FSBI-DB Tutorial
A guide to using this resource and its features
FSBI-DB Overview
Food Systems Biology Database (FSBI-DB) integrates odorant database from Leibniz Institute of Food System Biology, Food Composition and Nutrition Tables Souci-Fachmann-Kraut, and taste quality and receptor data from publication of this institute. It is a high- quality, science-based comprehensive and curated database platform incorporating multidisciplinary expertise in food chemistry, molecular biology, neuroscience, sensory evaluation, chemometrics, computational pharmacology and data science.
Structure Similarity Search
The FSBI-DB´s structure similarity search tool is modified from the R ChemDoodle package (version 0.3.0), which is published on an R shiny app server hosted by LSB. Users may sketch or paste a SMILES string of a query compound. Submitting the query launches a structure-similarity-search-tool which looks for common substructures from the query compound that match the FSBI-DB database. Result is sorted based on similarity scores, which indicates a high to low similarity among those compounds found in the database. Package RCPI [Dong-Sheng Cao, Nan Xiao, Qing-Song Xu, and Alex F. Chen. (2015). Rcpi: R/Bioconductor package to generate various descriptors of proteins, compounds and their interactions. Bioinformatics 31 (2), 279-281.] (1.26.0) is used to calculate the similarity with a fingerprint distance matrix being calculated with the Fingerprint type “kr”.
Compound Network and Page
Compound page includes molecular general identities such as common Name, IUPAC Name, SMILES, CAS ID, PubChem ID.
Further, 2D image of the molecule, using chemViewer, which transforms into 3D view upon clicking ‘Click to view/hide 3D structure’ button. Further, an option is provided to download the molecule data in Mol2, SDF, 2D image, JSON format.
The panel also provides classification,compound toxicity and food additive safety (OFAS), flavor profile with curated taste and odor quality data, relative publication,and food occurrence linking to food pages.
In the receptor session, one can explore the already know receptors and visite their page for more information like familiy, sequence,protein diagram, 3d model, and known ligands in FSBI-DB network.
FSBI-DB Food description and food taxonomy tree
LanguaL™ - the international framework for food descriptions is used to describe and index the food in FSBI-DB. It is a multilingual thesaural system using facetted classification, as well as an automated method for describing, capturing and retrieving data about food, categorized into viewpoints and coded for computer processing. Therefore, it is widely used for describing, capturing and retrieving data about food in national and international food composition and consumption databanks.
In LanguaL™, each food is described by a set of standard, controlled terms chosen from facets characteristic of the nutritional and/or hygienic quality of a food, for example the biological origin, the methods of cooking and conservation, and technological treatments. With this standardized language for describing FSBI foods, the generated food codes enable the retrieving data about the food from external databases and reusability by other database.
Receptor Tree Explorer
The Receptor Tree Explorer is modified from TidyTree. On default, it shows you the Receptor Phylogenetic Tree of FSBI-DB with customized layout settings . One can render his own Phylogenetic Trees in-browser with Source Your Data function or style your own FSBI-DB receptor tree then export it. Green nodes are taste receptors while blue nodes are olfactory receptors. Activate tooltips in Meta setting, to read more about the receptors and to go to the single receptor page.