportionality. These relations may b - - Material anatomical entity that is a member of an individual species or is a viral or viroid particle. - organism or virus - Melissa Haendel - 9/18/11 + organism or virus or viroid @@ -4057,90 +3516,9 @@ Association is weaker than correlation or proportionality. These relations may b - - - - A chemical entity is a physical entity of interest in chemistry including molecular entities, parts thereof, and chemical substances. - chemical entity - chebi_ontology - CHEBI:24431 - - chemical entity - - - - - chemical entity - UniProt - - - - - - - In general, a mineral is a chemical substance that is normally crystalline formed and has been formed as a result of geological processes. The term also includes metamict substances (naturally occurring, formerly crystalline substances whose crystallinity has been destroyed by ionising radiation) and can include naturally occurring amorphous substances that have never been crystalline ('mineraloids') such as georgite and calciouranoite as well as substances formed by the action of geological processes on bigenic compounds ('biogenic minerals'). - mineral - chebi_ontology - Minerale - minerales - minerals - mineraux - CHEBI:46662 - - mineral - - - - - mineral - ChEBI - - - - - Minerale - ChEBI - - - - - minerales - ChEBI - - - - - minerals - ChEBI - - - - - mineraux - ChEBI - - - - - - - - - A chemical substance is a portion of matter of constant composition, composed of molecular entities of the same type or of different types. - chebi_ontology - Chemische Substanz - CHEBI:59999 - - chemical substance - - - - - Chemische Substanz - ChEBI - + @@ -4154,505 +3532,12 @@ Association is weaker than correlation or proportionality. These relations may b - - - - - - - - - - - - - - - - - - - - - - A material entity which determines an environmental system. - environmental feature - - - - - A material entity which determines an environmental system. - DOI:10.1186/2041-1480-4-43 - NM:nm - ORCID:0000-0002-4366-3088 - - - - - - - - - A portion of environmental material is a fiat object which forms the medium or part of the medium of an environmental system. - portion of environmental material - environmental material - - - - - A portion of environmental material is a fiat object which forms the medium or part of the medium of an environmental system. - DOI:10.1186/2041-1480-4-43 - MA:ma - ORCID:0000-0002-4366-3088 - URL:http://ontology.buffalo.edu/smith/articles/niches.html - - - - - A system which has the disposition to environ one or more material entities. - environment environmental system - - - - A system which has the disposition to environ one or more material entities. - DOI:10.1186/2041-1480-4-43 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - An anthropogenic environment is an environmental system which is the product of human activity. - anthropogenic environment - - - - - - - - - - - - - - - - - - - - - - - - An environmental system in which minimal to no anthropisation has occurred and non-human agents are the primary determinants of the system's dynamics and composition. - natural environment - - - - - An environmental system in which minimal to no anthropisation has occurred and non-human agents are the primary determinants of the system's dynamics and composition. - https://en.wikipedia.org/wiki/Anthropization - https://en.wikipedia.org/wiki/Natural_environment - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A process during which a natural environmental system is altered by human action. - anthropization - anthropisation - - - - - A process during which a natural environmental system is altered by human action. - https://en.wikipedia.org/wiki/Anthropization - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - An environmental system which is determined by materials bearing roughly homogeneous qualities. - environmental system determined by a quality - - - - - - - - - - - - - - - - - - - - - - - - - - An environmental system within which an environmental material strongly influences the system's composition and properties. - environmental system determined by a material - - - - - - - - - - - - - - - - - - - - - - - - - - An environmental system which is determined by a living organism. - host-associated environment - environmental system determined by an organism - - - - - - - - - - - - - - - - - - - - - - - - - - An environmental system determined by an animal. - animal environment - Metazoan-associated environment - animal-associated environment - - - - - - - - - - - - - - - - - - - - - - - - - - An environmental system determined by part of a living or dead animal, or a whole small animal. - environment associated with an animal part or small animal - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - An environmental system determined by part of a living or dead plant, or a whole small plant. - environment associated with a plant part or small plant - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - An environmental system which includes both living and non-living components. - ecosystem - - - - - An environmental system which includes both living and non-living components. - https://en.wikipedia.org/wiki/Ecosystem - - - - - - - - - - - - - - - - - - - - - - - A process in which includes the components of an environmental system as participants. - environmental system process - - - - - - - - - - - - - - - - - - - - - - - - - - An environmental process which is driven by the action of humans. - anthropogenic environmental process - @@ -4725,7 +3610,6 @@ Association is weaker than correlation or proportionality. These relations may b - receptor activity true @@ -5204,7 +4088,6 @@ Association is weaker than correlation or proportionality. These relations may b A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. - Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end. janelomax 2012-09-19T15:05:24Z GO:0000004 @@ -5235,13 +4118,6 @@ Association is weaker than correlation or proportionality. These relations may b A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. GOC:pdt - - - - Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end. - GOC:go_curators - GOC:isa_complete - @@ -5776,7 +4652,7 @@ Association is weaker than correlation or proportionality. These relations may b - + A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. @@ -6873,7 +5749,7 @@ Association is weaker than correlation or proportionality. These relations may b A prolongation or process extending from a cell, e.g. a flagellum or axon. GOC:jl - http://www.cogsci.princeton.edu/~wn/ + http://www.cogsci.princeton.edu/~wn/ @@ -9403,793 +8279,6 @@ Association is weaker than correlation or proportionality. These relations may b - - - - - data item - - - - - - - - - information content entity - - - - - - - - - - - - - - - - - - - - - - - - curation status specification - - The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. - Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting) - PERSON:Bill Bug - GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - OBI_0000266 - curation status specification - - - - - - - - - data about an ontology part is a data item about a part of an ontology, for example a term - Person:Alan Ruttenberg - data about an ontology part - - - - - - - - - - - - - - - - - - - - obsolescence reason specification - - The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. - The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology. - PERSON: Alan Ruttenberg - PERSON: Melanie Courtot - obsolescence reason specification - - - - - - - - - - - - - - - - - - The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are "natural kinds" and the latter arbitrary collections of entities. - A denotator type indicates how a term should be interpreted from an ontological perspective. - Alan Ruttenberg - Barry Smith, Werner Ceusters - denotator type - - - - - - - - - all - root - - - - - all - - - - - - all - - - - - - - - - - Teleostomi - - - - - - - - - bony vertebrates - Euteleostomi - - - - - bony vertebrates - - - - - - - - - - biota - cellular organisms - - - - - biota - - - - - - biota - - - - - - - - - - Dipnotetrapodomorpha - - - - - - - - - Boreotheria - Boreoeutheria - - - - - Boreotheria - - - - - - - - - - Homo/Pan/Gorilla group - Homininae - - - - - Homo/Pan/Gorilla group - - - - - - - - - - eucaryotes - eukaryotes - Eucarya - Eucaryotae - Eukarya - Eukaryotae - eukaryotes - Eukaryota - - - - - eucaryotes - - - - - - eucaryotes - - - - - - eukaryotes - - - - - - eukaryotes - - - - - - Eucarya - - - - - - Eucarya - - - - - - Eucaryotae - - - - - - Eucaryotae - - - - - - Eukarya - - - - - - Eukarya - - - - - - Eukaryotae - - - - - - Eukaryotae - - - - - - eukaryotes - - - - - - eukaryotes - - - - - - - - - - Euarchontoglires - - - - - - - - - Anthropoidea - Simiiformes - - - - - Anthropoidea - - - - - - - - - - ape - apes - Hominoidea - - - - - ape - - - - - - apes - - - - - - - - - - tetrapods - Tetrapoda - - - - - tetrapods - - - - - - - - - - amniotes - Amniota - - - - - amniotes - - - - - - - - - - Theria - Theria <Mammalia> - - - - - Theria - - - - - - - - - - Fungi/Metazoa group - opisthokonts - Opisthokonta - - - - - Fungi/Metazoa group - - - - - - opisthokonts - - - - - - - - - - metazoans - multicellular animals - Animalia - animals - Metazoa - - - - - metazoans - - - - - - multicellular animals - - - - - - Animalia - - - - - - animals - - - - - - - - - - Bilateria - - - - - - - - - deuterostomes - Deuterostomia - - - - - deuterostomes - - - - - - - - - - Haplorrhini - - - - - - - - - mammals - mammals - Mammalia - - - - - mammals - - - - - - mammals - - - - - - - - - - Eumetazoa - - - - - - - - - chordates - chordates - Chordata - - - - - chordates - - - - - - chordates - - - - - - - - - - Vertebrata - vertebrates - vertebrates - Vertebrata <Metazoa> - - - - - Vertebrata - - - - - - vertebrates - - - - - - vertebrates - - - - - - - - - - Gnathostomata - jawed vertebrates - Gnathostomata <vertebrate> - - - - - Gnathostomata - - - - - - jawed vertebrates - - - - - - - - - - Sarcopterygii - - - - - - - - - Craniata - Craniata <chordata> - - - - - Craniata - - - - - - - - - - eutherian mammals - placental mammals - placentals - Placentalia - placentals - Eutheria - - - - - eutherian mammals - - - - - - placental mammals - - - - - - placentals - - - - - - Placentalia - - - - - - placentals - - - - - - - - - - primate - Primata - primates - Primates - - - - - primate - - - - - - Primata - - - - - - primates - - - - - - - - - - Catarrhini - - - - - - - - - great apes - Pongidae - Hominidae - - - - - great apes - - - - - - Pongidae - - - - - - - - - - humans - Homo - - - - - humans - - - - - - - - - - human - man - humans - Homo sapiens - - - - - human - - - - - - man - - - - - @@ -10208,7 +8297,6 @@ Association is weaker than correlation or proportionality. These relations may b A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities quality (PATO) PATO:0000072 - trait quality PATO:0000001 quality @@ -10972,7 +9060,7 @@ Association is weaker than correlation or proportionality. These relations may b - A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure. + A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure. quality PATO:0000051 @@ -10981,7 +9069,7 @@ Association is weaker than correlation or proportionality. These relations may b - A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure. + A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure. PATOC:GVG @@ -11259,7 +9347,7 @@ Association is weaker than correlation or proportionality. These relations may b - A quality inhering in a bearer by virtue of the whether the bearer differs from normal or average. + A quality inhering in a bearer by virtue of the whether the bearer differs from normal or average. quality PATO:0000069 @@ -11268,7 +9356,7 @@ Association is weaker than correlation or proportionality. These relations may b - A quality inhering in a bearer by virtue of the whether the bearer differs from normal or average. + A quality inhering in a bearer by virtue of the whether the bearer differs from normal or average. PATOC:GVG @@ -11879,7 +9967,7 @@ Association is weaker than correlation or proportionality. These relations may b - A morphology quality inhering in a bearer by virtue of the bearer's physical magnitude. + A morphology quality inhering in a bearer by virtue of the bearer's physical magnitude. quality PATO:0000117 @@ -11889,7 +9977,7 @@ Association is weaker than correlation or proportionality. These relations may b - A morphology quality inhering in a bearer by virtue of the bearer's physical magnitude. + A morphology quality inhering in a bearer by virtue of the bearer's physical magnitude. WordNet:WordNet @@ -18592,7 +16680,7 @@ Association is weaker than correlation or proportionality. These relations may b - A size quality which is relatively low. + A size quality which is relatively low. hypoplasia underdeveloped @@ -18607,7 +16695,7 @@ Association is weaker than correlation or proportionality. These relations may b - A size quality which is relatively low. + A size quality which is relatively low. PATOC:GVG @@ -30733,7 +28821,7 @@ Association is weaker than correlation or proportionality. These relations may b - A polyploidy quality inhering in a bearer by virtue of the bearer's containing four homologous sets of chromosomes. + A polyploidy quality inhering in a bearer by virtue of the bearer's containing six homologous sets of chromosomes. quality PATO:0001384 @@ -30743,7 +28831,7 @@ Association is weaker than correlation or proportionality. These relations may b - A polyploidy quality inhering in a bearer by virtue of the bearer's containing four homologous sets of chromosomes. + A polyploidy quality inhering in a bearer by virtue of the bearer's containing six homologous sets of chromosomes. Wikipedia:http://en.wikipedia.org/wiki/Hexaploid @@ -51349,7 +49437,7 @@ Association is weaker than correlation or proportionality. These relations may b - A quality that has a value that is decreased compared to normal or average. + A quality that has a value that is decreased compared to normal or average. George Gkoutos 2011-06-16T06:40:15Z @@ -51360,7 +49448,7 @@ Association is weaker than correlation or proportionality. These relations may b - A quality that has a value that is decreased compared to normal or average. + A quality that has a value that is decreased compared to normal or average. PATOC:GVG @@ -51415,7 +49503,7 @@ Association is weaker than correlation or proportionality. These relations may b - A quality of an object that has a value that is decreased compared to normal or average. + A quality of an object that has a value that is decreased compared to normal or average. George Gkoutos 2011-06-16T06:51:54Z @@ -51426,7 +49514,7 @@ Association is weaker than correlation or proportionality. These relations may b - A quality of an object that has a value that is decreased compared to normal or average. + A quality of an object that has a value that is decreased compared to normal or average. PATOC:GVG @@ -59026,6 +57114,27 @@ height'). + + + + + A ploidy quality inhering in a bearer by virtue of the bearer's haploid cells undergo chromosome doubling. + http://orcid.org/0000-0001-5208-3432 + double haploid + double-haploid + quality + PATO:0040027 + doubled haploid + + + + + A ploidy quality inhering in a bearer by virtue of the bearer's haploid cells undergo chromosome doubling. + Wikipedia:https://en.wikipedia.org/wiki/Doubled_haploidy + + + + @@ -61120,7 +59229,7 @@ height'). - A variability which is relatively normal or average + A variability of color which is relatively normal or average Luke Slater 2017-12-22T14:16:43Z quality @@ -61784,361 +59893,15 @@ height'). - - - - - - - - - - - - - 2 - - - - - - - - - - - - - - Examples include: population, community, species (meaning the collection of organisms that makes up a species, not the taxonomic rank), and family. - - A material entity that consists of two or more organisms, viruses, or viroids. - A material entity that consists of two or more organisms, viruses, or viroids. - group of organism - organism collection - May be of the same or different species. - collection of organisms - collection of organisms - - - - - - - - This a general term that can include every organism of a species living in an area or any subset of them. Subclasses can be more specific as needed. - - A collection of organisms, all of the same species, that live in the same place. - ISBN:0878932739 - It is sometimes difficult to define the physical boundaries of a population. In the case of sexually reproducing organisms, the individuals within a population have the potential to reproduce with one another during the course of their lifetimes. 'Community', as often used to describe a group of humans, is a type of population. - -Classes for population already exist in IDO ('organism population', IDO_0000509) and OBI ('population', OBI_0000181). The definitions should be standardized across OBO Foundry ontologies and only one term used. - population of organisms - - - - - - - - - - - - - - 2 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A community of at least two different species, living in a particular area. Must have at least two populations of different species as members. - Not sure if the equivalancy axiom specifies that both populations are located in the same site. - multispecies community - ISBN:0865423504 - Ecological community is defined broadly here, but includes both ecological interactions (inherited from parent term community) and spatial co-existence. It may be used to describe every organisms living in an area, but is often used to refer only to organisms of a particular taxon or guild (e.g., the plant community, the insect community, the herbivore community). The word community, as it often used to describe a group of humans living together, is a type of single-species collection of organisms, not an ecological community. - ecological community - + - - - - - - - - - - - - - - - - - - - - - A quality that inheres in a biological population. - See Chris's comments on population qualities at: http://code.google.com/p/popcomm-ontology/issues/detail?id=4. These may not belong under BFO:quality. May be better to call them population characteristics, and classify as specifically dependent continuants. Need to look at process profiles in BFO2. - Includes qualities like population size, population growth rate, carrying capacity, immigration rate, emigration rate, fecundity, and death rate. A population quality may depend on the qualities of individual organisms in the population, but cannot be measured or described for a single organism. This term may be replaced by a PATO term. - quality of a population - - - - - - - - - - - - - - - - - - - - - - - - - - - A quality that inheres in a community. - These may not belong under BFO:quality. May be better to call them community characteristics, and classify as specifically dependent continuants. Need to look at process profiles in BFO2. - Includes qualities like diversity, species richness, stability, resilience, community structure, number of trophic levels. A community quality may depend on the qualities of individual organism in the community, but cannot be measured or described for a single individual. - quality of an ecological community - - - - - - - - - - A collection of organisms that has as parts every organism of given species and no organisms of any other species. - At the moment there is no way to specify in an OWL axiom that the collection includes every individual of a species. This should be added, if possible. - This term is neutral with respect to which organisms are included in a species. Membership will depend on the species concept and the taxonomic assertions used to define the species. These criteria must be specified by the user. - species as a collection of organisms - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - 2 - - - - - - - - A material entity that has as parts two or more organisms, viruses, or viroids of the same species and no members of any other species. - collection of organisms of the same species - single-species collection of organisms - - - - - - - - - - - - - - - - - - 2 - - - - - - - - - - - - - - A collection of organisms of the same species that has as members only humans. - human community - human population - collection of humans - - - - - - - - - - A collection of organisms of the same species whose members are all either genealogically related to each other or have mated with each other. - Biological or social relations are covered by RO_0002437 (biotically interacts with), but that relations does provide an easy way to specify that two entities are interacting with each other (participating in the same interaction). Until that axiom is specified, the logical definition of this term is incomplete. - These relations can include shared values, occupying the same spatial regkion. A community be be a single species collection of organsisms (as in a human community, which is also a type of population) or a or multi-species collection of organisms (as in an ecological community). - community - - - - - - - - - - A collection of organisms that consists of two or more organisms from at least two species. - Need to add axiom to specify that it has at a mimum members of two different species, but not sure how to specify that. Can't say "('has member' only ('member of' min 2 'species as a collection of organisms'))". - - multi-species collection of organisms - - - - - - - - - - - - - - - - - - A material entity that is one or more organisms, viruses or viroids. - organismal entity - - - - - - - - - A plant structure (PO:0005679) which is a whole organism. - genet (broad) - ramet (broad) - planta entera (Spanish, exact) - 植物体全体 (Japanese, exact) - bush (narrow) - frutex (narrow) - frutices (narrow) - gametophyte (narrow) - herb (narrow) - liana (narrow) - prothalli (narrow) - prothallium (narrow) - prothallus (narrow) - seedling (narrow) - shrub (narrow) - sporophyte (narrow) - suffrutex (narrow) - suffrutices (narrow) - tree (narrow) - vine (narrow) - woody clump (narrow) - clonal colony (related) - colony (related) - whole plant - - - - - - - - - An anatomical structure that is or was part of a plant, or was derived from a part of a plant. - estructura vegetal (Spanish, exact) - 植物 構造 (Japanese, exact) - plant structure - - - - - - - - - An anatomical entity that is or was part of a plant. - entidad anat&#243mica vegetal (Spanish, exact) - 植物 解剖学（形態）的実体 (Japanese, exact) - plant anatomical entity - + @@ -62155,66 +59918,6 @@ Classes for population already exist in IDO ('organism population', I - - - - - Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species. - - AAO:0010841 - AEO:0000000 - BILA:0000000 - BIRNLEX:6 - CARO:0000000 - EHDAA2:0002229 - FBbt:10000000 - FBbt_root:00000000 - FMA:62955 - HAO:0000000 - MA:0000001 - NCIT:C12219 - TAO:0100000 - TGMA:0001822 - UMLS:C1515976 - WBbt:0000100 - XAO:0000000 - ZFA:0100000 - uberon - UBERON:0001062 - - anatomical entity - - - - - Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species. - - FMA:62955 - - - - - UMLS:C1515976 - ncithesaurus:Anatomic_Structure_System_or_Substance - - - - - - - - - - - - - - - - - - - - - - - example to be eventually removed - - - - - - - - - The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job - Person:Alan Ruttenberg - failed exploratory term - - - - - - - - - Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete. - metadata complete - - - - - - - - - term created to ease viewing/sort terms for development purpose, and will not be included in a release - organizational term - - - - - - Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release." ready for release - - - - - Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors. - metadata incomplete - - - - - - - - - Nothing done yet beyond assigning a unique class ID and proposing a preferred term. - uncurated - - - - - - All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor. pending final vetting - - - - - Core is an instance of a grouping of terms from an ontology or ontologies. It is used by the ontology to identify main classes. - PERSON: Alan Ruttenberg - PERSON: Melanie Courtot - core - - - - - - - - - placeholder removed - - - - - - - - - An editor note should explain what were the merged terms and the reason for the merge. - terms merged - - - - - - - - - This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use. - term imported - - - - - - - - - This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created. - term split - - - - - - - - - Hard to give a definition for. Intuitively a "natural kind" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents. - Alan Ruttenberg - A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf - universal - - - - - - - - - A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal - "definitions", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal. - Alan Ruttenberg - defined class - - - - - - - - - A named class expression is a logical expression that is given a name. The name can be used in place of the expression. - named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions - Alan Ruttenberg - named class expression - - - - - - - - - Terms with this status should eventually replaced with a term from another ontology. - Alan Ruttenberg - group:OBI - to be replaced with external ontology term - - - - - - A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues. - Alan Ruttenberg - group:OBI requires discussion @@ -62468,29 +60004,34 @@ This interpretation is *not* the same as an at-all-times relation --> - + + - + - + - + - - - + + + + + + + - + - + @@ -62655,14 +60196,6 @@ This interpretation is *not* the same as an at-all-times relation - - - - - - - - @@ -62673,28 +60206,6 @@ This interpretation is *not* the same as an at-all-times relation - - - - - - - - - - - - - - - - - - - - - - @@ -62712,19 +60223,19 @@ This interpretation is *not* the same as an at-all-times relation - + - + - + - + @@ -62831,9 +60342,10 @@ This interpretation is *not* the same as an at-all-times relation - - - + + + + @@ -62841,9 +60353,10 @@ This interpretation is *not* the same as an at-all-times relation - - - + + + + @@ -62851,10 +60364,9 @@ This interpretation is *not* the same as an at-all-times relation - - + + - @@ -62862,10 +60374,9 @@ This interpretation is *not* the same as an at-all-times relation - - - - + + + @@ -62892,65 +60403,6 @@ This interpretation is *not* the same as an at-all-times relation - - true - GP(X) part_of complex(Y) enables MF(Z) -> X contributes_to Z - contrib to MF - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z), e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity' @@ -62961,10 +60413,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - - + + + @@ -62973,9 +60424,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -62983,9 +60434,10 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + + @@ -63020,10 +60472,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - - + + + @@ -63042,9 +60493,10 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + + @@ -63424,9 +60876,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -63435,9 +60887,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + diff --git a/pato-simple.json b/pato-simple.json index 6f1ee030..e8a9dada 100644 --- a/pato-simple.json +++ b/pato-simple.json @@ -417,11 +417,6 @@ "val" : "A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities", "xrefs" : [ "PATOC:GVG" ] }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "trait", - "xrefs" : [ ] - } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", "val" : "quality (PATO)" @@ -3488,9 +3483,6 @@ "val" : "a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence", "xrefs" : [ ] }, - "xrefs" : [ { - "val" : "RO:0000053" - } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist." @@ -3500,9 +3492,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "is bearer of" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" @@ -3515,9 +3504,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "this apple is bearer of this red color" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "bearer_of" } ] }, "type" : "PROPERTY", @@ -7137,6 +7123,32 @@ }, "type" : "CLASS", "lbl" : "flared" + }, { + "id" : "http://purl.obolibrary.org/obo/PATO_0040027", + "meta" : { + "definition" : { + "val" : "A ploidy quality inhering in a bearer by virtue of the bearer's haploid cells undergo chromosome doubling.", + "xrefs" : [ "Wikipedia:https://en.wikipedia.org/wiki/Doubled_haploidy" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "double haploid", + "xrefs" : [ ] + }, { + "pred" : "hasExactSynonym", + "val" : "double-haploid", + "xrefs" : [ ] + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "quality" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "http://orcid.org/0000-0001-5208-3432" + } ] + }, + "type" : "CLASS", + "lbl" : "doubled haploid" }, { "id" : "http://purl.obolibrary.org/obo/PATO_0000808", "meta" : { @@ -13135,25 +13147,6 @@ "lbl" : "has_dividend_quality" }, { "id" : "http://purl.obolibrary.org/obo/IAO_0100001", - "meta" : { - "definition" : { - "val" : "Add as annotation triples in the granting ontology", - "xrefs" : [ ] - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Person:Alan Ruttenberg" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "Person:Alan Ruttenberg" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "term replaced by" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - } ] - }, "type" : "PROPERTY", "lbl" : "term replaced by" }, { @@ -26816,21 +26809,12 @@ "xrefs" : [ ] }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "RO:0002473" - } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Chris Mungall" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "composed_primarily_of" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate'" @@ -28324,25 +28308,9 @@ }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000115", "meta" : { - "definition" : { - "val" : "The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.", - "xrefs" : [ ] - }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "definition" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "GROUP:OBI:" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "2012-04-05: \nBarry Smith\n\nThe official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible.\n\nCan you fix to something like:\n\nA statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property.\n\nAlan Ruttenberg\n\nYour proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. \n\nOn the specifics of the proposed definition:\n\nWe don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. \n\nPersonally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. \n\nWe also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. " - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000122" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "PERSON:Daniel Schober" } ] }, "type" : "PROPERTY", @@ -34394,7 +34362,7 @@ "id" : "http://purl.obolibrary.org/obo/PATO_0045075", "meta" : { "definition" : { - "val" : "A variability which is relatively normal or average", + "val" : "A variability of color which is relatively normal or average", "xrefs" : [ ] }, "subsets" : [ "http://purl.obolibrary.org/obo/pato#value_slim" ], @@ -42385,26 +42353,6 @@ }, "type" : "CLASS", "lbl" : "scarred" - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000231", - "meta" : { - "definition" : { - "val" : "Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification.", - "xrefs" : [ ] - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "PERSON:Melanie Courtot" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "has obsolescence reason" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "PERSON:Alan Ruttenberg" - } ] - }, - "type" : "PROPERTY", - "lbl" : "has obsolescence reason" }, { "id" : "http://purl.obolibrary.org/obo/PATO_0000539", "meta" : { @@ -46747,9 +46695,6 @@ }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)" @@ -46925,9 +46870,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "this year has part this day (occurrent parthood)" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_cyclic", - "val" : "false" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime" @@ -46952,15 +46894,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "chebi_ontology" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)\n\nA continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'." - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "has part" @@ -48652,7 +48588,7 @@ "id" : "http://purl.obolibrary.org/obo/PATO_0001384", "meta" : { "definition" : { - "val" : "A polyploidy quality inhering in a bearer by virtue of the bearer's containing four homologous sets of chromosomes.", + "val" : "A polyploidy quality inhering in a bearer by virtue of the bearer's containing six homologous sets of chromosomes.", "xrefs" : [ "Wikipedia:http://en.wikipedia.org/wiki/Hexaploid" ] }, "subsets" : [ "http://purl.obolibrary.org/obo/pato#cell_quality", "http://purl.obolibrary.org/obo/pato#value_slim" ], @@ -49592,13 +49528,7 @@ "xrefs" : [ ] }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "RO:0002180" - } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "has_component" - }, { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" }, { @@ -49607,9 +49537,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit." - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity." @@ -50252,14 +50179,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0001629", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000330" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0001729", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0001995" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002178", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000628" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0001729", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0001995" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0005004", "pred" : "is_a", @@ -50532,14 +50459,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0001480", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000141" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0045077", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0001956" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002464", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000140" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0045077", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0001956" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001713", "pred" : "is_a", @@ -50568,14 +50495,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0002189", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0002182" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0001516", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0001300" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001632", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000140" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0001516", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0001300" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001465", "pred" : "is_a", @@ -50584,6 +50511,10 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0002488", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001590" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0001659", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0001599" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0000941", "pred" : "is_a", @@ -50592,10 +50523,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0000912", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0002304" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0001659", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0001599" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0045070", "pred" : "is_a", @@ -50676,14 +50603,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0002471", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0002305" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0001656", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0002303" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001957", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001956" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0001656", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0002303" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001824", "pred" : "is_a", @@ -50704,14 +50631,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0002250", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0002248" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0001966", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0000405" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001776", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0002305" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0001966", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0000405" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001986", "pred" : "is_a", @@ -51096,14 +51023,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0045001", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001241" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0001778", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0001230" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001752", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001490" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0001778", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0001230" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001539", "pred" : "is_a", @@ -51128,14 +51055,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0001773", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000083" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0001643", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0000052" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0045047", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001178" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0001643", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0000052" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001402", "pred" : "is_a", @@ -51280,14 +51207,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0001964", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000405" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0000998", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0000992" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002507", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000025" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0000998", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0000992" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0025001", "pred" : "is_a", @@ -52112,14 +52039,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0015002", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001236" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0001243", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0000318" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002026", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000057" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0001243", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0000318" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002228", "pred" : "is_a", @@ -52152,14 +52079,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0000300", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000004" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0001055", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0002326" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001269", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000319" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0001055", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0002326" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002287", "pred" : "is_a", @@ -52236,6 +52163,10 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0002467", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000052" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0040027", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0001393" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002057", "pred" : "is_a", @@ -52332,14 +52263,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0001418", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0002265" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0001372", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0001294" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001487", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000011" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0001372", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0001294" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002322", "pred" : "is_a", @@ -52864,22 +52795,22 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0001440", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001531" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0002376", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0002014" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001855", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000140" }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0002163", + "sub" : "http://purl.obolibrary.org/obo/PATO_0002376", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0001645" + "obj" : "http://purl.obolibrary.org/obo/PATO_0002014" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001619", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001439" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0002163", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0001645" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001570", "pred" : "is_a", @@ -52944,14 +52875,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0002029", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0002027" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0040014", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0000052" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0045009", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000404" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0040014", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0000052" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002150", "pred" : "is_a", @@ -53452,14 +53383,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0045016", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0045001" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0000992", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0001548" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001997", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0002301" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0000992", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0001548" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002348", "pred" : "is_a", @@ -53500,14 +53431,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0045061", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000921" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0045021", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0001544" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001408", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001396" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0045021", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0001544" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0000273", "pred" : "is_a", @@ -53516,14 +53447,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0045030", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000125" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0001335", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0001895" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001386", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001385" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0001335", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0001895" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002333", "pred" : "is_a", @@ -53728,14 +53659,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0000643", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001598" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0002138", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0001018" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002050", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000467" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0002138", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0001018" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0045013", "pred" : "is_a", @@ -53764,14 +53695,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0001873", "pred" : "http://purl.obolibrary.org/obo/pato#has_cross_section", "obj" : "http://purl.obolibrary.org/obo/PATO_0000411" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0000946", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0002006" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002132", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0002011" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0000946", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0002006" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001384", "pred" : "is_a", @@ -54040,14 +53971,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0002279", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0002278" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0002101", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0001397" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002306", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001875" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0002101", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0001397" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002262", "pred" : "is_a", @@ -54200,14 +54131,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0001552", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001457" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0045051", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0001323" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0045073", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001236" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0045051", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0001323" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001739", "pred" : "is_a", @@ -54252,14 +54183,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0045058", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0045057" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0001761", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0001767" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0045037", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0045001" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0001761", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0001767" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001957", "pred" : "is_a", @@ -54324,14 +54255,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0002283", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0002303" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0000626", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0000140" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0000634", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000060" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0000626", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0000140" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002370", "pred" : "is_a", @@ -54352,14 +54283,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0002056", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0002303" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0002283", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0000299" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0000374", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0002305" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0002283", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0000299" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002385", "pred" : "is_a", @@ -54580,14 +54511,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0002303", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0002301" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0002373", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0001769" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002110", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0002099" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0002373", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0001769" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002300", "pred" : "is_a", @@ -54772,14 +54703,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0015018", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0015017" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0000161", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0002062" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0000039", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001018" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0000161", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0002062" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001835", "pred" : "is_a", @@ -54844,14 +54775,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0002304", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0002300" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0000757", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0000185" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002328", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0002326" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0000757", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0000185" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002111", "pred" : "is_a", @@ -55044,14 +54975,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0000375", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000040" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0001193", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0000140" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0045049", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0045001" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0001193", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0000140" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0045057", "pred" : "is_a", @@ -55096,14 +55027,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0000011", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000165" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0001875", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0002006" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001861", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0002013" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0001875", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0002006" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0000152", "pred" : "is_a", @@ -55384,14 +55315,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0001833", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0002303" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0001230", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0001018" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0005008", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0002266" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0001230", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0001018" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0000276", "pred" : "is_a", @@ -55428,14 +55359,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0000623", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001598" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0002313", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0000052" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002424", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000140" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0002313", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0000052" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0000622", "pred" : "is_a", @@ -55616,14 +55547,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0000025", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000141" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0001814", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0001439" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002345", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0002007" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0001814", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0001439" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0045034", "pred" : "is_a", @@ -55640,14 +55571,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0001834", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0002303" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0045047", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0045001" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0045055", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0045054" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0045047", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0045001" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0040012", "pred" : "is_a", @@ -55692,14 +55623,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0005007", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0002266" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0000638", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0000141" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002430", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000052" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0000638", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0000141" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002062", "pred" : "is_a", @@ -55756,14 +55687,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0002167", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001646" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0002327", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0001475" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002456", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000052" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0002327", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0001475" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0000499", "pred" : "is_a", @@ -55984,14 +55915,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0001470", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001018" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0002023", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0001769" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002000", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001999" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0002023", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0001769" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002422", "pred" : "is_a", @@ -56028,14 +55959,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0000624", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000140" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0002007", - "pred" : "http://purl.obolibrary.org/obo/pato#has_cross_section", - "obj" : "http://purl.obolibrary.org/obo/PATO_0002006" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002328", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001476" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0002007", + "pred" : "http://purl.obolibrary.org/obo/pato#has_cross_section", + "obj" : "http://purl.obolibrary.org/obo/PATO_0002006" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002435", "pred" : "is_a", @@ -56232,14 +56163,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0045053", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0045050" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0001430", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0001428" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0015005", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", "obj" : "http://purl.obolibrary.org/obo/PATO_0002212" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0001430", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0001428" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002324", "pred" : "is_a", @@ -56356,14 +56287,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0001636", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001634" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0001893", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0001331" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001528", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001519" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0001893", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0001331" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0000018", "pred" : "is_a", @@ -56448,14 +56379,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0001783", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0002301" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0001770", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0000169" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001782", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000049" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0001770", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0000169" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002229", "pred" : "is_a", @@ -56524,14 +56455,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0000983", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000970" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0001900", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0000039" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001250", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000320" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0001900", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0000039" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0000956", "pred" : "is_a", @@ -56608,14 +56539,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0001188", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000261" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0001758", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0001757" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001748", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001857" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0001758", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0001757" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001746", "pred" : "is_a", @@ -56764,14 +56695,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0002518", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000140" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0002196", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0002193" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0050001", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000161" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0002196", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0002193" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002019", "pred" : "is_a", @@ -56828,22 +56759,22 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0000701", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000150" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0045069", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0045001" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0005011", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000140" }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0045062", + "sub" : "http://purl.obolibrary.org/obo/PATO_0045069", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0001537" + "obj" : "http://purl.obolibrary.org/obo/PATO_0045001" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0000574", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000122" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0045062", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0001537" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001275", "pred" : "is_a", @@ -56932,14 +56863,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0001717", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001299" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0001674", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0000033" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001537", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001536" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0001674", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0000033" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001480", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", @@ -57020,14 +56951,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0002214", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001979" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0001743", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0001741" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001776", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001544" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0001743", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0001741" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001606", "pred" : "is_a", @@ -57036,14 +56967,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0002106", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0002099" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0002054", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0002254" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002078", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0002014" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0002054", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0002254" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002403", "pred" : "is_a", @@ -57112,14 +57043,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0000462", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000070" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0001744", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0001739" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0000488", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000077" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0001744", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0001739" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0000330", "pred" : "is_a", @@ -57164,14 +57095,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0002034", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000052" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0001161", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0000033" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001306", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000146" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0001161", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0000033" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0005024", "pred" : "is_a", @@ -57280,14 +57211,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0040021", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000467" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0002503", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0000133" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001576", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001025" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0002503", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0000133" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001405", "pred" : "is_a", @@ -57328,14 +57259,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0002323", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0002062" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0001943", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0000951" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0045076", "pred" : "http://purl.obolibrary.org/obo/pato#has_relative_magnitude", "obj" : "http://purl.obolibrary.org/obo/PATO_0000461" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0001943", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0000951" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002341", "pred" : "is_a", @@ -57488,14 +57419,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0001264", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000324" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0000403", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0001857" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0045086", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0045073" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0000403", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0001857" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0000321", "pred" : "is_a", @@ -57652,26 +57583,26 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0015012", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001547" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0001874", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0001873" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002405", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000141" }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0001290", + "sub" : "http://purl.obolibrary.org/obo/PATO_0001874", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0000018" + "obj" : "http://purl.obolibrary.org/obo/PATO_0001873" }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0002534", + "sub" : "http://purl.obolibrary.org/obo/PATO_0001290", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0000052" + "obj" : "http://purl.obolibrary.org/obo/PATO_0000018" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001753", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001752" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0002534", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0000052" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001535", "pred" : "is_a", @@ -57848,14 +57779,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0001454", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000085" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0000632", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0000965" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002501", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000133" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0000632", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0000965" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002407", "pred" : "is_a", @@ -57972,14 +57903,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0001887", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001886" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0002535", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0000052" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001754", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001752" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0002535", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0000052" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0045084", "pred" : "is_a", @@ -58060,14 +57991,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0045060", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0045050" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0002011", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0000141" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002073", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0002182" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0002011", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0000141" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001284", "pred" : "is_a", @@ -58288,14 +58219,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0001302", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000014" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0000761", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0001707" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001321", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0002326" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0000761", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0001707" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001826", "pred" : "is_a", @@ -58448,14 +58379,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0001194", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0002303" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0002155", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0001599" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002261", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000140" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0002155", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0001599" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001793", "pred" : "is_a", @@ -58468,14 +58399,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0001317", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001305" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0001885", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0001884" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002426", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000052" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0001885", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0001884" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002070", "pred" : "is_a", @@ -58598,22 +58529,22 @@ "subsets" : [ ], "xrefs" : [ ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#auto-generated-by", - "val" : "OBO-Edit 2.3.1" + "pred" : "http://purl.org/dc/elements/1.1/description", + "val" : "An ontology of phenotypic qualities (properties, attributes or characteristics)." }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#date", - "val" : "07:02:2018 10:27" + "pred" : "http://purl.org/dc/elements/1.1/title", + "val" : "PATO - the Phenotype And Trait Ontology" + }, { + "pred" : "http://purl.org/dc/terms/license", + "val" : "https://creativecommons.org/licenses/by/3.0/" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#default-namespace", "val" : "quality" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBOFormatVersion", "val" : "1.2" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#saved-by", - "val" : "segerdel" } ], - "version" : "http://purl.obolibrary.org/obo/pato/releases/2019-11-05/pato-simple.json" + "version" : "http://purl.obolibrary.org/obo/pato/releases/2019-12-03/pato-simple.json" }, "equivalentNodesSets" : [ ], "logicalDefinitionAxioms" : [ ], diff --git a/pato-simple.obo b/pato-simple.obo index 33a56a76..9eb56902 100644 --- a/pato-simple.obo +++ b/pato-simple.obo @@ -1,8 +1,5 @@ format-version: 1.2 -data-version: pato/releases/2019-11-05/pato-simple.owl -date: 07:02:2018 10:27 -saved-by: segerdel -auto-generated-by: OBO-Edit 2.3.1 +data-version: pato/releases/2019-12-03/pato-simple.owl subsetdef: abnormal_slim "Abnormal/normal slim" subsetdef: absent_slim "Absent/present slim" subsetdef: attribute_slim "Attribute slim" @@ -16,6 +13,9 @@ subsetdef: scalar_slim "Scalar slim" subsetdef: value_slim "Value slim" default-namespace: quality ontology: pato/pato-simple +property_value: http://purl.org/dc/elements/1.1/description "An ontology of phenotypic qualities (properties, attributes or characteristics)." xsd:string +property_value: http://purl.org/dc/elements/1.1/title "PATO - the Phenotype And Trait Ontology" xsd:string +property_value: http://purl.org/dc/terms/license https://creativecommons.org/licenses/by/3.0/ xsd:string [Term] id: PATO:0000000 @@ -27,7 +27,6 @@ id: PATO:0000001 name: quality alt_id: PATO:0000072 def: "A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities" [PATOC:GVG] -synonym: "trait" EXACT [] property_value: IAO:0000589 "quality (PATO)" xsd:string [Term] @@ -8691,7 +8690,7 @@ is_a: PATO:0001377 ! polyploid [Term] id: PATO:0001384 name: hexaploid -def: "A polyploidy quality inhering in a bearer by virtue of the bearer's containing four homologous sets of chromosomes." [Wikipedia:http\://en.wikipedia.org/wiki/Hexaploid] +def: "A polyploidy quality inhering in a bearer by virtue of the bearer's containing six homologous sets of chromosomes." [Wikipedia:http\://en.wikipedia.org/wiki/Hexaploid] subset: cell_quality subset: value_slim is_a: PATO:0001377 ! polyploid @@ -20042,6 +20041,15 @@ synonym: "structurally interrupted" EXACT [] is_a: PATO:0001241 ! physical object quality created_by: http://orcid.org/0000-0001-5208-3432 +[Term] +id: PATO:0040027 +name: doubled haploid +def: "A ploidy quality inhering in a bearer by virtue of the bearer's haploid cells undergo chromosome doubling." [Wikipedia:https\://en.wikipedia.org/wiki/Doubled_haploidy] +synonym: "double haploid" EXACT [] +synonym: "double-haploid" EXACT [] +is_a: PATO:0001393 ! euploid +created_by: http://orcid.org/0000-0001-5208-3432 + [Term] id: PATO:0045000 name: normal rate @@ -20828,7 +20836,7 @@ creation_date: 2017-12-22T14:16:43Z [Term] id: PATO:0045075 name: normal variability of color -def: "A variability which is relatively normal or average" [] +def: "A variability of color which is relatively normal or average" [] subset: value_slim is_a: PATO:0001615 ! variant color relationship: has_relative_magnitude PATO:0000461 ! normal @@ -21069,6 +21077,18 @@ is_a: PATO:0060001 ! sex-specific created_by: http://orcid.org/0000-0002-1373-1705 creation_date: 2019-08-23T08:51:22Z +[Typedef] +id: RO:0000053 +name: bearer of +def: "a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence" [] +property_value: IAO:0000111 "bearer of" xsd:string +property_value: IAO:0000112 "this apple is bearer of this red color" xsd:string +property_value: IAO:0000112 "this vase is bearer of this fragility" xsd:string +property_value: IAO:0000116 "A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist." xsd:string +property_value: IAO:0000118 "bearer_of" xsd:string +property_value: IAO:0000118 "is bearer of" xsd:string +property_value: RO:0001900 RO:0001901 + [Typedef] id: RO:0000057 name: has participant @@ -21083,27 +21103,22 @@ property_value: IAO:0000118 "has_participant" xsd:string holds_over_chain: has_part RO:0000057 [Typedef] -id: bearer_of -name: bearer of -namespace: uberon -def: "a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence" [] -xref: RO:0000053 -property_value: IAO:0000111 "bearer of" xsd:string -property_value: IAO:0000112 "this apple is bearer of this red color" xsd:string -property_value: IAO:0000112 "this vase is bearer of this fragility" xsd:string -property_value: IAO:0000116 "A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist." xsd:string -property_value: IAO:0000118 "bearer_of" xsd:string -property_value: IAO:0000118 "is bearer of" xsd:string +id: RO:0002180 +name: has component +def: "w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type." [] +subset: ro-eco +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000116 "The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity." xsd:string +property_value: IAO:0000232 "For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit." xsd:string property_value: RO:0001900 RO:0001901 +property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:Componency +is_a: has_part ! has part [Typedef] -id: composed_primarily_of +id: RO:0002473 name: composed primarily of -namespace: uberon def: "x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y." [] -def: "x composed_primarily_of y iff: more than half of the mass of x is made from parts of y" [] subset: ro-eco -xref: RO:0002473 property_value: IAO:0000112 "'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate'" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 @@ -21141,20 +21156,6 @@ range: PATO:0000001 ! quality created_by: cjm creation_date: 2009-08-26T02:50:08Z -[Typedef] -id: has_component -name: has component -namespace: uberon -def: "w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type." [] -subset: ro-eco -xref: RO:0002180 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000116 "The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity." xsd:string -property_value: IAO:0000232 "For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit." xsd:string -property_value: RO:0001900 RO:0001901 -property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:Componency -is_a: has_part ! has part - [Typedef] id: has_cross_section name: has_cross_section @@ -21189,9 +21190,7 @@ is_a: has_ratio_quality ! has_ratio_quality id: has_part name: has part name: has_part -namespace: chebi_ontology namespace: external -namespace: uberon def: "a core relation that holds between a whole and its part" [] def: "Q1 has_part Q2 if and only if: every instance of Q1 is a quality_of an entity that has_quality some Q2." [PATOC:CJM] comment: We use the has_part relation to relate complex qualities to more primitive ones. A complex quality is a collection of qualities. The complex quality cannot exist without the sub-qualities. For example, the quality 'swollen' necessarily comes with the qualities of 'protruding' and 'increased size'. @@ -21205,7 +21204,6 @@ property_value: IAO:0000116 "Occurrents are not subject to change and so parthoo property_value: IAO:0000116 "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)\n\nA continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'." xsd:string property_value: IAO:0000118 "has_part" xsd:string property_value: RO:0001900 RO:0001901 -is_cyclic: false is_transitive: true [Typedef] @@ -21269,7 +21267,6 @@ id: part_of name: part of name: part_of namespace: external -namespace: uberon def: "a core relation that holds between a part and its whole" [] xref: BFO:0000050 property_value: IAO:0000111 "is part of" xsd:string diff --git a/pato-simple.owl