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Database Commons - MetaCyc database

MetaCyc database

Citations: 199

z-index 17.91

Short name MetaCyc database
Full name A database describing metabolic pathways and enzymes from all domains of life.
Description The MetaCyc database is a comprehensive and freely accessible database describing metabolic pathways and enzymes from all domains of life.
URL http://metacyc.org/
Year founded 2013
Last update & version 2015-11-12    v19.5
Availability Free to all users
University/Institution hosted SRI International
Address 333 Ravenswood,Menlo Park,CA 94025,USA
City Menlo Park
Province/State CA
Country/Region United States
Contact name Peter D. Karp
Contact email pkarp@ai.sri.com
Data type(s)
Major organism(s)
Keyword(s)
  • enzyme
Publication(s)
  • The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. [PMID: 26527732]

    Ron Caspi, Richard Billington, Luciana Ferrer, Hartmut Foerster, Carol A Fulcher, Ingrid M Keseler, Anamika Kothari, Markus Krummenacker, Mario Latendresse, Lukas A Mueller, Quang Ong, Suzanne Paley, Pallavi Subhraveti, Daniel S Weaver, Peter D Karp
    Nucleic acids research 2016:44(D1)
    1 Citations (Google Scholar as of 2016-01-29)

    Abstract: 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. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  • The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases. [PMID: 24225315]

    Ron Caspi, Tomer Altman, Richard Billington, Kate Dreher, Hartmut Foerster, Carol A Fulcher, Timothy A Holland, Ingrid M Keseler, Anamika Kothari, Aya Kubo, Markus Krummenacker, Mario Latendresse, Lukas A Mueller, Quang Ong, Suzanne Paley, Pallavi Subhraveti, Daniel S Weaver, Deepika Weerasinghe, Peifen Zhang, Peter D Karp
    Nucleic acids research 2014:42(Database issue)
    198 Citations (Google Scholar as of 2016-01-24)

    Abstract: The MetaCyc database (MetaCyc.org) is a comprehensive and freely accessible database describing metabolic pathways and enzymes from all domains of life. MetaCyc pathways are experimentally determined, mostly small-molecule metabolic pathways and are curated from the primary scientific literature. MetaCyc contains >2100 pathways derived from >37,000 publications, and is the largest curated collection of metabolic pathways currently available. BioCyc (BioCyc.org) is a collection of >3000 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. Additions to BioCyc over the past 2 years include YeastCyc, a PGDB for Saccharomyces cerevisiae, and 891 new genomes from the Human Microbiome Project. The BioCyc Web site offers a variety of tools for querying and analysis of PGDBs, including Omics Viewers and tools for comparative analysis. New developments include atom mappings in reactions, a new representation of glycan degradation pathways, improved compound structure display, better coverage of enzyme kinetic data, enhancements of the Web Groups functionality, improvements to the Omics viewers, a new representation of the Enzyme Commission system and, for the desktop version of the software, the ability to save display states.

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200 OK2016-03-14
200 OK2016-03-11
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200 OK2016-03-07
200 OK2016-03-04
200 OK2016-03-02
200 OK2016-02-29
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200 OK2016-02-19
200 OK2016-02-17
200 OK2016-02-15
200 OK2016-02-14
200 OK2016-02-12
200 OK2016-02-10
200 OK2016-02-08
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200 OK2016-02-05
200 OK2016-02-03
200 OK2016-02-01
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200 OK2016-01-29
200 OK2016-01-27
200 OK2016-01-25
200 OK2016-01-24
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200 OK2016-01-17
200 OK2016-01-15
200 OK2016-01-13
200 OK2016-01-11
200 OK2016-01-10
200 OK2016-01-08
200 OK2016-01-06
200 OK2016-01-04

Tags

DNA Metabolic and Signaling Pathway Standard, Ontology and Nomenclature
enzyme

Record metadata

  • Created on: 2015-06-20
  • Curated by:
    • Lin Liu [2016-03-26]
    • Lin Liu [2016-01-29]
    • Lin Liu [2016-01-14]
    • Li Yang [2015-11-23]
    • Li Yang [2015-06-26]
Stats