Difference between revisions of "CTS2 RDF Plugin"

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== CTS2 REST Services ==
 
== CTS2 REST Services ==
 +
 +
=== Known Issues ===
 +
* Unbound predicate queries are expensive to execute on the triple store, and CTS2 requires all Properties of a given subject to be displayed. This will cause all CTS2 Read services to have a delay in returning results.
 +
 +
All Read Services are executed by a SPARQL query similar to:
 +
 +
<code>
 +
<nowiki>
 +
<http://some/uri...> ?p ?o
 +
</nowiki>
 +
</code>
 +
 +
This ends up being a very expensive query to the triple store
 +
 +
* URI Mismatch: Certain portions of the RDF Plugin utilize the NCBO REST service for searching. Sometimes, the URIs returned by the NCBO REST service are not identical to those int the triple store. This will manifest on Entity Read by Name queries.
 +
 +
* URIs for Entities in Views: Some Entities in Views have different URIs then the resource in the actual code system. For instance
 +
 +
{{CTS2_RDF_base}}valueset/SNOMED-ETHNIC-GROUP/definition/SNOMED-ETHNIC-GROUP-43057/resolution/43057
 +
 +
refers to a SNOMEDCT Entity, but Entities have URIs starting with:
 +
 +
<code>
 +
<nowiki>
 +
http://purl.bioontology.org/ontology/SNOMED-Ethnic-Group#
 +
</nowiki>
 +
</code>
  
 
=== CodeSystemCatalogQuery ===
 
=== CodeSystemCatalogQuery ===
−
* Query: {{CTS2_RDF_base}}codesystems
+
* Query: {{CTS2_RDF_base}}codesystems?maxtoreturn=10
−
* Query with 'name' filter: {{CTS2_RDF_base}}codesystems?matchvalue=nci&filtercomponent=resourceName
+
* Query with 'name' filter: {{CTS2_RDF_base}}codesystems?matchvalue=go&filtercomponent=resourceName
 
* Query with 'description' filter: {{CTS2_RDF_base}}codesystems?matchvalue=databases&filtercomponent=resourceSynopsis
 
* Query with 'description' filter: {{CTS2_RDF_base}}codesystems?matchvalue=databases&filtercomponent=resourceSynopsis
 
* Get CodeSystems With Specified Limit: http://informatics.mayo.edu/cts2/services/bioportal-rdf/codesystems?maxtoreturn=5
 
* Get CodeSystems With Specified Limit: http://informatics.mayo.edu/cts2/services/bioportal-rdf/codesystems?maxtoreturn=5
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=== CodeSystemCatalogRead ===
 
=== CodeSystemCatalogRead ===
 
* Read by name: {{CTS2_RDF_base}}codesystem/TGMA
 
* Read by name: {{CTS2_RDF_base}}codesystem/TGMA
−
* Read by uri: {{CTS2_RDF_base}}codesystembyuri?uri=http://bioportal.bioontology.org/ontologies/1030
+
* Read by uri: {{CTS2_RDF_base}}codesystembyuri?uri=http://bioportal.bioontology.org/ontologies/TGMA
−
* Find CodeSystemByURI: {{CTS2_RDF_base}}codesystembyuri?uri=http://bioportal.bioontology.org/ontologies/1030
+
* Find CodeSystemByURI: {{CTS2_RDF_base}}codesystembyuri?uri=http://bioportal.bioontology.org/ontologies/TGMA
−
* Find CodeSystemByURI with redirect: {{CTS2_RDF_base}}codesystembyuri?uri=http://bioportal.bioontology.org/ontologies/1030&redirect=true
+
* Find CodeSystemByURI with redirect: {{CTS2_RDF_base}}codesystembyuri?uri=http://bioportal.bioontology.org/ontologies/TGMA&redirect=true
−
 
 
−
 
 
−
 
 
  
 
=== CodeSystemCatalogVersionQuery ===
 
=== CodeSystemCatalogVersionQuery ===
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* Query by Description (default) {{CTS2_RDF_base}}codesystemversions?matchvalue=bioinformatics
 
