title: Extraction of pharmacokinetic evidence of drug-drug interactions from the literature.
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.
authors.affiliation: School of Informatics and Computing, Indiana University, Bloomington, IN, USA; Instituto Gulbenkian de Ciência, Oeiras, Portugal.
authors.forename: Artemy
authors.initials: A
authors.lastname: Kolchinsky
authors.affiliation: ESEI: Escuela Superior de Ingeniería Informática, University of Vigo, Edificio Politécnico, Campus Universitario As Lagoas s/n 32004, Ourense, Spain; CEB-Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal.
authors.forename: Anália
authors.initials: A
authors.lastname: Lourenço
authors.affiliation: Center for Computational Biology and Bioinformatics and Department of Medical & Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA.
authors.forename: Heng-Yi
authors.initials: HY
authors.lastname: Wu
authors.affiliation: Center for Computational Biology and Bioinformatics and Department of Medical & Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA.
authors.forename: Lang
authors.initials: L
authors.lastname: Li
authors.affiliation: School of Informatics and Computing, Indiana University, Bloomington, IN, USA; Instituto Gulbenkian de Ciência, Oeiras, Portugal.
authors.forename: Luis M
authors.initials: LM
authors.lastname: Rocha
mesh_terms: D057225:Data Mining; D004347:Drug Interactions; D006801:Humans; D046650:Medical Subject Headings; D009323:Natural Language Processing; D010599:Pharmacokinetics; D039781:PubMed