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The Ontology for Biomedical Investigations
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stimulation/inhibition/dosage titration #107

Closed obi-bot closed 7 years ago

obi-bot commented 16 years ago

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

Reported by: mcourtot

Original Ticket: "obi/obi-terms/107":https://sourceforge.net/p/obi/obi-terms/107

obi-bot commented 16 years ago

* 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.

Original comment by: bpeters42

obi-bot commented 16 years ago

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.

Original comment by: alanruttenberg

obi-bot commented 9 years ago

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.

Original comment by: zhengj2007

obi-bot commented 9 years ago

Original comment by: bpeters42

obi-bot commented 9 years ago

Confirmed with Ryan that this original request can be closed. We will re-open tickets if/when updated term requests are made.

Original comment by: bpeters42