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Refreshed imports

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matentzn committed Aug 9, 2019
1 parent 44c6f2f commit 48d1d2f3c20c1cd6171e663cc9d120b1c81ae188
Showing with 7,436 additions and 12,408 deletions.
  1. +47 −9 imports/chebi_import.json
  2. +14 −1 imports/chebi_import.obo
  3. +37 −1 imports/chebi_import.owl
  4. +233 −166 imports/clo_import.json
  5. +59 −27 imports/clo_import.obo
  6. +76 −39 imports/clo_import.owl
  7. +605 −605 imports/go_import.json
  8. +1 −1 imports/go_import.obo
  9. +1 −1 imports/go_import.owl
  10. +1 −1 imports/pato_import.json
  11. +1 −1 imports/pato_import.obo
  12. +1 −1 imports/pato_import.owl
  13. +36 −32 imports/ro_import.json
  14. +1 −1 imports/ro_import.obo
  15. +4 −2 imports/ro_import.owl
  16. +1,442 −1,400 imports/uberon_import.json
  17. +23 −8 imports/uberon_import.obo
  18. +165 −128 imports/uberon_import.owl
  19. +1 −1 patterns/definitions.owl
  20. +6 −2,817 reports/cl-edit-obo-report.tsv
  21. +47 −9 src/ontology/imports/chebi_import.json
  22. +14 −1 src/ontology/imports/chebi_import.obo
  23. +37 −1 src/ontology/imports/chebi_import.owl
  24. +233 −166 src/ontology/imports/clo_import.json
  25. +59 −27 src/ontology/imports/clo_import.obo
  26. +76 −39 src/ontology/imports/clo_import.owl
  27. +605 −605 src/ontology/imports/go_import.json
  28. +1 −1 src/ontology/imports/go_import.obo
  29. +1 −1 src/ontology/imports/go_import.owl
  30. +1 −1 src/ontology/imports/pato_import.json
  31. +1 −1 src/ontology/imports/pato_import.obo
  32. +1 −1 src/ontology/imports/pato_import.owl
  33. +36 −32 src/ontology/imports/ro_import.json
  34. +1 −1 src/ontology/imports/ro_import.obo
  35. +4 −2 src/ontology/imports/ro_import.owl
  36. +1,442 −1,400 src/ontology/imports/uberon_import.json
  37. +23 −8 src/ontology/imports/uberon_import.obo
  38. +165 −128 src/ontology/imports/uberon_import.owl
  39. +1,923 −1,919 src/ontology/ontologyterms.txt
  40. +6 −2,817 src/ontology/reports/cl-edit-obo-report.tsv
  41. +1 −1 src/patterns/definitions.owl
  42. +5 −5 src/patterns/pattern_owl_seed.txt
@@ -667,14 +667,14 @@
"pred" : "hasRelatedSynonym",
"val" : "Kationen",
"xrefs" : [ "ChEBI" ]
}, {
"pred" : "hasExactSynonym",
"val" : "Cation",
"xrefs" : [ "KEGG_COMPOUND" ]
}, {
"pred" : "hasExactSynonym",
"val" : "cation",
"xrefs" : [ "IUPAC" ]
}, {
"pred" : "hasExactSynonym",
"val" : "Cation",
"xrefs" : [ "KEGG_COMPOUND" ]
}, {
"pred" : "hasRelatedSynonym",
"val" : "Kation",
@@ -2133,6 +2133,33 @@
},
"type" : "CLASS",
"lbl" : "azanide"
}, {
"id" : "http://purl.obolibrary.org/obo/CHEBI_23357",
"meta" : {
"definition" : {
"val" : "An organic molecule or ion (usually a metal ion) that is required by an enzyme for its activity. It may be attached either loosely (coenzyme) or tightly (prosthetic group).",
