ArticleBioinformatics (Oxford, England)2023
RaMP-DB 2.0: a renovated knowledgebase for deriving biological and chemical insight from metabolites, proteins, and genes.
Article in Bioinformatics (Oxford, England), 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 43 papers.
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Who cites it
43 citing papers in PubMed.
- Computational metabolomics at scale: from open data to insight.Current opinion in biotechnology · 2026Review
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- Gut-liver metabolic and enterohormonal remodeling drives progression from metabolic dysfunction-associated steatotic liver disease to steatohepatitis.Metabolism: clinical and experimental · 2026Article
- SpaMTP: integrative statistical analysis and visualization of spatial metabolomics and transcriptomics data.Nature methods · 2026Article
- Metabolic reprogramming in polyol pathway contributes to anti-inflammatory effect of glucosamine salts on synovial fibroblasts.npj metabolic health and disease · 2026Article
- Effect biomonitoring in a controlled firefighting setting: an untargeted metabolomic pilot study.Archives of toxicology · 2026Article
- Targeting sialic acid metabolism: a therapeutic strategy against gastric cancer driven by WZ35.Cellular oncology (Dordrecht, Netherlands) · 2026Article
- Metabolite names and identifiers: how far are we from interoperability?Metabolomics : Official journal of the Metabolomic Society · 2026Article
- Multi-omics analysis identifies TBCB as a therapeutic target in sepsis-induced liver injury.International journal of surgery (London, England) · 2026Article
- OmniPath: integrated knowledgebase for multi-omics analysis.Nucleic acids research · 2026Article
- Multiomic profiling of canine immune and metabolic aging in a cohort of young and senior beagles.Frontiers in immunology · 2026Article
- Urinary metabolite profiles differ by tumor size and malignancy in dogs with mammary tumors.Frontiers in veterinary science · 2026Article
- Deciphering the causal relationships between plasma metabolites, peripheral cells, inflammatory factors and DLBCL for discovering novel therapeutic targets.Discover oncology · 2025Article
- Metabolomic profiling reveals distinct lipid signatures in progressive versus stable fibrotic lung disease.Metabolomics : Official journal of the Metabolomic Society · 2025Article
- Butyrate rescues chlorpyrifos-induced social deficits through inhibition of class I histone deacetylases.bioRxiv : the preprint server for biology · 2025Article
- Perioperative IDH inhibition in treatment-naive IDH-mutant glioma: a pilot trial.Nature medicine · 2025Article
- Metabolomic, Lipidomic, and Enterohormone Changes in the Progression from MASLD to MASH.bioRxiv : the preprint server for biology · 2025Article
- Metabolic alterations in diabetic patients: aqueous humor profiling for biomarker discovery.Amino acids · 2025Article
- Nitrogen limitation causes a seismic shift in redox state and phosphorylation of proteins implicated in carbon flux and lipidome remodeling in Rhodotorula toruloides.Biotechnology for biofuels and bioproducts · 2025Article
Corrections and comments
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Authors and funding
8 authors.
Funding
Abstract
motivationFunctional 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.
resultsRaMP-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. AVAILABILITY AND IMPLEMENTATION: 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 INFORMATION: Supplementary data are available at Bioinformatics online.
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What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.