Linking the RxNorm Database - w3.org • Created by NIH’s National Library of Medicine • Combines several different drug vocabularies • A standardized nomenclature for drug names

Linking the RxNorm DatabaseJanos G. Hajagos

Medical InformaticsStony Brook University School of

Medicine

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RxNorm

• Created by NIH’s National Library of Medicine• Combines several different drug vocabularies• A standardized nomenclature for drug names• Unifies vocabularies around RXCUI, a concept

unique identifier

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RxNorm

• Full updates are made monthly• Weekly change updates• Part of the UMLS releases, e.g., 2009AB• Release files are in Rich Release Format (RRF)• Scripts to Load into relational databases

(MySQL and Oracle)• Requires a UMLS license agreement to

download

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RXAUI: A Source Identifier

http://link.informatics.stonybrook.edu/rxnorm/RXAUI/1666487

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RXAUI: Attributes

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http://link.informatics.stonybrook.edu/rxnorm/RXAUI/3051392

RXCUI: A Concept Identifier

6rxnorm:hasRXCUI rdfs:subPropertyOf owl:sameAs .

Relationships

• Mapping relationships between RXAUI and RXCUI

• Had to switch the order of the relationships to make “semantic” sense– ingredient_of– has_ingredient

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RXCUI: Relationships

http://link.informatics.stonybrook.edu/rxnorm/RXCUI/4044068

Details on publication of first draftBased on the March 2010 RxNorm Release

Count

Total Number of Triples 8,428,160

Number of Classes 4

Number of Distinct Predicates 37

Number of attributes (links to literals) 3,576,351

Number of connections (RXAUIs) 835,683

Number of connections (RXCUIs) 831,306

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http://download.nlm.nih.gov/umls/kss/rxnorm/RxNorm_full_03012010.zip

Finalizing the RXNorm draft

• Make RXCUI class richer– Create URI for HIPAA style NDC codes– Publish RXNSTY (semantic types)

• Linking into the LODD cloud– Mesh terminology

• May require publishing of Supplementary Mesh Terms

– DBPedia and Drugbank through ACS registry #– Dailymed needs structured product id to create link

• Adding Dublin Core Metadata

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Example

• A patient was prescribed Singulair 4 Mg Granules on 4/1/2010 – HIPAA compliant NDC is“00006384104”

• What do we know about this drug?• Can we utilize the LODD to learn more about

this drug?

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Follow the Links

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SPARQL QuerySELECT distinct ?RXCUI ?CASWHERE {?RXAUI1 <http://link.informatics.stonybrook.edu/rxnorm/ATN#NDC> "00006384104" .?RXAUI1 <http://link.informatics.stonybrook.edu/rxnorm/hasRXCUI> ?RXCUI .?RXAUI2 <http://link.informatics.stonybrook.edu/rxnorm/hasRXCUI> ?RXCUI .?RXAUI2 <http://link.informatics.stonybrook.edu/rxnorm/REL#has_ingredient>

?RXAUIingredient .?RXAUIingredient <http://link.informatics.stonybrook.edu/rxnorm/hasRXCUI>

?RXCUIingredient .?RXAUI3 <http://link.informatics.stonybrook.edu/rxnorm/hasRXCUI>

?RXCUIingredient .?RXAUI3 <http://link.informatics.stonybrook.edu/rxnorm/ATN#RN> ?CAS}

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SPARQL Endpoint: http://link.informatics.stonybrook.edu/sparql/

Named graph: http://nlm.nih.gov/research/umls/rxnorm/

Result:

Mesh Record

http://www.nlm.nih.gov/cgi/mesh/2010/MB_cgi?mode=&term=montelukast 14

Montelukast in Drugbank

http://www4.wiwiss.fu-berlin.de/drugbank/page/drugs/DB00471 15

Montelukast in DBpedia

16http://dbpedia.org/resource/Montelukast

The Challenge

• For clinical use connections should be based on chemical identifiers

• Differentiating between active and non active forms of an ingredient– Montelukast Sodium (CAS: 151767-02-1)– Montelukast (CAS: 158966-92-8)

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Linking to external URIs

• Pubmed (Mesh identifiers)• Pubchem (FDA UNII Codes)• Dailymed (should link by Structured Product

label Id)• RXNorm (rest interface):

http://rxnav.nlm.nih.gov/REST/rxcui/404406/

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Acknowledgements

• Erich Bremer (SBU) for awakening me to the semantic web and in depth discussions

• Sampurna Shrestha (SBU) for installing the server

• Moises Eisenberg and Margaret Morris (SBU/SUNY) for understanding the potential of linked data

• Susie Stephens and HCLS LODD Group for allowing me to present on this material

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