Hi,
I am trying to go though one of our Flow Cytometry use case: we are looking into using OBI as a controlled vocabulary to guide users when submitting experiments to our repository.
In order to do so, I need to define the stimulator and inhibitor roles, for which I would need the stimulation and inhibition processes.
Unfortunately, like for "activation" I don't have an optimal definition to propose, it sounds always a bit circular.
- stimulation: a process in which level of physiological or nervous activity in the body or any biological system are raised
- inhibition: a process in which level of physiological or nervous activity in the body or any biological system are decreased
I would also need a dosage titration process, which could maybe be defined as the the process of gradually adjusting the dose of a biomaterial bearing the role drug until the desired effect is achieved. I am also aware that this is not very satisfactory. It might also be nice to be able to say that this process has input a biomaterial which has_quality concentration?
Thanks,
Melanie
* I think we need to more generally define 'stimulation' and 'inhibition', as I know I will want to have the same terms for processes other than those in the body.
* Are you only thinking about 'objective driven' inhibition and stimulation done as part of an experiment, or also about natural ones, e.g stimulation of nerves in the visual cortex while I read this?
* It seems that GO must already have something to deal with these terms for e.g. genes in signalling pathways. Have you looked into that?
My preliminary take is: We should have process X stimulates/inhibits process Y outside of OBI. For the experimental version, we would create 'induced stimulation', 'induced inhibition' etc. as a planned process with the objective to inhibit process Y by doing X.
My next take is: This will be hard to do complete and well. Maybe we should aim for a generalizable solution now.
Quick thoughts:
In pathway discourse inhibition and activation are a pair of opposite. Generally we have some process P. In the case of activation P is not happening and the activation process A results in P being enabled. In the case of inactivation, P is possible but the inactivation process I makes it not possible. The prototypical case is that I or A changes some potential participant pp in P, e.g. by phosphorylation, cleavage, or complex formation (in which I include receptor-ligand binding) so that the qualities of pp that make is suitable for participating in P are changed.
Bjoern's point about experimental versus natural are good ones. For stimulation we might focus on application of the stimulus, which is a distinct process from the resultant stimulation, and easier to define.
Discussed on OBI call 9/21/2015. We definitely want to have experimental stimulation and inhibition in OBI. Bjoern will contact Ryan for it. We want to start with examples like cell culture stimulation.
Confirmed with Ryan that this original request can be closed. We will re-open tickets if/when updated term requests are made.