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Draft:Human Metabolome Project

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  • Comment: In preparing this draft, I disclose that AI assistance was used as follows: No AI was used to create this article. PaperTempo (talk) 16:53, 26 October 2026 (UTC)
  • Comment: Neutrality issues are still there. Further, I'm not sure this has standalone notability from Human Metabolome Database and likely any useful info from this should just be incorporated there. Sulfurboy (talk) 03:16, 26 July 2026 (UTC)
  • Comment: Needs to be rewritten from scratch without the use of LLMs. Helpful Raccoon (talk) 00:06, 9 June 2026 (UTC)


Human Metabolome Project

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The Human Metabolome Project (HMP) is a Canadian initiative aimed at identifying and quantifying all known and unknown metabolites in human tissues and biofluids. Metabolites are small molecules produced, consumed or found in living organisms. The collection of all metabolites in a given cell, tissue or organism is known as the metabolome.

The HMP was started at the University of Alberta under the direction of Dr. David Wishart. Since its inception in January 2005, the HMP has built and continues to develop and maintain databases such as the Human Metabolome Database or HMDB[1] and webservers such as MetaboAnaylst.[2] These HMP resources were developed to help identify metabolites and to facilitate metabolomic applications in human health.

Background and History

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In 1999, Dr. Wishart published a paper that showed how machine learning could enable automated metabolite identification and quantification from nuclear magnetic resonance (NMR) spectra of a human biofluid.[3] However, at that time, there were no public, centralized databases containing metabolite structures or their corresponding reference spectra. The lack of a centralized metabolomics database meant that automated metabolite identification would be very limited in its scope. To remedy the situation, Wishart obtained funding from Genome Canada to launch the HMP and create the "chemical equivalent of the human genome".[4] The overarching goal was to provide free, open-access tools and infrastructure, similar to those established for genomics and proteomics, to enable high throughput metabolomics studies.[5][6]

Cataloguing Human Metabolites

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The HMP's initial efforts focused on creating a centralized, online, web-based database to help metabolomics researchers, in the same way that GenBank[7] serves genomic researchers and UniProt[8] serves proteomics researchers. Rather than containing gene or protein sequences, this database would contain chemical structures and their corresponding reference NMR or mass spectrometry (MS) spectra to enable metabolite searching and identification.

The database, called the Human Metabolome Database or HMDB, was first released on Jan. 1, 2007. It contained metabolite structures, descriptions, concentrations and spectral data for 2180 human metabolites in various biofluids and tissues. Prior to the HMDB’s appearance, only 690 human metabolites had been catalogued in other databases or data collections.[9] The release of the HMDB led to significant press coverage of the HMP,[4][10] with analogies being made to the HMP’s equivalency to the human genome project.[10][11][12] However, others in the metabolomics community were more skeptical of how useful the HMDB could be.[12][13] Dr. Oliver Fiehn of the University of California-Davis said "HMDB is a good first step," before adding, "It's far from where we have to go."[11] Gary Siuzdak of the Scripps Research Institute was more specific, asserting that he “would be surprised if 2500 [entries] represents even 10%” of the human metabolome.[12]

As metabolomics technologies improved over the years, the HMP was able to significantly expand its annotation efforts and increase its metabolome coverage through successive HMDB updates.[14][15][16][17] As of October 26, 2026, HMDB houses 253,245 metabolites.[18]

Human Biofluid and Excreta Metabolomes

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To complement the work being done on the HMDB, the HMP team began in 2011 to systematically characterize the metabolomes of human biofluids (serum,saliva, and cerebrospinal fluid or CSF) and excreta (urine and feces). This was done to establish clinically useful, biofluid-specific, metabolite reference ranges. It was also done to conduct objective tests on the efficacy of different metabolomics assays and platforms. Using gas chromatography–mass spectrometry (GC-MS), liquid chromatography mass spectrometry (LC-MS), NMR spectroscopy, inductively coupled plasma mass spectrometry (ICP-MS) and comprehensive literature surveys, the HMP team identified and quantified thousands of biofluid-specific metabolites between 2011 and 2018. This included 4,200 compounds in the serum metabolome (in 2011),[19] 2,651 metabolites in the urine metabolome (in 2013),[20] 476 metabolites in the CSF metabolome (in 2012),[21] 1008 compounds in the saliva metabolome (in 2015)[22] and 6700 compounds in the fecal metabolome (in 2018).[23]

