Journal of Inherited Metabolic Disease

, Volume 41, Issue 3, pp 329–336 | Cite as

The role of the Human Metabolome Database in inborn errors of metabolism

  • Rupasri Mandal
  • Danuta Chamot
  • David S. Wishart


Metabolomics holds considerable promise to advance our understanding of human disease, including our understanding of inborn errors of metabolism (IEM). The application of metabolomics in IEM research has already led to the discovery of several novel IEMs and the identification of novel IEM biomarkers. However, with hundreds of known IEMs and more than 700 associated IEM metabolites, it is becoming increasingly challenging for clinical researchers to keep track of IEMs, their associated metabolites, and their corresponding metabolic mechanisms. Furthermore, when using metabolomics to assist in IEM biomarker discovery or even in IEM diagnosis, it is becoming much more difficult to properly identify metabolites from the complex NMR and MS spectra collected from IEM patients. To that end, comprehensive, open access metabolite databases that provide up-to-date referential information about metabolites, metabolic pathways, normal/abnormal metabolite concentrations, and reference NMR or MS spectra for compound identification are essential. Over the last few years, a number of compound databases, including the Human Metabolome Database (HMDB), have been developed to address these challenges. First described in 2007, the HMDB is now the world’s largest and most comprehensive metabolomic resource for human metabolic studies. The latest release of the HMDB contains 114,100 metabolite entries (with 247 being relevant to IEMs), thousands of metabolite concentrations (with 600 being relevant to IEMs), and ~33,000 metabolic and disease-associated pathways (with 202 being relevant to IEMs). Here we provide a summary of the HMDB and offer some guidance on how it can be used in metabolomic studies of IEMs.


Databases metabolomics Human Metabolome Database bioinformatics inborn errors of metabolism 



Funding for the HMDB and many of the programs described in this review has been provided by Genome Canada, Genome Alberta, The Canadian Institutes of Health Research, Alberta Innovates Health Solutions, and The Canada Foundation for Innovation.

Compliance with ethical standards

Conflict of interest

Rupasri Mandal, Danuta Chamot, David S. Wishart declare that they have no conflict of interest.

Informed consent and animals rights

This article does not contain any studies with human or animal subjects performed by any of the authors.


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Copyright information

© SSIEM 2018

Authors and Affiliations

  1. 1.Departments of Biological SciencesUniversity of AlbertaEdmontonCanada
  2. 2.Computing ScienceUniversity of AlbertaEdmontonCanada
  3. 3.National Institute for NanotechnologyEdmontonCanada

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