Ontological considerations for templates

[cthoyt]

Many of the transitions we'll want to model with high-level templates correspond to some subclass of the Basic Formal Ontology (BFO)'s process (BFO:0000015). Therefore, we could consider annotating all templates with a subclass of this entity.

Further, we've already got a notion of subject and outcome, which could generalize to using the following relationships from the Relation Ontology (RO):

• has input (RO:0002233) - relation to connect to the input of the process
• has output (RO:0002234) - relation to connect to the output of the process

Further, in the ControlledConversion template, we've also go a notion of a controller. This corresponds to regulates (RO:0002211) - relation to connect to the controller (e.g., enzyme) of the process. Further, subproperties could be use to even further contextualize this including:

• positively regulates (RO:0002213)
• negative regulates (RO:0002212)

There are additional members of this hierarchy that have mixins for "direct" physical interactions