b/pato-simple.owl index 3580bd4d..40656742 100644 --- a/pato-simple.owl +++ b/pato-simple.owl @@ -9,15 +9,16 @@ xmlns:xsd="http://www.w3.org/2001/XMLSchema#" xmlns:pato="http://purl.obolibrary.org/obo/pato#" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" + xmlns:terms="http://purl.org/dc/terms/" xmlns:subsets="http://purl.obolibrary.org/obo/ro/subsets#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - - OBO-Edit 2.3.1 - 07:02:2018 10:27 + + An ontology of phenotypic qualities (properties, attributes or characteristics). + PATO - the Phenotype And Trait Ontology + https://creativecommons.org/licenses/by/3.0/ quality 1.2 - segerdel @@ -54,31 +55,7 @@ - definition - The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. - 2012-04-05: -Barry Smith - -The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. - -Can you fix to something like: - -A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. - -Alan Ruttenberg - -Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. - -On the specifics of the proposed definition: - -We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. - -Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. - -We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. - PERSON:Daniel Schober - GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition definition @@ -111,13 +88,7 @@ We also have the outstanding issue of how to aim different definitions to differ - - has obsolescence reason - Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification. - PERSON:Alan Ruttenberg - PERSON:Melanie Courtot - has obsolescence reason - + @@ -136,14 +107,7 @@ We also have the outstanding issue of how to aim different definitions to differ - term replaced by - - Add as annotation triples in the granting ontology - Use on obsolete terms, relating the term to another term that can be used as a substitute - Person:Alan Ruttenberg - Person:Alan Ruttenberg term replaced by - term replaced by @@ -296,12 +260,6 @@ We also have the outstanding issue of how to aim different definitions to differ - - - - - - @@ -322,12 +280,6 @@ We also have the outstanding issue of how to aim different definitions to differ - - - - - - @@ -418,24 +370,12 @@ We also have the outstanding issue of how to aim different definitions to differ - - - - - - - - - - - - @@ -500,7 +440,6 @@ A continuant cannot be part of an occurrent: use 'participates in'. An BFO:0000050 external quality - uberon part_of part_of part of @@ -531,12 +470,9 @@ A continuant cannot have an occurrent as part: use 'participates in'. has_part BFO:0000051 - chebi_ontology external quality - uberon has_part - false has_part We use the has_part relation to relate complex qualities to more primitive ones. A complex quality is a collection of qualities. The complex quality cannot exist without the sub-qualities. For example, the quality 'swollen' necessarily comes with the qualities of 'protruding' and 'increased size'. has part @@ -563,11 +499,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. bearer_of is bearer of - RO:0000053 - uberon - bearer_of - bearer_of - bearer of bearer of @@ -602,12 +533,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity. For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit. - RO:0002180 - uberon - has_component - has_component - has component has component @@ -620,16 +546,10 @@ A continuant cannot have an occurrent as part: use 'participates in'. 'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate' x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y. - x composed_primarily_of y iff: more than half of the mass of x is made from parts of y Chris Mungall - RO:0002473 - uberon - RO:0002473 - composed_primarily_of - composed_primarily_of composed primarily of @@ -971,7 +891,6 @@ Association is weaker than correlation or proportionality. These relations may b A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities quality (PATO) PATO:0000072 - trait quality PATO:0000001 quality @@ -1623,7 +1542,7 @@ Association is weaker than correlation or proportionality. These relations may b A physical quality which inheres in a bearer by virtue of the number of the bearer's repetitive actions in a particular time. - Wikipedia:http://en.wikipedia.org/wiki/frequency + Wikipedia:http://en.wikipedia.org/wiki/frequency @@ -19162,7 +19081,7 @@ Association is weaker than correlation or proportionality. These relations may b A physical quality that inheres in an bearer by virtue of how that bearer interacts with electromagnetic radiation. - Wikipedia:http://en.wikipedia.org/wiki/Electromagnetic_radiation + Wikipedia:http://en.wikipedia.org/wiki/Electromagnetic_radiation @@ -21033,7 +20952,7 @@ Association is weaker than correlation or proportionality. These relations may b - A polyploidy quality inhering in a bearer by virtue of the bearer's containing four homologous sets of chromosomes. + A polyploidy quality inhering in a bearer by virtue of the bearer's containing six homologous sets of chromosomes. quality PATO:0001384 @@ -21043,7 +20962,7 @@ Association is weaker than correlation or proportionality. These relations may b - A polyploidy quality inhering in a bearer by virtue of the bearer's containing four homologous sets of chromosomes. + A polyploidy quality inhering in a bearer by virtue of the bearer's containing six homologous sets of chromosomes. Wikipedia:http://en.wikipedia.org/wiki/Hexaploid @@ -21852,7 +21771,7 @@ Association is weaker than correlation or proportionality. These relations may b A color hue with very low wavelength of that portion of the visible spectrum lying between reddish blue or bluish purple, evoked in the human observer by radiant energy with wavelengths of approximately 420 to 380 nanometers. - Wikipedia:http://en.wikipedia.org/wiki/Violet + Wikipedia:http://en.wikipedia.org/wiki/Violet @@ -22133,7 +22052,7 @@ Association is weaker than correlation or proportionality. These relations may b A attachment quality inhering in a bearer by virtue of the bearer's having or being supported by a pedicel or pedicle. - MedTerms:MedTerms + MedTerms:MedTerms @@ -22337,7 +22256,7 @@ Association is weaker than correlation or proportionality. These relations may b A composition quality inhering in an bearer by virtue of the bearer's being hardened by the deposition of calcium into bone. - MAMMALOGY:MAMMALOGY + MAMMALOGY:MAMMALOGY @@ -23119,7 +23038,7 @@ Association is weaker than correlation or proportionality. These relations may b An age quality that exists by virtue of the time (years and months) that the bearer has existed. - WordNet:Wordnet + WordNet:Wordnet @@ -29371,7 +29290,7 @@ Association is weaker than correlation or proportionality. These relations may b A shape quality inhering in a bearer by virtue of the bearer's being wound in a continuous series of loops. - Online_Dictionary:Online_Dictionary + Online_Dictionary:Online_Dictionary @@ -31366,7 +31285,7 @@ Association is weaker than correlation or proportionality. These relations may b A surface feature shape quality inhering in a bearer by virtue of the bearer's having the border, edge, or outline cut into a series of segments of circles resembling a scallop-shell. - Oxford:EnglishDictionary + Oxford:EnglishDictionary @@ -38054,7 +37973,7 @@ Association is weaker than correlation or proportionality. These relations may b A concave 3-D shape quality inhering in a bearer by virtue of the bearer's being shaped in the form of a spoon. - thefreedictionary:http://www.thefreedictionary.com/spoon-shaped + thefreedictionary:http://www.thefreedictionary.com/spoon-shaped @@ -38120,7 +38039,7 @@ Association is weaker than correlation or proportionality. These relations may b A curvature quality inhering in a bearer by virtue of the bearer's being curved backward or inward. - merriam-webster:http://www.merriam-webster.com/dictionary/recurved + merriam-webster:http://www.merriam-webster.com/dictionary/recurved @@ -38372,7 +38291,7 @@ Association is weaker than correlation or proportionality. These relations may b A quality inhering in a bearer by virtue of the bearer's being phosphorylated to a lesser than normal extent, or less than fully. - Wikipedia:http://en.wiktionary.org/wiki/hypophosphorylated + Wikipedia:http://en.wiktionary.org/wiki/hypophosphorylated @@ -40289,7 +40208,7 @@ Association is weaker than correlation or proportionality. These relations may b A convex 3-D shape quality inhering in a bearer by virtue of the bearer's exhibiting a by virtue of the bearer's exhibiting a consistently sized and approximately round cross-section along its length, which is many times larger than its diameter. - PATOC:DC + PATOC:DC @@ -41120,7 +41039,7 @@ Association is weaker than correlation or proportionality. These relations may b A conical quality inhering in a bearer by virtue of the bearer's resembling a cone, with the pointed end attached to an organism. - wiktionary:http://en.wiktionary.org/wiki/obconical + wiktionary:http://en.wiktionary.org/wiki/obconical @@ -41141,7 +41060,7 @@ Association is weaker than correlation or proportionality. These relations may b A structural quality inhering in a bearer by virtue of the bearer resembling wood. - merriam-webster:http://www.merriam-webster.com/dictionary/ligneous + merriam-webster:http://www.merriam-webster.com/dictionary/ligneous @@ -41162,7 +41081,7 @@ Association is weaker than correlation or proportionality. These relations may b A spatial quality inhering in a bearer by virtue of the bearer's being located toward the base of an organism relative to another entity. - merriam-webster:http://www.merriam-webster.com/dictionary/basal + merriam-webster:http://www.merriam-webster.com/dictionary/basal @@ -41183,7 +41102,7 @@ Association is weaker than correlation or proportionality. These relations may b A spatial quality inhering in a bearer by virtue of the bearer's being located toward the stalk of an organism relative to another entity. - merriam-webster:http://www.merriam-webster.com/dictionary/cauline + merriam-webster:http://www.merriam-webster.com/dictionary/cauline @@ -47440,6 +47359,27 @@ height'). + + + + + A ploidy quality inhering in a bearer by virtue of the bearer's haploid cells undergo chromosome doubling. + http://orcid.org/0000-0001-5208-3432 + double haploid + double-haploid + quality + PATO:0040027 + doubled haploid + + + + + A ploidy quality inhering in a bearer by virtue of the bearer's haploid cells undergo chromosome doubling. + Wikipedia:https://en.wikipedia.org/wiki/Doubled_haploidy + + + + @@ -48698,7 +48638,7 @@ height'). - A variability which is relatively normal or average + A variability of color which is relatively normal or average Luke Slater 2017-12-22T14:16:43Z quality diff --git a/pato.json b/pato.json index bdfea45c..b898756e 100644 --- a/pato.json +++ b/pato.json @@ -183,46 +183,6 @@ }, "type" : "CLASS", "lbl" : "obsolete mild response" - }, { - "id" : "http://purl.obolibrary.org/obo/PCO_0000004", - "meta" : { - "definition" : { - "val" : "A quality that inheres in a community.", - "xrefs" : [ ] - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000428" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "These may not belong under BFO:quality. May be better to call them community characteristics, and classify as specifically dependent continuants. Need to look at process profiles in BFO2." - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", - "val" : "Includes qualities like diversity, species richness, stability, resilience, community structure, number of trophic levels. A community quality may depend on the qualities of individual organism in the community, but cannot be measured or described for a single individual." - } ] - }, - "type" : "CLASS", - "lbl" : "quality of an ecological community" - }, { - "id" : "http://purl.obolibrary.org/obo/PCO_0000003", - "meta" : { - "definition" : { - "val" : "A quality that inheres in a biological population.", - "xrefs" : [ ] - }, - "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", - "val" : "Includes qualities like population size, population growth rate, carrying capacity, immigration rate, emigration rate, fecundity, and death rate. A population quality may depend on the qualities of individual organisms in the population, but cannot be measured or described for a single organism. This term may be replaced by a PATO term." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "See Chris's comments on population qualities at: http://code.google.com/p/popcomm-ontology/issues/detail?id=4. These may not belong under BFO:quality. May be better to call them population characteristics, and classify as specifically dependent continuants. Need to look at process profiles in BFO2." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000428" - } ] - }, - "type" : "CLASS", - "lbl" : "quality of a population" }, { "id" : "http://purl.obolibrary.org/obo/PATO_0000499", "meta" : { @@ -415,43 +375,6 @@ }, "type" : "CLASS", "lbl" : "obsolete phase value" - }, { - "id" : "http://purl.obolibrary.org/obo/PCO_0000017", - "meta" : { - "definition" : { - "val" : "A collection of organisms that has as parts every organism of given species and no organisms of any other species.", - "xrefs" : [ ] - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "At the moment there is no way to specify in an OWL axiom that the collection includes every individual of a species. This should be added, if possible." - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", - "val" : "This term is neutral with respect to which organisms are included in a species. Membership will depend on the species concept and the taxonomic assertions used to define the species. These criteria must be specified by the user." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000120" - } ] - }, - "type" : "CLASS", - "lbl" : "species as a collection of organisms" - }, { - "id" : "http://purl.obolibrary.org/obo/PCO_0000018", - "meta" : { - "definition" : { - "val" : "A material entity that has as parts two or more organisms, viruses, or viroids of the same species and no members of any other species.", - "xrefs" : [ ] - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "collection of organisms of the same species" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000120" - } ] - }, - "type" : "CLASS", - "lbl" : "single-species collection of organisms" }, { "id" : "http://purl.obolibrary.org/obo/PATO_0002205", "meta" : { @@ -668,32 +591,6 @@ }, "type" : "CLASS", "lbl" : "vaporizability" - }, { - "id" : "http://purl.obolibrary.org/obo/PCO_0000000", - "meta" : { - "definition" : { - "val" : "A material entity that consists of two or more organisms, viruses, or viroids.", - "xrefs" : [ ] - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "group of organism" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", - "val" : "May be of the same or different species." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "Examples include: population, community, species (meaning the collection of organisms that makes up a species, not the taxonomic rank), and family." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "organism collection" - } ] - }, - "type" : "CLASS", - "lbl" : "collection of organisms" }, { "id" : "http://purl.obolibrary.org/obo/RO_0000080", "meta" : { @@ -717,58 +614,6 @@ }, "type" : "PROPERTY", "lbl" : "quality of" - }, { - "id" : "http://purl.obolibrary.org/obo/PCO_0000002", - "meta" : { - "definition" : { - "val" : "A community of at least two different species, living in a particular area. Must have at least two populations of different species as members.", - "xrefs" : [ ] - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "ISBN:0865423504" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000123" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "multispecies community" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", - "val" : "Ecological community is defined broadly here, but includes both ecological interactions (inherited from parent term community) and spatial co-existence. It may be used to describe every organisms living in an area, but is often used to refer only to organisms of a particular taxon or guild (e.g., the plant community, the insect community, the herbivore community). The word community, as it often used to describe a group of humans living together, is a type of single-species collection of organisms, not an ecological community." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Not sure if the equivalancy axiom specifies that both populations are located in the same site." - } ] - }, - "type" : "CLASS", - "lbl" : "ecological community" - }, { - "id" : "http://purl.obolibrary.org/obo/PCO_0000001", - "meta" : { - "definition" : { - "val" : "A collection of organisms, all of the same species, that live in the same place.", - "xrefs" : [ ] - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "This a general term that can include every organism of a species living in an area or any subset of them. Subclasses can be more specific as needed." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "ISBN:0878932739" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", - "val" : "It is sometimes difficult to define the physical boundaries of a population. In the case of sexually reproducing organisms, the individuals within a population have the potential to reproduce with one another during the course of their lifetimes. 'Community', as often used to describe a group of humans, is a type of population. \n\nClasses for population already exist in IDO ('organism population', IDO_0000509) and OBI ('population', OBI_0000181). The definitions should be standardized across OBO Foundry ontologies and only one term used." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - } ] - }, - "type" : "CLASS", - "lbl" : "population of organisms" }, { "id" : "http://purl.obolibrary.org/obo/PATO_0002216", "meta" : { @@ -940,21 +785,12 @@ "val" : "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence", "xrefs" : [ ] }, - "xrefs" : [ { - "val" : "RO:0000086" - } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "has_quality" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "this apple has quality this red color" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "has_quality" @@ -1845,20 +1681,6 @@ }, "type" : "CLASS", "lbl" : "increased intensity" - }, { - "id" : "http://purl.obolibrary.org/obo/PCO_0000031", - "meta" : { - "definition" : { - "val" : "A material entity that is one or more organisms, viruses or viroids.", - "xrefs" : [ ] - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - } ] - }, - "type" : "CLASS", - "lbl" : "organismal entity" }, { "id" : "http://purl.obolibrary.org/obo/PATO_0001798", "meta" : { @@ -2075,15 +1897,9 @@ "val" : "a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence", "xrefs" : [ ] }, - "xrefs" : [ { - "val" : "RO:0000053" - } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist." - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "this apple is bearer of this red color" @@ -2102,9 +1918,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "bearer of" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "bearer_of" } ] }, "type" : "PROPERTY", @@ -2357,66 +2170,6 @@ }, "type" : "CLASS", "lbl" : "right side of" - }, { - "id" : "http://purl.obolibrary.org/obo/PCO_0000028", - "meta" : { - "definition" : { - "val" : "A collection of organisms of the same species whose members are all either genealogically related to each other or have mated with each other.", - "xrefs" : [ ] - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Biological or social relations are covered by RO_0002437 (biotically interacts with), but that relations does provide an easy way to specify that two entities are interacting with each other (participating in the same interaction). Until that axiom is specified, the logical definition of this term is incomplete." - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", - "val" : "These relations can include shared values, occupying the same spatial regkion. A community be be a single species collection of organsisms (as in a human community, which is also a type of population) or a or multi-species collection of organisms (as in an ecological community)." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000123" - } ] - }, - "type" : "CLASS", - "lbl" : "community" - }, { - "id" : "http://purl.obolibrary.org/obo/PCO_0000027", - "meta" : { - "definition" : { - "val" : "A collection of organisms of the same species that has as members only humans.", - "xrefs" : [ ] - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "human population" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "human community" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - } ] - }, - "type" : "CLASS", - "lbl" : "collection of humans" - }, { - "id" : "http://purl.obolibrary.org/obo/PCO_0000029", - "meta" : { - "definition" : { - "val" : "A collection of organisms that consists of two or more organisms from at least two species.", - "xrefs" : [ ] - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Need to add axiom to specify that it has at a mimum members of two different species, but not sure how to specify that. Can't say \"('has member' only ('member of' min 2 'species as a collection of organisms'))\"." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000123" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", - "val" : "" - } ] - }, - "type" : "CLASS", - "lbl" : "multi-species collection of organisms" }, { "id" : "http://purl.obolibrary.org/obo/PATO_0000477", "meta" : { @@ -2606,26 +2359,6 @@ }, "type" : "CLASS", "lbl" : "obsolete shattering value" - }, { - "id" : "http://purl.obolibrary.org/obo/ENVO_01001055", - "meta" : { - "definition" : { - "val" : "An environmental system determined by part of a living or dead animal, or a whole small animal.", - "xrefs" : [ ] - } - }, - "type" : "CLASS", - "lbl" : "environment associated with an animal part or small animal" - }, { - "id" : "http://purl.obolibrary.org/obo/ENVO_01001057", - "meta" : { - "definition" : { - "val" : "An environmental system determined by part of a living or dead plant, or a whole small plant.", - "xrefs" : [ ] - } - }, - "type" : "CLASS", - "lbl" : "environment associated with a plant part or small plant" }, { "id" : "http://purl.obolibrary.org/obo/PATO_0000408", "meta" : { @@ -4729,17 +4462,6 @@ }, "type" : "CLASS", "lbl" : "cell" - }, { - "id" : "http://purl.obolibrary.org/obo/NCBITaxon_89593", - "meta" : { - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "Craniata", - "xrefs" : [ ] - } ] - }, - "type" : "CLASS", - "lbl" : "Craniata " }, { "id" : "http://purl.obolibrary.org/obo/PATO_0002186", "meta" : { @@ -5188,9 +4910,6 @@ } ] }, "type" : "PROPERTY" - }, { - "id" : "http://www.geneontology.org/formats/oboInOwl#Subset", - "type" : "CLASS" }, { "id" : "http://purl.obolibrary.org/obo/PATO_0002148", "meta" : { @@ -5413,40 +5132,6 @@ }, "type" : "CLASS", "lbl" : "decreased radiopacity" - }, { - "id" : "http://purl.obolibrary.org/obo/ENVO_01001000", - "meta" : { - "definition" : { - "val" : "An environmental system which is determined by a living organism.", - "xrefs" : [ ] - }, - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "host-associated environment", - "xrefs" : [ ] - } ] - }, - "type" : "CLASS", - "lbl" : "environmental system determined by an organism" - }, { - "id" : "http://purl.obolibrary.org/obo/ENVO_01001002", - "meta" : { - "definition" : { - "val" : "An environmental system determined by an animal.", - "xrefs" : [ ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "Metazoan-associated environment", - "xrefs" : [ ] - }, { - "pred" : "hasBroadSynonym", - "val" : "animal environment", - "xrefs" : [ ] - } ] - }, - "type" : "CLASS", - "lbl" : "animal-associated environment" }, { "id" : "http://purl.obolibrary.org/obo/PATO_0002159", "meta" : { @@ -6361,16 +6046,6 @@ }, "type" : "CLASS", "lbl" : "peripheral" - }, { - "id" : "http://purl.obolibrary.org/obo/ENVO_02500000", - "meta" : { - "definition" : { - "val" : "A process in which includes the components of an environmental system as participants.", - "xrefs" : [ ] - } - }, - "type" : "CLASS", - "lbl" : "environmental system process" }, { "id" : "http://purl.obolibrary.org/obo/PATO_0002104", "meta" : { @@ -6832,21 +6507,6 @@ }, "type" : "CLASS", "lbl" : "phosphorylation" - }, { - "id" : "http://purl.obolibrary.org/obo/NCBITaxon_33154", - "meta" : { - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "opisthokonts", - "xrefs" : [ ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "Fungi/Metazoa group", - "xrefs" : [ ] - } ] - }, - "type" : "CLASS", - "lbl" : "Opisthokonta" }, { "id" : "http://purl.obolibrary.org/obo/GO_0005634", "meta" : { @@ -6970,16 +6630,6 @@ }, "type" : "CLASS", "lbl" : "scirrhous" - }, { - "id" : "http://purl.obolibrary.org/obo/ENVO_02500027", - "meta" : { - "definition" : { - "val" : "An environmental process which is driven by the action of humans.", - "xrefs" : [ ] - } - }, - "type" : "CLASS", - "lbl" : "anthropogenic environmental process" }, { "id" : "http://purl.obolibrary.org/obo/PATO_0002120", "meta" : { @@ -7900,30 +7550,6 @@ }, "type" : "CLASS", "lbl" : "decreased distance" - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000409", - "meta" : { - "definition" : { - "val" : "A denotator type indicates how a term should be interpreted from an ontological perspective.", - "xrefs" : [ ] - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "Barry Smith, Werner Ceusters" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are \"natural kinds\" and the latter arbitrary collections of entities." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Alan Ruttenberg" - } ] - }, - "type" : "CLASS", - "lbl" : "denotator type" - }, { - "id" : "http://purl.obolibrary.org/obo/NCBITaxon_314146", - "type" : "CLASS", - "lbl" : "Euarchontoglires" }, { "id" : "http://purl.obolibrary.org/obo/PATO_0000389", "meta" : { @@ -8137,75 +7763,13 @@ }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000412", "meta" : { - "definition" : { - "val" : "For external terms/classes, the ontology from which the term was imported", - "xrefs" : [ ] - }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "imported from" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "PERSON:Melanie Courtot" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "GROUP:OBI:" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "PERSON:Alan Ruttenberg" } ] }, "type" : "PROPERTY", "lbl" : "imported from" - }, { - "id" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "meta" : { - "definition" : { - "val" : "An alternate textual definition for a class taken unmodified from an external source. This definition may have been used to derive a generalized definition for the new class.", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] - }, - "xrefs" : [ { - "val" : "UBPROP:0000001" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", - "val" : "This annotation property may be replaced with an annotation property from an external ontology such as IAO" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "external_definition" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", - "val" : "true" - } ] - }, - "type" : "PROPERTY", - "lbl" : "external_definition" - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000410", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Hard to give a definition for. Intuitively a \"natural kind\" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Alan Ruttenberg" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf" - } ] - }, - "type" : "INDIVIDUAL", - "lbl" : "universal" - }, { - "id" : "http://purl.obolibrary.org/obo/NCBITaxon_8287", - "type" : "CLASS", - "lbl" : "Sarcopterygii" }, { "id" : "http://purl.obolibrary.org/obo/pato#has_dividend_quality", "meta" : { @@ -8342,75 +7906,8 @@ "lbl" : "obsolete slight" }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000424", - "meta" : { - "definition" : { - "val" : "A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones", - "xrefs" : [ ] - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "ObjectProperty: RO_0002104\nLabel: has plasma membrane part\nAnnotations: IAO_0000424 \"http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.org/obo/owl/GO#GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)\"\n" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "expand expression to" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - } ] - }, "type" : "PROPERTY", "lbl" : "expand expression to" - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000423", - "meta" : { - "definition" : { - "val" : "Terms with this status should eventually replaced with a term from another ontology.", - "xrefs" : [ ] - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "group:OBI" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Alan Ruttenberg" - } ] - }, - "type" : "INDIVIDUAL", - "lbl" : "to be replaced with external ontology term" - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000420", - "meta" : { - "definition" : { - "val" : "A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal", - "xrefs" : [ ] - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "\"definitions\", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Alan Ruttenberg" - } ] - }, - "type" : "INDIVIDUAL", - "lbl" : "defined class" - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000421", - "meta" : { - "definition" : { - "val" : "A named class expression is a logical expression that is given a name. The name can be used in place of the expression.", - "xrefs" : [ ] - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Alan Ruttenberg" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions" - } ] - }, - "type" : "INDIVIDUAL", - "lbl" : "named class expression" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", "type" : "PROPERTY", @@ -10994,56 +10491,13 @@ }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000428", "meta" : { - "definition" : { - "val" : "A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues.", - "xrefs" : [ ] - }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Alan Ruttenberg" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "group:OBI" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" } ] }, "type" : "INDIVIDUAL", "lbl" : "requires discussion" - }, { - "id" : "http://purl.obolibrary.org/obo/NCBITaxon_32525", - "meta" : { - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "Theria", - "xrefs" : [ ] - } ] - }, - "type" : "CLASS", - "lbl" : "Theria " - }, { - "id" : "http://purl.obolibrary.org/obo/NCBITaxon_32524", - "meta" : { - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "amniotes", - "xrefs" : [ ] - } ] - }, - "type" : "CLASS", - "lbl" : "Amniota" - }, { - "id" : "http://purl.obolibrary.org/obo/NCBITaxon_32523", - "meta" : { - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "tetrapods", - "xrefs" : [ ] - } ] - }, - "type" : "CLASS", - "lbl" : "Tetrapoda" }, { "id" : "http://purl.obolibrary.org/obo/PATO_0001608", "meta" : { @@ -11806,51 +11260,6 @@ }, "type" : "CLASS", "lbl" : "increased affinity" - }, { - "id" : "http://purl.obolibrary.org/obo/NCBITaxon_9604", - "meta" : { - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "Pongidae", - "xrefs" : [ ] - }, { - "pred" : "hasExactSynonym", - "val" : "great apes", - "xrefs" : [ ] - } ] - }, - "type" : "CLASS", - "lbl" : "Hominidae" - }, { - "id" : "http://purl.obolibrary.org/obo/NCBITaxon_9605", - "meta" : { - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "humans", - "xrefs" : [ ] - } ] - }, - "type" : "CLASS", - "lbl" : "Homo" - }, { - "id" : "http://purl.obolibrary.org/obo/NCBITaxon_9606", - "meta" : { - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "man", - "xrefs" : [ ] - }, { - "pred" : "hasExactSynonym", - "val" : "human", - "xrefs" : [ ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "humans", - "xrefs" : [ ] - } ] - }, - "type" : "CLASS", - "lbl" : "Homo sapiens" }, { "id" : "http://purl.obolibrary.org/obo/PATO_0002087", "meta" : { @@ -12358,109 +11767,6 @@ }, "type" : "CLASS", "lbl" : "ballooning" - }, { - "id" : "http://purl.obolibrary.org/obo/PO_0000003", - "meta" : { - "definition" : { - "val" : "A plant structure (PO:0005679) which is a whole organism.", - "xrefs" : [ ] - }, - "synonyms" : [ { - "pred" : "hasNarrowSynonym", - "val" : "prothalli (narrow)", - "xrefs" : [ ] - }, { - "pred" : "hasExactSynonym", - "val" : "植物体全体 (Japanese, exact)", - "xrefs" : [ ] - }, { - "pred" : "hasNarrowSynonym", - "val" : "shrub (narrow)", - "xrefs" : [ ] - }, { - "pred" : "hasExactSynonym", - "val" : "planta entera (Spanish, exact)", - "xrefs" : [ ] - }, { - "pred" : "hasNarrowSynonym", - "val" : "gametophyte (narrow)", - "xrefs" : [ ] - }, { - "pred" : "hasNarrowSynonym", - "val" : "suffrutex (narrow)", - "xrefs" : [ ] - }, { - "pred" : "hasNarrowSynonym", - "val" : "herb (narrow)", - "xrefs" : [ ] - }, { - "pred" : "hasNarrowSynonym", - "val" : "suffrutices (narrow)", - "xrefs" : [ ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "clonal colony (related)", - "xrefs" : [ ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "colony (related)", - "xrefs" : [ ] - }, { - "pred" : "hasNarrowSynonym", - "val" : "frutices (narrow)", - "xrefs" : [ ] - }, { - "pred" : "hasBroadSynonym", - "val" : "ramet (broad)", - "xrefs" : [ ] - }, { - "pred" : "hasNarrowSynonym", - "val" : "prothallium (narrow)", - "xrefs" : [ ] - }, { - "pred" : "hasNarrowSynonym", - "val" : "woody clump (narrow)", - "xrefs" : [ ] - }, { - "pred" : "hasNarrowSynonym", - "val" : "vine (narrow)", - "xrefs" : [ ] - }, { - "pred" : "hasBroadSynonym", - "val" : "genet (broad)", - "xrefs" : [ ] - }, { - "pred" : "hasNarrowSynonym", - "val" : "prothallus (narrow)", - "xrefs" : [ ] - }, { - "pred" : "hasNarrowSynonym", - "val" : "tree (narrow)", - "xrefs" : [ ] - }, { - "pred" : "hasNarrowSynonym", - "val" : "sporophyte (narrow)", - "xrefs" : [ ] - }, { - "pred" : "hasNarrowSynonym", - "val" : "bush (narrow)", - "xrefs" : [ ] - }, { - "pred" : "hasNarrowSynonym", - "val" : "seedling (narrow)", - "xrefs" : [ ] - }, { - "pred" : "hasNarrowSynonym", - "val" : "liana (narrow)", - "xrefs" : [ ] - }, { - "pred" : "hasNarrowSynonym", - "val" : "frutex (narrow)", - "xrefs" : [ ] - } ] - }, - "type" : "CLASS", - "lbl" : "whole plant" }, { "id" : "http://purl.obolibrary.org/obo/PATO_0002029", "meta" : { @@ -13825,10 +13131,6 @@ }, "type" : "CLASS", "lbl" : "obsolete surface shape" - }, { - "id" : "http://purl.obolibrary.org/obo/NCBITaxon_1338369", - "type" : "CLASS", - "lbl" : "Dipnotetrapodomorpha" }, { "id" : "http://purl.obolibrary.org/obo/PATO_0002001", "meta" : { @@ -14080,22 +13382,6 @@ }, "type" : "CLASS", "lbl" : "fasciculation" - }, { - "id" : "http://xmlns.com/foaf/0.1/page", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "foaf-page" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", - "val" : "true" - } ] - }, - "type" : "PROPERTY", - "lbl" : "page" }, { "id" : "http://purl.obolibrary.org/obo/PATO_0002425", "meta" : { @@ -15359,7 +14645,7 @@ "meta" : { "definition" : { "val" : "A relationship that holds between between a receptor and an chemical entity, typically a small molecule or peptide, that carries information between cells or compartments of a cell and which binds the receptor and regulates its effector function.", - "xrefs" : [ "GOC:dos" ] + "xrefs" : [ ] }, "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", @@ -17757,10 +17043,6 @@ }, "type" : "CLASS", "lbl" : "obsolete solid substance value" - }, { - "id" : "http://purl.obolibrary.org/obo/NCBITaxon_376913", - "type" : "CLASS", - "lbl" : "Haplorrhini" }, { "id" : "http://purl.obolibrary.org/obo/PATO_0000675", "meta" : { @@ -19332,48 +18614,13 @@ }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000589", "meta" : { - "definition" : { - "val" : "An alternative name for a class or property which is unique across the OBO Foundry.", - "xrefs" : [ ] - }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "PERSON:Chris Mungall" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "GROUP:OBO Foundry " - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "OBO foundry unique label" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "PERSON:Bjoern Peters" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "The intended usage of that property is as follow: OBO foundry unique labels are automatically generated based on regular expressions provided by each ontology, so that SO could specify unique label = 'sequence ' + [label], etc. , MA could specify 'mouse + [label]' etc. Upon importing terms, ontology developers can choose to use the 'OBO foundry unique label' for an imported term or not. The same applies to tools ." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "PERSON:Alan Ruttenberg" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "PERSON:Melanie Courtot" } ] }, "type" : "PROPERTY", "lbl" : "OBO foundry unique label" - }, { - "id" : "http://purl.obolibrary.org/obo/ENVO_01000313", - "meta" : { - "definition" : { - "val" : "An anthropogenic environment is an environmental system which is the product of human activity.", - "xrefs" : [ ] - } - }, - "type" : "CLASS", - "lbl" : "anthropogenic environment" }, { "id" : "http://purl.obolibrary.org/obo/PATO_0001905", "meta" : { @@ -21540,51 +20787,15 @@ }, { "id" : "http://purl.obolibrary.org/obo/RO_0002087", "meta" : { - "definition" : { - "val" : "X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)", - "xrefs" : [ ] - }, - "xrefs" : [ { - "val" : "RO:0002087" - } ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "starts_at_end_of", - "xrefs" : [ ] - }, { - "pred" : "hasExactSynonym", - "val" : "directly preceded by", - "xrefs" : [ ] - }, { - "pred" : "hasExactSynonym", - "val" : "is directly preceded by", - "xrefs" : [ ] - }, { - "pred" : "hasExactSynonym", - "val" : "is immediately preceded by", - "xrefs" : [ "SIO:000251" ] - } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "David Osumi-Sutherland" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "immediately_preceded_by" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", "val" : "X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "A non-transitive temporal relation in which one process immediately precedes another process, such that there is no interval of time between the two processes[SIO:000251]." