Abstract
The mutual interactions among genes, diseases, and drugs are at the heart of biomedical research, and are especially important for the pharmacological industry. The recent trend towards personalized medicine makes it increasingly relevant to be able to tailor drugs to specific genetic makeups. The pharmacogenetics and pharmacogenomics knowledge base (PharmGKB) aims at capturing relevant information about such interactions from several sources, including curation of the biomedical literature. Advanced text mining tools which can support the process of manual curation are increasingly necessary in order to cope with the deluge of new published results. However, effective evaluation of those tools requires the availability of manually curated data as gold standard. In this paper we discuss how the existing PharmGKB database can be used for such an evaluation task in a way similar to the usage of gold standard data derived from protein-protein interaction databases in one of the recent BioCreative shared tasks. Additionally, we present our own considerations and results on the feasibility and difficulty of such a task.
References
Mar 23, 2002·The Pharmacogenomics Journal·T E KleinR B Altman
Mar 26, 2002·FEBS Letters·Andreas ZanzoniGianni Cesareni
Dec 19, 2003·Nucleic Acids Research·Henning HermjakobRolf Apweiler
Sep 24, 2004·PLoS Biology·Hans-Michael MüllerPaul W Sternberg
Dec 31, 2005·Nucleic Acids Research·Chris StarkMike Tyers
Dec 1, 2006·BMC Bioinformatics·Fabio RinaldiMartin Romacker
Dec 5, 2006·Bioinformatics·Katrin FundelRalf Zimmer
Jul 25, 2007·Bioinformatics·William A BaumgartnerLawrence Hunter
Apr 16, 2008·BMC Bioinformatics·Nikiforos KaramanisTed Briscoe
Oct 18, 2008·Genome Biology·Beatrice AlexXinglong Wang
Oct 18, 2008·Genome Biology·Fabio RinaldiTherese Vachon
Oct 18, 2008·Genome Biology·Martin KrallingerAlfonso Valencia
Oct 25, 2008·Neuroinformatics·Hans-Michael MüllerPaul W Sternberg
Oct 25, 2008·Drug Metabolism Reviews·Katrin SangkuhlTeri E Klein
May 28, 2010·Bioinformatics·Hyrum D CarrollJohn L Spouge
Jul 31, 2010·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Fabio RinaldiMartin Romacker
Aug 13, 2010·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Florian LeitnerAlfonso Valencia
Jun 10, 2011·Artificial Intelligence in Medicine·Fabio RinaldiRune Sætre
Dec 22, 2011·BMC Bioinformatics·Gerold SchneiderFabio Rinaldi
Dec 22, 2011·BMC Bioinformatics·Zhiyong LuW John Wilbur
Dec 22, 2011·BMC Bioinformatics·Martin KrallingerAlfonso Valencia
Dec 22, 2011·BMC Bioinformatics·Cecilia N ArighiCathy H Wu
Dec 15, 2011·Journal of Biomedical Semantics·Dietrich Rebholz-SchuhmannUdo Hahn
Apr 25, 2012·Database : the Journal of Biological Databases and Curation·Fabio RinaldiRuss B Altman
Citations
Apr 25, 2012·Database : the Journal of Biological Databases and Curation·Fabio RinaldiRuss B Altman
Feb 12, 2013·Database : the Journal of Biological Databases and Curation·Fabio RinaldiTherese Vachon
Dec 5, 2014·BMC Bioinformatics·Fabio RinaldiRaul Rodriguez-Esteban
Jun 10, 2015·Artificial Intelligence in Medicine·Yun Niu, Yuwei Wang
Feb 11, 2015·Journal of Biomedical Informatics·Yan WangGenevieve B Melton
Apr 4, 2017·Database : the Journal of Biological Databases and Curation·Fabio RinaldiJulio Collado-Vides
Jul 28, 2019·Nature Communications·Volodymyr KuleshovMichael Snyder
Jan 4, 2020·Scientific Data·Joël LegrandAdrien Coulet
Dec 21, 2017·PloS One·A S M Ashique MahmoodK Vijay-Shanker