Home LiteratureArticle Details
PMID: 34986597 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

HMDB 5.0: the Human Metabolome Database for 2022.

Nucleic acids research ·Vol. 50 ·No. D1 ·2022-00-07 ·Pages D622-D631

Wishart DS, Guo A, Oler E, Wang F, Anjum A, Peters H, Dizon R, Sayeeda Z, Tian S, Lee BL, Berjanskii M, Mah R, Yamamoto M, Jovel J, Torres-Calzada C, Hiebert-Giesbrecht M, Lui VW, Varshavi D, Varshavi D, Allen D, Arndt D, Khetarpal N, Sivakumaran A, Harford K, Sanford S, Yee K, Cao X, Budinski Z, Liigand J, Zhang L, Zheng J, Mandal R, Karu N, Dambrova M, Schiöth HB, Greiner R, Gautam V

Abstract

The Human Metabolome Database or HMDB (https://hmdb.ca) has been providing comprehensive reference information about human metabolites and their associated biological, physiological and chemical properties since 2007. Over the past 15 years, the HMDB has grown and evolved significantly to meet the needs of the metabolomics community and respond to continuing changes in internet and computing technology. This year's update, HMDB 5.0, brings a number of important improvements and upgrades to the database. These should make the HMDB more useful and more appealing to a larger cross-section of users. In particular, these improvements include: (i) a significant increase in the number of metabolite entries (from 114 100 to 217 920 compounds); (ii) enhancements to the quality and depth of metabolite descriptions; (iii) the addition of new structure, spectral and pathway visualization tools; (iv) the inclusion of many new and much more accurately predicted spectral data sets, including predicted NMR spectra, more accurately predicted MS spectra, predicted retention indices and predicted collision cross section data and (v) enhancements to the HMDB's search functions to facilitate better compound identification. Many other minor improvements and updates to the content, the interface, and general performance of the HMDB website have also been made. Overall, we believe these upgrades and updates should greatly enhance the HMDB's ease of use and its potential applications not only in human metabolomics but also in exposomics, lipidomics, nutritional science, biochemistry and clinical chemistry.

