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Curation accuracy of model organism databases.

Ingrid M Keseler1, Marek Skrzypek1, Deepika Weerasinghe1

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Database : the Journal of Biological Databases and Curation
|June 14, 2014
PubMed
Summary

Manual biocuration for biological databases like EcoCyc and Candida Genome Database (CGD) is highly accurate. A study found an overall error rate of 1.58% in curated data, supporting its reliability for researchers.

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Area of Science:

  • Bioinformatics
  • Biocuration
  • Database Development

Background:

  • Manual extraction of biomedical literature (biocuration) is crucial for building biological databases such as UniProt, EcoCyc, and CGD.
  • These databases are vital resources for life science researchers, aiding in data interpretation and bioinformatics algorithm development.

Purpose of the Study:

  • To assess the accuracy of manual biocuration in biological databases.
  • To quantify the error rate in curated assertions within the EcoCyc and Candida Genome Database (CGD).

Main Methods:

  • Randomly selected gene pages from EcoCyc and CGD.
  • Manually validated curated assertions against their cited publications.
  • Identified errors where assertions were not supported by the referenced source.

Main Results:

  • An overall error rate of 1.58% was identified across 633 validated assertions.
  • EcoCyc exhibited an error rate of 1.40%, while CGD had an error rate of 1.82%.

Conclusions:

  • Manual biocuration by Ph.D.-level scientists is a highly accurate method for constructing biological databases.
  • The low error rates suggest that these curated databases are reliable resources for the scientific community.