CTS2 BioPortal wrapper summary
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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
ResolvedValueSetQueryService
- Query: http://informatics.mayo.edu/cts2/rest/resolvedvaluesets
- Query (with value set restriction): http://informatics.mayo.edu/cts2/rest/resolvedvaluesets?valueset=SNOMEDCT-MAS
ResolvedValueSetResolutionService
- Resolve: http://informatics.mayo.edu/cts2/rest/valueset/ECGT/definition/ECGT_1-0_OWL/resolution/43082
- Resolve (to EntityDirectory): http://informatics.mayo.edu/cts2/rest/valueset/ECGT/definition/ECGT_1-0_OWL/resolution/43082/entities
- 'Exists' via HEAD call
AssociationQuery
- Query 'children' associations of entity: http://informatics.mayo.edu/cts2/rest/codesystem/MSH/version/MSH_2009_2009_02_13_RRF/entity/D006321/children
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:
- http://rest.bioontology.org/bioportal/search/core?apikey=880e5e30-0fa9-4cba-b25f-3069b15577f9
<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