exposures to organisms and immunity

[diatomsRcool]

ECTO needs to contain classes that will be useful for others modeling immune responses. The latest release has a pattern for exposure to organism. I would like to keep this pattern for other use cases, but this is likely not sufficient for the immunity use case. For example, someone could be exposed to a cat without being exposed to toxoplasmodium. Someone could be exposed to toxoplasmodium without developing an infection. Then someone could be exposed to an infected person or be infected themselves. I could use some help thinking through this to arrive at a suite of patterns that satisfies use cases. @bpeters42

[bpeters42]

Thank you. Our immune modeling patterns are not solely including exposure to other organisms (like pathogens), but also to administration of vaccines, exposure to allergens, prescriptions of drugs, etc. For our use case, we don't deal with exposure to non-material entities (e.g. bullying, lack-of sunlight), which are undoubtedly important, and we might want to include those later for us as well, and will be happy to adopt anything you come up with. So what we need to coordinate in my mind is: "Exposure of organism to material entity" The common pattern I see is: "a process in which organism O is exposed to material entity ME at anatomical entity AE as part of process X".

We have normally done this by spelling out the roles different entities play in the process. Attempting to align them with yours:
O has_role some 'exposed organism' ME has_role some 'exposure stimulus' AE has_role some 'exposure route' X ''''has_role'''' 'exposure event' (processes can't have roles, and this one doesn't need one; just including for symmetry

Stopping here to get feedback.

[diatomsRcool]

Interesting. ECTO is not intended to model the entire exposure process. So I think what might work is "AE part of some O has exposure some ECTO class and part of process X" Or some combination. ECTO would include the ME which is the stimulus/stressor as well as information about the route (ingestion, inhalation, etc) and medium (air, water, soil, etc) if applicable. Does that make sense? I don't normally use roles, so I'm not entirely sure if this suggestion messes that up. I think that ECTO can provide a class containing the ME that the immune modeling patterns can use.

[bpeters42]

The anatomical entity in what I had above is meant to capture what you have as route (or at least important parts of it). Inhalation = exposure through the airways; ingestion = exposure through digestive tract, and similarly oral administration (mouth), intradermal injection (skin epidermis). What you have as 'route' seems to mix that anatomical entity with 'part of process X' (breathing, eating)?

[diatomsRcool]

OK. I think this is fine. They way I am thinking about ECTO is that there will be classes that will include just the ME - no route or medium. I think you can use these classes in your patterns? In my use case, sometimes the route and medium will be known, but sometimes not. So, I need very general classes and more specific classes. It sounds like your patterns will be very specific. In which case you would use the more general ECTO classes. I take your point about the mixing of AE and process. I'm going to think more on that. I think I would like to fold the AE into the logical definition of the process.