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 ChEBI (Chemical Entities of Biological Interest) ontology.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/; Rhea at https://www.rhea-db.org.
Highlights
The UniProt Knowledgebase (UniProtKB, at https://www.uniprot.org) is a reference resource of protein sequences and functional annotation that covers proteins from all branches of the tree of life (The UniProt Consortium, 2019)
We describe the introduction of a new reference vocabulary for the annotation of enzymes in UniProtKB – the Rhea knowledgebase of biochemical reactions (Lombardot, et al, 2019; Morgat, et al, 2017)
The EC number annotations for Rhea reactions are optional in UniProtKB, as Rhea contains thousands of reactions not described by the IUBMB Enzyme Classification
Summary
The UniProt Knowledgebase (UniProtKB, at https://www.uniprot.org) is a reference resource of protein sequences and functional annotation that covers proteins from all branches of the tree of life (The UniProt Consortium, 2019). Half of all protein sequence entries in UniProtKB/Swiss-Prot describe enzymes, whose function has traditionally been annotated using reference vocabularies such as the hierarchical enzyme classification of the Enzyme Nomenclature Committee of the IUBMB (often referred to as EC numbers) (Bairoch, 2000; McDonald, et al, 2009; McDonald and Tipton, 2014). We describe the introduction of a new reference vocabulary for the annotation of enzymes in UniProtKB – the Rhea knowledgebase of biochemical reactions (https://www.rhea-db.org) (Lombardot, et al, 2019; Morgat, et al, 2017).
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