Expanded Metabolome Coverage

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As metabolites can originate from both endogenous (within the organism) and exogenous (from food, drugs, microbiota, cosmetics, and environment) sources, the HMP pivoted in 2010 to create additional resources, specifically designed to enable the identification of exogenous compounds that might be found in humans or human biofluids. These resources included DrugBank (a drug compound database),[24] the Toxic Exposure Database or T3DB (a toxic chemical database),[25] FooDB (a database of food chemicals),[26] and the Microbial Metabolome Database or MiMeDB (a database of microbially derived metabolites).[27] As with the HMDB, these databases contain chemical structures, descriptions and reference spectral data designed to facilitate their identification in metabolomic assays. This collection of exogenous chemicals is often called the chemical exposome.[28]

Exogenous chemicals are metabolized differently than endogenous compounds, with many going through phase I, phase II or microbial biotransformations.[29][30] This is done so that they can be more easily excreted from the body. Many products of xenobiotic metabolism or biotransformations are still unknown or poorly characterized. To facilitate the identification of these unknown biotransformed chemicals, the HMP team created BioTransformer.[31][32] This tool uses known chemical reactions combined with machine learning to predict likely biochemical transformations that a starting compound may go through. By applying BioTransformer to known exogenous compounds such as those found in DrugBank, T3DB, FooDB and MiMeDB, it has been possible to generate millions of metabolite structures. Some of these predicted metabolite structures have already been identified in real biological samples[33] and are part of an ongoing effort by the HMP to characterize the “dark metabolome”.[32][34]

Legacy

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Beyond the databases, software and technologies, the HMP also led to the establishment of The Metabolomics Innovation Centre (TMIC[35]), Canada's national metabolomics laboratory, which is headquartered at the University of Alberta. Using advanced technologies, databases and software acquired or developed for the HMP, it supports metabolomics research.

