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Enzyme annotation in UniProtKB using Rhea
Anne Morgat1, Thierry Lombardot1, Elisabeth Coudert1
1Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, Geneva 1211-4, Switzerland.
Bioinformatics (Oxford, England)
|November 6, 2019
Summary
UniProtKB now uses Rhea for enzyme annotation, improving data quality and enabling advanced searches. This integration enhances biochemical reaction information accessibility and computational tractability.
Area of Science:
- Biochemistry
- Bioinformatics
- Computational Biology
Background:
- UniProtKB provides protein sequence and functional information.
- Enzyme annotation in UniProtKB relied on textual descriptions of biochemical reactions.
- There was a need for standardized, computationally tractable reaction data.
Purpose of the Study:
- To enhance enzyme annotation quality in UniProtKB using the Rhea knowledgebase.
- To integrate ChEBI ontology for standardized chemical entity representation.
- To improve search and query functionalities for biochemical reactions.
Main Methods:
- Replaced existing textual reaction descriptions in UniProtKB with Rhea equivalents.
- Leveraged Rhea's expert-curated biochemical reactions and ChEBI ontology.
- Developed enhanced search and query facilities for UniProt website, REST API, and SPARQL endpoint.
Main Results:
- Rhea is now the standard for enzymatic reaction annotation in UniProtKB.
- Improved search capabilities utilize chemical structure, nomenclature, and classification data.
- Enhanced data accessibility and computational tractability for biochemical reactions.
Conclusions:
- The integration of Rhea significantly improves UniProtKB's enzyme annotation.
- Enhanced search and query tools facilitate deeper analysis of biochemical data.
- This work establishes a new standard for representing enzymatic reactions in biological databases.
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