* Query by Description (default) {{CTS2_RDF_base}}codesystemversions?matchvalue=bioinformatics
 
* Query by Name {{CTS2_RDF_base}}codesystemversions?filtercomponent=resourceName&matchvalue=bioa
 
* Query by Name {{CTS2_RDF_base}}codesystemversions?filtercomponent=resourceName&matchvalue=bioa
−
* Query  by CodeSystem URI {{CTS2_RDF_base}}/codesystembyuri/versions?uri=http://bioportal.bioontology.org/ontologies/1030
+
* Query  by CodeSystem URI {{CTS2_RDF_base}}codesystembyuri/versions?uri=http://bioportal.bioontology.org/ontologies/TGMA
−
* Query by CodeSystem URI (with redirect) {{CTS2_RDF_base}}/codesystembyuri/versions?uri=http://bioportal.bioontology.org/ontologies/1030&redirect=true
+
* Query by CodeSystem URI (with redirect) {{CTS2_RDF_base}}codesystembyuri/versions?uri=http://bioportal.bioontology.org/ontologies/TGMA&redirect=true
  
 
=== CodeSystemVersionCatalogRead ===
 
=== CodeSystemVersionCatalogRead ===
−
* CodeSystemCatalogRead by Name ** {{CTS2_RDF_base}}codesystem/CARO/version/CARO-46255
+
* CodeSystemCatalogRead by Name {{CTS2_RDF_base}}codesystem/CARO/version/CARO-46255
−
* CodeSystemCatalogRead by Official Version Id ** {{CTS2_RDF_base}}codesystem/CL/version/2011-06-03
+
* CodeSystemCatalogRead by Official Version Id {{CTS2_RDF_base}}codesystem/CL/version/2011-06-03
−
 
 
−
 
 
  
 
=== EntityDescriptionQuery ===
 
=== EntityDescriptionQuery ===
 
* Query with 'description' {{CTS2_RDF_base}}entities?matchvalue=swelling
 
* Query with 'description' {{CTS2_RDF_base}}entities?matchvalue=swelling
 
* Get all entities of code system version: {{CTS2_RDF_base}}codesystem/AIR/version/AIR-42298/entities
 
* Get all entities of code system version: {{CTS2_RDF_base}}codesystem/AIR/version/AIR-42298/entities
−
* Query entities of code system version with 'keyword' filter: {{CTS2_REST_base}}codesystem/LNC/version/LNC_226_RRF/entities?matchvalue=100
+
* Get all entities of code system version by official version id: {{CTS2_RDF_base}}codesystem/LNC/version/232/entities
 +
* Query entities of code system version with 'keyword' filter: {{CTS2_RDF_base}}codesystem/LNC/version/232/entities?matchvalue=100
  
 
=== EntityDescriptionRead ===
 
=== EntityDescriptionRead ===
 
* Read by name: {{CTS2_RDF_base}}codesystem/LNC/version/LNC-44774/entity/LNC:LP97322-9
 
* Read by name: {{CTS2_RDF_base}}codesystem/LNC/version/LNC-44774/entity/LNC:LP97322-9
−
* Read using entity reference {{CTS2_REST_base}}entity/LNC:LP97322-9
+
* Read using entity reference {{CTS2_RDF_base}}entity/LNC:LP97322-9
−
 
+
* Read using entity references (mutliple Code System Versions) {{CTS2_RDF_base}}entity/obo:IAO_0000030
−
 
 
  
 
=== ValueSetCatalogQuery ===
 
=== ValueSetCatalogQuery ===
 
* Query: {{CTS2_RDF_base}}valuesets
 
* Query: {{CTS2_RDF_base}}valuesets
−
* ValueSetCatalogQuery by Description (default) {{CTS2_RDF_base}}/valuesets?matchvalue=subtree
+
* ValueSetCatalogQuery by Description (default) {{CTS2_RDF_base}}valuesets?matchvalue=subtree
 
* Query with 'name' filter: {{CTS2_RDF_base}}valuesets?matchvalue=set&filtercomponent=resourceName
 
