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

Updates in Rhea: SPARQLing biochemical reaction data

Thierry Lombardot  1 , Anne Morgat  1 , Kristian B Axelsen  1 , Lucila Aimo  1 , Nevila Hyka-Nouspikel  1 , Anne Niknejad  2 , Alex Ignatchenko  3 , Ioannis Xenarios  4   5 , Elisabeth Coudert  1 , Nicole Redaschi  1 , Alan Bridge  1
Affiliations

Updates in Rhea: SPARQLing biochemical reaction data

Thierry Lombardot et al. Nucleic Acids Res. .

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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Figures

Figure 1.
Figure 1.
The Rhea SPARQL endpoint https://sparql.rhea-db.org/sparql. The Rhea SPARQL endpoint provides users with a portal to query Rhea RDF and other endpoints using the SPARQL 1.1 standards as well as a comprehensive set of sample queries and documentation on the Rhea RDF data model.
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