"xrefs" : [ ]
},
"subsets" : [ "http://purl.obolibrary.org/obo/chebi#3_STAR" ],
"xrefs" : [ {
"val" : "Wikipedia:Cofactor_(biochemistry)"
} ],
"synonyms" : [ {
"pred" : "hasExactSynonym",
"val" : "cofactors",
"xrefs" : [ "IUPAC" ]
}, {
"pred" : "hasExactSynonym",
"val" : "cofactor",
"xrefs" : [ "IUPAC" ]
} ],
"basicPropertyValues" : [ {
"pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
"val" : "chebi_ontology"
} ]
},
"type" : "CLASS",
"lbl" : "cofactor"
}, {
"id" : "http://purl.obolibrary.org/obo/CHEBI_76969",
"meta" : {
@@ -2866,6 +2893,9 @@
}, {
"pred" : "http://purl.obolibrary.org/obo/chebi/mass",
"val" : "44.00950"
}, {
"pred" : "http://purl.obolibrary.org/obo/chebi/charge",
"val" : "-1"
}, {
"pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
"val" : "CHEBI:23026"
@@ -5577,6 +5607,10 @@
"sub" : "http://purl.obolibrary.org/obo/CHEBI_35106",
"pred" : "is_a",
"obj" : "http://purl.obolibrary.org/obo/CHEBI_35881"
}, {
"sub" : "http://purl.obolibrary.org/obo/CHEBI_28938",
"pred" : "http://purl.obolibrary.org/obo/RO_0000087",
"obj" : "http://purl.obolibrary.org/obo/CHEBI_23357"
}, {
"sub" : "http://purl.obolibrary.org/obo/CHEBI_33595",
"pred" : "is_a",
@@ -5741,14 +5775,14 @@
"sub" : "http://purl.obolibrary.org/obo/CHEBI_33304",
"pred" : "is_a",
"obj" : "http://purl.obolibrary.org/obo/CHEBI_33675"
}, {
"sub" : "http://purl.obolibrary.org/obo/CHEBI_64909",
"pred" : "is_a",
"obj" : "http://purl.obolibrary.org/obo/CHEBI_24432"
}, {
"sub" : "http://purl.obolibrary.org/obo/CHEBI_33832",
"pred" : "is_a",
"obj" : "http://purl.obolibrary.org/obo/CHEBI_33595"
}, {
"sub" : "http://purl.obolibrary.org/obo/CHEBI_64909",
"pred" : "is_a",
"obj" : "http://purl.obolibrary.org/obo/CHEBI_24432"
}, {
"sub" : "http://purl.obolibrary.org/obo/CHEBI_25699",
"pred" : "is_a",
@@ -5817,6 +5851,10 @@
"sub" : "http://purl.obolibrary.org/obo/CHEBI_33252",
"pred" : "http://purl.obolibrary.org/obo/BFO_0000051",
"obj" : "http://purl.obolibrary.org/obo/CHEBI_33253"
}, {
"sub" : "http://purl.obolibrary.org/obo/CHEBI_23357",
"pred" : "is_a",
"obj" : "http://purl.obolibrary.org/obo/CHEBI_52206"
}, {
"sub" : "http://purl.obolibrary.org/obo/CHEBI_52208",
"pred" : "is_a",
@@ -6035,7 +6073,7 @@
"subsets" : [ ],
"xrefs" : [ ],
"basicPropertyValues" : [ ],
"version" : "http://purl.obolibrary.org/obo/cl/releases/2019-07-16/imports/chebi_import.owl"
"version" : "http://purl.obolibrary.org/obo/cl/releases/2019-08-09/imports/chebi_import.owl"
},
"equivalentNodesSets" : [ ],
"logicalDefinitionAxioms" : [ ],
@@ -1,5 +1,5 @@
format-version: 1.2
data-version: cl/releases/2019-07-16/imports/chebi_import.owl
data-version: cl/releases/2019-08-09/imports/chebi_import.owl
ontology: cl/imports/chebi_import

