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. 2020 Mar 1;36(6):1896-1901.
doi: 10.1093/bioinformatics/btz817.

Enzyme annotation in UniProtKB using Rhea

Anne Morgat  1 , Thierry Lombardot  1 , Elisabeth Coudert  1 , Kristian Axelsen  1 , Teresa Batista Neto  1 , Sebastien Gehant  1 , Parit Bansal  1 , Jerven Bolleman  1 , Elisabeth Gasteiger  1 , Edouard de Castro  1 , Delphine Baratin  1 , Monica Pozzato  1 , Ioannis Xenarios  2 , Sylvain Poux  1 , Nicole Redaschi  1 , Alan Bridge  1 ; UniProt Consortium
Affiliations

Enzyme annotation in UniProtKB using Rhea

Anne Morgat et al. Bioinformatics. .

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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Figures

Fig. 1.
Fig. 1.
UniProtKB entry view showing Rhea annotation for the Streptomyces globisporus enzyme 2-amino-4-deoxychorismate synthase (UniProt: Q8GMH4 annotated with RHEA: 25512). The search and link-out options available for each reaction participant are illustrated using ‘l-glutamine’; users can search in UniProtKB or Rhea, or link out to ChEBI to learn more about the metabolite in question. We omit most sections for clarity
Fig. 2.
Fig. 2.
Advanced search in UniProtKB for enzymatic reactions. (a) Advanced search using chemical nomenclature. The autocomplete feature is shown. (b) Advanced search using InChIKeys of choline (HMDB00097) and trimethylamine (TMA) (HMDB0000906) to identify bacterial enzymes metabolizing both compounds. The result table can be customized to display Rhea reaction data, which can be used to launch further searches and link out precisely as in the entry view
Fig. 3.
Fig. 3.
A sample federated SPARQL query that leverages Rhea annotation in UniProtKB. The query retrieves information about drugs that target enzymes involved in human sterol (ChEBI: 15889) metabolism from the UniProt, Rhea and ChEMBL SPARQL endpoints, federating the three SPARQL endpoints with two SERVICE calls
See this image and copyright information in PMC

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