2012-04-08T13:41:11-07:00
Resource:BioCyc
curated
http://biocyc.org/
BioCyc is a collection of 1129 Pathway/Genome Databases (2011). Each database in the BioCyc collection describes the genome and metabolic pathways of a single organism. The BioCyc collection of Pathway/Genome Databases (PGDBs) provides an electronic reference source on the genomes and metabolic pathways of sequenced organisms.
BioCyc PGDBs are generated by software that predicts the metabolic pathway complements of completely sequenced organisms from their genome sequences. Furthermore, BioCyc PGDBs include the results of a number of other computational inference procedures applied to these genomes, including predictions of which genes code for missing enzymes in metabolic pathways, and predicted operons. The BioCyc Web site provides a suite of software tools for database searching and visualization, for omics data analysis, and for comparative genomics and comparative pathway questions.
The databases (DBs) within the BioCyc collection are organized into tiers according to the amount of manual review and updating they have received.
* Tier 1 PGDBs have been created through intensive manual efforts, and receive continuous updating. The BioCyc Tier 1 DBs are EcoCyc (Escherichia coli K-12) and MetaCyc (experimentally elucidated enzymes and metabolic pathways from more than 2000 organisms.)
* Tier 2 PGDBs were computationally generated by the PathoLogic program, and have undergone moderate amounts of review and updating.
* Tier 3 PGDBs were computationally generated by the PathoLogic program, and have undergone no review and updating. There are 967 DBs in Tier 3.
The downloadable version of BioCyc that includes the Pathway Tools software provides more speed and power than the BioCyc Web site. Multiple database configurations are available for installation with the software including multiple E. coli and Shigella genomes, multiple Bacillus genomes, multiple Mycobacterium genomes, and multiple mammalian genomes. Additionally, BioCyc data is available in XML format via several different REST-based web services (as well as in a variety of XML and non-XML based downloadable formats), subject to the terms of the BioCyc Databases Limited Use License.
Category:GM080746
nif-0000-00369
Resource:BioCyc
2011-08-24T00:00:00
16246909
BioCyc Database Collection
Resource:EcoCyc
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Synonym
National Institute of General Medical Sciences
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PMID
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Resource:Stanford Research Institute International
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Web service
Software resource
Data analysis service
Downloadable Database
Web accessible database
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Grant
File:Biocyc.jpg
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