Relabel “3D structure determination assay” and its subclasses, and adding new term.

[hectorguzor]

The IEDB team is looking to clean up the epitope-assays.tsv. Currently we are looking at the detection technique column to determine whether the terms under the column are correctly classified as detection techniques, or whether they should be entered under the parent class column for the assays in question.

In order to accomplish this, we also looked at general techniques (assays in the assays.tsv ) used across all kinds of investigations (not specific to the IEDB). We have started by looking at “3D structure determination assay” and its subclasses. We are proposing relabeling the terms below to better capture how they are related. This will help with cleaning up the detection technique column in the epitope-assays.tsv.

Relabel -“3D structure determination assay” (OBI:0600045 ) → relabel as “3D molecular structure determination assay”
-“nuclear magnetic resonance 3D structure assay” (OBI:0000182) → relabel as “NMR molecular structure determination assay”

• “small-angle scattering assay” (OBI:0002108) →relabel as “small-angle scattering molecular structure determination assay”
  • “X-ray crystallography assay” (OBI:0000912) → relabel as “X-ray crystallography molecular structure determination assay” -“3D structure determination of bound complex assay” (OBI:000 1145 ) → relabel as “3D structure determination of bound molecular complex assay”

New term We are also proposing a possible new term as a subclass of “3D molecular structure determination assay”

• “electron-microscopy molecular structure determination assay” related term: (electron microscopy imaging assay OBI:0001631)

[patrick-lloyd-ray]

I have a few terms in an application ontology that I have as subclasses of '3D structure determination assay'. They are terms related to neuron (cell) morphology assays. Can it be assumed that changing the label will imply that the scope of the class is now more narrow? In other words, is it the case that (in the future) all subclasses of '3D molecular structure determination assay' will involve determination of only molecular structure, and not something like structure of a cell?

[bpeters42]

Thanks Patrick for pointing that out!

The '3D structure determination assay' class was underdefined, and if you are using it more general, that was perfectly valid with the last definition, so we should keep it as such, and define a 'molecular structure determination assay' as a subclass.

Any chance you could submit your assay terms to OBI? cellular morphology assays would be very much in scope, and are pretty much a blank slate in OBI.

On Mon, May 3, 2021 at 11:40 AM Patrick Lloyd Ray @.***> wrote:

I have a few terms in an application ontology that I have as subclasses of '3D structure determination assay'. They are terms related to neuron (cell) morphology assays. Can it be assumed that changing the label will imply that the scope of the class is now more narrow? In other words, is it the case that (in the future) all subclasses of '3D molecular structure determination assay' will involve determination of only molecular structure, and not something like structure of a cell?

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[patrick-lloyd-ray]

Thank you. This is a very helpful response.

Yes, I can submit those terms to OBI. Would you like them submitted via issues as New Term Requests or would you like them in ROBOT template format? I have about 20 terms that would be in scope for OBI at the moment, if information is pertinent to your response.

[jamesaoverton]

Hi @patrick-lloyd-ray. A ROBOT template is easier for OBI developers, and hopefully fairly easy for you as well. Then you can either attach/link the template to an issue or jump right to a pull request. Let us know if you need help with anything.

[hectorguzor]

Hi @patrick-lloyd-ray you can reach out to me if you need help with the ROBOT template.

[patrick-lloyd-ray]

Here's a link to the terms I think would be of interest to OBI. I doubt this requires no further curation, so perhaps @hectorguzor could help identify the problems.

[hectorguzor]

Thanks @patrick-lloyd-ray I will take a look at these.

[hectorguzor]

Discussed in OBI call 2021-08-16: new labels should reflect '3D' component of the textual definition. For example, "x-ray crystallography assay" should be "x-ray crystallography 3D molecular structure determination assay".