Table 1.
Coverage of initial Foundry ontologies
| Granularity | Continuant | Occurrent | |||
|---|---|---|---|---|---|
| Independent | Dependent | ||||
| Organ and organism | Organism (NCBI taxonomy or similar) | Anatomical entity (FMA, CARO) | Organ function (Physiology ontology, to be determined) | Phenotypic quality (PATO) | Organism-level process (GO) |
| Cell and cellular component | Cell (CL, FMA) | Cellular component (FMA,GO) | Cellular function (GO) | Cellular process (GO) | |
| Molecule | Molecule (ChEBI, SO, RnaO, PRO) | Molecular function (GO) | Molecular process (GO) | ||
Down the left column is the granularities (spatial scales) of the entities represented in the ontologies; along the top is a division corresponding to the ways these entities exist in time47. ‘Continuants’ endure through time. ‘Occurrents’ (processes) unfold through time in successive stages. Continuants are divided into physical things, on the one hand, and qualities and functions, on the other. The latter are dependent continuants: a quality such as the shape of a fly’s wing depends for its existence on, and endures through time in tandem with, the wing that is its bearer; a function, such as the function of an enzyme to catalyze reactions of a certain type, similarly endures through time in tandem with the enzyme itself and exists even when it is not being exercised in any instance of that reaction. NCBI, US National Center for Biotechnology Information; CL, Cell Ontology; SO, Sequence Ontology; RnaO, RNA Ontology; PRO, Protein Ontology.