The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases

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The MetaCyc database (MetaCyc.org) is a freely accessible comprehensive database describing metabolic pathways and enzymes from all domains of life. The majority of MetaCyc pathways are small-molecule metabolic pathways that have been experimentally determined. MetaCyc contains more than 2400 pathwa...

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Autores principales: Caspi, Ron, Billington, Richard, Ferrer, Luciana, Foerster, Hartmut, Fulcher, Carol A., Keseler, Ingrid M., Kothari, Anamika, Krummenacker, Markus, Latendresse, Mario, Mueller, Lukas A., Ong, Quang, Paley, Suzanne, Subhraveti, Pallavi, Weaver, Daniel S., Karp, Peter D.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2016
Materias:
Database Issue
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4702838/
https://www.ncbi.nlm.nih.gov/pubmed/26527732
http://dx.doi.org/10.1093/nar/gkv1164
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author Caspi, Ron
Billington, Richard
Ferrer, Luciana
Foerster, Hartmut
Fulcher, Carol A.
Keseler, Ingrid M.
Kothari, Anamika
Krummenacker, Markus
Latendresse, Mario
Mueller, Lukas A.
Ong, Quang
Paley, Suzanne
Subhraveti, Pallavi
Weaver, Daniel S.
Karp, Peter D.
author_facet Caspi, Ron
Billington, Richard
Ferrer, Luciana
Foerster, Hartmut
Fulcher, Carol A.
Keseler, Ingrid M.
Kothari, Anamika
Krummenacker, Markus
Latendresse, Mario
Mueller, Lukas A.
Ong, Quang
Paley, Suzanne
Subhraveti, Pallavi
Weaver, Daniel S.
Karp, Peter D.
author_sort Caspi, Ron
collection PubMed
description The MetaCyc database (MetaCyc.org) is a freely accessible comprehensive database describing metabolic pathways and enzymes from all domains of life. The majority of MetaCyc pathways are small-molecule metabolic pathways that have been experimentally determined. MetaCyc contains more than 2400 pathways derived from >46 000 publications, and is the largest curated collection of metabolic pathways. BioCyc (BioCyc.org) is a collection of 5700 organism-specific Pathway/Genome Databases (PGDBs), each containing the full genome and predicted metabolic network of one organism, including metabolites, enzymes, reactions, metabolic pathways, predicted operons, transport systems, and pathway-hole fillers. The BioCyc website offers a variety of tools for querying and analyzing PGDBs, including Omics Viewers and tools for comparative analysis. This article provides an update of new developments in MetaCyc and BioCyc during the last two years, including addition of Gibbs free energy values for compounds and reactions; redesign of the primary gene/protein page; addition of a tool for creating diagrams containing multiple linked pathways; several new search capabilities, including searching for genes based on sequence patterns, searching for databases based on an organism's phenotypes, and a cross-organism search; and a metabolite identifier translation service.
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spelling pubmed-47028382016-01-07 The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases Caspi, Ron Billington, Richard Ferrer, Luciana Foerster, Hartmut Fulcher, Carol A. Keseler, Ingrid M. Kothari, Anamika Krummenacker, Markus Latendresse, Mario Mueller, Lukas A. Ong, Quang Paley, Suzanne Subhraveti, Pallavi Weaver, Daniel S. Karp, Peter D. Nucleic Acids Res Database Issue The MetaCyc database (MetaCyc.org) is a freely accessible comprehensive database describing metabolic pathways and enzymes from all domains of life. The majority of MetaCyc pathways are small-molecule metabolic pathways that have been experimentally determined. MetaCyc contains more than 2400 pathways derived from >46 000 publications, and is the largest curated collection of metabolic pathways. BioCyc (BioCyc.org) is a collection of 5700 organism-specific Pathway/Genome Databases (PGDBs), each containing the full genome and predicted metabolic network of one organism, including metabolites, enzymes, reactions, metabolic pathways, predicted operons, transport systems, and pathway-hole fillers. The BioCyc website offers a variety of tools for querying and analyzing PGDBs, including Omics Viewers and tools for comparative analysis. This article provides an update of new developments in MetaCyc and BioCyc during the last two years, including addition of Gibbs free energy values for compounds and reactions; redesign of the primary gene/protein page; addition of a tool for creating diagrams containing multiple linked pathways; several new search capabilities, including searching for genes based on sequence patterns, searching for databases based on an organism's phenotypes, and a cross-organism search; and a metabolite identifier translation service. Oxford University Press 2016-01-04 2015-11-02 /pmc/articles/PMC4702838/ /pubmed/26527732 http://dx.doi.org/10.1093/nar/gkv1164 Text en © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Database Issue
Caspi, Ron
Billington, Richard
Ferrer, Luciana
Foerster, Hartmut
Fulcher, Carol A.
Keseler, Ingrid M.
Kothari, Anamika
Krummenacker, Markus
Latendresse, Mario
Mueller, Lukas A.
Ong, Quang
Paley, Suzanne
Subhraveti, Pallavi
Weaver, Daniel S.
Karp, Peter D.
The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases
title The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases
title_full The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases
title_fullStr The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases
title_full_unstemmed The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases
title_short The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases
title_sort metacyc database of metabolic pathways and enzymes and the biocyc collection of pathway/genome databases
topic Database Issue
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4702838/
https://www.ncbi.nlm.nih.gov/pubmed/26527732
http://dx.doi.org/10.1093/nar/gkv1164
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