PGxMine: Text Mining for Curation of PharmGKB

Lever, J. , Barbarino, J. M., Gong, L., Huddart, R., Sangkuhl, K., Whaley, R., Whirl-Carrillo, M., Woon, M., Klein, T. E. and Altman, R. B. (2020) PGxMine: Text Mining for Curation of PharmGKB. In: 25th Pacific Symposium on Biocomputing, Puako, HI, USA, 03-07 Jan 2020, pp. 611-622.

Abstract

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.

• Item Type: Conference Proceedings
• Status: Published
• Refereed: Yes
• Glasgow Author(s) Enlighten ID: Lever, Dr Jake
• Authors: Lever, J., Barbarino, J. M., Gong, L., Huddart, R., Sangkuhl, K., Whaley, R., Whirl-Carrillo, M., Woon, M., Klein, T. E., and Altman, R. B.
• College/School: College of Science and Engineering > School of Computing Science
• Copyright Holders: Copyright © 2019 The Authors
• First Published: First published in Proceedings of the 2020 Pacific Symposium on Biocomputing: 611-622
• Publisher Policy: Reproduced under a Creative Commons License