From 82653c3416afea9e97836d63fb46d7f6557361bb Mon Sep 17 00:00:00 2001 From: Jules Jacobsen Date: Fri, 21 Feb 2020 14:21:58 +0000 Subject: [PATCH 1/5] Add Jackson annotations to allow de-serialisation. Addresses issue #52. Update OgJsonReader to return a GraphDocument rather than Graph --- examples/basic.json | 16 +- examples/basic.yaml | 12 +- examples/equivNodeSetTest.json | 38 +- examples/equivNodeSetTest.yaml | 30 +- examples/logicalDefinitionTest.json | 16 +- examples/logicalDefinitionTest.yaml | 12 +- examples/nucleus.json | 60 +- examples/nucleus.yaml | 66 +- examples/obsoletion_example.json | 26 +- examples/obsoletion_example.yaml | 18 +- examples/ro.json | 596 +++++++++--------- examples/ro.yaml | 548 ++++++++-------- .../obographs/io/OgJsonReader.java | 17 +- .../geneontology/obographs/model/Edge.java | 14 +- .../geneontology/obographs/model/Graph.java | 23 +- .../obographs/model/GraphDocument.java | 23 +- .../geneontology/obographs/model/Meta.java | 18 + .../geneontology/obographs/model/Node.java | 18 +- .../obographs/model/axiom/AbstractAxiom.java | 8 +- .../model/axiom/AbstractExpression.java | 8 - .../model/axiom/DomainRangeAxiom.java | 17 +- .../model/axiom/EquivalentNodesSet.java | 11 +- .../ExistentialRestrictionExpression.java | 8 +- .../model/axiom/LogicalDefinitionAxiom.java | 12 +- .../model/axiom/PropertyChainAxiom.java | 17 +- .../model/meta/AbstractPropertyValue.java | 26 +- .../model/meta/BasicPropertyValue.java | 30 +- .../model/meta/DefinitionPropertyValue.java | 19 +- .../model/meta/SynonymPropertyValue.java | 41 +- .../model/meta/XrefPropertyValue.java | 12 +- .../obographs/io/OgJsonGeneratorTest.java | 53 +- 31 files changed, 960 insertions(+), 853 deletions(-) diff --git a/examples/basic.json b/examples/basic.json index 7eee13b..6e1b35c 100644 --- a/examples/basic.json +++ b/examples/basic.json @@ -4,10 +4,6 @@ "id" : "http://purl.obolibrary.org/obo/UBERON_0002470", "type" : "CLASS", "lbl" : "autopod region" - }, { - "id" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "type" : "PROPERTY", - "lbl" : "shorthand" }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000050", "meta" : { @@ -20,6 +16,10 @@ } ] }, "type" : "PROPERTY" + }, { + "id" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "type" : "PROPERTY", + "lbl" : "shorthand" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#hasDbXref", "type" : "PROPERTY", @@ -32,10 +32,6 @@ "id" : "http://purl.obolibrary.org/obo/UBERON_0002102", "type" : "CLASS", "lbl" : "forelimb" - }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0002101", - "type" : "CLASS", - "lbl" : "limb" }, { "id" : "http://purl.obolibrary.org/obo/UBERON_0002398", "meta" : { @@ -46,6 +42,10 @@ }, "type" : "CLASS", "lbl" : "manus" + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0002101", + "type" : "CLASS", + "lbl" : "limb" } ], "edges" : [ { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002102", diff --git a/examples/basic.yaml b/examples/basic.yaml index c65787a..c3bffcd 100644 --- a/examples/basic.yaml +++ b/examples/basic.yaml @@ -4,9 +4,6 @@ graphs: - id: "http://purl.obolibrary.org/obo/UBERON_0002470" type: "CLASS" lbl: "autopod region" - - id: "http://www.geneontology.org/formats/oboInOwl#shorthand" - type: "PROPERTY" - lbl: "shorthand" - id: "http://purl.obolibrary.org/obo/BFO_0000050" meta: xrefs: @@ -15,6 +12,9 @@ graphs: - pred: "http://www.geneontology.org/formats/oboInOwl#shorthand" val: "part_of" type: "PROPERTY" + - id: "http://www.geneontology.org/formats/oboInOwl#shorthand" + type: "PROPERTY" + lbl: "shorthand" - id: "http://www.geneontology.org/formats/oboInOwl#hasDbXref" type: "PROPERTY" lbl: "database_cross_reference" @@ -24,9 +24,6 @@ graphs: - id: "http://purl.obolibrary.org/obo/UBERON_0002102" type: "CLASS" lbl: "forelimb" - - id: "http://purl.obolibrary.org/obo/UBERON_0002101" - type: "CLASS" - lbl: "limb" - id: "http://purl.obolibrary.org/obo/UBERON_0002398" meta: definition: @@ -34,6 +31,9 @@ graphs: xrefs: [] type: "CLASS" lbl: "manus" + - id: "http://purl.obolibrary.org/obo/UBERON_0002101" + type: "CLASS" + lbl: "limb" edges: - sub: "http://purl.obolibrary.org/obo/UBERON_0002102" pred: "is_a" diff --git a/examples/equivNodeSetTest.json b/examples/equivNodeSetTest.json index 834369d..4c19101 100644 --- a/examples/equivNodeSetTest.json +++ b/examples/equivNodeSetTest.json @@ -9,35 +9,35 @@ }, "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "Hemangiosarcoma", + "val" : "hemangiosarcoma", "xrefs" : [ ] }, { "pred" : "hasExactSynonym", - "val" : "HEMANGIOSARCOMA, MALIGNANT", + "val" : "Hemangiosarcoma", "xrefs" : [ ] }, { "pred" : "hasExactSynonym", - "val" : "angiosarcoma", + "val" : "HEMANGIOSARCOMA, MALIGNANT", "xrefs" : [ ] }, { "pred" : "hasExactSynonym", - "val" : "Hemangiosarcoma", + "val" : "Malignant Angioendothelioma", "xrefs" : [ ] }, { "pred" : "hasExactSynonym", - "val" : "Angiosarcoma", + "val" : "Hemangiosarcoma", "xrefs" : [ ] }, { "pred" : "hasExactSynonym", - "val" : "hemangiosarcoma", + "val" : "Malignant Hemangioendothelioma", "xrefs" : [ ] }, { "pred" : "hasExactSynonym", - "val" : "Malignant Angioendothelioma", + "val" : "angiosarcoma", "xrefs" : [ ] }, { "pred" : "hasExactSynonym", - "val" : "Malignant Hemangioendothelioma", + "val" : "Angiosarcoma", "xrefs" : [ ] } ] }, @@ -80,10 +80,6 @@ "id" : "http://www.geneontology.org/formats/oboInOwl#hasDbXref", "type" : "PROPERTY", "lbl" : "database_cross_reference" - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000115", - "type" : "PROPERTY", - "lbl" : "definition" }, { "id" : "http://purl.obolibrary.org/obo/DOID_267", "meta" : { @@ -97,6 +93,10 @@ "deprecated" : true }, "type" : "CLASS" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000115", + "type" : "PROPERTY", + "lbl" : "definition" }, { "id" : "http://purl.obolibrary.org/obo/DOID_0001816", "meta" : { @@ -106,23 +106,23 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/TEMP#NCIthesaurus" ], "xrefs" : [ { - "val" : "SCTID:33176006" + "val" : "MESH:D006394" }, { - "val" : "UMLS:C0018923" + "val" : "NCIT:C9275" }, { - "val" : "Orphanet:263413" + "val" : "SCTID:33176006" }, { "val" : "SCTID:39000009" }, { - "val" : "MESH:D006394" - }, { - "val" : "UMLS:C0854893" + "val" : "UMLS:C0018923" }, { "val" : "SCTID:403977003" }, { - "val" : "NCIT:C9275" + "val" : "UMLS:C0854893" }, { "val" : "NCIT:C3088" + }, { + "val" : "Orphanet:263413" } ], "synonyms" : [ { "pred" : "hasExactSynonym", diff --git a/examples/equivNodeSetTest.yaml b/examples/equivNodeSetTest.yaml index 8c5e5f4..b95752f 100644 --- a/examples/equivNodeSetTest.yaml +++ b/examples/equivNodeSetTest.yaml @@ -12,6 +12,9 @@ graphs: \ lymphedema are at increased risk of developing angiosarcoma." xrefs: [] synonyms: + - pred: "hasExactSynonym" + val: "hemangiosarcoma" + xrefs: [] - pred: "hasExactSynonym" val: "Hemangiosarcoma" xrefs: [] @@ -19,22 +22,19 @@ graphs: val: "HEMANGIOSARCOMA, MALIGNANT" xrefs: [] - pred: "hasExactSynonym" - val: "angiosarcoma" + val: "Malignant Angioendothelioma" xrefs: [] - pred: "hasExactSynonym" val: "Hemangiosarcoma" xrefs: [] - pred: "hasExactSynonym" - val: "Angiosarcoma" - xrefs: [] - - pred: "hasExactSynonym" - val: "hemangiosarcoma" + val: "Malignant Hemangioendothelioma" xrefs: [] - pred: "hasExactSynonym" - val: "Malignant Angioendothelioma" + val: "angiosarcoma" xrefs: [] - pred: "hasExactSynonym" - val: "Malignant Hemangioendothelioma" + val: "Angiosarcoma" xrefs: [] type: "CLASS" lbl: "Angiosarcoma" @@ -67,9 +67,6 @@ graphs: - id: "http://www.geneontology.org/formats/oboInOwl#hasDbXref" type: "PROPERTY" lbl: "database_cross_reference" - - id: "http://purl.obolibrary.org/obo/IAO_0000115" - type: "PROPERTY" - lbl: "definition" - id: "http://purl.obolibrary.org/obo/DOID_267" meta: basicPropertyValues: @@ -79,6 +76,9 @@ graphs: val: "http://purl.obolibrary.org/obo/IAO_0000227" deprecated: true type: "CLASS" + - id: "http://purl.obolibrary.org/obo/IAO_0000115" + type: "PROPERTY" + lbl: "definition" - id: "http://purl.obolibrary.org/obo/DOID_0001816" meta: definition: @@ -92,15 +92,15 @@ graphs: subsets: - "http://purl.obolibrary.org/obo/TEMP#NCIthesaurus" xrefs: + - val: "MESH:D006394" + - val: "NCIT:C9275" - val: "SCTID:33176006" - - val: "UMLS:C0018923" - - val: "Orphanet:263413" - val: "SCTID:39000009" - - val: "MESH:D006394" - - val: "UMLS:C0854893" + - val: "UMLS:C0018923" - val: "SCTID:403977003" - - val: "NCIT:C9275" + - val: "UMLS:C0854893" - val: "NCIT:C3088" + - val: "Orphanet:263413" synonyms: - pred: "hasExactSynonym" val: "hemangiosarcoma" diff --git a/examples/logicalDefinitionTest.json b/examples/logicalDefinitionTest.json index 8f60647..d15a383 100644 --- a/examples/logicalDefinitionTest.json +++ b/examples/logicalDefinitionTest.json @@ -4,10 +4,6 @@ "id" : "http://purl.obolibrary.org/obo/UBERON_0002470", "type" : "CLASS", "lbl" : "autopod region" - }, { - "id" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "type" : "PROPERTY", - "lbl" : "shorthand" }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000050", "meta" : { @@ -20,6 +16,10 @@ } ] }, "type" : "PROPERTY" + }, { + "id" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "type" : "PROPERTY", + "lbl" : "shorthand" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#hasDbXref", "type" : "PROPERTY", @@ -32,10 +32,6 @@ "id" : "http://purl.obolibrary.org/obo/UBERON_0002102", "type" : "CLASS", "lbl" : "forelimb" - }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0002101", - "type" : "CLASS", - "lbl" : "limb" }, { "id" : "http://purl.obolibrary.org/obo/UBERON_0002398", "meta" : { @@ -46,6 +42,10 @@ }, "type" : "CLASS", "lbl" : "manus" + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0002101", + "type" : "CLASS", + "lbl" : "limb" } ], "edges" : [ { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002102", diff --git a/examples/logicalDefinitionTest.yaml b/examples/logicalDefinitionTest.yaml index 8656d6f..483ce81 100644 --- a/examples/logicalDefinitionTest.yaml +++ b/examples/logicalDefinitionTest.yaml @@ -4,9 +4,6 @@ graphs: - id: "http://purl.obolibrary.org/obo/UBERON_0002470" type: "CLASS" lbl: "autopod region" - - id: "http://www.geneontology.org/formats/oboInOwl#shorthand" - type: "PROPERTY" - lbl: "shorthand" - id: "http://purl.obolibrary.org/obo/BFO_0000050" meta: xrefs: @@ -15,6 +12,9 @@ graphs: - pred: "http://www.geneontology.org/formats/oboInOwl#shorthand" val: "part_of" type: "PROPERTY" + - id: "http://www.geneontology.org/formats/oboInOwl#shorthand" + type: "PROPERTY" + lbl: "shorthand" - id: "http://www.geneontology.org/formats/oboInOwl#hasDbXref" type: "PROPERTY" lbl: "database_cross_reference" @@ -24,9 +24,6 @@ graphs: - id: "http://purl.obolibrary.org/obo/UBERON_0002102" type: "CLASS" lbl: "forelimb" - - id: "http://purl.obolibrary.org/obo/UBERON_0002101" - type: "CLASS" - lbl: "limb" - id: "http://purl.obolibrary.org/obo/UBERON_0002398" meta: definition: @@ -34,6 +31,9 @@ graphs: xrefs: [] type: "CLASS" lbl: "manus" + - id: "http://purl.obolibrary.org/obo/UBERON_0002101" + type: "CLASS" + lbl: "limb" edges: - sub: "http://purl.obolibrary.org/obo/UBERON_0002102" pred: "is_a" diff --git a/examples/nucleus.json b/examples/nucleus.json index a8b5e2b..424d14e 100644 --- a/examples/nucleus.json +++ b/examples/nucleus.json @@ -37,22 +37,6 @@ "id" : "http://www.geneontology.org/formats/oboInOwl#hasDbXref", "type" : "PROPERTY", "lbl" : "database_cross_reference" - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0044424", - "meta" : { - "definition" : { - "val" : "Any constituent part of the living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.", - "xrefs" : [ "GOC:jl" ] - }, - "comments" : [ "Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC." ], - "subsets" : [ "http://purl.obolibrary.org/obo/go-test#gocheck_do_not_annotate", "http://purl.obolibrary.org/obo/go-test#gosubset_prok", "http://purl.obolibrary.org/obo/go-test#goantislim_grouping" ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "cellular_component" - } ] - }, - "type" : "CLASS", - "lbl" : "intracellular part" }, { "id" : "http://purl.obolibrary.org/obo/GO_0005575", "meta" : { @@ -68,28 +52,44 @@ "val" : "NIF_Subcellular:sao-1337158144" } ], "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "cellular component", - "xrefs" : [ ] - }, { "pred" : "hasRelatedSynonym", "val" : "subcellular entity", "xrefs" : [ "NIF_Subcellular:nlx_subcell_100315" ] + }, { + "pred" : "hasExactSynonym", + "val" : "cellular component", + "xrefs" : [ ] }, { "pred" : "hasExactSynonym", "val" : "cell or subcellular entity", "xrefs" : [ ] } ], "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "cellular_component" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", "val" : "GO:0008372" - }, { + } ] + }, + "type" : "CLASS", + "lbl" : "cellular_component" + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0044424", + "meta" : { + "definition" : { + "val" : "Any constituent part of the living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.", + "xrefs" : [ "GOC:jl" ] + }, + "comments" : [ "Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC." ], + "subsets" : [ "http://purl.obolibrary.org/obo/go-test#gocheck_do_not_annotate", "http://purl.obolibrary.org/obo/go-test#gosubset_prok", "http://purl.obolibrary.org/obo/go-test#goantislim_grouping" ], + "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" } ] }, "type" : "CLASS", - "lbl" : "cellular_component" + "lbl" : "intracellular part" }, { "id" : "http://purl.obolibrary.org/obo/GO_0044464", "meta" : { @@ -158,6 +158,10 @@ "id" : "http://www.geneontology.org/formats/oboInOwl#SynonymTypeProperty", "type" : "PROPERTY", "lbl" : "synonym_type_property" + }, { + "id" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "type" : "PROPERTY", + "lbl" : "shorthand" }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000050", "meta" : { @@ -174,10 +178,6 @@ }, "type" : "PROPERTY", "lbl" : "part of" - }, { - "id" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "type" : "PROPERTY", - "lbl" : "shorthand" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#inSubset", "type" : "PROPERTY", @@ -323,14 +323,14 @@ "id" : "http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym", "type" : "PROPERTY", "lbl" : "has_related_synonym" - }, { - "id" : "http://www.geneontology.org/formats/oboInOwl#SubsetProperty", - "type" : "PROPERTY", - "lbl" : "subset_property" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#hasScope", "type" : "PROPERTY", "lbl" : "has_scope" + }, { + "id" : "http://www.geneontology.org/formats/oboInOwl#SubsetProperty", + "type" : "PROPERTY", + "lbl" : "subset_property" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", "type" : "PROPERTY", diff --git a/examples/nucleus.yaml b/examples/nucleus.yaml index c4c3854..7f16e44 100644 --- a/examples/nucleus.yaml +++ b/examples/nucleus.yaml @@ -41,29 +41,6 @@ graphs: - id: "http://www.geneontology.org/formats/oboInOwl#hasDbXref" type: "PROPERTY" lbl: "database_cross_reference" - - id: "http://purl.obolibrary.org/obo/GO_0044424" - meta: - definition: - val: "Any constituent part of the living contents of a cell; the matter contained\ - \ within (but not including) the plasma membrane, usually taken to exclude\ - \ large vacuoles and masses of secretory or ingested material. In eukaryotes\ - \ it includes the nucleus and cytoplasm." - xrefs: - - "GOC:jl" - comments: - - "Note that this term is in the subset of terms that should not be used for\ - \ direct gene product annotation. Instead, select a child term or, if no appropriate\ - \ child term exists, please request a new term. Direct annotations to this\ - \ term may be amended during annotation QC." - subsets: - - "http://purl.obolibrary.org/obo/go-test#gocheck_do_not_annotate" - - "http://purl.obolibrary.org/obo/go-test#gosubset_prok" - - "http://purl.obolibrary.org/obo/go-test#goantislim_grouping" - basicPropertyValues: - - pred: "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace" - val: "cellular_component" - type: "CLASS" - lbl: "intracellular part" - id: "http://purl.obolibrary.org/obo/GO_0005575" meta: definition: @@ -96,23 +73,46 @@ graphs: - val: "NIF_Subcellular:sao1337158144" - val: "NIF_Subcellular:sao-1337158144" synonyms: - - pred: "hasExactSynonym" - val: "cellular component" - xrefs: [] - pred: "hasRelatedSynonym" val: "subcellular entity" xrefs: - "NIF_Subcellular:nlx_subcell_100315" + - pred: "hasExactSynonym" + val: "cellular component" + xrefs: [] - pred: "hasExactSynonym" val: "cell or subcellular entity" xrefs: [] basicPropertyValues: + - pred: "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace" + val: "cellular_component" - pred: "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId" val: "GO:0008372" + type: "CLASS" + lbl: "cellular_component" + - id: "http://purl.obolibrary.org/obo/GO_0044424" + meta: + definition: + val: "Any constituent part of the living contents of a cell; the matter contained\ + \ within (but not including) the plasma membrane, usually taken to exclude\ + \ large vacuoles and masses of secretory or ingested material. In eukaryotes\ + \ it includes the nucleus and cytoplasm." + xrefs: + - "GOC:jl" + comments: + - "Note that this term is in the subset of terms that should not be used for\ + \ direct gene product annotation. Instead, select a child term or, if no appropriate\ + \ child term exists, please request a new term. Direct annotations to this\ + \ term may be amended during annotation QC." + subsets: + - "http://purl.obolibrary.org/obo/go-test#gocheck_do_not_annotate" + - "http://purl.obolibrary.org/obo/go-test#gosubset_prok" + - "http://purl.obolibrary.org/obo/go-test#goantislim_grouping" + basicPropertyValues: - pred: "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace" val: "cellular_component" type: "CLASS" - lbl: "cellular_component" + lbl: "intracellular part" - id: "http://purl.obolibrary.org/obo/GO_0044464" meta: definition: @@ -181,6 +181,9 @@ graphs: - id: "http://www.geneontology.org/formats/oboInOwl#SynonymTypeProperty" type: "PROPERTY" lbl: "synonym_type_property" + - id: "http://www.geneontology.org/formats/oboInOwl#shorthand" + type: "PROPERTY" + lbl: "shorthand" - id: "http://purl.obolibrary.org/obo/BFO_0000050" meta: xrefs: @@ -192,9 +195,6 @@ graphs: val: "external" type: "PROPERTY" lbl: "part of" - - id: "http://www.geneontology.org/formats/oboInOwl#shorthand" - type: "PROPERTY" - lbl: "shorthand" - id: "http://www.geneontology.org/formats/oboInOwl#inSubset" type: "PROPERTY" lbl: "in_subset" @@ -336,12 +336,12 @@ graphs: - id: "http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym" type: "PROPERTY" lbl: "has_related_synonym" - - id: "http://www.geneontology.org/formats/oboInOwl#SubsetProperty" - type: "PROPERTY" - lbl: "subset_property" - id: "http://www.geneontology.org/formats/oboInOwl#hasScope" type: "PROPERTY" lbl: "has_scope" + - id: "http://www.geneontology.org/formats/oboInOwl#SubsetProperty" + type: "PROPERTY" + lbl: "subset_property" - id: "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId" type: "PROPERTY" lbl: "has_alternative_id" diff --git a/examples/obsoletion_example.json b/examples/obsoletion_example.json index c0e02c3..c7933aa 100644 --- a/examples/obsoletion_example.json +++ b/examples/obsoletion_example.json @@ -27,6 +27,19 @@ }, "type" : "CLASS", "lbl" : "x1" + }, { + "id" : "http://purl.obolibrary.org/obo/Y_1", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "Y:2" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "y" + } ] + }, + "type" : "CLASS", + "lbl" : "y1" }, { "id" : "http://purl.obolibrary.org/obo/X_2", "meta" : { @@ -41,19 +54,6 @@ }, "type" : "CLASS", "lbl" : "obsolete x2" - }, { - "id" : "http://purl.obolibrary.org/obo/Y_1", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "Y:2" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "y" - } ] - }, - "type" : "CLASS", - "lbl" : "y1" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "type" : "PROPERTY", diff --git a/examples/obsoletion_example.yaml b/examples/obsoletion_example.yaml index 72af9e3..9d220ab 100644 --- a/examples/obsoletion_example.yaml +++ b/examples/obsoletion_example.yaml @@ -20,6 +20,15 @@ graphs: val: "x" type: "CLASS" lbl: "x1" + - id: "http://purl.obolibrary.org/obo/Y_1" + meta: + basicPropertyValues: + - pred: "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId" + val: "Y:2" + - pred: "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace" + val: "y" + type: "CLASS" + lbl: "y1" - id: "http://purl.obolibrary.org/obo/X_2" meta: basicPropertyValues: @@ -30,15 +39,6 @@ graphs: deprecated: true type: "CLASS" lbl: "obsolete x2" - - id: "http://purl.obolibrary.org/obo/Y_1" - meta: - basicPropertyValues: - - pred: "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId" - val: "Y:2" - - pred: "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace" - val: "y" - type: "CLASS" - lbl: "y1" - id: "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace" type: "PROPERTY" lbl: "has_obo_namespace" diff --git a/examples/ro.json b/examples/ro.json index 0198c91..87d5538 100644 --- a/examples/ro.json +++ b/examples/ro.json @@ -204,6 +204,9 @@ "xrefs" : [ ] }, "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_maturation_of" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Chris Mungall" }, { @@ -218,9 +221,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474)" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "results_in_maturation_of" } ] }, "type" : "PROPERTY", @@ -296,14 +296,14 @@ "xrefs" : [ ] }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "results_in_developmental_progression_of" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://wiki.geneontology.org/index.php/Ontology_extensions" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_developmental_progression_of" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Chris Mungall" @@ -363,11 +363,11 @@ "xrefs" : [ ] }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "results_in_development_of" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Chris Mungall" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_development_of" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "every flower development (GO:0009908) results in development of some flower (PO:0009046)" @@ -665,10 +665,10 @@ }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "ancestral_stucture_of" + "val" : "evolutionarily_descended_from" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "evolutionarily_descended_from" + "val" : "ancestral_stucture_of" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" @@ -677,34 +677,34 @@ "type" : "PROPERTY", "lbl" : "derived by descent from" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002157", + "id" : "http://purl.obolibrary.org/obo/RO_0003003", "meta" : { "definition" : { - "val" : "inverse of derived by descent from", + "val" : "Holds between protein a (a transcription factor) and DNA element b if and only if a activates the process of transcription of b.", "xrefs" : [ ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Logical axioms to be added after the relevant branch of GO is MIREOTed in" } ] }, "type" : "PROPERTY", - "lbl" : "has derived by descendant" + "lbl" : "increases expression of" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0003003", + "id" : "http://purl.obolibrary.org/obo/RO_0002157", "meta" : { "definition" : { - "val" : "Holds between protein a (a transcription factor) and DNA element b if and only if a activates the process of transcription of b.", + "val" : "inverse of derived by descent from", "xrefs" : [ ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Logical axioms to be added after the relevant branch of GO is MIREOTed in" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" } ] }, "type" : "PROPERTY", - "lbl" : "increases expression of" + "lbl" : "has derived by descendant" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002150", "meta" : { @@ -1384,6 +1384,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000426", + "val" : "(forall (?x ?y) \n\t(iff \n\t\t(has_fasciculating_neuron_projection ?x ?y)\n\t\t(exists (?nps ?npbs)\t\t\n\t\t\t(and \n\t\t\t\t(\"neuron projection bundle ; CARO_0001001\" ?x)\n\t\t\t\t(\"neuron projection ; GO0043005\" ?y)\n\t\t\t\t(\"neuron projection segment ; CARO_0001502\" ?nps)\n\t\t\t\t(\"neuron projection bundle segment ; CARO_0001500\" ?npbs)\n\t\t\t\t(part_of ?nps ?y)\n\t\t\t\t(part_of ?npbs ?x)\n\t\t\t\t(part_of ?nps ?npbs)\n\t\t\t\t(forall (?npbss)\n\t\t\t\t\t(if\n\t\t\t\t\t\t(and \n\t\t\t\t\t\t\t(\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n\t\t\t\t\t\t\t(part_of ?npbss ?npbs) \n\t\t\t\t\t\t)\n\t\t\t\t\t\t(overlaps ?nps ?npbss)\n\t\t\t\t\t))))))\n\n\n" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "David Osumi-Sutherland" @@ -1396,9 +1399,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000426", - "val" : "(forall (?x ?y) \n\t(iff \n\t\t(has_fasciculating_neuron_projection ?x ?y)\n\t\t(exists (?nps ?npbs)\t\t\n\t\t\t(and \n\t\t\t\t(\"neuron projection bundle ; CARO_0001001\" ?x)\n\t\t\t\t(\"neuron projection ; GO0043005\" ?y)\n\t\t\t\t(\"neuron projection segment ; CARO_0001502\" ?nps)\n\t\t\t\t(\"neuron projection bundle segment ; CARO_0001500\" ?npbs)\n\t\t\t\t(part_of ?nps ?y)\n\t\t\t\t(part_of ?npbs ?x)\n\t\t\t\t(part_of ?nps ?npbs)\n\t\t\t\t(forall (?npbss)\n\t\t\t\t\t(if\n\t\t\t\t\t\t(and \n\t\t\t\t\t\t\t(\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n\t\t\t\t\t\t\t(part_of ?npbss ?npbs) \n\t\t\t\t\t\t)\n\t\t\t\t\t\t(overlaps ?nps ?npbss)\n\t\t\t\t\t))))))\n\n\n" } ] }, "type" : "PROPERTY", @@ -1888,33 +1888,33 @@ "type" : "PROPERTY", "lbl" : "cell expresses" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002488", + "id" : "http://purl.obolibrary.org/obo/RO_0002004", "meta" : { "definition" : { - "val" : "x existence starts during y if and only if the time point at which x starts is after or equivalent to the time point at which y starts and before or equivalent to the time point at which y ends. Formally: x existence starts during y iff α(x) >= α(y) & α(x) <= ω(y).", + "val" : "The relationship that holds between a trachea or tracheole and an antomical structure that is contained in (and so provides an oxygen supply to).", "xrefs" : [ ] }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "val" : "David Osumi-Sutherland" } ] }, "type" : "PROPERTY", - "lbl" : "existence starts during" + "lbl" : "tracheates" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002004", + "id" : "http://purl.obolibrary.org/obo/RO_0002488", "meta" : { "definition" : { - "val" : "The relationship that holds between a trachea or tracheole and an antomical structure that is contained in (and so provides an oxygen supply to).", + "val" : "x existence starts during y if and only if the time point at which x starts is after or equivalent to the time point at which y starts and before or equivalent to the time point at which y ends. Formally: x existence starts during y iff α(x) >= α(y) & α(x) <= ω(y).", "xrefs" : [ ] }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "David Osumi-Sutherland" + "val" : "Chris Mungall" } ] }, "type" : "PROPERTY", - "lbl" : "tracheates" + "lbl" : "existence starts during" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002246", "meta" : { @@ -4035,6 +4035,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "fasciculates with" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000426", + "val" : "(forall (?x ?y) \n\t(iff \n\t\t(fasciculates_with ?x ?y)\n\t\t(exists (?nps ?npbs)\n\t\t\t(and \n\t\t\t\t(\"neuron ; CL_0000540\" ?x)\n\t\t\t\t(\"neuron projection bundle ; CARO_0001001\" ?y) \n\t\t\t\t(\"neuron projection segment ; CARO_0001502\" ?nps)\n\t\t\t\t(\"neuron projection bundle segment ; CARO_0001500' \" ?npbs)\n\t\t\t\t(part_of ?npbs ?y) \t\t\t\n\t\t\t\t(part_of ?nps ?x)\n\t\t\t\t(part_of ?nps ?npbs)\n\t\t\t\t(forall (?npbss)\n\t\t\t\t\t(if\n\t\t\t\t\t\t(and \n\t\t\t\t\t\t\t(\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n\t\t\t\t\t\t\t(part_of ?npbss ?npbs) \n\t\t\t\t\t\t)\n\t\t\t\t\t\t(overlaps ?nps ?npbss)\n\t\t\t\t\t))))))" }, { "pred" : "http://purl.org/spar/cito/citesAsAuthority", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" @@ -4044,9 +4047,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "David Osumi-Sutherland" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000426", - "val" : "(forall (?x ?y) \n\t(iff \n\t\t(fasciculates_with ?x ?y)\n\t\t(exists (?nps ?npbs)\n\t\t\t(and \n\t\t\t\t(\"neuron ; CL_0000540\" ?x)\n\t\t\t\t(\"neuron projection bundle ; CARO_0001001\" ?y) \n\t\t\t\t(\"neuron projection segment ; CARO_0001502\" ?nps)\n\t\t\t\t(\"neuron projection bundle segment ; CARO_0001500' \" ?npbs)\n\t\t\t\t(part_of ?npbs ?y) \t\t\t\n\t\t\t\t(part_of ?nps ?x)\n\t\t\t\t(part_of ?nps ?npbs)\n\t\t\t\t(forall (?npbss)\n\t\t\t\t\t(if\n\t\t\t\t\t\t(and \n\t\t\t\t\t\t\t(\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n\t\t\t\t\t\t\t(part_of ?npbss ?npbs) \n\t\t\t\t\t\t)\n\t\t\t\t\t\t(overlaps ?nps ?npbss)\n\t\t\t\t\t))))))" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" @@ -6643,14 +6643,14 @@ }, "type" : "PROPERTY", "lbl" : "involved in regulation of" - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0008150", - "type" : "CLASS", - "lbl" : "biological_process" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002549", "type" : "PROPERTY", "lbl" : "start, weeks post birth" + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0008150", + "type" : "CLASS", + "lbl" : "biological_process" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002429", "meta" : { @@ -8417,13 +8417,13 @@ "xrefs" : [ "http://dx.doi.org/10.1146/annurev.es.20.110189.000411", "http://purl.obolibrary.org/obo/HOM_0000027" ] }, "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "serial homologous to", - "xrefs" : [ ] - }, { "pred" : "hasRelatedSynonym", "val" : "homonomy", "xrefs" : [ ] + }, { + "pred" : "hasExactSynonym", + "val" : "serial homologous to", + "xrefs" : [ ] } ], "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/elements/1.1/creator", @@ -8494,6 +8494,32 @@ }, "type" : "PROPERTY", "lbl" : "in approximate one to one relationship with" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000301", + "meta" : { + "definition" : { + "val" : "A relation that holds between a neuron that is synapsed_to another neuron or a neuron that is connected indirectly to another by a chain of neurons, each synapsed_to the next.", + "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_0000426", + "val" : "(forall (?x ?y) \n\t(iff \n\t\t(upstream_neural_circuit_path ?x ?y)\n\t\t(and\n\t\t\t(\"neuron ; CL_0000540\" ?x)\n\t\t\t(\"neuron ; CL_0000540\" ?y)\n\t\t\t(synapsed_to ?x ?y))))\n\n\n(forall (...s ?x ?y ?z) \n\t(iff \n\t\t(upstream_neural_circuit_path ...s ?x ?y ?z )\n\t\t(and\n\t\t\t(upstream_neural_circuit_path ...s ?x ?y)\n\t\t\t(\"neuron ; CL_0000540\" ?z)\n\t\t\t(synapsed_to ?y ?z))))\n\t\t\t\n(forall (?x ?y) \n\t(iff \n\t\t(upstream_in_neural_circuit_with ?x ?y)\n\t\t(exists (...s)\n\t\t\t(upstream_neural_circuit_path ?x ...s ?y))))" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + } ] + }, + "type" : "PROPERTY", + "lbl" : "upstream in neural circuit with" }, { "id" : "http://purl.obolibrary.org/obo/RO_HOM0000032", "meta" : { @@ -8503,11 +8529,11 @@ }, "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "neotenous to", + "val" : "juvenilization", "xrefs" : [ ] }, { "pred" : "hasExactSynonym", - "val" : "juvenilization", + "val" : "neotenous to", "xrefs" : [ ] } ], "basicPropertyValues" : [ { @@ -8523,32 +8549,6 @@ }, "type" : "PROPERTY", "lbl" : "in neoteny relationship with" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0000301", - "meta" : { - "definition" : { - "val" : "A relation that holds between a neuron that is synapsed_to another neuron or a neuron that is connected indirectly to another by a chain of neurons, each synapsed_to the next.", - "xrefs" : [ ] - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://purl.org/spar/cito/citesAsAuthority", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "David Osumi-Sutherland" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000426", - "val" : "(forall (?x ?y) \n\t(iff \n\t\t(upstream_neural_circuit_path ?x ?y)\n\t\t(and\n\t\t\t(\"neuron ; CL_0000540\" ?x)\n\t\t\t(\"neuron ; CL_0000540\" ?y)\n\t\t\t(synapsed_to ?x ?y))))\n\n\n(forall (...s ?x ?y ?z) \n\t(iff \n\t\t(upstream_neural_circuit_path ...s ?x ?y ?z )\n\t\t(and\n\t\t\t(upstream_neural_circuit_path ...s ?x ?y)\n\t\t\t(\"neuron ; CL_0000540\" ?z)\n\t\t\t(synapsed_to ?y ?z))))\n\t\t\t\n(forall (?x ?y) \n\t(iff \n\t\t(upstream_in_neural_circuit_with ?x ?y)\n\t\t(exists (...s)\n\t\t\t(upstream_neural_circuit_path ?x ...s ?y))))" - } ] - }, - "type" : "PROPERTY", - "lbl" : "upstream in neural circuit with" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002603", "meta" : { @@ -8563,23 +8563,6 @@ }, "type" : "PROPERTY", "lbl" : "is approximately equivalent to" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002604", - "meta" : { - "definition" : { - "val" : "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).", - "xrefs" : [ ] - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "'anterior end of organism' is-opposite-of 'posterior end of organism'" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "'increase in temperature' is-opposite-of 'decrease in temperature'" - } ] - }, - "type" : "PROPERTY", - "lbl" : "is opposite of" }, { "id" : "http://purl.obolibrary.org/obo/RO_0000300", "meta" : { @@ -8588,6 +8571,9 @@ "xrefs" : [ ] }, "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000426", + "val" : "(forall (?x ?y) \n\t(iff \n\t\t(neural_circuit_path ?x ?y)\n\t\t(and\n\t\t\t(\"neuron ; CL_0000540\" ?x)\n\t\t\t(\"neuron ; CL_0000540\" ?y)\n\t\t\t(or \n\t\t\t\t(synapsed_by ?x ?y) \n\t\t\t\t(synapsed_to ?x ?y))))) \n\n(forall (...s ?x ?y ?z) \n\t(iff \n\t\t(neural_circuit_path ...s ?x ?y ?z)\n\t\t(and\n\t\t\t(neural_circuit_path ...s ?x ?y)\n\t\t\t(\"neuron ; CL_0000540\" ?z)\n\t\t\t(or \n\t\t\t\t(synapsed_by ?y ?z) \n\t\t\t\t(synapsed_to ?y ?z))))) \n\n(forall (?x ?y) \n\t(iff \n\t\t(in_neural_circuit_with ?x ?y)\n\t\t(exists (...s)\n\t\t\t(neural_circuit_path ?x ...s ?y)))) " + }, { "pred" : "http://purl.org/spar/cito/citesAsAuthority", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" }, { @@ -8599,13 +8585,27 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000426", - "val" : "(forall (?x ?y) \n\t(iff \n\t\t(neural_circuit_path ?x ?y)\n\t\t(and\n\t\t\t(\"neuron ; CL_0000540\" ?x)\n\t\t\t(\"neuron ; CL_0000540\" ?y)\n\t\t\t(or \n\t\t\t\t(synapsed_by ?x ?y) \n\t\t\t\t(synapsed_to ?x ?y))))) \n\n(forall (...s ?x ?y ?z) \n\t(iff \n\t\t(neural_circuit_path ...s ?x ?y ?z)\n\t\t(and\n\t\t\t(neural_circuit_path ...s ?x ?y)\n\t\t\t(\"neuron ; CL_0000540\" ?z)\n\t\t\t(or \n\t\t\t\t(synapsed_by ?y ?z) \n\t\t\t\t(synapsed_to ?y ?z))))) \n\n(forall (?x ?y) \n\t(iff \n\t\t(in_neural_circuit_with ?x ?y)\n\t\t(exists (...s)\n\t\t\t(neural_circuit_path ?x ...s ?y)))) " } ] }, "type" : "PROPERTY", "lbl" : "in neural circuit with" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002604", + "meta" : { + "definition" : { + "val" : "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).", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'anterior end of organism' is-opposite-of 'posterior end of