Open Majpuc opened 3 years ago
@Majpuc are these all proteins?
No, not only proteins. I mentioned neurotransmitters here in the first round, but actually also need controlled term lists for receptors, transporters, ions, etc.. I think we could have an umbrella term like "molecule" allowing to include all these "study target" without going into too much details. Open to suggestions and discussion
molecules is a bit too general I would say. I would not mind maybe splitting to:
[I would do these separations because the controlledTerms and corresponding instances will be used across openMINDS metadata models and the distinction could be very nice for the in-depth models.]
Would that be a good start?
Yes, good idea. Let's define these lists or fetch them from somewhere :)
I think we have several of those already in the old KG. I will see how many I can automatically generated until tomorrow. @Majpuc thanks again for making the request!
Example for neurotransmitters:
Maybe use "compounds" instead of "molecules" as a general term? If we need a general term to group neurotransmitters, receptors and so on, that is :)
..but this would not cover receptors, though
The plan is to make several lists of controlled terms as Lyuba suggested above. The one I proposed covers main neurotransmitters. Similar lists could be created for the other categories (receptors, transporters, ion channels, ions, hormones, etc..)
@Majpuc I agree. @amkvello thanks for preparing this and as discussed: define some groups now and I can rearrange later if necessary. @Majpuc I might get back to you about the groupings then.
@lzehl was this topic moved to another github project?
I lack the possibility to be able to have different molecules as study target. Similarly to "cell type" I suggest that we have the instance "molecule" where the entries could be a set of controlled terms as follows:
Glutamate (Glu) Acetylcholine (ACh) Histamine Dopamine (DA) Norepinephrine (NE); also known as noradrenaline (NAd) Epinephrine (Epi); also known as adrenaline (Ad) gamma-Aminobutyric acid (GABA) Serotonin (5-HT) Dopamine (DA) Oxytocin (Oxt) Vasopressin; also known as antidiuretic hormone (ADH)
They have of course properties, like excitatory, inhibitory, modulatory but this info could be added later.