From: <cmu...@us...> - 2011-08-31 01:59:44
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Revision: 4007 http://obo.svn.sourceforge.net/obo/?rev=4007&view=rev Author: cmungall Date: 2011-08-31 01:53:36 +0000 (Wed, 31 Aug 2011) Log Message: ----------- Modified Paths: -------------- ontologies/trunk/UBERON/composite-vertebrate.owl Modified: ontologies/trunk/UBERON/composite-vertebrate.owl =================================================================== --- ontologies/trunk/UBERON/composite-vertebrate.owl 2011-08-31 01:45:26 UTC (rev 4006) +++ ontologies/trunk/UBERON/composite-vertebrate.owl 2011-08-31 01:53:36 UTC (rev 4007) @@ -1,17 +1,16 @@ <?xml version="1.0"?> -<rdf:RDF xmlns="http://purl.obolibrary.org/obo/uberon.owl#" - xml:base="http://purl.obolibrary.org/obo/uberon.owl" +<rdf:RDF xmlns="http://purl.obolibrary.org/obo/merged.owl#" + xml:base="http://purl.obolibrary.org/obo/merged.owl" xmlns:obo="http://purl.obolibrary.org/obo/" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" xmlns:owl="http://www.w3.org/2002/07/owl#" xmlns:xsd="http://www.w3.org/2001/XMLSchema#" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" - xmlns:uberon="http://purl.obolibrary.org/obo/uberon#" - xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - <owl:Ontology rdf:about="http://purl.obolibrary.org/obo/uberon.owl"> + xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#" + xmlns:merged="http://purl.obolibrary.org/obo/merged#"> + <owl:Ontology rdf:about="http://purl.obolibrary.org/obo/merged.owl"> <oboInOwl:hasOBOFormatVersion rdf:datatype="http://www.w3.org/2001/XMLSchema#string">1.2</oboInOwl:hasOBOFormatVersion> <oboInOwl:treat-xrefs-as-genus-differentia rdf:datatype="http://www.w3.org/2001/XMLSchema#string">AAO part_of NCBITaxon:8292</oboInOwl:treat-xrefs-as-genus-differentia> - <oboInOwl:treat-xrefs-as-reverse-genus-differentia rdf:datatype="http://www.w3.org/2001/XMLSchema#string">AAO part_of NCBITaxon:8292</oboInOwl:treat-xrefs-as-reverse-genus-differentia> <oboInOwl:treat-xrefs-as-equivalent rdf:datatype="http://www.w3.org/2001/XMLSchema#string">BILA</oboInOwl:treat-xrefs-as-equivalent> <oboInOwl:treat-xrefs-as-equivalent rdf:datatype="http://www.w3.org/2001/XMLSchema#string">BSPO</oboInOwl:treat-xrefs-as-equivalent> <oboInOwl:treat-xrefs-as-equivalent rdf:datatype="http://www.w3.org/2001/XMLSchema#string">CARO</oboInOwl:treat-xrefs-as-equivalent> @@ -19,36 +18,23 @@ <oboInOwl:treat-xrefs-as-has-subclass rdf:datatype="http://www.w3.org/2001/XMLSchema#string">EHDAA2</oboInOwl:treat-xrefs-as-has-subclass> <oboInOwl:treat-xrefs-as-has-subclass rdf:datatype="http://www.w3.org/2001/XMLSchema#string">EMAPA</oboInOwl:treat-xrefs-as-has-subclass> <oboInOwl:treat-xrefs-as-genus-differentia rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FBbt part_of NCBITaxon:7227</oboInOwl:treat-xrefs-as-genus-differentia> - <oboInOwl:treat-xrefs-as-reverse-genus-differentia rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FBbt part_of NCBITaxon:7227</oboInOwl:treat-xrefs-as-reverse-genus-differentia> - <oboInOwl:treat-xrefs-as-reverse-genus-differentia rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FMA part_of NCBITaxon:9606</oboInOwl:treat-xrefs-as-reverse-genus-differentia> <oboInOwl:treat-xrefs-as-genus-differentia rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FMA part_of NCBITaxon:9606</oboInOwl:treat-xrefs-as-genus-differentia> <oboInOwl:treat-xrefs-as-equivalent rdf:datatype="http://www.w3.org/2001/XMLSchema#string">GO</oboInOwl:treat-xrefs-as-equivalent> - <oboInOwl:treat-xrefs-as-reverse-genus-differentia rdf:datatype="http://www.w3.org/2001/XMLSchema#string">HAO part_of NCBITaxon:7399</oboInOwl:treat-xrefs-as-reverse-genus-differentia> <oboInOwl:treat-xrefs-as-genus-differentia rdf:datatype="http://www.w3.org/2001/XMLSchema#string">HAO part_of NCBITaxon:7399</oboInOwl:treat-xrefs-as-genus-differentia> <oboInOwl:treat-xrefs-as-genus-differentia rdf:datatype="http://www.w3.org/2001/XMLSchema#string">KUPO part_of NCBITaxon:9606</oboInOwl:treat-xrefs-as-genus-differentia> - <oboInOwl:treat-xrefs-as-reverse-genus-differentia rdf:datatype="http://www.w3.org/2001/XMLSchema#string">MA part_of NCBITaxon:10088</oboInOwl:treat-xrefs-as-reverse-genus-differentia> <oboInOwl:treat-xrefs-as-genus-differentia rdf:datatype="http://www.w3.org/2001/XMLSchema#string">MA part_of NCBITaxon:10088</oboInOwl:treat-xrefs-as-genus-differentia> <oboInOwl:treat-xrefs-as-genus-differentia rdf:datatype="http://www.w3.org/2001/XMLSchema#string">MFO part_of NCBITaxon:8089</oboInOwl:treat-xrefs-as-genus-differentia> - <oboInOwl:treat-xrefs-as-reverse-genus-differentia rdf:datatype="http://www.w3.org/2001/XMLSchema#string">MFO part_of NCBITaxon:8089</oboInOwl:treat-xrefs-as-reverse-genus-differentia> <oboInOwl:treat-xrefs-as-equivalent rdf:datatype="http://www.w3.org/2001/XMLSchema#string">NIF_GrossAnatomy</oboInOwl:treat-xrefs-as-equivalent> <oboInOwl:treat-xrefs-as-equivalent rdf:datatype="http://www.w3.org/2001/XMLSchema#string">OG</oboInOwl:treat-xrefs-as-equivalent> - <oboInOwl:treat-xrefs-as-reverse-genus-differentia rdf:datatype="http://www.w3.org/2001/XMLSchema#string">SPD part_of NCBITaxon:6893</oboInOwl:treat-xrefs-as-reverse-genus-differentia> <oboInOwl:treat-xrefs-as-genus-differentia rdf:datatype="http://www.w3.org/2001/XMLSchema#string">SPD part_of NCBITaxon:6893</oboInOwl:treat-xrefs-as-genus-differentia> - <oboInOwl:treat-xrefs-as-reverse-genus-differentia rdf:datatype="http://www.w3.org/2001/XMLSchema#string">TADS part_of NCBITaxon:6939</oboInOwl:treat-xrefs-as-reverse-genus-differentia> <oboInOwl:treat-xrefs-as-genus-differentia rdf:datatype="http://www.w3.org/2001/XMLSchema#string">TADS part_of NCBITaxon:6939</oboInOwl:treat-xrefs-as-genus-differentia> - <oboInOwl:treat-xrefs-as-reverse-genus-differentia rdf:datatype="http://www.w3.org/2001/XMLSchema#string">TAO part_of NCBITaxon:32443</oboInOwl:treat-xrefs-as-reverse-genus-differentia> <oboInOwl:treat-xrefs-as-genus-differentia rdf:datatype="http://www.w3.org/2001/XMLSchema#string">TAO part_of NCBITaxon:32443</oboInOwl:treat-xrefs-as-genus-differentia> - <oboInOwl:treat-xrefs-as-reverse-genus-differentia rdf:datatype="http://www.w3.org/2001/XMLSchema#string">TGMA part_of NCBITaxon:44484</oboInOwl:treat-xrefs-as-reverse-genus-differentia> <oboInOwl:treat-xrefs-as-genus-differentia rdf:datatype="http://www.w3.org/2001/XMLSchema#string">TGMA part_of