VIVO Mini-Grant: Integrating the UMLS Ontology into VIVO for Linking Biomedical Scientists
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VIVO 2011 presentation on mini-grant award that Stony Brook won from the NIH VIVO consortium.
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VIVO Mini-Grant: Integrating the UMLS Ontology into VIVO for Linking Biomedical Scientists
- 1. Stony Brook University School of Medicine 8/25/2011 1 VIVO Mini-Grant: Integrating the UMLS Ontology into VIVO for Linking Biomedical Scientists Moises Eisenberg* and Janos Hajagos*
- 2. Contributors: Erich Bremer* JizuZhi** Tammy DiPrima* Ann Gardner*** Naresh Singh**** AniketDivecha**** 2 Dept. of Medical Informatics* | OSA**| SOM***|Dept. of Computer Science****
- 3. SUNY REACH 3
- 4. 4
- 5. 5
- 6. 6
- 7. VIVO has an ontology 7
- 8. The Semantic Web starts simple with a RDF triple Subject Object Predicate 8
- 9. Builds into a more complex network of interlinked URIs Source data from NCIt 9
- 10. 10
- 11. The CUI: Concept Unique Identifier 11
- 12. UMLS as linked data Developed tool to publish large databases into RDFS Published 2011AA version of the UMLS and corresponding RxNorm Release Public available sources (SRL=0) RxNorm is linked to DrugBank Includes attributes, relationships, and semantic types from the UMLS 12
- 13. UMLS RDF in the wider world 13
- 14. Faceted browser view 14
- 15. UMLS CUI Alignment Tool 15
- 16. 16
- 17. Algorithm for aligning free text Parse free text into component words Build phrases of different word length Query UMLS if phrase exists Sort in descending order of number of words Tie criteria based on number of occurrences in different source vocabularies Most widely used gets a higher rank 17
- 18. UMLS Web Service Base address: http://link.informatics.stonybrook.edu Sample call: /MeaningLookup/MlServiceServlet?textToProcess=Pediatric%20HIV&format=json Response format: JSON, N-triples, RDF/XML Response content: Best choices and all choices for matching CUIs 18
- 19. 19 Alignment to the UMLS CUIs
- 20. PubMed RDF Conversion Started with XSLT published in 2008 by Pierre Lindenbaum A prototype project linked 2010 PubMed to the internal Health Sciences Library MARC holdings data (>800,000,000 triples) Allowed linked data search joining article data with holdings data PubMed XSLT updated to 2011 schema with MeSH aligned to the UMLS CUIs Current translation generated 1,973,880,813 triples 20
- 21. 21
- 22. PubMed CUI Web Service Base address: http://link.informatics.stonybrook.edu Sample call: /weaver/pubmed2cuis?pmid=17952453 Response format: JSON Response content: UMLS CUIs with labels 22
- 23. Linking subject areas to publications 23
- 25. Links SPARQL endpoint: http://link.informatics.stonybrook.edu/sparql/ CUI alignment tool: http://link.informatics.stonybrook.edu/MeaningLookup/ Points to start browsing linked data: http://link.informatics.stonybrook.edu/umls/ http://link.informatics.stonybrook.edu/umls/SAB Open source code developed at SBU: http://code.google.com/p/py-triple-simple/ Native Python RDF utility http://code.google.com/p/sbu-mi-vivo-tools/ Automated dumping of VIVO sites RDF and alignment to UMLS and PubMed http://code.google.com/p/spyder-web/ Faceted browser and lightweight web service for parameterized SPARQL queries 25
- 26. Acknowledgements Supported through: VIVO: Enabling National Networking of Scientists NIH U24 RR029822 Original interactive CUI alignment tool created by JakubPezacki (SBU Class of 2010) 26