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Related Experiment Videos

EcoCyc: a comprehensive database resource for Escherichia coli.

Ingrid M Keseler1, Julio Collado-Vides, Socorro Gama-Castro

  • 1SRI International, 333 Ravenswood Avenue, Menlo Park, CA 94025, USA.

Nucleic Acids Research
|December 21, 2004
PubMed
Summary

The EcoCyc database provides comprehensive biological data for Escherichia coli K12, including genes, proteins, and pathways. This resource aids in computational biology research and bioinformatics predictions.

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Area of Science:

  • Microbiology
  • Bioinformatics
  • Systems Biology

Background:

  • The EcoCyc database is a vital resource for understanding the biology of Escherichia coli K12.
  • It aims to catalog all genes, proteins, pathways, and molecular interactions within E. coli.

Purpose of the Study:

  • To update and expand the EcoCyc database with manually curated information.
  • To provide enhanced computational exploration capabilities through downloadable software and data files.

Main Methods:

  • Manual curation of information from 8862 publications.
  • Integration of summary comments, regulatory information, literature citations, and evidence types.
  • Development of computable descriptions and detailed comments for biological entities.

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Main Results:

  • Version 8.5 of the EcoCyc database now contains extensive, manually curated biological information.
  • The database is accessible via a web interface and downloadable Pathway Tools software.
  • Curated data serves as training sets for bioinformatics predictions.

Conclusions:

  • EcoCyc is a continuously updated, comprehensive resource for E. coli K12 biology.
  • The database facilitates in-depth computational analysis and supports the development of predictive bioinformatics tools.
  • It serves as a valuable platform for systems biology research.