NCBITaxon:44484</oboInOwl:treat-xrefs-as-genus-differentia> <oboInOwl:treat-xrefs-as-equivalent rdf:datatype="http://www.w3.org/2001/XMLSchema#string">VAO</oboInOwl:treat-xrefs-as-equivalent> <oboInOwl:treat-xrefs-as-genus-differentia rdf:datatype="http://www.w3.org/2001/XMLSchema#string">WBbt part_of NCBITaxon:6237</oboInOwl:treat-xrefs-as-genus-differentia> - <oboInOwl:treat-xrefs-as-reverse-genus-differentia rdf:datatype="http://www.w3.org/2001/XMLSchema#string">WBbt part_of NCBITaxon:6237</oboInOwl:treat-xrefs-as-reverse-genus-differentia> - <oboInOwl:treat-xrefs-as-reverse-genus-differentia rdf:datatype="http://www.w3.org/2001/XMLSchema#string">XAO part_of NCBITaxon:8353</oboInOwl:treat-xrefs-as-reverse-genus-differentia> <oboInOwl:treat-xrefs-as-genus-differentia rdf:datatype="http://www.w3.org/2001/XMLSchema#string">XAO part_of NCBITaxon:8353</oboInOwl:treat-xrefs-as-genus-differentia> <oboInOwl:treat-xrefs-as-genus-differentia rdf:datatype="http://www.w3.org/2001/XMLSchema#string">ZFA part_of NCBITaxon:7954</oboInOwl:treat-xrefs-as-genus-differentia> - <oboInOwl:treat-xrefs-as-reverse-genus-differentia rdf:datatype="http://www.w3.org/2001/XMLSchema#string">ZFA part_of NCBITaxon:7954</oboInOwl:treat-xrefs-as-reverse-genus-differentia> <oboInOwl:treat-xrefs-as-genus-differentia rdf:datatype="http://www.w3.org/2001/XMLSchema#string">ncithesaurus part_of NCBITaxon:40674</oboInOwl:treat-xrefs-as-genus-differentia> - <oboInOwl:treat-xrefs-as-reverse-genus-differentia rdf:datatype="http://www.w3.org/2001/XMLSchema#string">ncithesaurus part_of NCBITaxon:40674</oboInOwl:treat-xrefs-as-reverse-genus-differentia> </owl:Ontology> @@ -61,170 +47,127 @@ /////////////////////////////////////////////////////////////////////////////////////// --> - <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/uberon#vertebrate_core"> - <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">core classes typically found across vertebrates. one purpose is to create a rough set of terms that could be used to start a new vertebrate AO</rdfs:comment> + <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/merged#inconsistent_with_fma"> + <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">classes that have some inconsistency with FMA</rdfs:comment> <rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SubsetProperty"/> </owl:AnnotationProperty> - <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/uberon#emapa_ehdaa2"> - <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">derived from the union of EHDAA2 and EMAPA - still to be checked</rdfs:comment> - <rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SubsetProperty"/> + <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/merged#PLURAL"> + <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PLURAL</rdfs:label> + <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Plural</rdfs:label> + <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">plural term</rdfs:label> + <rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SynonymTypeProperty"/> </owl:AnnotationProperty> - <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/uberon#developmental_classification"> - <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">developmental_classification</rdfs:comment> - <rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SubsetProperty"/> - </owl:AnnotationProperty> <owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#hasScope"> <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">has_scope</rdfs:label> </owl:AnnotationProperty> - <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/uberon#systematic_synonym"> - <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Systematic synonym</rdfs:label> + <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/merged#InChI"> + <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"></rdfs:label> + <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">InChI</rdfs:label> <rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SynonymTypeProperty"/> - <oboInOwl:hasScope rdf:resource="http://www.geneontology.org/formats/oboInOwl#hasExactSynonym"/> </owl:AnnotationProperty> - <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/uberon#SENSU"> - <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">taxonomic disambiguation</rdfs:label> - <rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SynonymTypeProperty"/> + <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/merged#goslim_pir"> + <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PIR GO slim</rdfs:comment> + <rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SubsetProperty"/> </owl:AnnotationProperty> - <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/uberon#goslim_yeast"> + <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/merged#abnormal_slim"> + <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Abnormal/normal slim</rdfs:comment> + <rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SubsetProperty"/> + </owl:AnnotationProperty> + <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/merged#goslim_yeast"> <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Yeast GO slim</rdfs:comment> <rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SubsetProperty"/> </owl:AnnotationProperty> - <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/uberon#spatially_disjoint_from"> - <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">spatially_disjoint_from</rdfs:label> - <obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A is spatially_disjoint_from B if they have no parts in common.</obo:IAO_0000115> - <obo:IAO_0000424 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">BFO_0000051 exactly 0 (BFO_0000050 some ?Y)</obo:IAO_0000424> - <oboInOwl:hasExactSynonym rdf:datatype="http://www.w3.org/2001/XMLSchema#string">non_overlapping_with</oboInOwl:hasExactSynonym> - <oboInOwl:hasExactSynonym rdf:datatype="http://www.w3.org/2001/XMLSchema#string">shares_no_parts_with</oboInOwl:hasExactSynonym> - <oboInOwl:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">spatially_disjoint_from</oboInOwl:id> - <oboInOwl:is_metadata_tag rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</oboInOwl:is_metadata_tag> - <oboInOwl:is_class_level rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</oboInOwl:is_class_level> - <oboInOwl:hasOBONamespace rdf:datatype="http://www.w3.org/2001/XMLSchema#string">uberon</oboInOwl:hasOBONamespace> + <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/merged#goslim_pombe"> + <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Fission yeast GO slim</rdfs:comment> + <rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SubsetProperty"/> </owl:AnnotationProperty> - <owl:Axiom> - <owl:annotatedTarget rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A is spatially_disjoint_from B if they have no parts in common.