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. SRI International Bioinformatics Pathway Tools Software PathoLogic l Predicts operons, metabolic network, pathway hole fillers (from genome) l Computational creation of new Pathway/Genome Databases Pathway/Genome Editors l Distributed curation of PGDBs l Distributed object database system, interactive editing tools Pathway/Genome Navigator l WWW publishing of PGDBs l Querying, visualization of pathways, chromosomes, operons l Analysis operations u Pathway visualization of gene-expression data u Global comparisons of metabolic networks Bioinformatics 18:S225 2002

3. SRI International Bioinformatics BioCyc Collection of Pathway/Genome Databases Pathway/Genome Database (PGDB) – combines information about l Pathways, reactions, substrates l Enzymes, transporters l Genes, replicons l Transcription factors/sites, promoters, operons Tier 1: Literature-derived PGDBs l MetaCyc l EcoCyc Tier 2: Computationally-derived DBs featuring some curation l 13 databases Tier 3: Computationally-derived DBs l More than 300 databases

4. SRI International Bioinformatics EcoCyc ( EcoCyc.org) E. coli Encyclopedia l Review-level model organism database for E. coli l Tracks evolving annotation of the E. coli genome and cellular networks Contains l Curated commentary for all experimentally described genes (3,300) l 15,000 supporting citations l Both a text and a computational reference Nuc. Acids. Res. 33:D334 2005 ASM News 70:25 2004 Science 293:2040

5. SRI International Bioinformatics MetaCyc (MetaCyc.org) Metabolic Encyclopedia l Nonredundant metabolic pathway database l Goal is to describe a representative sample of every experimentally determined metabolic pathway Contains l Literature-based curation of pathways, reactions, enzymes, substrates l Over 800 pathways from over 700 organisms Jointly developed by SRI and Carnegie Institution Nucleic Acids Research 34:D511-D516 2006

6. SRI International Bioinformatics Comparative Tools