Enzyme Annotation in UniProtKB Using Rhea

Overview

Journal Bioinformatics

Publisher Oxford University Press

Specialty Biology

Date 2019 Nov 6

PMID 31688925

Citations 51

Authors

Anne Morgat

Thierry Lombardot

Elisabeth Coudert

Kristian Axelsen

Teresa Batista Neto

Sebastien Gehant

Parit Bansal

Jerven Bolleman

Elisabeth Gasteiger

Edouard de Castro

Delphine Baratin

Monica Pozzato

Ioannis Xenarios

Sylvain Poux

Nicole Redaschi

Alan Bridge

Affiliations

Soon will be listed here.

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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