</owl:annotatedTarget> - <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">SO:cjm</oboInOwl:hasDbXref> - <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/> - <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/uberon#spatially_disjoint_from"/> - </owl:Axiom> + <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/merged#inherited_grouping_class"> + <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A grouping class that originates in two or more separate anatomical ontologies. Includes 'region of X' type terms</rdfs:comment> + <rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SubsetProperty"/> + </owl:AnnotationProperty> <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0100001"> <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">term replaced by</rdfs:label> </owl:AnnotationProperty> - <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/uberon#cell_quality"> - <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">cell_quality</rdfs:comment> - <rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SubsetProperty"/> + <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/merged#InChIKey"> + <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"></rdfs:label> + <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">InChIKey</rdfs:label> + <rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SynonymTypeProperty"/> </owl:AnnotationProperty> - <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/uberon#unvetted"> - <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">unvetted</rdfs:comment> - <rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SubsetProperty"/> - </owl:AnnotationProperty> <owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#hasSynonymType"> <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">has_synonym_type</rdfs:label> </owl:AnnotationProperty> - <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/uberon#goslim_pir"> - <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PIR GO slim</rdfs:comment> - <rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SubsetProperty"/> + <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/merged#homologous_to"> + <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">homologous_to</rdfs:label> + <oboInOwl:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">homologous_to</oboInOwl:id> + <oboInOwl:is_metadata_tag rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</oboInOwl:is_metadata_tag> </owl:AnnotationProperty> <owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#hasDbXref"> <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">database_cross_reference</rdfs:label> </owl:AnnotationProperty> - <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/uberon#metazoa_core"> - <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">core classes typically found across metazoa. one purpose is to create a rough set of terms that could be used to start a new metazoan AO. Note this subset is not yet fully fleshed out</rdfs:comment> + <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/merged#early_development"> + <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A class that represents an early developmental structure, like a blastocyst. This part of the ontology is undergoing review to remove inappropriate grouping classes.</rdfs:comment> <rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SubsetProperty"/> </owl:AnnotationProperty> - <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/uberon#FORMULA"> - <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FORMULA</rdfs:label> - <rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SynonymTypeProperty"/> - </owl:AnnotationProperty> - <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/uberon#InChI"> - <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">InChI</rdfs:label> - <rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SynonymTypeProperty"/> - </owl:AnnotationProperty> - <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/uberon#relational_slim"> - <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Relational slim: types of quality that require an additional entity in order to exist</rdfs:comment> + <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/merged#goslim_plant"> + <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Plant GO slim</rdfs:comment> <rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SubsetProperty"/> </owl:AnnotationProperty> <owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#hasOBONamespace"> <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">has_obo_namespace</rdfs:label> </owl:AnnotationProperty> - <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/uberon#anatomical_site_slim"> - <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Anatomical Site slim</rdfs:comment> - <rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SubsetProperty"/> - </owl:AnnotationProperty> - <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/uberon#defined_by_ordinal_series"> - <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">classes that are defined by relative position counting from first in a series in an individual organism rather than by homology</rdfs:comment> - <rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SubsetProperty"/> - </owl:AnnotationProperty> - <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/uberon#DUBIOUS"> - <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">dubious or contested synonym</rdfs:label> - <rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SynonymTypeProperty"/> - </owl:AnnotationProperty> <owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#SubsetProperty"> <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">subset_property</rdfs:label> </owl:AnnotationProperty> - <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/uberon#scalar_slim"> - <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Scalar slim</rdfs:comment> - <rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SubsetProperty"/> + <owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#is_class_level"/> + <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/merged#INN"> + <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"></rdfs:label> + <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">INN</rdfs:label> + <rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SynonymTypeProperty"/> </owl:AnnotationProperty> - <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/uberon#disjointness_axiom_removed"> - <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A class which has a weakened disjointness axiom, to avoid inconsistency. These are kept separately in the uberon_disjoint_from_strict ontology.