Extraction of pharmacokinetic evidence of drug-drug interactions from the literature

Artemy Kolchinsky, Anália Lourenço, Heng Yi Wu, Lang Li, Luis M. Rocha

Research output: Contribution to journalArticle

9 Citations (Scopus)

Abstract

Drug-drug interaction (DDI) is a major cause of morbidity and mortality and a subject of intense scientific interest. Biomedical literature mining can aid DDI research by extracting evidence for large numbers of potential interactions from published literature and clinical databases. Though DDI is investigated in domains ranging in scale from intracellular biochemistry to human populations, literature mining has not been used to extract specific types of experimental evidence, which are reported differently for distinct experimental goals. We focus on pharmacokinetic evidence for DDI, essential for identifying causal mechanisms of putative interactions and as input for further pharmacological and pharmacoepidemiology investigations. We used manually curated corpora of PubMed abstracts and annotated sentences to evaluate the efficacy of literature mining on two tasks: first, identifying PubMed abstracts containing pharmacokinetic evidence of DDIs; second, extracting sentences containing such evidence from abstracts. We implemented a text mining pipeline and evaluated it using several linear classifiers and a variety of feature transforms. The most important textual features in the abstract and sentence classification tasks were analyzed. We also investigated the performance benefits of using features derived from PubMed metadata fields, various publicly available named entity recognizers, and pharmacokinetic dictionaries. Several classifiers performed very well in distinguishing relevant and irrelevant abstracts (reaching F1≈0.93, MCC≈0.74, iAUC≈0.99) and sentences (F1≈0.76, MCC≈0.65, iAUC≈0.83). We found that word bigram features were important for achieving optimal classifier performance and that features derived from Medical Subject Headings (MeSH) terms significantly improved abstract classification. We also found that some drug-related named entity recognition tools and dictionaries led to slight but significant improvements, especially in classification of evidence sentences. Based on our thorough analysis of classifiers and feature transforms and the high classification performance achieved, we demonstrate that literature mining can aid DDI discovery by supporting automatic extraction of specific types of experimental evidence.

Original languageEnglish
Article numbere0122199
JournalPLoS One
Volume10
Issue number5
DOIs
StatePublished - May 11 2015

Fingerprint

Drug interactions
drug interactions
Pharmacokinetics
Drug Interactions
pharmacokinetics
drugs
Classifiers
PubMed
Pharmaceutical Preparations
Glossaries
Pharmacoepidemiology
Medical Subject Headings
Biochemistry
Data Mining
Drug Discovery
Metadata
human population
biochemistry
morbidity
Pipelines

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Medicine(all)

Cite this

Kolchinsky, A., Lourenço, A., Wu, H. Y., Li, L., & Rocha, L. M. (2015). Extraction of pharmacokinetic evidence of drug-drug interactions from the literature. PLoS One, 10(5), [e0122199]. https://doi.org/10.1371/journal.pone.0122199

Extraction of pharmacokinetic evidence of drug-drug interactions from the literature. / Kolchinsky, Artemy; Lourenço, Anália; Wu, Heng Yi; Li, Lang; Rocha, Luis M.

In: PLoS One, Vol. 10, No. 5, e0122199, 11.05.2015.

Research output: Contribution to journalArticle

Kolchinsky, A, Lourenço, A, Wu, HY, Li, L & Rocha, LM 2015, 'Extraction of pharmacokinetic evidence of drug-drug interactions from the literature', PLoS One, vol. 10, no. 5, e0122199. https://doi.org/10.1371/journal.pone.0122199
Kolchinsky, Artemy ; Lourenço, Anália ; Wu, Heng Yi ; Li, Lang ; Rocha, Luis M. / Extraction of pharmacokinetic evidence of drug-drug interactions from the literature. In: PLoS One. 2015 ; Vol. 10, No. 5.
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