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 comprehensive and freely accessible resource for metabolic pathways and enzymes from all domains of life. The pathways in MetaCyc are experimentally determined, small-molecule metabolic pathways and are curated from the primary scientific literature. With more...

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Autores principales: Caspi, Ron, Altman, Tomer, Dale, Joseph M., Dreher, Kate, Fulcher, Carol A., Gilham, Fred, Kaipa, Pallavi, Karthikeyan, Athikkattuvalasu S., Kothari, Anamika, Krummenacker, Markus, Latendresse, Mario, Mueller, Lukas A., Paley, Suzanne, Popescu, Liviu, Pujar, Anuradha, Shearer, Alexander G., Zhang, Peifen, Karp, Peter D.
Formato: Texto
Lenguaje:English
Publicado: Oxford University Press 2010
Materias:
Articles
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2808959/
https://www.ncbi.nlm.nih.gov/pubmed/19850718
http://dx.doi.org/10.1093/nar/gkp875
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author Caspi, Ron
Altman, Tomer
Dale, Joseph M.
Dreher, Kate
Fulcher, Carol A.
Gilham, Fred
Kaipa, Pallavi
Karthikeyan, Athikkattuvalasu S.
Kothari, Anamika
Krummenacker, Markus
Latendresse, Mario
Mueller, Lukas A.
Paley, Suzanne
Popescu, Liviu
Pujar, Anuradha
Shearer, Alexander G.
Zhang, Peifen
Karp, Peter D.
author_facet Caspi, Ron
Altman, Tomer
Dale, Joseph M.
Dreher, Kate
Fulcher, Carol A.
Gilham, Fred
Kaipa, Pallavi
Karthikeyan, Athikkattuvalasu S.
Kothari, Anamika
Krummenacker, Markus
Latendresse, Mario
Mueller, Lukas A.
Paley, Suzanne
Popescu, Liviu
Pujar, Anuradha
Shearer, Alexander G.
Zhang, Peifen
Karp, Peter D.
author_sort Caspi, Ron
collection PubMed
description The MetaCyc database (MetaCyc.org) is a comprehensive and freely accessible resource for metabolic pathways and enzymes from all domains of life. The pathways in MetaCyc are experimentally determined, small-molecule metabolic pathways and are curated from the primary scientific literature. With more than 1400 pathways, MetaCyc is the largest collection of metabolic pathways currently available. Pathways reactions are linked to one or more well-characterized enzymes, and both pathways and enzymes are annotated with reviews, evidence codes, and literature citations. BioCyc (BioCyc.org) is a collection of more than 500 organism-specific Pathway/Genome Databases (PGDBs). Each BioCyc PGDB contains the full genome and predicted metabolic network of one organism. The network, which is predicted by the Pathway Tools software using MetaCyc as a reference, consists of metabolites, enzymes, reactions and metabolic pathways. BioCyc PGDBs also contain additional features, such as predicted operons, transport systems, and pathway hole-fillers. The BioCyc Web site offers several tools for the analysis of the PGDBs, including Omics Viewers that enable visualization of omics datasets on two different genome-scale diagrams and tools for comparative analysis. The BioCyc PGDBs generated by SRI are offered for adoption by any party interested in curation of metabolic, regulatory, and genome-related information about an organism.
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spelling pubmed-28089592010-01-20 The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases Caspi, Ron Altman, Tomer Dale, Joseph M. Dreher, Kate Fulcher, Carol A. Gilham, Fred Kaipa, Pallavi Karthikeyan, Athikkattuvalasu S. Kothari, Anamika Krummenacker, Markus Latendresse, Mario Mueller, Lukas A. Paley, Suzanne Popescu, Liviu Pujar, Anuradha Shearer, Alexander G. Zhang, Peifen Karp, Peter D. Nucleic Acids Res Articles The MetaCyc database (MetaCyc.org) is a comprehensive and freely accessible resource for metabolic pathways and enzymes from all domains of life. The pathways in MetaCyc are experimentally determined, small-molecule metabolic pathways and are curated from the primary scientific literature. With more than 1400 pathways, MetaCyc is the largest collection of metabolic pathways currently available. Pathways reactions are linked to one or more well-characterized enzymes, and both pathways and enzymes are annotated with reviews, evidence codes, and literature citations. BioCyc (BioCyc.org) is a collection of more than 500 organism-specific Pathway/Genome Databases (PGDBs). Each BioCyc PGDB contains the full genome and predicted metabolic network of one organism. The network, which is predicted by the Pathway Tools software using MetaCyc as a reference, consists of metabolites, enzymes, reactions and metabolic pathways. BioCyc PGDBs also contain additional features, such as predicted operons, transport systems, and pathway hole-fillers. The BioCyc Web site offers several tools for the analysis of the PGDBs, including Omics Viewers that enable visualization of omics datasets on two different genome-scale diagrams and tools for comparative analysis. The BioCyc PGDBs generated by SRI are offered for adoption by any party interested in curation of metabolic, regulatory, and genome-related information about an organism. Oxford University Press 2010-01 2009-10-22 /pmc/articles/PMC2808959/ /pubmed/19850718 http://dx.doi.org/10.1093/nar/gkp875 Text en © The Author(s) 2009. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/2.5/uk/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Articles
Caspi, Ron
Altman, Tomer
Dale, Joseph M.
Dreher, Kate
Fulcher, Carol A.
Gilham, Fred
Kaipa, Pallavi
Karthikeyan, Athikkattuvalasu S.
Kothari, Anamika
Krummenacker, Markus
Latendresse, Mario
Mueller, Lukas A.
Paley, Suzanne
Popescu, Liviu
Pujar, Anuradha
Shearer, Alexander G.
Zhang, Peifen
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 Articles
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2808959/
https://www.ncbi.nlm.nih.gov/pubmed/19850718
http://dx.doi.org/10.1093/nar/gkp875
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