ontologies

This repository carries the set of ontologies that are used for various mapping tasks, including:

ISO11179

This image was derived from the XMDR ISO/IEC 11179 project, and represents a slightly dated version (CD2 RC7, 2008-09-17) of ISO/IEC 11179 Edition 3 Part 3. To date, the most significant difference between this version and the current version (ISO/IEC 11179-3:2013(E)) is that Characteristic has been renamed to `Propertyin theData_Element_Concept`` region.

Additional changes:

• ontology.owl -- the following lines were removed from the definition of Ontology because they resulted in a classification error:

<rdfs:subClassOf>
      <owl:Restriction>
        <owl:onProperty rdf:resource="http://xmdr.org/ont/iso11179-3e3cd2rc7.owl#notation"/>
        <owl:cardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#int"
        >1</owl:cardinality>
      </owl:Restriction>
</rdfs:subClassOf>

• data.owl -- the following lines were removed for the same reason:

<rdfs:subClassOf>
      <owl:Restriction>
        <owl:cardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#int"
        >1</owl:cardinality>
        <owl:onProperty rdf:resource="http://xmdr.org/ont/iso11179-3e3cd2rc7.owl#notation"/>
      </owl:Restriction>
</rdfs:subClassOf>

• All files were converted from rdf/xml format to turtle format for readability purposes.
• The base URI was changed from http://xmdr.org/ont/iso11179-3e3cd2rc7.owl# to http://iso.org/iso11179-3e3/
• An rdfs:label was created for every non-BNode subject with an 'ISO ' prefix, to allow 11179 entities to be readily identified.

Note that the root module for ISO11179 is caDSR.ttl, which, in turn imports all of the other modules.

OCRE

The Ontology of Clinical Research

It is a bit of a challenge to convince Protege to load the sources locally rather than off of the interwebs. We removed the ".owl" suffixes on both the namespaces and the import statements, but that didn't appear to be sufficient. We finally just blocked access to the network when loading OCRe.ttl, which forced Protege to look locally. The ".owl" changes have been kept for the time being...

Additionally, we added the text "OCRe " to all rdfs:labels in the local files and preserved the original name as skos:prefLabel

dbGaP

This is a conversion of the XML Schema for dbGaPEx2.1.5, with "GAP" prefixes on the labels.

MMS

This is the mapping directory. The file, dbGaPMap.ttl imports iso11179, OCRe and the dbGaP schema. This is the file that we are using to prototype maps between dbGaP schema elements, ISO 11179 ObjectClass, Characteristic, DataElement, DataElementConcept, etc.