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The Ontology for Biomedical Investigations
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Question regarding intra cellular electrophysiology recording assay hierarchy #1458

Closed patrick-lloyd-ray closed 2 years ago

patrick-lloyd-ray commented 3 years ago

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).

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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 commented 3 years ago

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?

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-- 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 commented 2 years ago

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 commented 2 years ago

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 commented 2 years ago

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 commented 2 years ago

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.