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Computational Metabolomics Operations at BioCyc.org

BioCyc.org is a genome and metabolic pathway web portal covering 5500 organisms, including Homo sapiens, Arabidopsis thaliana, Saccharomyces cerevisiae and Escherichia coli. These organism-specific databases have undergone variable degrees of curation. The EcoCyc (Escherichia coli Encyclopedia) data...

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Autores principales: Karp, Peter D., Billington, Richard, Holland, Timothy A., Kothari, Anamika, Krummenacker, Markus, Weaver, Daniel, Latendresse, Mario, Paley, Suzanne
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2015
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4495374/
https://www.ncbi.nlm.nih.gov/pubmed/26011592
http://dx.doi.org/10.3390/metabo5020291
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author Karp, Peter D.
Billington, Richard
Holland, Timothy A.
Kothari, Anamika
Krummenacker, Markus
Weaver, Daniel
Latendresse, Mario
Paley, Suzanne
author_facet Karp, Peter D.
Billington, Richard
Holland, Timothy A.
Kothari, Anamika
Krummenacker, Markus
Weaver, Daniel
Latendresse, Mario
Paley, Suzanne
author_sort Karp, Peter D.
collection PubMed
description BioCyc.org is a genome and metabolic pathway web portal covering 5500 organisms, including Homo sapiens, Arabidopsis thaliana, Saccharomyces cerevisiae and Escherichia coli. These organism-specific databases have undergone variable degrees of curation. The EcoCyc (Escherichia coli Encyclopedia) database is the most highly curated; its contents have been derived from 27,000 publications. The MetaCyc (Metabolic Encyclopedia) database within BioCyc is a “universal” metabolic database that describes pathways, reactions, enzymes and metabolites from all domains of life. Metabolic pathways provide an organizing framework for analyzing metabolomics data, and the BioCyc website provides computational operations for metabolomics data that include metabolite search and translation of metabolite identifiers across multiple metabolite databases. The site allows researchers to store and manipulate metabolite lists using a facility called SmartTables, which supports metabolite enrichment analysis. That analysis operation identifies metabolite sets that are statistically over-represented for the substrates of specific metabolic pathways. BioCyc also enables visualization of metabolomics data on individual pathway diagrams and on the organism-specific metabolic map diagrams that are available for every BioCyc organism. Most of these operations are available both interactively and as programmatic web services.
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spelling pubmed-44953742015-07-08 Computational Metabolomics Operations at BioCyc.org Karp, Peter D. Billington, Richard Holland, Timothy A. Kothari, Anamika Krummenacker, Markus Weaver, Daniel Latendresse, Mario Paley, Suzanne Metabolites Article BioCyc.org is a genome and metabolic pathway web portal covering 5500 organisms, including Homo sapiens, Arabidopsis thaliana, Saccharomyces cerevisiae and Escherichia coli. These organism-specific databases have undergone variable degrees of curation. The EcoCyc (Escherichia coli Encyclopedia) database is the most highly curated; its contents have been derived from 27,000 publications. The MetaCyc (Metabolic Encyclopedia) database within BioCyc is a “universal” metabolic database that describes pathways, reactions, enzymes and metabolites from all domains of life. Metabolic pathways provide an organizing framework for analyzing metabolomics data, and the BioCyc website provides computational operations for metabolomics data that include metabolite search and translation of metabolite identifiers across multiple metabolite databases. The site allows researchers to store and manipulate metabolite lists using a facility called SmartTables, which supports metabolite enrichment analysis. That analysis operation identifies metabolite sets that are statistically over-represented for the substrates of specific metabolic pathways. BioCyc also enables visualization of metabolomics data on individual pathway diagrams and on the organism-specific metabolic map diagrams that are available for every BioCyc organism. Most of these operations are available both interactively and as programmatic web services. MDPI 2015-05-22 /pmc/articles/PMC4495374/ /pubmed/26011592 http://dx.doi.org/10.3390/metabo5020291 Text en © 2015 by the authors; licensee MDPI, Basel, Switzerland This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Karp, Peter D.
Billington, Richard
Holland, Timothy A.
Kothari, Anamika
Krummenacker, Markus
Weaver, Daniel
Latendresse, Mario
Paley, Suzanne
Computational Metabolomics Operations at BioCyc.org
title Computational Metabolomics Operations at BioCyc.org
title_full Computational Metabolomics Operations at BioCyc.org
title_fullStr Computational Metabolomics Operations at BioCyc.org
title_full_unstemmed Computational Metabolomics Operations at BioCyc.org
title_short Computational Metabolomics Operations at BioCyc.org
title_sort computational metabolomics operations at biocyc.org
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4495374/
https://www.ncbi.nlm.nih.gov/pubmed/26011592
http://dx.doi.org/10.3390/metabo5020291
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