MeSH Terms
Databases, Genetic Humans Lipidomics/classification Mass Spectrometry Metabolome/genetics Metabolomics/classification User-Computer Interface
Authors & Affiliations
37 authors, click to expand affiliations / ORCID
Wishart David S ORCID
Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada. | Department of Computing Science, University of Alberta, Edmonton, AB T6G 2E8, Canada. | Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB T6G 2B7, Canada. | Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, AB T6G 2H7, Canada.
Guo AnChi
Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada.
Oler Eponine
Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada.
Wang Fei
Department of Computing Science, University of Alberta, Edmonton, AB T6G 2E8, Canada.
Anjum Afia
Department of Computing Science, University of Alberta, Edmonton, AB T6G 2E8, Canada.
Peters Harrison
Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada.
Dizon Raynard
Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada.
Sayeeda Zinat
Department of Computing Science, University of Alberta, Edmonton, AB T6G 2E8, Canada.
Tian Siyang
Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada.
Lee Brian L
Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada.
Berjanskii Mark
Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada.
Mah Robert
Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada.
Yamamoto Mai
Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada.
Jovel Juan
Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada.
Torres-Calzada Claudia
Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada.
Hiebert-Giesbrecht Mickel
Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada.
Lui Vicki W
Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada.
Varshavi Dorna
Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada.
Varshavi Dorsa
Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada.
Allen Dana
Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada.
Arndt David
Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada.
Khetarpal Nitya
Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada.
Sivakumaran Aadhavya
Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada.
Harford Karxena
Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada.
Sanford Selena
Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada.
Yee Kristen
Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada.
Cao Xuan
Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada.
Budinski Zachary
Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada.
Liigand Jaanus
Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada.
Zhang Lun
Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada.
Zheng Jiamin
Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada.
Mandal Rupasri
Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada.
Karu Naama
Leiden Academic Centre for Drug Research LACDR/Analytical Biosciences, Leiden University, Leiden, Netherlands.
Dambrova Maija
Laboratory of Pharmaceutical Pharmacology, Latvian Institute of Organic Synthesis, Riga, Latvia.
Schiöth Helgi B
Section of Functional Pharmacology, Department of Neuroscience, Uppsala University, Uppsala, Sweden. | Institute for Translational Medicine and Biotechnology, Sechenov First Moscow State Medical University, Moscow, Russia.
Greiner Russell
Department of Computing Science, University of Alberta, Edmonton, AB T6G 2E8, Canada.
Gautam Vasuk
Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada.
References (42)
42 references, click to expand
  1. CEU Mass Mediator 3.0: A Metabolite Annotation Tool.
    J Proteome Res. 2019 Feb 1;18(2):797-802 PMID: 30574788
  2. Predicting Density Functional Theory-Quality Nuclear Magnetic Resonance Chemical Shifts via Δ-Machine Learning.
    J Chem Theory Comput. 2021 Feb 9;17(2):826-840 PMID: 33428408
  3. BioMagResBank.
    Nucleic Acids Res. 2008 Jan;36(Database issue):D402-8 PMID: 17984079
  4. The MetaCyc database of metabolic pathways and enzymes - a 2019 update.
    Nucleic Acids Res. 2020 Jan 8;48(D1):D445-D453 PMID: 31586394
  5. Predicting Ion Mobility Collision Cross-Sections Using a Deep Neural Network: DeepCCS.
    Anal Chem. 2019 Apr 16;91(8):5191-5199 PMID: 30932474
  6. Identification of endogenous acyl amino acids based on a targeted lipidomics approach.
    J Lipid Res. 2010 Jan;51(1):112-9 PMID: 19584404
  7. Acylcarnitines: Nomenclature, Biomarkers, Therapeutic Potential, Drug Targets, and Clinical Trials.
    Pharmacol Rev. 2022 Jul;74(3):506-551 PMID: 35710135
  8. Computational Prediction of Electron Ionization Mass Spectra to Assist in GC/MS Compound Identification.
    Anal Chem. 2016 Aug 2;88(15):7689-97 PMID: 27381172
  9. nmrML: A Community Supported Open Data Standard for the Description, Storage, and Exchange of NMR Data.
    Anal Chem. 2018 Jan 2;90(1):649-656 PMID: 29035042
  10. MarkerDB: an online database of molecular biomarkers.
    Nucleic Acids Res. 2021 Jan 8;49(D1):D1259-D1267 PMID: 33245771
  11. Using MetaboAnalyst 4.0 for Comprehensive and Integrative Metabolomics Data Analysis.
    Curr Protoc Bioinformatics. 2019 Dec;68(1):e86 PMID: 31756036
