About BioCyc
BioCyc is a collection of 1763 Pathway/Genome Databases (PGDBs). Each PGDB
in the BioCyc collection describes the genome and metabolic pathways of a
single organism.
New to BioCyc? Typical usage:
- Select a database (genome) to search by clicking "change organism database" at top right
- Enter a gene name or pathway name in the box at top right and click Quick Search
Windows users: We strongly suggest you use Firefox instead of Internet Explorer to interact with this web site [more].
To learn more about BioCyc, read the Introduction to
BioCyc or watch our instructional videos.
BioCyc Software: Pathway Tools
The BioCyc Web site contains many tools for navigating and analyzing
these databases, and for analyzing omics data, including the following.
- Genome browser
- Display of individual metabolic pathways, and of full metabolic maps
- Visual analysis of user-supplied omics datasets by painting onto
metabolic map, regulatory map, and genome map
- Comparative analysis tools
The downloadable version of BioCyc that includes the Pathway Tools
software provides more speed and power than the BioCyc Web site [more],
and allows you to create your own PGDBs and build metabolic flux models.
Multiple database configurations are available with Pathway Tools including multiple E. coli and Shigella
genomes, multiple Bacillus genomes, multiple Mycobacterium genomes, and multiple mammalian genomes.
BioCyc Pathway/Genome Databases
The BioCyc databases are divided into three tiers, based on their
quality.
Tier 1 databases have received person-decades of literature-based curation, and are the most accurate. Tier 2 and Tier 3 databases contain computationally predicted metabolic
pathways, predictions as to which genes code for missing enzymes in
metabolic pathways, and predicted operons.
PGDBs for many other organisms are available outside the BioCyc
collection, created by other users of Pathway Tools [more].
BioCyc Tier 1: Intensively Curated Databases
| Database |
Scope |
Highlights |
Organization |
|
EcoCyc
|
Escherichia coli K-12 MG1655
Model-Organism Database |
- Literature curation of complete
genome
- Information from 22,895 publications
- Transcriptional
regulatory network
- Flux-balance metabolic model
|
SRI International |
| MetaCyc |
Multiorganism Metabolic Pathway
and Enzyme Database |
- 1,842 metabolic pathways from 2263 organisms
- Extensive commentary
- Information from 33,541 publications
|
SRI International |
|
HumanCyc
|
Homo sapiens |
|
SRI International |
| AraCyc |
Arabidopsis thaliana |
- 400 metabolic pathways
- Information from 3,500 publications
|
S. Rhee, Department of Plant Biology, Carnegie Institution, USA |
|
YeastCyc
|
Saccharomyces cerevisiae |
- 152 metabolic pathways
- Information from 1,000 publications
|
SGD Curators, Stanford U., USA |
|
LeishCyc
|
Leishmania major Friedlin |
|
Bio21 Molecular Science and Biotechnology Institute, University of Melbourne |
BioCyc Tier 2: Computationally-Derived Databases Subject to
Moderate Curation
34 databases are available. [list
of tier 2 DBs]
BioCyc Tier 3: Computationally-Derived Databases Subject to No
Curation
1653 databases are available [list
of tier 3 DBs] and ready for adoption [more] by interested scientists for curation and updating.
Create Your Own Pathway/Genome Database
Interested in creating a Pathway/Genome Database for a genome of interest?
Credits
BioCyc is developed by the Bioinformatics Research Group at SRI International, directed by Dr. Peter Karp.
Some databases within the BioCyc collection were developed by groups
outside SRI International. The authors of each BioCyc database are listed
on the database summary page for each database.
Acknowledgments
The NIH National Institute for General Medical Sciences funds
development of the MetaCyc database and the BioCyc collection under grant
GM080746.
The NIH National Institute for General Medical Sciences and National
Center for Research Resources co-fund development of the EcoCyc database
under grant GM077678.
The Department of Energy funded development of the CauloCyc database
under grant DE-FG03-01ER63219.
Development of the MtbRvCyc and the MtbCdcCyc databases was funded by
the Defense Advanced Research Projects Agency (DARPA) under contract
N66001-01-C-8011 and by the NIH National Institute of Allergy and
Infectious Diseases under grant AI44826.
DARPA funded development of the VchoCyc database under contract
N66001-01-C-8011.
|
