A key element of fermented foods are microorganisms that transform raw materials to create a distinct end product. For this reason, microbial composition and metabolism must be considered as key ontological features. The microbial community diversity and composition is strongly influenced by substrates that might be uniquely present in a particular geographic location. The Fermented Food Ontology (FFO) aims to provide a description of fermented foods while considering raw materials as the main drivers of microbial diversity. This ontology is based on i) FoodON low-level categories and on ii) manually curated categories obtained for the foods from the curated FermDB database. We defined three ontology levels (level 1-3) to classify the categories, such levels are based exclusively on the raw materials used to elaborate the fermented foods while excluding processing information. Level 1 corresponds to broad categories of raw material and level 3 a narrow anatomical and fluid classification. This approach better elaborates on features of raw material used to produce the fermented foods while at the same time simplifying the complexity of FoodON to keep the hierarchical relationship between components of foods.
The Fermented Food Ontology (FOO) can be visualized interactively at https://bokulich-lab.github.io/FermDB/#graphs
To suggest a new category or changes in the ontology please submit an issue in the current repository. For new categories please indicate the proposed 3-level hierarchy.
The Fermented Food Ontology can be downloaded as a JSON file or python dictionary structure.
If you have used the FOO please consider citing: Reference DOI