The Rhea SPARQL endpoint supports integrated analyses of genome, proteome and metabolome
journal contributionposted on 01.12.2018 by Thierry Lombardot, Anne Morgat, Sebastien Gehant, Nicole Redaschi, Alan Bridge
Any type of content formally published in an academic journal, usually following a peer-review process.
‘Omics technologies enable comprehensive analyses of how genetic variation (genomics), gene expression patterns (transcriptomics), proteins and complexes (proteomics), and small molecules (metabolomics) interact in complex biological systems. RDF and SPARQL can connect these ‘omics domains and help us realize the full potential of this valuable experimental data. Rhea is a comprehensive and non-redundant resource of expert-curated biochemical reactions based on the ChEBI ontology. Here we demonstrate how to link genome (Ensembl), proteome (UniProt), and metabolome (ChEBI) data using federated queries that leverage the SPARQL endpoint of Rhea (https://sparql.rhea-db.org/sparql) and data from these other resources.