FooDB (The Food Database) (version 1.0) is a freely available, open-access database containing chemical composition data of macronutrient, micronutrients as well as extensive data on flavor and aroma constituents, on common, unprocessed food.
FooDB is the world’s largest and most comprehensive resource on food constituents, chemistry and biology. The database contains information of about 28,000 chemicals found in around 1,000 raw or unprocessed food products. Each chemical entry in the FooDB contains more than 100 separate data fields covering detailed compositional, biochemical and physiological information (obtained from the literature). This includes data on the compound’s nomenclature, its description, information on its structure, chemical class, physico-chemical data, food source(s), color, aroma, taste, physiological effect, presumptive health effects (from published studies), and concentrations in foods.
Tutorial - How to use: Users are able to search FooDB by food source, compound name, or other descriptors. Also users are able to view the content of FooDB from the Food Browse (listing foods by their chemical composition) or the Compound Browse (listing chemicals by their food sources), Nutrients Browse (listing the different Nutrients in a food) or Contents Browse (listing by the concentrations of compounds in a particular food). It also can be used ‘ChemQuery Search’ to search by molecular structure, ‘Advanced Search’ for customization the criteria to look for the compounds, or the Spectra Search option, an extremely useful choice for searching compounds’ masses for MS as well as chemical shifts (1H- 13C for 1D) and (TOCSY and HSQC for 2D) for NMR, in the compounds’ identification process.
Given the complexity of food constituents, the diversity of known food metabolites, and the rapidly growing number of studies on the food metabolome, it is becoming clear that well-curated databases are of utmost importance to keep track of this information. These “omic era” databases are being developed to help researchers understand the origins and fate of many food metabolites.
|Exposome-Explorer is the first database dedicated to biomarkers of exposure to environmental risk factors for diseases. It contains detailed information on the nature of biomarkers, populations and subjects in which biomarkers have been measured, samples analysed, methods used for biomarker analyses, concentrations in biospecimens, correlations with external exposure measurements, and biological reproducibility over time. This information can be used by researchers to compare the performance and field of application of various biomarkers and to identify the specific biomarkers or panels of biomarkers that are most useful for biomonitoring or disease etiology studies.
|FoodComEx is a new chemical library initiated in the FoodBAll project to facilitate the sharing of not easily accessible standards for food compounds and their human metabolites. FoodComEx is a virtual library, with compounds stored in the laboratory where they have been isolated or synthesized. Anyone interested in one compound will directly contact the laboratory offering to share the compound. A reference spectral library for food-derived compounds and their metabolites will be made available from the data shared by users.
PhytoHub is a freely available database containing detailed information on all phytochemicals present in commonly consumed foods, and their human metabolites. It is designed for use in nutritional metabolomics studies, with many search possibilities. For every compound, the following is available:
|Phenol-Explorer is a comprehensive database on polyphenol content in foods. The database contains more than 35,000 content values for 500 different polyphenols in over 400 foods. These data are derived from the systematic collection of more than 60,000 original content values found in more than 1,300 scientific publications. Each of these publications has been critically evaluated before inclusion in the database. Phenol-Explorer includes pharmacokinetic data on polyphenol metabolism and retention factors that describe the effects of food processing and cooking. A wide range of queries on foods, polyphenols and metabolites can be executed.
The Human Metabolome Database (HMDB) is the most widely used database for human studies. It contains detailed information about small molecule metabolites found in the human body and is intended to be used for applications in metabolomics, clinical chemistry, biomarker discovery and general education. The open-access database (version 3.6) contains over 42,000 metabolite entries including 3821 metabolites actually detected in human biofluids or tissues and 38,172 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). Each MetaboCard entry contains more than 110 data fields with compound description, chemical identifyers, chemical structure, taxonomy and ontology, physical properties, NMR and MS spectra (4868 metabolites have searchable spectral data), concentration in human biofluids as well as biological properties. Many data fields are hyperlinked to other databases (KEGG, PubChem, MetaCyc, ChEBI, PDB, Swiss-Prot, and GenBank) and a variety of structure and pathway viewing applets. The HMDB database supports extensive text, chemical structure, spectral data and relational query searches.
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 ~3,600 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.
