title: Automated extraction of information on chemical-P-glycoprotein interactions from the literature.
abstract: Knowledge of the interactions between drugs and transporters is important for drug discovery and development as well as for the evaluation of their clinical safety. We recently developed a text-mining system for the automatic extraction of information on chemical-CYP3A4 interactions from the literature. This system is based on natural language processing and can extract chemical names and their interaction patterns according to sentence context. The present study aimed to extend this system to the extraction of information regarding chemical-transporter interactions. For this purpose, the key verb list designed for cytochrome P450 enzymes was replaced with that for known drug transporters. The performance of the system was then tested by examining the accuracy of information on chemical-P-glycoprotein (P-gp) interactions extracted from randomly selected PubMed abstracts. The system achieved 89.8% recall and 84.2% precision for the identification of chemical names and 71.7% recall and 78.6% precision for the extraction of chemical-P-gp interactions.
authors.affiliation: Department of Drug Delivery Research, Graduate School of Pharmaceutical Sciences, and ⊥Institute for Integrated Cell-Material Sciences, Kyoto University , 46-29 Yoshidashimoadachi-cho, Sakyo-ku, Kyoto 606-8501, Japan.
authors.forename: Shuya
authors.initials: S
authors.lastname: Yoshida
authors.forename: Fumiyoshi
authors.initials: F
authors.lastname: Yamashita
authors.forename: Atsushi
authors.initials: A
authors.lastname: Ose
authors.forename: Kazuya
authors.initials: K
authors.lastname: Maeda
authors.forename: Yuichi
authors.initials: Y
authors.lastname: Sugiyama
authors.forename: Mitsuru
authors.initials: M
authors.lastname: Hashida
mesh_terms: D018435:ATP Binding Cassette Transporter, Subfamily B / Q000819:agonists / Q000037:antagonists & inhibitors / Q000737:chemistry*; D051544:Cytochrome P-450 CYP3A / Q000737:chemistry*; D065692:Cytochrome P-450 CYP3A Inhibitors; D057225:Data Mining; D016206:Databases, Bibliographic; D062126:Databases, Chemical; D062313:Databases, Pharmaceutical; D055808:Drug Discovery; D006801:Humans; D008024:Ligands; D026901:Membrane Transport Proteins / Q000819:agonists / Q000737:chemistry*; D009323:Natural Language Processing; D054852:Small Molecule Libraries / Q000737:chemistry*; D013379:Substrate Specificity
chemical_list: D018435:ATP Binding Cassette Transporter, Subfamily B; D065692:Cytochrome P-450 CYP3A Inhibitors; D008024:Ligands; D026901:Membrane Transport Proteins; D054852:Small Molecule Libraries; D051544:Cytochrome P-450 CYP3A; C510163:CYP3A4 protein, human