RaMP-DB 2.0: a renovated knowledgebase for deriving biological and chemical insight from metabolites, proteins, and genes.

Software Metabolomics Databases, Factual Gene Expression Profiling Knowledge Bases Proteins

Journal

Bioinformatics (Oxford, England)
ISSN: 1367-4811
Titre abrégé: Bioinformatics
Pays: England
ID NLM: 9808944

Informations de publication

Date de publication:
01 01 2023
Historique:
received: 08 04 2022
revised: 19 09 2022
pubmed: 15 11 2022
medline: 11 1 2023
entrez: 14 11 2022
Statut: ppublish

Résumé

Functional interpretation of high-throughput metabolomic and transcriptomic results is a crucial step in generating insight from experimental data. However, pathway and functional information for genes and metabolites are distributed among many siloed resources, limiting the scope of analyses that rely on a single knowledge source. RaMP-DB 2.0 is a web interface, relational database, API and R package designed for straightforward and comprehensive functional interpretation of metabolomic and multi-omic data. RaMP-DB 2.0 has been upgraded with an expanded breadth and depth of functional and chemical annotations (ClassyFire, LIPID MAPS, SMILES, InChIs, etc.), with new data types related to metabolites and lipids incorporated. To streamline entity resolution across multiple source databases, we have implemented a new semi-automated process, thereby lessening the burden of harmonization and supporting more frequent updates. The associated RaMP-DB 2.0 R package now supports queries on pathways, common reactions (e.g. metabolite-enzyme relationship), chemical functional ontologies, chemical classes and chemical structures, as well as enrichment analyses on pathways (multi-omic) and chemical classes. Lastly, the RaMP-DB web interface has been completely redesigned using the Angular framework. The code used to build all components of RaMP-DB 2.0 are freely available on GitHub at https://github.com/ncats/ramp-db, https://github.com/ncats/RaMP-Client/ and https://github.com/ncats/RaMP-Backend. The RaMP-DB web application can be accessed at https://rampdb.nih.gov/. Supplementary data are available at Bioinformatics online.

Identifiants

DOI: 10.1093/bioinformatics/btac726 PMID: 36373969 PMC: PMC9825745
pubmed: 36373969
pii: 6827287
doi: 10.1093/bioinformatics/btac726
pmc: PMC9825745
pii:
doi:

Substances chimiques

Proteins 0

Types de publication

Journal Article Research Support, N.I.H., Intramural

Langues

eng

Sous-ensembles de citation

IM

Subventions

Organisme : Intramural NIH HHS
ID : ZIC TR000410
Pays : United States

Informations de copyright

Published by Oxford University Press 2022.

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Auteurs

John Braisted (J)

Division of Preclinical Innovation, National Center for Advancing Translational Sciences, Rockville, MD 20850, USA.
ORCID: 0000-0001-8093-6463

Andrew Patt (A)

Division of Preclinical Innovation, National Center for Advancing Translational Sciences, Rockville, MD 20850, USA.
ORCID: 0000-0002-6373-9545

Cole Tindall (C)

Division of Preclinical Innovation, National Center for Advancing Translational Sciences, Rockville, MD 20850, USA.

Timothy Sheils (T)

Division of Preclinical Innovation, National Center for Advancing Translational Sciences, Rockville, MD 20850, USA.
ORCID: 0000-0002-9987-3738

Jorge Neyra (J)

Somatus, McLean, VA 22102, USA.

Kyle Spencer (K)

Division of Preclinical Innovation, National Center for Advancing Translational Sciences, Rockville, MD 20850, USA.
Department of Biomedical Informatics, The Ohio State University, Columbus, OH 43210, USA.
ORCID: 0000-0002-6720-5348

Tara Eicher (T)

Division of Preclinical Innovation, National Center for Advancing Translational Sciences, Rockville, MD 20850, USA.
Department of Computer Science and Engineering, The Ohio State University, Columbus OH 43210, USA.
ORCID: 0000-0003-1809-4458

Ewy A Mathé (EA)

Division of Preclinical Innovation, National Center for Advancing Translational Sciences, Rockville, MD 20850, USA.
ORCID: 0000-0003-4491-8107

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Classifications MeSH

questionsmedicales.fr › Sciences de l'information › Méthodologies informatiques › Logiciel › RaMP-DB 2.0: a renovated knowledgebase for...
questionsmedicales.fr › Disciplines des sciences naturelles › Chimie › Biochimie › Métabolomique › RaMP-DB 2.0: a renovated knowledgebase for...
questionsmedicales.fr › Sciences de l'information › Mémorisation et recherche des informations › Bases de données comme sujet › Bases de données factuelles › RaMP-DB 2.0: a renovated knowledgebase for...
questionsmedicales.fr › Techniques d'investigation › Techniques génétiques › Analyse de profil d'expression de gènes › RaMP-DB 2.0: a renovated knowledgebase for...
questionsmedicales.fr › Sciences de l'information › Informatique › Informatique médicale › Applications de l'informatique médicale › Systèmes d'information › Bases de connaissances › RaMP-DB 2.0: a renovated knowledgebase for...
questionsmedicales.fr › Acides aminés, peptides et protéines › Protéines › RaMP-DB 2.0: a renovated knowledgebase for...