The BioCyc Collection of Pathway/Genome Databases Alexander Shearer Bioinformatics Research Group...

The BioCyc Collection of Pathway/Genome

Databases

Alexander ShearerBioinformatics Research Group

SRI International

[email protected]

BioCyc.org

EcoCyc.org

MetaCyc.org

HumanCyc.org

SRI InternationalBioinformaticsPathway Tools Software

PathoLogic Predicts operons, metabolic network, pathway hole fillers (from genome) Computational creation of new Pathway/Genome Databases

Pathway/Genome Editors Distributed curation of PGDBs Distributed object database system, interactive editing tools

Pathway/Genome Navigator WWW publishing of PGDBs Querying, visualization of pathways, chromosomes, operons Analysis operations

Pathway visualization of gene-expression data Global comparisons of metabolic networks

Bioinformatics 18:S225 2002

SRI InternationalBioinformaticsBioCyc Collection of

Pathway/Genome Databases

Pathway/Genome Database (PGDB) – combines information about

Pathways, reactions, substrates Enzymes, transporters Genes, replicons Transcription factors/sites, promoters,

operonsTier 1: Literature-derived PGDBs

MetaCyc EcoCyc

Tier 2: Computationally-derived DBs featuring some curation

13 databasesTier 3: Computationally-derived DBs

More than 300 databases

SRI InternationalBioinformatics

EcoCyc ( EcoCyc.org)

E. coli Encyclopedia Review-level model organism database for E. coli Tracks evolving annotation of the E. coli genome and

cellular networks

Contains Curated commentary for all experimentally described

genes (3,300) 15,000 supporting citations Both a text and a computational reference

Nuc. Acids. Res. 33:D334 2005 ASM News 70:25 2004 Science 293:2040


MetaCyc (MetaCyc.org)

Metabolic Encyclopedia Nonredundant metabolic pathway database Goal is to describe a representative sample of every

experimentally determined metabolic pathway

Contains Literature-based curation of pathways, reactions, enzymes,

substrates Over 800 pathways from over 700 organisms

Jointly developed by SRI and Carnegie Institution

Nucleic Acids Research 34:D511-D516 2006


Comparative Tools

The BioCyc Collection of Pathway/Genome Databases Alexander Shearer Bioinformatics Research Group...

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