</rdfs:comment> + <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/merged#goslim_candida"> + <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Candida GO slim</rdfs:comment> <rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SubsetProperty"/> </owl:AnnotationProperty> - <owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#is_class_level"/> - <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/uberon#goslim_goa"> - <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">GOA and proteome slim</rdfs:comment> - <rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SubsetProperty"/> - </owl:AnnotationProperty> <owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#SynonymTypeProperty"> <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">synonym_type_property</rdfs:label> </owl:AnnotationProperty> - <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/uberon#IUPAC_NAME"> - <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">IUPAC NAME</rdfs:label> + <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/merged#systematic_synonym"> + <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"></rdfs:label> + <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Systematic synonym</rdfs:label> <rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SynonymTypeProperty"/> + <oboInOwl:hasScope rdf:resource="http://www.geneontology.org/formats/oboInOwl#hasExactSynonym"/> </owl:AnnotationProperty> <owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#treat-xrefs-as-has-subclass"> <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">treat-xrefs-as-has-subclass</rdfs:label> </owl:AnnotationProperty> - <owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#hasExactSynonym"> - <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">has_exact_synonym</rdfs:label> - </owl:AnnotationProperty> - <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/uberon#BRAND_NAME"> - <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">BRAND NAME</rdfs:label> + <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/merged#DUBIOUS"> + <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">dubious or contested synonym</rdfs:label> <rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SynonymTypeProperty"/> </owl:AnnotationProperty> - <owl:AnnotationProperty rdf:about="http://www.w3.org/2000/01/rdf-schema#comment"/> - <owl:AnnotationProperty rdf:about="http://www.w3.org/2002/07/owl#deprecated"/> - <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/uberon#inherited_grouping_class"> - <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A grouping class that originates in two or more separate anatomical ontologies. Includes 'region of X' type terms</rdfs:comment> + <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/merged#relational_slim"> + <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Relational slim: types of quality that require an additional entity in order to exist</rdfs:comment> <rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SubsetProperty"/> </owl:AnnotationProperty> - <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/uberon#grouping_class"> - <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Subset consisting of classes creating for grouping purposes</rdfs:comment> + <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/merged#disjointness_axiom_removed"> + <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A class which has a weakened disjointness axiom, to avoid inconsistency. These are kept separately in the uberon_disjoint_from_strict ontology.</rdfs:comment> <rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SubsetProperty"/> </owl:AnnotationProperty> - <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/uberon#absent_slim"> - <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Absent/present slim</rdfs:comment> + <owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#hasExactSynonym"> + <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">has_exact_synonym</rdfs:label> + </owl:AnnotationProperty> + <owl:AnnotationProperty rdf:about="http://www.w3.org/2000/01/rdf-schema#comment"/> + <owl:AnnotationProperty rdf:about="http://www.w3.org/2002/07/owl#deprecated"/> + <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/merged#upper_level"> + <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">abstract upper-level terms not directly useful for analysis</rdfs:comment> <rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SubsetProperty"/> </owl:AnnotationProperty> - <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/uberon#homologous_to"> - <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">homologous_to</rdfs:label> - <oboInOwl:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">homologous_to</oboInOwl:id> - <oboInOwl:is_metadata_tag rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</oboInOwl:is_metadata_tag> - <oboInOwl:hasOBONamespace rdf:datatype="http://www.w3.org/2001/XMLSchema#string">uberon</oboInOwl:hasOBONamespace> - </owl:AnnotationProperty> - <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/uberon#SMILES"> - <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">SMILES</rdfs:label> - <rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SynonymTypeProperty"/> - </owl:AnnotationProperty> <owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#is_metadata_tag"/> - <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/uberon#INCONSISTENT"> - <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">indicates that a synonym is used in an inconsistent or confusing way, typically between