Ontology


 * PRO Ontology
 * OBI Ontology
 * OBO Foundry

There is a SPARQL endpoint that loads the OBO ontologies into separate named graphs: http://sparql.obo.neurocommons.org/

Example query, finding the subclasses of the OBI "assay" term,

prefix rdfs:  prefix rdf:  prefix owl:  prefix obo:  prefix obi:  select ?x ?lbl ?def where { graph obo:OBI { ?x a owl:Class ; rdfs:subClassOf [ a owl:Class ; rdfs:label "assay"@en ]. OPTIONAL { ?x rdfs:label ?lbl. }       OPTIONAL { ?x  ?def. }    }  }

Some ontologies use the skos:definition property to define them:

select distinct ?x ?lbl ?def where { graph obo:NIF_Cell { ?x a owl:Class. optional { ?x skos:definition ?def. }     optional { ?x skos:prefLabel ?lbl. }     }  }

The complete set of OBO named graphs in the store, as of 8/30/2010:

http://purl.org/science/graph/obo/AAO http://purl.org/science/graph/obo/APO http://purl.org/science/graph/obo/ATO http://purl.org/science/graph/obo/BILA http://purl.org/science/graph/obo/BOOTStrep http://purl.org/science/graph/obo/BSPO http://purl.org/science/graph/obo/BTO http://purl.org/science/graph/obo/CARO http://purl.org/science/graph/obo/CHEMINF http://purl.org/science/graph/obo/CL http://purl.org/science/graph/obo/CL-EMAPA http://purl.org/science/graph/obo/COG2GO http://purl.org/science/graph/obo/DC_CL http://purl.org/science/graph/obo/DDANAT http://purl.org/science/graph/obo/DOID http://purl.org/science/graph/obo/EC2GO http://purl.org/science/graph/obo/ECO http://purl.org/science/graph/obo/EGAD2GO http://purl.org/science/graph/obo/EHDA http://purl.org/science/graph/obo/EHDAA http://purl.org/science/graph/obo/EHDAA2 http://purl.org/science/graph/obo/EMAP http://purl.org/science/graph/obo/ENVO http://purl.org/science/graph/obo/ENVO_XP http://purl.org/science/graph/obo/EO http://purl.org/science/graph/obo/EV http://purl.org/science/graph/obo/FAO http://purl.org/science/graph/obo/FBbi http://purl.org/science/graph/obo/FBbt http://purl.org/science/graph/obo/FBbt_XP http://purl.org/science/graph/obo/FBdv http://purl.org/science/graph/obo/FBsp http://purl.org/science/graph/obo/FIX http://purl.org/science/graph/obo/FLU http://purl.org/science/graph/obo/GENPROTECGO http://purl.org/science/graph/obo/GO http://purl.org/science/graph/obo/GO_XP_ALL http://purl.org/science/graph/obo/GO_XP_INTERNAL http://purl.org/science/graph/obo/GO_XRF_ABBS http://purl.org/science/graph/obo/HAMAP2GO http://purl.org/science/graph/obo/HAO http://purl.org/science/graph/obo/HOM http://purl.org/science/graph/obo/HP http://purl.org/science/graph/obo/HP_XP http://purl.org/science/graph/obo/HP_XP_ALL http://purl.org/science/graph/obo/HP_XP_FMA http://purl.org/science/graph/obo/HP_XP_REL http://purl.org/science/graph/obo/IAO http://purl.org/science/graph/obo/IEV http://purl.org/science/graph/obo/IMR http://purl.org/science/graph/obo/LiPrO http://purl.org/science/graph/obo/MA http://purl.org/science/graph/obo/METACYC2GO http://purl.org/science/graph/obo/MFO http://purl.org/science/graph/obo/MI http://purl.org/science/graph/obo/MIPS2GO http://purl.org/science/graph/obo/MO http://purl.org/science/graph/obo/MPATH http://purl.org/science/graph/obo/MS http://purl.org/science/graph/obo/NIF_Cell http://purl.org/science/graph/obo/OBI http://purl.org/science/graph/obo/OBO_REL_BFO_BRIDGE http://purl.org/science/graph/obo/PATO http://purl.org/science/graph/obo/PD_ST http://purl.org/science/graph/obo/PLO http://purl.org/science/graph/obo/PRO http://purl.org/science/graph/obo/PROSITE2GO http://purl.org/science/graph/obo/ProPreO http://purl.org/science/graph/obo/REX http://purl.org/science/graph/obo/RNAO http://purl.org/science/graph/obo/SAO http://purl.org/science/graph/obo/SO http://purl.org/science/graph/obo/SO_XP http://purl.org/science/graph/obo/SPKW2GO http://purl.org/science/graph/obo/SYMP http://purl.org/science/graph/obo/TAO http://purl.org/science/graph/obo/TGMA http://purl.org/science/graph/obo/TIGR2GO http://purl.org/science/graph/obo/TO http://purl.org/science/graph/obo/TRANS http://purl.org/science/graph/obo/UMBBDENZYMEID2GO http://purl.org/science/graph/obo/UO http://purl.org/science/graph/obo/WBPhenotype http://purl.org/science/graph/obo/WBls http://purl.org/science/graph/obo/WP_XP_GO http://purl.org/science/graph/obo/WP_XP_REL http://purl.org/science/graph/obo/WP_XP_WBbt_WBls http://purl.org/science/graph/obo/ZFA

