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Missing in action: enzyme functional annotations in biological databases

Nature Chemical Biology volume 5, pages 521–525 (2009)Cite this article

Annotations of enzyme function provide critical starting points for generating and testing biological hypotheses, but the quality of functional annotations is hindered by uncertain assignments for uncharacterized sequences and by the relative sparseness of validated experimental data. Given the relentless increase in genomic data, new thinking and validation methods are urgently needed to provide high confidence in enzyme functional assignments.

Automatically assigning function to a gene product remains a challenging task to perform accurately. Unfortunately, the lack of high-throughput experimental pipelines to reveal biological function results in a chronic lack of validated data. This in turn hampers the generation of curated annotations, and as these are used as the basis for automated annotations, it is often impossible to provide any annotations at all. Notwithstanding this basic problem, the automatic assignment of enzyme function remains an essential undertaking given the relentless increase in genomic data and the necessity to have such annotations for performing day-to-day work in biology. Here we describe the process and some of the current challenges and identify the advantages to be gained by the development of better tools that integrate all the available data to improve the quality of the annotations and provide a measure of confidence.

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Figure 1: Overview of the UniProtKB annotation process.
Figure 2
Figure 3: The conservation of E.C. by homology in the CSA.

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Authors and Affiliations

  1. Nicholas Furnham, John S. Garavelli, Rolf Apweiler and Janet M. Thornton are in the European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.,

    Nicholas Furnham, John S Garavelli, Rolf Apweiler & Janet M Thornton

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  1. Nicholas Furnham
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Correspondence to Nicholas Furnham.

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Furnham, N., Garavelli, J., Apweiler, R. et al. Missing in action: enzyme functional annotations in biological databases. Nat Chem Biol 5, 521–525 (2009). https://doi.org/10.1038/nchembio0809-521

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