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BioCyc database collection

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The BioCyc database collection is an assortment of organism specific Pathway/ Genome Databases (PGDBs). They provide reference to genome and metabolic pathways of few thousand organisms.[1] As of June 23, 2014, there are 3563 databases within BioCyc. The list of databases can be found here. SRI International, based in Menlo Park, California, maintains the BioCyc database family.

Categories of Databases within BioCyc:

Based on the manual curation done, BioCyc database family is divided into 3 tiers:

Tier 1: Databases which have received at least one year literature based manual curation. Currently there are seven databases in Tier 1. Out of the seven, MetaCyc is a major database that contains metabolic pathways for 2063 organisms.[1][2] The other important Tier 1 database is HumanCyc which contains around 250 metabolic pathways found in humans.[3] The remaining five databases include, EcoCyc (E. coli),[4] AraCyc (Arabidopsis thaliana), YeastCyc (Saccharomyces cerevisiae), LeishCyc (Leishmania major Friedlin) and TrypanoCyc (Trypanosoma brucei).

Tier 2: Databases which are computationally predicted by PathoLogic but have received moderate manual curation (most with 1–4 months curation). Tier 2 Databases are available for manual curation by scientists who are interested in any particular organism. Tier 2 databases currently contain 36 different organism databases.

Tier 3: Databases which are computationally predicted by PathoLogic and received no manual curation. As with Tier 2, Tier 3 databases are also available for curation for interested scientists.

Software Tools within BioCyc:

The BioCyc website contains a variety of software tools for searching, visualizing, comparing, and analyzing genome and pathway information. It includes a genome browser, and browsers for metabolic and regulatory networks. The website also includes tools for painting large-scale ("omics") datasets onto metabolic and regulatory networks, and onto the genome.

Pathway Tools Software: The Pathway Tools is a comprehensive systems biology software that allows:

  • Development of Organism specific databases
  • Scientific Visualization, web publishing, and dissemination of organism-specific databases
  • Development of metabolic-flux models
  • Visual analysis of omics datasets
  • Computational inferences
  • Comparative analyses of organism-specific databases
  • Analysis of biological networks

The Pathway Tools software had four main components:

  1. PathoLogic: Algorithm that takes Genbank entry as input and creates the new PGDB containing the predicted metabolic pathways of an organism.
  2. Pathway/Genome Navigator: Allows query, visualization, and analysis of PGDBs.
  3. MetaFlux: Allows development of metabolic flux models.
  4. Pathway/Genome Editors: Provides interactive editing capabilities for PGDBs.

BioCyc databases rely on a software system called Pathway Tools for their initial generation, subsequent updating, and for querying their content. The databases can also be installed locally.

All BioCyc databases share the same database schema, which facilitates comparisons across the databases.

References

  1. ^ a b Caspi R, Altman T, Dreher K, Fulcher CA, Subhraveti P, Keseler IM, Kothari A, Krummenacker M, Latendresse M, Mueller LA,Ong Q, Paley S, Pujar A, Shearer AG, Travers M, Weerasinghe D, Zhang P,Karp PD. "The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases," Nucleic Acids Research 40:D742-53 2011
  2. ^ Karp, PD, and Caspi, R. "A survey of metabolic databases emphasizing the MetaCyc family" Archives of Toxicology 85:1015-33 2011
  3. ^ P. Romero, J. Wagg, M.L. Green, D. Kaiser, M. Krummenacker, and P.D. Karp "Computational prediction of human metabolic pathways from the complete human genome", Genome Biology 6:R2 R2.1-17 2004
  4. ^ Keseler, I.M., Collado-Vides, J., Santos-Zavaleta, A., Peralta-Gil, M., Gama-Castro, S., Muniz-Rascado, L., Bonavides-Martinez, C., Paley, S., Krummenacker, M., Altman, T., Kaipa, P., Spaulding, A., Pacheco, J., Latendresse, M., Fulcher, C., Sarker, M., Shearer, A.G., Mackie, A., Paulsen, I., Gunsalus, R.P., and Karp, P.D. "EcoCyc: a comprehensive database of Escherichia coli biology" Nucleic Acids Research 39:D583-590 2011
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