organism'" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'increase in temperature' is-opposite-of 'decrease in temperature'" + } ] + }, + "type" : "PROPERTY", + "lbl" : "is opposite of" }, { "id" : "http://purl.obolibrary.org/obo/CL_0000000", "meta" : { @@ -8655,15 +8655,15 @@ }, "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "many-to-many homology", + "val" : "many:many homology ", "xrefs" : [ ] }, { "pred" : "hasExactSynonym", - "val" : "many:many homology ", + "val" : "many to many homologous to", "xrefs" : [ ] }, { "pred" : "hasExactSynonym", - "val" : "many to many homologous to", + "val" : "many-to-many homology", "xrefs" : [ ] } ], "basicPropertyValues" : [ { @@ -8735,6 +8735,10 @@ "pred" : "hasExactSynonym", "val" : "one-to-many orthology", "xrefs" : [ ] + }, { + "pred" : "hasExactSynonym", + "val" : "1:many orthology", + "xrefs" : [ ] }, { "pred" : "hasRelatedSynonym", "val" : "co-orthology", @@ -8743,10 +8747,6 @@ "pred" : "hasRelatedSynonym", "val" : "many to 1 orthology", "xrefs" : [ ] - }, { - "pred" : "hasExactSynonym", - "val" : "1:many orthology", - "xrefs" : [ ] }, { "pred" : "hasExactSynonym", "val" : "1 to many orthologous to", @@ -8859,9 +8859,9 @@ }, "comments" : [ "The term is sometimes also used for anatomical structures." ], "xrefs" : [ { - "val" : "ECO:00000060" - }, { "val" : "SO:0000855" + }, { + "val" : "ECO:00000060" }, { "val" : "SO:0000858" }, { @@ -8950,13 +8950,13 @@ "val" : "SO:non_functional_homolog_of" } ], "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "non functional homologous to", - "xrefs" : [ ] - }, { "pred" : "hasBroadSynonym", "val" : "pseudogene", "xrefs" : [ ] + }, { + "pred" : "hasExactSynonym", + "val" : "non functional homologous to", + "xrefs" : [ ] } ], "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/elements/1.1/source", @@ -9141,15 +9141,15 @@ }, "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "symparalogy", + "val" : "inparalogy", "xrefs" : [ ] }, { "pred" : "hasExactSynonym", - "val" : "in-paralogous to", + "val" : "symparalogy", "xrefs" : [ ] }, { "pred" : "hasExactSynonym", - "val" : "inparalogy", + "val" : "in-paralogous to", "xrefs" : [ ] } ], "basicPropertyValues" : [ { @@ -9177,9 +9177,9 @@ "xrefs" : [ "http://dx.doi.org/10.1016/j.jhevol.2006.11.014", "http://dx.doi.org/10.1146/annurev.es.20.110189.000411", "http://purl.obolibrary.org/obo/HOM_0000006", "ISBN:0123195837" ] }, "xrefs" : [ { - "val" : "ECO:0000071" - }, { "val" : "MI:2163" + }, { + "val" : "ECO:0000071" } ], "synonyms" : [ { "pred" : "hasExactSynonym", @@ -9211,19 +9211,19 @@ "xrefs" : [ "http://dx.doi.org/10.1016/S0169-5347(97)01125-7", "http://purl.obolibrary.org/obo/HOM_0000007", "ISBN:0123195837" ] }, "xrefs" : [ { - "val" : "SO:0000853" + "val" : "TAO:homologous_to" }, { - "val" : "SO:0000857" + "val" : "RO_proposed_relation:homologous_to" }, { - "val" : "SO:0000330" + "val" : "SO:0000857" }, { - "val" : "ECO:0000080" + "val" : "SO:0000853" }, { "val" : "SO:homologous_to" }, { - "val" : "TAO:homologous_to" + "val" : "SO:0000330" }, { - "val" : "RO_proposed_relation:homologous_to" + "val" : "ECO:0000080" } ], "synonyms" : [ { "pred" : "hasExactSynonym", @@ -9231,7 +9231,7 @@ "xrefs" : [ ] }, { "pred" : "hasExactSynonym", - "val" : "taxic homology", + "val" : "phylogenetic homology", "xrefs" : [ ] }, { "pred" : "hasBroadSynonym", @@ -9243,7 +9243,7 @@ "xrefs" : [ ] }, { "pred" : "hasExactSynonym", - "val" : "phylogenetic homology", + "val" : "taxic homology", "xrefs" : [ ] }, { "pred" : "hasRelatedSynonym", @@ -9327,13 +9327,13 @@ "val" : "ECO:0000067" } ], "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "transformational homology", - "xrefs" : [ ] - }, { "pred" : "hasExactSynonym", "val" : "biological homologous to", "xrefs" : [ ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "transformational homology", + "xrefs" : [ ] } ], "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/elements/1.1/creator", @@ -9356,10 +9356,6 @@ "xrefs" : [ "http://dx.doi.org/10.1016/j.jhevol.2006.11.010", "http://purl.obolibrary.org/obo/HOM_0000009" ] }, "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "rudiment", - "xrefs" : [ ] - }, { "pred" : "hasRelatedSynonym", "val" : "reversion", "xrefs" : [ ] @@ -9367,6 +9363,10 @@ "pred" : "hasExactSynonym", "val" : "atavism", "xrefs" : [ ] + }, { + "pred" : "hasExactSynonym", + "val" : "rudiment", + "xrefs" : [ ] } ], "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/elements/1.1/creator", @@ -9450,24 +9450,24 @@ "xrefs" : [ "http://purl.obolibrary.org/obo/HOM_0000014", "ISBN:0123195837", "ISBN:978-0471984931" ] }, "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "fractional homology", + "pred" : "hasRelatedSynonym", + "val" : "percent homology", "xrefs" : [ ] }, { "pred" : "hasExactSynonym", "val" : "segmental homology", "xrefs" : [ ] }, { - "pred" : "hasExactSynonym", - "val" : "partial homologous to", + "pred" : "hasRelatedSynonym", + "val" : "mixed homology", "xrefs" : [ ] }, { - "pred" : "hasRelatedSynonym", - "val" : "partial correspondence", + "pred" : "hasExactSynonym", + "val" : "partial homologous to", "xrefs" : [ ] }, { - "pred" : "hasRelatedSynonym", - "val" : "mixed homology", + "pred" : "hasExactSynonym", + "val" : "fractional homology", "xrefs" : [ ] }, { "pred" : "hasRelatedSynonym", @@ -9475,7 +9475,7 @@ "xrefs" : [ ] }, { "pred" : "hasRelatedSynonym", - "val" : "percent homology", + "val" : "partial correspondence", "xrefs" : [ ] } ], "basicPropertyValues" : [ { @@ -9531,6 +9531,10 @@ "xrefs" : [ "http://dx.doi.org/10.1186/1471-213X-7-100", "http://purl.obolibrary.org/obo/HOM_0000012", "DOI:10.1002/1097-010X(20001215)288:4<345::AID-JEZ7>3.0.CO;2-Y" ] }, "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "duplicon", + "xrefs" : [ ] + }, { "pred" : "hasExactSynonym", "val" : "syntenic paralogous to", "xrefs" : [ ] @@ -9538,10 +9542,6 @@ "pred" : "hasRelatedSynonym", "val" : "paralogon", "xrefs" : [ ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "duplicon", - "xrefs" : [ ] } ], "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/elements/1.1/creator", @@ -9627,21 +9627,21 @@ "val" : "SO:similar_to" } ], "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "resemblance", + "xrefs" : [ ] + }, { "pred" : "hasExactSynonym", "val" : "sameness", "xrefs" : [ ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "correspondence", - "xrefs" : [ "http://dx.doi.org/10.1007/BF02814479" ] }, { "pred" : "hasExactSynonym", "val" : "similar to", "xrefs" : [ ] }, { "pred" : "hasRelatedSynonym", - "val" : "resemblance", - "xrefs" : [ ] + "val" : "correspondence", + "xrefs" : [ "http://dx.doi.org/10.1007/BF02814479" ] } ], "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/elements/1.1/creator", @@ -9898,11 +9898,11 @@ }, "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "duplicate xenology", + "val" : "multiple xenology", "xrefs" : [ ] }, { "pred" : "hasExactSynonym", - "val" : "multiple xenology", + "val" : "duplicate xenology", "xrefs" : [ ] }, { "pred" : "hasExactSynonym", @@ -9993,7 +9993,7 @@ "comments" : [ "The genes are actually paralogs but appear to be orthologous due to differential, lineage-specific gene loss." ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "pseudoorthology", + "val" : "apparent 1:1 orthology", "xrefs" : [ ] }, { "pred" : "hasExactSynonym", @@ -10005,7 +10005,7 @@ "xrefs" : [ ] }, { "pred" : "hasExactSynonym", - "val" : "apparent 1:1 orthology", + "val" : "pseudoorthology", "xrefs" : [ ] } ], "basicPropertyValues" : [ { @@ -10055,24 +10055,24 @@ "xrefs" : [ "http://dx.doi.org/10.1038/415741a", "http://purl.obolibrary.org/obo/HOM_0000048", "http://www.ensembl.org/info/docs/compara/homology_method.html" ] }, "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "many-to-many orthology", + "pred" : "hasRelatedSynonym", + "val" : "co-orthology", "xrefs" : [ ] }, { "pred" : "hasRelatedSynonym", - "val" : "co-orthology", + "val" : "trans-homology", "xrefs" : [ ] }, { "pred" : "hasExactSynonym", - "val" : "many:many orthology", + "val" : "many-to-many orthology", "xrefs" : [ ] }, { "pred" : "hasExactSynonym", "val" : "trans-orthology", "xrefs" : [ ] }, { - "pred" : "hasRelatedSynonym", - "val" : "trans-homology", + "pred" : "hasExactSynonym", + "val" : "many:many orthology", "xrefs" : [ ] }, { "pred" : "hasExactSynonym", @@ -10285,11 +10285,11 @@ "comments" : [ "Cannot be used when orthologous patterning gene are organizing obviously non-homologous structures in different organisms due for example to pleiotropic functions of these genes." ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "generative homology", + "val" : "syngenous to", "xrefs" : [ ] }, { "pred" : "hasExactSynonym", - "val" : "syngenous to", + "val" : "generative homology", "xrefs" : [ ] } ], "basicPropertyValues" : [ { @@ -10313,6 +10313,10 @@ "xrefs" : [ "http://dx.doi.org/10.1016/S0168-9525(00)02005-9", "http://purl.obolibrary.org/obo/HOM_0000055", "ISBN:978-0878932665" ] }, "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "iterative paralogy", + "xrefs" : [ ] + }, { "pred" : "hasRelatedSynonym", "val" : "serial paralogy", "xrefs" : [ ] @@ -10320,10 +10324,6 @@ "pred" : "hasExactSynonym", "val" : "tandem paralogous to", "xrefs" : [ ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "iterative paralogy", - "xrefs" : [ ] } ], "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/elements/1.1/creator", @@ -10372,13 +10372,13 @@ "xrefs" : [ "http://purl.obolibrary.org/obo/HOM_0000037", "BGEE:curator" ] }, "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "one-to-many homology", - "xrefs" : [ ] - }, { "pred" : "hasRelatedSynonym", "val" : "1:many homology", "xrefs" : [ ] + }, { + "pred" : "hasExactSynonym", + "val" : "one-to-many homology", + "xrefs" : [ ] }, { "pred" : "hasExactSynonym", "val" : "1 to many homologous to", @@ -10435,13 +10435,13 @@ }, "comments" : [ "This term is usually contrasted to apomorphy." ], "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "plesiomorphous to", - "xrefs" : [ ] - }, { "pred" : "hasRelatedSynonym", "val" : "symplesiomorphy", "xrefs" : [ ] + }, { + "pred" : "hasExactSynonym", + "val" : "plesiomorphous to", + "xrefs" : [ ] } ], "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/elements/1.1/creator", @@ -10528,20 +10528,20 @@ }, "comments" : [ "Used for structures in distantly related taxa." ], "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "deep homologous to", + "pred" : "hasRelatedSynonym", + "val" : "homoiology", "xrefs" : [ ] }, { - "pred" : "hasRelatedSynonym", - "val" : "generative homology", + "pred" : "hasExactSynonym", + "val" : "deep genetic homology", "xrefs" : [ ] }, { "pred" : "hasRelatedSynonym", - "val" : "homoiology", + "val" : "generative homology", "xrefs" : [ ] }, { "pred" : "hasExactSynonym", - "val" : "deep genetic homology", + "val" : "deep homologous to", "xrefs" : [ ] } ], "basicPropertyValues" : [ { @@ -10773,14 +10773,14 @@ }, "type" : "INDIVIDUAL", "lbl" : "relation has no temporal argument" - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0051816", - "type" : "CLASS", - "lbl" : "acquisition of nutrients from other organism during symbiotic interaction" }, { "id" : "http://purl.obolibrary.org/obo/GO_0007610", "type" : "CLASS", "lbl" : "behavior" + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0051816", + "type" : "CLASS", + "lbl" : "acquisition of nutrients from other organism during symbiotic interaction" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass", "type" : "CLASS", @@ -10789,14 +10789,14 @@ "id" : "http://purl.obolibrary.org/obo/GO_0072519", "type" : "CLASS", "lbl" : "parasitism" - }, { - "id" : "http://purl.obolibrary.org/obo/PATO_0001199", - "type" : "CLASS", - "lbl" : "linear" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#hasOBOFormatVersion", "type" : "PROPERTY", "lbl" : "has_obo_format_version" + }, { + "id" : "http://purl.obolibrary.org/obo/PATO_0001199", + "type" : "CLASS", + "lbl" : "linear" }, { "id" : "http://purl.obolibrary.org/obo/GO_0051702", "type" : "CLASS", @@ -11150,6 +11150,10 @@ "id" : "http://purl.obolibrary.org/obo/PATO_0000052", "type" : "CLASS", "lbl" : "shape" + }, { + "id" : "http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym", + "type" : "PROPERTY", + "lbl" : "has_broad_synonym" }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000002", "meta" : { @@ -11160,10 +11164,6 @@ }, "type" : "CLASS", "lbl" : "continuant" - }, { - "id" : "http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym", - "type" : "PROPERTY", - "lbl" : "has_broad_synonym" }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000003", "meta" : { @@ -11414,14 +11414,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002200", "pred" : "subPropertyOf", "obj" : "http://www.w3.org/2002/07/owl#topObjectProperty" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002614", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002616" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002615", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0003301" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002614", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002616" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0016301", "pred" : "is_a", @@ -11458,14 +11458,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002210", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002203" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0000302", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0000300" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0003307", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002410" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0000302", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0000300" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002009", "pred" : "subPropertyOf", @@ -11846,14 +11846,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002291", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002206" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002225", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002202" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002223", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002222" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002225", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002202" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002492", "pred" : "subPropertyOf", @@ -11938,14 +11938,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002350", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/BFO_0000050" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000022", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_HOM0000011" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002230", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/BFO_0000051" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000022", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_HOM0000011" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002590", "pred" : "subPropertyOf", @@ -12106,14 +12106,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002509", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002131" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_0030425", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_0043005" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001199", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000052" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0030425", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GO_0043005" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002478", "pred" : "subPropertyOf", @@ -12146,10 +12146,6 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002406", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002629" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002252", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002375" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002455", "pred" : "subPropertyOf", @@ -12158,6 +12154,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002466", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002465" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002252", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002375" }, { "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000007", "pred" : "subPropertyOf", @@ -12282,10 +12282,6 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002430", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002428" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002113", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002130" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002379", "pred" : "subPropertyOf", @@ -12294,6 +12290,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002114", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002120" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002113", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002130" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002329", "pred" : "subPropertyOf", @@ -12346,14 +12346,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002006", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002131" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000062", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_HOM0000065" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002618", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002619" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000062", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_HOM0000065" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002600", "pred" : "subPropertyOf", @@ -12770,14 +12770,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002245", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002206" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002180", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000051" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002231", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002479" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002180", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000051" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002230", "pred" : "subPropertyOf", @@ -12798,14 +12798,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000075", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_HOM0000007" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002241", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002244" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002211", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002411" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002241", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002244" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002293", "pred" : "subPropertyOf", @@ -12826,14 +12826,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002087", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002090" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002085", - "pred" : "inverseOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002092" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002084", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002093" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002085", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002092" }, { "sub" : "http://purl.obolibrary.org/obo/CARO_0000011", "pred" : "is_a", @@ -12866,14 +12866,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002233", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0000057" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002006", - "pred" : "inverseOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002130" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0001020", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0001022" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002006", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002130" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002622", "pred" : "inverseOf", @@ -12922,14 +12922,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002350", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002351" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002473", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000051" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002624", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002625" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002473", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000051" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002216", "pred" : "subPropertyOf", @@ -12998,14 +12998,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0003302", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002410" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002460", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002459" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002373", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002567" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002460", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002459" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002264", "pred" : "subPropertyOf", @@ -13018,14 +13018,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0000081", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0000052" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000057", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_HOM0000005" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002403", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002234" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000057", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_HOM0000005" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002500", "pred" : "subPropertyOf", @@ -13231,17 +13231,17 @@ "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0000057" }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002090", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000063" + "sub" : "http://purl.obolibrary.org/obo/RO_0000079", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0000085" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002159", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002320" }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0000079", - "pred" : "inverseOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0000085" + "sub" : "http://purl.obolibrary.org/obo/RO_0002090", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000063" }, { "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000045", "pred" : "subPropertyOf", @@ -13418,26 +13418,26 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002459", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002574" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0003305", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0003304" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002177", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002323" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0003305", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0003304" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002551", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002576" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002381", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002375" }, { "sub" : "http://purl.obolibrary.org/obo/BFO_0000054", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/BFO_0000055" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002381", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002375" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002000", "pred" : "subPropertyOf", @@ -13514,14 +13514,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002380", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002569" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002331", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002431" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002256", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002257" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002331", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002431" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002286", "pred" : "subPropertyOf", @@ -13874,14 +13874,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002297", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002295" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000060", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_HOM0000050" }, { "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000065", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_HOM0000000" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000060", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_HOM0000050" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0051705", "pred" : "is_a", @@ -13910,14 +13910,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002641", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002635" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002091", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002222" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002326", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002329" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002091", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002222" }, { "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000032", "pred" : "subPropertyOf", @@ -14064,50 +14064,50 @@ "subsets" : [ ], "xrefs" : [ ], "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", - "val" : "Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 276 Logical Axioms: 56]" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", - "val" : "Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 146 Logical Axioms: 45]" - }, { "pred" : "http://purl.org/dc/elements/1.1/description", "val" : "The OBO Relations Ontology (RO) is a collection of OWL relations (ObjectProperties) intended for use across a wide variety of biological ontologies." + }, { + "pred" : "http://purl.org/dc/elements/1.1/source", + "val" : "http://obofoundry.org/ro" + }, { + "pred" : "http://purl.org/dc/elements/1.1/title", + "val" : "OBO Relations Ontology" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", - "val" : "Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 42 Logical Axioms: 16]" + "val" : "Includes Ontology(OntologyID(Anonymous-21)) [Axioms: 26 Logical Axioms: 0]" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", - "val" : "Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 20 Logical Axioms: 6]" + "val" : "Includes Ontology(OntologyID(Anonymous-21)) [Axioms: 32 Logical Axioms: 0]" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", - "val" : "Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 29 Logical Axioms: 9]" + "val" : "Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 61 Logical Axioms: 0]" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", - "val" : "Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 6 Logical Axioms: 2]" + "val" : "Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 53 Logical Axioms: 12]" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", - "val" : "Includes Ontology(OntologyID(Anonymous-21)) [Axioms: 26 Logical Axioms: 0]" + "val" : "Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 276 Logical Axioms: 56]" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", - "val" : "Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 61 Logical Axioms: 0]" + "val" : "Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 6 Logical Axioms: 2]" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", - "val" : "Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 731 Logical Axioms: 148]" + "val" : "Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 42 Logical Axioms: 16]" }, { - "pred" : "http://xmlns.com/foaf/0.1/homepage", - "val" : " https://github.com/oborel/obo-relations/" + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 29 Logical Axioms: 9]" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", - "val" : "Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 53 Logical Axioms: 12]" + "val" : "Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 20 Logical Axioms: 6]" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", - "val" : "Includes Ontology(OntologyID(Anonymous-21)) [Axioms: 32 Logical Axioms: 0]" + "val" : "Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 731 Logical Axioms: 148]" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", - "val" : "http://obofoundry.org/ro" + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 146 Logical Axioms: 45]" }, { - "pred" : "http://purl.org/dc/elements/1.1/title", - "val" : "OBO Relations Ontology" + "pred" : "http://xmlns.com/foaf/0.1/homepage", + "val" : " https://github.com/oborel/obo-relations/" } ], "version" : "http://purl.obolibrary.org/obo/ro/releases/2016-09-02/ro.owl" }, @@ -14182,13 +14182,13 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002207", "allValuesFromEdges" : [ { - "sub" : "http://purl.obolibrary.org/obo/CARO_0010000", - "pred" : "http://purl.obolibrary.org/obo/RO_0002207", - "obj" : "http://purl.obolibrary.org/obo/CARO_0010000" - }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000000", "pred" : "http://purl.obolibrary.org/obo/RO_0002207", "obj" : "http://purl.obolibrary.org/obo/CL_0000000" + }, { + "sub" : "http://purl.obolibrary.org/obo/CARO_0010000", + "pred" : "http://purl.obolibrary.org/obo/RO_0002207", + "obj" : "http://purl.obolibrary.org/obo/CARO_0010000" } ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002009", diff --git a/examples/ro.yaml b/examples/ro.yaml index ef83010..83c493c 100644 --- a/examples/ro.yaml +++ b/examples/ro.yaml @@ -171,6 +171,8 @@ graphs: \ in it's shape and results in an end point state of that entity." xrefs: [] basicPropertyValues: + - pred: "http://www.geneontology.org/formats/oboInOwl#shorthand" + val: "results_in_maturation_of" - pred: "http://purl.obolibrary.org/obo/IAO_0000117" val: "Chris Mungall" - pred: "http://purl.obolibrary.org/obo/IAO_0000114" @@ -183,8 +185,6 @@ graphs: val: "GOC:mtg_berkeley_2013" - pred: "http://purl.obolibrary.org/obo/IAO_0000112" val: "bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474)" - - pred: "http://www.geneontology.org/formats/oboInOwl#shorthand" - val: "results_in_maturation_of" type: "PROPERTY" lbl: "results in maturation of" - id: "http://purl.obolibrary.org/obo/RO_0002179" @@ -253,8 +253,6 @@ graphs: \ its loss)." xrefs: [] basicPropertyValues: - - pred: "http://www.geneontology.org/formats/oboInOwl#shorthand" - val: "results_in_developmental_progression_of" - pred: "http://www.w3.org/2000/01/rdf-schema#seeAlso" val: "http://wiki.geneontology.org/index.php/Ontology_extensions" - pred: "http://purl.obolibrary.org/obo/IAO_0000116" @@ -265,6 +263,8 @@ graphs: \ we require highly specific relations to avoid incorrect entailments. To\ \ avoid this, the corresponding genus terms in GO should be declared mutually\ \ disjoint." + - pred: "http://www.geneontology.org/formats/oboInOwl#shorthand" + val: "results_in_developmental_progression_of" - pred: "http://purl.obolibrary.org/obo/IAO_0000117" val: "Chris Mungall" - pred: "http://purl.obolibrary.org/obo/IAO_0000114" @@ -316,10 +316,10 @@ graphs: \ as a primordium or anlage through its mature state and to its final state." xrefs: [] basicPropertyValues: - - pred: "http://www.geneontology.org/formats/oboInOwl#shorthand" - val: "results_in_development_of" - pred: "http://purl.obolibrary.org/obo/IAO_0000117" val: "Chris Mungall" + - pred: "http://www.geneontology.org/formats/oboInOwl#shorthand" + val: "results_in_development_of" - pred: "http://purl.obolibrary.org/obo/IAO_0000112" val: "every flower development (GO:0009908) results in development of some\ \ flower (PO:0009046)" @@ -564,26 +564,14 @@ graphs: \ that is sequence-inherited-from a genetic program that specifies a." xrefs: [] basicPropertyValues: - - pred: "http://purl.obolibrary.org/obo/IAO_0000118" - val: "ancestral_stucture_of" - pred: "http://purl.obolibrary.org/obo/IAO_0000118" val: "evolutionarily_descended_from" + - pred: "http://purl.obolibrary.org/obo/IAO_0000118" + val: "ancestral_stucture_of" - pred: "http://purl.obolibrary.org/obo/IAO_0000114" val: "http://purl.obolibrary.org/obo/IAO_0000125" type: "PROPERTY" lbl: "derived by descent from" - - id: "http://purl.obolibrary.org/obo/RO_0002157" - meta: - definition: - val: "inverse of derived by descent from" - xrefs: [] - subsets: - - "http://purl.obolibrary.org/obo/RO_0002259" - basicPropertyValues: - - pred: "http://purl.obolibrary.org/obo/IAO_0000114" - val: "http://purl.obolibrary.org/obo/IAO_0000125" - type: "PROPERTY" - lbl: "has derived by descendant" - id: "http://purl.obolibrary.org/obo/RO_0003003" meta: definition: @@ -596,6 +584,18 @@ graphs: \ in" type: "PROPERTY" lbl: "increases expression of" + - id: "http://purl.obolibrary.org/obo/RO_0002157" + meta: + definition: + val: "inverse of derived by descent from" + xrefs: [] + subsets: + - "http://purl.obolibrary.org/obo/RO_0002259" + basicPropertyValues: + - pred: "http://purl.obolibrary.org/obo/IAO_0000114" + val: "http://purl.obolibrary.org/obo/IAO_0000125" + type: "PROPERTY" + lbl: "has derived by descendant" - id: "http://purl.obolibrary.org/obo/RO_0002150" meta: definition: @@ -1161,14 +1161,6 @@ graphs: basicPropertyValues: - pred: "http://purl.obolibrary.org/obo/RO_0001900" val: "http://purl.obolibrary.org/obo/RO_0001901" - - pred: "http://purl.obolibrary.org/obo/IAO_0000117" - val: "David Osumi-Sutherland" - - pred: "http://purl.org/spar/cito/citesAsAuthority" - val: "http://www.ncbi.nlm.nih.gov/pubmed/22402613" - - pred: "http://purl.obolibrary.org/obo/IAO_0000118" - val: "has fasciculating component" - - pred: "http://purl.obolibrary.org/obo/IAO_0000114" - val: "http://purl.obolibrary.org/obo/IAO_0000125" - pred: "http://purl.obolibrary.org/obo/IAO_0000426" val: "(forall (?x ?y) \n\t(iff \n\t\t(has_fasciculating_neuron_projection\ \ ?x ?y)\n\t\t(exists (?nps ?npbs)\t\t\n\t\t\t(and \n\t\t\t\t(\"neuron projection\ @@ -1180,6 +1172,14 @@ graphs: \t(\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n\t\t\t\ \t\t\t\t(part_of ?npbss ?npbs) \n\t\t\t\t\t\t)\n\t\t\t\t\t\t(overlaps ?nps\ \ ?npbss)\n\t\t\t\t\t))))))\n\n\n" + - pred: "http://purl.obolibrary.org/obo/IAO_0000117" + val: "David Osumi-Sutherland" + - pred: "http://purl.org/spar/cito/citesAsAuthority" + val: "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + - pred: "http://purl.obolibrary.org/obo/IAO_0000118" + val: "has fasciculating component" + - pred: "http://purl.obolibrary.org/obo/IAO_0000114" + val: "http://purl.obolibrary.org/obo/IAO_0000125" type: "PROPERTY" lbl: "has fasciculating neuron projection" - id: "http://purl.obolibrary.org/obo/RO_0002375" @@ -1607,6 +1607,17 @@ graphs: \ DNA templated (GO_0006351)'(t)\nAND t occurs_in x\nAND t has_input y" type: "PROPERTY" lbl: "cell expresses" + - id: "http://purl.obolibrary.org/obo/RO_0002004" + meta: + definition: + val: "The relationship that holds between a trachea or tracheole and an antomical\ + \ structure that is contained in (and so provides an oxygen supply to)." + xrefs: [] + basicPropertyValues: + - pred: "http://purl.obolibrary.org/obo/IAO_0000117" + val: "David Osumi-Sutherland" + type: "PROPERTY" + lbl: "tracheates" - id: "http://purl.obolibrary.org/obo/RO_0002488" meta: definition: @@ -1620,17 +1631,6 @@ graphs: val: "Chris Mungall" type: "PROPERTY" lbl: "existence starts during" - - id: "http://purl.obolibrary.org/obo/RO_0002004" - meta: - definition: - val: "The relationship that holds between a trachea or tracheole and an antomical\ - \ structure that is contained in (and so provides an oxygen supply to)." - xrefs: [] - basicPropertyValues: - - pred: "http://purl.obolibrary.org/obo/IAO_0000117" - val: "David Osumi-Sutherland" - type: "PROPERTY" - lbl: "tracheates" - id: "http://purl.obolibrary.org/obo/RO_0002246" meta: definition: @@ -3426,12 +3426,6 @@ graphs: basicPropertyValues: - pred: "http://purl.obolibrary.org/obo/IAO_0000118" val: "fasciculates with" - - pred: "http://purl.org/spar/cito/citesAsAuthority" - val: "http://www.ncbi.nlm.nih.gov/pubmed/22402613" - - pred: "http://purl.obolibrary.org/obo/RO_0001900" - val: "http://purl.obolibrary.org/obo/RO_0001901" - - pred: "http://purl.obolibrary.org/obo/IAO_0000117" - val: "David Osumi-Sutherland" - pred: "http://purl.obolibrary.org/obo/IAO_0000426" val: "(forall (?x ?y) \n\t(iff \n\t\t(fasciculates_with ?x ?y)\n\t\t(exists\ \ (?nps ?npbs)\n\t\t\t(and \n\t\t\t\t(\"neuron ; CL_0000540\" ?x)\n\t\t\t\ @@ -3442,6 +3436,12 @@ graphs: \t\t\t\t\t(if\n\t\t\t\t\t\t(and \n\t\t\t\t\t\t\t(\"neuron projection bundle\ \ subsegment ; CARO_0001501\" ?npbss)\n\t\t\t\t\t\t\t(part_of ?npbss ?npbs)\ \ \n\t\t\t\t\t\t)\n\t\t\t\t\t\t(overlaps ?nps ?npbss)\n\t\t\t\t\t))))))" + - pred: "http://purl.org/spar/cito/citesAsAuthority" + val: "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + - pred: "http://purl.obolibrary.org/obo/RO_0001900" + val: "http://purl.obolibrary.org/obo/RO_0001901" + - pred: "http://purl.obolibrary.org/obo/IAO_0000117" + val: "David Osumi-Sutherland" - pred: "http://purl.obolibrary.org/obo/IAO_0000114" val: "http://purl.obolibrary.org/obo/IAO_0000125" type: "PROPERTY" @@ -5627,12 +5627,12 @@ graphs: val: "Chris Mungall" type: "PROPERTY" lbl: "involved in regulation of" - - id: "http://purl.obolibrary.org/obo/GO_0008150" - type: "CLASS" - lbl: "biological_process" - id: "http://purl.obolibrary.org/obo/RO_0002549" type: "PROPERTY" lbl: "start, weeks post birth" + - id: "http://purl.obolibrary.org/obo/GO_0008150" + type: "CLASS" + lbl: "biological_process" - id: "http://purl.obolibrary.org/obo/RO_0002429" meta: basicPropertyValues: @@ -7103,12 +7103,12 @@ graphs: - "http://dx.doi.org/10.1146/annurev.es.20.110189.000411" - "http://purl.obolibrary.org/obo/HOM_0000027" synonyms: - - pred: "hasExactSynonym" - val: "serial homologous to" - xrefs: [] - pred: "hasRelatedSynonym" val: "homonomy" xrefs: [] + - pred: "hasExactSynonym" + val: "serial homologous to" + xrefs: [] basicPropertyValues: - pred: "http://purl.org/dc/elements/1.1/creator" val: "http://bgee.unil.ch" @@ -7172,6 +7172,33 @@ graphs: xrefs: [] type: "PROPERTY" lbl: "in approximate one to one relationship with" + - id: "http://purl.obolibrary.org/obo/RO_0000301" + meta: + definition: + val: "A relation that holds between a neuron that is synapsed_to another neuron\ + \ or a neuron that is connected indirectly to another by a chain of neurons,\ + \ each synapsed_to the next." + 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_0000426" + val: "(forall (?x ?y) \n\t(iff \n\t\t(upstream_neural_circuit_path ?x ?y)\n\ + \t\t(and\n\t\t\t(\"neuron ; CL_0000540\" ?x)\n\t\t\t(\"neuron ; CL_0000540\"\ + \ ?y)\n\t\t\t(synapsed_to ?x ?y))))\n\n\n(forall (...s ?x ?y ?z) \n\t(iff\ + \ \n\t\t(upstream_neural_circuit_path ...s ?x ?y ?z )\n\t\t(and\n\t\t\t\ + (upstream_neural_circuit_path ...s ?x ?y)\n\t\t\t(\"neuron ; CL_0000540\"\ + \ ?z)\n\t\t\t(synapsed_to ?y ?z))))\n\t\t\t\n(forall (?x ?y) \n\t(iff \n\ + \t\t(upstream_in_neural_circuit_with ?x ?y)\n\t\t(exists (...s)\n\t\t\t\ + (upstream_neural_circuit_path ?x ...s ?y))))" + - pred: "http://purl.obolibrary.org/obo/RO_0001900" + val: "http://purl.obolibrary.org/obo/RO_0001901" + - pred: "http://purl.org/spar/cito/citesAsAuthority" + val: "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + - pred: "http://purl.obolibrary.org/obo/IAO_0000117" + val: "David Osumi-Sutherland" + type: "PROPERTY" + lbl: "upstream in neural circuit with" - id: "http://purl.obolibrary.org/obo/RO_HOM0000032" meta: definition: @@ -7182,10 +7209,10 @@ graphs: - "ISBN:978-0674639416" synonyms: - pred: "hasExactSynonym" - val: "neotenous to" + val: "juvenilization" xrefs: [] - pred: "hasExactSynonym" - val: "juvenilization" + val: "neotenous to" xrefs: [] basicPropertyValues: - pred: "http://purl.org/dc/elements/1.1/source" @@ -7196,33 +7223,6 @@ graphs: val: "http://bgee.unil.ch" type: "PROPERTY" lbl: "in neoteny relationship with" - - id: "http://purl.obolibrary.org/obo/RO_0000301" - meta: - definition: - val: "A relation that holds between a neuron that is synapsed_to another neuron\ - \ or a neuron that is connected indirectly to another by a chain of neurons,\ - \ each synapsed_to the next." - xrefs: [] - basicPropertyValues: - - pred: "http://purl.obolibrary.org/obo/IAO_0000114" - val: "http://purl.obolibrary.org/obo/IAO_0000125" - - pred: "http://purl.obolibrary.org/obo/RO_0001900" - val: "http://purl.obolibrary.org/obo/RO_0001901" - - pred: "http://purl.org/spar/cito/citesAsAuthority" - val: "http://www.ncbi.nlm.nih.gov/pubmed/22402613" - - pred: "http://purl.obolibrary.org/obo/IAO_0000117" - val: "David Osumi-Sutherland" - - pred: "http://purl.obolibrary.org/obo/IAO_0000426" - val: "(forall (?x ?y) \n\t(iff \n\t\t(upstream_neural_circuit_path ?x ?y)\n\ - \t\t(and\n\t\t\t(\"neuron ; CL_0000540\" ?x)\n\t\t\t(\"neuron ; CL_0000540\"\ - \ ?y)\n\t\t\t(synapsed_to ?x ?y))))\n\n\n(forall (...s ?x ?y ?z) \n\t(iff\ - \ \n\t\t(upstream_neural_circuit_path ...s ?x ?y ?z )\n\t\t(and\n\t\t\t\ - (upstream_neural_circuit_path ...s ?x ?y)\n\t\t\t(\"neuron ; CL_0000540\"\ - \ ?z)\n\t\t\t(synapsed_to ?y ?z))))\n\t\t\t\n(forall (?x ?y) \n\t(iff \n\ - \t\t(upstream_in_neural_circuit_with ?x ?y)\n\t\t(exists (...s)\n\t\t\t\ - (upstream_neural_circuit_path ?x ...s ?y))))" - type: "PROPERTY" - lbl: "upstream in neural circuit with" - id: "http://purl.obolibrary.org/obo/RO_0002603" meta: definition: @@ -7238,19 +7238,6 @@ graphs: \ that x=y\"" type: "PROPERTY" lbl: "is approximately equivalent to" - - id: "http://purl.obolibrary.org/obo/RO_0002604" - meta: - definition: - val: "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)." - xrefs: [] - basicPropertyValues: - - pred: "http://purl.obolibrary.org/obo/IAO_0000112" - val: "'anterior end of organism' is-opposite-of 'posterior end of organism'" - - pred: "http://purl.obolibrary.org/obo/IAO_0000112" - val: "'increase in temperature' is-opposite-of 'decrease in temperature'" - type: "PROPERTY" - lbl: "is opposite of" - id: "http://purl.obolibrary.org/obo/RO_0000300" meta: definition: @@ -7258,14 +7245,6 @@ graphs: \ or indirectly via a series of synaptically connected neurons." xrefs: [] basicPropertyValues: - - pred: "http://purl.org/spar/cito/citesAsAuthority" - val: "http://www.ncbi.nlm.nih.gov/pubmed/22402613" - - pred: "http://purl.obolibrary.org/obo/RO_0001900" - val: "http://purl.obolibrary.org/obo/RO_0001901" - - pred: "http://purl.obolibrary.org/obo/IAO_0000117" - val: "David Osumi-Sutherland" - - pred: "http://purl.obolibrary.org/obo/IAO_0000114" - val: "http://purl.obolibrary.org/obo/IAO_0000125" - pred: "http://purl.obolibrary.org/obo/IAO_0000426" val: "(forall (?x ?y) \n\t(iff \n\t\t(neural_circuit_path ?x ?y)\n\t\t(and\n\ \t\t\t(\"neuron ; CL_0000540\" ?x)\n\t\t\t(\"neuron ; CL_0000540\" ?y)\n\ @@ -7275,8 +7254,29 @@ graphs: neuron ; CL_0000540\" ?z)\n\t\t\t(or \n\t\t\t\t(synapsed_by ?y ?z) \n\t\t\ \t\t(synapsed_to ?y ?z))))) \n\n(forall (?x ?y) \n\t(iff \n\t\t(in_neural_circuit_with\ \ ?x ?y)\n\t\t(exists (...s)\n\t\t\t(neural_circuit_path ?x ...s ?y)))) " + - pred: "http://purl.org/spar/cito/citesAsAuthority" + val: "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + - pred: "http://purl.obolibrary.org/obo/RO_0001900" + val: "http://purl.obolibrary.org/obo/RO_0001901" + - pred: "http://purl.obolibrary.org/obo/IAO_0000117" + val: "David Osumi-Sutherland" + - pred: "http://purl.obolibrary.org/obo/IAO_0000114" + val: "http://purl.obolibrary.org/obo/IAO_0000125" type: "PROPERTY" lbl: "in neural circuit with" + - id: "http://purl.obolibrary.org/obo/RO_0002604" + meta: + definition: + val: "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)." + xrefs: [] + basicPropertyValues: + - pred: "http://purl.obolibrary.org/obo/IAO_0000112" + val: "'anterior end of organism' is-opposite-of 'posterior end of organism'" + - pred: "http://purl.obolibrary.org/obo/IAO_0000112" + val: "'increase in temperature' is-opposite-of 'decrease in temperature'" + type: "PROPERTY" + lbl: "is opposite of" - id: "http://purl.obolibrary.org/obo/CL_0000000" meta: basicPropertyValues: @@ -7317,15 +7317,15 @@ graphs: - "http://dx.doi.org/10.1093/molbev/msp002" - "http://purl.obolibrary.org/obo/HOM_0000036" synonyms: - - pred: "hasExactSynonym" - val: "many-to-many homology" - xrefs: [] - pred: "hasExactSynonym" val: "many:many homology " xrefs: [] - pred: "hasExactSynonym" val: "many to many homologous to" xrefs: [] + - pred: "hasExactSynonym" + val: "many-to-many homology" + xrefs: [] basicPropertyValues: - pred: "http://www.w3.org/2000/01/rdf-schema#seeAlso" val: "http://purl.obolibrary.org/obo/HOM_0000036" @@ -7385,15 +7385,15 @@ graphs: - pred: "hasExactSynonym" val: "one-to-many orthology" xrefs: [] + - pred: "hasExactSynonym" + val: "1:many orthology" + xrefs: [] - pred: "hasRelatedSynonym" val: "co-orthology" xrefs: [] - pred: "hasRelatedSynonym" val: "many to 1 orthology" xrefs: [] - - pred: "hasExactSynonym" - val: "1:many orthology" - xrefs: [] - pred: "hasExactSynonym" val: "1 to many orthologous to" xrefs: [] @@ -7493,8 +7493,8 @@ graphs: comments: - "The term is sometimes also used for anatomical structures." xrefs: - - val: "ECO:00000060" - val: "SO:0000855" + - val: "ECO:00000060" - val: "SO:0000858" - val: "SO:orthologous_to" synonyms: @@ -7569,12 +7569,12 @@ graphs: xrefs: - val: "SO:non_functional_homolog_of" synonyms: - - pred: "hasExactSynonym" - val: "non functional homologous to" - xrefs: [] - pred: "hasBroadSynonym" val: "pseudogene" xrefs: [] + - pred: "hasExactSynonym" + val: "non functional homologous to" + xrefs: [] basicPropertyValues: - pred: "http://purl.org/dc/elements/1.1/source" val: "http://www.ncbi.nlm.nih.gov/pubmed/20116127" @@ -7728,13 +7728,13 @@ graphs: - "http://purl.obolibrary.org/obo/HOM_0000023" synonyms: - pred: "hasExactSynonym" - val: "symparalogy" + val: "inparalogy" xrefs: [] - pred: "hasExactSynonym" - val: "in-paralogous to" + val: "symparalogy" xrefs: [] - pred: "hasExactSynonym" - val: "inparalogy" + val: "in-paralogous to" xrefs: [] basicPropertyValues: - pred: "http://purl.org/dc/elements/1.1/source" @@ -7759,8 +7759,8 @@ graphs: - "http://purl.obolibrary.org/obo/HOM_0000006" - "ISBN:0123195837" xrefs: - - val: "ECO:0000071" - val: "MI:2163" + - val: "ECO:0000071" synonyms: - pred: "hasExactSynonym" val: "structural homologous to" @@ -7786,19 +7786,19 @@ graphs: - "http://purl.obolibrary.org/obo/HOM_0000007" - "ISBN:0123195837" xrefs: - - val: "SO:0000853" + - val: "TAO:homologous_to" + - val: "RO_proposed_relation:homologous_to" - val: "SO:0000857" + - val: "SO:0000853" + - val: "SO:homologous_to" - val: "SO:0000330" - val: "ECO:0000080" - - val: "SO:homologous_to" - - val: "TAO:homologous_to" - - val: "RO_proposed_relation:homologous_to" synonyms: - pred: "hasExactSynonym" val: "historical homologous to" xrefs: [] - pred: "hasExactSynonym" - val: "taxic homology" + val: "phylogenetic homology" xrefs: [] - pred: "hasBroadSynonym" val: "homology" @@ -7807,7 +7807,7 @@ graphs: val: "cladistic homology" xrefs: [] - pred: "hasExactSynonym" - val: "phylogenetic homology" + val: "taxic homology" xrefs: [] - pred: "hasRelatedSynonym" val: "true homology" @@ -7882,12 +7882,12 @@ graphs: xrefs: - val: "ECO:0000067" synonyms: - - pred: "hasRelatedSynonym" - val: "transformational homology" - xrefs: [] - pred: "hasExactSynonym" val: "biological homologous to" xrefs: [] + - pred: "hasRelatedSynonym" + val: "transformational homology" + xrefs: [] basicPropertyValues: - pred: "http://purl.org/dc/elements/1.1/creator" val: "http://bgee.unil.ch" @@ -7906,15 +7906,15 @@ graphs: - "http://dx.doi.org/10.1016/j.jhevol.2006.11.010" - "http://purl.obolibrary.org/obo/HOM_0000009" synonyms: - - pred: "hasExactSynonym" - val: "rudiment" - xrefs: [] - pred: "hasRelatedSynonym" val: "reversion" xrefs: [] - pred: "hasExactSynonym" val: "atavism" xrefs: [] + - pred: "hasExactSynonym" + val: "rudiment" + xrefs: [] basicPropertyValues: - pred: "http://purl.org/dc/elements/1.1/creator" val: "http://bgee.unil.ch" @@ -7982,26 +7982,26 @@ graphs: - "ISBN:0123195837" - "ISBN:978-0471984931" synonyms: - - pred: "hasExactSynonym" - val: "fractional homology" + - pred: "hasRelatedSynonym" + val: "percent homology" xrefs: [] - pred: "hasExactSynonym" val: "segmental homology" xrefs: [] + - pred: "hasRelatedSynonym" + val: "mixed homology" + xrefs: [] - pred: "hasExactSynonym" val: "partial homologous to" xrefs: [] - - pred: "hasRelatedSynonym" - val: "partial correspondence" - xrefs: [] - - pred: "hasRelatedSynonym" - val: "mixed homology" + - pred: "hasExactSynonym" + val: "fractional homology" xrefs: [] - pred: "hasRelatedSynonym" val: "modular homology" xrefs: [] - pred: "hasRelatedSynonym" - val: "percent homology" + val: "partial correspondence" xrefs: [] basicPropertyValues: - pred: "http://www.w3.org/2000/01/rdf-schema#seeAlso" @@ -8048,15 +8048,15 @@ graphs: - "http://purl.obolibrary.org/obo/HOM_0000012" - "DOI:10.1002/1097-010X(20001215)288:4<345::AID-JEZ7>3.0.CO;2-Y" synonyms: + - pred: "hasRelatedSynonym" + val: "duplicon" + xrefs: [] - pred: "hasExactSynonym" val: "syntenic paralogous to" xrefs: [] - pred: "hasRelatedSynonym" val: "paralogon" xrefs: [] - - pred: "hasRelatedSynonym" - val: "duplicon" - xrefs: [] basicPropertyValues: - pred: "http://purl.org/dc/elements/1.1/creator" val: "http://bgee.unil.ch" @@ -8130,19 +8130,19 @@ graphs: - val: "ECO:0000041" - val: "SO:similar_to" synonyms: + - pred: "hasRelatedSynonym" + val: "resemblance" + xrefs: [] - pred: "hasExactSynonym" val: "sameness" xrefs: [] - - pred: "hasRelatedSynonym" - val: "correspondence" - xrefs: - - "http://dx.doi.org/10.1007/BF02814479" - pred: "hasExactSynonym" val: "similar to" xrefs: [] - pred: "hasRelatedSynonym" - val: "resemblance" - xrefs: [] + val: "correspondence" + xrefs: + - "http://dx.doi.org/10.1007/BF02814479" basicPropertyValues: - pred: "http://purl.org/dc/elements/1.1/creator" val: "http://bgee.unil.ch" @@ -8372,10 +8372,10 @@ graphs: - "http://www.ncbi.nlm.nih.gov/pubmed/3065587" synonyms: - pred: "hasExactSynonym" - val: "duplicate xenology" + val: "multiple xenology" xrefs: [] - pred: "hasExactSynonym" - val: "multiple xenology" + val: "duplicate xenology" xrefs: [] - pred: "hasExactSynonym" val: "paraxenologous to" @@ -8453,7 +8453,7 @@ graphs: \ lineage-specific gene loss." synonyms: - pred: "hasExactSynonym" - val: "pseudoorthology" + val: "apparent 1:1 orthology" xrefs: [] - pred: "hasExactSynonym" val: "apparent orthologous to" @@ -8462,7 +8462,7 @@ graphs: val: "1:1 paralogy" xrefs: [] - pred: "hasExactSynonym" - val: "apparent 1:1 orthology" + val: "pseudoorthology" xrefs: [] basicPropertyValues: - pred: "http://purl.org/dc/elements/1.1/source" @@ -8506,20 +8506,20 @@ graphs: - "http://purl.obolibrary.org/obo/HOM_0000048" - "http://www.ensembl.org/info/docs/compara/homology_method.html" synonyms: - - pred: "hasExactSynonym" - val: "many-to-many orthology" - xrefs: [] - pred: "hasRelatedSynonym" val: "co-orthology" xrefs: [] + - pred: "hasRelatedSynonym" + val: "trans-homology" + xrefs: [] - pred: "hasExactSynonym" - val: "many:many orthology" + val: "many-to-many orthology" xrefs: [] - pred: "hasExactSynonym" val: "trans-orthology" xrefs: [] - - pred: "hasRelatedSynonym" - val: "trans-homology" + - pred: "hasExactSynonym" + val: "many:many orthology" xrefs: [] - pred: "hasExactSynonym" val: "many to many orthologous to" @@ -8703,10 +8703,10 @@ graphs: \ functions of these genes." synonyms: - pred: "hasExactSynonym" - val: "generative homology" + val: "syngenous to" xrefs: [] - pred: "hasExactSynonym" - val: "syngenous to" + val: "generative homology" xrefs: [] basicPropertyValues: - pred: "http://www.w3.org/2000/01/rdf-schema#seeAlso" @@ -8727,15 +8727,15 @@ graphs: - "http://purl.obolibrary.org/obo/HOM_0000055" - "ISBN:978-0878932665" synonyms: + - pred: "hasRelatedSynonym" + val: "iterative paralogy" + xrefs: [] - pred: "hasRelatedSynonym" val: "serial paralogy" xrefs: [] - pred: "hasExactSynonym" val: "tandem paralogous to" xrefs: [] - - pred: "hasRelatedSynonym" - val: "iterative paralogy" - xrefs: [] basicPropertyValues: - pred: "http://purl.org/dc/elements/1.1/creator" val: "http://bgee.unil.ch" @@ -8777,12 +8777,12 @@ graphs: - "http://purl.obolibrary.org/obo/HOM_0000037" - "BGEE:curator" synonyms: - - pred: "hasExactSynonym" - val: "one-to-many homology" - xrefs: [] - pred: "hasRelatedSynonym" val: "1:many homology" xrefs: [] + - pred: "hasExactSynonym" + val: "one-to-many homology" + xrefs: [] - pred: "hasExactSynonym" val: "1 to many homologous to" xrefs: [] @@ -8829,12 +8829,12 @@ graphs: comments: - "This term is usually contrasted to apomorphy." synonyms: - - pred: "hasExactSynonym" - val: "plesiomorphous to" - xrefs: [] - pred: "hasRelatedSynonym" val: "symplesiomorphy" xrefs: [] + - pred: "hasExactSynonym" + val: "plesiomorphous to" + xrefs: [] basicPropertyValues: - pred: "http://purl.org/dc/elements/1.1/creator" val: "http://bgee.unil.ch" @@ -8907,17 +8907,17 @@ graphs: comments: - "Used for structures in distantly related taxa." synonyms: + - pred: "hasRelatedSynonym" + val: "homoiology" + xrefs: [] - pred: "hasExactSynonym" - val: "deep homologous to" + val: "deep genetic homology" xrefs: [] - pred: "hasRelatedSynonym" val: "generative homology" xrefs: [] - - pred: "hasRelatedSynonym" - val: "homoiology" - xrefs: [] - pred: "hasExactSynonym" - val: "deep genetic homology" + val: "deep homologous to" xrefs: [] basicPropertyValues: - pred: "http://purl.org/dc/elements/1.1/source" @@ -9152,24 +9152,24 @@ graphs: xrefs: [] type: "INDIVIDUAL" lbl: "relation has no temporal argument" - - id: "http://purl.obolibrary.org/obo/GO_0051816" - type: "CLASS" - lbl: "acquisition of nutrients from other organism during symbiotic interaction" - id: "http://purl.obolibrary.org/obo/GO_0007610" type: "CLASS" lbl: "behavior" + - id: "http://purl.obolibrary.org/obo/GO_0051816" + type: "CLASS" + lbl: "acquisition of nutrients from other organism during symbiotic interaction" - id: "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" type: "CLASS" lbl: "Obsolete Class" - id: "http://purl.obolibrary.org/obo/GO_0072519" type: "CLASS" lbl: "parasitism" - - id: "http://purl.obolibrary.org/obo/PATO_0001199" - type: "CLASS" - lbl: "linear" - id: "http://www.geneontology.org/formats/oboInOwl#hasOBOFormatVersion" type: "PROPERTY" lbl: "has_obo_format_version" + - id: "http://purl.obolibrary.org/obo/PATO_0001199" + type: "CLASS" + lbl: "linear" - id: "http://purl.obolibrary.org/obo/GO_0051702" type: "CLASS" lbl: "interaction with symbiont" @@ -9514,6 +9514,9 @@ graphs: - id: "http://purl.obolibrary.org/obo/PATO_0000052" type: "CLASS" lbl: "shape" + - id: "http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym" + type: "PROPERTY" + lbl: "has_broad_synonym" - id: "http://purl.obolibrary.org/obo/BFO_0000002" meta: definition: @@ -9523,9 +9526,6 @@ graphs: xrefs: [] type: "CLASS" lbl: "continuant" - - id: "http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym" - type: "PROPERTY" - lbl: "has_broad_synonym" - id: "http://purl.obolibrary.org/obo/BFO_0000003" meta: definition: @@ -9726,12 +9726,12 @@ graphs: - sub: "http://purl.obolibrary.org/obo/RO_0002200" pred: "subPropertyOf" obj: "http://www.w3.org/2002/07/owl#topObjectProperty" - - sub: "http://purl.obolibrary.org/obo/RO_0002614" - pred: "subPropertyOf" - obj: "http://purl.obolibrary.org/obo/RO_0002616" - sub: "http://purl.obolibrary.org/obo/RO_0002615" pred: "inverseOf" obj: "http://purl.obolibrary.org/obo/RO_0003301" + - sub: "http://purl.obolibrary.org/obo/RO_0002614" + pred: "subPropertyOf" + obj: "http://purl.obolibrary.org/obo/RO_0002616" - sub: "http://purl.obolibrary.org/obo/GO_0016301" pred: "is_a" obj: "http://purl.obolibrary.org/obo/GO_0016772" @@ -9759,12 +9759,12 @@ graphs: - sub: "http://purl.obolibrary.org/obo/RO_0002210" pred: "subPropertyOf" obj: "http://purl.obolibrary.org/obo/RO_0002203" - - sub: "http://purl.obolibrary.org/obo/RO_0000302" - pred: "subPropertyOf" - obj: "http://purl.obolibrary.org/obo/RO_0000300" - sub: "http://purl.obolibrary.org/obo/RO_0003307" pred: "subPropertyOf" obj: "http://purl.obolibrary.org/obo/RO_0002410" + - sub: "http://purl.obolibrary.org/obo/RO_0000302" + pred: "subPropertyOf" + obj: "http://purl.obolibrary.org/obo/RO_0000300" - sub: "http://purl.obolibrary.org/obo/RO_0002009" pred: "subPropertyOf" obj: "http://purl.obolibrary.org/obo/RO_0002292" @@ -10050,12 +10050,12 @@ graphs: - sub: "http://purl.obolibrary.org/obo/RO_0002291" pred: "subPropertyOf" obj: "http://purl.obolibrary.org/obo/RO_0002206" - - sub: "http://purl.obolibrary.org/obo/RO_0002225" - pred: "subPropertyOf" - obj: "http://purl.obolibrary.org/obo/RO_0002202" - sub: "http://purl.obolibrary.org/obo/RO_0002223" pred: "subPropertyOf" obj: "http://purl.obolibrary.org/obo/RO_0002222" + - sub: "http://purl.obolibrary.org/obo/RO_0002225" + pred: "subPropertyOf" + obj: "http://purl.obolibrary.org/obo/RO_0002202" - sub: "http://purl.obolibrary.org/obo/RO_0002492" pred: "subPropertyOf" obj: "http://purl.obolibrary.org/obo/RO_0002490" @@ -10119,12 +10119,12 @@ graphs: - sub: "http://purl.obolibrary.org/obo/RO_0002350" pred: "subPropertyOf" obj: "http://purl.obolibrary.org/obo/BFO_0000050" - - sub: "http://purl.obolibrary.org/obo/RO_HOM0000022" - pred: "subPropertyOf" - obj: "http://purl.obolibrary.org/obo/RO_HOM0000011" - sub: "http://purl.obolibrary.org/obo/RO_0002230" pred: "subPropertyOf" obj: "http://purl.obolibrary.org/obo/BFO_0000051" + - sub: "http://purl.obolibrary.org/obo/RO_HOM0000022" + pred: "subPropertyOf" + obj: "http://purl.obolibrary.org/obo/RO_HOM0000011" - sub: "http://purl.obolibrary.org/obo/RO_0002590" pred: "subPropertyOf" obj: "http://purl.obolibrary.org/obo/RO_0002586" @@ -10245,12 +10245,12 @@ graphs: - sub: "http://purl.obolibrary.org/obo/RO_0002509" pred: "subPropertyOf" obj: "http://purl.obolibrary.org/obo/RO_0002131" - - sub: "http://purl.obolibrary.org/obo/GO_0030425" - pred: "is_a" - obj: "http://purl.obolibrary.org/obo/GO_0043005" - sub: "http://purl.obolibrary.org/obo/PATO_0001199" pred: "is_a" obj: "http://purl.obolibrary.org/obo/PATO_0000052" + - sub: "http://purl.obolibrary.org/obo/GO_0030425" + pred: "is_a" + obj: "http://purl.obolibrary.org/obo/GO_0043005" - sub: "http://purl.obolibrary.org/obo/RO_0002478" pred: "subPropertyOf" obj: "http://purl.obolibrary.org/obo/RO_0002476" @@ -10275,15 +10275,15 @@ graphs: - sub: "http://purl.obolibrary.org/obo/RO_0002406" pred: "subPropertyOf" obj: "http://purl.obolibrary.org/obo/RO_0002629" - - sub: "http://purl.obolibrary.org/obo/RO_0002252" - pred: "subPropertyOf" - obj: "http://purl.obolibrary.org/obo/RO_0002375" - sub: "http://purl.obolibrary.org/obo/RO_0002455" pred: "subPropertyOf" obj: "http://purl.obolibrary.org/obo/RO_0002442" - sub: "http://purl.obolibrary.org/obo/RO_0002466" pred: "subPropertyOf" obj: "http://purl.obolibrary.org/obo/RO_0002465" + - sub: "http://purl.obolibrary.org/obo/RO_0002252" + pred: "subPropertyOf" + obj: "http://purl.obolibrary.org/obo/RO_0002375" - sub: "http://purl.obolibrary.org/obo/RO_HOM0000007" pred: "subPropertyOf" obj: "http://purl.obolibrary.org/obo/RO_HOM0000001" @@ -10377,15 +10377,15 @@ graphs: - sub: "http://purl.obolibrary.org/obo/RO_0002430" pred: "subPropertyOf" obj: "http://purl.obolibrary.org/obo/RO_0002428" - - sub: "http://purl.obolibrary.org/obo/RO_0002113" - pred: "subPropertyOf" - obj: "http://purl.obolibrary.org/obo/RO_0002130" - sub: "http://purl.obolibrary.org/obo/RO_0002379" pred: "subPropertyOf" obj: "http://purl.obolibrary.org/obo/RO_0002131" - sub: "http://purl.obolibrary.org/obo/RO_0002114" pred: "subPropertyOf" obj: "http://purl.obolibrary.org/obo/RO_0002120" + - sub: "http://purl.obolibrary.org/obo/RO_0002113" + pred: "subPropertyOf" + obj: "http://purl.obolibrary.org/obo/RO_0002130" - sub: "http://purl.obolibrary.org/obo/RO_0002329" pred: "subPropertyOf" obj: "http://purl.obolibrary.org/obo/RO_0002328" @@ -10425,12 +10425,12 @@ graphs: - sub: "http://purl.obolibrary.org/obo/RO_0002006" pred: "subPropertyOf" obj: "http://purl.obolibrary.org/obo/RO_0002131" - - sub: "http://purl.obolibrary.org/obo/RO_HOM0000062" - pred: "subPropertyOf" - obj: "http://purl.obolibrary.org/obo/RO_HOM0000065" - sub: "http://purl.obolibrary.org/obo/RO_0002618" pred: "inverseOf" obj: "http://purl.obolibrary.org/obo/RO_0002619" + - sub: "http://purl.obolibrary.org/obo/RO_HOM0000062" + pred: "subPropertyOf" + obj: "http://purl.obolibrary.org/obo/RO_HOM0000065" - sub: "http://purl.obolibrary.org/obo/RO_0002600" pred: "subPropertyOf" obj: "http://purl.obolibrary.org/obo/RO_0002598" @@ -10743,12 +10743,12 @@ graphs: - sub: "http://purl.obolibrary.org/obo/RO_0002245" pred: "subPropertyOf" obj: "http://purl.obolibrary.org/obo/RO_0002206" - - sub: "http://purl.obolibrary.org/obo/RO_0002180" - pred: "subPropertyOf" - obj: "http://purl.obolibrary.org/obo/BFO_0000051" - sub: "http://purl.obolibrary.org/obo/RO_0002231" pred: "subPropertyOf" obj: "http://purl.obolibrary.org/obo/RO_0002479" + - sub: "http://purl.obolibrary.org/obo/RO_0002180" + pred: "subPropertyOf" + obj: "http://purl.obolibrary.org/obo/BFO_0000051" - sub: "http://purl.obolibrary.org/obo/RO_0002230" pred: "subPropertyOf" obj: "http://purl.obolibrary.org/obo/RO_0002222" @@ -10764,12 +10764,12 @@ graphs: - sub: "http://purl.obolibrary.org/obo/RO_HOM0000075" pred: "subPropertyOf" obj: "http://purl.obolibrary.org/obo/RO_HOM0000007" - - sub: "http://purl.obolibrary.org/obo/RO_0002241" - pred: "subPropertyOf" - obj: "http://purl.obolibrary.org/obo/RO_0002244" - sub: "http://purl.obolibrary.org/obo/RO_0002211" pred: "subPropertyOf" obj: "http://purl.obolibrary.org/obo/RO_0002411" + - sub: "http://purl.obolibrary.org/obo/RO_0002241" + pred: "subPropertyOf" + obj: "http://purl.obolibrary.org/obo/RO_0002244" - sub: "http://purl.obolibrary.org/obo/RO_0002293" pred: "subPropertyOf" obj: "http://purl.obolibrary.org/obo/RO_0002292" @@ -10785,12 +10785,12 @@ graphs: - sub: "http://purl.obolibrary.org/obo/RO_0002087" pred: "inverseOf" obj: "http://purl.obolibrary.org/obo/RO_0002090" - - sub: "http://purl.obolibrary.org/obo/RO_0002085" - pred: "inverseOf" - obj: "http://purl.obolibrary.org/obo/RO_0002092" - sub: "http://purl.obolibrary.org/obo/RO_0002084" pred: "inverseOf" obj: "http://purl.obolibrary.org/obo/RO_0002093" + - sub: "http://purl.obolibrary.org/obo/RO_0002085" + pred: "inverseOf" + obj: "http://purl.obolibrary.org/obo/RO_0002092" - sub: "http://purl.obolibrary.org/obo/CARO_0000011" pred: "is_a" obj: "http://purl.obolibrary.org/obo/CARO_0000006" @@ -10815,12 +10815,12 @@ graphs: - sub: "http://purl.obolibrary.org/obo/RO_0002233" pred: "subPropertyOf" obj: "http://purl.obolibrary.org/obo/RO_0000057" - - sub: "http://purl.obolibrary.org/obo/RO_0002006" - pred: "inverseOf" - obj: "http://purl.obolibrary.org/obo/RO_0002130" - sub: "http://purl.obolibrary.org/obo/RO_0001020" pred: "inverseOf" obj: "http://purl.obolibrary.org/obo/RO_0001022" + - sub: "http://purl.obolibrary.org/obo/RO_0002006" + pred: "inverseOf" + obj: "http://purl.obolibrary.org/obo/RO_0002130" - sub: "http://purl.obolibrary.org/obo/RO_0002622" pred: "inverseOf" obj: "http://purl.obolibrary.org/obo/RO_0002623" @@ -10857,12 +10857,12 @@ graphs: - sub: "http://purl.obolibrary.org/obo/RO_0002350" pred: "inverseOf" obj: "http://purl.obolibrary.org/obo/RO_0002351" - - sub: "http://purl.obolibrary.org/obo/RO_0002473" - pred: "subPropertyOf" - obj: "http://purl.obolibrary.org/obo/BFO_0000051" - sub: "http://purl.obolibrary.org/obo/RO_0002624" pred: "inverseOf" obj: "http://purl.obolibrary.org/obo/RO_0002625" + - sub: "http://purl.obolibrary.org/obo/RO_0002473" + pred: "subPropertyOf" + obj: "http://purl.obolibrary.org/obo/BFO_0000051" - sub: "http://purl.obolibrary.org/obo/RO_0002216" pred: "subPropertyOf" obj: "http://purl.obolibrary.org/obo/RO_0002328" @@ -10914,12 +10914,12 @@ graphs: - sub: "http://purl.obolibrary.org/obo/RO_0003302" pred: "subPropertyOf" obj: "http://purl.obolibrary.org/obo/RO_0002410" - - sub: "http://purl.obolibrary.org/obo/RO_0002460" - pred: "subPropertyOf" - obj: "http://purl.obolibrary.org/obo/RO_0002459" - sub: "http://purl.obolibrary.org/obo/RO_0002373" pred: "subPropertyOf" obj: "http://purl.obolibrary.org/obo/RO_0002567" + - sub: "http://purl.obolibrary.org/obo/RO_0002460" + pred: "subPropertyOf" + obj: "http://purl.obolibrary.org/obo/RO_0002459" - sub: "http://purl.obolibrary.org/obo/RO_0002264" pred: "subPropertyOf" obj: "http://purl.obolibrary.org/obo/RO_0002500" @@ -10929,12 +10929,12 @@ graphs: - sub: "http://purl.obolibrary.org/obo/RO_0000081" pred: "subPropertyOf" obj: "http://purl.obolibrary.org/obo/RO_0000052" - - sub: "http://purl.obolibrary.org/obo/RO_HOM0000057" - pred: "subPropertyOf" - obj: "http://purl.obolibrary.org/obo/RO_HOM0000005" - sub: "http://purl.obolibrary.org/obo/RO_0002403" pred: "subPropertyOf" obj: "http://purl.obolibrary.org/obo/RO_0002234" + - sub: "http://purl.obolibrary.org/obo/RO_HOM0000057" + pred: "subPropertyOf" + obj: "http://purl.obolibrary.org/obo/RO_HOM0000005" - sub: "http://purl.obolibrary.org/obo/RO_0002500" pred: "subPropertyOf" obj: "http://purl.obolibrary.org/obo/RO_0002595" @@ -11088,15 +11088,15 @@ graphs: - sub: "http://purl.obolibrary.org/obo/RO_0002355" pred: "subPropertyOf" obj: "http://purl.obolibrary.org/obo/RO_0000057" - - sub: "http://purl.obolibrary.org/obo/RO_0002090" - pred: "subPropertyOf" - obj: "http://purl.obolibrary.org/obo/BFO_0000063" - - sub: "http://purl.obolibrary.org/obo/RO_0002159" - pred: "subPropertyOf" - obj: "http://purl.obolibrary.org/obo/RO_0002320" - sub: "http://purl.obolibrary.org/obo/RO_0000079" pred: "inverseOf" obj: "http://purl.obolibrary.org/obo/RO_0000085" + - sub: "http://purl.obolibrary.org/obo/RO_0002159" + pred: "subPropertyOf" + obj: "http://purl.obolibrary.org/obo/RO_0002320" + - sub: "http://purl.obolibrary.org/obo/RO_0002090" + pred: "subPropertyOf" + obj: "http://purl.obolibrary.org/obo/BFO_0000063" - sub: "http://purl.obolibrary.org/obo/RO_HOM0000045" pred: "subPropertyOf" obj: "http://purl.obolibrary.org/obo/RO_HOM0000007" @@ -11229,21 +11229,21 @@ graphs: - sub: "http://purl.obolibrary.org/obo/RO_0002459" pred: "subPropertyOf" obj: "http://purl.obolibrary.org/obo/RO_0002574" - - sub: "http://purl.obolibrary.org/obo/RO_0003305" - pred: "subPropertyOf" - obj: "http://purl.obolibrary.org/obo/RO_0003304" - sub: "http://purl.obolibrary.org/obo/RO_0002177" pred: "subPropertyOf" obj: "http://purl.obolibrary.org/obo/RO_0002323" + - sub: "http://purl.obolibrary.org/obo/RO_0003305" + pred: "subPropertyOf" + obj: "http://purl.obolibrary.org/obo/RO_0003304" - sub: "http://purl.obolibrary.org/obo/RO_0002551" pred: "inverseOf" obj: "http://purl.obolibrary.org/obo/RO_0002576" - - sub: "http://purl.obolibrary.org/obo/RO_0002381" - pred: "subPropertyOf" - obj: "http://purl.obolibrary.org/obo/RO_0002375" - sub: "http://purl.obolibrary.org/obo/BFO_0000054" pred: "inverseOf" obj: "http://purl.obolibrary.org/obo/BFO_0000055" + - sub: "http://purl.obolibrary.org/obo/RO_0002381" + pred: "subPropertyOf" + obj: "http://purl.obolibrary.org/obo/RO_0002375" - sub: "http://purl.obolibrary.org/obo/RO_0002000" pred: "subPropertyOf" obj: "http://purl.obolibrary.org/obo/RO_0002323" @@ -11301,12 +11301,12 @@ graphs: - sub: "http://purl.obolibrary.org/obo/RO_0002380" pred: "inverseOf" obj: "http://purl.obolibrary.org/obo/RO_0002569" - - sub: "http://purl.obolibrary.org/obo/RO_0002331" - pred: "subPropertyOf" - obj: "http://purl.obolibrary.org/obo/RO_0002431" - sub: "http://purl.obolibrary.org/obo/RO_0002256" pred: "inverseOf" obj: "http://purl.obolibrary.org/obo/RO_0002257" + - sub: "http://purl.obolibrary.org/obo/RO_0002331" + pred: "subPropertyOf" + obj: "http://purl.obolibrary.org/obo/RO_0002431" - sub: "http://purl.obolibrary.org/obo/RO_0002286" pred: "subPropertyOf" obj: "http://purl.obolibrary.org/obo/RO_0002384" @@ -11571,12 +11571,12 @@ graphs: - sub: "http://purl.obolibrary.org/obo/RO_0002297" pred: "subPropertyOf" obj: "http://purl.obolibrary.org/obo/RO_0002295" - - sub: "http://purl.obolibrary.org/obo/RO_HOM0000060" - pred: "subPropertyOf" - obj: "http://purl.obolibrary.org/obo/RO_HOM0000050" - sub: "http://purl.obolibrary.org/obo/RO_HOM0000065" pred: "subPropertyOf" obj: "http://purl.obolibrary.org/obo/RO_HOM0000000" + - sub: "http://purl.obolibrary.org/obo/RO_HOM0000060" + pred: "subPropertyOf" + obj: "http://purl.obolibrary.org/obo/RO_HOM0000050" - sub: "http://purl.obolibrary.org/obo/GO_0051705" pred: "is_a" obj: "http://purl.obolibrary.org/obo/GO_0007610" @@ -11598,12 +11598,12 @@ graphs: - sub: "http://purl.obolibrary.org/obo/RO_0002641" pred: "subPropertyOf" obj: "http://purl.obolibrary.org/obo/RO_0002635" - - sub: "http://purl.obolibrary.org/obo/RO_0002091" - pred: "subPropertyOf" - obj: "http://purl.obolibrary.org/obo/RO_0002222" - sub: "http://purl.obolibrary.org/obo/RO_0002326" pred: "subPropertyOf" obj: "http://purl.obolibrary.org/obo/RO_0002329" + - sub: "http://purl.obolibrary.org/obo/RO_0002091" + pred: "subPropertyOf" + obj: "http://purl.obolibrary.org/obo/RO_0002222" - sub: "http://purl.obolibrary.org/obo/RO_HOM0000032" pred: "subPropertyOf" obj: "http://purl.obolibrary.org/obo/RO_HOM0000029" @@ -11714,48 +11714,48 @@ graphs: subsets: [] xrefs: [] basicPropertyValues: - - pred: "http://www.w3.org/2000/01/rdf-schema#comment" - val: "Includes Ontology(OntologyID(OntologyIRI()\ - \ VersionIRI())) [Axioms: 276 Logical Axioms: 56]" - - pred: "http://www.w3.org/2000/01/rdf-schema#comment" - val: "Includes Ontology(OntologyID(OntologyIRI()\ - \ VersionIRI())) [Axioms: 146 Logical Axioms: 45]" - pred: "http://purl.org/dc/elements/1.1/description" val: "The OBO Relations Ontology (RO) is a collection of OWL relations (ObjectProperties)\ \ intended for use across a wide variety of biological ontologies." + - pred: "http://purl.org/dc/elements/1.1/source" + val: "http://obofoundry.org/ro" + - pred: "http://purl.org/dc/elements/1.1/title" + val: "OBO Relations Ontology" - pred: "http://www.w3.org/2000/01/rdf-schema#comment" - val: "Includes Ontology(OntologyID(OntologyIRI()\ - \ VersionIRI())) [Axioms: 42 Logical Axioms: 16]" + val: "Includes Ontology(OntologyID(Anonymous-21)) [Axioms: 26 Logical Axioms:\ + \ 0]" - pred: "http://www.w3.org/2000/01/rdf-schema#comment" - val: "Includes Ontology(OntologyID(OntologyIRI()\ - \ VersionIRI())) [Axioms: 20 Logical Axioms: 6]" + val: "Includes Ontology(OntologyID(Anonymous-21)) [Axioms: 32 Logical