Updates in Rhea: SPARQLing biochemical reaction data.

Details

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State: Public
Version: Final published version
License: CC BY 4.0
Serval ID
serval:BIB_593223E3F0D5
Type
Article: article from journal or magazin.
Collection
Publications
Title
Updates in Rhea: SPARQLing biochemical reaction data.
Journal
Nucleic Acids Research
Author(s)
Lombardot T., Morgat A., Axelsen K.B., Aimo L., Hyka-Nouspikel N., Niknejad A., Ignatchenko A., Xenarios I., Coudert E., Redaschi N., Bridge A.
ISSN
1362-4962 (Electronic)
ISSN-L
0305-1048
Publication state
Published
Issued date
2019
Peer-reviewed
Oui
Volume
47
Number
D1
Pages
D596-D600
Language
english
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.
Pubmed
Web of science
Open Access
Yes
Create date
16/10/2018 12:37
Last modification date
20/08/2019 15:12
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