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "starts_at_end_of" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/SIO_000251" } ] }, "type" : "PROPERTY", @@ -22414,10 +21625,6 @@ }, "type" : "CLASS", "lbl" : "mediolateral polarity" - }, { - "id" : "http://purl.obolibrary.org/obo/NCBITaxon_6072", - "type" : "CLASS", - "lbl" : "Eumetazoa" }, { "id" : "http://purl.obolibrary.org/obo/PATO_0001043", "meta" : { @@ -23980,28 +23187,16 @@ "id" : "http://purl.obolibrary.org/obo/RO_0002131", "meta" : { "definition" : { - "val" : "A overlaps B if they share some part in common.", + "val" : "x overlaps y if and only if there exists some z such that x has part z and z part of y", "xrefs" : [ ] }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "RO:0002131" - } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", - "val" : "BFO_0000051 some (BFO_0000050 some ?Y)" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "overlaps" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", "val" : "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)" @@ -24265,25 +23460,6 @@ }, "type" : "CLASS", "lbl" : "increased height" - }, { - "id" : "http://purl.obolibrary.org/obo/PO_0009011", - "meta" : { - "definition" : { - "val" : "An anatomical structure that is or was part of a plant, or was derived from a part of a plant.", - "xrefs" : [ ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "estructura vegetal (Spanish, exact)", - "xrefs" : [ ] - }, { - "pred" : "hasExactSynonym", - "val" : "植物 構造 (Japanese, exact)", - "xrefs" : [ ] - } ] - }, - "type" : "CLASS", - "lbl" : "plant structure" }, { "id" : "http://purl.obolibrary.org/obo/PATO_0000572", "meta" : { @@ -24376,21 +23552,6 @@ "lbl" : "increased length" }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000600", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "elucidation" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", - "val" : "Primitive terms in a highest-level ontology such as BFO are terms which are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "Person:Barry Smith" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "person:Alan Ruttenberg" - } ] - }, "type" : "PROPERTY", "lbl" : "elucidation" }, { @@ -24634,26 +23795,6 @@ }, "type" : "CLASS", "lbl" : "hypertrophic" - }, { - "id" : "http://purl.obolibrary.org/obo/CHEBI_24431", - "meta" : { - "definition" : { - "val" : "A chemical entity is a physical entity of interest in chemistry including molecular entities, parts thereof, and chemical substances.", - "xrefs" : [ ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/chebi#3_STAR" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "chemical entity", - "xrefs" : [ "UniProt" ] - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "chebi_ontology" - } ] - }, - "type" : "CLASS", - "lbl" : "chemical entity" }, { "id" : "http://purl.obolibrary.org/obo/PATO_0000598", "meta" : { @@ -24862,26 +24003,6 @@ }, "type" : "CLASS", "lbl" : "increased volume" - }, { - "id" : "http://purl.obolibrary.org/obo/CHEBI_59999", - "meta" : { - "definition" : { - "val" : "A chemical substance is a portion of matter of constant composition, composed of molecular entities of the same type or of different types.", - "xrefs" : [ ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/chebi#3_STAR" ], - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "Chemische Substanz", - "xrefs" : [ "ChEBI" ] - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "chebi_ontology" - } ] - }, - "type" : "CLASS", - "lbl" : "chemical substance" }, { "id" : "http://purl.obolibrary.org/obo/GO_0038023", "meta" : { @@ -25243,15 +24364,6 @@ }, "type" : "CLASS", "lbl" : "scarred" - }, { - "id" : "http://purl.obolibrary.org/obo/chebi#3_STAR", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", - "val" : "Manually annotated by ChEBI Team" - } ] - }, - "type" : "PROPERTY" }, { "id" : "http://purl.obolibrary.org/obo/PATO_0000539", "meta" : { @@ -26085,17 +25197,6 @@ }, "type" : "CLASS", "lbl" : "obsolete thermoinsensitive" - }, { - "id" : "http://purl.obolibrary.org/obo/NCBITaxon_207598", - "meta" : { - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "Homo/Pan/Gorilla group", - "xrefs" : [ ] - } ] - }, - "type" : "CLASS", - "lbl" : "Homininae" }, { "id" : "http://purl.obolibrary.org/obo/PATO_0001885", "meta" : { @@ -26277,17 +25378,6 @@ }, "type" : "CLASS", "lbl" : "obsolete absolute temperature sensitivity value" - }, { - "id" : "http://purl.obolibrary.org/obo/NCBITaxon_117571", - "meta" : { - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "bony vertebrates", - "xrefs" : [ ] - } ] - }, - "type" : "CLASS", - "lbl" : "Euteleostomi" }, { "id" : "http://purl.obolibrary.org/obo/PATO_0001880", "meta" : { @@ -26348,10 +25438,6 @@ }, "type" : "CLASS", "lbl" : "obsolete u v light sensitivity value" - }, { - "id" : "http://purl.obolibrary.org/obo/NCBITaxon_117570", - "type" : "CLASS", - "lbl" : "Teleostomi" }, { "id" : "http://purl.obolibrary.org/obo/PATO_0001817", "meta" : { @@ -26718,25 +25804,6 @@ }, "type" : "CLASS", "lbl" : "increased wetness" - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0010000", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Person:Alan Ruttenberg" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "Person:Alan Ruttenberg" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "has axiom id" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", - "val" : "A URI that is intended to be unique label for an axiom used for tracking change to the ontology. For an axiom expressed in different languages, each expression is given the same URI" - } ] - }, - "type" : "PROPERTY", - "lbl" : "has axiom label" }, { "id" : "http://purl.obolibrary.org/obo/PATO_0001822", "meta" : { @@ -27514,25 +26581,6 @@ }, "type" : "CLASS", "lbl" : "tolerant to" - }, { - "id" : "http://purl.obolibrary.org/obo/PO_0025131", - "meta" : { - "definition" : { - "val" : "An anatomical entity that is or was part of a plant.", - "xrefs" : [ ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "entidad anatómica vegetal (Spanish, exact)", - "xrefs" : [ ] - }, { - "pred" : "hasExactSynonym", - "val" : "植物 解剖学（形態）的実体 (Japanese, exact)", - "xrefs" : [ ] - } ] - }, - "type" : "CLASS", - "lbl" : "plant anatomical entity" }, { "id" : "http://purl.obolibrary.org/obo/PATO_0001806", "meta" : { @@ -27722,33 +26770,6 @@ } ] }, "type" : "PROPERTY" - }, { - "id" : "http://purl.obolibrary.org/obo/NCBITaxon_33213", - "type" : "CLASS", - "lbl" : "Bilateria" - }, { - "id" : "http://purl.obolibrary.org/obo/NCBITaxon_33208", - "meta" : { - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "multicellular animals", - "xrefs" : [ ] - }, { - "pred" : "hasExactSynonym", - "val" : "metazoans", - "xrefs" : [ ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "Animalia", - "xrefs" : [ ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "animals", - "xrefs" : [ ] - } ] - }, - "type" : "CLASS", - "lbl" : "Metazoa" }, { "id" : "http://purl.obolibrary.org/obo/CARO_0030000", "type" : "CLASS", @@ -28045,42 +27066,6 @@ }, "type" : "CLASS", "lbl" : "semi erect" - }, { - "id" : "http://purl.obolibrary.org/obo/CHEBI_46662", - "meta" : { - "definition" : { - "val" : "In general, a mineral is a chemical substance that is normally crystalline formed and has been formed as a result of geological processes. The term also includes metamict substances (naturally occurring, formerly crystalline substances whose crystallinity has been destroyed by ionising radiation) and can include naturally occurring amorphous substances that have never been crystalline ('mineraloids') such as georgite and calciouranoite as well as substances formed by the action of geological processes on bigenic compounds ('biogenic minerals').", - "xrefs" : [ ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/chebi#3_STAR" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "mineral", - "xrefs" : [ "ChEBI" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "minerals", - "xrefs" : [ "ChEBI" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "mineraux", - "xrefs" : [ "ChEBI" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "Minerale", - "xrefs" : [ "ChEBI" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "minerales", - "xrefs" : [ "ChEBI" ] - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "chebi_ontology" - } ] - }, - "type" : "CLASS", - "lbl" : "mineral" }, { "id" : "http://purl.obolibrary.org/obo/GO_0005102", "meta" : { @@ -29638,17 +28623,6 @@ "lbl" : "increased_in_magnitude_relative_to" }, { "id" : "http://purl.obolibrary.org/obo/ENVO_01000254", - "meta" : { - "definition" : { - "val" : "A system which has the disposition to environ one or more material entities.", - "xrefs" : [ "DOI:10.1186/2041-1480-4-43" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "environment", - "xrefs" : [ ] - } ] - }, "type" : "CLASS", "lbl" : "environmental system" }, { @@ -29659,13 +28633,7 @@ "xrefs" : [ ] }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "RO:0002180" - } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "has_component" - }, { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" }, { @@ -29674,9 +28642,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit." - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity." @@ -30347,11 +29312,6 @@ "val" : "A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities", "xrefs" : [ "PATOC:GVG" ] }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "trait", - "xrefs" : [ ] - } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", "val" : "quality (PATO)" @@ -31104,7 +30064,7 @@ "id" : "http://purl.obolibrary.org/obo/RO_0002264", "meta" : { "definition" : { - "val" : "c acts upstream of or within p if c is enables 'p' and p' causally upstream of or within p", + "val" : "c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process.", "xrefs" : [ ] }, "synonyms" : [ { @@ -31349,18 +30309,9 @@ "val" : "Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p", "xrefs" : [ ] }, - "xrefs" : [ { - "val" : "RO:0002258" - } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Chris Mungall" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "developmentally_preceded_by" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", "val" : "This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from" @@ -31497,24 +30448,15 @@ "val" : "x has developmental contribution from y iff x has some part z such that z develops from y", "xrefs" : [ ] }, - "xrefs" : [ { - "val" : "RO:0002254" - } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Chris Mungall" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "has_developmental_contribution_from" } ] }, "type" : "PROPERTY", @@ -31536,25 +30478,16 @@ "xrefs" : [ ] }, "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], - "xrefs" : [ { - "val" : "RO:0002255" - } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "developmentally_contributes_to" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Chris Mungall" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" } ] }, "type" : "PROPERTY", - "lbl" : "developmentally_contributes_to" + "lbl" : "developmentally contributes to" }, { "id" : "http://purl.obolibrary.org/obo/PATO_0002628", "meta" : { @@ -31912,7 +30845,7 @@ "id" : "http://purl.obolibrary.org/obo/RO_0002233", "meta" : { "definition" : { - "val" : "p has direct input c iff c is a participant in p, c is present at the start of p, and the state of c is modified during p.", + "val" : "p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p.", "xrefs" : [ ] }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], @@ -32135,9 +31068,6 @@ }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", "val" : "A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations." - }, { - "pred" : "http://purl.org/dc/elements/1.1/source", - "val" : "https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1" }, { "pred" : "http://purl.org/dc/terms/source", "val" : "https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1" @@ -32225,9 +31155,6 @@ "xrefs" : [ ] }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Chris Mungall" }, { @@ -32266,7 +31193,7 @@ } ] }, "type" : "PROPERTY", - "lbl" : "has active participant" + "lbl" : "obsolete has active participant" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002213", "meta" : { @@ -32340,30 +31267,18 @@ "xrefs" : [ ] }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "RO:0002215" - } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "For compatibility with BFO, this relation has a shortcut definition in which the expression \"capable of some P\" expands to \"bearer_of (some realized_by only P)\"." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/21208450" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "has function realized in" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "capable_of" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "osteoclast SubClassOf 'capable of' some 'bone resorption'" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", "val" : "RO_0000053 some (RO_0000054 only ?Y)" @@ -32402,24 +31317,12 @@ "val" : "c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p.", "xrefs" : [ ] }, - "xrefs" : [ { - "val" : "RO:0002216" - } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "has function in" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "capable_of_part_of" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Chris Mungall" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", "val" : "RO_0000053 some (RO_0000054 only (BFO_0000050 some ?Y))" @@ -32541,9 +31444,6 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "negatively_regulates" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", "val" : "negatively regulates (process to process)" @@ -32618,18 +31518,12 @@ "val" : "x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y", "xrefs" : [ ] }, - "xrefs" : [ { - "val" : "RO:0002202" - } ], "basicPropertyValues" : [ { "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", "val" : "This is the transitive form of the develops from relation" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "David Osumi-Sutherland" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "develops_from" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Terry Meehan" @@ -32639,9 +31533,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Melissa Haendel" @@ -32670,21 +31561,12 @@ "xrefs" : [ ] }, "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], - "xrefs" : [ { - "val" : "RO:0002203" - } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "develops_into" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Chris Mungall" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "David Osumi-Sutherland" @@ -32897,21 +31779,6 @@ "id" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "type" : "PROPERTY", "lbl" : "has_obo_namespace" - }, { - "id" : "http://purl.obolibrary.org/obo/NCBITaxon_40674", - "meta" : { - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "mammals", - "xrefs" : [ ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "mammals", - "xrefs" : [ ] - } ] - }, - "type" : "CLASS", - "lbl" : "Mammalia" }, { "id" : "http://purl.obolibrary.org/obo/GO_0060089", "meta" : { @@ -33480,17 +32347,6 @@ }, "type" : "CLASS", "lbl" : "obsolete relative neurobehavioral function value" - }, { - "id" : "http://purl.obolibrary.org/obo/NCBITaxon_1437010", - "meta" : { - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "Boreotheria", - "xrefs" : [ ] - } ] - }, - "type" : "CLASS", - "lbl" : "Boreoeutheria" }, { "id" : "http://purl.obolibrary.org/obo/PATO_0000804", "meta" : { @@ -33644,6 +32500,32 @@ }, "type" : "CLASS", "lbl" : "obsolete reflex value" + }, { + "id" : "http://purl.obolibrary.org/obo/PATO_0040027", + "meta" : { + "definition" : { + "val" : "A ploidy quality inhering in a bearer by virtue of the bearer's haploid cells undergo chromosome doubling.", + "xrefs" : [ "Wikipedia:https://en.wikipedia.org/wiki/Doubled_haploidy" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "double-haploid", + "xrefs" : [ ] + }, { + "pred" : "hasExactSynonym", + "val" : "double haploid", + "xrefs" : [ ] + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "quality" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "http://orcid.org/0000-0001-5208-3432" + } ] + }, + "type" : "CLASS", + "lbl" : "doubled haploid" }, { "id" : "http://purl.obolibrary.org/obo/PATO_0000807", "meta" : { @@ -34270,17 +33152,6 @@ }, "type" : "CLASS", "lbl" : "obsolete quinine taste" - }, { - "id" : "http://purl.obolibrary.org/obo/NCBITaxon_33511", - "meta" : { - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "deuterostomes", - "xrefs" : [ ] - } ] - }, - "type" : "CLASS", - "lbl" : "Deuterostomia" }, { "id" : "http://purl.obolibrary.org/obo/PATO_0040012", "meta" : { @@ -34690,16 +33561,6 @@ }, "type" : "CLASS", "lbl" : "increased porosity" - }, { - "id" : "http://purl.obolibrary.org/obo/ENVO_01000997", - "meta" : { - "definition" : { - "val" : "An environmental system which is determined by materials bearing roughly homogeneous qualities.", - "xrefs" : [ ] - } - }, - "type" : "CLASS", - "lbl" : "environmental system determined by a quality" }, { "id" : "http://purl.obolibrary.org/obo/PATO_0015021", "meta" : { @@ -34715,16 +33576,6 @@ }, "type" : "CLASS", "lbl" : "combustibility" - }, { - "id" : "http://purl.obolibrary.org/obo/ENVO_01000998", - "meta" : { - "definition" : { - "val" : "An environmental system within which an environmental material strongly influences the system's composition and properties.", - "xrefs" : [ ] - } - }, - "type" : "CLASS", - "lbl" : "environmental system determined by a material" }, { "id" : "http://purl.obolibrary.org/obo/PATO_0015022", "meta" : { @@ -36395,33 +35246,6 @@ }, "type" : "CLASS", "lbl" : "desaturated yellow" - }, { - "id" : "http://purl.obolibrary.org/obo/NCBITaxon_9347", - "meta" : { - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "Placentalia", - "xrefs" : [ ] - }, { - "pred" : "hasExactSynonym", - "val" : "placentals", - "xrefs" : [ ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "placentals", - "xrefs" : [ ] - }, { - "pred" : "hasExactSynonym", - "val" : "placental mammals", - "xrefs" : [ ] - }, { - "pred" : "hasExactSynonym", - "val" : "eutherian mammals", - "xrefs" : [ ] - } ] - }, - "type" : "CLASS", - "lbl" : "Eutheria" }, { "id" : "http://purl.obolibrary.org/obo/PATO_0001287", "meta" : { @@ -37082,25 +35906,6 @@ "type" : "PROPERTY" }, { "id" : "http://purl.obolibrary.org/obo/IAO_0100001", - "meta" : { - "definition" : { - "val" : "Add as annotation triples in the granting ontology", - "xrefs" : [ ] - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Person:Alan Ruttenberg" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "Person:Alan Ruttenberg" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "term replaced by" - } ] - }, "type" : "PROPERTY", "lbl" : "term replaced by" }, { @@ -37110,21 +35915,12 @@ "val" : "x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y", "xrefs" : [ ] }, - "xrefs" : [ { - "val" : "RO:0002385" - } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000428" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Chris Mungall" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "has_potential_to_developmentally_contribute_to" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" } ] }, "type" : "PROPERTY", @@ -37159,6 +35955,21 @@ }, "type" : "CLASS", "lbl" : "dark green" + }, { + "id" : "http://purl.obolibrary.org/obo/PATO_0001246", + "meta" : { + "definition" : { + "val" : "A color consisting of brown hue and high brightness.", + "xrefs" : [ "PATOC:GVG" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/pato#mpath_slim", "http://purl.obolibrary.org/obo/pato#value_slim" ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "quality" + } ] + }, + "type" : "CLASS", + "lbl" : "light brown" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002387", "meta" : { @@ -37166,16 +35977,7 @@ "val" : "x has the potential to develop into y iff x develops into y or if x is capable of developing into y", "xrefs" : [ ] }, - "xrefs" : [ { - "val" : "RO:0002387" - } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "has_potential_to_develop_into" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Chris Mungall" }, { @@ -37185,21 +35987,6 @@ }, "type" : "PROPERTY", "lbl" : "has potential to develop into" - }, { - "id" : "http://purl.obolibrary.org/obo/PATO_0001246", - "meta" : { - "definition" : { - "val" : "A color consisting of brown hue and high brightness.", - "xrefs" : [ "PATOC:GVG" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/pato#mpath_slim", "http://purl.obolibrary.org/obo/pato#value_slim" ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "quality" - } ] - }, - "type" : "CLASS", - "lbl" : "light brown" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002388", "meta" : { @@ -37207,21 +35994,12 @@ "val" : "x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y", "xrefs" : [ ] }, - "xrefs" : [ { - "val" : "RO:0002388" - } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Chris Mungall" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000428" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "has_potential_to_directly_develop_into" } ] }, "type" : "PROPERTY", @@ -37962,27 +36740,18 @@ "val" : "a relation between two independent continuants, the target and the location, in which the target is entirely within the location", "xrefs" : [ ] }, - "xrefs" : [ { - "val" : "RO:0001025" - } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "located in" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "my brain is located in my head" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "located_in" }, { "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" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "this rat is located in this cage" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://purl.org/dc/elements/1.1/source", "val" : "http://www.obofoundry.org/ro/#OBO_REL:located_in" @@ -37998,7 +36767,7 @@ } ] }, "type" : "PROPERTY", - "lbl" : "located_in" + "lbl" : "located in" }, { "id" : "http://purl.obolibrary.org/obo/PATO_0002510", "meta" : { @@ -38028,18 +36797,9 @@ "xrefs" : [ ] }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco", "http://purl.obolibrary.org/obo/RO_0002259" ], - "xrefs" : [ { - "val" : "RO:0002352" - } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Chris Mungall" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "input_of" } ] }, "type" : "PROPERTY", @@ -38073,18 +36833,9 @@ "xrefs" : [ ] }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco", "http://purl.obolibrary.org/obo/RO_0002259" ], - "xrefs" : [ { - "val" : "RO:0002353" - } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "output_of" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Chris Mungall" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" } ] }, "type" : "PROPERTY", @@ -38207,18 +36958,9 @@ "val" : "is member of is a mereological relation between a item and a collection.", "xrefs" : [ ] }, - "xrefs" : [ { - "val" : "RO:0002350" - } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "is member of" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "member_of" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "An organism that is a member of a population of organisms" @@ -38270,21 +37012,12 @@ "val" : "has member is a mereological relation between a collection and an item.", "xrefs" : [ ] }, - "xrefs" : [ { - "val" : "RO:0002351" - } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "SIO" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "has_member" } ] }, "type" : "PROPERTY", @@ -38347,21 +37080,12 @@ "id" : "http://purl.obolibrary.org/obo/RO_0001019", "meta" : { "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "RO:0001019" - } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "contains" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "contains" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" } ] }, "type" : "PROPERTY", @@ -38419,24 +37143,15 @@ "val" : "a relation between two independent continuants, the location and the target, in which the target is entirely within the location", "xrefs" : [ ] }, - "xrefs" : [ { - "val" : "RO:0001015" - } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "this cage is the location of this rat" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "location_of" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "location_of" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "is location of" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Most location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime" @@ -38449,7 +37164,7 @@ } ] }, "type" : "PROPERTY", - "lbl" : "location_of" + "lbl" : "location of" }, { "id" : "http://purl.obolibrary.org/obo/pato#hpo_slim", "meta" : { @@ -38895,31 +37610,6 @@ }, "type" : "CLASS", "lbl" : "obsolete episodic" - }, { - "id" : "http://purl.obolibrary.org/obo/ENVO_01000952", - "meta" : { - "definition" : { - "val" : "A process during which a natural environmental system is altered by human action.", - "xrefs" : [ "https://en.wikipedia.org/wiki/Anthropization" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "anthropization", - "xrefs" : [ ] - } ] - }, - "type" : "CLASS", - "lbl" : "anthropisation" - }, { - "id" : "http://purl.obolibrary.org/obo/ENVO_01000951", - "meta" : { - "definition" : { - "val" : "An environmental system in which minimal to no anthropisation has occurred and non-human agents are the primary determinants of the system's dynamics and composition.", - "xrefs" : [ "https://en.wikipedia.org/wiki/Anthropization", "https://en.wikipedia.org/wiki/Natural_environment" ] - } - }, - "type" : "CLASS", - "lbl" : "natural environment" }, { "id" : "http://purl.obolibrary.org/obo/PATO_0000763", "meta" : { @@ -39198,21 +37888,12 @@ "val" : "A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities.", "xrefs" : [ ] }, - "xrefs" : [ { - "val" : "RO:0002328" - } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "This is a grouping relation that collects relations used for the purpose of connecting structure and function" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Chris Mungall" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "functionally_related_to" } ] }, "type" : "PROPERTY", @@ -39224,18 +37905,9 @@ "val" : "this relation holds between c and p when c is part of some c', and c' is capable of p.", "xrefs" : [ ] }, - "xrefs" : [ { - "val" : "RO:0002329" - } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Chris Mungall" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "part_of_structure_that_is_capable_of" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "false" @@ -39521,10 +38193,6 @@ }, "type" : "CLASS", "lbl" : "aversion" - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000002", - "type" : "INDIVIDUAL", - "lbl" : "example to be eventually removed" }, { "id" : "http://purl.obolibrary.org/obo/PATO_0000785", "meta" : { @@ -39612,9 +38280,6 @@ }, { "pred" : "http://purl.org/dc/terms/creator", "val" : "cjm" - }, { - "pred" : "http://purl.org/dc/elements/1.1/creator", - "val" : "cjm" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", "val" : "holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y" @@ -39686,9 +38351,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0004049", "val" : "http://purl.obolibrary.org/obo/RO_0002411" - }, { - "pred" : "http://purl.org/dc/elements/1.1/creator", - "val" : "cjm" } ] }, "type" : "PROPERTY", @@ -39852,10 +38514,6 @@ }, "type" : "CLASS", "lbl" : "obsolete immubocompetent value" - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000027", - "type" : "CLASS", - "lbl" : "data item" }, { "id" : "http://purl.obolibrary.org/obo/PATO_0000727", "meta" : { @@ -40529,21 +39187,6 @@ }, "type" : "CLASS", "lbl" : "obsolete learning and memory value" - }, { - "id" : "http://purl.obolibrary.org/obo/NCBITaxon_1", - "meta" : { - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "all", - "xrefs" : [ ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "all", - "xrefs" : [ ] - } ] - }, - "type" : "CLASS", - "lbl" : "root" }, { "id" : "http://purl.obolibrary.org/obo/GO_0050789", "meta" : { @@ -40944,8 +39587,7 @@ "val" : "http://purl.obolibrary.org/obo/GO_0038023" } ] }, - "type" : "CLASS", - "lbl" : "receptor activity" + "type" : "CLASS" }, { "id" : "http://purl.obolibrary.org/obo/PATO_0000719", "meta" : { @@ -41050,16 +39692,6 @@ }, "type" : "CLASS", "lbl" : "molecular function regulator" - }, { - "id" : "http://purl.obolibrary.org/obo/ENVO_00002297", - "meta" : { - "definition" : { - "val" : "A material entity which determines an environmental system.", - "xrefs" : [ "DOI:10.1186/2041-1480-4-43", "NM:nm", "ORCID:0000-0002-4366-3088" ] - } - }, - "type" : "CLASS", - "lbl" : "environmental feature" }, { "id" : "http://purl.obolibrary.org/obo/PATO_0001174", "meta" : { @@ -41551,22 +40183,6 @@ }, "type" : "CLASS", "lbl" : "medial to" - }, { - "id" : "http://purl.org/dc/elements/1.1/source", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "dc-source" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", - "val" : "true" - } ] - }, - "type" : "PROPERTY", - "lbl" : "derived from resource" }, { "id" : "http://purl.obolibrary.org/obo/PATO_0002469", "meta" : { @@ -41993,58 +40609,6 @@ }, "type" : "CLASS", "lbl" : "obsolete relative resistance value" - }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0001062", - "meta" : { - "definition" : { - "val" : "Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species.", - "xrefs" : [ "http://orcid.org/0000-0001-9114-8737", "FMA:62955" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], - "xrefs" : [ { - "val" : "NCIT:C12219" - }, { - "val" : "HAO:0000000" - }, { - "val" : "TAO:0100000" - }, { - "val" : "CARO:0000000" - }, { - "val" : "FBbt:10000000" - }, { - "val" : "AAO:0010841" - }, { - "val" : "EHDAA2:0002229" - }, { - "val" : "AEO:0000000" - }, { - "val" : "FMA:62955" - }, { - "val" : "WBbt:0000100" - }, { - "val" : "ZFA:0100000" - }, { - "val" : "XAO:0000000" - }, { - "val" : "TGMA:0001822" - }, { - "val" : "BIRNLEX:6" - }, { - "val" : "BILA:0000000" - }, { - "val" : "FBbt_root:00000000" - }, { - "val" : "UMLS:C1515976" - }, { - "val" : "MA:0000001" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] - }, - "type" : "CLASS", - "lbl" : "anatomical entity" }, { "id" : "http://purl.obolibrary.org/obo/PATO_0002472", "meta" : { @@ -44463,21 +43027,6 @@ }, "type" : "CLASS", "lbl" : "obsolete digestive function" - }, { - "id" : "http://purl.obolibrary.org/obo/NCBITaxon_131567", - "meta" : { - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "biota", - "xrefs" : [ ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "biota", - "xrefs" : [ ] - } ] - }, - "type" : "CLASS", - "lbl" : "cellular organisms" }, { "id" : "http://purl.obolibrary.org/obo/PATO_0001534", "meta" : { @@ -45219,9 +43768,6 @@ "xrefs" : [ ] }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "RO:0002473" - } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate'" @@ -45231,15 +43777,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Chris Mungall" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "composed_primarily_of" } ] }, "type" : "PROPERTY", @@ -45603,21 +44143,6 @@ }, "type" : "CLASS", "lbl" : "increased sensitivity of a process" - }, { - "id" : "http://purl.obolibrary.org/obo/NCBITaxon_314295", - "meta" : { - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "ape", - "xrefs" : [ ] - }, { - "pred" : "hasExactSynonym", - "val" : "apes", - "xrefs" : [ ] - } ] - }, - "type" : "CLASS", - "lbl" : "Hominoidea" }, { "id" : "http://purl.obolibrary.org/obo/GO_0005488", "meta" : { @@ -45712,9 +44237,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000428" } ] }, "type" : "PROPERTY", @@ -45831,17 +44353,6 @@ } ] }, "type" : "CLASS" - }, { - "id" : "http://purl.obolibrary.org/obo/NCBITaxon_314293", - "meta" : { - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "Anthropoidea", - "xrefs" : [ ] - } ] - }, - "type" : "CLASS", - "lbl" : "Simiiformes" }, { "id" : "http://purl.obolibrary.org/obo/PATO_0001560", "meta" : { @@ -46016,22 +44527,6 @@ "lbl" : "obsolete taste" }, { "id" : "http://purl.obolibrary.org/obo/CARO_0001010", - "meta" : { - "definition" : { - "val" : "Material anatomical entity that is a member of an individual species or is a viral or viroid particle.", - "xrefs" : [ ] - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_creation_date", - "val" : "9/18/11" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_created_by", - "val" : "Melissa Haendel" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "organism or virus" - } ] - }, "type" : "CLASS", "lbl" : "organism or virus or viroid" }, { @@ -46096,7 +44591,7 @@ } ] }, "type" : "PROPERTY", - "lbl" : "molecularly decreases activity of" + "lbl" : "activity directly negatively regulates activity of" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002447", "meta" : { @@ -46116,34 +44611,9 @@ }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000116", "meta" : { - "definition" : { - "val" : "An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology.", - "xrefs" : [ ] - }, - "xrefs" : [ { - "val" : "IAO:0000116" - } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "editor_note" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "editor note" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000122" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "GROUP:OBI:" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "PERSON:Daniel Schober" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", - "val" : "true" } ] }, "type" : "PROPERTY", @@ -46151,71 +44621,21 @@ }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000117", "meta" : { - "definition" : { - "val" : "Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people", - "xrefs" : [ ] - }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "term editor" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "20110707, MC: label update to term editor and definition modified accordingly. See http://code.google.com/p/information-artifact-ontology/issues/detail?id=115." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "PERSON:Daniel Schober" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000122" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "GROUP:OBI:" } ] }, "type" : "PROPERTY", "lbl" : "term editor" }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000114", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "PERSON:Melanie Courtot" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "PERSON:Bill Bug" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "has curation status" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "OBI_0000281" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "PERSON:Alan Ruttenberg" - } ] - }, "type" : "PROPERTY", "lbl" : "has curation status" }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000115", "meta" : { - "definition" : { - "val" : "The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.", - "xrefs" : [ ] - }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "definition" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "PERSON:Daniel Schober" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "GROUP:OBI:" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "2012-04-05: \nBarry Smith\n\nThe official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible.\n\nCan you fix to something like:\n\nA statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property.\n\nAlan Ruttenberg\n\nYour proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. \n\nOn the specifics of the proposed definition:\n\nWe don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. \n\nPersonally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. \n\nWe also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. " - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000122" } ] @@ -46225,59 +44645,15 @@ }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000112", "meta" : { - "definition" : { - "val" : "A phrase describing how a class name should be used. May also include other kinds of examples that facilitate immediate understanding of a class semantics, such as widely known prototypical subclasses or instances of the class. Although essential for high level terms, examples for low level terms (e.g., Affymetrix HU133 array) are not", - "xrefs" : [ ] - }, - "xrefs" : [ { - "val" : "IAO:0000112" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "GROUP:OBI:" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "example_of_usage" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "example" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", - "val" : "true" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000122" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "PERSON:Daniel Schober" } ] }, "type" : "PROPERTY", "lbl" : "example of usage" }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000111", - "meta" : { - "definition" : { - "val" : "The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English)", - "xrefs" : [ ] - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000122" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "PERSON:Daniel Schober" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "GROUP:OBI:" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "editor preferred term" - } ] - }, "type" : "PROPERTY", "lbl" : "editor preferred term" }, { @@ -46328,22 +44704,9 @@ }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000118", "meta" : { - "definition" : { - "val" : "An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent)", - "xrefs" : [ ] - }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "alternative term" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "GROUP:OBI:" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "PERSON:Daniel Schober" } ] }, "type" : "PROPERTY", @@ -46351,23 +44714,7 @@ }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000119", "meta" : { - "definition" : { - "val" : "formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007", - "xrefs" : [ ] - }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "PERSON:Daniel Schober" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "definition source" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "GROUP:OBI:" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000122" } ] @@ -46508,16 +44855,6 @@ }, "type" : "CLASS", "lbl" : "complex" - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000120", - "meta" : { - "definition" : { - "val" : "Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete.", - "xrefs" : [ ] - } - }, - "type" : "INDIVIDUAL", - "lbl" : "metadata complete" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002434", "meta" : { @@ -46582,10 +44919,6 @@ }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000125", "meta" : { - "definition" : { - "val" : "All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor.", - "xrefs" : [ ] - }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" @@ -46593,43 +44926,9 @@ }, "type" : "INDIVIDUAL", "lbl" : "pending final vetting" - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000123", - "meta" : { - "definition" : { - "val" : "Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors.", - "xrefs" : [ ] - } - }, - "type" : "INDIVIDUAL", - "lbl" : "metadata incomplete" - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000124", - "meta" : { - "definition" : { - "val" : "Nothing done yet beyond assigning a unique class ID and proposing a preferred term.", - "xrefs" : [ ] - } - }, - "type" : "INDIVIDUAL", - "lbl" : "uncurated" - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000121", - "meta" : { - "definition" : { - "val" : "term created to ease viewing/sort terms for development purpose, and will not be included in a release", - "xrefs" : [ ] - } - }, - "type" : "INDIVIDUAL", - "lbl" : "organizational term" }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000122", "meta" : { - "definition" : { - "val" : "Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking \"ready_for_release\" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed \"ready_for_release\" will also derived from a chain of ancestor classes that are also \"ready_for_release.