Literature mining on pharmacokinetics numerical data: a feasibility study

J Biomed Inform. 2009 Aug;42(4):726-35. doi: 10.1016/j.jbi.2009.03.010. Epub 2009 Apr 2.

Abstract

A feasibility study of literature mining is conducted on drug PK parameter numerical data with a sequential mining strategy. Firstly, an entity template library is built to retrieve pharmacokinetics relevant articles. Then a set of tagging and extraction rules are applied to retrieve PK data from the article abstracts. To estimate the PK parameter population-average mean and between-study variance, a linear mixed meta-analysis model and an E-M algorithm are developed to describe the probability distributions of PK parameters. Finally, a cross-validation procedure is developed to ascertain false-positive mining results. Using this approach to mine midazolam (MDZ) PK data, an 88% precision rate and 92% recall rate are achieved, with an F-score=90%. It greatly out-performs a conventional data mining approach (support vector machine), which has an F-score of 68.1%. Further investigate on 7 more drugs reveals comparable performances of our sequential mining approach.

MeSH terms

  • Algorithms
  • Artificial Intelligence
  • Databases, Factual
  • Humans
  • Information Storage and Retrieval / methods*
  • Linear Models*
  • Midazolam / pharmacokinetics
  • Models, Biological*
  • Pharmacokinetics*
  • PubMed
  • Reproducibility of Results

Substances

  • Midazolam