We can query to see which properties are used to assign literal values to classes,

select distinct ?p ?lbl where { ?x a owl:Class ; ?p ?o. optional { ?p rdfs:label ?lbl }. FILTER ( isLiteral(?o) && (datatype(?o) = xsd:string || isBlank(?o)) ) }

The resulting set can be filtered into those properties that appear to assign either an identifier or a description (or definition of some sort) to the target term.

The following properties appear to define simple names, synonyms, acronyms, or alternative terms which should be indexed (but not analyzed) and used to search or annotate OBO terms:

http://purl.obolibrary.org/obo/IAO_0000111	editor preferred term http://purl.obolibrary.org/obo/IAO_0000118	alternative term http://www.bootstrep.eu/ontology/GRO#synonym http://www.ebi.ac.uk/efo/alternative_term http://ccdb.ucsd.edu/SAO/1.2#synonym http://ccdb.ucsd.edu/SAO/1.2#abbreviation http://mged.sourceforge.net/ontologies/MGEDOntology.owl#unique_identifier http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Chemical_Formula	Chemical_Formula http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Display_Name	Display_Name http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#FULL_SYN	FULL_SYN http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Preferred_Name	Preferred_Name http://ontology.neuinfo.org/NIF/Backend/OBO_annotation_properties.owl#abbrev http://ontology.neuinfo.org/NIF/Backend/OBO_annotation_properties.owl#acronym http://www.nbirn.net/birnlex/1.0/OBO_annotation_properties.owl#acronym http://www.nbirn.net/birnlex/1.0/OBO_annotation_properties.owl#synonym http://www.w3.org/2000/01/rdf-schema#label http://www.w3.org/2000/01/rdf-schema#seeAlso http://www.w3.org/2004/02/skos/core#altLabel http://www.w3.org/2004/02/skos/core#definition http://www.w3.org/2004/02/skos/core#prefLabel http://ontology.neuinfo.org/NIF/Backend/OBO_annotation_properties.owl#synonym