\"", - "xrefs" : [ ] - }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" @@ -46667,15 +44966,6 @@ }, "type" : "CLASS", "lbl" : "sound quality" - }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#upper_level", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", - "val" : "abstract upper-level terms not directly useful for analysis" - } ] - }, - "type" : "PROPERTY" }, { "id" : "http://purl.obolibrary.org/obo/PATO_0001512", "meta" : { @@ -46927,7 +45217,7 @@ "id" : "http://purl.obolibrary.org/obo/RO_0002428", "meta" : { "definition" : { - "val" : "c involved in regulation of p if c is involved in some 'p' and p' regulates some p", + "val" : "c involved in regulation of p if c is involved in some p' and p' regulates some p", "xrefs" : [ ] }, "basicPropertyValues" : [ { @@ -46954,6 +45244,10 @@ }, "type" : "PROPERTY", "lbl" : "involved in positive regulation of" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002423", + "type" : "PROPERTY", + "lbl" : "logical macro assertion on an annotation property" }, { "id" : "http://purl.obolibrary.org/obo/PATO_0001529", "meta" : { @@ -47241,25 +45535,6 @@ }, "type" : "PROPERTY", "lbl" : "immediately causally downstream of" - }, { - "id" : "http://purl.obolibrary.org/obo/NCBITaxon_7742", - "meta" : { - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "Vertebrata", - "xrefs" : [ ] - }, { - "pred" : "hasExactSynonym", - "val" : "vertebrates", - "xrefs" : [ ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "vertebrates", - "xrefs" : [ ] - } ] - }, - "type" : "CLASS", - "lbl" : "Vertebrata " }, { "id" : "http://www.geneontology.org/formats/oboInOwl#hasDbXref", "type" : "PROPERTY", @@ -47409,49 +45684,6 @@ }, "type" : "CLASS", "lbl" : "ventralized" - }, { - "id" : "http://purl.obolibrary.org/obo/NCBITaxon_7711", - "meta" : { - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "chordates", - "xrefs" : [ ] - }, { - "pred" : "hasExactSynonym", - "val" : "chordates", - "xrefs" : [ ] - } ] - }, - "type" : "CLASS", - "lbl" : "Chordata" - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000103", - "meta" : { - "definition" : { - "val" : "The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job", - "xrefs" : [ ] - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Person:Alan Ruttenberg" - } ] - }, - "type" : "INDIVIDUAL", - "lbl" : "failed exploratory term" - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000102", - "meta" : { - "definition" : { - "val" : "data about an ontology part is a data item about a part of an ontology, for example a term", - "xrefs" : [ ] - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Person:Alan Ruttenberg" - } ] - }, - "type" : "CLASS", - "lbl" : "data about an ontology part" }, { "id" : "http://purl.obolibrary.org/obo/GO_0048585", "meta" : { @@ -47799,35 +46031,6 @@ }, "type" : "CLASS", "lbl" : "plumose" - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000078", - "meta" : { - "definition" : { - "val" : "The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value.", - "xrefs" : [ ] - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "GROUP:OBI:" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "curation status specification" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "PERSON:Bill Bug" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "OBI_0000266" - } ] - }, - "type" : "CLASS", - "lbl" : "curation status specification" }, { "id" : "http://purl.obolibrary.org/obo/pato#cell_quality", "meta" : { @@ -47837,21 +46040,6 @@ } ] }, "type" : "PROPERTY" - }, { - "id" : "http://purl.obolibrary.org/obo/NCBITaxon_7776", - "meta" : { - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "jawed vertebrates", - "xrefs" : [ ] - }, { - "pred" : "hasExactSynonym", - "val" : "Gnathostomata", - "xrefs" : [ ] - } ] - }, - "type" : "CLASS", - "lbl" : "Gnathostomata " }, { "id" : "http://www.geneontology.org/formats/oboInOwl#consider", "type" : "PROPERTY", @@ -47961,10 +46149,6 @@ }, "type" : "CLASS", "lbl" : "unicuspidate" - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000030", - "type" : "CLASS", - "lbl" : "information content entity" }, { "id" : "http://purl.obolibrary.org/obo/pato#value_slim", "meta" : { @@ -48437,10 +46621,6 @@ "id" : "http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym", "type" : "PROPERTY", "lbl" : "has_narrow_synonym" - }, { - "id" : "http://purl.obolibrary.org/obo/NCBITaxon_9526", - "type" : "CLASS", - "lbl" : "Catarrhini" }, { "id" : "http://purl.obolibrary.org/obo/GO_0048523", "meta" : { @@ -49134,7 +47314,7 @@ "id" : "http://purl.obolibrary.org/obo/PATO_0045075", "meta" : { "definition" : { - "val" : "A variability which is relatively normal or average", + "val" : "A variability of color which is relatively normal or average", "xrefs" : [ ] }, "subsets" : [ "http://purl.obolibrary.org/obo/pato#value_slim" ], @@ -50474,69 +48654,6 @@ }, "type" : "CLASS", "lbl" : "aerobic (for occurrence)" - }, { - "id" : "http://purl.obolibrary.org/obo/NCBITaxon_2759", - "meta" : { - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "eukaryotes", - "xrefs" : [ ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "Eucarya", - "xrefs" : [ ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "Eucaryotae", - "xrefs" : [ ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "eukaryotes", - "xrefs" : [ ] - }, { - "pred" : "hasExactSynonym", - "val" : "eucaryotes", - "xrefs" : [ ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "Eukarya", - "xrefs" : [ ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "Eukaryotae", - "xrefs" : [ ] - }, { - "pred" : "hasExactSynonym", - "val" : "eucaryotes", - "xrefs" : [ ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "Eucaryotae", - "xrefs" : [ ] - }, { - "pred" : "hasExactSynonym", - "val" : "eukaryotes", - "xrefs" : [ ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "Eukaryotae", - "xrefs" : [ ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "eukaryotes", - "xrefs" : [ ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "Eucarya", - "xrefs" : [ ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "Eukarya", - "xrefs" : [ ] - } ] - }, - "type" : "CLASS", - "lbl" : "Eukaryota" }, { "id" : "http://purl.obolibrary.org/obo/PATO_0001450", "meta" : { @@ -51556,25 +49673,16 @@ "xrefs" : [ ] }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "RO:0003001" - } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "produced_by" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Melissa Haendel" } ] }, "type" : "PROPERTY", - "lbl" : "produced_by" + "lbl" : "produced by" }, { "id" : "http://purl.obolibrary.org/obo/PATO_0000146", "meta" : { @@ -51663,18 +49771,9 @@ "xrefs" : [ ] }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "RO:0003000" - } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "produces" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Melissa Haendel" @@ -51730,21 +49829,6 @@ }, "type" : "CLASS", "lbl" : "decreased depth" - }, { - "id" : "http://purl.obolibrary.org/obo/ENVO_00010483", - "meta" : { - "definition" : { - "val" : "A portion of environmental material is a fiat object which forms the medium or part of the medium of an environmental system.", - "xrefs" : [ "DOI:10.1186/2041-1480-4-43", "MA:ma", "ORCID:0000-0002-4366-3088", "URL:http://ontology.buffalo.edu/smith/articles/niches.html" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "portion of environmental material", - "xrefs" : [ ] - } ] - }, - "type" : "CLASS", - "lbl" : "environmental material" }, { "id" : "http://purl.obolibrary.org/obo/PATO_0000141", "meta" : { @@ -54168,26 +52252,6 @@ }, "type" : "CLASS", "lbl" : "negative regulation of signal transduction" - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000228", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use." - } ] - }, - "type" : "INDIVIDUAL", - "lbl" : "term imported" - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000229", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created." - } ] - }, - "type" : "INDIVIDUAL", - "lbl" : "term split" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002575", "meta" : { @@ -54198,9 +52262,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "The general property hierarchy is:\n\n \"directly P\" SubPropertyOf \"P\"\n Transitive(P)\n\nWhere we have an annotation assertion\n\n \"directly P\" \"is direct form of\" \"P\"" - }, { - "pred" : "http://purl.org/dc/elements/1.1/creator", - "val" : "Chris Mungall" }, { "pred" : "http://purl.org/dc/terms/creator", "val" : "Chris Mungall" @@ -54257,58 +52318,16 @@ }, "type" : "PROPERTY", "lbl" : "causally influences" - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000231", - "meta" : { - "definition" : { - "val" : "Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification.", - "xrefs" : [ ] - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "PERSON:Melanie Courtot" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "has obsolescence reason" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "PERSON:Alan Ruttenberg" - } ] - }, - "type" : "PROPERTY", - "lbl" : "has obsolescence reason" }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000232", "meta" : { - "definition" : { - "val" : "An administrative note of use for a curator but of no use for a user", - "xrefs" : [ ] - }, - "xrefs" : [ { - "val" : "IAO:0000232" - } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "curator_notes" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "PERSON:Alan Ruttenberg" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "curator note" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", - "val" : "true" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000122" } ] }, "type" : "PROPERTY", - "lbl" : "curator notes" + "lbl" : "curator note" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002563", "meta" : { @@ -54492,22 +52511,6 @@ }, "type" : "CLASS", "lbl" : "nucleate quality" - }, { - "id" : "http://purl.org/dc/elements/1.1/creator", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", - "val" : "true" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "dc-creator" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] - }, - "type" : "PROPERTY", - "lbl" : "creator" }, { "id" : "http://purl.obolibrary.org/obo/PATO_0001405", "meta" : { @@ -55203,15 +53206,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "The label for this relation is probably too general for its restricted use, where the domain is a system. It may be relabeled in future" - }, { - "pred" : "http://purl.org/dc/elements/1.1/creator", - "val" : "Pier Buttigieg" }, { "pred" : "http://purl.org/dc/terms/creator", "val" : "Pier Buttigieg" - }, { - "pred" : "http://purl.org/dc/elements/1.1/creator", - "val" : "Chris Mungall" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", "val" : "determined by (system to material entity)" @@ -55397,63 +53394,6 @@ }, "type" : "CLASS", "lbl" : "obsolete inconsistent" - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000226", - "type" : "INDIVIDUAL", - "lbl" : "placeholder removed" - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000227", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "An editor note should explain what were the merged terms and the reason for the merge." - } ] - }, - "type" : "INDIVIDUAL", - "lbl" : "terms merged" - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000224", - "meta" : { - "definition" : { - "val" : "Core is an instance of a grouping of terms from an ontology or ontologies. It is used by the ontology to identify main classes.", - "xrefs" : [ ] - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "PERSON: Melanie Courtot" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "PERSON: Alan Ruttenberg" - } ] - }, - "type" : "INDIVIDUAL", - "lbl" : "core" - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000225", - "meta" : { - "definition" : { - "val" : "The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value.", - "xrefs" : [ ] - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "PERSON: Alan Ruttenberg" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "PERSON: Melanie Courtot" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "obsolescence reason specification" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - } ] - }, - "type" : "CLASS", - "lbl" : "obsolescence reason specification" }, { "id" : "http://purl.obolibrary.org/obo/PATO_0000925", "meta" : { @@ -56009,7 +53949,7 @@ "id" : "http://purl.obolibrary.org/obo/RO_0002608", "meta" : { "definition" : { - "val" : "Inverse of 'causal agent in'", + "val" : "Inverse of 'causal agent in process'", "xrefs" : [ ] }, "basicPropertyValues" : [ { @@ -56018,7 +53958,7 @@ } ] }, "type" : "PROPERTY", - "lbl" : "has causal agent" + "lbl" : "process has causal agent" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002609", "meta" : { @@ -56974,9 +54914,6 @@ }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "my brain is part of my body (continuant parthood, two material entities)" @@ -57089,9 +55026,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "this year has part this day (occurrent parthood)" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_cyclic", - "val" : "false" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" @@ -57104,9 +55038,6 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "chebi_ontology" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)\n\nA continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'." @@ -57128,9 +55059,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" } ] }, "type" : "PROPERTY", @@ -57219,25 +55147,6 @@ }, "type" : "CLASS", "lbl" : "obsolete herbicide sensitivity" - }, { - "id" : "http://purl.obolibrary.org/obo/NCBITaxon_9443", - "meta" : { - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "primate", - "xrefs" : [ ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "primates", - "xrefs" : [ ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "Primata", - "xrefs" : [ ] - } ] - }, - "type" : "CLASS", - "lbl" : "Primates" }, { "id" : "http://purl.obolibrary.org/obo/PATO_0000096", "meta" : { @@ -57277,16 +55186,6 @@ }, "type" : "CLASS", "lbl" : "obsolete insecticide sensitivity" - }, { - "id" : "http://purl.obolibrary.org/obo/ENVO_01001110", - "meta" : { - "definition" : { - "val" : "An environmental system which includes both living and non-living components.", - "xrefs" : [ "https://en.wikipedia.org/wiki/Ecosystem" ] - } - }, - "type" : "CLASS", - "lbl" : "ecosystem" }, { "id" : "http://purl.obolibrary.org/obo/PATO_0000091", "meta" : { @@ -57394,18 +55293,9 @@ "val" : "[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t", "xrefs" : [ ] }, - "xrefs" : [ { - "val" : "BFO:0000067" - } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "contains_process" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", "val" : "Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant" @@ -57420,34 +55310,16 @@ "id" : "http://purl.obolibrary.org/obo/BFO_0000062", "meta" : { "definition" : { - "val" : "X preceded_by Y iff: end(Y) before_or_simultaneous_with start(X)", + "val" : "x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.", "xrefs" : [ ] }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "BFO:0000062" - } ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "is preceded by", - "xrefs" : [ "SIO:000249" ] - }, { - "pred" : "hasExactSynonym", - "val" : "takes place after", - "xrefs" : [ "Allen:precedes" ] - } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "is preceded by" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "preceded by" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "preceded_by" }, { "pred" : "http://purl.org/dc/elements/1.1/source", "val" : "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" @@ -57460,7 +55332,7 @@ } ] }, "type" : "PROPERTY", - "lbl" : "preceded_by" + "lbl" : "preceded by" }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000063", "meta" : { @@ -57469,18 +55341,9 @@ "xrefs" : [ ] }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "BFO:0000063" - } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "precedes" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "precedes" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" } ] }, "type" : "PROPERTY", @@ -57493,7 +55356,7 @@ "id" : "http://purl.obolibrary.org/obo/BFO_0000015", "meta" : { "definition" : { - "val" : "p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])", + "val" : "An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t.", "xrefs" : [ ] } }, @@ -57841,7 +55704,7 @@ "id" : "http://purl.obolibrary.org/obo/BFO_0000004", "meta" : { "definition" : { - "val" : "b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])", + "val" : "A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything.", "xrefs" : [ ] } }, @@ -57938,7 +55801,7 @@ "id" : "http://purl.obolibrary.org/obo/PATO_0001384", "meta" : { "definition" : { - "val" : "A polyploidy quality inhering in a bearer by virtue of the bearer's containing four homologous sets of chromosomes.", + "val" : "A polyploidy quality inhering in a bearer by virtue of the bearer's containing six homologous sets of chromosomes.", "xrefs" : [ "Wikipedia:http://en.wikipedia.org/wiki/Hexaploid" ] }, "subsets" : [ "http://purl.obolibrary.org/obo/pato#cell_quality", "http://purl.obolibrary.org/obo/pato#value_slim" ], @@ -58174,10 +56037,6 @@ }, "type" : "CLASS", "lbl" : "monosomy" - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000001", - "type" : "CLASS", - "lbl" : "entity" }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000002", "meta" : { @@ -58563,22 +56422,10 @@ "definition" : { "val" : "A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time.", "xrefs" : [ ] - }, - "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", - "val" : "http://purl.obolibrary.org/obo/bfo.owl" - } ] + } }, "type" : "CLASS", "lbl" : "generically dependent continuant" - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000027", - "type" : "CLASS", - "lbl" : "object aggregate" - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000029", - "type" : "CLASS", - "lbl" : "site" }, { "id" : "http://purl.obolibrary.org/obo/PATO_0000073", "meta" : { @@ -58721,7 +56568,7 @@ "id" : "http://purl.obolibrary.org/obo/BFO_0000020", "meta" : { "definition" : { - "val" : "b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])", + "val" : "A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same.", "xrefs" : [ ] } }, @@ -58847,10 +56694,6 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0045936", "pred" : "http://purl.obolibrary.org/obo/RO_0002212", "obj" : "http://purl.obolibrary.org/obo/GO_0006796" - }, { - "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_33154", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_2759" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0015003", "pred" : "is_a", @@ -58859,14 +56702,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0001629", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000330" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0002178", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0000628" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001729", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001995" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0002178", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0000628" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0005004", "pred" : "is_a", @@ -58895,10 +56738,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0002128", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000025" - }, { - "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_1", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000040" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001502", "pred" : "is_a", @@ -58971,10 +56810,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0000050", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000165" - }, { - "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_9526", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_314293" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0000599", "pred" : "is_a", @@ -58991,10 +56826,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0001890", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0002008" - }, { - "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_117570", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7776" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0008152", "pred" : "is_a", @@ -59003,6 +56834,10 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0015004", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0002304" + }, { + "sub" : "http://purl.obolibrary.org/obo/CARO_0001010", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000040" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001769", "pred" : "is_a", @@ -59111,10 +56946,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0001282", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000951" - }, { - "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_9606", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_9605" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002630", "pred" : "subPropertyOf", @@ -59187,10 +57018,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0000949", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000052" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0000409", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/IAO_0000102" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002126", "pred" : "is_a", @@ -59211,10 +57038,6 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0048519", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GO_0050789" - }, { - "sub" : "http://purl.obolibrary.org/obo/PCO_0000027", - "pred" : "http://purl.obolibrary.org/obo/RO_0002351", - "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001927", "pred" : "is_a", @@ -59387,14 +57210,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0002069", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0002067" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0001752", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0001490" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001778", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001230" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0001752", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0001490" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001539", "pred" : "is_a", @@ -59471,10 +57294,6 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0016740", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GO_0003824" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0000027", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/IAO_0000030" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001948", "pred" : "is_a", @@ -59491,10 +57310,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0001997", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000467" - }, { - "sub" : "http://www.geneontology.org/formats/oboInOwl#Subset", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/IAO_0000102" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0045070", "pred" : "is_a", @@ -59503,10 +57318,6 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0043393", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GO_0051098" - }, { - "sub" : "http://purl.obolibrary.org/obo/PCO_0000004", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0002003" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001904", "pred" : "is_a", @@ -59615,10 +57426,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0002259", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000140" - }, { - "sub" : "http://purl.obolibrary.org/obo/PO_0000003", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PO_0009011" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001645", "pred" : "is_a", @@ -59655,10 +57462,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0001877", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001419" - }, { - "sub" : "http://purl.obolibrary.org/obo/PCO_0000003", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0002003" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002482", "pred" : "is_a", @@ -59675,10 +57478,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0002043", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0002041" - }, { - "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_32525", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_40674" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0019220", "pred" : "http://purl.obolibrary.org/obo/RO_0002211", @@ -59727,10 +57526,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0001253", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000321" - }, { - "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_9605", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_207598" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001359", "pred" : "is_a", @@ -59791,10 +57586,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0000060", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000051" - }, { - "sub" : "http://purl.obolibrary.org/obo/ENVO_01001002", - "pred" : "http://purl.obolibrary.org/obo/RO_0002507", - "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001595", "pred" : "is_a", @@ -59839,10 +57630,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0000569", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000119" - }, { - "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_7776", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7742" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0000945", "pred" : "is_a", @@ -59899,14 +57686,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002013", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002334" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0055002", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0002304" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001706", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0002265" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0055002", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0002304" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001724", "pred" : "is_a", @@ -59967,18 +57754,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0002026", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000057" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002596", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002500" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0000719", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000169" }, { - "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_1437010", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_9347" + "sub" : "http://purl.obolibrary.org/obo/RO_0002596", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002500" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0015028", "pred" : "is_a", @@ -60003,10 +57786,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0000069", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000068" - }, { - "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_32524", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_32523" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002248", "pred" : "is_a", @@ -60019,10 +57798,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0000406", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001591" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0000421", - "pred" : "type", - "obj" : "http://purl.obolibrary.org/obo/IAO_0000409" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0005622", "pred" : "is_a", @@ -60043,6 +57818,10 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0002467", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000052" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0040027", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0001393" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0019220", "pred" : "is_a", @@ -60123,10 +57902,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0001487", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000011" - }, { - "sub" : "http://purl.obolibrary.org/obo/ENVO_01001110", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/ENVO_01000254" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001398", "pred" : "is_a", @@ -60139,10 +57914,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0000948", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0002008" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0000120", - "pred" : "type", - "obj" : "http://purl.obolibrary.org/obo/IAO_0000078" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002442", "pred" : "is_a", @@ -60251,10 +58022,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0001378", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001377" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0000226", - "pred" : "type", - "obj" : "http://purl.obolibrary.org/obo/IAO_0000225" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001287", "pred" : "is_a", @@ -60279,10 +58046,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0001555", "pred" : "http://purl.obolibrary.org/obo/pato#reciprocal_of", "obj" : "http://purl.obolibrary.org/obo/PATO_0000070" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0000121", - "pred" : "type", - "obj" : "http://purl.obolibrary.org/obo/IAO_0000078" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002508", "pred" : "subPropertyOf", @@ -60303,10 +58066,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0000761", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0002303" - }, { - "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_32523", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_1338369" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001907", "pred" : "is_a", @@ -60335,10 +58094,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0001460", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001458" - }, { - "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_33208", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_33154" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002028", "pred" : "is_a", @@ -60391,14 +58146,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0015010", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0015009" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0000381", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0000044" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0010004", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0010002" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0000381", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0000044" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0045083", "pred" : "is_a", @@ -60431,10 +58186,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0002342", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0002227" - }, { - "sub" : "http://purl.obolibrary.org/obo/ENVO_01001000", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/ENVO_01001110" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001989", "pred" : "is_a", @@ -60447,10 +58198,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0002334", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0002303" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0000103", - "pred" : "type", - "obj" : "http://purl.obolibrary.org/obo/IAO_0000225" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001716", "pred" : "is_a", @@ -60487,14 +58234,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0002113", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0002112" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0002222", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0002220" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0040005", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000133" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0002222", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0002220" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0048018", "pred" : "is_a", @@ -60527,10 +58274,6 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002352", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002328" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0000420", - "pred" : "type", - "obj" : "http://purl.obolibrary.org/obo/IAO_0000409" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0045015", "pred" : "is_a", @@ -60543,14 +58286,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0000014", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001300" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_0010563", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_0031324" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002181", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000140" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0010563", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GO_0031324" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002048", "pred" : "is_a", @@ -60664,9 +58407,9 @@ "pred" : "http://purl.obolibrary.org/obo/RO_0002212", "obj" : "http://purl.obolibrary.org/obo/GO_0009987" }, { - "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_314295", + "sub" : "http://purl.obolibrary.org/obo/GO_0016020", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_9526" + "obj" : "http://purl.obolibrary.org/obo/CARO_0000014" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002307", "pred" : "is_a", @@ -60731,10 +58474,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0002009", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000052" - }, { - "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_9347", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_32525" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0005515", "pred" : "is_a", @@ -60755,10 +58494,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0000410", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000052" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0000125", - "pred" : "type", - "obj" : "http://purl.obolibrary.org/obo/IAO_0000078" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001167", "pred" : "is_a", @@ -60767,10 +58502,6 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002216", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002500" - }, { - "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_33511", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_33213" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002024", "pred" : "subPropertyOf", @@ -60779,10 +58510,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0001397", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001396" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0000124", - "pred" : "type", - "obj" : "http://purl.obolibrary.org/obo/IAO_0000078" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0045080", "pred" : "is_a", @@ -60803,10 +58530,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0000304", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0002303" - }, { - "sub" : "http://purl.obolibrary.org/obo/PCO_0000000", - "pred" : "http://purl.obolibrary.org/obo/RO_0002351", - "obj" : "http://purl.obolibrary.org/obo/CARO_0001010" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002396", "pred" : "is_a", @@ -60875,10 +58598,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0045016", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0045001" - }, { - "sub" : "http://purl.obolibrary.org/obo/ENVO_01001055", - "pred" : "http://purl.obolibrary.org/obo/RO_0002507", - "obj" : "http://purl.obolibrary.org/obo/CARO_0000006" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0000078", "pred" : "is_a", @@ -60971,10 +58690,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0001983", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000141" - }, { - "sub" : "http://purl.obolibrary.org/obo/ENVO_00002297", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000040" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0045006", "pred" : "is_a", @@ -61043,10 +58758,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0002386", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0002008" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0000002", - "pred" : "type", - "obj" : "http://purl.obolibrary.org/obo/IAO_0000078" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0000642", "pred" : "is_a", @@ -61071,18 +58782,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002431", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002500" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0000227", - "pred" : "type", - "obj" : "http://purl.obolibrary.org/obo/IAO_0000225" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0000643", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001598" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0000122", - "pred" : "type", - "obj" : "http://purl.obolibrary.org/obo/IAO_0000078" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002050", "pred" : "is_a", @@ -61159,10 +58862,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0001940", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000586" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_0016020", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_0044464" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001817", "pred" : "is_a", @@ -61183,10 +58882,6 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0043227", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GO_0043226" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0000229", - "pred" : "type", - "obj" : "http://purl.obolibrary.org/obo/IAO_0000225" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001622", "pred" : "is_a", @@ -61219,26 +58914,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002354", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002353" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0000123", - "pred" : "type", - "obj" : "http://purl.obolibrary.org/obo/IAO_0000078" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002395", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000628" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0000228", - "pred" : "type", - "obj" : "http://purl.obolibrary.org/obo/IAO_0000225" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002131", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0002168" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0000102", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/IAO_0000027" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001505", "pred" : "is_a", @@ -61275,10 +58958,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0002453", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000141" - }, { - "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_314146", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_1437010" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002306", "pred" : "is_a", @@ -61439,10 +59118,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0045028", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000891" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0000078", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/IAO_0000102" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0000584", "pred" : "is_a", @@ -61543,10 +59218,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0001553", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001459" - }, { - "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_9443", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_314146" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001838", "pred" : "is_a", @@ -61699,14 +59370,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0002294", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000150" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0002060", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0001293" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002057", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001323" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0002060", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0001293" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0000052", "pred" : "inverseOf", @@ -61727,10 +59398,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0001727", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001241" - }, { - "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_8287", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_117571" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0000077", "pred" : "is_a", @@ -61779,10 +59446,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0001259", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000951" - }, { - "sub" : "http://purl.obolibrary.org/obo/ENVO_00010483", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000040" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002413", "pred" : "is_a", @@ -61867,10 +59530,6 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0071944", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GO_0110165" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002215", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002328" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0000402", "pred" : "is_a", @@ -61959,10 +59618,6 @@ "sub" : "http://purl.obolibrary.org/obo/BFO_0000062", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002086" - }, { - "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_1338369", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_8287" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0000405", "pred" : "is_a", @@ -62003,10 +59658,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0001832", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0002305" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0000030", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000031" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0000396", "pred" : "is_a", @@ -62127,10 +59778,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0001859", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0002305" - }, { - "sub" : "http://purl.obolibrary.org/obo/PCO_0000000", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000027" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0004034", "pred" : "subPropertyOf", @@ -62139,14 +59786,14 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0048522", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GO_0050794" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0002052", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0002302" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0000021", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000186" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0002052", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0002302" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001833", "pred" : "is_a", @@ -62215,14 +59862,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0001346", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001343" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002563", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002464" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002459", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000052" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002563", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002464" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002559", "pred" : "subPropertyOf", @@ -62287,14 +59934,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0001252", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000950" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0001278", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0000953" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0000938", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0002264" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0001278", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0000953" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002336", "pred" : "subPropertyOf", @@ -62319,10 +59966,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0045043", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0045040" - }, { - "sub" : "http://purl.obolibrary.org/obo/ENVO_01001057", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/ENVO_01000254" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002217", "pred" : "inverseOf", @@ -62419,14 +60062,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0001830", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0002303" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0002180", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0000052" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002135", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000502" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0002180", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0000052" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002167", "pred" : "is_a", @@ -62519,14 +60162,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0001561", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001564" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0001705", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0001424" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001714", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001334" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0001705", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0001424" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0043231", "pred" : "is_a", @@ -62643,10 +60286,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0001344", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001342" - }, { - "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_314293", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_376913" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0045045", "pred" : "is_a", @@ -62683,10 +60322,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0045089", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0045088" - }, { - "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_7742", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_89593" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001780", "pred" : "is_a", @@ -62715,14 +60350,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0045041", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0045040" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0001430", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0001428" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0015005", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", "obj" : "http://purl.obolibrary.org/obo/PATO_0002212" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0001430", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0001428" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002324", "pred" : "is_a", @@ -62931,18 +60566,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002577", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/BFO_0000040" - }, { - "sub" : "http://purl.obolibrary.org/obo/ENVO_01000951", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/ENVO_01000254" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0000592", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000915" - }, { - "sub" : "http://purl.obolibrary.org/obo/PCO_0000003", - "pred" : "http://purl.obolibrary.org/obo/RO_0000052", - "obj" : "http://purl.obolibrary.org/obo/PCO_0000001" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002449", "pred" : "subPropertyOf", @@ -62963,10 +60590,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0002632", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000068" - }, { - "sub" : "http://purl.obolibrary.org/obo/PO_0009011", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PO_0025131" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002141", "pred" : "is_a", @@ -63043,34 +60666,30 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0030545", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GO_0098772" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0050001", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0000161" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002196", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0002193" }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0045088", + "sub" : "http://purl.obolibrary.org/obo/PATO_0050001", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0045073" + "obj" : "http://purl.obolibrary.org/obo/PATO_0000161" }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0002197", + "sub" : "http://purl.obolibrary.org/obo/PATO_0045088", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0002182" + "obj" : "http://purl.obolibrary.org/obo/PATO_0045073" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0051174", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GO_0031323" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0002197", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0002182" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0045048", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001806" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002202", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002254" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0045069", "pred" : "is_a", @@ -63087,10 +60706,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0002630", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000057" - }, { - "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_207598", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_9604" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002418", "pred" : "subPropertyOf", @@ -63255,14 +60870,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0000985", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000973" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0001161", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0000033" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001306", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000146" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0001161", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0000033" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0005024", "pred" : "is_a", @@ -63471,10 +61086,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0045085", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0045084" - }, { - "sub" : "http://purl.obolibrary.org/obo/ENVO_01001055", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/ENVO_01000254" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002353", "pred" : "is_a", @@ -63575,14 +61186,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0015012", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001547" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0002405", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0000141" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001874", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001873" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0002405", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0000141" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002534", "pred" : "is_a", @@ -63879,10 +61490,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0000587", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000117" - }, { - "sub" : "http://purl.obolibrary.org/obo/ENVO_01000952", - "pred" : "http://purl.obolibrary.org/obo/RO_0002234", - "obj" : "http://purl.obolibrary.org/obo/ENVO_01000313" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0000591", "pred" : "is_a", @@ -64027,10 +61634,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0000645", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0002290" - }, { - "sub" : "http://purl.obolibrary.org/obo/PCO_0000018", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PCO_0000000" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001186", "pred" : "is_a", @@ -64047,14 +61650,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0000586", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000117" - }, { - "sub" : "http://purl.obolibrary.org/obo/PCO_0000017", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PCO_0000018" - }, { - "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_89593", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7711" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002298", "pred" : "is_a", @@ -64063,10 +61658,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0001328", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001325" - }, { - "sub" : "http://purl.obolibrary.org/obo/BFO_0000029", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000141" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001437", "pred" : "is_a", @@ -64127,10 +61718,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0002035", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000140" - }, { - "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_9604", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_314295" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0000760", "pred" : "is_a", @@ -64331,10 +61918,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0002339", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000454" - }, { - "sub" : "http://purl.obolibrary.org/obo/CHEBI_59999", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CHEBI_24431" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002507", "pred" : "inverseOf", @@ -64355,10 +61938,6 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0050794", "pred" : "http://purl.obolibrary.org/obo/RO_0002211", "obj" : "http://purl.obolibrary.org/obo/GO_0009987" - }, { - "sub" : "http://purl.obolibrary.org/obo/PCO_0000000", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PCO_0000031" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0005003", "pred" : "is_a", @@ -64368,17 +61947,13 @@ "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GO_0043393" }, { - "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_33213", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" + "sub" : "http://purl.obolibrary.org/obo/GO_0023056", + "pred" : "http://purl.obolibrary.org/obo/RO_0002213", + "obj" : "http://purl.obolibrary.org/obo/GO_0023052" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0023057", "pred" : "http://purl.obolibrary.org/obo/RO_0002212", "obj" : "http://purl.obolibrary.org/obo/GO_0023052" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_0023056", - "pred" : "http://purl.obolibrary.org/obo/RO_0002213", - "obj" : "http://purl.obolibrary.org/obo/GO_0023052" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0000409", "pred" : "is_a", @@ -64391,10 +61966,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0002221", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0002305" - }, { - "sub" : "http://purl.obolibrary.org/obo/PCO_0000029", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PCO_0000000" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0000008", "pred" : "is_a", @@ -64419,10 +61990,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0002260", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000622" - }, { - "sub" : "http://purl.obolibrary.org/obo/PCO_0000027", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PCO_0000018" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0045091", "pred" : "is_a", @@ -64447,10 +62014,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0000708", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0002303" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0000428", - "pred" : "type", - "obj" : "http://purl.obolibrary.org/obo/IAO_0000078" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0000122", "pred" : "is_a", @@ -64499,22 +62062,18 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0007165", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/GO_0051716" - }, { - "sub" : "http://purl.obolibrary.org/obo/PCO_0000001", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PCO_0000018" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002189", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0002182" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0001632", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0000140" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001516", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001300" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0001632", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0000140" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002488", "pred" : "is_a", @@ -64555,34 +62114,30 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0004034", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0004032" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0001656", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0002303" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001957", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001956" }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0001824", + "sub" : "http://purl.obolibrary.org/obo/PATO_0001656", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0001822" + "obj" : "http://purl.obolibrary.org/obo/PATO_0002303" }, { - "sub" : "http://purl.obolibrary.org/obo/PCO_0000028", + "sub" : "http://purl.obolibrary.org/obo/PATO_0001824", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PCO_0000000" + "obj" : "http://purl.obolibrary.org/obo/PATO_0001822" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002250", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0002248" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0001776", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0002305" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001966", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000405" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0001776", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0002305" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002245", "pred" : "is_a", @@ -64619,10 +62174,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0002383", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0002381" - }, { - "sub" : "http://purl.obolibrary.org/obo/PO_0025131", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000040" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0051348", "pred" : "is_a", @@ -64739,10 +62290,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0002251", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0002248" - }, { - "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_7711", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_33511" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002628", "pred" : "is_a", @@ -64907,14 +62454,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0001964", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000405" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0002507", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0000025" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0000998", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000992" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0002507", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0000025" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0025001", "pred" : "is_a", @@ -64975,18 +62522,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0001298", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000018" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0002125", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0000141" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002367", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000384" }, { - "sub" : "http://purl.obolibrary.org/obo/ENVO_01001000", - "pred" : "http://purl.obolibrary.org/obo/RO_0002507", - "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_131567" + "sub" : "http://purl.obolibrary.org/obo/PATO_0002125", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0000141" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001786", "pred" : "is_a", @@ -65039,14 +62582,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0002541", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001995" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0002331", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0001431" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002460", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000141" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0002331", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0001431" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0000261", "pred" : "is_a", @@ -65063,10 +62606,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0002080", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001444" - }, { - "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_2759", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_131567" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001293", "pred" : "is_a", @@ -65103,10 +62642,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0025000", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001018" - }, { - "sub" : "http://purl.obolibrary.org/obo/ENVO_01000998", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/ENVO_01000254" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0045044", "pred" : "is_a", @@ -65123,10 +62658,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0002300", "pred" : "http://purl.obolibrary.org/obo/pato#increased_in_magnitude_relative_to", "obj" : "http://purl.obolibrary.org/obo/PATO_0000461" - }, { - "sub" : "http://purl.obolibrary.org/obo/PCO_0000004", - "pred" : "http://purl.obolibrary.org/obo/RO_0000052", - "obj" : "http://purl.obolibrary.org/obo/PCO_0000002" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002270", "pred" : "is_a", @@ -65191,10 +62722,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0002295", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001925" - }, { - "sub" : "http://purl.obolibrary.org/obo/ENVO_01001002", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/ENVO_01001000" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002428", "pred" : "subPropertyOf", @@ -65236,17 +62763,13 @@ "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000186" }, { - "sub" : "http://purl.obolibrary.org/obo/CHEBI_46662", + "sub" : "http://purl.obolibrary.org/obo/PATO_0002185", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CHEBI_59999" + "obj" : "http://purl.obolibrary.org/obo/PATO_0002183" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002365", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000383" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0002185", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0002183" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0000646", "pred" : "is_a", @@ -65287,10 +62810,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0001319", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000189" - }, { - "sub" : "http://purl.obolibrary.org/obo/ENVO_01000997", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/ENVO_01000254" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0000694", "pred" : "is_a", @@ -65311,14 +62830,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0001518", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001516" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0001627", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0001626" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002091", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001309" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0001627", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0001626" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001594", "pred" : "is_a", @@ -65519,10 +63038,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0001702", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001424" - }, { - "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_117571", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_117570" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002057", "pred" : "is_a", @@ -65703,10 +63218,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0002058", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000587" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0000225", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/IAO_0000102" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001738", "pred" : "is_a", @@ -65911,14 +63422,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0001440", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001531" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0002376", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0002014" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001855", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000140" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0002376", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0002014" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002163", "pred" : "is_a", @@ -65999,10 +63510,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0002359", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000052" - }, { - "sub" : "http://purl.obolibrary.org/obo/ENVO_01000998", - "pred" : "http://purl.obolibrary.org/obo/RO_0002507", - "obj" : "http://purl.obolibrary.org/obo/ENVO_00010483" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002278", "pred" : "is_a", @@ -66079,10 +63586,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0001441", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001531" - }, { - "sub" : "http://purl.obolibrary.org/obo/ENVO_01000952", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/ENVO_02500027" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001291", "pred" : "is_a", @@ -66331,10 +63834,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0000274", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001434" - }, { - "sub" : "http://purl.obolibrary.org/obo/ENVO_01000952", - "pred" : "http://purl.obolibrary.org/obo/RO_0002233", - "obj" : "http://purl.obolibrary.org/obo/ENVO_01000951" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0015025", "pred" : "is_a", @@ -66363,14 +63862,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0045030", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000125" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0001386", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0001385" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001335", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001895" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0001386", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0001385" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0020000", "pred" : "is_a", @@ -66419,10 +63918,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0001850", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000141" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0000410", - "pred" : "type", - "obj" : "http://purl.obolibrary.org/obo/IAO_0000409" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0000309", "pred" : "is_a", @@ -66463,10 +63958,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0001922", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000628" - }, { - "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_40674", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_32524" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001929", "pred" : "http://purl.obolibrary.org/obo/pato#towards", @@ -66543,10 +64034,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0045019", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001720" - }, { - "sub" : "http://purl.obolibrary.org/obo/PCO_0000031", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000040" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0045027", "pred" : "is_a", @@ -66575,14 +64062,14 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0098796", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/GO_0016020" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0001884", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0001018" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001923", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000628" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0001884", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0001018" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0005102", "pred" : "is_a", @@ -66671,14 +64158,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0002172", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001786" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0002279", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0002278" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002299", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0002078" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0002279", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0002278" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002101", "pred" : "is_a", @@ -66751,10 +64238,6 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002405", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002087" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0000224", - "pred" : "type", - "obj" : "http://www.geneontology.org/formats/oboInOwl#Subset" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001688", "pred" : "is_a", @@ -66815,10 +64298,6 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002566", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002506" - }, { - "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_131567", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_1" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001917", "pred" : "is_a", @@ -66875,10 +64354,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0045011", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0045001" - }, { - "sub" : "http://purl.obolibrary.org/obo/BFO_0000003", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000001" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002282", "pred" : "is_a", @@ -66887,10 +64362,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0015004", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0015002" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002410", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002609" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0045059", "pred" : "is_a", @@ -66899,14 +64370,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0002283", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0002303" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0000634", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0000060" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0000626", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000140" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0000634", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0000060" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002370", "pred" : "is_a", @@ -67019,10 +64490,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0001695", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0002305" - }, { - "sub" : "http://purl.obolibrary.org/obo/BFO_0000002", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000001" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001751", "pred" : "is_a", @@ -67171,10 +64638,6 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0032091", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GO_0051100" - }, { - "sub" : "http://purl.obolibrary.org/obo/CARO_0001010", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PCO_0000031" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0045035", "pred" : "is_a", @@ -67379,10 +64842,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0002290", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001241" - }, { - "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_376913", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_9443" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0000595", "pred" : "is_a", @@ -67423,10 +64882,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0000380", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000912" - }, { - "sub" : "http://purl.obolibrary.org/obo/PCO_0000002", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/ENVO_01001110" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001478", "pred" : "is_a", @@ -67475,10 +64930,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0001476", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0002303" - }, { - "sub" : "http://purl.obolibrary.org/obo/ENVO_02500000", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000015" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0045054", "pred" : "is_a", @@ -67643,14 +65094,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002217", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0000056" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0002345", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0002007" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001814", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001439" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0002345", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0002007" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0045034", "pred" : "is_a", @@ -67699,10 +65150,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0002434", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000140" - }, { - "sub" : "http://purl.obolibrary.org/obo/ENVO_02500027", - "pred" : "http://purl.obolibrary.org/obo/RO_0002218", - "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002327", "pred" : "is_a", @@ -67763,10 +65210,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0045049", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000516" - }, { - "sub" : "http://purl.obolibrary.org/obo/ENVO_01000313", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/ENVO_01000254" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001547", "pred" : "is_a", @@ -68043,14 +65486,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0002330", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001199" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0045071", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0001439" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0045084", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001309" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0045071", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0001439" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0000320", "pred" : "is_a", @@ -68115,10 +65558,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0001975", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001976" - }, { - "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_6072", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001790", "pred" : "is_a", @@ -68199,10 +65638,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0001263", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000324" - }, { - "sub" : "http://purl.obolibrary.org/obo/ENVO_02500027", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/ENVO_02500000" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0000956", "pred" : "is_a", @@ -68215,14 +65650,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0005015", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000117" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0001567", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0000060" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001990", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001309" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0001567", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0000060" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0005012", "pred" : "is_a", @@ -68811,10 +66246,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0000366", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000039" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0000423", - "pred" : "type", - "obj" : "http://purl.obolibrary.org/obo/IAO_0000078" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0045075", "pred" : "is_a", @@ -68911,10 +66342,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0002428", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000052" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0001062", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000004" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0044093", "pred" : "is_a", @@ -68931,10 +66358,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0000186", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001995" - }, { - "sub" : "http://purl.obolibrary.org/obo/ENVO_00002297", - "pred" : "http://purl.obolibrary.org/obo/RO_0002508", - "obj" : "http://purl.obolibrary.org/obo/ENVO_01000254" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0051174", "pred" : "http://purl.obolibrary.org/obo/RO_0002211", @@ -69187,10 +66610,6 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0045936", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GO_0019220" - }, { - "sub" : "http://purl.obolibrary.org/obo/BFO_0000027", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000040" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001448", "pred" : "is_a", @@ -69215,14 +66634,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0002168", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000133" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0045092", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0045090" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002149", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001788" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0045092", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0045090" }, { "sub" : "http://purl.obolibrary.org/obo/GO_1900122", "pred" : "http://purl.obolibrary.org/obo/RO_0002213", @@ -69375,14 +66794,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0001317", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001305" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0002426", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0000052" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001885", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001884" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0002426", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0000052" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001365", "pred" : "is_a", @@ -69407,18 +66826,10 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0045093", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0045090" - }, { - "sub" : "http://purl.obolibrary.org/obo/PCO_0000002", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PCO_0000029" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001577", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0002305" - }, { - "sub" : "http://purl.obolibrary.org/obo/PCO_0000002", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PCO_0000028" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001857", "pred" : "is_a", @@ -69453,22 +66864,22 @@ "subsets" : [ ], "xrefs" : [ ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#auto-generated-by", - "val" : "OBO-Edit 2.3.1" + "pred" : "http://purl.org/dc/elements/1.1/description", + "val" : "An ontology of phenotypic qualities (properties, attributes or characteristics)." }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#date", - "val" : "07:02:2018 10:27" + "pred" : "http://purl.org/dc/elements/1.1/title", + "val" : "PATO - the Phenotype And Trait Ontology" + }, { + "pred" : "http://purl.org/dc/terms/license", + "val" : "https://creativecommons.org/licenses/by/3.0/" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#default-namespace", "val" : "quality" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBOFormatVersion", "val" : "1.2" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#saved-by", - "val" : "segerdel" } ], - "version" : "http://purl.obolibrary.org/obo/pato/releases/2019-11-05" + "version" : "http://purl.obolibrary.org/obo/pato/releases/2019-12-03" }, "equivalentNodesSets" : [ ], "logicalDefinitionAxioms" : [ { @@ -69555,16 +66966,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/pato#decreased_in_magnitude_relative_to", "fillerId" : "http://purl.obolibrary.org/obo/PATO_0000461" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/ENVO_01000952", - "genusIds" : [ "http://purl.obolibrary.org/obo/ENVO_02500027" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002233", - "fillerId" : "http://purl.obolibrary.org/obo/ENVO_01000951" - }, { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002234", - "fillerId" : "http://purl.obolibrary.org/obo/ENVO_01000313" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/PATO_0002298", "genusIds" : [ "http://purl.obolibrary.org/obo/PATO_0001488" ], @@ -69586,13 +66987,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/pato#towards", "fillerId" : "http://purl.obolibrary.org/obo/PATO_0000146" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/ENVO_02500027", - "genusIds" : [ "http://purl.obolibrary.org/obo/ENVO_02500000" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002218", - "fillerId" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/PATO_0000595", "genusIds" : [ "http://purl.obolibrary.org/obo/PATO_0000918" ], @@ -69726,13 +67120,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/pato#has_relative_magnitude", "fillerId" : "http://purl.obolibrary.org/obo/PATO_0000461" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/ENVO_01001002", - "genusIds" : [ "http://purl.obolibrary.org/obo/ENVO_01000254" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002507", - "fillerId" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/PATO_0001163", "genusIds" : [ "http://purl.obolibrary.org/obo/PATO_0001159" ], @@ -69915,10 +67302,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/pato#has_relative_magnitude", "fillerId" : "http://purl.obolibrary.org/obo/PATO_0000461" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/ENVO_01001057", - "genusIds" : [ "http://purl.obolibrary.org/obo/ENVO_01000254" ], - "restrictions" : [ null ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/PATO_0000386", "genusIds" : [ "http://purl.obolibrary.org/obo/PATO_0000048" ], @@ -69997,17 +67380,17 @@ "fillerId" : "http://purl.obolibrary.org/obo/PATO_0000461" } ] }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0009967", + "definedClassId" : "http://purl.obolibrary.org/obo/GO_0009968", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0008150" ], "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002213", + "propertyId" : "http://purl.obolibrary.org/obo/RO_0002212", "fillerId" : "http://purl.obolibrary.org/obo/GO_0007165" } ] }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0009968", + "definedClassId" : "http://purl.obolibrary.org/obo/GO_0009967", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0008150" ], "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002212", + "propertyId" : "http://purl.obolibrary.org/obo/RO_0002213", "fillerId" : "http://purl.obolibrary.org/obo/GO_0007165" } ] }, { @@ -70193,15 +67576,15 @@ "fillerId" : "http://purl.obolibrary.org/obo/PATO_0000461" } ] }, { - "definedClassId" : "http://purl.obolibrary.org/obo/PATO_0001552", - "genusIds" : [ "http://purl.obolibrary.org/obo/PATO_0001457" ], + "definedClassId" : "http://purl.obolibrary.org/obo/PATO_0001779", + "genusIds" : [ "http://purl.obolibrary.org/obo/PATO_0001230" ], "restrictions" : [ { "propertyId" : "http://purl.obolibrary.org/obo/pato#decreased_in_magnitude_relative_to", "fillerId" : "http://purl.obolibrary.org/obo/PATO_0000461" } ] }, { - "definedClassId" : "http://purl.obolibrary.org/obo/PATO_0001779", - "genusIds" : [ "http://purl.obolibrary.org/obo/PATO_0001230" ], + "definedClassId" : "http://purl.obolibrary.org/obo/PATO_0001552", + "genusIds" : [ "http://purl.obolibrary.org/obo/PATO_0001457" ], "restrictions" : [ { "propertyId" : "http://purl.obolibrary.org/obo/pato#decreased_in_magnitude_relative_to", "fillerId" : "http://purl.obolibrary.org/obo/PATO_0000461" @@ -70290,13 +67673,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/pato#has_relative_magnitude", "fillerId" : "http://purl.obolibrary.org/obo/PATO_0000461" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/ENVO_01001055", - "genusIds" : [ "http://purl.obolibrary.org/obo/ENVO_01000254" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002507", - "fillerId" : "http://purl.obolibrary.org/obo/CARO_0000006" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/PATO_0000570", "genusIds" : [ "http://purl.obolibrary.org/obo/PATO_0000119" ], @@ -70304,10 +67680,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/pato#increased_in_magnitude_relative_to", "fillerId" : "http://purl.obolibrary.org/obo/PATO_0000461" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/ENVO_01000997", - "genusIds" : [ "http://purl.obolibrary.org/obo/ENVO_01000254" ], - "restrictions" : [ null ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/PATO_0045053", "genusIds" : [ "http://purl.obolibrary.org/obo/PATO_0000119" ], @@ -70631,15 +68003,15 @@ "fillerId" : "http://purl.obolibrary.org/obo/PATO_0000461" } ] }, { - "definedClassId" : "http://purl.obolibrary.org/obo/PATO_0001551", - "genusIds" : [ "http://purl.obolibrary.org/obo/PATO_0001457" ], + "definedClassId" : "http://purl.obolibrary.org/obo/PATO_0001778", + "genusIds" : [ "http://purl.obolibrary.org/obo/PATO_0001230" ], "restrictions" : [ { "propertyId" : "http://purl.obolibrary.org/obo/pato#increased_in_magnitude_relative_to", "fillerId" : "http://purl.obolibrary.org/obo/PATO_0000461" } ] }, { - "definedClassId" : "http://purl.obolibrary.org/obo/PATO_0001778", - "genusIds" : [ "http://purl.obolibrary.org/obo/PATO_0001230" ], + "definedClassId" : "http://purl.obolibrary.org/obo/PATO_0001551", + "genusIds" : [ "http://purl.obolibrary.org/obo/PATO_0001457" ], "restrictions" : [ { "propertyId" : "http://purl.obolibrary.org/obo/pato#increased_in_magnitude_relative_to", "fillerId" : "http://purl.obolibrary.org/obo/PATO_0000461" @@ -70966,10 +68338,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/pato#has_relative_magnitude", "fillerId" : "http://purl.obolibrary.org/obo/PATO_0000461" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/ENVO_01000313", - "genusIds" : [ "http://purl.obolibrary.org/obo/ENVO_01000254" ], - "restrictions" : [ null ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/PATO_0045067", "genusIds" : [ "http://purl.obolibrary.org/obo/PATO_0000146" ], @@ -71005,13 +68373,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/pato#decreased_in_magnitude_relative_to", "fillerId" : "http://purl.obolibrary.org/obo/PATO_0000461" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/PCO_0000004", - "genusIds" : [ "http://purl.obolibrary.org/obo/PATO_0002003" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0000052", - "fillerId" : "http://purl.obolibrary.org/obo/PCO_0000002" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/PATO_0001693", "genusIds" : [ "http://purl.obolibrary.org/obo/PATO_0000998" ], @@ -71040,13 +68401,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/pato#decreased_in_magnitude_relative_to", "fillerId" : "http://purl.obolibrary.org/obo/PATO_0000461" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/PCO_0000003", - "genusIds" : [ "http://purl.obolibrary.org/obo/PATO_0002003" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0000052", - "fillerId" : "http://purl.obolibrary.org/obo/PCO_0000001" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/PATO_0001714", "genusIds" : [ "http://purl.obolibrary.org/obo/PATO_0001334" ], @@ -71188,15 +68542,15 @@ "fillerId" : "http://purl.obolibrary.org/obo/PATO_0000461" } ] }, { - "definedClassId" : "http://purl.obolibrary.org/obo/PATO_0045035", - "genusIds" : [ "http://purl.obolibrary.org/obo/PATO_0001655" ], + "definedClassId" : "http://purl.obolibrary.org/obo/PATO_0045075", + "genusIds" : [ "http://purl.obolibrary.org/obo/PATO_0001615" ], "restrictions" : [ { "propertyId" : "http://purl.obolibrary.org/obo/pato#has_relative_magnitude", "fillerId" : "http://purl.obolibrary.org/obo/PATO_0000461" } ] }, { - "definedClassId" : "http://purl.obolibrary.org/obo/PATO_0045075", - "genusIds" : [ "http://purl.obolibrary.org/obo/PATO_0001615" ], + "definedClassId" : "http://purl.obolibrary.org/obo/PATO_0045035", + "genusIds" : [ "http://purl.obolibrary.org/obo/PATO_0001655" ], "restrictions" : [ { "propertyId" : "http://purl.obolibrary.org/obo/pato#has_relative_magnitude", "fillerId" : "http://purl.obolibrary.org/obo/PATO_0000461" @@ -71229,13 +68583,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002213", "fillerId" : "http://purl.obolibrary.org/obo/GO_0016301" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/ENVO_01001000", - "genusIds" : [ "http://purl.obolibrary.org/obo/ENVO_01000254" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002507", - "fillerId" : "http://purl.obolibrary.org/obo/NCBITaxon_131567" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/PATO_0001831", "genusIds" : [ "http://purl.obolibrary.org/obo/PATO_0000888" ], @@ -71304,17 +68651,17 @@ "fillerId" : "http://purl.obolibrary.org/obo/PATO_0000461" } ] }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0010562", + "definedClassId" : "http://purl.obolibrary.org/obo/GO_0010563", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0008150" ], "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002213", + "propertyId" : "http://purl.obolibrary.org/obo/RO_0002212", "fillerId" : "http://purl.obolibrary.org/obo/GO_0006793" } ] }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0010563", + "definedClassId" : "http://purl.obolibrary.org/obo/GO_0010562", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0008150" ], "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002212", + "propertyId" : "http://purl.obolibrary.org/obo/RO_0002213", "fillerId" : "http://purl.obolibrary.org/obo/GO_0006793" } ] }, { @@ -71331,13 +68678,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002213", "fillerId" : "http://purl.obolibrary.org/obo/GO_0016310" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/ENVO_01000998", - "genusIds" : [ "http://purl.obolibrary.org/obo/ENVO_01000254" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002507", - "fillerId" : "http://purl.obolibrary.org/obo/ENVO_00010483" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/PATO_0045027", "genusIds" : [ "http://purl.obolibrary.org/obo/PATO_0001685" ], @@ -71556,17 +68896,17 @@ "fillerId" : "http://purl.obolibrary.org/obo/PATO_0000461" } ] }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0048523", + "definedClassId" : "http://purl.obolibrary.org/obo/GO_0048522", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0008150" ], "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002212", + "propertyId" : "http://purl.obolibrary.org/obo/RO_0002213", "fillerId" : "http://purl.obolibrary.org/obo/GO_0009987" } ] }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0048522", + "definedClassId" : "http://purl.obolibrary.org/obo/GO_0048523", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0008150" ], "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002213", + "propertyId" : "http://purl.obolibrary.org/obo/RO_0002212", "fillerId" : "http://purl.obolibrary.org/obo/GO_0009987" } ] }, { @@ -71832,13 +69172,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/pato#increased_in_magnitude_relative_to", "fillerId" : "http://purl.obolibrary.org/obo/PATO_0000461" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0010647", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0008150" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002213", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0007154" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0010648", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0008150" ], @@ -71847,11 +69180,11 @@ "fillerId" : "http://purl.obolibrary.org/obo/GO_0007154" } ] }, { - "definedClassId" : "http://purl.obolibrary.org/obo/ENVO_00002297", - "genusIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ], + "definedClassId" : "http://purl.obolibrary.org/obo/GO_0010647", + "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0008150" ], "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002508", - "fillerId" : "http://purl.obolibrary.org/obo/ENVO_01000254" + "propertyId" : "http://purl.obolibrary.org/obo/RO_0002213", + "fillerId" : "http://purl.obolibrary.org/obo/GO_0007154" } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/PATO_0001723", @@ -72166,8 +69499,8 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002254", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000004", "http://purl.obolibrary.org/obo/CARO_0000000" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000000", "http://purl.obolibrary.org/obo/CARO_0000003" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000000" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000000" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002595", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ], @@ -72213,6 +69546,10 @@ "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_0000004", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000004" }, { "sub" : "http://purl.obolibrary.org/obo/BFO_0000003", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -72221,10 +69558,6 @@ "sub" : "http://purl.obolibrary.org/obo/BFO_0000002", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/BFO_0000002" - }, { - "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_0000031", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -72391,15 +69724,9 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002598", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002215", "http://purl.obolibrary.org/obo/RO_0002213" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002202", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002202", "http://purl.obolibrary.org/obo/BFO_0000050" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002314", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0000052", "http://purl.obolibrary.org/obo/BFO_0000050" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002202", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/BFO_0000050", "http://purl.obolibrary.org/obo/RO_0002202" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002211", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002578", "http://purl.obolibrary.org/obo/RO_0002578" ] diff --git a/pato.obo b/pato.obo index cd1aa5d0..525d87b8 100644 --- a/pato.obo +++ b/pato.obo @@ -1,8 +1,5 @@ format-version: 1.2 -data-version: releases/2019-11-05/pato.obo -date: 07:02:2018 10:27 -saved-by: segerdel -auto-generated-by: OBO-Edit 2.3.1 +data-version: releases/2019-12-03/pato.obo subsetdef: abnormal_slim "Abnormal/normal slim" subsetdef: absent_slim "Absent/present slim" subsetdef: attribute_slim "Attribute slim" @@ -16,6 +13,9 @@ subsetdef: scalar_slim "Scalar slim" subsetdef: value_slim "Value slim" default-namespace: quality ontology: pato +property_value: http://purl.org/dc/elements/1.1/description "An ontology of phenotypic qualities (properties, attributes or characteristics)." xsd:string +property_value: http://purl.org/dc/elements/1.1/title "PATO - the Phenotype And Trait Ontology" xsd:string +property_value: http://purl.org/dc/terms/license https://creativecommons.org/licenses/by/3.0/ xsd:string [Term] id: PATO:0000000 @@ -27,7 +27,6 @@ id: PATO:0000001 name: quality alt_id: PATO:0000072 def: "A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities" [PATOC:GVG] -synonym: "trait" EXACT [] property_value: IAO:0000589 "quality (PATO)" xsd:string [Term] @@ -8691,7 +8690,7 @@ is_a: PATO:0001377 ! polyploid [Term] id: PATO:0001384 name: hexaploid -def: "A polyploidy quality inhering in a bearer by virtue of the bearer's containing four homologous sets of chromosomes." [Wikipedia:http\://en.wikipedia.org/wiki/Hexaploid] +def: "A polyploidy quality inhering in a bearer by virtue of the bearer's containing six homologous sets of chromosomes." [Wikipedia:http\://en.wikipedia.org/wiki/Hexaploid] subset: cell_quality subset: value_slim is_a: PATO:0001377 ! polyploid @@ -20042,6 +20041,15 @@ synonym: "structurally interrupted" EXACT [] is_a: PATO:0001241 ! physical object quality created_by: http://orcid.org/0000-0001-5208-3432 +[Term] +id: PATO:0040027 +name: doubled haploid +def: "A ploidy quality inhering in a bearer by virtue of the bearer's haploid cells undergo chromosome doubling." [Wikipedia:https\://en.wikipedia.org/wiki/Doubled_haploidy] +synonym: "double haploid" EXACT [] +synonym: "double-haploid" EXACT [] +is_a: PATO:0001393 ! euploid +created_by: http://orcid.org/0000-0001-5208-3432 + [Term] id: PATO:0045000 name: normal rate @@ -20828,7 +20836,7 @@ creation_date: 2017-12-22T14:16:43Z [Term] id: PATO:0045075 name: normal variability of color -def: "A variability which is relatively normal or average" [] +def: "A variability of color which is relatively normal or average" [] subset: value_slim is_a: PATO:0001615 ! variant color relationship: has_relative_magnitude PATO:0000461 ! normal @@ -21069,6 +21077,18 @@ is_a: PATO:0060001 ! sex-specific created_by: http://orcid.org/0000-0002-1373-1705 creation_date: 2019-08-23T08:51:22Z +[Typedef] +id: RO:0000053 +name: bearer of +def: "a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence" [] +property_value: IAO:0000111 "bearer of" xsd:string +property_value: IAO:0000112 "this apple is bearer of this red color" xsd:string +property_value: IAO:0000112 "this vase is bearer of this fragility" xsd:string +property_value: IAO:0000116 "A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist." xsd:string +property_value: IAO:0000118 "bearer_of" xsd:string +property_value: IAO:0000118 "is bearer of" xsd:string +property_value: RO:0001900 RO:0001901 + [Typedef] id: RO:0000057 name: has participant @@ -21083,27 +21103,22 @@ property_value: IAO:0000118 "has_participant" xsd:string holds_over_chain: has_part RO:0000057 [Typedef] -id: bearer_of -name: bearer of -namespace: uberon -def: "a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence" [] -xref: RO:0000053 -property_value: IAO:0000111 "bearer of" xsd:string -property_value: IAO:0000112 "this apple is bearer of this red color" xsd:string -property_value: IAO:0000112 "this vase is bearer of this fragility" xsd:string -property_value: IAO:0000116 "A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist." xsd:string -property_value: IAO:0000118 "bearer_of" xsd:string -property_value: IAO:0000118 "is bearer of" xsd:string +id: RO:0002180 +name: has component +def: "w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type." [] +subset: ro-eco +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000116 "The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity." xsd:string +property_value: IAO:0000232 "For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit." xsd:string property_value: RO:0001900 RO:0001901 +property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:Componency +is_a: has_part ! has part [Typedef] -id: composed_primarily_of +id: RO:0002473 name: composed primarily of -namespace: uberon def: "x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y." [] -def: "x composed_primarily_of y iff: more than half of the mass of x is made from parts of y" [] subset: ro-eco -xref: RO:0002473 property_value: IAO:0000112 "'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate'" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 @@ -21141,20 +21156,6 @@ range: PATO:0000001 ! quality created_by: cjm creation_date: 2009-08-26T02:50:08Z -[Typedef] -id: has_component -name: has component -namespace: uberon -def: "w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type." [] -subset: ro-eco -xref: RO:0002180 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000116 "The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity." xsd:string -property_value: IAO:0000232 "For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit." xsd:string -property_value: RO:0001900 RO:0001901 -property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:Componency -is_a: has_part ! has part - [Typedef] id: has_cross_section name: has_cross_section @@ -21189,9 +21190,7 @@ is_a: has_ratio_quality ! has_ratio_quality id: has_part name: has part name: has_part -namespace: chebi_ontology namespace: external -namespace: uberon def: "a core relation that holds between a whole and its part" [] def: "Q1 has_part Q2 if and only if: every instance of Q1 is a quality_of an entity that has_quality some Q2." [PATOC:CJM] comment: We use the has_part relation to relate complex qualities to more primitive ones. A complex quality is a collection of qualities. The complex quality cannot exist without the sub-qualities. For example, the quality 'swollen' necessarily comes with the qualities of 'protruding' and 'increased size'. @@ -21205,7 +21204,6 @@ property_value: IAO:0000116 "Occurrents are not subject to change and so parthoo property_value: IAO:0000116 "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)\n\nA continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'." xsd:string property_value: IAO:0000118 "has_part" xsd:string property_value: RO:0001900 RO:0001901 -is_cyclic: false is_transitive: true [Typedef] @@ -21269,7 +21267,6 @@ id: part_of name: part of name: part_of namespace: external -namespace: uberon def: "a core relation that holds between a part and its whole" [] xref: BFO:0000050 property_value: IAO:0000111 "is part of" xsd:string diff --git a/pato.owl b/pato.owl index 96a45765..99328413 100644 --- a/pato.owl +++ b/pato.owl @@ -8,24 +8,22 @@ xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:xml="http://www.w3.org/XML/1998/namespace" xmlns:xsd="http://www.w3.org/2001/XMLSchema#" - xmlns:core="http://purl.obolibrary.org/obo/uberon/core#" xmlns:foaf="http://xmlns.com/foaf/0.1/" xmlns:pato="http://purl.obolibrary.org/obo/pato#" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" xmlns:swrl="http://www.w3.org/2003/11/swrl#" - xmlns:chebi="http://purl.obolibrary.org/obo/chebi#3" xmlns:swrla="http://swrl.stanford.edu/ontologies/3.3/swrla.owl#" xmlns:swrlb="http://www.w3.org/2003/11/swrlb#" xmlns:terms="http://purl.org/dc/terms/" xmlns:subsets="http://purl.obolibrary.org/obo/ro/subsets#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - - OBO-Edit 2.3.1 - 07:02:2018 10:27 + + An ontology of phenotypic qualities (properties, attributes or characteristics). + PATO - the Phenotype And Trait Ontology + https://creativecommons.org/licenses/by/3.0/ quality 1.2 - segerdel @@ -44,11 +42,6 @@ - editor preferred term - - The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English) - PERSON:Daniel Schober - GROUP:OBI:<http://purl.obolibrary.org/obo/obi> editor preferred term @@ -57,17 +50,7 @@ - example - A phrase describing how a class name should be used. May also include other kinds of examples that facilitate immediate understanding of a class semantics, such as widely known prototypical subclasses or instances of the class. Although essential for high level terms, examples for low level terms (e.g., Affymetrix HU133 array) are not - PERSON:Daniel Schober - GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - IAO:0000112 - uberon - example_of_usage - true - example_of_usage - example of usage example of usage @@ -76,11 +59,6 @@ - has curation status - PERSON:Alan Ruttenberg - PERSON:Bill Bug - PERSON:Melanie Courtot - OBI_0000281 has curation status @@ -89,31 +67,7 @@ - definition - The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. - 2012-04-05: -Barry Smith - -The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. - -Can you fix to something like: - -A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. - -Alan Ruttenberg - -Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. - -On the specifics of the proposed definition: - -We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. - -Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. - -We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. - PERSON:Daniel Schober - GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition definition @@ -123,17 +77,7 @@ We also have the outstanding issue of how to aim different definitions to differ - editor note - An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology. - PERSON:Daniel Schober - GROUP:OBI:<http://purl.obfoundry.org/obo/obi> - IAO:0000116 - uberon - editor_note - true - editor_note - editor note editor note @@ -142,12 +86,7 @@ We also have the outstanding issue of how to aim different definitions to differ - term editor - Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people - 20110707, MC: label update to term editor and definition modified accordingly. See http://code.google.com/p/information-artifact-ontology/issues/detail?id=115. - PERSON:Daniel Schober - GROUP:OBI:<http://purl.obolibrary.org/obo/obi> term editor @@ -156,11 +95,7 @@ We also have the outstanding issue of how to aim different definitions to differ - alternative term - An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent) - PERSON:Daniel Schober - GROUP:OBI:<http://purl.obolibrary.org/obo/obi> alternative term @@ -169,12 +104,7 @@ We also have the outstanding issue of how to aim different definitions to differ - definition source - formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007 - PERSON:Daniel Schober - Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w - GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition source @@ -182,30 +112,15 @@ We also have the outstanding issue of how to aim different definitions to differ - - has obsolescence reason - Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification. - PERSON:Alan Ruttenberg - PERSON:Melanie Courtot - has obsolescence reason - + - curator note - An administrative note of use for a curator but of no use for a user - PERSON:Alan Ruttenberg - IAO:0000232 - uberon - curator_notes - true - curator_notes curator note - curator notes @@ -213,12 +128,7 @@ We also have the outstanding issue of how to aim different definitions to differ - imported from - For external terms/classes, the ontology from which the term was imported - PERSON:Alan Ruttenberg - PERSON:Melanie Courtot - GROUP:OBI:<http://purl.obolibrary.org/obo/obi> imported from @@ -227,14 +137,6 @@ We also have the outstanding issue of how to aim different definitions to differ - expand expression to - ObjectProperty: RO_0002104 -Label: has plasma membrane part -Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.org/obo/owl/GO#GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)" - - A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones - Chris Mungall - expand expression to expand expression to @@ -243,15 +145,7 @@ Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some ( - OBO foundry unique label - An alternative name for a class or property which is unique across the OBO Foundry. - The intended usage of that property is as follow: OBO foundry unique labels are automatically generated based on regular expressions provided by each ontology, so that SO could specify unique label = 'sequence ' + [label], etc. , MA could specify 'mouse + [label]' etc. Upon importing terms, ontology developers can choose to use the 'OBO foundry unique label' for an imported term or not. The same applies to tools . - PERSON:Alan Ruttenberg - PERSON:Bjoern Peters - PERSON:Chris Mungall - PERSON:Melanie Courtot - GROUP:OBO Foundry <http://obofoundry.org/> OBO foundry unique label @@ -260,54 +154,19 @@ Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some ( - elucidation - person:Alan Ruttenberg - Person:Barry Smith - Primitive terms in a highest-level ontology such as BFO are terms which are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms elucidation - - - - has axiom id - Person:Alan Ruttenberg - Person:Alan Ruttenberg - A URI that is intended to be unique label for an axiom used for tracking change to the ontology. For an axiom expressed in different languages, each expression is given the same URI - has axiom label - - - - - term replaced by - - Add as annotation triples in the granting ontology - Use on obsolete terms, relating the term to another term that can be used as a substitute - Person:Alan Ruttenberg - Person:Alan Ruttenberg - term replaced by term replaced by - - - - - - - - - - - - @@ -329,7 +188,9 @@ Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some ( - + + logical macro assertion on an annotation property + @@ -346,7 +207,6 @@ Where we have an annotation assertion "directly P" "is direct form of" "P" If we have the annotation P is-direct-form-of Q, and we have inverses P' and Q', then it follows that P' is-direct-form-of Q' - Chris Mungall Chris Mungall is direct form of @@ -423,36 +283,6 @@ Where we have an annotation assertion - - - - An alternate textual definition for a class taken unmodified from an external source. This definition may have been used to derive a generalized definition for the new class. - UBPROP:0000001 - uberon - external_definition - true - external_definition - This annotation property may be replaced with an annotation property from an external ontology such as IAO - external_definition - - - - - An alternate textual definition for a class taken unmodified from an external source. This definition may have been used to derive a generalized definition for the new class. - - - - - - - - - Manually annotated by ChEBI Team - - - - - @@ -678,25 +508,9 @@ Where we have an annotation assertion - - - - abstract upper-level terms not directly useful for analysis - - - - - - - - uberon - dc-creator - true - dc-creator - creator - + @@ -708,14 +522,7 @@ Where we have an annotation assertion - - - uberon - dc-source - true - dc-source - derived from resource - + @@ -745,12 +552,6 @@ Where we have an annotation assertion - - - - - - @@ -771,12 +572,6 @@ Where we have an annotation assertion - - - - - - @@ -875,24 +670,12 @@ Where we have an annotation assertion - - - - - - - - - - - - @@ -901,12 +684,6 @@ Where we have an annotation assertion - - - - - - @@ -927,14 +704,7 @@ Where we have an annotation assertion - - - uberon - foaf-page - true - foaf-page - page - + @@ -977,7 +747,6 @@ A continuant cannot be part of an occurrent: use 'participates in'. An BFO:0000050 external quality - uberon part_of part_of part of @@ -1009,12 +778,9 @@ A continuant cannot have an occurrent as part: use 'participates in'. has_part BFO:0000051 - chebi_ontology external quality - uberon has_part - false has_part We use the has_part relation to relate complex qualities to more primitive ones. A complex quality is a collection of qualities. The complex quality cannot exist without the sub-qualities. For example, the quality 'swollen' necessarily comes with the qualities of 'protruding' and 'increased size'. has part @@ -1043,34 +809,14 @@ A continuant cannot have an occurrent as part: use 'participates in'. preceded by - X preceded_by Y iff: end(Y) before_or_simultaneous_with start(X) x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other. is preceded by preceded_by http://www.obofoundry.org/ro/#OBO_REL:preceded_by - BFO:0000062 - is preceded by - takes place after - uberon - preceded_by - preceded_by preceded by - preceded_by - - - - is preceded by - SIO:000249 - - - - - takes place after - Allen:precedes - @@ -1087,12 +833,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. precedes x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. - BFO:0000063 - uberon - precedes - precedes - precedes precedes @@ -1134,13 +875,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. site of [copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t - BFO:0000067 - uberon - contains_process - contains_process Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant - contains process contains process @@ -1175,11 +911,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. bearer_of is bearer of - RO:0000053 - uberon - bearer_of - bearer_of - bearer of bearer of @@ -1248,11 +979,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist. has_quality - RO:0000086 - uberon - has_quality - has_quality - has quality has quality @@ -1270,12 +996,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. Most location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime location_of - RO:0001015 - uberon - location_of - location_of location of - location_of @@ -1310,12 +1031,7 @@ range: spatial region or site (immaterial continuant) contains - RO:0001019 - uberon - contains - contains - contains contains @@ -1356,12 +1072,7 @@ range: spatial region or site (immaterial continuant) located_in http://www.obofoundry.org/ro/#OBO_REL:located_in - RO:0001025 - uberon - located_in - located_in located in - located_in @@ -1455,12 +1166,6 @@ range: spatial region or site (immaterial continuant) 2017-07-19T17:30:36Z has ligand - - - - A relationship that holds between between a receptor and an chemical entity, typically a small molecule or peptide, that carries information between cells or compartments of a cell and which binds the receptor and regulates its effector function. - GOC:dos - @@ -1560,35 +1265,11 @@ range: spatial region or site (immaterial continuant) - X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) David Osumi-Sutherland starts_at_end_of - A non-transitive temporal relation in which one process immediately precedes another process, such that there is no interval of time between the two processes[SIO:000251]. - RO:0002087 - directly preceded by - is directly preceded by - is immediately preceded by - starts_at_end_of - uberon - immediately_preceded_by - immediately_preceded_by X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) immediately preceded by - immediately_preceded_by - - - - - A non-transitive temporal relation in which one process immediately precedes another process, such that there is no interval of time between the two processes[SIO:000251]. - SIO:000251 - - - - - is immediately preceded by - SIO:000251 - @@ -1628,17 +1309,10 @@ range: spatial region or site (immaterial continuant) - A overlaps B if they share some part in common. x overlaps y if and only if there exists some z such that x has part z and z part of y - BFO_0000051 some (BFO_0000050 some ?Y) http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y) - RO:0002131 - uberon - overlaps - overlaps - overlaps overlaps @@ -1662,12 +1336,7 @@ range: spatial region or site (immaterial continuant) The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity. For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit. - RO:0002180 - uberon - has_component - has_component - has component has component @@ -1677,33 +1346,19 @@ range: spatial region or site (immaterial continuant) - - - - - - - - - x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y Chris Mungall David Osumi-Sutherland Melissa Haendel Terry Meehan - RO:0002202 - uberon - develops_from - develops_from This is the transitive form of the develops from relation develops from - develops_from @@ -1720,13 +1375,8 @@ range: spatial region or site (immaterial continuant) Chris Mungall David Osumi-Sutherland Terry Meehan - RO:0002203 - uberon - develops_into - develops_into develops into - develops_into @@ -1770,7 +1420,6 @@ range: spatial region or site (immaterial continuant) - 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. Chris Mungall @@ -1816,12 +1465,10 @@ range: spatial region or site (immaterial continuant) - mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974) osteoclast SubClassOf 'capable of' some 'bone resorption' - A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. Chris Mungall has function realized in @@ -1829,12 +1476,7 @@ range: spatial region or site (immaterial continuant) For compatibility with BFO, this relation has a shortcut definition in which the expression "capable of some P" expands to "bearer_of (some realized_by only P)". RO_0000053 some (RO_0000054 only ?Y) - RO:0002215 - uberon - capable_of - capable_of - capable of capable of @@ -1849,16 +1491,10 @@ range: spatial region or site (immaterial continuant) - c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p. Chris Mungall has function in RO_0000053 some (RO_0000054 only (BFO_0000050 some ?Y)) - RO:0002216 - uberon - capable_of_part_of - capable_of_part_of - capable of part of capable of part of @@ -1879,7 +1515,6 @@ range: spatial region or site (immaterial continuant) - x actively participates in y if and only if x participates in y and x realizes some active role Chris Mungall agent in @@ -1899,7 +1534,6 @@ range: spatial region or site (immaterial continuant) Chris Mungall has agent - has active participant obsolete has active participant true @@ -1915,7 +1549,6 @@ range: spatial region or site (immaterial continuant) Chris Mungall Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends. - https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. @@ -1932,7 +1565,6 @@ range: spatial region or site (immaterial continuant) - p has direct input c iff c is a participant in p, c is present at the start of p, and the state of c is modified during p. p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p. Chris Mungall consumes @@ -1962,11 +1594,8 @@ range: spatial region or site (immaterial continuant) - - - @@ -1975,11 +1604,6 @@ range: spatial region or site (immaterial continuant) x has developmental contribution from y iff x has some part z such that z develops from y Chris Mungall - RO:0002254 - uberon - has_developmental_contribution_from - has_developmental_contribution_from - has developmental contribution from has developmental contribution from @@ -1997,13 +1621,8 @@ range: spatial region or site (immaterial continuant) inverse of has developmental contribution from Chris Mungall - RO:0002255 - uberon - developmentally_contributes_to - developmentally_contributes_to developmentally contributes to - developmentally_contributes_to @@ -2020,12 +1639,7 @@ range: spatial region or site (immaterial continuant) false Chris Mungall In general you should not use this relation to make assertions - use one of the more specific relations below this one - RO:0002258 - uberon - developmentally_preceded_by - developmentally_preceded_by This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from - developmentally preceded by developmentally preceded by @@ -2041,7 +1655,6 @@ range: spatial region or site (immaterial continuant) A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision. c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes. - c involved in regulation of p if c enables 'p' and p' causally upstream of p acts upstream of @@ -2057,7 +1670,6 @@ range: spatial region or site (immaterial continuant) A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway. - c acts upstream of or within p if c is enables 'p' and p' causally upstream of or within p c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process. affects acts upstream of or within @@ -2118,7 +1730,6 @@ range: spatial region or site (immaterial continuant) - cjm cjm holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y causally upstream of, positive effect @@ -2132,7 +1743,6 @@ range: spatial region or site (immaterial continuant) - cjm cjm holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y causally upstream of, negative effect @@ -2255,11 +1865,6 @@ However, this is not possible in OWL. We instead make this relation a sub-relati A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities. Chris Mungall This is a grouping relation that collects relations used for the purpose of connecting structure and function - RO:0002328 - uberon - functionally_related_to - functionally_related_to - functionally related to functionally related to @@ -2276,11 +1881,6 @@ However, this is not possible in OWL. We instead make this relation a sub-relati this relation holds between c and p when c is part of some c', and c' is capable of p. Chris Mungall false - RO:0002329 - uberon - part_of_structure_that_is_capable_of - part_of_structure_that_is_capable_of - part of structure that is capable of part of structure that is capable of @@ -2323,11 +1923,6 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - - - - - inverse of enables Chris Mungall enabled by @@ -2386,11 +1981,6 @@ However, this is not possible in OWL. We instead make this relation a sub-relati member part of SIO - RO:0002350 - uberon - member_of - member_of - member of member of @@ -2404,11 +1994,6 @@ However, this is not possible in OWL. We instead make this relation a sub-relati has member is a mereological relation between a collection and an item. SIO - RO:0002351 - uberon - has_member - has_member - has member has member @@ -2421,13 +2006,8 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inverse of has input Chris Mungall - RO:0002352 - uberon - input_of - input_of - input of input of @@ -2440,13 +2020,8 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inverse of has output Chris Mungall - RO:0002353 - uberon - output_of - output_of - output of output of @@ -2500,14 +2075,8 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y Chris Mungall - RO:0002385 - uberon - has_potential_to_developmentally_contribute_to - has_potential_to_developmentally_contribute_to - has potential to developmentally contribute to has potential to developmentally contribute to @@ -2518,14 +2087,8 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - x has the potential to develop into y iff x develops into y or if x is capable of developing into y x has the potential to develop into y iff x develops into y or if x is capable of developing into y Chris Mungall - RO:0002387 - uberon - has_potential_to_develop_into - has_potential_to_develop_into - has potential to develop into has potential to develop into @@ -2536,14 +2099,8 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y Chris Mungall - RO:0002388 - uberon - has_potential_to_directly_develop_into - has_potential_to_directly_develop_into - has potential to directly develop into has potential to directly develop into @@ -2579,7 +2136,6 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - This relation groups causal relations between material entities and causal relations between processes This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents. @@ -2675,7 +2231,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - c involved in regulation of p if c is involved in some 'p' and p' regulates some p c involved in regulation of p if c is involved in some p' and p' regulates some p Chris Mungall involved in regulation of @@ -2748,13 +2303,11 @@ Each of these 3 primitives can be composed to yield a cross-product of different A protein that enables activity in a cytosol. - c executes activity in d if and only if c enables p and p occurs_in d c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. Chris Mungall executes activity in enables activity in - enables activity in is active in @@ -2801,7 +2354,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - An interaction relationship in which the two partners are molecular entities and are executing molecular processes that are directly causally connected. An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other. Chris Mungall binds @@ -2836,11 +2388,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different Holds between molecular entities A and B where A can physically interact with B and in doing so regulates a process that B is capable of. