Abstract

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.

Keywords

UniProtSPARQLAnnotationComputer scienceOntologyLeverage (statistics)Information retrievalOomyceteWorld Wide WebComputational biologySemantic WebBiologyRDFArtificial intelligenceGenetics

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Publication Info

Year
2019
Type
article
Volume
36
Issue
6
Pages
1896-1901
Citations
98
Access
Closed

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Cite This

Anne Morgat, Thierry Lombardot, Elisabeth Coudert et al. (2019). Enzyme annotation in UniProtKB using Rhea. Bioinformatics , 36 (6) , 1896-1901. https://doi.org/10.1093/bioinformatics/btz817

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DOI
10.1093/bioinformatics/btz817