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Re: Orangebook data

From: Richard Boyce <rdb20@pitt.edu>
Date: Sat, 16 Mar 2013 23:26:58 -0400
Message-ID: <51453802.7070208@pitt.edu>
To: <public-semweb-lifesci@w3.org>
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




Received on Sunday, 17 March 2013 03:27:32 UTC

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