  12. Deep Learning to Generate in Silico Chemical Property Libraries and Candidate Molecules for Small Molecule Identification in Complex Samples.
    Anal Chem. 2020 Jan 21;92(2):1720-1729 PMID: 31661259
  13. METLIN: A Tandem Mass Spectral Library of Standards.
    Methods Mol Biol. 2020;2104:149-163 PMID: 31953817
  14. Predicting Kováts Retention Indices Using Graph Neural Networks.
    J Chromatogr A. 2021 Jun 7;1646:462100 PMID: 33892256
  15. A review on human fecal metabolomics: Methods, applications and the human fecal metabolome database.
    Anal Chim Acta. 2018 Nov 7;1030:1-24 PMID: 30032758
  16. Generating the Blood Exposome Database Using a Comprehensive Text Mining and Database Fusion Approach.
    Environ Health Perspect. 2019 Sep;127(9):97008 PMID: 31557052
  17. The FAIR Guiding Principles for scientific data management and stewardship.
    Sci Data. 2016 Mar 15;3:160018 PMID: 26978244
  18. NMRShiftDB -- compound identification and structure elucidation support through a free community-built web database.
    Phytochemistry. 2004 Oct;65(19):2711-7 PMID: 15464159
  19. SPLASH, a hashed identifier for mass spectra.
    Nat Biotechnol. 2016 Nov 8;34(11):1099-1101 PMID: 27824832
  20. HMDB: the Human Metabolome Database.
    Nucleic Acids Res. 2007 Jan;35(Database issue):D521-6 PMID: 17202168
  21. ClassyFire: automated chemical classification with a comprehensive, computable taxonomy.
    J Cheminform. 2016 Nov 4;8:61 PMID: 27867422
  22. KEGG: new perspectives on genomes, pathways, diseases and drugs.
    Nucleic Acids Res. 2017 Jan 4;45(D1):D353-D361 PMID: 27899662
  23. HMDB 4.0: the human metabolome database for 2018.
    Nucleic Acids Res. 2018 Jan 4;46(D1):D608-D617 PMID: 29140435
  24. The reactome pathway knowledgebase.
    Nucleic Acids Res. 2020 Jan 8;48(D1):D498-D503 PMID: 31691815
  25. HMDB: a knowledgebase for the human metabolome.
    Nucleic Acids Res. 2009 Jan;37(Database issue):D603-10 PMID: 18953024
  26. Ion mobility collision cross-section atlas for known and unknown metabolite annotation in untargeted metabolomics.
    Nat Commun. 2020 Aug 28;11(1):4334 PMID: 32859911
  27. A Web Tool for Generating High Quality Machine-readable Biological Pathways.
    J Vis Exp. 2017 Feb 8;(120): PMID: 28287524
  28. Comparative dietary sulfated metabolome analysis reveals unknown metabolic interactions of the gut microbiome and the human host.
    Free Radic Biol Med. 2020 Nov 20;160:745-754 PMID: 32927015
  29. Illuminating the dark matter in metabolomics.
    Proc Natl Acad Sci U S A. 2015 Oct 13;112(41):12549-50 PMID: 26430243
  30. BioTransformer: a comprehensive computational tool for small molecule metabolism prediction and metabolite identification.
    J Cheminform. 2019 Jan 5;11(1):2 PMID: 30612223
  31. Spinach--a software library for simulation of spin dynamics in large spin systems.
    J Magn Reson. 2011 Feb;208(2):179-94 PMID: 21169043
  32. Prediction of 1H NMR chemical shifts using neural networks.
    Anal Chem. 2002 Jan 1;74(1):80-90 PMID: 11795822
  33. mzML: a single, unifying data format for mass spectrometer output.
    Proteomics. 2008 Jul;8(14):2776-7 PMID: 18655045
  34. PathBank: a comprehensive pathway database for model organisms.
    Nucleic Acids Res. 2020 Jan 8;48(D1):D470-D478 PMID: 31602464
  35. HMDB 3.0--The Human Metabolome Database in 2013.
    Nucleic Acids Res. 2013 Jan;41(Database issue):D801-7 PMID: 23161693
  36. Global chemical effects of the microbiome include new bile-acid conjugations.
    Nature. 2020 Mar;579(7797):123-129 PMID: 32103176
  37. Metabolomic and Lipidomic Profiling of Bone Marrow Plasma Differentiates Patients with Monoclonal Gammopathy of Undetermined Significance from Multiple Myeloma.
    Sci Rep. 2020 Jun 24;10(1):10250 PMID: 32581232
  38. The Urinary Metabolome of Healthy Newborns.
    Metabolites. 2020 Apr 23;10(4): PMID: 32340350
  39. The Gene Ontology Resource: 20 years and still GOing strong.
    Nucleic Acids Res. 2019 Jan 8;47(D1):D330-D338 PMID: 30395331
  40. CFM-ID 4.0: More Accurate ESI-MS/MS Spectral Prediction and Compound Identification.
    Anal Chem. 2021 Aug 31;93(34):11692-11700 PMID: 34403256
  41. Evaluation of lipid quantification accuracy using HILIC and RPLC MS on the example of NIST® SRM® 1950 metabolites in human plasma.
    Anal Bioanal Chem. 2020 Jun;412(15):3573-3584 PMID: 32240327
  42. DrugBank 5.0: a major update to the DrugBank database for 2018.
    Nucleic Acids Res. 2018 Jan 4;46(D1):D1074-D1082 PMID: 29126136
Article Info
Journal
Nucleic acids research
Abbr.
Nucleic Acids Res
ISSN
1362-4962
DOI
10.1093/nar/gkab1062
Published
2022-00-07
Pages
D622-D631
Language
English
Region
England
NLM ID
0411011
PMCID
PMC8728138
Subset
IM
Grants
CIHR · Canada
External Links
PubMed source DOI: 10.1093/nar/gkab1062 PMC Full Text View journal details
Analysis Services
Analysis Services

Contact

No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong

Qilu Normal University · Genelibs Bioinformatics Lab

750 Shunhua Rd, Jinan

2F, Bldg F, University Science Park

Tel: 0531-88819269

WeChat Official Account

Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.


Business Email

E-mail: [email protected]

Copyright © 2026.Genelibs Jinan Honghui Biotechnology Co., Ltd. 鲁ICP备20007159号-2