alexa ECOMICS:Ecosystem Trans-OMICS Tools and Methods for Complex Environmental Samples and Datasets | OMICS International | Abstract
ISSN: 2157-7625

Journal of Ecosystem & Ecography
Open Access

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Research Article

ECOMICS:Ecosystem Trans-OMICS Tools and Methods for Complex Environmental Samples and Datasets

Jun Kikuchi1,2,3,4*, Yoshiyuki Ogata1 and Kazuo Shinozaki1,2

1RIKEN Plant Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan

2Biomass Engineering Research Program, RIKEN Research Cluster for Innovation, 2-1, Hirosawa, Wako, 351-0198, Japan

3Graduate School of Nanobioscience, Yokohama City University, 1-7-29 Suehirocho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan

4Graduate School of Bioagricultural Sciences, Nagoya University, 1 Furo-cho, Chikusa-ku, Nagoya, Aichi 464-0810, Japan

*Corresponding Author:
Jun Kikuchi
RIKEN Plant Science Center
1-7-22 Suehiro-cho
Tsurumi-ku, Yokohama
Kanagawa 230-0045, Japan
E-mail:[email protected]

Received date: August 02, 2010; Accepted date: August 22, 2011; Published date: August 25, 2011

Citation: Kikuchi J, Ogata Y, Shinozaki K (2011) ECOMICS: Ecosystem Trans-OMICS Tools and Methods for Complex Environmental Samples and Datasets. J Ecosys Ecograph S2:001. doi:10.4172/2157-7625.S2-001

Copyright: © 2011 Kikuchi J, et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and and source are credited.

Abstract

Despite the apparent detachment of modern industrial societies from natural ecosystems, such systems continue to provide enormous and essential benefits in the form of ecosystem services, including potable water, clean air, and forest products and fisheries. Further, engineered ecosystems, but ecosystems nevertheless, provide the majority of agricultural and additional forestry products. Relationships between ecosystem services and human needs can be identified by connecting genomic information of component organisms with enzyme functions, metabolic pathways and resulting product chemicals such as biomass. Tools that advance the understanding of ecosystem function from the perspective of both environmental and metabolic systems are an important aspect of the emerging systems approach to biological science. We introduce here a web service designated “ECOMICS” to provide an omics approach to clarify such relationships. ECOMICS comprises the E-class web tool for taxonomic (metagenomic) classification based on prokaryotic and eukaryotic ribosomal sequences and selected functional (enzymatic) classification based on sequential domains, FT2DB for the digitization of NMR spectra for chemicals from metabolic to macromolecular phenotyping, Bm-Char for the chemical (macromolecular biomass) assignment of lignocellulose components, and HetMap for identifying and viewing correlations between heterogeneous trans-omics data sets that are produced by such web tools. This website is open to the public domain: https://database.riken.jp/ecomics/.

Keywords

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