This folder contains design patterns for groupings of classes in the ontology.
The design patterns are specified in YAML, and follow the dead_simple_design_patterns specification
Consult each yaml file for details on the specific pattern.
The design patterns act as templates, with template values coming from the CSVs in the ontology/modules directory. pattern2owl is used to translate the TSVs to OWL. See the Makefile for more details
We strive for species-neutrality. This means that we do not bake in assumptions such as the surroundings of the organism being air; the ontology can be used for fish and other aquatic organisms.
In some circumstances some assumptions are already baked in, e.g. via CHEBI roles such as 'toxin'.
Some non-human use cases:
- http://www.nature.com/articles/srep33207 - bee exposome
Some ontologies designed for model organisms bake in assumptions that certain kinds of conditions are experiments - e.g. surgical manipulations.
In general, we try and represent conditions in a way that is neutral w.r.t the experimental context. When specifying the context is necessary, we will follow a standard subclass pattern, e.g.
- surgical manipulation
- surgical manipulation in experimental context
- surgical manipulation in clinical context