HMDB: a knowledgebase for the human metabolome

By David S. Wishart, Craig Knox, Anchi Guo, Roman Eisner, Nelson Young, Bijaya Gautam, D. Hau, Nick Psychogios, Edison Dong, Souhaila Bouatra and 28 more. 2008

1,846 citations recorded by the source corpus.

The Human Metabolome Database (HMDB, http://www.hmdb.ca) is a richly annotated resource that is designed to address the broad needs of biochemists, clinical chemists, physicians, medical geneticists, nutritionists and members of the metabolomics community. Since its first release in 2007, the HMDB has been used to facilitate the research for nearly 100 published studies in metabolomics, clinical biochemistry and systems biology. The most recent release of HMDB (version 2.0) has been significantly expanded and enhanced over the previous release (version 1.0). In particular, the number of fully annotated metabolite entries has grown from 2180 to more than 6800 (a 300% increase), while the number of metabolites with biofluid or tissue concentration data has grown by a factor of five (from 883 to 4413). Similarly, the number of purified compounds with reference to NMR, LC-MS and GC-MS spectra has more than doubled (from 380 to more than 790 compounds). In addition to this significant expansion in database size, many new database searching tools and new data content has been added or enhanced. These include better algorithms for spectral searching and matching, more powerful chemical substructure searches, faster text searching software, as well as dedicated pathway searching tools and customized, clickable metabolic maps. Changes to the user-interface have also been implemented to accommodate future expansion and to make database navigation much easier. These improvements should make the HMDB much more useful to a much wider community of users.

Subfields: Molecular Biology

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Citations in the corpus

MetaboAnalyst 2.0—a comprehensive server for metabolomic data analysis (2012, background): “This name standardization function is able to recognize common compound names and synonyms and map them to speciﬁc HMDB, KEGG, PubChem and ChEBI identiﬁers which are, in turn, linked to MetaboAnalyst’s extensive metabolite knowledgebases.”
Skyline for Small Molecules: A Unifying Software Package for Quantitative Metabolomics (2020, background): “…of small molecules, such as Metlin (http://metlin.scripps.edu/) 47, 48 , MassBank 49 , the Human Metabolome Database (HMDB, http://www.hmdb.ca/) 50, 51 and the National Institute of Standards and Technology Database (NIST https://chemdata.nist.gov/); similar workflows are already available for…”
HMDB 5.0: the Human Metabolome Database for 2022 (2021, background): “0, which was released in 2009, included more spectral data and much more literaturederived physiological and biochemical data for 6408 human metabolites (7).”
Ambiguity of non-systematic chemical identifiers within and between small-molecule databases (2015, background): “Databases We selected eight well-known chemical databases covering a wide range of bioactive compounds: Chemical Entities of Biological Interest (ChEBI) [18], ChEMBL [19], ChemSpider [20], DrugBank [21], the Human Metabolome Database (HMDB) [9, 22], the NCGC Pharmaceutical Collection (NPC) [23], Pub”
Virtual Screening with AutoDock: Theory and Practice (2010, background): “Other libraries are targeted for specific needs, such as the lead-like compounds [25], nutraceuticals [26], natural products [27] and metabolome [28] libraries, which bring together compounds that might be expected to have good biological properties.”
Somatic oxidative bioenergetics transitions into pluripotency-dependent glycolysis to facilitate nuclear reprogramming (2011, methodology): “Identities of (1)H NMR spectra peaks obtained on a Bruker Ultrashield 700 MHz spectrometer with a zgpr water suppression presaturation pulse were assigned by comparison to reference values for chemical shift and multiplicity, and confirmed by comparison to spectra of pure compounds in the Human Meta”
DrugBank 3.0: a comprehensive resource for ‘Omics’ research on drugs (2010, background): “These new links include numerous compound-specific, spectral, pathway and disease databases such as ChemSpider (11), HMDB (14), MMCD (23), SMPDB (15) and OMIM (24).”
Predicting Network Activity from High Throughput Metabolomics (2013, background): “For example, a number of metabolites in metabolomics databases [36,65,66] are not in any of these metabolic models.”
HMDB 3.0—The Human Metabolome Database in 2013 (2012, methodology): “This information is released publicly through the Human Metabolome Database or HMDB (3,4).”
The Human Urine Metabolome (2013, methodology): “This corresponds to less than 1% of the known human metabolome [15], [16].”
Competitive fragmentation modeling of ESI-MS/MS spectra for putative metabolite identification (2013, background): “However, the restriction to a list of candidate molecules means that this approach still falls short of de novo identification of ’unknown unknowns’ (Wishart et al. 2009), i.e. we cannot identify molecules not in the list.”
Structure and dynamics of molecular networks: A novel paradigm of drug discovery: A comprehensive review (2012, background): “…et al., 2005 SMPDB Small Molecule (e.g., drug) Pathway Database http://smpdb.ca Frolkis et al., 2010 HMDB Human Metabolome Database http://hmdb.ca Wishart et al., 2009 BRENDA Comprehensive enzyme data resource http://brenda-enzymes.info Scheer et al., 2011 YeastNet Yeast metabolic network…”
HMDB 4.0: the human metabolome database for 2018 (2017, background): “Details regarding the HMDB’s overall layout, navigation structure, data sources, curation protocols, data management system, and quality assurance criteria have been described previously (14,15).”