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UniRule: a unified rule resource for automatic annotation in the UniProt Knowledgebase.

Alistair MacDougall1, Vladimir Volynkin1, Rabie Saidi1

  • 1European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

Bioinformatics (Oxford, England)
|May 14, 2020
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Summary

UniProt developed UniRule, a rule-based system, to automatically annotate millions of proteins in the UniProt Knowledgebase. This scalable method enhances functional annotation for vast protein datasets.

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Area of Science:

  • Bioinformatics
  • Proteomics
  • Computational Biology

Background:

  • The UniProt Knowledgebase (UniProtKB) faces a growing challenge in functionally annotating an increasing number of protein records due to rapid genome sequencing.
  • Manual annotation struggles to keep pace with the expanding volume of protein data, necessitating automated solutions.

Purpose of the Study:

  • To address the challenge of annotating a rapidly growing protein database.
  • To introduce and describe the UniRule system for scalable protein functional annotation.

Main Methods:

  • Developed UniRule, an expert-curated rule-based annotation method integrating multiple existing systems (RuleBase, HAMAP, PIRSR, PIRNR).
  • Utilized protein family signatures from InterPro, alongside taxonomic and other constraints, to identify proteins with shared, experimentally supported functional properties.
  • Propagated annotations from reviewed to unreviewed UniProtKB records meeting specific criteria.

Main Results:

  • Release 2020_01 of UniProtKB incorporated 6496 UniRule rules, annotating 53 million proteins.
  • UniRule-annotated proteins constituted 30% of the 178 million records in UniProtKB.
  • Demonstrated scalable enrichment of functional annotation within UniProtKB.

Conclusions:

  • UniRule provides an effective and scalable solution for enriching functional annotation in the UniProt Knowledgebase.
  • The UniRule system successfully addresses the challenge of annotating large-scale, rapidly growing protein datasets.
  • Public availability of UniRule rules and the UniFIRE implementation facilitates broader research applications.