Question regarding intra cellular electrophysiology recording assay hierarchy

[patrick-lloyd-ray]

Looking at the classes under ‘intra cellular electrophysiology recording assay’ there are three classes: current clamp assay, patch clamp assay, and voltage clamp assay. I think that both current clamp assay and voltage clamp assay are types of patch clamp assay (they are the two ways that one can perform a patch clamp assay).

Perhaps there is a good reason for these three to be under ‘intra cellular electrophysiology recording assay’ – e.g., having only one child class under a parent is a “bad smell” for some ontologists. However, this could lead some users think that these classes are disjoint when they are not. Thoughts?

[rvita]

I am forwarding this to Brenda Farrell who initiated those terms to see if she has any comments. Thanks, Randi

…

On Tue, Nov 16, 2021 at 2:39 PM Patrick Lloyd Ray ***@***.***> wrote: Looking at the classes under ‘intra cellular electrophysiology recording assay’ there are three classes: current clamp assay, patch clamp assay, and voltage clamp assay. I think that both current clamp assay and voltage clamp assay are types of patch clamp assay (they are the two ways that one can perform a patch clamp assay). Perhaps there is a good reason for these three to be under ‘intra cellular electrophysiology recording assay’ – e.g., having only one child class under a parent is a “bad smell” for some ontologists. However, this could lead some users think that these classes are disjoint when they are not. Thoughts? — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or unsubscribe. Triage notifications on the go with GitHub Mobile for iOS or Android.

-- Randi Vita, M.D. Lead Ontology and Quality Manager Immune Epitope Database and Analysis Project La Jolla Institute for Allergy & Immunology 9420 Athena Circle La Jolla, Ca 92037 ***@***.*** www.immuneepitope.org 858-752-6912

[rvita]

I am sorry to say that Brenda Farrell is no longer working, so she will be unable to comment. These assays are not within my area of expertise, so I can offer no other input.

[nsuvarnaiari]

Hi All,

We have noticed that there is already a term - "electrophysiology assay" (OBI:0002176). But, extracellular electrophysiology recording assay (OBI:0000454) and intra cellular electrophysiology recording assay (OBI:0000447) are not the children of "electrophysiology assay". I think it makes more sense to add those relationships.

Thanks,
Suvvi and @mgiglio99

[hectorguzor]

Discussed on OBI call 2021-11-22: There were no comments on the hierarchy of ‘intra cellular electrophysiology recording assay’. There was agreement that 'extracellular electrophysiology recording assay' (OBI:0000454) and 'intra cellular electrophysiology recording assay' (OBI:0000447) should be made children of 'electrophysiology assay' (OBI:0002176).

[hectorguzor]

PR #1499 was merged. @hectorguzor discussed with @patrick-lloyd-ray that for now we will leave the intra cellular electrophysiology recording assay hierarchy as is. If changes need to be made in the future, we can reopen the issue.