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ncbo / umls2rdf

These python scripts connect to the Unified Medical Language System (UMLS) database and translate the ontologies into RDF/OWL files. This is part of the BioPortal project.
http://bioportal.bioontology.org/
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MRSAT and attributes on RELs #26

Closed rwynne closed 5 years ago

rwynne commented 6 years ago

For some sources, MRSAT has attributes on RELs not expressed in the output. Could these be added to the conversion, or is this a limitation of Turtle?

Examples: CHARACTERISTIC_TYPE_ID|SNOMEDCT_US 520746 MODIFIER_ID|SNOMEDCT_US 520746 MODULE_ID|SNOMEDCT_US 13884 MODULE_NAME|SNOMEDCT_US 13884 SMQ_TERM_ADDVERSION|MDR 150604 SMQ_TERM_CAT|MDR 150604 SMQ_TERM_LMVERSION|MDR 150604 SMQ_TERM_SCOPE|MDR 150604 SMQ_TERM_STATUS|MDR 150604 SMQ_TERM_WEIGHT|MDR 150604 SOURCE_EFFECTIVE_TIME|SNOMEDCT_US 6 TARGET_EFFECTIVE_TIME|SNOMEDCT_US 6 UI1_HAS_BOND_WITH|NPO 2 UI1_HAS_PROPERTY|NPO 15 UI1_HAS_QUALITY|NPO 20 UI1_HAS_ROLE|NPO 21 UI1_HAS_SINGLE_BOND_WITH|NPO 2 UI1_IS_REALIZED_IN|NPO 95

Some of us think this might be a concrete example, using SNOMED. Because RELs in RRF don't have inheritance, they can probably be considered one-to-one.

<http://purl.bioontology.org/ontology/SNOMEDCT/359905005> a owl:Class ;
               skos:prefLabel """Repair of abdominal fistula"""@en ;
               skos:notation """359905005"""^^xsd:string ;
               skos:altLabel """Repair of abdominal fistula (procedure)"""@en ;
               rdfs:subClassOf <http://purl.bioontology.org/ontology/SNOMEDCT/120171006> ;
               <http://purl.bioontology.org/ontology/SNOMEDCT/has_direct_morphology> <http://purl.bioontology.org/ontology/SNOMEDCT/118622000> ;
               <http://purl.bioontology.org/ontology/SNOMEDCT/has_direct_procedure_site> <http://purl.bioontology.org/ontology/SNOMEDCT/113345001> ;
               <http://purl.bioontology.org/ontology/SNOMEDCT/has_method> <http://purl.bioontology.org/ontology/SNOMEDCT/129357001> ;
               <http://purl.bioontology.org/ontology/SNOMEDCT/SUBSET_MEMBER> """900000000000497000~MAPTARGET~XU7bj"""^^xsd:string ;
               <http://purl.bioontology.org/ontology/SNOMEDCT/SUBSET_MEMBER> """900000000000509007~ACCEPTABILITYID~900000000000548007"""^^xsd:string ;
               <http://purl.bioontology.org/ontology/SNOMEDCT/TYPE_ID> """900000000000003001"""^^xsd:string ;
               <http://purl.bioontology.org/ontology/SNOMEDCT/SUBSET_MEMBER> """900000000000508004~ACCEPTABILITYID~900000000000548007"""^^xsd:string ;
               <http://purl.bioontology.org/ontology/SNOMEDCT/DEFINITION_STATUS_ID> """900000000000073002"""^^xsd:string ;
               <http://purl.bioontology.org/ontology/SNOMEDCT/SUBSET_MEMBER> """900000000000509007~ACCEPTABILITYID~900000000000548007"""^^xsd:string ;
               <http://purl.bioontology.org/ontology/SNOMEDCT/TYPE_ID> """900000000000013009"""^^xsd:string ;
               <http://purl.bioontology.org/ontology/SNOMEDCT/ACTIVE> """1"""^^xsd:string ;
               <http://purl.bioontology.org/ontology/SNOMEDCT/SUBSET_MEMBER> """900000000000508004~ACCEPTABILITYID~900000000000548007"""^^xsd:string ;
               <http://purl.bioontology.org/ontology/SNOMEDCT/EFFECTIVE_TIME> """20070731"""^^xsd:string ;
               <http://purl.bioontology.org/ontology/SNOMEDCT/CASE_SIGNIFICANCE_ID> """900000000000448009"""^^xsd:string ;
               <http://purl.bioontology.org/ontology/SNOMEDCT/CASE_SIGNIFICANCE_ID> """900000000000448009"""^^xsd:string ;
               <http://purl.bioontology.org/ontology/SNOMEDCT/CTV3ID> """XU7bj"""^^xsd:string ;
               umls:cui """C2937261"""^^xsd:string ;
               umls:tui """T061"""^^xsd:string ;
               umls:hasSTY <http://purl.bioontology.org/ontology/STY/T061> ;
_:genid12345678 a owl:Axiom ;
                owl:annotatedSource <http://purl.bioontology.org/ontology/SNOMEDCT/359905005> ;
                owl:annotatedProperty <http://purl.bioontology.org/ontology/SNOMEDCT/has_direct_procedure_site> ;
                owl:annotatedTarget <http://purl.bioontology.org/ontology/SNOMEDCT/113345001> ;
                <http://purl.bioontology.org/ontology/SNOMEDCT/MODIFIER_ID> “900000000000451002” ; 
 <http://purl.bioontology.org/ontology/SNOMEDCT/CHARACTERISTIC_TYPE_ID> “900000000000011006” ; .