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Nucleic Acids Res. 2019 Jan 8;47(D1):D596-D600. doi: 10.1093/nar/gky876.

Updates in Rhea: SPARQLing biochemical reaction data.

Author information

1
Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, CMU, 1 rue Michel-Servet, CH-1211 Geneva 4, Switzerland.
2
Vital-IT Group, SIB Swiss Institute of Bioinformatics, Quartier Sorge, Bâtiment Génopode, CH-1015 Lausanne, Switzerland.
3
European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
4
Department of Biochemistry, University of Geneva, CH-1211 Geneva, Switzerland.
5
Center for Integrative Genomics, University of Lausanne, CH-1015 Lausanne, Switzerland.

Abstract

Rhea (http://www.rhea-db.org) is a comprehensive and non-redundant resource of over 11 000 expert-curated biochemical reactions that uses chemical entities from the ChEBI ontology to represent reaction participants. Originally designed as an annotation vocabulary for the UniProt Knowledgebase (UniProtKB), Rhea also provides reaction data for a range of other core knowledgebases and data repositories including ChEBI and MetaboLights. Here we describe recent developments in Rhea, focusing on a new resource description framework representation of Rhea reaction data and an SPARQL endpoint (https://sparql.rhea-db.org/sparql) that provides access to it. We demonstrate how federated queries that combine the Rhea SPARQL endpoint and other SPARQL endpoints such as that of UniProt can provide improved metabolite annotation and support integrative analyses that link the metabolome through the proteome to the transcriptome and genome. These developments will significantly boost the utility of Rhea as a means to link chemistry and biology for a more holistic understanding of biological systems and their function in health and disease.

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