Disambiguation of PharmGKB drug-disease relations with NDF-RT and SPL

Journal of Biomedical Informatics

Volumn 46, Issue 4, 2013, Pages 690-696

  Zhu, Qian ^a   Freimuth, Robert R ^a   Pathak, Jyotishman ^a   Durski, Matthew J ^a   Chute, Christopher G ^a  

^a MAYO CLINIC   (United States)

Author keywords

Clinical associations; NDF RT; Pharmacogenomics; PharmGKB; SPL

Indexed keywords

BIOMEDICAL ONTOLOGIES; DISEASE ASSOCIATIONS; NDF-RT; PHARMACOGENOMICS; PHARMGKB; SEMANTIC RELATIONSHIPS; SPL; STRUCTURED PRODUCT;

BIOINFORMATICS; COMPUTER APPLICATIONS;

SEMANTICS;

ARTICLE; DISEASE ASSOCIATION; DRUG PACKAGING; DRUG RESPONSE; GENETIC VARIABILITY; HUMAN; MEDICAL TERMINOLOGY; PHARMACOGENOMICS; PRACTICE GUIDELINE; PRIORITY JOURNAL; SEMANTICS; UNIFIED MEDICAL LANGUAGE SYSTEM;

CLINICAL ASSOCIATIONS; NDF-RT; PHARMACOGENOMICS; PHARMGKB; SPL;

DISEASE; DRUG LABELING; HUMANS; PHARMACOGENETICS; PHARMACOKINETICS; PHARMACOLOGY;

EID: 84880329908     PISSN: 15320464     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jbi.2013.05.005     Document Type: Article

References (22)

1. Hewett M.O., Rubin D.E., Easton D.L., Stuart K.L., Altman J.M., Klein R.B. TE: PharmGKB: the pharmacogenetics knowledge base. Nucleic Acids Res 2002, 30(1):163-165.
2. Pathak J, Weiss LC, Durski MJ, Zhu Q, Freimuth RR, Chute CG. Integrating VAs NDF-RT drug terminology with PharmGKB: preliminary results. In: Pacific Symposium on Biocomputing (PSB); 2012.
3. Theobald M, Shah N, Shrager J. Extraction of conditional probabilities of the relationships between drugs, diseases and genes from PubMed guided by relationships in PharmGKB. In: Proceedings of the American medical informatics associated symposium; 2009. p. 124-8.
4. Whirl-Carrillo M., McDonagh E.M., Hebert J.M., Gong L., Sangkuhl K., Thorn C.F., et al. Pharmacogenomics knowledge for personalized medicine. Clin Pharmacol Ther 2012, 92(4):414-417. [PharmGKB, [accessed 11.04.13].
5. Vilar S., Harpaz R., Chase H.S., Costanzi S., Rabadan R., Friedman C. Facilitating adverse drug event detection in pharmacovigilance databases using molecular structure similarity: application to rhabdomyolysis. JAMIA 2011, 18(12):i73-i80. [Suppl. 1, Epub. 2011 Sep. 21].
6. Benton A., Ungar L., Hill S., Hennessy S., Mao J., Chung A., et al. Identifying potential adverse effects using the web: a new approach to medical hypothesis generation. J Biomed Inform 2011, 44(6):989-996. [Epub. 2011, Jul. 26].
7. Jiang G., Solbrig H.R., Chute C.G. ADEpedia: a scalable and standardized knowledge base of adverse drug events using semantic web technology. AMIA Annu Symp Proc 2011, 2011:607-616. [Epub. 2011, Oct. 22].
8. VA National Drug File Reference Terminology. <> [accessed 11.04.13]. http://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/NDFRT.
9. The FDA Structured Product Labeling URL. <> [accessed 11.04.13]. http://www.fda.gov/ForIndustry/DataStandards/StructuredProductLabeling/default.htm.
10. DailyMed. <> [accessed 11.04.13]. http://dailymed.nlm.nih.gov/dailymed/about.cfm.
11. McDonald C.J., Huff S.M., Suico J.G., Hill G., Leavelle D., Aller R., et al. LOINC, a universal standard for identifying laboratory observations: a 5-year update. Clin Chem 2003, 49:624-633.
12. Jonquet C., Shah N.H., Youn C.H., Callendar C., Storey M.A. NCBO annotator: semantic annotation of biomedical data. ISWC 2009, 170-173.
13. RxNav API. <> [accessed 11.04.13]. http://rxnav.nlm.nih.gov/RxNormRestAPI.html.
14. UMLS Semantic Types. <> [accessed 11.04.13]. http://www.nlm.nih.gov/research/umls/META3_current_semantic_types.html.
15. OpenNLP. <> [accessed 11.04.13]. http://opennlp.apache.org/.
16. Glibenclamide. <>http://en.wikipedia.org/wiki/Glibenclamide.
17. Arakawa R., Tamehiro N., Nishimaki-Mogami T., Ueda K., Yokoyama S. Fenofibric acid, an active form of fenofibrate, increases apolipoprotein A-I-mediated high-density lipoprotein biogenesis by enhancing transcription of ATP-binding cassette transporter A1 gene in a liver X receptor-dependent manner. Arterioscler Thromb Vasc Biol 2005, 25:1193-1197.
18. Cyanocobalamin. <>http://en.wikipedia.org/wiki/Cyanocobalamin.
19. Hassanzadeh O., Zhu Q., Freimuth R., Boyce R. Extending the "Web of Drug Identity" with knowledge extracted from United States product labels. AMIA Summit Clin Res Inform 2013, in press.
20. PubChem. <> [accessed 11.04.13]. http://pubchem.ncbi.nlm.nih.gov/.
21. DrugBank. <> [accessed 11.04.13]. http://www.drugbank.ca.
22. Parish C.R. Fluorescent dyes for lymphocyte migration and proliferation studies. Immunol Cell Biol 1999, 77:499-508.