The CyberCell Database (CCDB): a comprehensive, self-updating, relational database to coordinate and facilitate in silico modeling of Escherichia coli - PubMed (original) (raw)

The CyberCell Database (CCDB): a comprehensive, self-updating, relational database to coordinate and facilitate in silico modeling of Escherichia coli

Shan Sundararaj et al. Nucleic Acids Res. 2004.

Abstract

The CyberCell Database (CCDB: http://redpoll. pharmacy.ualberta.ca/CCDB) is a comprehensive, web-accessible database designed to support and coordinate international efforts in modeling an Escherichia coli cell on a computer. The CCDB brings together both observed and derived quantitative data from numerous independent sources covering many aspects of the genomic, proteomic and metabolomic character of E.coli (strain K12). The database is self-updating but also supports 'community' annotation, and provides an extensive array of viewing, querying and search options including a powerful, easy-to-use relational data extraction system.

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Figures

Figure 1

A screenshot montage of the CCDB showing several possible views of information describing the protein AsnA (aspartate ammonia ligase). Not all fields are shown.

Figure 2

An example of a complex query conducted using the CCDB’s data extractor. Results are shown for a query asking for all proteins in E.coli that are both <500 residues and homologous (>40% identity) to human proteins.

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