See also

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References

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  1. ↑ Wishart, D. S.; Tzur, D.; Knox, C.; Eisner, R.; Guo, A. C.; Young, N.; Cheng, D.; Jewell, K.; Arndt, D.; Sawhney, S.; Fung, C.; Nikolai, L.; Lewis, M.; Coutouly, M.-A.; Forsythe, I. (2007-01-03). "HMDB: the Human Metabolome Database". Nucleic Acids Research. 35 (Database): D521–D526. doi:10.1093/nar/gkl923. ISSN 0305-1048. PMC 1899095. PMID 17202168.
  2. ↑ Xia, Jianguo; Psychogios, Nick; Young, Nelson; Wishart, David S. (2009). "MetaboAnalyst: a web server for metabolomic data analysis and interpretation". Nucleic Acids Research. 37 (Web Server issue): W652–660. doi:10.1093/nar/gkp356. ISSN 1362-4962. PMC 2703878. PMID 19429898.
  3. ↑ Bamforth, F. J.; Dorian, V.; Vallance, H.; Wishart, D. S. (1999). "Diagnosis of inborn errors of metabolism using 1H NMR spectroscopic analysis of urine". Journal of Inherited Metabolic Disease. 22 (3): 297–301. doi:10.1023/A:1005531432766. ISSN 0141-8955. PMID 10384391.
  4. 1 2 "Alberta scientists map human metabolome chemicals". CBC/Radio-Canada. January 24, 2007. Retrieved July 7, 2026.
  5. ↑ Ph.D, Dr Sanchari Sinha Dutta (2020-02-14). "The Human Metabolome Project". AZoLifeSciences. Retrieved 2026-07-07.
  6. ↑ Villas-Boas, Silas G.; Nielsen, Jens; Smedsgaard, Jorn; Hansen, Michael A. E.; Roessner-Tunali, Ute (2007-02-16). Metabolome Analysis: An Introduction. John Wiley & Sons. ISBN 978-0-471-74344-6.
  7. ↑ Sayers, Eric W.; Cavanaugh, Mark; Frisse, Linda; Pruitt, Kim D.; Schneider, Valerie A.; Underwood, Beverly A.; Yankie, Linda; Karsch-Mizrachi, Ilene (2025-01-06). "GenBank 2025 update". Nucleic Acids Research. 53 (D1): D56–D61. doi:10.1093/nar/gkae1114. ISSN 1362-4962. PMC 11701615. PMID 39558184.
  8. ↑ UniProt Consortium (2015). "UniProt: a hub for protein information". Nucleic Acids Research. 43 (Database issue): D204–212. doi:10.1093/nar/gku989. ISSN 1362-4962. PMC 4384041. PMID 25348405.
  9. ↑ Kanehisa, Minoru (2002). "The KEGG database". Novartis Foundation Symposium. 247: 91–101, discussion 101–103, 119–128, 244–252. ISSN 1528-2511. PMID 12539951.
  10. 1 2 Sinnema, Jodie (January 24, 2007). "Project Deciphers Chemical Recipes for Human Diseases". Edmonton Journal. pp. A3.{{cite news}}: CS1 maint: url-status (link)
  11. 1 2 Scudellari, Megan. "Charting the Human Metabolome | The Scientist". The Scientist. Archived from the original on 2026-10-08. Retrieved 2026-10-19.
  12. 1 2 3 Marshall, Eliot (2007-02-02). "Canadian Group Claims 'Unique' Database". Science. 315 (5812): 583–584. doi:10.1126/science.315.5812.583b. ISSN 0036-8075.
  13. ↑ Pearson, Helen (2007-03-01). "Meet the human metabolome". Nature. 446 (7131): 8–8. doi:10.1038/446008a. ISSN 0028-0836.
  14. ↑ Wishart, David S.; Knox, Craig; Guo, An Chi; Eisner, Roman; Young, Nelson; Gautam, Bijaya; Hau, David D.; Psychogios, Nick; Dong, Edison; Bouatra, Souhaila; Mandal, Rupasri; Sinelnikov, Igor; Xia, Jianguo; Jia, Leslie; Cruz, Joseph A. (2009). "HMDB: a knowledgebase for the human metabolome". Nucleic Acids Research. 37 (Database issue): D603–610. doi:10.1093/nar/gkn810. ISSN 1362-4962. PMC 2686599. PMID 18953024.
