Human Metabolome Database

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This article is about the Human Metabolome Database (HMDB.ca). For the Historical Marker Database (HMdb.org), see Historical Marker Database.
Human Metabolome Database
Research center
University of Alberta and The Metabolomics Innovation Centre
LaboratoryDavid S. Wishart
Primary citationHMDB: the Human Metabolome Database.[1]
Access
Websitehttp://www.hmdb.ca
Download URLhttp://www.hmdb.ca/downloads
Miscellaneous
Data release
frequency		Every 2 years with monthly corrections and updates
Curation policyManually curated

The Human Metabolome Database (HMDB)

LC/MS spectrometry. To aid in this discovery process, the HMDB contains three kinds of data: 1) chemical data, 2) clinical data, and 3) molecular biology/biochemistry
data (Fig. 1–3). The chemical data includes 41,514 metabolite structures with detailed descriptions along with nearly 10,000 NMR, GC-MS and LC/MS spectra.

The clinical data includes information on >10,000 metabolite-

relational query searches. It has been widely used in metabolomics, clinical chemistry, biomarker
discovery and general biochemistry education.

Four additional databases, DrugBank,[6][7][8] T3DB,[9] SMPDB [10] and FooDB are also part of the HMDB suite of databases. DrugBank contains equivalent information on ~1,600 drug and drug metabolites, T3DB contains information on 3,100 common toxins and environmental pollutants, SMPDB contains pathway diagrams for 700 human metabolic and disease pathways, while FooDB contains equivalent information on ~28,000 food components and food additives.

Version history

The first version of HMDB was released on January 1, 2007,[1] followed by two subsequent versions on January 1, 2009 (version 2.0),[2] August 1, 2009 (version 2.5), September 18, 2012 (version 3.0)[4] and Jan. 1, 2013 (version 3.5),[11] 2017 (version 4.0).[12], 2022 (version 5.0).[11] Details for each of the major HMDB versions (up to version 5.0) is provided in Table 1.

Table 1. Content comparison of HMDB versions
Database Feature or Content Status HMDB (v1.0) HMDB (v2.0) HMDB (v3.0) HMDB (v4.0) HMDB (v5.0)
Number of metabolites 2,180 6,408 37,170 114,100 220,945
Number of unique metabolite synonyms 27,700 43,882 152,364 − −
Number of compounds with disease links 862 1,002 3,948 22,605 22,600
Number of compounds with biofluid or tissue concentration data 883 4,413 6,796 − −
Number of compounds with chemical synthesis references 220 1,647 8,863 72,604 78,841
Number of compounds with experimental reference 1H and or 13C NMR spectra 385 792 1,054 2,801 12,216
Number of compounds with reference MS/MS spectra 390 799 1,249 1,544 4,064
Number of compounds with reference GC-MS reference data 0 279 884 7,418 11,493
Number of human-specific pathway maps 26 58 442 − −
Number of compounds in Human Metabolome Library 607 920 1,031 − −
Number of HMDB data fields 91 102 114 130 130
'Number of predicted molecular properties 2 2 10 − −

Scope and access

All data in HMDB is non-proprietary or is derived from a non-proprietary source. It is freely accessible and available to anyone. In addition, nearly every data item is fully traceable and explicitly referenced to the original source. HMDB data is available through a public web interface and downloads.

See also

References

  1. ^
    PMID 17202168
    .
  2. ^
    PMID 18953024
    .
  3. S2CID 24291704
    .
  4. ^
    PMID 23161693
    .
  5. ^ a b "Human Metabolome Project". Retrieved 13 February 2013.
  6. PMID 16381955
    .
  7. PMID 18048412
    .
  8. PMID 21059682
    .
  9. PMID 19897546
    .
  10. PMID 19948758
    .
  11. ^ a b "Human Metabolome Database Release Notes".
  12. PMID 29140435
    .
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