Difference between revisions of "SPARQL BioPortal"
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| Line 13: | Line 13: | ||
| Ontology Versions | | Ontology Versions | ||
| At the moment only the last version of each ontology is kept in our RDF database. | | At the moment only the last version of each ontology is kept in our RDF database. | ||
| − | | | + | | In the future the data store will keep metadata with links to download old ontology versions. But the triple store will only contain data for the latest ontology version. |
| + | |- | ||
| + | | RRF/UMLS | ||
| + | | Not all the predicates from RRF/UMLS have been transformed into RDF triples. Labels, descriptions and hierarchies are the only predicates that we support for the moment. | ||
| + | | Actions to fully transform the UMLS database into RDF are scheduledf for 2012 Q1. | ||
| + | |- | ||
| + | |NCI Metathesaurus | ||
| + | |Currently the process that transforms RRF/UMLS into RDF triples is unable to process NCI Metathesaurus. We are working to fix this issue but meanwhile NCI Metathesaurus cannot be accessed via our SPARQL service. | ||
| + | | This issue will be addressed together with the RRF/UMLS conversion (2012 Q1). | ||
| + | |- | ||
| + | |Ontology Mappings | ||
| + | |The ontology mapping data from BioPortal has not been migrated into the SPARQL database yet. | ||
| + | |Planned to be implemented in 2012 Q1. | ||
| + | |- | ||
| + | |Synchronization with BioPortal | ||
| + | |The offline process that syncs BioPortal with our RDF database runs once a day (6pm PST). Therefore, new ontology uploads in BioPortal will be reflected in the SPARQL endpoint after that time. | ||
| + | |This policy will remain in-place unless other policy is required. | ||
| + | |- | ||
| + | |Hierarchy Closure | ||
| + | |The SPARQL queries in the alpha release do not handle any semantics. The queries only work on the asserted triples and therefore, closures need to be resolve by recursively issuing SPARQL queries. | ||
| + | | Planned to be implemented in 2012 Q1. | ||
| + | |- | ||
| + | |<del>Synonyms</del> | ||
| + | |<del>At the moment, synonyms are not handled in SPARQL queries. We are on the mechanism we will use to implement this feature, probably equivalent property reasoning.</del> | ||
| + | | Implemented, see ''Preferred Names, Synonyms and other common predicates'' | ||
|- | |- | ||
|} | |} | ||
<div style="margin-top: 10px; background: #FFEFC6; padding: 6px; border: 1px solid #FFD700; margin-bottom: 20px;"> | <div style="margin-top: 10px; background: #FFEFC6; padding: 6px; border: 1px solid #FFD700; margin-bottom: 20px;"> | ||
| − | We understand that some of these points are limitations to the service as is provided today. The NCBO team is addressing these issues and working on the production infrastructure | + | We understand that some of these points are limitations to the service as is provided today. The NCBO team is addressing these issues and working on the future SPARQL production infrastructure. Meanwhile, we offer this alpha release. Even though, the service is in alpha we plan to keep high up-time ratios. Please, contact us to provide feedback. Our support mailing list is: [mailto:support@bioontology.org support@bioontology.org] |
| − | Please, contact us to provide feedback. Our support mailing list is: [mailto:support@bioontology.org support@bioontology.org] | ||
</div> | </div> | ||
| Line 29: | Line 52: | ||
| − | === | + | === Preferred Names, Synonyms and other common predicates === |
yyyyyyyyyyy | yyyyyyyyyyy | ||
Revision as of 19:08, 29 November 2011
lorem ipsu ....
Alpha Release
This SPARQL endpoint is currently in alpha release. This alpha release is provided with the following limitations:
| Item | Description | Status/Actions |
|---|---|---|
| Ontology Versions | At the moment only the last version of each ontology is kept in our RDF database. | In the future the data store will keep metadata with links to download old ontology versions. But the triple store will only contain data for the latest ontology version. |
| RRF/UMLS | Not all the predicates from RRF/UMLS have been transformed into RDF triples. Labels, descriptions and hierarchies are the only predicates that we support for the moment. | Actions to fully transform the UMLS database into RDF are scheduledf for 2012 Q1. |
| NCI Metathesaurus | Currently the process that transforms RRF/UMLS into RDF triples is unable to process NCI Metathesaurus. We are working to fix this issue but meanwhile NCI Metathesaurus cannot be accessed via our SPARQL service. | This issue will be addressed together with the RRF/UMLS conversion (2012 Q1). |
| Ontology Mappings | The ontology mapping data from BioPortal has not been migrated into the SPARQL database yet. | Planned to be implemented in 2012 Q1. |
| Synchronization with BioPortal | The offline process that syncs BioPortal with our RDF database runs once a day (6pm PST). Therefore, new ontology uploads in BioPortal will be reflected in the SPARQL endpoint after that time. | This policy will remain in-place unless other policy is required. |
| Hierarchy Closure | The SPARQL queries in the alpha release do not handle any semantics. The queries only work on the asserted triples and therefore, closures need to be resolve by recursively issuing SPARQL queries. | Planned to be implemented in 2012 Q1. |
| Implemented, see Preferred Names, Synonyms and other common predicates |
We understand that some of these points are limitations to the service as is provided today. The NCBO team is addressing these issues and working on the future SPARQL production infrastructure. Meanwhile, we offer this alpha release. Even though, the service is in alpha we plan to keep high up-time ratios. Please, contact us to provide feedback. Our support mailing list is: support@bioontology.org
BioPortal SPARQL Usage Policy
Submitting SPARQL queries programmatically
yyyyyyyyyyy
Preferred Names, Synonyms and other common predicates
yyyyyyyyyyy