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NTR: Has exposure medium #477
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@diatomsRcool Should we try to move this along? |
Can you use of the occurs in object property? That is, an exposure event |
I'm wondering if the 'occurs in' object property would give the impression that the exposure is occurring in a specific location or medium. |
Hmmm... teasing out this distinction may be difficult. Let's say you are exposed to secondhand smoke. The medium (I assume) would be the air containing the smoke. The exposure event occurs in: you (e.g., your lungs?), the air around you, the room (or some other location) where you breathed in the air. All these seem to be encompassed by the occurs in relation:
Is the |
Could be a subproperty? |
The exposure medium is not intended to pick out the location where the exposure occurs (e.g. lungs vs air vs room), but rather denote the entity that is allowing for the stimulus to be transmitted to the actual site of the exposure. So in your example, the medium would be air, stimulus is the smoke, and the location of the exposure is the lungs (because you and your lungs are the exposure receptor). |
think of it more as a vehicle |
So, it sounds like the relation needs to hold between the stimulus (e.g., smoke) and the environmental material through which the stimulus moves? In other words, do you want the relation to be:
or
If the latter, then it might help to change the definition to explicitly refer to the stimulus and the stimulus' medium. |
Hmm we currently use the second approach offered, but I wonder if it would be more meaningful to assign the medium to the stimulus itself instead of the exposure event generally? thoughts @diatomsRcool ? Also spitballing on the first proposal, |
You can also have relations for both situations:
For the definition of X |
@laurenechan that is essentially what we do because the assigning of the medium and the route is a part of the class itself. Exposure to mercury in food via ingestion is a separate class from exposure to mercury in air via inhalation. |
Thanks @diatomsRcool |
I think @diatomsRcool is correct and maybe we should omit the mention of organisms being a potential medium as to avoid confusion for what the medium is actually supposed to represent as opposed to the receptor. |
Great! |
Revising my initial definition proposal, Relation label: has exposure medium Doesn't seem to particularly different, but removes organism from the example entities (although I am still thinking about whether there could be a separate organism/organism substance outside the receptor that could serve as a medium, maybe contaminated honey?). I've also strictly included stimulus int he definition as the entity being transmitted through the medium. Were you looking for other revisions as well @wdduncan ? |
I don't know what the standards are regrading how definitions are to be written in RO. I often write definitions in the form:
to make it painstakingly clear what the domains and ranges are. Also, it makes the definition a bit more formal. I see a lot of variety in how definitions are written in RO, though. Perhaps @matentzn knows if there are guidelines about how definitions should be submitted to RO? |
I was using the other relations under the 'related via exposure to' branch as examples which don't have that format, but I think you are right @wdduncan , it seems like other relations use that format. I just slightly modified your proposed definition from above: X has exposure medium Y if X is an exposure event (process), Y is a material entity or food material, and the stimulus for X is transmitted or carried in Y. @diatomsRcool can you confirm whether or not we need further options for what Y can be? We only use terms from ENVO and FoodOn as media at this point, but if we want the definition to range further we can add that now. |
@diatomsRcool did you have any comments on this or should I go ahead and create a pull request for this relation? |
I think this is fine. Isn't food material a material entity? |
@diatomsRcool yes, it is, shall we pare down to just 'Y is a material entity' then? |
yes - then its fine |
@diatomsRcool @cmungall
Hello,
Within the Environmental Conditions, Treatments, and Exposures Ontology (ECTO) we are using the higher level model of Exposure Ontology (ExO) to develop our exposure event classes. This includes documenting the route, stressor, and medium of the exposure when available.
We are currently using relations including 'has exposure stressor' and 'has exposure receptor', but we do not have a relation for 'has exposure medium'.
We propose the following details for this term:
Label: has exposure medium
Parent: related via exposure (RO:0002244)
Definition: A broad relationship between an exposure event or process and any entity (e.g., an organism or environmental substance) through which something else is transmitted or carried during an exposure event.
Definition source: ExO_0000083
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