ECOMICS: a web-based toolkit for investigating the biomolecular web in ecosystems using a trans-omics approach.
Ecosystems can be conceptually thought of as interconnected environmental and metabolic systems, in which small molecules to macro-molecules interact through diverse networks. State-of-the-art technologies in post-genomic science offer ways to inspect and analyze this biomolecular web using omics-ba...
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2012
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oai:doaj.org-article:c6e78c8a885e4437aa92070842a9cae92021-11-18T07:29:02ZECOMICS: a web-based toolkit for investigating the biomolecular web in ecosystems using a trans-omics approach.1932-620310.1371/journal.pone.0030263https://doaj.org/article/c6e78c8a885e4437aa92070842a9cae92012-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/22319563/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203Ecosystems can be conceptually thought of as interconnected environmental and metabolic systems, in which small molecules to macro-molecules interact through diverse networks. State-of-the-art technologies in post-genomic science offer ways to inspect and analyze this biomolecular web using omics-based approaches. Exploring useful genes and enzymes, as well as biomass resources responsible for anabolism and catabolism within ecosystems will contribute to a better understanding of environmental functions and their application to biotechnology. Here we present ECOMICS, a suite of web-based tools for ECosystem trans-OMICS investigation that target metagenomic, metatranscriptomic, and meta-metabolomic systems, including biomacromolecular mixtures derived from biomass. ECOMICS is made of four integrated webtools. E-class allows for the sequence-based taxonomic classification of eukaryotic and prokaryotic ribosomal data and the functional classification of selected enzymes. FT2B allows for the digital processing of NMR spectra for downstream metabolic or chemical phenotyping. Bm-Char allows for statistical assignment of specific compounds found in lignocellulose-based biomass, and HetMap is a data matrix generator and correlation calculator that can be applied to trans-omics datasets as analyzed by these and other web tools. This web suite is unique in that it allows for the monitoring of biomass metabolism in a particular environment, i.e., from macromolecular complexes (FT2DB and Bm-Char) to microbial composition and degradation (E-class), and makes possible the understanding of relationships between molecular and microbial elements (HetMap). This website is available to the public domain at: https://database.riken.jp/ecomics/.Yoshiyuki OgataEisuke ChikayamaYusuke MoriokaR Craig EverroadAmiu ShinoAkihiro MatsushimaHideaki HarunaShigeharu MoriyaTetsuro ToyodaJun KikuchiPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 7, Iss 2, p e30263 (2012) |
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Medicine R Science Q |
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Medicine R Science Q Yoshiyuki Ogata Eisuke Chikayama Yusuke Morioka R Craig Everroad Amiu Shino Akihiro Matsushima Hideaki Haruna Shigeharu Moriya Tetsuro Toyoda Jun Kikuchi ECOMICS: a web-based toolkit for investigating the biomolecular web in ecosystems using a trans-omics approach. |
| description |
Ecosystems can be conceptually thought of as interconnected environmental and metabolic systems, in which small molecules to macro-molecules interact through diverse networks. State-of-the-art technologies in post-genomic science offer ways to inspect and analyze this biomolecular web using omics-based approaches. Exploring useful genes and enzymes, as well as biomass resources responsible for anabolism and catabolism within ecosystems will contribute to a better understanding of environmental functions and their application to biotechnology. Here we present ECOMICS, a suite of web-based tools for ECosystem trans-OMICS investigation that target metagenomic, metatranscriptomic, and meta-metabolomic systems, including biomacromolecular mixtures derived from biomass. ECOMICS is made of four integrated webtools. E-class allows for the sequence-based taxonomic classification of eukaryotic and prokaryotic ribosomal data and the functional classification of selected enzymes. FT2B allows for the digital processing of NMR spectra for downstream metabolic or chemical phenotyping. Bm-Char allows for statistical assignment of specific compounds found in lignocellulose-based biomass, and HetMap is a data matrix generator and correlation calculator that can be applied to trans-omics datasets as analyzed by these and other web tools. This web suite is unique in that it allows for the monitoring of biomass metabolism in a particular environment, i.e., from macromolecular complexes (FT2DB and Bm-Char) to microbial composition and degradation (E-class), and makes possible the understanding of relationships between molecular and microbial elements (HetMap). This website is available to the public domain at: https://database.riken.jp/ecomics/. |
| format |
article |
| author |
Yoshiyuki Ogata Eisuke Chikayama Yusuke Morioka R Craig Everroad Amiu Shino Akihiro Matsushima Hideaki Haruna Shigeharu Moriya Tetsuro Toyoda Jun Kikuchi |
| author_facet |
Yoshiyuki Ogata Eisuke Chikayama Yusuke Morioka R Craig Everroad Amiu Shino Akihiro Matsushima Hideaki Haruna Shigeharu Moriya Tetsuro Toyoda Jun Kikuchi |
| author_sort |
Yoshiyuki Ogata |
| title |
ECOMICS: a web-based toolkit for investigating the biomolecular web in ecosystems using a trans-omics approach. |
| title_short |
ECOMICS: a web-based toolkit for investigating the biomolecular web in ecosystems using a trans-omics approach. |
| title_full |
ECOMICS: a web-based toolkit for investigating the biomolecular web in ecosystems using a trans-omics approach. |
| title_fullStr |
ECOMICS: a web-based toolkit for investigating the biomolecular web in ecosystems using a trans-omics approach. |
| title_full_unstemmed |
ECOMICS: a web-based toolkit for investigating the biomolecular web in ecosystems using a trans-omics approach. |
| title_sort |
ecomics: a web-based toolkit for investigating the biomolecular web in ecosystems using a trans-omics approach. |
| publisher |
Public Library of Science (PLoS) |
| publishDate |
2012 |
| url |
https://doaj.org/article/c6e78c8a885e4437aa92070842a9cae9 |
| work_keys_str_mv |
AT yoshiyukiogata ecomicsawebbasedtoolkitforinvestigatingthebiomolecularwebinecosystemsusingatransomicsapproach AT eisukechikayama ecomicsawebbasedtoolkitforinvestigatingthebiomolecularwebinecosystemsusingatransomicsapproach AT yusukemorioka ecomicsawebbasedtoolkitforinvestigatingthebiomolecularwebinecosystemsusingatransomicsapproach AT rcraigeverroad ecomicsawebbasedtoolkitforinvestigatingthebiomolecularwebinecosystemsusingatransomicsapproach AT amiushino ecomicsawebbasedtoolkitforinvestigatingthebiomolecularwebinecosystemsusingatransomicsapproach AT akihiromatsushima ecomicsawebbasedtoolkitforinvestigatingthebiomolecularwebinecosystemsusingatransomicsapproach AT hideakiharuna ecomicsawebbasedtoolkitforinvestigatingthebiomolecularwebinecosystemsusingatransomicsapproach AT shigeharumoriya ecomicsawebbasedtoolkitforinvestigatingthebiomolecularwebinecosystemsusingatransomicsapproach AT tetsurotoyoda ecomicsawebbasedtoolkitforinvestigatingthebiomolecularwebinecosystemsusingatransomicsapproach AT junkikuchi ecomicsawebbasedtoolkitforinvestigatingthebiomolecularwebinecosystemsusingatransomicsapproach |
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