  15. ↑ Wishart, David S.; Jewison, Timothy; Guo, An Chi; Wilson, Michael; Knox, Craig; Liu, Yifeng; Djoumbou, Yannick; Mandal, Rupasri; Aziat, Farid; Dong, Edison; Bouatra, Souhaila; Sinelnikov, Igor; Arndt, David; Xia, Jianguo; Liu, Philip (2013). "HMDB 3.0--The Human Metabolome Database in 2013". Nucleic Acids Research. 41 (Database issue): D801–807. doi:10.1093/nar/gks1065. ISSN 1362-4962. PMC 3531200. PMID 23161693.
  16. ↑ Wishart, David S.; Feunang, Yannick Djoumbou; Marcu, Ana; Guo, An Chi; Liang, Kevin; Vázquez-Fresno, Rosa; Sajed, Tanvir; Johnson, Daniel; Li, Carin; Karu, Naama; Sayeeda, Zinat; Lo, Elvis; Assempour, Nazanin; Berjanskii, Mark; Singhal, Sandeep (2018-01-04). "HMDB 4.0: the human metabolome database for 2018". Nucleic Acids Research. 46 (D1): D608–D617. doi:10.1093/nar/gkx1089. ISSN 1362-4962. PMC 5753273. PMID 29140435.
  17. ↑ Wishart, David S.; Guo, AnChi; Oler, Eponine; Wang, Fei; Anjum, Afia; Peters, Harrison; Dizon, Raynard; Sayeeda, Zinat; Tian, Siyang; Lee, Brian L.; Berjanskii, Mark; Mah, Robert; Yamamoto, Mai; Jovel, Juan; Torres-Calzada, Claudia (2022-01-07). "HMDB 5.0: the Human Metabolome Database for 2022". Nucleic Acids Research. 50 (D1): D622–D631. doi:10.1093/nar/gkab1062. ISSN 1362-4962. PMC 8728138. PMID 34986597.
  18. ↑ "Human Metabolome Database". hmdb.ca. Archived from the original on 2026-02-11. Retrieved 2026-10-21.
  19. ↑ Psychogios, Nikolaos; Hau, David D.; Peng, Jun; Guo, An Chi; Mandal, Rupasri; Bouatra, Souhaila; Sinelnikov, Igor; Krishnamurthy, Ramanarayan; Eisner, Roman; Gautam, Bijaya; Young, Nelson; Xia, Jianguo; Knox, Craig; Dong, Edison; Huang, Paul (2011-02-16). "The human serum metabolome". PLOS ONE. 6 (2) e16957. Bibcode:2011PLoSO...616957P. doi:10.1371/journal.pone.0016957. ISSN 1932-6203. PMC 3040193. PMID 21359215.
  20. ↑ Bouatra, Souhaila; Aziat, Farid; Mandal, Rupasri; Guo, An Chi; Wilson, Michael R.; Knox, Craig; Bjorndahl, Trent C.; Krishnamurthy, Ramanarayan; Saleem, Fozia; Liu, Philip; Dame, Zerihun T.; Poelzer, Jenna; Huynh, Jessica; Yallou, Faizath S.; Psychogios, Nick (2013). "The human urine metabolome". PLOS ONE. 8 (9) e73076. Bibcode:2013PLoSO...873076B. doi:10.1371/journal.pone.0073076. ISSN 1932-6203. PMC 3762851. PMID 24023812.
  21. ↑ Mandal, Rupasri; Guo, An Chi; Chaudhary, Kruti K.; Liu, Philip; Yallou, Faizath S.; Dong, Edison; Aziat, Farid; Wishart, David S. (2012-04-30). "Multi-platform characterization of the human cerebrospinal fluid metabolome: a comprehensive and quantitative update". Genome Medicine. 4 (4): 38. doi:10.1186/gm337. ISSN 1756-994X. PMC 3446266. PMID 22546835.
  22. ↑ Dame, Zerihun T.; Aziat, Farid; Mandal, Rupasri; Krishnamurthy, Ram; Bouatra, Souhaila; Borzouie, Shima; Guo, An Chi; Sajed, Tanvir; Deng, Lu; Lin, Hong; Liu, Philip; Dong, Edison; Wishart, David S. (2015). "The human saliva metabolome". Metabolomics. 11 (6): 1864–1883. doi:10.1007/s11306-015-0840-5. ISSN 1573-3882.
  23. ↑ Karu, Naama; Deng, Lu; Slae, Mordechai; Guo, An Chi; Sajed, Tanvir; Huynh, Hien; Wine, Eytan; Wishart, David S. (2018-11-07). "A review on human fecal metabolomics: Methods, applications and the human fecal metabolome database". Analytica Chimica Acta. 1030: 1–24. Bibcode:2018AcAC.1030....1K. doi:10.1016/j.aca.2018.05.031. ISSN 1873-4324. PMID 30032758.
  24. ↑ Knox, Craig; Wilson, Mike; Klinger, Christen M.; Franklin, Mark; Oler, Eponine; Wilson, Alex; Pon, Allison; Cox, Jordan; Chin, Na Eun Lucy; Strawbridge, Seth A.; Garcia-Patino, Marysol; Kruger, Ray; Sivakumaran, Aadhavya; Sanford, Selena; Doshi, Rahil (2024-01-05). "DrugBank 6.0: the DrugBank Knowledgebase for 2024". Nucleic Acids Research. 52 (D1): D1265–D1275. doi:10.1093/nar/gkad976. ISSN 1362-4962. PMC 10767804. PMID 37953279.
