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Enzyme annotation in UniProtKB using Rhea

Authors :
Sylvain Poux
Delphine Baratin
Ioannis Xenarios
Teresa Batista Neto
Elisabeth Gasteiger
Sebastien Gehant
Nicole Redaschi
Anne Morgat
Thierry Lombardot
Jerven Bolleman
Edouard de Castro
Parit Bansal
Monica Pozzato
Elisabeth Coudert
Kristian B. Axelsen
Alan Bridge
Source :
Bioinformatics
Publication Year :
2019
Publisher :
Oxford University Press (OUP), 2019.

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).ResultsWe 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 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/.Contactanne.morgat@sib.swiss

Details

ISSN :
14602059 and 13674803
Database :
OpenAIRE
Journal :
Bioinformatics
Accession number :
edsair.doi.dedup.....094df19a76493513f1d0258b3b046420
Full Text :
https://doi.org/10.1093/bioinformatics/btz817