Difference between revisions of "CTS2 RDF Plugin"
Jump to navigation
Jump to search
| (31 intermediate revisions by 2 users not shown) | |||
| Line 1: | Line 1: | ||
== 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= | + | * 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 | ||
| Line 10: | Line 37: | ||
=== 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/ | + | * 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/ | + | * 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/ | + | * Find CodeSystemByURI with redirect: {{CTS2_RDF_base}}codesystembyuri?uri=http://bioportal.bioontology.org/ontologies/TGMA&redirect=true |
=== CodeSystemCatalogVersionQuery === | === CodeSystemCatalogVersionQuery === | ||
| Line 19: | Line 46: | ||
* Query with 'name' filter: {{CTS2_RDF_base}}codesystemversions?matchvalue=nci&filtercomponent=resourceName | * Query with 'name' filter: {{CTS2_RDF_base}}codesystemversions?matchvalue=nci&filtercomponent=resourceName | ||
* Query with 'description' filter: {{CTS2_RDF_base}}codesystemversions?matchvalue=anatomy&filtercomponent=resourceSynopsis | * Query with 'description' filter: {{CTS2_RDF_base}}codesystemversions?matchvalue=anatomy&filtercomponent=resourceSynopsis | ||
| − | * | + | * Query by Description (default) {{CTS2_RDF_base}}codesystemversions?matchvalue=bioinformatics |
| − | * | + | * 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/TGMA |
| − | * | + | * 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 | + | * CodeSystemCatalogRead by Name {{CTS2_RDF_base}}codesystem/CARO/version/CARO-46255 |
| − | * CodeSystemCatalogRead by Official Version Id | + | * 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: {{ | + | * 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/ | + | * Read by name: {{CTS2_RDF_base}}codesystem/LNC/version/LNC-44774/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}} | + | * 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 | ||
| Line 48: | Line 75: | ||
=== 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 === | ||
| Line 64: | Line 90: | ||
* AssociationQuery (subjectof) {{CTS2_RDF_base}}codesystem/ICD9CM/version/ICD9CM-47178/entity/E008/subjectof | * AssociationQuery (subjectof) {{CTS2_RDF_base}}codesystem/ICD9CM/version/ICD9CM-47178/entity/E008/subjectof | ||
* AssociationQuery (targetof) {{CTS2_RDF_base}}codesystem/ICD9CM/version/ICD9CM-47178/entity/E008/targetof | * AssociationQuery (targetof) {{CTS2_RDF_base}}codesystem/ICD9CM/version/ICD9CM-47178/entity/E008/targetof | ||
| − | |||
| − | |||
| − | |||
| − | |||
Latest revision as of 18:30, 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
refers to a SNOMEDCT Entity, but Entities have URIs starting with:
http://purl.bioontology.org/ontology/SNOMED-Ethnic-Group#
CodeSystemCatalogQuery
- Query: http://informatics.mayo.edu/cts2/services/bioportal-rdf/codesystems?maxtoreturn=10
- Query with 'name' filter: http://informatics.mayo.edu/cts2/services/bioportal-rdf/codesystems?matchvalue=go&filtercomponent=resourceName
- Query with 'description' filter: http://informatics.mayo.edu/cts2/services/bioportal-rdf/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 and Page: http://informatics.mayo.edu/cts2/services/bioportal-rdf/codesystems?maxtoreturn=5&page=10
CodeSystemCatalogRead
- Read by name: http://informatics.mayo.edu/cts2/services/bioportal-rdf/codesystem/TGMA
- Read by uri: http://informatics.mayo.edu/cts2/services/bioportal-rdf/codesystembyuri?uri=http://bioportal.bioontology.org/ontologies/TGMA
- Find CodeSystemByURI: http://informatics.mayo.edu/cts2/services/bioportal-rdf/codesystembyuri?uri=http://bioportal.bioontology.org/ontologies/TGMA
- Find CodeSystemByURI with redirect: http://informatics.mayo.edu/cts2/services/bioportal-rdf/codesystembyuri?uri=http://bioportal.bioontology.org/ontologies/TGMA&redirect=true
CodeSystemCatalogVersionQuery
- Query: http://informatics.mayo.edu/cts2/services/bioportal-rdf/codesystemversions
- Query code system versions of code system: http://informatics.mayo.edu/cts2/services/bioportal-rdf/codesystem/SNOMEDCT/versions
- Query with 'name' filter: http://informatics.mayo.edu/cts2/services/bioportal-rdf/codesystemversions?matchvalue=nci&filtercomponent=resourceName
- Query with 'description' filter: http://informatics.mayo.edu/cts2/services/bioportal-rdf/codesystemversions?matchvalue=anatomy&filtercomponent=resourceSynopsis