  25. ↑ Wishart, David; Arndt, David; Pon, Allison; Sajed, Tanvir; Guo, An Chi; Djoumbou, Yannick; Knox, Craig; Wilson, Michael; Liang, Yongjie; Grant, Jason; Liu, Yifeng; Goldansaz, Seyed Ali; Rappaport, Stephen M. (2015). "T3DB: the toxic exposome database". Nucleic Acids Research. 43 (Database issue): D928–934. doi:10.1093/nar/gku1004. ISSN 1362-4962. PMC 4383875. PMID 25378312.
  26. ↑ Wishart, David S. (2024-09-01). "Knowledge translation and knowledge mobilization from the FoodBAll project". Applied Physiology, Nutrition, and Metabolism = Physiologie Appliquee, Nutrition et Metabolisme. 49 (9): 1279–1285. doi:10.1139/apnm-2023-0573. ISSN 1715-5320. PMID 39011902.
  27. ↑ Wishart, David S.; Oler, Eponine; Peters, Harrison; Guo, AnChi; Girod, Sagan; Han, Scott; Saha, Sukanta; Lui, Vicki W.; LeVatte, Marcia; Gautam, Vasuk; Kaddurah-Daouk, Rima; Karu, Naama (2023-01-06). "MiMeDB: the Human Microbial Metabolome Database". Nucleic Acids Research. 51 (D1): D611–D620. doi:10.1093/nar/gkac868. ISSN 1362-4962. PMC 9825614. PMID 36215042.
  28. ↑ David, Arthur; Lennon, Sarah; Mercier, Fabien; Bouhlel, Jihene; Chaker, Jade; Appenzeller, Brice M. R.; Audouze, Karine; Ayeni, Kolawole I.; Bailly-Chouriberry, Ludovic; El Balkhi, Souleiman; Barouki, Robert; Belova, Lidia; Benmarhnia, Tarik; Bonnefille, Bénilde; Bessonneau, Vincent (2026). "Mapping the human chemical exposome for public health". Nature Medicine. 32 (8). Nature Publishing Group: 2708–2710. doi:10.1038/s41591-026-04289-7. ISSN 1546-170X.
  29. ↑ Testa, Bernard; Pedretti, Alessandro; Vistoli, Giulio (2012). "Reactions and enzymes in the metabolism of drugs and other xenobiotics". Drug Discovery Today. 17 (11–12): 549–560. doi:10.1016/j.drudis.2012.01.017.
  30. ↑ Koppel, Nitzan; Maini Rekdal, Vayu; Balskus, Emily P. (2017-06-23). "Chemical transformation of xenobiotics by the human gut microbiota". Science. 356 (6344). doi:10.1126/science.aag2770. ISSN 0036-8075. PMC 5534341. PMID 28642381.
  31. ↑ Wishart, David S; Tian, Siyang; Allen, Dana; Oler, Eponine; Peters, Harrison; Lui, Vicki W; Gautam, Vasuk; Djoumbou-Feunang, Yannick; Greiner, Russell; Metz, Thomas O (2022-07-05). "BioTransformer 3.0—a web server for accurately predicting metabolic transformation products". Nucleic Acids Research. 50 (W1): W115–W123. doi:10.1093/nar/gkac313. ISSN 0305-1048. PMC 9252798. PMID 35536252.
  32. 1 2 Outreach, Research (2019-09-26). "Using metabolomics and artificial intelligence to explore the universe of the dark metabolome". Research Outreach. Retrieved 2026-10-21.
  33. ↑ Qiang, Hantao; Wang, Fei; Lu, Wenyun; Xing, Xi; Kim, Hahn; Mérette, Sandrine A. M.; Ayres, Lucas B.; Oler, Eponine; AbuSalim, Jenna E.; Roichman, Asael; Neinast, Michael; Cordova, Ricardo A.; Lee, Won Dong; Herbst, Ehud; Gupta, Vishu (2026). "Language model-guided anticipation and discovery of mammalian metabolites". Nature. 651 (8104). Nature Publishing Group: 211–220. doi:10.1038/s41586-025-09969-x. ISSN 1476-4687.
  34. ↑ Mitchell Crow, James (2021-11-18). "Canada's scientists are elucidating the dark metabolome". Nature. 599 (7885): S14–S15. doi:10.1038/d41586-021-03062-9. ISSN 0028-0836.
  35. ↑ "Home". The Metabolomics Innovation Centre. Retrieved 2026-10-21.
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