species</rdfs:label> - <rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SynonymTypeProperty"/> + <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/merged#functional_classification"> + <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">functional_classification</rdfs:comment> + <rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SubsetProperty"/> </owl:AnnotationProperty> - <owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#treat-xrefs-as-reverse-genus-differentia"> - <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">treat-xrefs-as-reverse-genus-differentia</rdfs:label> - </owl:AnnotationProperty> - <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/uberon#sectional_anatomy_items"> - <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Sectional Anatomy Item slim</rdfs:comment> + <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/merged#high_level_annotation_qc"> + <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">High-level terms not to be used for direct annotation</rdfs:comment> <rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SubsetProperty"/> </owl:AnnotationProperty> <owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#treat-xrefs-as-genus-differentia"> @@ -236,159 +179,207 @@ <owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#consider"> <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">consider</rdfs:label> </owl:AnnotationProperty> + <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/merged#spatially_disjoint_from"> + <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">spatially_disjoint_from</rdfs:label> + <obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A is spatially_disjoint_from B if they have no parts in common.</obo:IAO_0000115> + <obo:IAO_0000424 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">BFO_0000051 exactly 0 (BFO_0000050 some ?Y)</obo:IAO_0000424> + <oboInOwl:hasExactSynonym rdf:datatype="http://www.w3.org/2001/XMLSchema#string">non_overlapping_with</oboInOwl:hasExactSynonym> + <oboInOwl:hasExactSynonym rdf:datatype="http://www.w3.org/2001/XMLSchema#string">shares_no_parts_with</oboInOwl:hasExactSynonym> + <oboInOwl:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">spatially_disjoint_from</oboInOwl:id> + <oboInOwl:is_metadata_tag rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</oboInOwl:is_metadata_tag> + <oboInOwl:is_class_level rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</oboInOwl:is_class_level> + </owl:AnnotationProperty> + <owl:Axiom> + <owl:annotatedTarget rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A is spatially_disjoint_from B if they have no parts in common.</owl:annotatedTarget> + <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">SO:cjm</oboInOwl:hasDbXref> + <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/> + <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/merged#spatially_disjoint_from"/> + </owl:Axiom> <owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym"> <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">has_broad_synonym</rdfs:label> </owl:AnnotationProperty> - <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/uberon#upper_level"> - <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">abstract upper-level terms not directly useful for analysis</rdfs:comment> - <rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SubsetProperty"/> + <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/merged#ATTRIBUTION_REQUIRED"> + <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">expert consultation and attribution required</rdfs:label> + <rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SynonymTypeProperty"/> </owl:AnnotationProperty> - <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/uberon#frequent_anatomy_items"> - <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Frequently Used Anatomy slim</rdfs:comment> + <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/merged#upper_ontology_conflict"> + <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Terms in this subset group together terms from different anatomy ontologies that have conflicting upper ontology/CARO assignments. For example, in FMA the naris is immaterial and in ZFA it is an organism subdivision.</rdfs:comment> <rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SubsetProperty"/> </owl:AnnotationProperty> - <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/uberon#PLURAL"> - <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PLURAL</rdfs:label> - <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Plural</rdfs:label> - <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">plural term</rdfs:label> - <rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SynonymTypeProperty"/> - </owl:AnnotationProperty> <owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#shorthand"> <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">shorthand</rdfs:label> </owl:AnnotationProperty> - <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/uberon#goslim_candida"> - <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Candida GO slim</rdfs:comment> - <rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SubsetProperty"/> - </owl:AnnotationProperty> <owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#hasOBOFormatVersion"> <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">has_obo_format_version</rdfs:label> </owl:AnnotationProperty> <owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#inSubset"> <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">in_subset</rdfs:label> </owl:AnnotationProperty> - <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/uberon#high_level_annotation_qc"> - <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">High-level terms not to be used for direct annotation</rdfs:comment> + <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/merged#dubious_grouping"> + <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Indicates that subclasses in AOs may be inappropriately linked</rdfs:comment> <rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SubsetProperty"/> </owl:AnnotationProperty> + <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/merged#absent_slim"> + <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Absent/present slim</rdfs:comment> + <rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SubsetProperty"/> + </owl:AnnotationProperty> + <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/merged#anatomical_site_slim"> + <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Anatomical