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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
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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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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