The following properties appear to indicate associate identifiers, URIs, or names. These should (again) be indexed but not analyzed for annotation purposes:

http://www.geneontology.org/formats/oboInOwl#hasURI	has_URI http://www.geneontology.org/formats/oboInOwl#hasDbXref	has_dbxref http://www.geneontology.org/formats/oboInOwl#hasAlternativeId	has_alternative_id http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#EntrezGene_ID	EntrezGene_ID http://ccdb.ucsd.edu/SAO/1.2#bonfire_ID http://ccdb.ucsd.edu/SAO/1.2#cell_ontology_ID http://ccdb.ucsd.edu/SAO/1.2#gene_Ontology_ID http://ccdb.ucsd.edu/SAO/1.2#sao_ID http://ccdb.ucsd.edu/SAO/1.2#umls_ID http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#BioCarta_ID	BioCarta_ID http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#CAS_Registry	CAS_Registry http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#FDA_UNII_Code	FDA_UNII_Code http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#GO_Annotation	GO_Annotation http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#GenBank_Accession_Number	GenBank_Accession_Number http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Gene_Encodes_Product	Gene_Encodes_Product http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Homologous_Gene	Homologous_Gene http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#ICD-O-3_Code	ICD-O-3_Code http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#KEGG_ID	KEGG_ID http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Locus_ID	Locus_ID http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#MGI_Accession_ID	MGI_Accession_ID http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Maps_To_LASH	Maps_To_LASH http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Mitelman_Code	Mitelman_Code http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#NCBI_Taxon_ID	NCBI_Taxon_ID http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#NCI_META_CUI	NCI_META_CUI http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#NDFRT_Code	NDFRT_Code http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#NDFRT_Name	NDFRT_Name http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#NSC_Code	NSC_Code http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#OID	OID http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#OMIM_Number	OMIM_Number http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Related_Lash_Concept	Related_Lash_Concept http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Related_MedDRA_Code	Related_MedDRA_Code http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#SNP_ID	SNP_ID http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Swiss_Prot	Swiss_Prot http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#UMLS_CUI	UMLS_CUI http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#USDA_ID	USDA_ID http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#code http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#miRBase_ID	miRBase_ID http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#PMID http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#bamsID http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#bonfireID http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#bonfire_ID http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#cell_ontology_ID http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#gene_Ontology_ID http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#neuroNamesAncillaryTerm http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#neuronamesID http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#sao_ID http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#umls_ID http://ontology.neuinfo.org/NIF/Backend/OBO_annotation_properties.owl#MeshUid http://ontology.neuinfo.org/NIF/Backend/OBO_annotation_properties.owl#UmlsCui http://ontology.neuinfo.org/NIF/Backend/OBO_annotation_properties.owl#nifID http://ontology.neuinfo.org/NIF/Backend/OBO_annotation_properties.owl#taxonomicCommonName http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-Cell.owl#cell_ontology_ID http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-Cell.owl#sao_ID http://protege.stanford.edu/plugins/owl/protege#sao_ID

Finally, the following properties appear to designate definitions, descriptions, comments, or other textual notes that should be analyzed and indexed for search purposes:

http://ccdb.ucsd.edu/SAO/1.2#definition http://ccdb.ucsd.edu/SAO/1.2#externallySourcedDefinition http://ccdb.ucsd.edu/SAO/1.2#note http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#ALT_DEFINITION http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#DEFINITION	DEFINITION http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#birnlexComment http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#birnlexDefinition http://ontology.neuinfo.org/NIF/Backend/OBO_annotation_properties.owl#altDefinition http://www.w3.org/2000/01/rdf-schema#comment http://purl.obolibrary.org/obo/IAO_0000115	definition http://purl.org/dc/elements/1.1/description http://www.bootstrep.eu/ontology/GRO#definition http://www.ebi.ac.uk/efo/definition http://www.nbirn.net/birnlex/1.0/OBO_annotation_properties.owl#tempDefinition http://www.nbirn.net/birnlex/1.0/OBO_annotation_properties.owl#externallySourcedDefinition http://ontology.neuinfo.org/NIF/Backend/OBO_annotation_properties.owl#externallySourcedDefinition http://ontology.neuinfo.org/NIF/Backend/OBO_annotation_properties.owl#tempDefinition