Relation mining experiments in the pharmacogenomics domain

Journal of Biomedical Informatics
Fabio RinaldiSimon Clematide

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

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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

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