- Query by Description (default) http://informatics.mayo.edu/cts2/services/bioportal-rdf/codesystemversions?matchvalue=bioinformatics
- Query by Name http://informatics.mayo.edu/cts2/services/bioportal-rdf/codesystemversions?filtercomponent=resourceName&matchvalue=bioa
- Query by CodeSystem URI http://informatics.mayo.edu/cts2/services/bioportal-rdf/codesystembyuri/versions?uri=http://bioportal.bioontology.org/ontologies/TGMA
- Query by CodeSystem URI (with redirect) http://informatics.mayo.edu/cts2/services/bioportal-rdf/codesystembyuri/versions?uri=http://bioportal.bioontology.org/ontologies/TGMA&redirect=true
CodeSystemVersionCatalogRead
- CodeSystemCatalogRead by Name http://informatics.mayo.edu/cts2/services/bioportal-rdf/codesystem/CARO/version/CARO-46255
- CodeSystemCatalogRead by Official Version Id http://informatics.mayo.edu/cts2/services/bioportal-rdf/codesystem/CL/version/2011-06-03
EntityDescriptionQuery
- Query with 'description' http://informatics.mayo.edu/cts2/services/bioportal-rdf/entities?matchvalue=swelling
- Get all entities of code system version: http://informatics.mayo.edu/cts2/services/bioportal-rdf/codesystem/AIR/version/AIR-42298/entities
- Get all entities of code system version by official version id: http://informatics.mayo.edu/cts2/services/bioportal-rdf/codesystem/LNC/version/232/entities
- Query entities of code system version with 'keyword' filter: http://informatics.mayo.edu/cts2/services/bioportal-rdf/codesystem/LNC/version/232/entities?matchvalue=100
EntityDescriptionRead
- Read by name: http://informatics.mayo.edu/cts2/services/bioportal-rdf/codesystem/LNC/version/LNC-44774/entity/LNC:LP97322-9
- Read using entity reference http://informatics.mayo.edu/cts2/services/bioportal-rdf/entity/LNC:LP97322-9
- Read using entity references (mutliple Code System Versions) http://informatics.mayo.edu/cts2/services/bioportal-rdf/entity/obo:IAO_0000030
ValueSetCatalogQuery
- Query: http://informatics.mayo.edu/cts2/services/bioportal-rdf/valuesets
- ValueSetCatalogQuery by Description (default) http://informatics.mayo.edu/cts2/services/bioportal-rdf/valuesets?matchvalue=subtree
- Query with 'name' filter: http://informatics.mayo.edu/cts2/services/bioportal-rdf/valuesets?matchvalue=set&filtercomponent=resourceName
- Query with 'description' filter: http://informatics.mayo.edu/cts2/services/bioportal-rdf/valuesets?matchvalue=anatomy&filtercomponent=resourceSynopsis
- Query based on code system restriction: http://informatics.mayo.edu/cts2/services/bioportal-rdf/valuesets?codesystem=SNOMEDCT
ValueSetCatalogRead
- Read by name: http://informatics.mayo.edu/cts2/services/bioportal-rdf/valueset/SNOMEDCT-MAS
- Read by uri http://informatics.mayo.edu/cts2/services/bioportal-rdf/valuesetbyuri?uri=http://bioportal.bioontology.org/ontologies/SNOMEDCT-TF
- Read by uri with redirect http://informatics.mayo.edu/cts2/services/bioportal-rdf/valuesetbyuri?uri=http://bioportal.bioontology.org/ontologies/SNOMEDCT-TF&redirect=true
ResolvedValueSetQuery
- Get all ResolvedValueSets http://informatics.mayo.edu/cts2/services/bioportal-rdf/resolvedvaluesets
- Get ResolvedValueSet http://informatics.mayo.edu/cts2/services/bioportal-rdf/valueset/SNOMEDCT-TF/definition/SNOMEDCT-TF-43049/resolution/43049
- Get ResolvedValueSet (with filter) http://informatics.mayo.edu/cts2/services/bioportal-rdf/valueset/SNOMEDCT-TF/definition/SNOMEDCT-TF-43049/resolution/43049?matchvalue=toe
- Get ResolvedValueSet entities http://informatics.mayo.edu/cts2/services/bioportal-rdf/valueset/SNOMEDCT-TF/definition/SNOMEDCT-TF-43049/resolution/43049/entities
- Get ResolvedValueSet entities (with filter) http://informatics.mayo.edu/cts2/services/bioportal-rdf/valueset/SNOMEDCT-TF/definition/SNOMEDCT-TF-43049/resolution/43049/entities?matchvalue=toe
AssociationQuery
- AssociationQuery (all of CodeSystemVersion) http://informatics.mayo.edu/cts2/services/bioportal-rdf/codesystem/ICD9CM/version/ICD9CM-47178/associations
- AssociationQuery (children) http://informatics.mayo.edu/cts2/services/bioportal-rdf/codesystem/ICD9CM/version/ICD9CM-47178/entity/E008/children
- AssociationQuery (subjectof) http://informatics.mayo.edu/cts2/services/bioportal-rdf/codesystem/ICD9CM/version/ICD9CM-47178/entity/E008/subjectof
- AssociationQuery (targetof) http://informatics.mayo.edu/cts2/services/bioportal-rdf/codesystem/ICD9CM/version/ICD9CM-47178/entity/E008/targetof