Semantic Web Applications and Tools for Healthcare and Life Sciences
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The Rhea SPARQL endpoint supports integrated analyses of genome, proteome and metabolome

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posted on 2018-12-01, 20:39 authored by Thierry Lombardot, Anne Morgat, Sebastien Gehant, Nicole Redaschi, Alan Bridge
‘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.

Funding

Swiss Federal Government through the State Secretariat for Education, Research and Innovation (SERI)

ELIXIR Implementation study on ‘A microbial metabolism resource for Systems Biology’

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    Semantic Web Applications and Tools for Healthcare and Life Sciences

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    Keywords

    Biochemical reactionsmetabolitesRDFRheaSPARQLOrganisation of Information and Knowledge ResourcesBioinformaticsMedical Biochemistry: Amino Acids and Metabolites

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