Axioms:\ + \ 0]" - pred: "http://www.w3.org/2000/01/rdf-schema#comment" - val: "Includes Ontology(OntologyID(OntologyIRI()\ - \ VersionIRI())) [Axioms: 29 Logical Axioms: 9]" + val: "Includes Ontology(OntologyID(OntologyIRI()\ + \ VersionIRI())) [Axioms: 61 Logical Axioms: 0]" + - pred: "http://www.w3.org/2000/01/rdf-schema#comment" + val: "Includes Ontology(OntologyID(OntologyIRI()\ + \ VersionIRI())) [Axioms: 53 Logical Axioms: 12]" + - pred: "http://www.w3.org/2000/01/rdf-schema#comment" + val: "Includes Ontology(OntologyID(OntologyIRI()\ + \ VersionIRI())) [Axioms: 276 Logical Axioms: 56]" - pred: "http://www.w3.org/2000/01/rdf-schema#comment" val: "Includes Ontology(OntologyID(OntologyIRI()\ \ VersionIRI())) [Axioms: 6 Logical Axioms: 2]" - pred: "http://www.w3.org/2000/01/rdf-schema#comment" - val: "Includes Ontology(OntologyID(Anonymous-21)) [Axioms: 26 Logical Axioms:\ - \ 0]" + val: "Includes Ontology(OntologyID(OntologyIRI()\ + \ VersionIRI())) [Axioms: 42 Logical Axioms: 16]" - pred: "http://www.w3.org/2000/01/rdf-schema#comment" - val: "Includes Ontology(OntologyID(OntologyIRI()\ - \ VersionIRI())) [Axioms: 61 Logical Axioms: 0]" + val: "Includes Ontology(OntologyID(OntologyIRI()\ + \ VersionIRI())) [Axioms: 29 Logical Axioms: 9]" + - pred: "http://www.w3.org/2000/01/rdf-schema#comment" + val: "Includes Ontology(OntologyID(OntologyIRI()\ + \ VersionIRI())) [Axioms: 20 Logical Axioms: 6]" - pred: "http://www.w3.org/2000/01/rdf-schema#comment" val: "Includes Ontology(OntologyID(OntologyIRI()\ \ VersionIRI())) [Axioms: 731 Logical Axioms: 148]" + - pred: "http://www.w3.org/2000/01/rdf-schema#comment" + val: "Includes Ontology(OntologyID(OntologyIRI()\ + \ VersionIRI())) [Axioms: 146 Logical Axioms: 45]" - pred: "http://xmlns.com/foaf/0.1/homepage" val: " https://github.com/oborel/obo-relations/" - - pred: "http://www.w3.org/2000/01/rdf-schema#comment" - val: "Includes Ontology(OntologyID(OntologyIRI()\ - \ VersionIRI())) [Axioms: 53 Logical Axioms: 12]" - - pred: "http://www.w3.org/2000/01/rdf-schema#comment" - val: "Includes Ontology(OntologyID(Anonymous-21)) [Axioms: 32 Logical Axioms:\ - \ 0]" - - pred: "http://purl.org/dc/elements/1.1/source" - val: "http://obofoundry.org/ro" - - pred: "http://purl.org/dc/elements/1.1/title" - val: "OBO Relations Ontology" version: "http://purl.obolibrary.org/obo/ro/releases/2016-09-02/ro.owl" equivalentNodesSets: [] logicalDefinitionAxioms: [] @@ -11840,12 +11840,12 @@ graphs: - "http://purl.obolibrary.org/obo/BFO_0000004" - predicateId: "http://purl.obolibrary.org/obo/RO_0002207" allValuesFromEdges: - - sub: "http://purl.obolibrary.org/obo/CARO_0010000" - pred: "http://purl.obolibrary.org/obo/RO_0002207" - obj: "http://purl.obolibrary.org/obo/CARO_0010000" - sub: "http://purl.obolibrary.org/obo/CL_0000000" pred: "http://purl.obolibrary.org/obo/RO_0002207" obj: "http://purl.obolibrary.org/obo/CL_0000000" + - sub: "http://purl.obolibrary.org/obo/CARO_0010000" + pred: "http://purl.obolibrary.org/obo/RO_0002207" + obj: "http://purl.obolibrary.org/obo/CARO_0010000" - predicateId: "http://purl.obolibrary.org/obo/RO_0002009" domainClassIds: - "http://purl.obolibrary.org/obo/CL_0000000" diff --git a/src/main/java/org/geneontology/obographs/io/OgJsonReader.java b/src/main/java/org/geneontology/obographs/io/OgJsonReader.java index 1d49ab0..6d92f93 100644 --- a/src/main/java/org/geneontology/obographs/io/OgJsonReader.java +++ b/src/main/java/org/geneontology/obographs/io/OgJsonReader.java @@ -1,27 +1,26 @@ package org.geneontology.obographs.io; +import com.fasterxml.jackson.databind.ObjectMapper; +import org.geneontology.obographs.model.GraphDocument; + import java.io.File; import java.io.IOException; import java.io.InputStream; -import org.geneontology.obographs.model.Graph; - -import com.fasterxml.jackson.databind.ObjectMapper; - public class OgJsonReader { - public static Graph readFile(String fileName) throws IOException { + public static GraphDocument readFile(String fileName) throws IOException { return readFile(new File(fileName)); } - public static Graph readFile(File file) throws IOException { + public static GraphDocument readFile(File file) throws IOException { ObjectMapper objectMapper = new ObjectMapper(); - return objectMapper.readValue(file, Graph.class); + return objectMapper.readValue(file, GraphDocument.class); } - public static Graph readInputStream(InputStream stream) throws IOException { + public static GraphDocument readInputStream(InputStream stream) throws IOException { ObjectMapper objectMapper = new ObjectMapper(); - return objectMapper.readValue(stream, Graph.class); + return objectMapper.readValue(stream, GraphDocument.class); } } diff --git a/src/main/java/org/geneontology/obographs/model/Edge.java b/src/main/java/org/geneontology/obographs/model/Edge.java index ab53b51..2066d65 100644 --- a/src/main/java/org/geneontology/obographs/model/Edge.java +++ b/src/main/java/org/geneontology/obographs/model/Edge.java @@ -1,6 +1,8 @@ package org.geneontology.obographs.model; +import com.fasterxml.jackson.annotation.JsonCreator; import com.fasterxml.jackson.annotation.JsonProperty; +import com.fasterxml.jackson.databind.annotation.JsonDeserialize; /** * An edge connects two nodes via a predicate @@ -8,6 +10,7 @@ * @author cjm * */ +@JsonDeserialize(builder = Edge.Builder.class) public class Edge implements NodeOrEdge { private Edge(Builder builder) { @@ -48,7 +51,15 @@ public String getObj() { return obj; } - + @Override + public String toString() { + return "Edge{" + + "sub='" + sub + '\'' + + ", pred='" + pred + '\'' + + ", obj='" + obj + '\'' + + ", meta=" + meta + + '}'; + } /** * @return the meta @@ -90,6 +101,7 @@ public Builder meta(Meta meta) { return this; } + @JsonCreator public Edge build() { return new Edge(this); } diff --git a/src/main/java/org/geneontology/obographs/model/Graph.java b/src/main/java/org/geneontology/obographs/model/Graph.java index 16f86c8..f42f8dd 100644 --- a/src/main/java/org/geneontology/obographs/model/Graph.java +++ b/src/main/java/org/geneontology/obographs/model/Graph.java @@ -1,13 +1,14 @@ package org.geneontology.obographs.model; -import java.util.List; - +import com.fasterxml.jackson.annotation.JsonCreator; +import com.fasterxml.jackson.annotation.JsonProperty; +import com.fasterxml.jackson.databind.annotation.JsonDeserialize; import org.geneontology.obographs.model.axiom.DomainRangeAxiom; import org.geneontology.obographs.model.axiom.EquivalentNodesSet; import org.geneontology.obographs.model.axiom.LogicalDefinitionAxiom; import org.geneontology.obographs.model.axiom.PropertyChainAxiom; -import com.fasterxml.jackson.annotation.JsonProperty; +import java.util.List; /** * A graph object holds a collection of nodes and edges @@ -33,6 +34,7 @@ * @author cjm * */ +@JsonDeserialize(builder = Graph.Builder.class) public class Graph { private Graph(Builder builder) { @@ -139,6 +141,20 @@ public List getPropertyChainAxioms() { } + @Override + public String toString() { + return "Graph{" + + "nodes=" + nodes + + ", edges=" + edges + + ", id='" + id + '\'' + + ", lbl='" + lbl + '\'' + + ", meta=" + meta + + ", equivalentNodesSets=" + equivalentNodesSets + + ", logicalDefinitionAxioms=" + logicalDefinitionAxioms + + ", domainRangeAxioms=" + domainRangeAxioms + + ", propertyChainAxioms=" + propertyChainAxioms + + '}'; + } public static class Builder { @@ -202,6 +218,7 @@ public Builder domainRangeAxioms(List domainRangeAxioms) { return this; } + @JsonCreator public Graph build() { return new Graph(this); } diff --git a/src/main/java/org/geneontology/obographs/model/GraphDocument.java b/src/main/java/org/geneontology/obographs/model/GraphDocument.java index c79cea6..be361c2 100644 --- a/src/main/java/org/geneontology/obographs/model/GraphDocument.java +++ b/src/main/java/org/geneontology/obographs/model/GraphDocument.java @@ -1,8 +1,10 @@ package org.geneontology.obographs.model; -import java.util.List; - +import com.fasterxml.jackson.annotation.JsonCreator; import com.fasterxml.jackson.annotation.JsonProperty; +import com.fasterxml.jackson.databind.annotation.JsonDeserialize; + +import java.util.List; /** * Holds a collection of graphs, plus document-level metadata @@ -23,6 +25,7 @@ * @author cjm * */ +@JsonDeserialize(builder = GraphDocument.Builder.class) public class GraphDocument { private GraphDocument(Builder builder) { @@ -61,9 +64,14 @@ public Meta getMeta() { } - - - + @Override + public String toString() { + return "GraphDocument{" + + "graphs=" + graphs + + ", meta=" + meta + + ", context=" + context + + '}'; + } public static class Builder { @@ -71,11 +79,9 @@ public static class Builder { private Meta meta; @JsonProperty private List graphs; - @JsonProperty + @JsonProperty("@context") private Object context; - - public Builder meta(Meta meta) { this.meta = meta; return this; @@ -89,6 +95,7 @@ public Builder context(Object context) { return this; } + @JsonCreator public GraphDocument build() { return new GraphDocument(this); } diff --git a/src/main/java/org/geneontology/obographs/model/Meta.java b/src/main/java/org/geneontology/obographs/model/Meta.java index d6a498a..0856fe1 100644 --- a/src/main/java/org/geneontology/obographs/model/Meta.java +++ b/src/main/java/org/geneontology/obographs/model/Meta.java @@ -1,7 +1,9 @@ package org.geneontology.obographs.model; +import com.fasterxml.jackson.annotation.JsonCreator; import com.fasterxml.jackson.annotation.JsonIgnore; import com.fasterxml.jackson.annotation.JsonProperty; +import com.fasterxml.jackson.databind.annotation.JsonDeserialize; import org.geneontology.obographs.model.meta.*; import java.util.ArrayList; @@ -25,6 +27,7 @@ * @author cjm * */ +@JsonDeserialize(builder = Meta.Builder.class) public class Meta { private Meta(Builder builder) { @@ -107,6 +110,20 @@ public Boolean getDeprecated() { return deprecated; } + @Override + public String toString() { + return "Meta{" + + "definition=" + definition + + ", comments=" + comments + + ", subsets=" + subsets + + ", xrefs=" + xrefs + + ", synonyms=" + synonyms + + ", basicPropertyValues=" + basicPropertyValues + + ", version='" + version + '\'' + + ", deprecated=" + deprecated + + '}'; + } + public static class Builder { @JsonProperty @@ -205,6 +222,7 @@ public Builder deprecated(Boolean deprecated) { } + @JsonCreator public Meta build() { return new Meta(this); } diff --git a/src/main/java/org/geneontology/obographs/model/Node.java b/src/main/java/org/geneontology/obographs/model/Node.java index 2a69290..29bcde1 100644 --- a/src/main/java/org/geneontology/obographs/model/Node.java +++ b/src/main/java/org/geneontology/obographs/model/Node.java @@ -1,6 +1,8 @@ package org.geneontology.obographs.model; +import com.fasterxml.jackson.annotation.JsonCreator; import com.fasterxml.jackson.annotation.JsonProperty; +import com.fasterxml.jackson.databind.annotation.JsonDeserialize; /** * A graph node corresponds to a class, individual or property @@ -19,6 +21,7 @@ * @author cjm * */ +@JsonDeserialize(builder = Node.Builder.class) public class Node implements NodeOrEdge { public enum RDFTYPES { CLASS, INDIVIDUAL, PROPERTY }; @@ -77,11 +80,21 @@ public Meta getMeta() { return meta; } - public static class Builder { + @Override + public String toString() { + return "Node{" + + "id='" + id + '\'' + + ", label='" + label + '\'' + + ", meta=" + meta + + ", type=" + type + + '}'; + } + + public static class Builder { @JsonProperty private String id; - @JsonProperty + @JsonProperty("lbl") private String label; @JsonProperty private Meta meta; @@ -108,6 +121,7 @@ public Builder type(RDFTYPES type) { return this; } + @JsonCreator public Node build() { return new Node(this); } diff --git a/src/main/java/org/geneontology/obographs/model/axiom/AbstractAxiom.java b/src/main/java/org/geneontology/obographs/model/axiom/AbstractAxiom.java index 7abae99..115fcc0 100644 --- a/src/main/java/org/geneontology/obographs/model/axiom/AbstractAxiom.java +++ b/src/main/java/org/geneontology/obographs/model/axiom/AbstractAxiom.java @@ -1,11 +1,7 @@ package org.geneontology.obographs.model.axiom; -import java.util.Set; - -import org.geneontology.obographs.model.Meta; -import org.geneontology.obographs.model.axiom.EquivalentNodesSet.Builder; - import com.fasterxml.jackson.annotation.JsonProperty; +import org.geneontology.obographs.model.Meta; public abstract class AbstractAxiom implements Axiom { @@ -31,7 +27,7 @@ public static class Builder { @JsonProperty private Meta meta; - + public Builder meta(Meta meta) { this.meta = meta; return this; diff --git a/src/main/java/org/geneontology/obographs/model/axiom/AbstractExpression.java b/src/main/java/org/geneontology/obographs/model/axiom/AbstractExpression.java index 8588b28..b089421 100644 --- a/src/main/java/org/geneontology/obographs/model/axiom/AbstractExpression.java +++ b/src/main/java/org/geneontology/obographs/model/axiom/AbstractExpression.java @@ -1,10 +1,5 @@ package org.geneontology.obographs.model.axiom; -import org.geneontology.obographs.model.Meta; -import org.geneontology.obographs.model.axiom.AbstractAxiom.Builder; - -import com.fasterxml.jackson.annotation.JsonProperty; - public class AbstractExpression implements Expression { protected AbstractExpression(Builder builder) { @@ -12,8 +7,5 @@ protected AbstractExpression(Builder builder) { public static class Builder { - - - } } diff --git a/src/main/java/org/geneontology/obographs/model/axiom/DomainRangeAxiom.java b/src/main/java/org/geneontology/obographs/model/axiom/DomainRangeAxiom.java index 92f68bc..ca7b78d 100644 --- a/src/main/java/org/geneontology/obographs/model/axiom/DomainRangeAxiom.java +++ b/src/main/java/org/geneontology/obographs/model/axiom/DomainRangeAxiom.java @@ -1,14 +1,14 @@ package org.geneontology.obographs.model.axiom; -import java.util.ArrayList; -import java.util.Collections; -import java.util.HashSet; -import java.util.Set; - +import com.fasterxml.jackson.annotation.JsonCreator; +import com.fasterxml.jackson.annotation.JsonProperty; +import com.fasterxml.jackson.databind.annotation.JsonDeserialize; import org.geneontology.obographs.model.Edge; import org.geneontology.obographs.model.Meta; -import com.fasterxml.jackson.annotation.JsonProperty; +import java.util.Collections; +import java.util.HashSet; +import java.util.Set; /** * This combined ObjectPropertyDomain, ObjectPropertyRange, and some AllValuesFrom expressions into a single convenience structure @@ -17,6 +17,7 @@ * @author cjm * */ +@JsonDeserialize(builder = DomainRangeAxiom.Builder.class) public class DomainRangeAxiom extends AbstractAxiom { private DomainRangeAxiom(Builder builder) { @@ -137,13 +138,13 @@ public Builder addAllValuesFrom(Edge edge) { allValuesFromEdges = new HashSet<>(); this.allValuesFromEdges.add(edge); return this; - } + + @JsonCreator public DomainRangeAxiom build() { return new DomainRangeAxiom(this); } - } diff --git a/src/main/java/org/geneontology/obographs/model/axiom/EquivalentNodesSet.java b/src/main/java/org/geneontology/obographs/model/axiom/EquivalentNodesSet.java index a634fbb..192fa88 100644 --- a/src/main/java/org/geneontology/obographs/model/axiom/EquivalentNodesSet.java +++ b/src/main/java/org/geneontology/obographs/model/axiom/EquivalentNodesSet.java @@ -1,10 +1,11 @@ package org.geneontology.obographs.model.axiom; -import java.util.Set; - +import com.fasterxml.jackson.annotation.JsonCreator; +import com.fasterxml.jackson.annotation.JsonProperty; +import com.fasterxml.jackson.databind.annotation.JsonDeserialize; import org.geneontology.obographs.model.Meta; -import com.fasterxml.jackson.annotation.JsonProperty; +import java.util.Set; /** * A set of nodes that all stand in a mutual equivalence or identity relationship to one another @@ -15,6 +16,7 @@ * @author cjm * */ +@JsonDeserialize(builder = EquivalentNodesSet.Builder.class) public class EquivalentNodesSet extends AbstractAxiom { private EquivalentNodesSet(Builder builder) { @@ -64,7 +66,8 @@ public Builder nodeIds(Set nodeIds) { this.nodeIds = nodeIds; return this; } - + + @JsonCreator public EquivalentNodesSet build() { return new EquivalentNodesSet(this); } diff --git a/src/main/java/org/geneontology/obographs/model/axiom/ExistentialRestrictionExpression.java b/src/main/java/org/geneontology/obographs/model/axiom/ExistentialRestrictionExpression.java index 2691d50..095f184 100644 --- a/src/main/java/org/geneontology/obographs/model/axiom/ExistentialRestrictionExpression.java +++ b/src/main/java/org/geneontology/obographs/model/axiom/ExistentialRestrictionExpression.java @@ -1,10 +1,8 @@ package org.geneontology.obographs.model.axiom; -import java.util.Set; - -import org.geneontology.obographs.model.Meta; - +import com.fasterxml.jackson.annotation.JsonCreator; import com.fasterxml.jackson.annotation.JsonProperty; +import com.fasterxml.jackson.databind.annotation.JsonDeserialize; /** * Corresponds to an axiom of the form C = X1 and ... and Xn, @@ -14,6 +12,7 @@ * @author cjm * */ +@JsonDeserialize(builder = ExistentialRestrictionExpression.Builder.class) public class ExistentialRestrictionExpression extends AbstractExpression { private ExistentialRestrictionExpression(Builder builder) { @@ -64,6 +63,7 @@ public Builder fillerId(String fillerId) { return this; } + @JsonCreator public ExistentialRestrictionExpression build() { return new ExistentialRestrictionExpression(this); } diff --git a/src/main/java/org/geneontology/obographs/model/axiom/LogicalDefinitionAxiom.java b/src/main/java/org/geneontology/obographs/model/axiom/LogicalDefinitionAxiom.java index f5cc97b..8ff5d87 100644 --- a/src/main/java/org/geneontology/obographs/model/axiom/LogicalDefinitionAxiom.java +++ b/src/main/java/org/geneontology/obographs/model/axiom/LogicalDefinitionAxiom.java @@ -1,11 +1,11 @@ package org.geneontology.obographs.model.axiom; -import java.util.List; -import java.util.Set; - +import com.fasterxml.jackson.annotation.JsonCreator; +import com.fasterxml.jackson.annotation.JsonProperty; +import com.fasterxml.jackson.databind.annotation.JsonDeserialize; import org.geneontology.obographs.model.Meta; -import com.fasterxml.jackson.annotation.JsonProperty; +import java.util.List; /** * Corresponds to an axiom of the form C = X1 and ... and Xn, @@ -15,6 +15,7 @@ * @author cjm * */ +@JsonDeserialize(builder = LogicalDefinitionAxiom.Builder.class) public class LogicalDefinitionAxiom extends AbstractAxiom { private LogicalDefinitionAxiom(Builder builder) { @@ -81,7 +82,8 @@ public Builder restrictions(List restrictions) this.restrictions = restrictions; return this; } - + + @JsonCreator public LogicalDefinitionAxiom build() { return new LogicalDefinitionAxiom(this); } diff --git a/src/main/java/org/geneontology/obographs/model/axiom/PropertyChainAxiom.java b/src/main/java/org/geneontology/obographs/model/axiom/PropertyChainAxiom.java index e246c75..865f5a9 100644 --- a/src/main/java/org/geneontology/obographs/model/axiom/PropertyChainAxiom.java +++ b/src/main/java/org/geneontology/obographs/model/axiom/PropertyChainAxiom.java @@ -1,15 +1,10 @@ package org.geneontology.obographs.model.axiom; -import java.util.ArrayList; -import java.util.Collections; -import java.util.HashSet; -import java.util.List; -import java.util.Set; - -import org.geneontology.obographs.model.Edge; -import org.geneontology.obographs.model.Meta; - +import com.fasterxml.jackson.annotation.JsonCreator; import com.fasterxml.jackson.annotation.JsonProperty; +import com.fasterxml.jackson.databind.annotation.JsonDeserialize; + +import java.util.List; /** * P <- P1 ... Pn @@ -18,6 +13,7 @@ * @author cjm * */ +@JsonDeserialize(builder = PropertyChainAxiom.Builder.class) public class PropertyChainAxiom extends AbstractAxiom { private PropertyChainAxiom(Builder builder) { @@ -63,7 +59,8 @@ public Builder chainPredicateIds(List chainPredicateIds) { this.chainPredicateIds = chainPredicateIds; return this; } - + + @JsonCreator public PropertyChainAxiom build() { return new PropertyChainAxiom(this); } diff --git a/src/main/java/org/geneontology/obographs/model/meta/AbstractPropertyValue.java b/src/main/java/org/geneontology/obographs/model/meta/AbstractPropertyValue.java index 1ec918f..c6e92a1 100644 --- a/src/main/java/org/geneontology/obographs/model/meta/AbstractPropertyValue.java +++ b/src/main/java/org/geneontology/obographs/model/meta/AbstractPropertyValue.java @@ -1,11 +1,9 @@ package org.geneontology.obographs.model.meta; -import java.util.Collection; -import java.util.List; - +import com.fasterxml.jackson.annotation.JsonProperty; import org.geneontology.obographs.model.Meta; -import com.fasterxml.jackson.annotation.JsonProperty; +import java.util.List; public abstract class AbstractPropertyValue implements PropertyValue { @@ -18,10 +16,14 @@ protected AbstractPropertyValue(Builder builder) { xrefs = builder.xrefs; } - private final String pred; + @JsonProperty + private final String pred; + @JsonProperty private final String val; + @JsonProperty private final List xrefs; - private final Meta meta; + @JsonProperty + private final Meta meta; @@ -62,9 +64,17 @@ public Meta getMeta() { return meta; } + @Override + public String toString() { + return "AbstractPropertyValue{" + + "pred='" + pred + '\'' + + ", val='" + val + '\'' + + ", xrefs=" + xrefs + + ", meta=" + meta + + '}'; + } - - public static class Builder { + public static class Builder { @JsonProperty private String pred; diff --git a/src/main/java/org/geneontology/obographs/model/meta/BasicPropertyValue.java b/src/main/java/org/geneontology/obographs/model/meta/BasicPropertyValue.java index 6641df6..fea6664 100644 --- a/src/main/java/org/geneontology/obographs/model/meta/BasicPropertyValue.java +++ b/src/main/java/org/geneontology/obographs/model/meta/BasicPropertyValue.java @@ -1,40 +1,40 @@ package org.geneontology.obographs.model.meta; -import java.util.List; - -import org.geneontology.obographs.model.Meta; +import com.fasterxml.jackson.annotation.JsonCreator; +import com.fasterxml.jackson.databind.annotation.JsonDeserialize; -import com.fasterxml.jackson.annotation.JsonProperty; +import java.util.List; /** * A generic {@link PropertyValue} that is not explicitly modeled - * - * @author cjm * + * @author cjm */ -public class BasicPropertyValue extends AbstractPropertyValue implements PropertyValue { - - private BasicPropertyValue(Builder builder) { - super(builder); - } +@JsonDeserialize(builder = BasicPropertyValue.Builder.class) +public class BasicPropertyValue extends AbstractPropertyValue { + private BasicPropertyValue(Builder builder) { + super(builder); + } - public static class Builder extends AbstractPropertyValue.Builder { + public static class Builder extends AbstractPropertyValue.Builder { public Builder pred(String pred) { return (Builder) super.pred(pred); } + public Builder val(String val) { return (Builder) super.val(val); } + public Builder xrefs(List xrefs) { return (Builder) super.xrefs(xrefs); } - + @JsonCreator public BasicPropertyValue build() { - return new BasicPropertyValue(this); + return new BasicPropertyValue(this); } } - + } diff --git a/src/main/java/org/geneontology/obographs/model/meta/DefinitionPropertyValue.java b/src/main/java/org/geneontology/obographs/model/meta/DefinitionPropertyValue.java index 3c9d287..ac57e49 100644 --- a/src/main/java/org/geneontology/obographs/model/meta/DefinitionPropertyValue.java +++ b/src/main/java/org/geneontology/obographs/model/meta/DefinitionPropertyValue.java @@ -1,19 +1,20 @@ package org.geneontology.obographs.model.meta; -import java.util.List; +import com.fasterxml.jackson.annotation.JsonCreator; +import com.fasterxml.jackson.databind.annotation.JsonDeserialize; -import org.geneontology.obographs.model.meta.AbstractPropertyValue.Builder; +import java.util.List; /** * A {@link PropertyValue} that represents a textual definition of an ontology class or * property - * - * @author cjm * + * @author cjm */ -public class DefinitionPropertyValue extends AbstractPropertyValue implements PropertyValue { - +@JsonDeserialize(builder = DefinitionPropertyValue.Builder.class) +public class DefinitionPropertyValue extends AbstractPropertyValue { + private DefinitionPropertyValue(Builder builder) { super(builder); } @@ -24,13 +25,15 @@ public static class Builder extends AbstractPropertyValue.Builder { public Builder val(String val) { return (Builder) super.val(val); } + public Builder xrefs(List xrefs) { return (Builder) super.xrefs(xrefs); } - + + @JsonCreator public DefinitionPropertyValue build() { return new DefinitionPropertyValue(this); } } - + } diff --git a/src/main/java/org/geneontology/obographs/model/meta/SynonymPropertyValue.java b/src/main/java/org/geneontology/obographs/model/meta/SynonymPropertyValue.java index 7e52dd6..8c9b29c 100644 --- a/src/main/java/org/geneontology/obographs/model/meta/SynonymPropertyValue.java +++ b/src/main/java/org/geneontology/obographs/model/meta/SynonymPropertyValue.java @@ -1,49 +1,46 @@ package org.geneontology.obographs.model.meta; +import com.fasterxml.jackson.annotation.JsonCreator; +import com.fasterxml.jackson.annotation.JsonIgnore; +import com.fasterxml.jackson.databind.annotation.JsonDeserialize; +import org.geneontology.obographs.model.Meta; + import java.util.ArrayList; import java.util.Collections; import java.util.List; -import org.geneontology.obographs.model.Meta; -import org.geneontology.obographs.model.meta.DefinitionPropertyValue.Builder; - -import com.fasterxml.jackson.annotation.JsonIgnore; - /** * A {@link PropertyValue} that represents a an alternative term for a node - * - * @author cjm * + * @author cjm */ - -public class SynonymPropertyValue extends AbstractPropertyValue implements PropertyValue { +@JsonDeserialize(builder = SynonymPropertyValue.Builder.class) +public class SynonymPropertyValue extends AbstractPropertyValue { /** * OBO-style synonym scopes - * - * @author cjm * + * @author cjm */ public enum SCOPES { EXACT, NARROW, BROAD, RELATED - }; - + } + /** * properties from oboInOwl vocabulary that represent scopes - * - * @author cjm * + * @author cjm */ public enum PREDS { hasExactSynonym, hasNarrowSynonym, hasBroadSynonym, hasRelatedSynonym - }; + } private SynonymPropertyValue(Builder builder) { super(builder); @@ -65,7 +62,6 @@ public List getTypes() { return new ArrayList<>(); } - public static class Builder extends AbstractPropertyValue.Builder { @Override @@ -87,17 +83,16 @@ public Builder addType(String type) { public Builder scope(SCOPES scope) { PREDS pred = PREDS.hasRelatedSynonym; switch (scope) { - case EXACT: pred = PREDS.hasExactSynonym; break; - case RELATED: pred = PREDS.hasRelatedSynonym; break; - case BROAD: pred = PREDS.hasBroadSynonym; break; - case NARROW: pred = PREDS.hasNarrowSynonym; break; - + case EXACT: pred = PREDS.hasExactSynonym; break; + case RELATED: pred = PREDS.hasRelatedSynonym; break; + case BROAD: pred = PREDS.hasBroadSynonym; break; + case NARROW: pred = PREDS.hasNarrowSynonym; break; } super.pred(pred.toString()); return this; - } + @JsonCreator public SynonymPropertyValue build() { return new SynonymPropertyValue(this); } diff --git a/src/main/java/org/geneontology/obographs/model/meta/XrefPropertyValue.java b/src/main/java/org/geneontology/obographs/model/meta/XrefPropertyValue.java index f057018..470f9b0 100644 --- a/src/main/java/org/geneontology/obographs/model/meta/XrefPropertyValue.java +++ b/src/main/java/org/geneontology/obographs/model/meta/XrefPropertyValue.java @@ -1,11 +1,14 @@ package org.geneontology.obographs.model.meta; -import java.util.List; +import com.fasterxml.jackson.annotation.JsonCreator; +import com.fasterxml.jackson.annotation.JsonProperty; +import com.fasterxml.jackson.databind.annotation.JsonDeserialize; -import org.geneontology.obographs.model.meta.DefinitionPropertyValue.Builder; +import java.util.List; -public class XrefPropertyValue extends AbstractPropertyValue implements PropertyValue { +@JsonDeserialize(builder = XrefPropertyValue.Builder.class) +public class XrefPropertyValue extends AbstractPropertyValue { private final String lbl; @@ -27,12 +30,14 @@ public String getLbl() { public static class Builder extends AbstractPropertyValue.Builder { + @JsonProperty private String lbl; @Override public Builder val(String val) { return (Builder) super.val(val); } + public Builder lbl(String lbl) { this.lbl= lbl; return this; @@ -43,6 +48,7 @@ public Builder xrefs(List xrefs) { return (Builder) super.xrefs(xrefs); } + @JsonCreator public XrefPropertyValue build() { return new XrefPropertyValue(this); } diff --git a/src/test/java/org/geneontology/obographs/io/OgJsonGeneratorTest.java b/src/test/java/org/geneontology/obographs/io/OgJsonGeneratorTest.java index 6f7ba39..54a118b 100644 --- a/src/test/java/org/geneontology/obographs/io/OgJsonGeneratorTest.java +++ b/src/test/java/org/geneontology/obographs/io/OgJsonGeneratorTest.java @@ -1,17 +1,16 @@ package org.geneontology.obographs.io; -import static org.junit.Assert.*; +import org.apache.commons.io.FileUtils; +import org.geneontology.obographs.model.*; +import org.geneontology.obographs.model.meta.SynonymPropertyValue; +import org.geneontology.obographs.model.meta.XrefPropertyValue; +import org.junit.Test; import java.io.File; import java.io.IOException; +import java.util.Arrays; -import org.apache.commons.io.FileUtils; -import org.geneontology.obographs.model.Graph; -import org.geneontology.obographs.model.GraphDocument; -import org.geneontology.obographs.model.GraphDocumentTest; -import org.junit.Test; - -import com.fasterxml.jackson.core.JsonProcessingException; +import static org.junit.Assert.assertEquals; public class OgJsonGeneratorTest { @@ -23,6 +22,42 @@ public void test() throws IOException { FileUtils.writeStringToFile(new File("target/simple-example.json"), s); } - + @Test + public void testRead() throws IOException { + GraphDocument graphDocument = OgJsonReader.readFile(new File("target/simple-example.json")); + assertEquals(1, graphDocument.getGraphs().size()); + Graph graph = graphDocument.getGraphs().get(0); + assertEquals(2, graph.getNodes().size()); + + Node node1 = graph.getNodes().get(0); + assertEquals("GO:0005634", node1.getId()); + assertEquals("nucleus", node1.getLabel()); + Meta node1Meta = node1.getMeta(); + assertEquals("A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and " + + "replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar " + + "chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell" + + " types, RNA metabolism or DNA replication may be absent.", node1Meta.getDefinition().getVal()); + assertEquals(Arrays.asList("GOC:go_curators"), node1Meta.getDefinition().getXrefs()); + assertEquals(Arrays.asList("goslim_yeast", "goslim_plant"), node1Meta.getSubsets()); + + XrefPropertyValue xrefPropertyValue = node1Meta.getXrefs().get(0); + assertEquals("ICD10:111", xrefPropertyValue.getVal()); + assertEquals("foo disease", xrefPropertyValue.getLbl()); + + SynonymPropertyValue synonymPropertyValue = node1Meta.getSynonyms().get(0); + assertEquals("cell nucleus", synonymPropertyValue.getVal()); + assertEquals("hasExactSynonym", synonymPropertyValue.getPred()); + assertEquals(Arrays.asList("GOC:go_curators"), synonymPropertyValue.getXrefs()); + + Node node2 = graph.getNodes().get(1); + assertEquals("GO:0005623", node2.getId()); + assertEquals("cell", node2.getLabel()); + + assertEquals(1, graph.getEdges().size()); + Edge edge = graph.getEdges().get(0); + assertEquals("GO:0005634", edge.getSub()); + assertEquals("part_of", edge.getPred()); + assertEquals("GO:0005623", edge.getObj()); + } } From 6ff9929de27eba88ccd00e4a37dfdf9f57f39261 Mon Sep 17 00:00:00 2001 From: Jules Jacobsen Date: Tue, 25 Feb 2020 16:04:41 +0000 Subject: [PATCH 2/5] Add missing @JsonProperty to AbstractPropertyValue.Builder --- .../geneontology/obographs/model/meta/SynonymPropertyValue.java | 2 ++ 1 file changed, 2 insertions(+) diff --git a/src/main/java/org/geneontology/obographs/model/meta/SynonymPropertyValue.java b/src/main/java/org/geneontology/obographs/model/meta/SynonymPropertyValue.java index 1881cdf..53ed9f5 100644 --- a/src/main/java/org/geneontology/obographs/model/meta/SynonymPropertyValue.java +++ b/src/main/java/org/geneontology/obographs/model/meta/SynonymPropertyValue.java @@ -2,6 +2,7 @@ import com.fasterxml.jackson.annotation.JsonCreator; import com.fasterxml.jackson.annotation.JsonIgnore; +import com.fasterxml.jackson.annotation.JsonProperty; import com.fasterxml.jackson.databind.annotation.JsonDeserialize; import org.geneontology.obographs.model.Meta; @@ -74,6 +75,7 @@ public List getTypes() { public static class Builder extends AbstractPropertyValue.Builder { + @JsonProperty private String synonymType; @Override From 223dcc9d5d93a52255bdf01e5e43bf6433284ef4 Mon Sep 17 00:00:00 2001 From: Jules Jacobsen Date: Tue, 25 Feb 2020 16:27:31 +0000 Subject: [PATCH 3/5] Make OgJsonGeneratorTest.testRead() independent of testWrite() --- .../geneontology/obographs/io/OgJsonGeneratorTest.java | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/src/test/java/org/geneontology/obographs/io/OgJsonGeneratorTest.java b/src/test/java/org/geneontology/obographs/io/OgJsonGeneratorTest.java index 54a118b..139829e 100644 --- a/src/test/java/org/geneontology/obographs/io/OgJsonGeneratorTest.java +++ b/src/test/java/org/geneontology/obographs/io/OgJsonGeneratorTest.java @@ -8,6 +8,8 @@ import java.io.File; import java.io.IOException; +import java.nio.file.Files; +import java.nio.file.Path; import java.util.Arrays; import static org.junit.Assert.assertEquals; @@ -24,7 +26,12 @@ public void test() throws IOException { @Test public void testRead() throws IOException { - GraphDocument graphDocument = OgJsonReader.readFile(new File("target/simple-example.json")); + GraphDocument testGraphDocument = GraphDocumentTest.build(); + + Path tempFile = Files.createTempFile("simple-example", ".json"); + FileUtils.writeStringToFile(tempFile.toFile(), OgJsonGenerator.render(testGraphDocument)); + + GraphDocument graphDocument = OgJsonReader.readFile(tempFile.toFile()); assertEquals(1, graphDocument.getGraphs().size()); Graph graph = graphDocument.getGraphs().get(0); assertEquals(2, graph.getNodes().size()); From 08539a001c6b1a7b9ad3ab75cce8881c74aa6f16 Mon Sep 17 00:00:00 2001 From: Jules Jacobsen Date: Wed, 26 Feb 2020 17:01:12 +0000 Subject: [PATCH 4/5] Fix maven warning about javadoc-plugin versions --- pom.xml | 24 +++++++++--------------- 1 file changed, 9 insertions(+), 15 deletions(-) diff --git a/pom.xml b/pom.xml index 1d496e5..6f4d570 100644 --- a/pom.xml +++ b/pom.xml @@ -162,6 +162,15 @@ org.apache.maven.plugins maven-javadoc-plugin 2.9.1 + + ch.raffael.doclets.pegdown.PegdownDoclet + + ch.raffael.pegdown-doclet + pegdown-doclet + 1.1 + + true + attach-javadocs @@ -171,21 +180,6 @@ - - - maven-javadoc-plugin - 2.9 - - ch.raffael.doclets.pegdown.PegdownDoclet - - ch.raffael.pegdown-doclet - pegdown-doclet - 1.1 - - true - - - From a38ef83554b71eb7bea7adc1aff6dfffd9c5a3ff Mon Sep 17 00:00:00 2001 From: Jules Jacobsen Date: Wed, 26 Feb 2020 17:02:30 +0000 Subject: [PATCH 5/5] Bump version to 0.2.1 --- pom.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pom.xml b/pom.xml index 6f4d570..2708af6 100644 --- a/pom.xml +++ b/pom.xml @@ -3,7 +3,7 @@ 4.0.0 org.geneontology obographs - 0.2.0 + 0.2.1 jar ${project.groupId}:${project.artifactId} Reference implementation for Obo Graphs