Site slim</rdfs:comment> + <rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SubsetProperty"/> + </owl:AnnotationProperty> + <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/merged#BRAND_NAME"> + <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"></rdfs:label> + <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">BRAND NAME</rdfs:label> + <rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SynonymTypeProperty"/> + </owl:AnnotationProperty> + <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/merged#value_slim"> + <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Value slim</rdfs:comment> + <rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SubsetProperty"/> + </owl:AnnotationProperty> <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000115"> <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">definition</rdfs:label> </owl:AnnotationProperty> <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000424"> <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">expand expression to</rdfs:label> </owl:AnnotationProperty> - <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/uberon#upper_ontology_conflict"> - <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Terms in this subset group together terms from different anatomy ontologies that have conflicting upper ontology/CARO assignments. For example, in FMA the naris is immaterial and in ZFA it is an organism subdivision.</rdfs:comment> + <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/merged#cell_slim"> + <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">cell_slim</rdfs:comment> <rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SubsetProperty"/> </owl:AnnotationProperty> + <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/merged#attribute_slim"> + <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Attribute slim</rdfs:comment> + <rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SubsetProperty"/> + </owl:AnnotationProperty> + <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/merged#IUPAC_NAME"> + <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"></rdfs:label> + <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">IUPAC NAME</rdfs:label> + <rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SynonymTypeProperty"/> + </owl:AnnotationProperty> <owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#transitive_over"/> + <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/merged#SENSU"> + <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">taxonomic disambiguation</rdfs:label> + <rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SynonymTypeProperty"/> + </owl:AnnotationProperty> <owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#hasAlternativeId"> <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">has_alternative_id</rdfs:label> </owl:AnnotationProperty> - <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/uberon#disposition_slim"> - <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Disposition slim</rdfs:comment> + <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/merged#goslim_goa"> + <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">GOA and proteome slim</rdfs:comment> <rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SubsetProperty"/> </owl:AnnotationProperty> - <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/uberon#goslim_generic"> - <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Generic GO slim</rdfs:comment> + <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/merged#vertebrate_core"> + <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">core classes typically found across vertebrates. one purpose is to create a rough set of terms that could be used to start a new vertebrate AO</rdfs:comment> <rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SubsetProperty"/> </owl:AnnotationProperty> - <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/uberon#functional_classification"> - <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">functional_classification</rdfs:comment> - <rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SubsetProperty"/> + <owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#id"/> + <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/merged#HOMOLOGY"> + <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">a synonym made on the basis of a possibly homologous structure in another species</rdfs:label> + <rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SynonymTypeProperty"/> </owl:AnnotationProperty> - <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/uberon#early_development"> - <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A class that represents an early developmental structure, like a blastocyst. This part of the ontology is undergoing review to remove inappropriate grouping classes.</rdfs:comment> - <rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SubsetProperty"/> + <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/merged#SMILES"> + <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"></rdfs:label> + <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">SMILES</rdfs:label> + <rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SynonymTypeProperty"/> </owl:AnnotationProperty> - <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/uberon#inconsistent_with_fma"> - <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">classes that have some inconsistency with FMA</rdfs:comment> + <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/merged#major_organ"> + <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">somewhat fuzzy grouping for analysis purposes, currently composed of something like: liver, heart, skeletal, kidney, bladder, brain, skin, mouth, esophagus, stomach, small intestine, large intestines, trachea nose, lungs, brain, spinal cord, peripheral nerves, kidneys, ureters, bladder, urethra, gonads</rdfs:comment> <rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SubsetProperty"/> </owl:AnnotationProperty> - <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/uberon#uberon_slim"> - <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Uberon slim</rdfs:comment> - <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Uberon slim - somewhat arbitrary subset that excludes obscure terms and deep compositional