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Related Experiment Videos

Genome annotation errors in pathway databases due to semantic ambiguity in partial EC numbers.

M L Green1, P D Karp

  • 1Bioinformatics Research Group, Artificial Intelligence Center, SRI International Menlo Park, CA 94025, USA. green@ai.sri.com

Nucleic Acids Research
|July 22, 2005
PubMed
Summary

Database errors misinterpreting partial Enzyme Commission (EC) numbers affect genome and pathway annotations. This systematic error impacts gene-reaction assignments in databases like KEGG, affecting scientific research and bioinformatics.

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Area of Science:

  • Bioinformatics
  • Genomics
  • Systems Biology

Background:

  • Genome and pathway databases are crucial resources for biological research.
  • Enzyme Commission (EC) numbers systematically classify enzymes based on catalyzed reactions.
  • Partial EC numbers, like '1.1.1.-', present ambiguity in enzyme function annotation.

Purpose of the Study:

  • To identify and characterize a novel systematic annotation error in genome and pathway databases.
  • To investigate the impact of misinterpreting partial EC numbers on gene-reaction assignments.
  • To highlight the consequences of these errors for researchers and bioinformaticians.

Main Methods:

  • Analysis of gene-reaction assignments in multiple databases (KEGG, VIMSS, IMG).
  • Examination of the Escherichia coli subset within the KEGG database.

Related Experiment Videos

  • Comparison of gene function descriptions with assigned reaction activities.

    • Main Results:

    • A systematic error was identified due to misinterpretation of partial EC numbers.
    • This error leads to incorrect assignment of genes to numerous reactions.
    • The Escherichia coli KEGG subset shows this error in 6.8% of gene-reaction assignments.
    • Internal database inconsistencies were observed between gene functions and assigned reactions.

    Conclusions:

    • Misinterpretation of partial EC numbers creates significant annotation errors in biological databases.
    • These errors compromise the reliability of databases used as scientific references.
    • The findings necessitate improvements in database annotation processes to ensure accuracy.