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HMDB specifications


Unique identifier OMICS_02532
Alternative name Human Metabolome DataBase
Restrictions to use None
Database management system MySQL
Community driven No
Data access File download, Browse
User data submission Not allowed
Version 4.0
Maintained Yes


  • Primates
    • Homo sapiens


  • person_outline David Wishart

Publications for Human Metabolome DataBase

HMDB citations


Metabolic alterations in urine extracellular vesicles are associated to prostate cancer pathogenesis and progression

J Extracell Vesicles
PMCID: 5944373
PMID: 29760869
DOI: 10.1080/20013078.2018.1470442

[…] p/kegg/pathway.html). Primary enzymes involved in the metabolism of the metabolite of interest, and their corresponding coding genes were retrieved from KEGG ( and HMDB ( databases, using dbWalk utility on bioDBnet database searching online utility and specifying “9606” (Homo sapiens) Taxon ID on Organism box (https://biodbnet-abcc.ncifcrf.go […]


Tissue storage affects lipidome profiling in comparison to in vivo microsampling approach

Sci Rep
PMCID: 5934459
PMID: 29725071
DOI: 10.1038/s41598-018-25428-2

[…] 2 H”,   “M + H”,   “M + NH4”,   “M + Na”,   “M + ACN + H”,   “M + ACN + Na”,   “M + 2ACN + H”,   “2 M + H”,   “2 M + Na”,   “2 M + ACN + H”,   “M + 2Na-H”,   “M + H-H2O”,   “M + H-2H2O” ), db_name = ‘HMDB’, …) { data <- xcms::groupval(xset, ‘medret’, “into”) adduct_weights = = c(‘M + H’,‘M-H’),Weight = c(5,5)) mz <- xcms::groups(xset)[, 1] time <- xcms::groups(xset)[, 4] da […]


Integrative metabolic and microbial profiling on patients with Spleen yang deficiency syndrome

Sci Rep
PMCID: 5920061
PMID: 29700349
DOI: 10.1038/s41598-018-24130-7

[…] differentiated metabolite ions. Then they were structurally identified and interpreted based on searches of their accurate masses in metabolomic associated databases: METLIN (, HMDB ( and KEGG ( Lastly, the isotopic distribution, retention time and fragments of commercial standards were further confirmed for the metabolites of interest. […]


A prototypic small molecule database for bronchoalveolar lavage based metabolomics

Sci Data
PMCID: 5903367
PMID: 29664467
DOI: 10.1038/sdata.2018.60

[…] le for download from a GitHub repository at: Included are code written in the R language for obtaining the ion statistics, computing the isotope ratios from the HMDB and LipidMaps databases and filtering of compounds. Also included are code for searching and processing MS/MS search results, storing the results in a SQL database, and plotting the MS/MS results […]


Metabolome Integrated Analysis of High Temperature Response in Pinus radiata

Front Plant Sci
PMCID: 5914196
PMID: 29719546
DOI: 10.3389/fpls.2018.00485

[…] s performed against an in-house library (>100 compounds) and manual annotation considering m/z and retention times. In the second step, masses were assigned using the KEGG, PubChem, METLIN, MassBank, HMDB, and Plantcyc databases as reported by with built-in MZmine plugins with a 5 ppm threshold and considering as “identified” beyond doubt those metabolites that were defined after the comparison t […]


Metabolomic study of human tissue and urine in clear cell renal carcinoma by LC HRMS and PLS DA

Anal Bioanal Chem
PMCID: 5956006
PMID: 29658093
DOI: 10.1007/s00216-018-1059-x
call_split See protocol

[…] served RT was 5% for authentic standards and 45% for other metabolites. Putative identifications were also guided by searches on the Madison-Qingdao Metabolomics Consortium Database (MMCD) [] and the Human Metabolome Database (HMDB) [].Multivariate statistical analyses were performed using Metaboanalyst 3.0 []. […]


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HMDB institution(s)
Department of Biological Sciences University of Alberta, Edmonton, AB, Canada; Department of Computing Science, University of Alberta, Edmonton, AB, Canada; Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, AB, Canada; International Agency for Research on Cancer (IARC), Lyon, France; OMx Personal Health Analytics, Inc., Edmonton, AB, Canada; Institut National de la Recherche Agronomique (INRA) – Human Nutrition Unit, Universite Clermont Auvergne, Clermont-Ferrand, France
HMDB funding source(s)
Supported by Genome Alberta (a division of Genome Canada); The Canadian Institutes of Health Research (CIHR); Western Economic Diversification (WED); Alberta Innovates Health Solutions (AIHS).

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