* Query with 'name' filter: {{CTS2_RDF_base}}valuesets?matchvalue=set&filtercomponent=resourceName
 
* Query with 'description' filter: {{CTS2_RDF_base}}valuesets?matchvalue=anatomy&filtercomponent=resourceSynopsis
 
* Query with 'description' filter: {{CTS2_RDF_base}}valuesets?matchvalue=anatomy&filtercomponent=resourceSynopsis
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=== ValueSetCatalogRead ===
 
=== ValueSetCatalogRead ===
 
* Read by name: {{CTS2_RDF_base}}valueset/SNOMEDCT-MAS
 
* Read by name: {{CTS2_RDF_base}}valueset/SNOMEDCT-MAS
−
 
+
* Read by uri {{CTS2_RDF_base}}valuesetbyuri?uri=http://bioportal.bioontology.org/ontologies/SNOMEDCT-TF
−
 
+
* Read by uri with redirect {{CTS2_RDF_base}}valuesetbyuri?uri=http://bioportal.bioontology.org/ontologies/SNOMEDCT-TF&redirect=true
  
 
=== ResolvedValueSetQuery ===
 
=== ResolvedValueSetQuery ===
 
* Get all ResolvedValueSets {{CTS2_RDF_base}}resolvedvaluesets
 
* Get all ResolvedValueSets {{CTS2_RDF_base}}resolvedvaluesets
 
* Get ResolvedValueSet {{CTS2_RDF_base}}valueset/SNOMEDCT-TF/definition/SNOMEDCT-TF-43049/resolution/43049
 
* Get ResolvedValueSet {{CTS2_RDF_base}}valueset/SNOMEDCT-TF/definition/SNOMEDCT-TF-43049/resolution/43049
−
* Get ResolvedValueSet {{CTS2_RDF_base}}valueset/SNOMEDCT-TF/definition/SNOMEDCT-TF-43049/resolution/43049?matchvalue=toe
+
* Get ResolvedValueSet (with filter) {{CTS2_RDF_base}}valueset/SNOMEDCT-TF/definition/SNOMEDCT-TF-43049/resolution/43049?matchvalue=toe
−
 
+
* Get ResolvedValueSet entities {{CTS2_RDF_base}}valueset/SNOMEDCT-TF/definition/SNOMEDCT-TF-43049/resolution/43049/entities
−
 
+
* Get ResolvedValueSet entities (with filter) {{CTS2_RDF_base}}valueset/SNOMEDCT-TF/definition/SNOMEDCT-TF-43049/resolution/43049/entities?matchvalue=toe
  
 
=== AssociationQuery ===
 
=== AssociationQuery ===

Latest revision as of 17:30, 11 June 2012

CTS2 REST Services

Known Issues

  • Unbound predicate queries are expensive to execute on the triple store, and CTS2 requires all Properties of a given subject to be displayed. This will cause all CTS2 Read services to have a delay in returning results.

All Read Services are executed by a SPARQL query similar to:

<http://some/uri...> ?p ?o

This ends up being a very expensive query to the triple store

  • URI Mismatch: Certain portions of the RDF Plugin utilize the NCBO REST service for searching. Sometimes, the URIs returned by the NCBO REST service are not identical to those int the triple store. This will manifest on Entity Read by Name queries.
  • URIs for Entities in Views: Some Entities in Views have different URIs then the resource in the actual code system. For instance

http://informatics.mayo.edu/cts2/services/bioportal-rdf/valueset/SNOMED-ETHNIC-GROUP/definition/SNOMED-ETHNIC-GROUP-43057/resolution/43057

refers to a SNOMEDCT Entity, but Entities have URIs starting with:

http://purl.bioontology.org/ontology/SNOMED-Ethnic-Group#

CodeSystemCatalogQuery

CodeSystemCatalogRead

CodeSystemCatalogVersionQuery

CodeSystemVersionCatalogRead

EntityDescriptionQuery

EntityDescriptionRead

ValueSetCatalogQuery

ValueSetCatalogRead

ResolvedValueSetQuery

AssociationQuery

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