VIVO Mini-Grant: Integrating the UMLS Ontology into VIVO for Linking Biomedical Scientists

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This document discusses a project to integrate the Unified Medical Language System (UMLS) ontology into the VIVO system to link biomedical scientists. It describes developing tools to publish large biomedical databases like UMLS and RxNorm as linked data. This includes aligning biomedical subject areas and publications in the VIVO system to concepts in UMLS to create connections between people, organizations, and publications. Web services were also created to facilitate working with the UMLS and PubMed linked data.

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*

Contributors: Erich Bremer* JizuZhi** Tammy DiPrima* Ann Gardner*** Naresh Singh**** AniketDivecha**** 2 Dept. of Medical Informatics* | OSA**| SOM***|Dept. of Computer Science****

The Semantic Web starts simple with a RDF triple Subject Object Predicate 8

Builds into a more complex network of interlinked URIs Source data from NCIt 9

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

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

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

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

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

Linking subject areas to publications 23

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 ,[object Object],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 24

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

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

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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

24.

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

VIVO Mini-Grant: Integrating the UMLS Ontology into VIVO for Linking Biomedical Scientists

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