Difference between revisions of "CTS2 BioPortal wrapper summary"

From NCBO Wiki
Jump to: navigation, search
(AssociationQuery)
 
(10 intermediate revisions by the same user not shown)
Line 56: Line 56:
 
* 'Exists' via HEAD call
 
* 'Exists' via HEAD call
  
=== ValueSetDefinitionQuery ===
+
=== ResolvedValueSetQueryService ===
* Read by name: {{CTS2_REST_base}}valueset/SCTSPA/definitions
+
* Query: {{CTS2_REST_base}}resolvedvaluesets
* 'Exists' via HEAD call
+
* Query (with value set restriction): {{CTS2_REST_base}}resolvedvaluesets?valueset=SNOMEDCT-MAS
 
 
=== ValueSetDefinitionRead ===
 
* Read by name: {{CTS2_REST_base}}valueset/SCTSPA/definition/42157
 
* 'Exists' via HEAD call
 
  
=== ValueSetDefinitionResolutionService ===
+
=== ResolvedValueSetResolutionService ===
* Read by name: {{CTS2_REST_base}}valueset/SCTSPA/definition/42157/resolution?resolutiontype=entitydirectory
+
* Resolve: {{CTS2_REST_base}}valueset/ECGT/definition/ECGT_1-0_OWL/resolution/43082
 +
* Resolve (to EntityDirectory): {{CTS2_REST_base}}valueset/ECGT/definition/ECGT_1-0_OWL/resolution/43082/entities
 
* 'Exists' via HEAD call
 
* 'Exists' via HEAD call
  
 
=== AssociationQuery ===
 
=== AssociationQuery ===
* Query 'sourceOf' associations of entity: {{CTS2_REST_base}}codesystem/SNOMEDCT/version/SNOMEDCT_2010_01_31_RRF/entity/100001001/sourceof
 
 
* Query 'children' associations of entity: {{CTS2_REST_base}}codesystem/MSH/version/MSH_2009_2009_02_13_RRF/entity/D006321/children
 
* Query 'children' associations of entity: {{CTS2_REST_base}}codesystem/MSH/version/MSH_2009_2009_02_13_RRF/entity/D006321/children
 
=== AdvancedAssociationQuery ===
 
* Get root nodes of a code system version: {{CTS2_REST_base}}codesystem/SNOMEDCT/version/SNOMEDCT_2010_01_31_RRF/graph?focus=TOP_NODE&direction=FORWARD
 
* Get graph of focusn node in code system version:{{CTS2_REST_base}}codesystem/SNOMEDCT/version/SNOMEDCT_2010_01_31_RRF/graph?focus=243796009&direction=FORWARD
 
* NOTES: Currently only supports direction=FORWARD and depth=1
 
  
 
== ISSUES ==
 
== ISSUES ==

Latest revision as of 12:26, 11 June 2012

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