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Release 5.0 - January 2022

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.

Release 4.0 - January, 2018

HMDB 4.0 represents the most significant upgrade to the database in its history. For instance, the number of fully annotated metabolites has increased by nearly threefold, the number of experimental spectra has grown by almost fourfold and the number of illustrated metabolic pathways has grown by a factor of almost 60. Significant improvements have also been made to the HMDB’s chemical taxonomy, chemical ontology, spectral viewing, and spectral/text searching tools. A great deal of brand new data has also been added to HMDB 4.0. This includes large quantities of predicted MS/MS and GC–MS reference spectral data as well as predicted (physiologically feasible) metabolite structures to facilitate novel metabolite identification. Additional information on metabolite-SNP interactions and the influence of drugs on metabolite levels (pharmacometabolomics) has also been added. Many other important improvements in the content, the interface, and the performance of the HMDB website have been made and these should greatly enhance its ease of use and its potential applications in nutrition, biochemistry, clinical chemistry, clinical genetics, medicine, and metabolomics science.

The substantial expansion of annotated metabolites in HMDB 4.0 has necessitated an important change to the HMDB’s original 5-digit accession numbers. Since its inception, the HMDB has used unique accession numbers consisting of a 4-letter prefix (HMDB) and a 5-number suffix. With the release of HMDB 4.0, the 5-digit accession numbers have had to be adjusted to a 7-digit suffix to maintain consistency. This has been accomplished by appending two zeroes after the 4-letter prefix and before each 5-number suffix (e.g. HMDB00001 becomes HMDB0000001). In order to minimize disruption in dependent applications, the original 5-digit accession numbers have become secondary accession numbers to their 7-digit counterparts. This ensures that access to metabolite entries via their URLs is preserved.

Release 3.0 - September, 2012

Version 3.0 of the HMDB is has been significantly expanded and enhanced over the 2009 release (version 2.0). In particular, the number of annotated metabolite entries has grown from 6500 to more than 37,166. This enormous expansion is a result of the inclusion of both “Confirmed” metabolites (those with measured concentrations or experimental confirmation of their existence) and “Expected” metabolites (those for which biochemical pathways are known or human intake/exposure is frequent but the compound has yet to be detected in the body). The latest release also has greatly increased the number of metabolites with biofluid or tissue concentration data, the number of compounds with reference spectra and the number of data fields per entry. In addition to this expansion in data quantity, new database visualization tools and new data content has been added or enhanced. These include better spectral viewing tools, more powerful chemical substructure searches, an improved chemical taxonomy and better, more interactive pathway maps.

Release 2.5 - August 1, 2009

Version 2.5 of the HMDB represents an evolution in the richness and depth of the data available in the HMDB. In addition, it includes several enhancements and refinements to the search and visualization tools available on the website. The following table provides a summary of the major changes and enhancements in version 2.5.

Database feature/content status HMDB Version 1.0 HMDB Version 2.0 HMDB Version 2.5
Number of metabolites 2180 6826 7982
Number of unique metabolite synonyms 27700 43882 69287
Number of compounds with disease links 862 1002 1064
Number of compounds with biofluid or tissue concentration data 883 4413 4857
Number of compounds with urine concentration data 231 472 782
Number of compounds with serum concentration data 174 3976 4418
Number of compounds with cerebrospinal fluid concentration data 47 360 363
Number of compounds with experimental reference 13C NMR spectra 380 784 899
Number of compounds with experimental reference 1H NMR spectra 385 792 905
Number of compounds with reference MS-MS spectra 390 799 2654
Number of compounds with reference GC-MS spectra 0 279 318
Number of human-specific pathway maps 26 58 71
Number of compounds in the Human Metabolome Library (HML) 607 920 1016
Number of HMDB data fields 91 102 111
Pathway search/browse capability No Yes Enhanced
Disease search/browse capability No Yes Enhanced
Chemical class search/browse capability No Yes Enhanced
Chemical substructure search capability No Yes Enhanced
Biofluid search/sort tools No Yes Enhanced
Advanced (multipeak or multicompound) NMR search No Yes Enhanced
Advanced (multipeak or multicompound) MS-MS search No Yes Enhanced
Advanced (retention index or MS peak) GC-MS search No Yes Enhanced

Release 2.0 - January 1, 2009

Release 1.0 - January 1, 2006