The omics discovery REST interface.

Databases, Genetic Datasets as Topic Gene Expression Profiling / methods Genomics / methods Metabolomics / methods Proteomics / methods Software User-Computer Interface

Journal

Nucleic acids research
ISSN: 1362-4962
Titre abrégé: Nucleic Acids Res
Pays: England
ID NLM: 0411011

Informations de publication

Date de publication:
02 07 2020
Historique:
accepted: 21 04 2020
revised: 11 04 2020
received: 10 02 2020
pubmed: 7 5 2020
medline: 26 11 2020
entrez: 7 5 2020
Statut: ppublish

Résumé

The Omics Discovery Index is an open source platform that can be used to access, discover and disseminate omics datasets. OmicsDI integrates proteomics, genomics, metabolomics, models and transcriptomics datasets. Using an efficient indexing system, OmicsDI integrates different biological entities including genes, transcripts, proteins, metabolites and the corresponding publications from PubMed. In addition, it implements a group of pipelines to estimate the impact of each dataset by tracing the number of citations, reanalysis and biological entities reported by each dataset. Here, we present the OmicsDI REST interface (www.omicsdi.org/ws/) to enable programmatic access to any dataset in OmicsDI or all the datasets for a specific provider (database). Clients can perform queries on the API using different metadata information such as sample details (species, tissues, etc), instrumentation (mass spectrometer, sequencer), keywords and other provided annotations. In addition, we present two different libraries in R and Python to facilitate the development of tools that can programmatically interact with the OmicsDI REST interface.

Identifiants

DOI: 10.1093/nar/gkaa326 PMID: 32374843 PMC: PMC7319562
pubmed: 32374843
pii: 5831190
doi: 10.1093/nar/gkaa326
pmc: PMC7319562
doi:

Types de publication

Journal Article Research Support, Non-U.S. Gov't

Langues

eng

Sous-ensembles de citation

IM

Pagination

W380-W384

Subventions

Organisme : Biotechnology and Biological Sciences Research Council
ID : BB/N022432/1
Pays : United Kingdom
Organisme : Wellcome Trust
ID : 208391/Z/17/Z
Pays : United Kingdom

Informations de copyright

© The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research.

Références

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Auteurs

Gaurhari Dass (G)

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge CB10 1SD, UK.

Manh-Tu Vu (MT)

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge CB10 1SD, UK.

Pan Xu (P)

State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Lifeomics, National Center for Protein Sciences Beijing, 102206 Beijing, China.

Enrique Audain (E)

Department of Human Genetics, University Medical Center Schleswig-Holstein (UKSH), Kiel, Germany.

Marc-Phillip Hitz (MP)

Department of Human Genetics, University Medical Center Schleswig-Holstein (UKSH), Kiel, Germany.

Björn A Grüning (BA)

Bioinformatics Group, Department of Computer Science, University of Freiburg, Georges-Köhler-Allee 106, 79110 Freiburg, Germany.

Henning Hermjakob (H)

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge CB10 1SD, UK.
State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Lifeomics, National Center for Protein Sciences Beijing, 102206 Beijing, China.

Yasset Perez-Riverol (Y)

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge CB10 1SD, UK.

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Classifications MeSH

questionsmedicales.fr › Sciences de l'information › Mémorisation et recherche des informations › Bases de données comme sujet › Bases de données factuelles › Bases de données génétiques › The omics discovery REST interface.
questionsmedicales.fr › Environnement et santé publique › Santé publique › Méthodes épidémiologiques › Collecte de données › Jeux de données comme sujet › The omics discovery REST interface.
questionsmedicales.fr › Techniques d'investigation › Techniques génétiques › Analyse de profil d'expression de gènes › The omics discovery REST interface.
questionsmedicales.fr › Disciplines des sciences naturelles › Disciplines des sciences biologiques › Biologie › Génétique › Génomique › The omics discovery REST interface.
questionsmedicales.fr › Disciplines des sciences naturelles › Chimie › Biochimie › Métabolomique › The omics discovery REST interface.
questionsmedicales.fr › Disciplines des sciences naturelles › Chimie › Biochimie › Protéomique › The omics discovery REST interface.
questionsmedicales.fr › Sciences de l'information › Méthodologies informatiques › Logiciel › The omics discovery REST interface.
questionsmedicales.fr › Sciences de l'information › Méthodologies informatiques › Logiciel › Interface utilisateur › The omics discovery REST interface.