An iterative searching and ranking algorithm for prioritising pharmacogenomics genes

Int J Comput Biol Drug Des. 2013;6(1-2):18-31. doi: 10.1504/IJCBDD.2013.052199. Epub 2013 Feb 21.

Abstract

Pharmacogenomics (PGx) studies are to identify genetic variants that may affect drug efficacy and toxicity. A machine understandable drug-gene relationship knowledge is important for many computational PGx studies and for personalised medicine. A comprehensive and accurate PGx-specific gene lexicon is important for automatic drug-gene relationship extraction from the scientific literature, rich knowledge source for PGx studies. In this study, we present a bootstrapping learning technique to rank 33,310 human genes with respect to their relevance to drug response. The algorithm uses only one seed PGx gene to iteratively extract and rank co-occurred genes using 20 million MEDLINE abstracts. Our ranking method is able to accurately rank PGx-specific genes highly among all human genes. Compared to randomly ranked genes (precision: 0.032, recall: 0.013, F1: 0.018), the algorithm has achieved significantly better performance (precision: 0.861, recall: 0.548, F1: 0.662) in ranking the top 2.5% of genes.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms*
  • Data Mining / methods*
  • Drug Design
  • Genomics / methods*
  • Humans
  • Natural Language Processing
  • Pharmacogenetics / methods*
  • Pharmacological Phenomena
  • Precision Medicine