Human Metabolome Database-Overview
August 5, 2019The Human Metabolome Database or HMDB (www.hmdb.ca) is a piece of web-enabled metabolomic information containing comprehensive information regarding human metabolites in conjunction with their biological roles, physiological concentrations, sickness associations, chemical reactions, metabolic pathways, and reference spectra. The first release in 2007, the HMDB is currently thought of the quality metabolomic resource for human metabolic studies. Over the past decade the HMDB has continued to grow and evolve in response to rising desires for metabolomics researchers and continued changes in internet standards. This year’s update, HMDB 4.0, represents the foremost vital upgrade to the information in its history. As an example, the quantity of absolutely annotated metabolites has enlarged by nearly threefold, the quantity of experimental spectra has fully grown by almost fourfold and therefore the number of illustrated metabolic pathways has grown by an element of virtually sixty. Vital enhancements have conjointly been created to the HMDB’s chemical taxonomy, chemical metaphysics, spectral viewing, and spectral/text looking tools. An excellent deal of name new knowledge has conjointly been further to HMDB 4.0. This includes giant quantities of foretold MS/MS and GC–MS reference spectral knowledge furthermore as predicted (physiologically feasible) matter structures to facilitate novel metabolite identification. Extra data on matter-SNP interactions and the influence of medication on metabolite levels (pharmacometabolomics) has also been further. Several different vital enhancements within the content, the interface, and therefore the performance of the HMDB web site is created and these ought to greatly enhance its easy use and its potential applications in nutrition, organic chemistry, clinical chemistry, clinical biological science, medicine, and metabolomics science.
FEATURES
The Human Metabolomes Database (HMDB) contains files for more than 2180 endogenous metabolites with records gathered from thousands of books, journal articles and digital database. In addition to its comprehensive literature-derived data, the HMDB also consists of a vast collection of experimental metabolite concentration information compiled from hundreds of mass spectra (MS) and Nuclear Magnetic resonance (NMR) metabolomic analyses performed on urine, blood and cerebrospinal fluid samples Therefore, it is very useful for the researchers as it can save the energy and time of the researchers to find and gather information about human metabolomics.
There are several features available at HMDB and these features organized by various categories that can help the researchers to find information more easily.
Figure 1 : Homepage of HMDB
The first feature is the browse tab. In this browse tab , it contains several menu options that we can choose such as metabolites, diseases,pathways, biospecimens, classes, proteins, reactions, metabolite library (HML), BMI Metabolomics , Age Metabolomics , Gender Metabolomics ,Geno Metabolomics ,Pharmaco Metabolomics and Diurnal Metabolomics. The researcher can browse information that they need based on their categories. For example if the researcher wants to browse the metabolites categories, just click the metabolites and it will redirect the researcher to the browsing metabolites page. In the metabolites page, there are four filters available. These four filters are metabolites status, bio specimen, origin and subcellular location. With the existence of this filter, it can help researchers to find information more accurately. In another category, it contains the same filter that researchers can use to find information in more detail based on the category they want
Figure 2 : browsing metabolites page.
The second feature is the search tab. There are several different menu options available in the search tab such as ChemQuery Structure Search,Molecular Weight Search,Text Query,Sequence Search,Advanced Search,LC-MS Search,LC-MS/MS Search,GC-MS Search,1D NMR Search,2D NMR Search and LC-MS CMM Search (New). This feature helps the researcher to do a search by clicking the search tab. For example, the researchers can find metabolites from their various molecular weight by clicking the tab of the molecular weight search and it will redirect the researchers to the molecular weight search page. After that, the researchers need to enter the amount of range search of molecular weight they want on the box provided and click search. The researcher can find either molecular weight/average mass or monoisotopic mass in this molecular weight search page. Besides that, the researcher also can set the status they want for the molecular weight search. Click the button search to find metabolites based on the range search of molecular weight and status after done entering the amount of range search of molecular weight and status. The metabolites will appears based on the amount and the status the researcher wants.
Figure 3: Molecular weight search page with the amount of range search molecular weight and selected status
Figure 3.1: The result of metabolites searching
The third feature is download tab. In the download tab, the reaschers can choose to download any of dataset provided such as the researchers can download protein/ gene sequences in FASTA format, structure in SDF format or metabolites or protein data in XML format. The researchers can download this data set based on the version provided. There are four versions available which is version 1.0, 2.5, 3.6 and 4.0 but the researchers are highly recommended to download the latest version as it updates and contain more information about metabolites.
Figure 4 : The download tab page of version 4.0
Forth feature is about tab. In the about tab, the researcher will find the information and guides on how to use the Human Metabolome Database (HMDB), release notes , a link to the data source used in HMDB and more about Human Metabolome Project . Last but not least, contact us tab feature. The contact us tab provide contact information and a nice feedback information form that the researcher can fill in to give feedback about the Human Metabolome Database (HMDB).
