CTS2 BioPortal wrapper summary

CTS2 REST Services

CodeSystemCatalogQuery

• Query: http://informatics.mayo.edu/cts2/rest/codesystems
  • Query with 'about' filter: http://informatics.mayo.edu/cts2/rest/codesystems?matchvalue=oid&filtercomponent=about
  • Query with 'name' filter: http://informatics.mayo.edu/cts2/rest/codesystems?matchvalue=nci&filtercomponent=resourceName
  • Query with 'description' filter: http://informatics.mayo.edu/cts2/rest/codesystems?matchvalue=databases&filtercomponent=resourceSynopsis
  • Query with 'keyword' filter: http://informatics.mayo.edu/cts2/rest/codesystems?matchvalue=100&filtercomponent=keyword
  • Query with 'bioportalId' filter: http://informatics.mayo.edu/cts2/rest/codesystems?matchvalue=1007&filtercomponent=ontologyId&referencetype=property
  • ('contains' and 'exactmatch' algorithms supported)
• 'Count' via HEAD call

CodeSystemCatalogRead

• Read by name: http://informatics.mayo.edu/cts2/rest/codesystem/SNOMEDCT
• Read by uri: http://informatics.mayo.edu/cts2/rest/codesystembyuri?uri=http://purl.bioontology.org/ontology/SNOMEDCT
• 'Exists' via HEAD call

CodeSystemCatalogVersionQuery

• Query: http://informatics.mayo.edu/cts2/rest/codesystemversions
• Query code system versions of code system: http://informatics.mayo.edu/cts2/rest/codesystem/SNOMEDCT/versions
  • Query with 'about' filter: http://informatics.mayo.edu/cts2/rest/codesystemversions?matchvalue=oid&filtercomponent=about
  • Query with 'name' filter: http://informatics.mayo.edu/cts2/rest/codesystemversions?matchvalue=nci&filtercomponent=resourceName
  • Query with 'description' filter: http://informatics.mayo.edu/cts2/rest/codesystemversions?matchvalue=anatomy&filtercomponent=resourceSynopsis
  • ('contains' and 'exactmatch' algorithms supported)
• 'Count' via HEAD call

CodeSystemVersionCatalogRead

• Read by name: http://informatics.mayo.edu/cts2/rest/codesystem/LNC/version/LNC_226_RRF
• Or OfficialResourceVersionId: http://informatics.mayo.edu/cts2/rest/codesystem/LNC/version/226
• 'Exists' via HEAD call

EntityDescriptionQuery

• Query with 'description' http://informatics.mayo.edu/cts2/rest/entities?matchvalue=swelling
• Get all entities of code system version: http://informatics.mayo.edu/cts2/rest/codesystem/AIR/version/AIR_1993_RRF/entities
• Query entities of code system version with 'keyword' filter: http://informatics.mayo.edu/cts2/rest/codesystem/LNC/version/LNC_226_RRF/entities?matchvalue=100
  • ('contains' and 'exactmatch' algorithms supported)
• 'Count' via HEAD call

EntityDescriptionRead

• Read by name: http://informatics.mayo.edu/cts2/rest/codesystem/LNC/version/LNC_226_RRF/entity/LP31957-1
• Or using CSV OfficialResourceVersionId : http://informatics.mayo.edu/cts2/rest/codesystem/LNC/version/226/entity/LP31957-1

  NOTE: Does not support Entity lookup by URI (See notes below)

• 'Exists' via HEAD call

ValueSetCatalogQuery

• Query: http://informatics.mayo.edu/cts2/rest/valuesets
  • Query with 'about' filter: http://informatics.mayo.edu/cts2/rest/valuesets?matchvalue=FMA_subset&filtercomponent=about
  • Query with 'name' filter: http://informatics.mayo.edu/cts2/rest/valuesets?matchvalue=set&filtercomponent=resourceName
  • Query with 'description' filter: http://informatics.mayo.edu/cts2/rest/valuesets?matchvalue=anatomy&filtercomponent=resourceSynopsis
  • Query based on code system restriction: http://informatics.mayo.edu/cts2/rest/valuesets?codesystem=SNOMEDCT
  • ('contains' and 'exactmatch' algorithms supported)
• 'Count' via HEAD call

ValueSetCatalogRead

• Read by name: http://informatics.mayo.edu/cts2/rest/valueset/SNOMEDCT-MAS
• 'Exists' via HEAD call

ValueSetDefinitionQuery

• Read by name: http://informatics.mayo.edu/cts2/rest/valueset/SCTSPA/definitions
• 'Exists' via HEAD call

ValueSetDefinitionRead

• Read by name: http://informatics.mayo.edu/cts2/rest/valueset/SCTSPA/definition/42157
• 'Exists' via HEAD call

ValueSetDefinitionResolutionService

• Resolve: http://informatics.mayo.edu/cts2/rest/valueset/ECGT/definition/ECGT_1-0_OWL/resolution/43082
• 'Exists' via HEAD call

AssociationQuery

• Query 'sourceOf' associations of entity: http://informatics.mayo.edu/cts2/rest/codesystem/SNOMEDCT/version/SNOMEDCT_2010_01_31_RRF/entity/100001001/sourceof
• Query 'children' associations of entity: http://informatics.mayo.edu/cts2/rest/codesystem/MSH/version/MSH_2009_2009_02_13_RRF/entity/D006321/children

AdvancedAssociationQuery

• Get root nodes of a code system version: http://informatics.mayo.edu/cts2/rest/codesystem/SNOMEDCT/version/SNOMEDCT_2010_01_31_RRF/graph?focus=TOP_NODE&direction=FORWARD
• Get graph of focusn node in code system version:http://informatics.mayo.edu/cts2/rest/codesystem/SNOMEDCT/version/SNOMEDCT_2010_01_31_RRF/graph?focus=243796009&direction=FORWARD
• NOTES: Currently only supports direction=FORWARD and depth=1

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>
 	 ...
   

• • "1634" is not found in the results from http://rest.bioontology.org/bioportal/ontologies?apikey=YourAPIKey

• 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