- From: Richard Boyce <rdb20@pitt.edu>
- Date: Sat, 16 Mar 2013 23:26:58 -0400
- To: <public-semweb-lifesci@w3.org>
- Message-ID: <51453802.7070208@pitt.edu>
If Orangebook uses active ingredient names from the FDA's Unique Ingredient Identifier system [1] then you can take advantage of the mappings that we have created in LinkedSPLs [2] for American Structured Product Labels. There will likely be an unambiguous link from DrugBank drug to Orangebook data via SPL active ingredient for a generic.... We used three different approaches [3, attached] to achieve ~1246 *manually validated* mappings [4]. In LinkedSPLs, active ingredients and their UNII codes are derived from a weekly-updated list of drug products. These are linked to RxNorm CUIs, the drug classes provided by NDF-RT, and other things in development like semantically annotated pharmacogenomics statements [5, also attached] and experimental dynamic enhancements such as NDF-RT drug-drug interactions and automatically extracted efficacy study conclusion statements from ClinicalTrials.gov [6]. -Rich Boyce 1. http://www.fda.gov/ForIndustry/DataStandards/SubstanceRegistrationSystem-UniqueIngredientIdentifierUNII/ 2. D2R sample: http://dbmi-icode-01.dbmi.pitt.edu/linkedSPLs/; Complete graph updated 3/12/2013: http://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/linkedSPLs-dump.nt.bz2; Example queries: http://www.pitt.edu/~rdb20/data/example-queries-against-the-UPITT-NLP-LDSI.txt) 3. Hassanzadeh, O., Zhu, Qian., Freimuth, RR., Boyce R. Extending the "Web of Drug Identity" with Knowledge Extracted from United States Product Labels. Proceedings of the 2013 AMIA Summit on Translational Bioinformatics. San Francisco, March 2013. 4. https://code.google.com/p/swat-4-med-safety/source/browse/trunk/linkedSPLs/ChEBI-DrugBank-bio2rdf-mapping/fda-substance-preferred-name-to-drugbank-09292012.csv 5. Boyce, RD., Freimuth, RR., Romagnoli, KM., Pummer, T., Hochheiser, H., Empey, PE. Toward semantic modeling of pharmacogenomic knowledge for clinical and translational decision support. Proceedings of the 2013 AMIA Summit on Translational Bioinformatics. San Francisco, March 2013. 6. http://www.jbiomedsem.com/content/4/1/5 On 03/16/2013 04:35 PM, Umutcan ŞİMŞEK wrote: > I'm thinking of using fda orangebook data in my mashup which includes > dbpedia, drugbank, diseasesome, linkedct etc. AFAIK there is no rdf > serialization for orangebook in lodd project, I found one dataset from > 2008 and I'm considering convert ~ seperated .txt data to rdf through > coding a custom mapper. Do you have any suggestions to link drugbank > data to orangebook data? Is there a mapper that I can customize tokens? > Are there any work to include orangebook data in lodd?Oran > -- Richard D Boyce, PhD Assistant Professor of Biomedical Informatics Faculty, Geriatric Pharmaceutical Outcomes and Gero-Informatics Research and Training Program Scholar, Comparative Effectiveness Research Program University of Pittsburgh rdb20@pitt.edu Office: 412-648-9219 Twitter: @bhaapgh
Attachments
- application/pdf attachment: drug-entity-mapping-TBI-manuscript-camera-ready.pdf
- application/pdf attachment: PharmgxStatementAnnotation-TBI-2012-camera-ready-01232013.pdf
Received on Sunday, 17 March 2013 03:27:32 UTC