A SNPshot of PubMed to associate genetic variants with drugs, diseases, and adverse reactions

Journal of Biomedical Informatics
Jörg HakenbergChitta Baral

Abstract

Genetic factors determine differences in pharmacokinetics, drug efficacy, and drug responses between individuals and sub-populations. Wrong dosages of drugs can lead to severe adverse drug reactions in individuals whose drug metabolism drastically differs from the "assumed average". Databases such as PharmGKB are excellent sources of pharmacogenetic information on enzymes, genetic variants, and drug response affected by changes in enzymatic activity. Here, we seek to aid researchers, database curators, and clinicians in their search for relevant information by automatically extracting these data from literature. We automatically populate a repository of information on genetic variants, relations to drugs, occurrence in sub-populations, and associations with disease. We mine textual data from PubMed abstracts to discover such genotype-phenotype associations, focusing on SNPs that can be associated with variations in drug response. The overall repository covers relations found between genes, variants, alleles, drugs, diseases, adverse drug reactions, populations, and allele frequencies. We cross-reference these data to EntrezGene, PharmGKB, PubChem, and others. The performance regarding entity recognition and relation extraction ...Continue Reading

References

Apr 29, 1998·JAMA : the Journal of the American Medical Association·J LazarouP N Corey
Oct 12, 2004·Pharmacogenetics·Jeffrey T Chang, Russ B Altman
Dec 27, 2005·Drug Discovery Today·Andreas P Russ, Stefan Lampel
May 15, 2007·Bioinformatics·J Gregory CaporasoLawrence Hunter
May 26, 2010·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Jörg HakenbergGraciela Gonzalez
Dec 22, 2010·BMC Genomics·Jonas B LaurilaChristopher J O Baker

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Citations

Aug 24, 2013·Bioinformatics·Robert LeamanZhiyong Lu
Sep 26, 2013·BMC Bioinformatics·David CamposJosé Luís Oliveira
Feb 14, 2013·BMC Bioinformatics·Carlo A TrugenbergerSvetlana Bureeva
Feb 13, 2014·Database : the Journal of Biological Databases and Curation·Antonio Jimeno Yepes, Karin Verspoor
Sep 24, 2014·Database : the Journal of Biological Databases and Curation·John D BurgerLynette Hirschman
May 9, 2015·BMC Medical Genomics·Nevin Z GerekSudhir Kumar
Aug 22, 2013·Journal of Molecular Biology·Thomas A PetersonMaricel G Kann
Jun 17, 2016·Database : the Journal of Biological Databases and Curation·Àlex BravoLaura I Furlong
Jul 28, 2016·BMC Medical Informatics and Decision Making·Karin M VerspoorMin Song
Jan 26, 2018·BMC Bioinformatics·Kyubum LeeJaewoo Kang
Aug 27, 2019·Frontiers in Pharmacology·Debleena GuinRitushree Kukreti
Dec 21, 2017·PloS One·A S M Ashique MahmoodK Vijay-Shanker
Jul 23, 2021·Journal of Biomedical Semantics·Ton E Becker, Eric Jakobsson
May 6, 2017·Chemical Reviews·Martin KrallingerAlfonso Valencia

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