title: XMetDB: an open access database for xenobiotic metabolism.
abstract: Xenobiotic metabolism is an active research topic but the limited amount of openly available high-quality biotransformation data constrains predictive modeling. Current database often default to commonly available information: which enzyme metabolizes a compound, but neither experimental conditions nor the atoms that undergo metabolization are captured. We present XMetDB, an open access database for drugs and other xenobiotics and their respective metabolites. The database contains chemical structures of xenobiotic biotransformations with substrate atoms annotated as reaction centra, the resulting product formed, and the catalyzing enzyme, type of experiment, and literature references. Associated with the database is a web interface for the submission and retrieval of experimental metabolite data for drugs and other xenobiotics in various formats, and a web API for programmatic access is also available. The database is open for data deposition, and a curation scheme is in place for quality control. An extensive guide on how to enter experimental data into is available from the XMetDB wiki. XMetDB formalizes how biotransformation data should be reported, and the openly available systematically labeled data is a big step forward towards better models for predictive metabolism.
authors.affiliation: Department of Pharmaceutical Biosciences and Science for Life Laboratory, Uppsala University, 75124 Uppsala, Sweden.
authors.forename: Ola
authors.identifier: 0000-0002-8083-2864
authors.initials: O
authors.lastname: Spjuth
authors.affiliation: Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark.
authors.forename: Patrik
authors.initials: P
authors.lastname: Rydberg
authors.affiliation: Department of Bioinformatics - BiGCaT, Maastricht University, P.O. Box 616, UNS50 Box 19, 6200 MD Maastricht, The Netherlands.
authors.forename: Egon L
authors.initials: EL
authors.lastname: Willighagen
authors.affiliation: Department of Bioinformatics - BiGCaT, Maastricht University, P.O. Box 616, UNS50 Box 19, 6200 MD Maastricht, The Netherlands.
authors.forename: Chris T
authors.initials: CT
authors.lastname: Evelo
authors.affiliation: IdeaConsult Ltd, 4 A.Kanchev str., 1000 Sofia, Bulgaria.
authors.forename: Nina
authors.initials: N
authors.lastname: Jeliazkova
keywords: Cytochrome; Database; Metabolism; P450; Xenobiotic