ArticleNucleic acids research2009
HMDB: a knowledgebase for the human metabolome.
Article in Nucleic acids research, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 809 papers, 2 of them syntheses that pooled it.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
809 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Meta-analysis of probiotics metabolites in gastrointestinal tract and metabolic health.Frontiers in cellular and infection microbiology · 2025Pooled it
- Metabolomic biomarkers of low BMD: a systematic review.Osteoporosis international : a journal established as result of cooperation between the European Foundation for Osteoporosis and the National Osteoporosis Foundation of the USA · 2021Pooled it
- Acute aerobic exercise reveals that FAHFAs distinguish the metabolomes of overweight and normal-weight runners.JCI insight · 2022Trial
- Action Spectroscopy of Mass-Selected Ions-From Principles to Applications.Journal of mass spectrometry : JMS · 2026Review
- Advancing spatial-omics through Pyxis, vendor-neutral software for ion mobility mass spectrometry imaging data analysis.Analytical and bioanalytical chemistry · 2026Article
- Multi-omics integration of proteomics and metabolomics in pediatric health and disease.Communications medicine · 2026Review
- Integrated metabolomics and DNA methylation signatures and their association with flare remission in SLE.Lupus science & medicine · 2026Article
- Comprehensive Identification of the Chemical Components in the Classical Prescription Shashen Maidong Decoction Based on UPLC-Q-Orbitrap MS and Molecular Networking.Pharmaceuticals (Basel, Switzerland) · 2026Article
- Dietary yacon concentrate reshapes microbial-metabolite crosstalk to inhibit colorectal cancer.NPJ science of food · 2026Article
- Data-Driven Electrochemistry Reveals the Impact of Hydrophobicity on Aptamer Cross-Reactivity.ACS measurement science au · 2026Article
- Lipidomic and sterolomic profiles of different brain regions in the mouse model of Alzheimer's disease.Neural regeneration research · 2026Article
- 1H MR-based detection of human plasma metabolic alterations in clear cell renal cell carcinoma.BJUI compass · 2026Article
- Lifespan trajectories of serum sphingolipids in a clinically healthy Swiss population, towards precision medicine in cardiometabolic health assessment.Communications medicine · 2026Article
- The NMR Exchange Format (NEF): Specification and Applications.bioRxiv : the preprint server for biology · 2026Article
- First comprehensive GC-MS profile of Echinops erinaceus with antimicrobial and cytotoxic activities and in-silico model.Scientific reports · 2026Article
- Cholecalciferol (vitamin D3) is an agonist of the Alzheimer's disease-associated immune receptor TREM2.Neurotherapeutics : the journal of the American Society for Experimental NeuroTherapeutics · 2026Article
- Mass spectrometry imaging tutorial: From cancer biomarker discovery to clinical applications.Analytica chimica acta · 2026Review
- Retrieval-Augmented Language Models Enable Scalable Chemical Source Classification in Metabolomics Workflows.Analytical chemistry · 2026Article
- Live Metabolomics with NMR.Analytical chemistry · 2026Review
- Virtual Colon: spatiotemporal modeling of metabolic interactions in a computational colonic environment.mSystems · 2026Article
749 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
38 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The Human Metabolome Database (HMDB, http://www.hmdb.ca) is a richly annotated resource that is designed to address the broad needs of biochemists, clinical chemists, physicians, medical geneticists, nutritionists and members of the metabolomics community. Since its first release in 2007, the HMDB has been used to facilitate the research for nearly 100 published studies in metabolomics, clinical biochemistry and systems biology. The most recent release of HMDB (version 2.0) has been significantly expanded and enhanced over the previous release (version 1.0). In particular, the number of fully annotated metabolite entries has grown from 2180 to more than 6800 (a 300% increase), while the number of metabolites with biofluid or tissue concentration data has grown by a factor of five (from 883 to 4413). Similarly, the number of purified compounds with reference to NMR, LC-MS and GC-MS spectra has more than doubled (from 380 to more than 790 compounds). In addition to this significant expansion in database size, many new database searching tools and new data content has been added or enhanced. These include better algorithms for spectral searching and matching, more powerful chemical substructure searches, faster text searching software, as well as dedicated pathway searching tools and customized, clickable metabolic maps. Changes to the user-interface have also been implemented to accommodate future expansion and to make database navigation much easier. These improvements should make the HMDB much more useful to a much wider community of users.
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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.