MetaCyc statistics

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Protocols

MetaCyc specifications

Information


Unique identifier OMICS_29033
Name MetaCyc
Restrictions to use None
Community driven No
Data access File download, Browse
User data submission Not allowed
Version 22.0
Maintained Yes
Wikipedia https://en.wikipedia.org/wiki/MetaCyc

Documentation


Maintainers


  • person_outline Peter D Karp
  • person_outline Ron Caspi

Additional information


A downloadable version of the database can be obtained here: https://metacyc.org/download.shtml

Publications for MetaCyc

MetaCyc citations

 (209)
library_books

SolCyc: a database hub at the Sol Genomics Network (SGN) for the manual curation of metabolic networks in Solanum and Nicotiana specific databases

2018
PMCID: 5946812
PMID: 29762652
DOI: 10.1093/database/bay035

[…] of Peter Karp at SRI International, who also develops the Pathway tools software; the group has also developed extensive guidelines for the curation of primary and specialized metabolism (http://www.metacyc.org/) (). MetaCyc contains metabolic reference pathways, which have been extracted from the literature by experts and as such represents an experimentally validated, universal repository for m […]

call_split

A Prospective Metagenomic and Metabolomic Analysis of the Impact of Exercise and/or Whey Protein Supplementation on the Gut Microbiome of Sedentary Adults

2018
mSystems
PMCID: 5915698
PMID: 29719871
DOI: 10.1128/mSystems.00044-18
call_split See protocol

[…] ilitated by use of the Human Microbiome Project (HMP) Unified Metabolic Analysis Network (HUMAnN2 V.0.99) pipeline (). Models of microbial metabolic pathways produced by HUMAnN2 were derived from the MetaCyc database () and were the basis for analyses performed on microbial metabolic profiling. Taxonomic profiling was facilitated by use of the Kraken taxonomy assignment software tool (V.0.10.6) () […]

library_books

Synergistic Killing of Polymyxin B in Combination With the Antineoplastic Drug Mitotane Against Polymyxin Susceptible and Resistant Acinetobacter baumannii: A Metabolomic Study

2018
Front Pharmacol
PMCID: 5911485
PMID: 29713282
DOI: 10.3389/fphar.2018.00359

[…] Other metabolites were putatively identified (Level 2 identification based on MSI standards) using exact mass and predicted retention time based on the Kyoto Encyclopedia of Genes and Genomes (KEGG), MetaCyc, and LIPIDMAPS databases, using preference to bacterial metabolites annotated in EcoCyc. Raw peak intensity was used to quantify each metabolite. The free online tool MetaboAnalyst 3.0 was use […]

library_books

A Computational Approach Using Bioinformatics to Screening Drug Targets for Leishmania infantum Species

2018
PMCID: 5896251
PMID: 29785196
DOI: 10.1155/2018/6813467

[…] identified references. In the case of [“Aldo-keto reductase”], only one reference was found. Data were extracted, analyzed, and compared with the metabolic pathway information present in the KEGG and MetaCyc servers. The results showed that the mechanism of action of strychnobiflavone was based on the inhibition of the methylglyoxal degradation superpathway (). […]

library_books

Exploring Linkages between Taxonomic and Functional Profiles of the Human Microbiome

2018
mSystems
PMCID: 5881027
PMID: 29629420
DOI: 10.1128/mSystems.00163-17

[…] ntity cutoff commonly used in OTUs. In addition, PICRUSt 2.0 will be based on over 39,000 genomes (a nearly 10-fold increase in reference genomes) and will provide predictions that integrate with the MetaCyc functional framework (). The accuracy of predicting the eukaryotic functional proportion of the microbiome based on 18S rRNA gene profiles is also being tested and validated. A major limitatio […]

library_books

A Retrospective Review of Microbiological Methods Applied in Studies Following the Deepwater Horizon Oil Spill

2018
Front Microbiol
PMCID: 5876298
PMID: 29628913
DOI: 10.3389/fmicb.2018.00520

[…] o Encyclopedia of Genes and Genomes (KEGG, DB; Ogata et al., ), The Carbohydrate-Active EnZymes (CAZY, DB; Cantarel et al., ), Clusters of Orthologous Groups of proteins (COGs, DB; Tatusov et al., ), MetaCyc (DB; Caspi et al., ), and RefSeq (DB; Pruitt et al., ), Transporter Classification Database (TCDB, DB; Saier et al., ), MetaPathways (ST; Konwar et al., ), RAxML version 8 (ST; Stamatakis, ), […]

Citations

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MetaCyc institution(s)
SRI International, Menlo Park, CA, USA
MetaCyc funding source(s)
Supported by National Institute of General Medical Sciences of the National Institutes of Health (NIH) [GM080746, GM077678, GM75742].

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