[Term]
@@ -212,6 +212,17 @@ property_value: http://purl.obolibrary.org/obo/chebi/formula "CO" xsd:string
property_value: http://purl.obolibrary.org/obo/chebi/mass "28.01010" xsd:string
property_value: http://purl.obolibrary.org/obo/chebi/monoisotopicmass "27.99491" xsd:string

[Term]
id: CHEBI:23357
name: cofactor
namespace: chebi_ontology
def: "An organic molecule or ion (usually a metal ion) that is required by an enzyme for its activity. It may be attached either loosely (coenzyme) or tightly (prosthetic group)." []
subset: 3_STAR
synonym: "cofactor" EXACT [IUPAC]
synonym: "cofactors" EXACT IUPAC_NAME [IUPAC]
xref: Wikipedia:Cofactor_(biochemistry)
is_a: CHEBI:52206 ! biochemical role

[Term]
id: CHEBI:23367
name: molecular entity
@@ -572,6 +583,7 @@ is_a: CHEBI:35106 ! nitrogen hydride
is_a: CHEBI:35274 ! ammonium ion
is_a: CHEBI:50313 ! onium cation
is_a: CHEBI:60242 ! monovalent inorganic cation
relationship: has_role CHEBI:23357 ! cofactor
relationship: has_role CHEBI:75772 ! Saccharomyces cerevisiae metabolite
relationship: has_role CHEBI:76971 ! Escherichia coli metabolite
relationship: has_role CHEBI:77746 ! human metabolite
@@ -600,6 +612,7 @@ synonym: "carboxylic anions" RELATED [ChEBI]
is_a: CHEBI:25696 ! organic anion
is_a: CHEBI:35406 ! oxoanion
relationship: is_conjugate_base_of CHEBI:33575 ! carboxylic acid
property_value: http://purl.obolibrary.org/obo/chebi/charge "-1" xsd:string
property_value: http://purl.obolibrary.org/obo/chebi/formula "CO2R" xsd:string
property_value: http://purl.obolibrary.org/obo/chebi/mass "44.00950" xsd:string
property_value: http://purl.obolibrary.org/obo/chebi/monoisotopicmass "43.98983" xsd:string
@@ -13,7 +13,7 @@
xmlns:chebi3="http://purl.obolibrary.org/obo/chebi#1"
xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#">
<owl:Ontology rdf:about="http://purl.obolibrary.org/obo/cl/imports/chebi_import.owl">
<owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/cl/releases/2019-07-16/imports/chebi_import.owl"/>
<owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/cl/releases/2019-08-09/imports/chebi_import.owl"/>
</owl:Ontology>


@@ -1207,6 +1207,35 @@



<!-- http://purl.obolibrary.org/obo/CHEBI_23357 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/CHEBI_23357">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/CHEBI_52206"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">An organic molecule or ion (usually a metal ion) that is required by an enzyme for its activity. It may be attached either loosely (coenzyme) or tightly (prosthetic group).</obo:IAO_0000115>
<oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Wikipedia:Cofactor_(biochemistry)</oboInOwl:hasDbXref>
<oboInOwl:hasExactSynonym rdf:datatype="http://www.w3.org/2001/XMLSchema#string">cofactor</oboInOwl:hasExactSynonym>
<oboInOwl:hasExactSynonym rdf:datatype="http://www.w3.org/2001/XMLSchema#string">cofactors</oboInOwl:hasExactSynonym>
<oboInOwl:hasOBONamespace rdf:datatype="http://www.w3.org/2001/XMLSchema#string">chebi_ontology</oboInOwl:hasOBONamespace>
<oboInOwl:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">CHEBI:23357</oboInOwl:id>
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/chebi#3_STAR"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">cofactor</rdfs:label>
</owl:Class>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/CHEBI_23357"/>
<owl:annotatedProperty rdf:resource="http://www.geneontology.org/formats/oboInOwl#hasExactSynonym"/>
<owl:annotatedTarget rdf:datatype="http://www.w3.org/2001/XMLSchema#string">cofactor</owl:annotatedTarget>
<oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">IUPAC</oboInOwl:hasDbXref>
</owl:Axiom>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/CHEBI_23357"/>
<owl:annotatedProperty rdf:resource="http://www.geneontology.org/formats/oboInOwl#hasExactSynonym"/>
<owl:annotatedTarget rdf:datatype="http://www.w3.org/2001/XMLSchema#string">cofactors</owl:annotatedTarget>
<oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">IUPAC</oboInOwl:hasDbXref>
<oboInOwl:hasSynonymType rdf:resource="http://purl.obolibrary.org/obo/chebi#IUPAC_NAME"/>
</owl:Axiom>



<!-- http://purl.obolibrary.org/obo/CHEBI_23367 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/CHEBI_23367">
@@ -2236,6 +2265,12 @@
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/CHEBI_35274"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/CHEBI_50313"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/CHEBI_60242"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000087"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/CHEBI_23357"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000087"/>
@@ -2512,6 +2547,7 @@
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The conjugate base formed when the carboxy group of a carboxylic acid is deprotonated.</obo:IAO_0000115>
<chebi:charge rdf:datatype="http://www.w3.org/2001/XMLSchema#string">-1</chebi:charge>
<chebi:formula rdf:datatype="http://www.w3.org/2001/XMLSchema#string">CO2R</chebi:formula>
<chebi:mass rdf:datatype="http://www.w3.org/2001/XMLSchema#string">44.00950</chebi:mass>
<chebi:monoisotopicmass rdf:datatype="http://www.w3.org/2001/XMLSchema#string">43.98983</chebi:monoisotopicmass>

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