The BioCyc Collection of PathwayGenome Databases

1
The BioCyc Collection of Pathway/Genome Databases

• Alexander Shearer
• Bioinformatics Research Group
• SRI International
• shearer_at_ai.sri.com
• BioCyc.org
• EcoCyc.org
• MetaCyc.org
• HumanCyc.org

2
Pathway 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 18S225 2002
3
BioCyc Collection of Pathway/Genome Databases

• Pathway/Genome Database (PGDB) combines
  information about
• Pathways, reactions, substrates
• Enzymes, transporters
• Genes, replicons
• Transcription factors/sites, promoters, operons
• Tier 1 Literature-derived PGDBs
• MetaCyc
• EcoCyc
• Tier 2 Computationally-derived DBs featuring
  some curation
• 13 databases
• Tier 3 Computationally-derived DBs
• More than 300 databases

4
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. 33D334 2005 ASM News
7025 2004 Science 2932040
5
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 34D511-D516 2006
6
Comparative Tools