FoodOn’s organism facet, under the OBI “organism” term, contains taxonomic terms that reference a whole prototypical plant, animal or fungus organism, and semantically include its roots, leaves, arms, legs, fur, etc. as the case may be.
A food item may be an organism facet organism directly, as in a reference to a whole sardine. In ontology speak we say that a given sardine is an instance of the NCBITaxon sardine class. Alternately a food item may be an anatomical part of organism, or a more arbitrarily processed part, either of which “derives from” the organism, for example an apple.
The facet’s branches enable two different ways to approach the species and subspecies level of organism taxonomy, described below. A given organism reference often hast two parents, each belonging to one of the branches below.
Most FoodOn references to a plant, animal, or fungus are to an NCBITaxon organismal classification ontology term at the species or sub-species level. The organism facet includes an entire path from a given NCBITaxon item all the way up its parent family, genus etc. until finally reaching Bacteria or Eukaryota under the organism facet root (itself actually an OBI ontology term). Bacteria are included to encompass those that distinguish cheeses etc.
In the farm to fork journey, an organism as a whole may be commodified as a food product for agricultural purposes, but also towards the consumer end where say fish or chickens can be sold at market with scales or feathers intact.
Food product organismal source
A second approach for navigational convenience, but also to cope with the ambiguous use of food terms that reference more than one species, is through a food product organismal source minimal taxonomic hierarchy that selectively echoes upper level taxa that exist in the NCBITaxon full hierarchy, but also introduces common language groupings that span taxa. It still usually culminates in NCBITaxon species / sub-species organism taxa terms, or in some cases the FoodOn ids for organisms not in NCBITaxon. It provides a much shallower hierarchy than the NCBITaxon one which can have a depth of 20, 30 or 40 taxa.
The Food product organismal source also houses identifiers for organisms that are not yet in NCBITaxon but which exist in other taxonomies like ITIS. As well, it also houses a number of FoodOn organisms imported from LanguaL that may have NCBITaxon counterparts, but for whatever reason were not recognized as such in the initial automated setup of FoodOn. Such terms will eventually be migrated into NCBITaxon ones.