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The BioCyc Collection of Pathway/Genome Databases

The BioCyc Collection of Pathway/Genome Databases. Alexander Shearer Bioinformatics Research Group SRI International shearer@ai.sri.com BioCyc.org EcoCyc.org MetaCyc.org HumanCyc.org. Pathway Tools Software. PathoLogic

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The BioCyc Collection of Pathway/Genome Databases

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  1. The BioCyc Collection of Pathway/Genome Databases Alexander Shearer Bioinformatics Research Group SRI International shearer@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 18:S225 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. 33:D334 2005 ASM News 70:25 2004 Science 293:2040

  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 Research34:D511-D516 2006

  6. Comparative Tools

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