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用于代谢组学数据预处理、挖掘和传播的KOMICS网络门户的工具和数据库。

Tools and databases of the KOMICS web portal for preprocessing, mining, and dissemination of metabolomics data.

作者信息

Sakurai Nozomu, Ara Takeshi, Enomoto Mitsuo, Motegi Takeshi, Morishita Yoshihiko, Kurabayashi Atsushi, Iijima Yoko, Ogata Yoshiyuki, Nakajima Daisuke, Suzuki Hideyuki, Shibata Daisuke

机构信息

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.

Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba 292-0818, Japan.

出版信息

Biomed Res Int. 2014;2014:194812. doi: 10.1155/2014/194812. Epub 2014 Apr 9.

DOI:10.1155/2014/194812
PMID:24949426
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC4052814/
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.

摘要

代谢组（即生物体中代谢物综合定量数据的集合）已越来越多地用于诸如数据密集型系统生物学、疾病诊断、生物标志物发现以及食品质量评估等应用中。迄今为止，已经开发了大量工具和数据库，用于分析由色谱法和质谱法的各种组合产生的数据。我们在此报告一个名为KOMICS（Kazusa代谢组学门户）的门户网站，我们开发的工具和数据库可供学术用户免费使用。KOMICS包括用于代谢组学数据预处理、挖掘、可视化和发表的工具和数据库。改进未知代谢物的注释以及全面代谢组学数据的传播是开发此门户的主要目的。为此，PowerGet和FragmentAlign包括代谢物特征比对结果的人工整理功能。一个特定于元数据的基于维基的数据库Metabolonote，充当与提交者工作相关的网络资源中心。此功能有望增加提交者工作的引用率，从而促进数据发表。作为KOMICS实际应用的一个例子，展示了麻疯树研究的工作流程。KOMICS提供的工具和数据库应有助于增强代谢组学大数据的生成、解释和利用。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2ef2/4052814/f0cbc0e8e618/BMRI2014-194812.005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2ef2/4052814/4b2e0b311311/BMRI2014-194812.001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2ef2/4052814/7712732c2f2e/BMRI2014-194812.002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2ef2/4052814/017ac099c863/BMRI2014-194812.003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2ef2/4052814/6f47b6b44db3/BMRI2014-194812.004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2ef2/4052814/f0cbc0e8e618/BMRI2014-194812.005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2ef2/4052814/4b2e0b311311/BMRI2014-194812.001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2ef2/4052814/7712732c2f2e/BMRI2014-194812.002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2ef2/4052814/017ac099c863/BMRI2014-194812.003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2ef2/4052814/6f47b6b44db3/BMRI2014-194812.004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2ef2/4052814/f0cbc0e8e618/BMRI2014-194812.005.jpg

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