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

Autores
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.
Año de publicación
2016
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
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.
Fil: Caspi, Ron. SRI International; Estados Unidos
Fil: Billington, Richard. SRI International; Estados Unidos
Fil: Ferrer, Luciana. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Foerster, Hartmut. Boyce Thompson Institute for Plant Research; Estados Unidos
Fil: Fulcher, Carol A.. SRI International; Estados Unidos
Fil: Keseler, Ingrid M.. SRI International; Estados Unidos
Fil: Kothari, Anamika. SRI International; Estados Unidos
Fil: Krummenacker, Markus. SRI International; Estados Unidos
Fil: Latendresse, Mario. SRI International; Estados Unidos
Fil: Mueller, Lukas A.. Boyce Thompson Institute for Plant Research; Estados Unidos
Fil: Ong, Quang. SRI International; Estados Unidos
Fil: Paley, Suzanne. SRI International; Estados Unidos
Fil: Subhraveti, Pallavi. SRI International; Estados Unidos
Fil: Weaver, Daniel S.. SRI International; Estados Unidos
Fil: Karp, Peter D.. SRI International; Estados Unidos
Materia
METABOLIC PATHWAYS
ENZYMES
DATABASE
GENOME
Nivel de accesibilidad
acceso abierto
Condiciones de uso
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
Repositorio
CONICET Digital (CONICET)
Institución
Consejo Nacional de Investigaciones Científicas y Técnicas
OAI Identificador
oai:ri.conicet.gov.ar:11336/85389
Acceder
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oai_identifier_str oai:ri.conicet.gov.ar:11336/85389
network_acronym_str CONICETDig
repository_id_str 3498
network_name_str CONICET Digital (CONICET)
spelling The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databasesCaspi, RonBillington, RichardFerrer, LucianaFoerster, HartmutFulcher, Carol A.Keseler, Ingrid M.Kothari, AnamikaKrummenacker, MarkusLatendresse, MarioMueller, Lukas A.Ong, QuangPaley, SuzanneSubhraveti, PallaviWeaver, Daniel S.Karp, Peter D.METABOLIC PATHWAYSENZYMESDATABASEGENOMEhttps://purl.org/becyt/ford/1.2https://purl.org/becyt/ford/1The 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.Fil: Caspi, Ron. SRI International; Estados UnidosFil: Billington, Richard. SRI International; Estados UnidosFil: Ferrer, Luciana. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Foerster, Hartmut. Boyce Thompson Institute for Plant Research; Estados UnidosFil: Fulcher, Carol A.. SRI International; Estados UnidosFil: Keseler, Ingrid M.. SRI International; Estados UnidosFil: Kothari, Anamika. SRI International; Estados UnidosFil: Krummenacker, Markus. SRI International; Estados UnidosFil: Latendresse, Mario. SRI International; Estados UnidosFil: Mueller, Lukas A.. Boyce Thompson Institute for Plant Research; Estados UnidosFil: Ong, Quang. SRI International; Estados UnidosFil: Paley, Suzanne. SRI International; Estados UnidosFil: Subhraveti, Pallavi. SRI International; Estados UnidosFil: Weaver, Daniel S.. SRI International; Estados UnidosFil: Karp, Peter D.. SRI International; Estados UnidosOxford University Press2016-01info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/85389Caspi, Ron; Billington, Richard; Ferrer, Luciana; Foerster, Hartmut; Fulcher, Carol A.; et al.; The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases; Oxford University Press; Nucleic Acids Research; 44; D1; 1-2016; D471-D4800305-10481362-4962CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/doi/10.1093/nar/gkv1164info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-sa/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-29T10:25:16Zoai:ri.conicet.gov.ar:11336/85389instacron:CONICETInstitucionalhttp://ri.conicet.gov.ar/Organismo científico-tecnológicoNo correspondehttp://ri.conicet.gov.ar/oai/requestdasensio@conicet.gov.ar; lcarlino@conicet.gov.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:34982025-09-29 10:25:17.227CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv 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
spellingShingle The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases
Caspi, Ron
METABOLIC PATHWAYS
ENZYMES
DATABASE
GENOME
title_short 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_sort The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases
dc.creator.none.fl_str_mv 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 Caspi, Ron
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_role author
author2 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.
author2_role author
author
author
author
author
author
author
author
author
author
author
author
author
author
dc.subject.none.fl_str_mv METABOLIC PATHWAYS
ENZYMES
DATABASE
GENOME
topic METABOLIC PATHWAYS
ENZYMES
DATABASE
GENOME
purl_subject.fl_str_mv https://purl.org/becyt/ford/1.2
https://purl.org/becyt/ford/1
dc.description.none.fl_txt_mv 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.
Fil: Caspi, Ron. SRI International; Estados Unidos
Fil: Billington, Richard. SRI International; Estados Unidos
Fil: Ferrer, Luciana. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Foerster, Hartmut. Boyce Thompson Institute for Plant Research; Estados Unidos
Fil: Fulcher, Carol A.. SRI International; Estados Unidos
Fil: Keseler, Ingrid M.. SRI International; Estados Unidos
Fil: Kothari, Anamika. SRI International; Estados Unidos
Fil: Krummenacker, Markus. SRI International; Estados Unidos
Fil: Latendresse, Mario. SRI International; Estados Unidos
Fil: Mueller, Lukas A.. Boyce Thompson Institute for Plant Research; Estados Unidos
Fil: Ong, Quang. SRI International; Estados Unidos
Fil: Paley, Suzanne. SRI International; Estados Unidos
Fil: Subhraveti, Pallavi. SRI International; Estados Unidos
Fil: Weaver, Daniel S.. SRI International; Estados Unidos
Fil: Karp, Peter D.. SRI International; Estados Unidos
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.
publishDate 2016
dc.date.none.fl_str_mv 2016-01
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
http://purl.org/coar/resource_type/c_6501
info:ar-repo/semantics/articulo
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/11336/85389
Caspi, Ron; Billington, Richard; Ferrer, Luciana; Foerster, Hartmut; Fulcher, Carol A.; et al.; The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases; Oxford University Press; Nucleic Acids Research; 44; D1; 1-2016; D471-D480
0305-1048
1362-4962
CONICET Digital
CONICET
url http://hdl.handle.net/11336/85389
identifier_str_mv Caspi, Ron; Billington, Richard; Ferrer, Luciana; Foerster, Hartmut; Fulcher, Carol A.; et al.; The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases; Oxford University Press; Nucleic Acids Research; 44; D1; 1-2016; D471-D480
0305-1048
1362-4962
CONICET Digital
CONICET
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/doi/10.1093/nar/gkv1164
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
eu_rights_str_mv openAccess
rights_invalid_str_mv https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
dc.format.none.fl_str_mv application/pdf
application/pdf
dc.publisher.none.fl_str_mv Oxford University Press
publisher.none.fl_str_mv Oxford University Press
dc.source.none.fl_str_mv reponame:CONICET Digital (CONICET)
instname:Consejo Nacional de Investigaciones Científicas y Técnicas
reponame_str CONICET Digital (CONICET)
collection CONICET Digital (CONICET)
instname_str Consejo Nacional de Investigaciones Científicas y Técnicas
repository.name.fl_str_mv CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicas
repository.mail.fl_str_mv dasensio@conicet.gov.ar; lcarlino@conicet.gov.ar
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score 13.070432

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