title: Tools and databases of the KOMICS web portal for preprocessing, mining, and dissemination of metabolomics data.
abstract: A metabolome--the collection of comprehensive quantitative data on metabolites in an organism--has been increasingly utilized for applications such as data-intensive systems biology, disease diagnostics, biomarker discovery, and assessment of food quality. A considerable number of tools and databases have been developed to date for the analysis of data generated by various combinations of chromatography and mass spectrometry. We report here a web portal named KOMICS (The Kazusa Metabolomics Portal), where the tools and databases that we developed are available for free to academic users. KOMICS includes the tools and databases for preprocessing, mining, visualization, and publication of metabolomics data. Improvements in the annotation of unknown metabolites and dissemination of comprehensive metabolomic data are the primary aims behind the development of this portal. For this purpose, PowerGet and FragmentAlign include a manual curation function for the results of metabolite feature alignments. A metadata-specific wiki-based database, Metabolonote, functions as a hub of web resources related to the submitters' work. This feature is expected to increase citation of the submitters' work, thereby promoting data publication. As an example of the practical use of KOMICS, a workflow for a study on Jatropha curcas is presented. The tools and databases available at KOMICS should contribute to enhanced production, interpretation, and utilization of metabolomic Big Data.
authors.affiliation: Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba 292-0818, Japan ; JST, National Bioscience Database Center (NBDC), 5-3 Yonbancho, Chiyoda-ku, Tokyo 102-0081, Japan.
authors.forename: Nozomu
authors.identifier: 0000-0001-5861-6228
authors.initials: N
authors.lastname: Sakurai
authors.affiliation: Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba 292-0818, Japan ; JST, National Bioscience Database Center (NBDC), 5-3 Yonbancho, Chiyoda-ku, Tokyo 102-0081, Japan.
authors.forename: Takeshi
authors.identifier: 0000-0003-1754-2837
authors.initials: T
authors.lastname: Ara
authors.affiliation: Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba 292-0818, Japan ; JST, National Bioscience Database Center (NBDC), 5-3 Yonbancho, Chiyoda-ku, Tokyo 102-0081, Japan.
authors.forename: Mitsuo
authors.initials: M
authors.lastname: Enomoto
authors.affiliation: Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba 292-0818, Japan.
authors.forename: Takeshi
authors.identifier: 0000-0001-5174-4374
authors.initials: T
authors.lastname: Motegi
authors.affiliation: Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba 292-0818, Japan.
authors.forename: Yoshihiko
authors.initials: Y
authors.lastname: Morishita
authors.affiliation: Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba 292-0818, Japan.
authors.forename: Atsushi
authors.initials: A
authors.lastname: Kurabayashi
authors.affiliation: Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba 292-0818, Japan ; Department of Nutrition and Life Science, Kanagawa Institute of Technology, 1030 Shimo-ogino, Atsugi, Kanagawa 243-0292, Japan.
authors.forename: Yoko
authors.initials: Y
authors.lastname: Iijima
authors.affiliation: Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba 292-0818, Japan ; Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Sakai, Osaka 599-8531, Japan.
authors.forename: Yoshiyuki
authors.initials: Y
authors.lastname: Ogata
authors.affiliation: Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba 292-0818, Japan.
authors.forename: Daisuke
authors.initials: D
authors.lastname: Nakajima
authors.affiliation: Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba 292-0818, Japan.
authors.forename: Hideyuki
authors.initials: H
authors.lastname: Suzuki
authors.affiliation: Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba 292-0818, Japan.
authors.forename: Daisuke
authors.initials: D
authors.lastname: Shibata
mesh_terms: D016208:Databases, Factual; D006801:Humans; D020407:Internet; D055442:Metabolome; D055432:Metabolomics; D012984:Software; D049490:Systems Biology