Closed andreagaede closed 5 months ago
Hi @andreagaede these are two very good questions which tackle first version schemas in openMINDS (meaning based on your feedback, use case we will find that we need a refinement here in openMINDS). Currently you will have the following options:
I'm sorry if that summary is a bit confusing. What we indeed currently not offer is a way of specifying an anatomical target within a SubjectState (to avoid the definition of TissueSamples/TissueSampleStates). I will bring this to the developers to discuss this further.
Additionally you can define the type and amount of treatment (unstructured) in the additional remarks of the SubjectStates or descriptions of the ProtocolExecutions. You can also use the CustomPropertySet in ProtocolExecutions to define your own structured metadata for the treatment. Moreover, you can define the relative time relation between the SubjectStates or which SubjectState descended from which to highlight the order in which the activities happened that produced these states. Depending on your needs all ProtocolExecutions could link to the same Protocol which describes (unstructured) the whole process (because it might be fixed for all subjects). So far we did not develop an extension that would capture treatments of subjects in more detailed/structured way.
I'm happy to discuss further. I'm not sure if every option became clear. Feel free to also get in touch with us for a video call (it might be easier to discuss in person, but I hope I was able to somewhat describe what you could do).
@andreagaede : Maybe this one is solved for us? I was looking as to whether to add on or not.
@stevewds oh you're right -- the new issue is more about a new ontology in addition to what we ask about here. We will still also want to use StimulationApproach as suggested though I think
@andreagaede Do you think we should close it, to take it off their plates? Or is there more info we need? If you want to close it go ahead!
A couple of things I could use help with:
When using StimulationApproach, I would like to specify which body part the stimulus is applied to (e.g., left eye, right eye, left ear, left hindlimb, etc...). Is there a way to add controlled terms for this somewhere, rather than adding this as a 'description' at either the StimulationApproach or Protocol levels?
In a case where a treatment has been applied to an animal (e.g., developmental intervention) that will be present for many epochs, where should this be indicated? I think maybe SubjectAttribute is the answer, but these are general attributes, so is there a place where I can put more details. Also, if this happens at postnatal day 4, for instance, where should I indicate that since it is not the animal's current age, just the age at intervention/treatment/etc...?