Subject(s)
ATP-Binding Cassette Transporters/genetics , Anticonvulsants/pharmacology , Anticonvulsants/pharmacokinetics , Brain/metabolism , Lamotrigine/pharmacology , Lamotrigine/pharmacokinetics , Monosaccharide Transport Proteins/genetics , Receptors, GABA/genetics , ATP-Binding Cassette Transporters/metabolism , Anticonvulsants/adverse effects , Calcium Channels, Q-Type/genetics , Calcium Channels, Q-Type/metabolism , Humans , Lamotrigine/adverse effects , Monosaccharide Transport Proteins/metabolism , Polymorphism, Genetic , Receptors, GABA/metabolismABSTRACT
Precision medicine tailors treatment to individuals personal data including differences in their genome. The Pharmacogenomics Knowledgebase (PharmGKB) provides highly curated information on the effect of genetic variation on drug response and side effects for a wide range of drugs. PharmGKB's scientific curators triage, review and annotate a large number of papers each year but the task is challenging. We present the PGxMine resource, a text-mined resource of pharmacogenomic associations from all accessible published literature to assist in the curation of PharmGKB. We developed a supervised machine learning pipeline to extract associations between a variant (DNA and protein changes, star alleles and dbSNP identifiers) and a chemical. PGxMine covers 452 chemicals and 2,426 variants and contains 19,930 mentions of pharmacogenomic associations across 7,170 papers. An evaluation by PharmGKB curators found that 57 of the top 100 associations not found in PharmGKB led to 83 curatable papers and a further 24 associations would likely lead to curatable papers through citations. The results can be viewed at https://pgxmine.pharmgkb.org/ and code can be downloaded at https://github.com/jakelever/pgxmine.
Subject(s)
Pharmacogenetics , Precision Medicine , Computational Biology , Data Mining/methods , Databases, Genetic , Humans , Knowledge Bases , Precision Medicine/methodsABSTRACT
As precision medicine becomes increasingly relevant in healthcare, the field of pharmacogenomics (PGx) also continues to gain prominence in the clinical setting. Leading institutions have begun to implement PGx testing and the amount of published PGx literature increases yearly. The Pharmacogenomics Knowledgebase (PharmGKB; www.pharmgkb.org) is one of the foremost worldwide resources for PGx knowledge, and the organization has been adapting and refocusing its mission along with the current revolution in genomic medicine. The PharmGKB website provides a diverse array of PGx information, from annotations of the primary literature to guidelines for adjusting drug treatment based on genetic information. It is freely available and accessible to everyone from researchers to clinicians to everyday citizens. PharmGKB was found over 17 years ago, but continues to be a vital resource for the entire PGx community and the general public. This article is categorized under: Translational, Genomic, and Systems Medicine > Translational Medicine.