CTS2 BioPortal wrapper summary

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Contents

CTS2 REST Services

CodeSystemCatalogQuery

CodeSystemCatalogRead

CodeSystemCatalogVersionQuery

CodeSystemVersionCatalogRead

EntityDescriptionQuery

EntityDescriptionRead

ValueSetCatalogQuery

ValueSetCatalogRead

ResolvedValueSetQueryService

ResolvedValueSetResolutionService

AssociationQuery

ISSUES

  • URI issues
  • Views as ontologies is problematic
  • Search returns hits back from views. We can restrict the search to only ontologyIds that are ontologies, but that tested to be a 4-5x performance hit on the searc
  • A search will sometimes return results with an 'ontologyId' that doesn't match to anything. For example:
    • http://rest.bioontology.org/bioportal/search/core?apikey=880e5e30-0fa9-4cba-b25f-3069b15577f9
      results in:
	 <searchBean>
	 <ontologyVersionId>45952</ontologyVersionId>
	 <ontologyId>1634</ontologyId>
 	 <ontologyDisplayLabel>Infectious DIsease Ontology</ontologyDisplayLabel>
 	 <recordType>apreferredname</recordType>
 	 <objectType>individual</objectType>
 	 <conceptId>http://purl.obolibrary.org/obo/IAO_0000224</conceptId>
 	 <conceptIdShort>obo:IAO_0000224</conceptIdShort>
 	 <preferredName>core</preferredName>
 	 <contents>core</contents>
 	 </searchBean>
 	 ...
   
  • No bioportal REST signature to search for an entity based on ontologyVersionId
  • No bioportal REST signation to get an Entity by its URI (or 'fullId') in bioportal
  • No good way to get all entities in the system (can get all of an ontologyId)
  • Can't get all associations, so we can't do /codesystem/CSNAME/version/VERSION/associations -- there is no efficient way to do this in bioportal.

SVN

SVN url

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