terms</rdfs:comment> - <rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SubsetProperty"/> + <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/merged#INCONSISTENT"> + <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">indicates that a synonym is used in an inconsistent or confusing way, typically between species</rdfs:label> + <rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SynonymTypeProperty"/> </owl:AnnotationProperty> - <owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#id"/> - <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/uberon#abnormal_slim"> - <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Abnormal/normal slim</rdfs:comment> + <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/merged#cell_quality"> + <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">cell_quality</rdfs:comment> <rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SubsetProperty"/> </owl:AnnotationProperty> - <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/uberon#attribute_slim"> - <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Attribute slim</rdfs:comment> + <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/merged#sectional_anatomy_items"> + <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Sectional Anatomy Item slim</rdfs:comment> <rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SubsetProperty"/> </owl:AnnotationProperty> - <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/uberon#value_slim"> - <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Value slim</rdfs:comment> - <rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SubsetProperty"/> + <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/merged#has_fused_element"> + <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">has_fused_element</rdfs:label> + <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A single bone in one species may correspond to the fusion of two or more bones found as distinct elements in another. For example, tibiofibula has_fused_element tibia. A has_fused_element B does not imply that A has_part some B, rather than A has_part some B', where B' is not a subtype of B (because B is a distinct element but B' is a regional part) but has some evolutionary relationship to B.</rdfs:comment> + <oboInOwl:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">has_fused_element</oboInOwl:id> + <oboInOwl:is_class_level rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</oboInOwl:is_class_level> + <oboInOwl:is_metadata_tag rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</oboInOwl:is_metadata_tag> </owl:AnnotationProperty> - <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/uberon#gosubset_prok"> - <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Prokaryotic GO subset</rdfs:comment> + <owl:AnnotationProperty rdf:about="http://www.w3.org/2000/01/rdf-schema#label"/> + <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/merged#unvetted"> + <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">unvetted</rdfs:comment> <rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SubsetProperty"/> </owl:AnnotationProperty> - <owl:AnnotationProperty rdf:about="http://www.w3.org/2000/01/rdf-schema#label"/> - <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/uberon#ATTRIBUTION_REQUIRED"> - <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">expert consultation and attribution required</rdfs:label> + <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/merged#FORMULA"> + <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"></rdfs:label> + <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FORMULA</rdfs:label> <rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SynonymTypeProperty"/> </owl:AnnotationProperty> <owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#treat-xrefs-as-equivalent"> <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">treat-xrefs-as-equivalent</rdfs:label> </owl:AnnotationProperty> - <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/uberon#INN"> - <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">INN</rdfs:label> - <rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SynonymTypeProperty"/> + <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/merged#scalar_slim"> + <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Scalar slim</rdfs:comment> + <rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SubsetProperty"/> </owl:AnnotationProperty> - <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/uberon#major_organ"> - <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">somewhat fuzzy grouping for analysis purposes, currently composed of something like: liver, heart, skeletal, kidney, bladder, brain, skin, mouth, esophagus, stomach, small intestine, large intestines, trachea nose, lungs, brain, spinal cord, peripheral nerves, kidneys, ureters, bladder, urethra, gonads</rdfs:comment> + <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/merged#developmental_classification"> + <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">developmental_classification</rdfs:comment> <rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SubsetProperty"/> </owl:AnnotationProperty> <owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym"> <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">has_related_synonym</rdfs:label> </owl:AnnotationProperty> - <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/uberon#goslim_plant"> - <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Plant GO slim</rdfs:comment> + <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/merged#organism_views"> + <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Organism View slim</rdfs:comment> <rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SubsetProperty"/> </owl:AnnotationProperty> - <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/uberon#cell_slim"> - <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">cell_slim</rdfs:comment> + <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/merged#metazoa_core"> + <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">core classes typically found across metazoa. one purpose is to create a rough set of terms that could be used to start a new metazoan AO. Note this subset is not yet fully fleshed out</rdfs:comment> <rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SubsetProperty"/> </owl:AnnotationProperty> - <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/uberon#HOMOLOGY"> - <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">a