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Bioinformatics. 2020 Mar 1;36(6):1896-1901. doi: 10.1093/bioinformatics/btz817.

Enzyme annotation in UniProtKB using Rhea.

Author information

1
Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, Geneva 1211-4, Switzerland.
2
University of Lausanne, Lausanne 1015, Switzerland.

Abstract

MOTIVATION:

To provide high quality computationally tractable enzyme annotation in UniProtKB using Rhea, a comprehensive expert-curated knowledgebase of biochemical reactions which describes reaction participants using the ChEBI (Chemical Entities of Biological Interest) ontology.

RESULTS:

We replaced existing textual descriptions of biochemical reactions in UniProtKB with their equivalents from Rhea, which is now the standard for annotation of enzymatic reactions in UniProtKB. We developed improved search and query facilities for the UniProt website, REST API and SPARQL endpoint that leverage the chemical structure data, nomenclature and classification that Rhea and ChEBI provide.

AVAILABILITY AND IMPLEMENTATION:

UniProtKB at https://www.uniprot.org; UniProt REST API at https://www.uniprot.org/help/api; UniProt SPARQL endpoint at https://sparql.uniprot.org/; Rhea at https://www.rhea-db.org.

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