References: Wishart DS, Jewison T, Guo AC, Wilson M, Knox C, et al., HMDB 3.0 — The Human Metabolome Database in 2013. Nucleic Acids Res. 2013. Jan 1;41(D1):D801-7.
Tutorial - How to use: The simple text query supports general text queries of the entire textual component of the database. Clicking on the Browse menu header generates a tabular synopsis of the HMDB's content. This browse view allows users to casually scroll through the database or re-sort its contents. Clicking on a given HMDB ID brings up the full data content for the corresponding metabolite. The Biofluids link in the Browse menu generates hyperlinked tables listing normal and abnormal concentrations of different metabolites for 23 different biofluids. In the Search menu, the ChemQuery Structure Search link allows users to draw (using a ChemSketch applet) or write (using a SMILES string) a chemical compound and to search HMDB for chemicals similar or identical to the query compound. The Text Query supports a more sophisticated text search (partial word matches, case sensitive, misspellings, etc.) of the text portion of HMDB. The Sequence Search allows users to conduct BLAST sequence searches of the over 5,701 gene and protein sequences contained in HMDB. Both single and multiple sequence BLAST queries are supported. The Advanced Search link opens an easy-to-use relational query search tool that allows users to select or search over various combinations of subfields. The Advanced Search is the most sophisticated search tool for HMDB. The MS Search allows users to submit Mass spectral files (MoverZ format) that will be searched against the HMDB's library of MS/MS spectra. This allows the identification of metabolites from mixtures via MS/MS spectroscopy. The 1D and 2D NMR Searches allow users to submit peak lists from 1H or 13C NMR spectra (both pure and mixtures) or 2D TOCSY or 13C HSQC spectra, respectively, and to have these spectra compared to the NMR libraries contained in the HMDB. This allows the identification of metabolites from mixtures via NMR spectroscopy. The Downloads link provides links to collected sequence, image and text files associated with the HMDB. The HML Home button links to the Human Metabolome Library (HML) home page. The HML lists metabolites that can be ordered for a fee by researchers around the world. Finally, under the About menu there are links for HMDB Statistics, and information about the Data Sources used to assemble the HMDB.
ChEBI (Chemical Entities of Biological Interest) is a freely available dictionary of molecular entities focused on ‘small’ chemical entities (n=99274). ChEBI has a high quality manual annotation by chemists. It provides standardized descriptions of molecular entities, using nomenclature, symbolism and terminology endorsed by the International Union of Pure and Applied Chemistry (IUPAC) and the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (NC-IUBMB). ChEBI database entries contain a unique, unambiguous, recommended ChEBI name and an associated stable unique identifier, a chemical structure downloadable as a molfile, a collection of synonyms, including the IUPAC recommended name for the entity where appropriate, and brand names and INNs for drugs, an InChI, InChIKey and a SMILES, a collection of cross-references to other databases, a link to the ChEBI chemical ontology, which allows the relationships between molecular entities or classes of entities and their parents and/or children to be specified in a structured way.
|Dictionary of Food Compounds
|The Dictionary of Food Compounds is an online database with access fees. Simple search can be made in free access with a monoisotopic mass or an elemental formula, but the metabocards of the matching compounds are not freely accessible. DFC contains the 50,000 most popular compounds found in food. The information contained on the chemical database includes systematic and common names of compounds, chemical structures, descriptive and numerical data on physicochemical properties of compounds including accurate mass, literature references, and for some compounds information on their occurrence in food.
|KNApSAcK Core System: An extensive species-metabolite database for plants, including edible and non-edible plants, which contains > 50,000 metabolites. A search engine was developed within the KNApSAcK Core DB for use in metabolomics research, making it possible to search for metabolites based on an accurate mass, molecular formula, or metabolite name. Name, chemical structure, and latin names of plant species containing the compound are given.
|Dr. Duke’s Phytochemical and Ethnobotanical Database is a freely electronic database containing phytochemical and ethnobotanical data. Entity types are of chemicals and phytochemicals, plants and ethnobotanical plants, biological activities, syndromes and ethnobotanical uses. This database contains more than 29,000 entries of chemical and phytochemical compounds of plants. The search engine allows to retrieve all chemicals and phytochemicals present in a given plant, with information on the part of the plant where the compound is found and the range of concentrations. It can also serve to list all plant sources of a given compound.