synonym made on the basis of a possibly homologous structure in another species</rdfs:label> - <rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SynonymTypeProperty"/> + <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/merged#disposition_slim"> + <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Disposition slim</rdfs:comment> + <rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SubsetProperty"/> </owl:AnnotationProperty> - <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/uberon#dubious_for_taxon"> + <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/merged#defined_by_ordinal_series"> + <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">classes that are defined by relative position counting from first in a series in an individual organism rather than by homology</rdfs:comment> + <rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SubsetProperty"/> + </owl:AnnotationProperty> + <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/merged#uberon_slim"> + <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Uberon slim</rdfs:comment> + <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Uberon slim - somewhat arbitrary subset that excludes obscure terms and deep compositional terms</rdfs:comment> + <rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SubsetProperty"/> + </owl:AnnotationProperty> + <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/merged#dubious_for_taxon"> <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">dubious_for_taxon</rdfs:label> <oboInOwl:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">dubious_for_taxon</oboInOwl:id> <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">this relation lacks a strong logical interpretation, but can be used in place of never_in_taxon where it is desirable to state that the definition of the class is too strict for the taxon under consideration, but placing a never_in_taxon link would result in a chain of inconsistencies that will take time to resolve. Example: metencephalon in teleost</rdfs:comment> <oboInOwl:is_metadata_tag rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</oboInOwl:is_metadata_tag> <oboInOwl:is_class_level rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</oboInOwl:is_class_level> - <oboInOwl:hasOBONamespace rdf:datatype="http://www.w3.org/2001/XMLSchema#string">uberon</oboInOwl:hasOBONamespace> </owl:AnnotationProperty> - <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/uberon#InChIKey"> - <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">InChIKey</rdfs:label> - <rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SynonymTypeProperty"/> + <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/merged#goslim_generic"> + <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Generic GO slim</rdfs:comment> + <rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SubsetProperty"/> </owl:AnnotationProperty> - <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/uberon#organism_views"> - <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Organism View slim</rdfs:comment> + <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/merged#frequent_anatomy_items"> + <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Frequently Used Anatomy slim</rdfs:comment> <rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SubsetProperty"/> </owl:AnnotationProperty> - <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/uberon#goslim_pombe"> - <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Fission yeast GO slim</rdfs:comment> + <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/merged#emapa_ehdaa2"> + <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">derived from the union of EHDAA2 and EMAPA - still to be checked</rdfs:comment> <rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SubsetProperty"/> </owl:AnnotationProperty> - <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/uberon#has_fused_element"> - <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">has_fused_element</rdfs:label> - <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A single bone in one species may correspond to the fusion of two or more bones found as distinct elements in another. For example, tibiofibula has_fused_element tibia. A has_fused_element B does not imply that A has_part some B, rather than A has_part some B', where B' is not a subtype of B (because B is a distinct element but B' is a regional part) but has some evolutionary relationship to B.</rdfs:comment> - <oboInOwl:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">has_fused_element</oboInOwl:id> - <oboInOwl:is_metadata_tag rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</oboInOwl:is_metadata_tag> - <oboInOwl:is_class_level rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</oboInOwl:is_class_level> - <oboInOwl:hasOBONamespace rdf:datatype="http://www.w3.org/2001/XMLSchema#string">uberon</oboInOwl:hasOBONamespace> + <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/merged#PSI-MOD-label"> + <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"></rdfs:label> + <rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SynonymTypeProperty"/> </owl:AnnotationProperty> - <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/uberon#dubious_grouping"> - <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Indicates that subclasses in AOs may be inappropriately linked</rdfs:comment> + <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/merged#grouping_class"> + <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Subset consisting of classes creating for grouping purposes</rdfs:comment> <rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SubsetProperty"/> </owl:AnnotationProperty> + <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/merged#gosubset_prok"> + <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Prokaryotic GO subset</rdfs:comment> + <rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SubsetProperty"/> + </owl:AnnotationProperty> @@ -425,7 +416,6 @@ <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">BFO:0000051</oboInOwl:hasDbXref> <oboInOwl:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">has_part</oboInOwl:id> <oboInOwl:shorthand rdf:datatype="http://www.w3.org/2001/XMLSchema#string">has_part</oboInOwl:shorthand> - <oboInOwl:hasOBONamespace rdf:datatype="http://www.w3.org/2... 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