Updates in Rhea: SPARQLing biochemical reaction data.

Détails

Ressource 1Télécharger: gky876.pdf (1603.06 [Ko])
Etat: Public
Version: Final published version
Licence: CC BY 4.0
ID Serval
serval:BIB_593223E3F0D5
Type
Article: article d'un périodique ou d'un magazine.
Collection
Publications
Titre
Updates in Rhea: SPARQLing biochemical reaction data.
Périodique
Nucleic Acids Research
Auteur(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
Statut éditorial
Publié
Date de publication
2019
Peer-reviewed
Oui
Volume
47
Numéro
D1
Pages
D596-D600
Langue
anglais
Résumé
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
Oui
Création de la notice
16/10/2018 11:37
Dernière modification de la notice
20/08/2019 14:12
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