Мы используем файлы cookie.
Продолжая использовать сайт, вы даете свое согласие на работу с этими файлами.
Biological database
Human Metabolome Database
Другие языки:

    Human Metabolome Database

    Подписчиков: 0, рейтинг: 0
    This article is about the Human Metabolome Database (HMDB.ca). For the Historical Marker Database (HMdb.org), see Historical Marker Database.
    Human Metabolome Database
    Human Metabolome Database logo.png
    Content
    Description Metabolomics database
    Data types
    captured    		 Human metabolite structures, metabolite descriptions, metabolite reactions, metabolite enzymes and transporters, human enzyme and transporter sequences, human metabolic pathways, normal and abnormal metabolite concentrations in humans, associated diseases, chemical properties, nomenclature, synonyms, chemical taxonomy, metabolite NMR spectra, metabolite GC-MS spectra, metabolite LC-MS spectra
    Contact
    Research center University of Alberta and The Metabolomics Innovation Centre
    Laboratory David S. Wishart
    Primary citation HMDB: the Human Metabolome Database.
    Access
    Website http://www.hmdb.ca
    Download URL http://www.hmdb.ca/downloads
    Miscellaneous
    Data release
    frequency    		 Every 2 years with monthly corrections and updates
    Curation policy Manually curated

    The Human Metabolome Database (HMDB) is a comprehensive, high-quality, freely accessible, online database of small molecule metabolites found in the human body. It bas been created by the Human Metabolome Project funded by Genome Canada and is one of the first dedicated metabolomics databases. The HMDB facilitates human metabolomics research, including the identification and characterization of human metabolites using NMR spectroscopy, GC-MS spectrometry and LC/MS spectrometry. To aid in this discovery process, the HMDB contains three kinds of data: 1) chemical data, 2) clinical data, and 3) molecular biology/biochemistry data (Fig. 1–3). The chemical data includes 41,514 metabolite structures with detailed descriptions along with nearly 10,000 NMR, GC-MS and LC/MS spectra.

    The clinical data includes information on >10,000 metabolite-biofluid concentrations and metabolite concentration information on more than 600 different human diseases. The biochemical data includes 5,688 protein (and DNA) sequences and more than 5,000 biochemical reactions that are linked to these metabolite entries. Each metabolite entry in the HMDB contains more than 110 data fields with 2/3 of the information being devoted to chemical/clinical data and the other 1/3 devoted to enzymatic or biochemical data. Many data fields are hyperlinked to other databases (KEGG, MetaCyc, PubChem, Protein Data Bank, ChEBI, Swiss-Prot, and GenBank) and a variety of structure and pathway viewing applets. The HMDB database supports extensive text, sequence, spectral, chemical structure and relational query searches. It has been widely used in metabolomics, clinical chemistry, biomarker discovery and general biochemistry education.

    Four additional databases, DrugBank, T3DB, SMPDB and FooDB are also part of the HMDB suite of databases. DrugBank contains equivalent information on ~1,600 drug and drug metabolites, T3DB contains information on 3,100 common toxins and environmental pollutants, SMPDB contains pathway diagrams for 700 human metabolic and disease pathways, while FooDB contains equivalent information on ~28,000 food components and food additives.

    Version history

    The first version of HMDB was released on January 1, 2007, followed by two subsequent versions on January 1, 2009 (version 2.0), August 1, 2009 (version 2.5), September 18, 2012 (version 3.0) and Jan. 1, 2013 (version 3.5), 2017 (version 4.0). Details for each of the major HMDB versions (up to version 4.0) is provided in Table 1.

    Table 1. Content comparison of HMDB versions
    Database Feature or Content Status HMDB (v1.0) HMDB (v2.0) HMDB (v3.0) HMDB (v4.0)
    Number of metabolites 2,180 6,408 37,170 114,100
    Number of unique metabolite synonyms 27,700 43,882 152,364 −
    Number of compounds with disease links 862 1,002 3,948 22,605
    Number of compounds with biofluid or tissue concentration data 883 4,413 6,796 −
    Number of compounds with chemical synthesis references 220 1,647 8,863 72,604
    Number of compounds with experimental reference 1H and or 13C NMR spectra 385 792 1,054 2,801
    Number of compounds with reference MS/MS spectra 390 799 1,249 1,544
    Number of compounds with reference GC-MS reference data 0 279 884 7,418
    Number of human-specific pathway maps 26 58 442 −
    Number of compounds in Human Metabolome Library 607 920 1,031 −
    Number of HMDB data fields 91 102 114 130
    'Number of predicted molecular properties 2 2 10 −

    Scope and access

    All data in HMDB is non-proprietary or is derived from a non-proprietary source. It is freely accessible and available to anyone. In addition, nearly every data item is fully traceable and explicitly referenced to the original source. HMDB data is available through a public web interface and downloads.

    See also


    Новое сообщение