vivo mini-grant: integrating the umls ontology into vivo for linking biomedical scientists
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Stony Brook University
School of Medicine
8/25/2011
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VIVO Mini-Grant: Integrating the UMLS Ontology into VIVO for Linking Biomedical Scientists
Moises Eisenberg* and Janos Hajagos*
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Contributors:
• Erich Bremer*
• Jizu Zhi**
• Tammy DiPrima*
• Ann Gardner***
• Naresh Singh****
• Aniket Divecha****
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Dept. of Medical Informatics* | OSA**| SOM***|Dept. of Computer Science****
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SUNY REACH
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VIVO has an ontology
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The Semantic Web starts simple with a RDF triple
Subject ObjectPredicate
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Builds into a more complex network of interlinked URIs
Source data from NCIt
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The CUI: Concept Unique Identifier
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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
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UMLS RDF in the wider world
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Faceted browser view
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UMLS CUI Alignment Tool
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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
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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
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Alignment to the UMLS CUIs
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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
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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
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Linking subject areas to publications
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Data facts
• UMLS RDF (2011AA release; English language; SRL=0)– Number of triples: 110,415,427– Number of different sources: 46– Number of CUIs: 2,404,344– Number of AUIs: 3,594,372
• REACH VIVO (Data extracted 8/23/2011)– Number of people: 684– Number of triples: 448,112
• UMLS alignment of subject areas– Number of subject areas: 425– Number of UMLS CUIs generated: 899– Number of distinct UMLS CUIs: 604
• PubMed alignment to REACH– Number of UMLS CUIs generated: 192,450– Number of distinct UMLS CUIs: 11,039– Articles with no MeSH is 1,293 out of 15,975
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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
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Acknowledgements
• Supported through:
VIVO: Enabling National Networking of ScientistsNIH U24 RR029822
• Original interactive CUI alignment tool created by Jakub Pezacki (SBU Class of 2010)
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