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B. - Holds between molecular entities a and b when the execution of a activates or inhibits the activity of b Chris Mungall molecularly controls activity directly regulates activity of - molecularly controls @@ -2855,12 +2405,10 @@ Each of these 3 primitives can be composed to yield a cross-product of different Holds between molecular entities A and B where A can physically interact with B and in doing so negatively regulates a process that B is capable of. For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B. - Holds between molecules a and b if and only if a executes a process that directly diminishes a process executed by b. Chris Mungall inhibits molecularly decreases activity of activity directly negatively regulates activity of - molecularly decreases activity of @@ -2875,12 +2423,10 @@ Each of these 3 primitives can be composed to yield a cross-product of different Holds between molecular entities A and B where A can physically interact with B and in doing so positively regulates a process that B is capable of. For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B. - Holds between molecules a and b if and only if a executes a process that directly activates a process executed by b. Chris Mungall activates molecularly increases activity of activity directly positively regulates activity of - molecularly increases activity of @@ -2888,10 +2434,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - Chris Mungall This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning. - helper property helper property (not for use in curation) @@ -2905,16 +2449,10 @@ Each of these 3 primitives can be composed to yield a cross-product of different 'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate' x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y. - x composed_primarily_of y iff: more than half of the mass of x is made from parts of y Chris Mungall - RO:0002473 - uberon - RO:0002473 - composed_primarily_of - composed_primarily_of composed primarily of @@ -2963,7 +2501,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different A relationship between a material entity and a process where the material entity has some causal role that influences the process - causal agent in causal agent in process @@ -3024,8 +2561,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different Chris Mungall determined by (system to material entity) - Chris Mungall - Pier Buttigieg Chris Mungall Pier Buttigieg @@ -3233,9 +2768,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different Inverse of 'causal agent in process' - Inverse of 'causal agent in' - has causal agent process has causal agent @@ -3247,7 +2780,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different A relationship that holds between two entities, where the relationship holds based on the presence or absence of statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. obsolete related via dependence to - related via dependence to true @@ -3259,7 +2791,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different Process(P1) directly postively regulates process(P2) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P1 directly positively regulates P2. - Process(P1) directly regulates process(P2) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P1 directly positively regulates P2. directly positively regulates (process to process) @@ -3274,7 +2805,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different Process(P1) directly negatively regulates process(P2) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P1 directly negatively regulates P2. - Process(P1) directly regulates process(P2) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P1 directly negatively regulates P2. directly negatively regulates (process to process) @@ -3298,13 +2828,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix. Melissa Haendel - RO:0003000 - uberon - produces - produces Note that this definition doesn't quite distinguish the output of a transformation process from a production process, which is related to the identity/granularity issue. - produces produces @@ -3318,13 +2843,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different a produced_by b iff some process that occurs_in b has_output a. Melissa Haendel - RO:0003001 - uberon - produced_by - produced_by produced by - produced_by @@ -3759,18 +3279,9 @@ Association is weaker than correlation or proportionality. These relations may b - - - - entity - - - - - @@ -3793,7 +3304,6 @@ Association is weaker than correlation or proportionality. These relations may b - @@ -3825,15 +3335,8 @@ Association is weaker than correlation or proportionality. These relations may b A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. - b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) independent continuant - - - - b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) - - @@ -3851,15 +3354,8 @@ Association is weaker than correlation or proportionality. These relations may b An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. - p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) process - - - - p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) - - @@ -3907,34 +3403,8 @@ Association is weaker than correlation or proportionality. These relations may b A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. - b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n &gt; 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i &lt; j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004]) - b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) specifically dependent continuant - - - - b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) - - - - - - - - - - object aggregate - - - - - - - - - site - @@ -3949,8 +3419,6 @@ Association is weaker than correlation or proportionality. These relations may b A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time. - b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) - generically dependent continuant @@ -4003,7 +3471,6 @@ Association is weaker than correlation or proportionality. These relations may b - anatomical structure connected anatomical structure @@ -4034,11 +3501,7 @@ Association is weaker than correlation or proportionality. These relations may b - - Material anatomical entity that is a member of an individual species or is a viral or viroid particle. - organism or virus - Melissa Haendel - 9/18/11 + organism or virus or viroid @@ -4053,90 +3516,9 @@ Association is weaker than correlation or proportionality. These relations may b - - - - A chemical entity is a physical entity of interest in chemistry including molecular entities, parts thereof, and chemical substances. - chemical entity - chebi_ontology - CHEBI:24431 - - chemical entity - - - - - chemical entity - UniProt - - - - - - - In general, a mineral is a chemical substance that is normally crystalline formed and has been formed as a result of geological processes. The term also includes metamict substances (naturally occurring, formerly crystalline substances whose crystallinity has been destroyed by ionising radiation) and can include naturally occurring amorphous substances that have never been crystalline ('mineraloids') such as georgite and calciouranoite as well as substances formed by the action of geological processes on bigenic compounds ('biogenic minerals'). - mineral - chebi_ontology - Minerale - minerales - minerals - mineraux - CHEBI:46662 - - mineral - - - - - mineral - ChEBI - - - - - Minerale - ChEBI - - - - - minerales - ChEBI - - - - - minerals - ChEBI - - - - - mineraux - ChEBI - - - - - - - - - A chemical substance is a portion of matter of constant composition, composed of molecular entities of the same type or of different types. - chebi_ontology - Chemische Substanz - CHEBI:59999 - - chemical substance - - - - - Chemische Substanz - ChEBI - + @@ -4150,505 +3532,12 @@ Association is weaker than correlation or proportionality. These relations may b - - - - - - - - - - - - - - - - - - - - - - A material entity which determines an environmental system. - environmental feature - - - - - A material entity which determines an environmental system. - DOI:10.1186/2041-1480-4-43 - NM:nm - ORCID:0000-0002-4366-3088 - - - - - - - - - A portion of environmental material is a fiat object which forms the medium or part of the medium of an environmental system. - portion of environmental material - environmental material - - - - - A portion of environmental material is a fiat object which forms the medium or part of the medium of an environmental system. - DOI:10.1186/2041-1480-4-43 - MA:ma - ORCID:0000-0002-4366-3088 - URL:http://ontology.buffalo.edu/smith/articles/niches.html - - - - - A system which has the disposition to environ one or more material entities. - environment environmental system - - - - A system which has the disposition to environ one or more material entities. - DOI:10.1186/2041-1480-4-43 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - An anthropogenic environment is an environmental system which is the product of human activity. - anthropogenic environment - - - - - - - - - - - - - - - - - - - - - - - - An environmental system in which minimal to no anthropisation has occurred and non-human agents are the primary determinants of the system's dynamics and composition. - natural environment - - - - - An environmental system in which minimal to no anthropisation has occurred and non-human agents are the primary determinants of the system's dynamics and composition. - https://en.wikipedia.org/wiki/Anthropization - https://en.wikipedia.org/wiki/Natural_environment - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A process during which a natural environmental system is altered by human action. - anthropization - anthropisation - - - - - A process during which a natural environmental system is altered by human action. - https://en.wikipedia.org/wiki/Anthropization - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - An environmental system which is determined by materials bearing roughly homogeneous qualities. - environmental system determined by a quality - - - - - - - - - - - - - - - - - - - - - - - - - - An environmental system within which an environmental material strongly influences the system's composition and properties. - environmental system determined by a material - - - - - - - - - - - - - - - - - - - - - - - - - - An environmental system which is determined by a living organism. - host-associated environment - environmental system determined by an organism - - - - - - - - - - - - - - - - - - - - - - - - - - An environmental system determined by an animal. - animal environment - Metazoan-associated environment - animal-associated environment - - - - - - - - - - - - - - - - - - - - - - - - - - An environmental system determined by part of a living or dead animal, or a whole small animal. - environment associated with an animal part or small animal - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - An environmental system determined by part of a living or dead plant, or a whole small plant. - environment associated with a plant part or small plant - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - An environmental system which includes both living and non-living components. - ecosystem - - - - - An environmental system which includes both living and non-living components. - https://en.wikipedia.org/wiki/Ecosystem - - - - - - - - - - - - - - - - - - - - - - - A process in which includes the components of an environmental system as participants. - environmental system process - - - - - - - - - - - - - - - - - - - - - - - - - - An environmental process which is driven by the action of humans. - anthropogenic environmental process - @@ -4721,7 +3610,6 @@ Association is weaker than correlation or proportionality. These relations may b - receptor activity true @@ -5200,7 +4088,6 @@ Association is weaker than correlation or proportionality. These relations may b A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. - Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end. janelomax 2012-09-19T15:05:24Z GO:0000004 @@ -5231,13 +4118,6 @@ Association is weaker than correlation or proportionality. These relations may b A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. GOC:pdt - - - - Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end. - GOC:go_curators - GOC:isa_complete - @@ -5772,7 +4652,7 @@ Association is weaker than correlation or proportionality. These relations may b - + A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. @@ -6869,7 +5749,7 @@ Association is weaker than correlation or proportionality. These relations may b A prolongation or process extending from a cell, e.g. a flagellum or axon. GOC:jl - http://www.cogsci.princeton.edu/~wn/ + http://www.cogsci.princeton.edu/~wn/ @@ -9399,793 +8279,6 @@ Association is weaker than correlation or proportionality. These relations may b - - - - - data item - - - - - - - - - information content entity - - - - - - - - - - - - - - - - - - - - - - - - curation status specification - - The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. - Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting) - PERSON:Bill Bug - GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - OBI_0000266 - curation status specification - - - - - - - - - data about an ontology part is a data item about a part of an ontology, for example a term - Person:Alan Ruttenberg - data about an ontology part - - - - - - - - - - - - - - - - - - - - obsolescence reason specification - - The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. - The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology. - PERSON: Alan Ruttenberg - PERSON: Melanie Courtot - obsolescence reason specification - - - - - - - - - - - - - - - - - - The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are "natural kinds" and the latter arbitrary collections of entities. - A denotator type indicates how a term should be interpreted from an ontological perspective. - Alan Ruttenberg - Barry Smith, Werner Ceusters - denotator type - - - - - - - - - all - root - - - - - all - - - - - - all - - - - - - - - - - Teleostomi - - - - - - - - - bony vertebrates - Euteleostomi - - - - - bony vertebrates - - - - - - - - - - biota - cellular organisms - - - - - biota - - - - - - biota - - - - - - - - - - Dipnotetrapodomorpha - - - - - - - - - Boreotheria - Boreoeutheria - - - - - Boreotheria - - - - - - - - - - Homo/Pan/Gorilla group - Homininae - - - - - Homo/Pan/Gorilla group - - - - - - - - - - eucaryotes - eukaryotes - Eucarya - Eucaryotae - Eukarya - Eukaryotae - eukaryotes - Eukaryota - - - - - eucaryotes - - - - - - eucaryotes - - - - - - eukaryotes - - - - - - eukaryotes - - - - - - Eucarya - - - - - - Eucarya - - - - - - Eucaryotae - - - - - - Eucaryotae - - - - - - Eukarya - - - - - - Eukarya - - - - - - Eukaryotae - - - - - - Eukaryotae - - - - - - eukaryotes - - - - - - eukaryotes - - - - - - - - - - Euarchontoglires - - - - - - - - - Anthropoidea - Simiiformes - - - - - Anthropoidea - - - - - - - - - - ape - apes - Hominoidea - - - - - ape - - - - - - apes - - - - - - - - - - tetrapods - Tetrapoda - - - - - tetrapods - - - - - - - - - - amniotes - Amniota - - - - - amniotes - - - - - - - - - - Theria - Theria <Mammalia> - - - - - Theria - - - - - - - - - - Fungi/Metazoa group - opisthokonts - Opisthokonta - - - - - Fungi/Metazoa group - - - - - - opisthokonts - - - - - - - - - - metazoans - multicellular animals - Animalia - animals - Metazoa - - - - - metazoans - - - - - - multicellular animals - - - - - - Animalia - - - - - - animals - - - - - - - - - - Bilateria - - - - - - - - - deuterostomes - Deuterostomia - - - - - deuterostomes - - - - - - - - - - Haplorrhini - - - - - - - - - mammals - mammals - Mammalia - - - - - mammals - - - - - - mammals - - - - - - - - - - Eumetazoa - - - - - - - - - chordates - chordates - Chordata - - - - - chordates - - - - - - chordates - - - - - - - - - - Vertebrata - vertebrates - vertebrates - Vertebrata <Metazoa> - - - - - Vertebrata - - - - - - vertebrates - - - - - - vertebrates - - - - - - - - - - Gnathostomata - jawed vertebrates - Gnathostomata <vertebrate> - - - - - Gnathostomata - - - - - - jawed vertebrates - - - - - - - - - - Sarcopterygii - - - - - - - - - Craniata - Craniata <chordata> - - - - - Craniata - - - - - - - - - - eutherian mammals - placental mammals - placentals - Placentalia - placentals - Eutheria - - - - - eutherian mammals - - - - - - placental mammals - - - - - - placentals - - - - - - Placentalia - - - - - - placentals - - - - - - - - - - primate - Primata - primates - Primates - - - - - primate - - - - - - Primata - - - - - - primates - - - - - - - - - - Catarrhini - - - - - - - - - great apes - Pongidae - Hominidae - - - - - great apes - - - - - - Pongidae - - - - - - - - - - humans - Homo - - - - - humans - - - - - - - - - - human - man - humans - Homo sapiens - - - - - human - - - - - - man - - - - - @@ -10204,7 +8297,6 @@ Association is weaker than correlation or proportionality. These relations may b A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities quality (PATO) PATO:0000072 - trait quality PATO:0000001 quality @@ -10968,7 +9060,7 @@ Association is weaker than correlation or proportionality. These relations may b - A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure. + A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure. quality PATO:0000051 @@ -10977,7 +9069,7 @@ Association is weaker than correlation or proportionality. These relations may b - A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure. + A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure. PATOC:GVG @@ -11255,7 +9347,7 @@ Association is weaker than correlation or proportionality. These relations may b - A quality inhering in a bearer by virtue of the whether the bearer differs from normal or average. + A quality inhering in a bearer by virtue of the whether the bearer differs from normal or average. quality PATO:0000069 @@ -11264,7 +9356,7 @@ Association is weaker than correlation or proportionality. These relations may b - A quality inhering in a bearer by virtue of the whether the bearer differs from normal or average. + A quality inhering in a bearer by virtue of the whether the bearer differs from normal or average. PATOC:GVG @@ -11875,7 +9967,7 @@ Association is weaker than correlation or proportionality. These relations may b - A morphology quality inhering in a bearer by virtue of the bearer's physical magnitude. + A morphology quality inhering in a bearer by virtue of the bearer's physical magnitude. quality PATO:0000117 @@ -11885,7 +9977,7 @@ Association is weaker than correlation or proportionality. These relations may b - A morphology quality inhering in a bearer by virtue of the bearer's physical magnitude. + A morphology quality inhering in a bearer by virtue of the bearer's physical magnitude. WordNet:WordNet @@ -18588,7 +16680,7 @@ Association is weaker than correlation or proportionality. These relations may b - A size quality which is relatively low. + A size quality which is relatively low. hypoplasia underdeveloped @@ -18603,7 +16695,7 @@ Association is weaker than correlation or proportionality. These relations may b - A size quality which is relatively low. + A size quality which is relatively low. PATOC:GVG @@ -30729,7 +28821,7 @@ Association is weaker than correlation or proportionality. These relations may b - A polyploidy quality inhering in a bearer by virtue of the bearer's containing four homologous sets of chromosomes. + A polyploidy quality inhering in a bearer by virtue of the bearer's containing six homologous sets of chromosomes. quality PATO:0001384 @@ -30739,7 +28831,7 @@ Association is weaker than correlation or proportionality. These relations may b - A polyploidy quality inhering in a bearer by virtue of the bearer's containing four homologous sets of chromosomes. + A polyploidy quality inhering in a bearer by virtue of the bearer's containing six homologous sets of chromosomes. Wikipedia:http://en.wikipedia.org/wiki/Hexaploid @@ -51345,7 +49437,7 @@ Association is weaker than correlation or proportionality. These relations may b - A quality that has a value that is decreased compared to normal or average. + A quality that has a value that is decreased compared to normal or average. George Gkoutos 2011-06-16T06:40:15Z @@ -51356,7 +49448,7 @@ Association is weaker than correlation or proportionality. These relations may b - A quality that has a value that is decreased compared to normal or average. + A quality that has a value that is decreased compared to normal or average. PATOC:GVG @@ -51411,7 +49503,7 @@ Association is weaker than correlation or proportionality. These relations may b - A quality of an object that has a value that is decreased compared to normal or average. + A quality of an object that has a value that is decreased compared to normal or average. George Gkoutos 2011-06-16T06:51:54Z @@ -51422,7 +49514,7 @@ Association is weaker than correlation or proportionality. These relations may b - A quality of an object that has a value that is decreased compared to normal or average. + A quality of an object that has a value that is decreased compared to normal or average. PATOC:GVG @@ -59022,6 +57114,27 @@ height'). + + + + + A ploidy quality inhering in a bearer by virtue of the bearer's haploid cells undergo chromosome doubling. + http://orcid.org/0000-0001-5208-3432 + double haploid + double-haploid + quality + PATO:0040027 + doubled haploid + + + + + A ploidy quality inhering in a bearer by virtue of the bearer's haploid cells undergo chromosome doubling. + Wikipedia:https://en.wikipedia.org/wiki/Doubled_haploidy + + + + @@ -61116,7 +59229,7 @@ height'). - A variability which is relatively normal or average + A variability of color which is relatively normal or average Luke Slater 2017-12-22T14:16:43Z quality @@ -61780,361 +59893,15 @@ height'). - - - - - - - - - - - - - 2 - - - - - - - - - - - - - - Examples include: population, community, species (meaning the collection of organisms that makes up a species, not the taxonomic rank), and family. - - A material entity that consists of two or more organisms, viruses, or viroids. - A material entity that consists of two or more organisms, viruses, or viroids. - group of organism - organism collection - May be of the same or different species. - collection of organisms - collection of organisms - - - - - - - - This a general term that can include every organism of a species living in an area or any subset of them. Subclasses can be more specific as needed. - - A collection of organisms, all of the same species, that live in the same place. - ISBN:0878932739 - It is sometimes difficult to define the physical boundaries of a population. In the case of sexually reproducing organisms, the individuals within a population have the potential to reproduce with one another during the course of their lifetimes. 'Community', as often used to describe a group of humans, is a type of population. - -Classes for population already exist in IDO ('organism population', IDO_0000509) and OBI ('population', OBI_0000181). The definitions should be standardized across OBO Foundry ontologies and only one term used. - population of organisms - - - - - - - - - - - - - - 2 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A community of at least two different species, living in a particular area. Must have at least two populations of different species as members. - Not sure if the equivalancy axiom specifies that both populations are located in the same site. - multispecies community - ISBN:0865423504 - Ecological community is defined broadly here, but includes both ecological interactions (inherited from parent term community) and spatial co-existence. It may be used to describe every organisms living in an area, but is often used to refer only to organisms of a particular taxon or guild (e.g., the plant community, the insect community, the herbivore community). The word community, as it often used to describe a group of humans living together, is a type of single-species collection of organisms, not an ecological community. - ecological community - + - - - - - - - - - - - - - - - - - - - - - A quality that inheres in a biological population. - See Chris's comments on population qualities at: http://code.google.com/p/popcomm-ontology/issues/detail?id=4. These may not belong under BFO:quality. May be better to call them population characteristics, and classify as specifically dependent continuants. Need to look at process profiles in BFO2. - Includes qualities like population size, population growth rate, carrying capacity, immigration rate, emigration rate, fecundity, and death rate. A population quality may depend on the qualities of individual organisms in the population, but cannot be measured or described for a single organism. This term may be replaced by a PATO term. - quality of a population - - - - - - - - - - - - - - - - - - - - - - - - - - - A quality that inheres in a community. - These may not belong under BFO:quality. May be better to call them community characteristics, and classify as specifically dependent continuants. Need to look at process profiles in BFO2. - Includes qualities like diversity, species richness, stability, resilience, community structure, number of trophic levels. A community quality may depend on the qualities of individual organism in the community, but cannot be measured or described for a single individual. - quality of an ecological community - - - - - - - - - - A collection of organisms that has as parts every organism of given species and no organisms of any other species. - At the moment there is no way to specify in an OWL axiom that the collection includes every individual of a species. This should be added, if possible. - This term is neutral with respect to which organisms are included in a species. Membership will depend on the species concept and the taxonomic assertions used to define the species. These criteria must be specified by the user. - species as a collection of organisms - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - 2 - - - - - - - - A material entity that has as parts two or more organisms, viruses, or viroids of the same species and no members of any other species. - collection of organisms of the same species - single-species collection of organisms - - - - - - - - - - - - - - - - - - 2 - - - - - - - - - - - - - - A collection of organisms of the same species that has as members only humans. - human community - human population - collection of humans - - - - - - - - - - A collection of organisms of the same species whose members are all either genealogically related to each other or have mated with each other. - Biological or social relations are covered by RO_0002437 (biotically interacts with), but that relations does provide an easy way to specify that two entities are interacting with each other (participating in the same interaction). Until that axiom is specified, the logical definition of this term is incomplete. - These relations can include shared values, occupying the same spatial regkion. A community be be a single species collection of organsisms (as in a human community, which is also a type of population) or a or multi-species collection of organisms (as in an ecological community). - community - - - - - - - - - - A collection of organisms that consists of two or more organisms from at least two species. - Need to add axiom to specify that it has at a mimum members of two different species, but not sure how to specify that. Can't say "('has member' only ('member of' min 2 'species as a collection of organisms'))". - - multi-species collection of organisms - - - - - - - - - - - - - - - - - - A material entity that is one or more organisms, viruses or viroids. - organismal entity - - - - - - - - - A plant structure (PO:0005679) which is a whole organism. - genet (broad) - ramet (broad) - planta entera (Spanish, exact) - 植物体全体 (Japanese, exact) - bush (narrow) - frutex (narrow) - frutices (narrow) - gametophyte (narrow) - herb (narrow) - liana (narrow) - prothalli (narrow) - prothallium (narrow) - prothallus (narrow) - seedling (narrow) - shrub (narrow) - sporophyte (narrow) - suffrutex (narrow) - suffrutices (narrow) - tree (narrow) - vine (narrow) - woody clump (narrow) - clonal colony (related) - colony (related) - whole plant - - - - - - - - - An anatomical structure that is or was part of a plant, or was derived from a part of a plant. - estructura vegetal (Spanish, exact) - 植物 構造 (Japanese, exact) - plant structure - - - - - - - - - An anatomical entity that is or was part of a plant. - entidad anat&#243mica vegetal (Spanish, exact) - 植物 解剖学（形態）的実体 (Japanese, exact) - plant anatomical entity - + @@ -62151,66 +59918,6 @@ Classes for population already exist in IDO ('organism population', I - - - - - Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species. - - AAO:0010841 - AEO:0000000 - BILA:0000000 - BIRNLEX:6 - CARO:0000000 - EHDAA2:0002229 - FBbt:10000000 - FBbt_root:00000000 - FMA:62955 - HAO:0000000 - MA:0000001 - NCIT:C12219 - TAO:0100000 - TGMA:0001822 - UMLS:C1515976 - WBbt:0000100 - XAO:0000000 - ZFA:0100000 - uberon - UBERON:0001062 - - anatomical entity - - - - - Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species. - - FMA:62955 - - - - - UMLS:C1515976 - ncithesaurus:Anatomic_Structure_System_or_Substance - - - - - - - - - - - - - - - - - - - - - - - example to be eventually removed - - - - - - - - - The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job - Person:Alan Ruttenberg - failed exploratory term - - - - - - - - - Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete. - metadata complete - - - - - - - - - term created to ease viewing/sort terms for development purpose, and will not be included in a release - organizational term - - - - - - Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release." ready for release - - - - - Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors. - metadata incomplete - - - - - - - - - Nothing done yet beyond assigning a unique class ID and proposing a preferred term. - uncurated - - - - - - All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor. pending final vetting - - - - - Core is an instance of a grouping of terms from an ontology or ontologies. It is used by the ontology to identify main classes. - PERSON: Alan Ruttenberg - PERSON: Melanie Courtot - core - - - - - - - - - placeholder removed - - - - - - - - - An editor note should explain what were the merged terms and the reason for the merge. - terms merged - - - - - - - - - This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use. - term imported - - - - - - - - - This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created. - term split - - - - - - - - - Hard to give a definition for. Intuitively a "natural kind" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents. - Alan Ruttenberg - A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf - universal - - - - - - - - - A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal - "definitions", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal. - Alan Ruttenberg - defined class - - - - - - - - - A named class expression is a logical expression that is given a name. The name can be used in place of the expression. - named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions - Alan Ruttenberg - named class expression - - - - - - - - - Terms with this status should eventually replaced with a term from another ontology. - Alan Ruttenberg - group:OBI - to be replaced with external ontology term - - - - - - A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues. - Alan Ruttenberg - group:OBI requires discussion @@ -62464,29 +60004,34 @@ This interpretation is *not* the same as an at-all-times relation --> - + + - + - + - + - - - + + + + + + + - + - + @@ -62651,14 +60196,6 @@ This interpretation is *not* the same as an at-all-times relation - - - - - - - - @@ -62669,28 +60206,6 @@ This interpretation is *not* the same as an at-all-times relation - - - - - - - - - - - - - - - - - - - - - - @@ -62708,19 +60223,19 @@ This interpretation is *not* the same as an at-all-times relation - + - + - + - + @@ -62827,9 +60342,10 @@ This interpretation is *not* the same as an at-all-times relation - - - + + + + @@ -62837,9 +60353,10 @@ This interpretation is *not* the same as an at-all-times relation - - - + + + + @@ -62847,10 +60364,9 @@ This interpretation is *not* the same as an at-all-times relation - - + + - @@ -62858,10 +60374,9 @@ This interpretation is *not* the same as an at-all-times relation - - - - + + + @@ -62888,65 +60403,6 @@ This interpretation is *not* the same as an at-all-times relation - - true - GP(X) part_of complex(Y) enables MF(Z) -> X contributes_to Z - contrib to MF - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z), e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity' @@ -62957,10 +60413,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - - + + + @@ -62969,9 +60424,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -62979,9 +60434,10 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + + @@ -63016,10 +60472,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - - + + + @@ -63038,9 +60493,10 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + + @@ -63420,9 +60876,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -63431,9 +60887,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + +