Enzyme annotation in UniProtKB using Rhea

Anne Morgat; Thierry Lombardot; Elisabeth Coudert; Kristian B. Axelsen; Teresa Batista Neto; Sébastien Géhant; Parit Bansal; Jerven Tjalling Bolleman; Elisabeth Gasteiger; Edouard de Castro; Delphine Baratin; Monica Pozzato; Ioannis Xénarios; Sylvain Poux; Nicole Redaschi; Alan James Bridge

doi:10.1093/bioinformatics/btz817

BioinformaticsBioinformaticsOct 31, 2019

Peer-reviewed journal article

Enzyme annotation in UniProtKB using Rhea

Anne Morgat iD, Thierry Lombardot iD, Elisabeth Coudert iD, Kristian B. Axelsen iD, Teresa Batista Neto iD, Sébastien Géhant iD, Parit Bansal iD, Jerven Tjalling Bolleman iD, Elisabeth Gasteiger iD, Edouard de Castro iD, Delphine Baratin iD, Monica Pozzato iD, Ioannis Xénarios iD, Sylvain Poux iD, Nicole Redaschi iD, Alan James Bridge iD

Abstract

MotivationTo 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 ontology ChEBI (Chemical Entities of Biological Interest).\n\nResultsWe 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.\n\nAvailability and ImplementationUniProtKB at https://www.uniprot.org/; UniProt REST API at https://www.uniprot.org/help/api; UniProt SPARQL endpoint at https://sparql.uniprot.org/sparql; Rhea at https://www.rhea-db.org/.\n\nContactanne.morgat@sib.swiss

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