Add three CRISPR assays

[sebastianduesing]

Closes #1784. Adds three CRISPR assay terms using assay template additions created by Bjoern during the 2024-07-08 OBI dev call.

[jamesaoverton]

Sebastian and I looked at this together, and it looks good to me.

[jenjou]

I noticed that the term name says "single RNA-seq"; I'm not sure if that's accidentally omitting the word "cell" (as in "single cell RNA-seq")?

Also, if it's OK, I'd like to share this pull request with some of our labs working on CRISPR screens to see if they are happy with the terminology.

[sebastianduesing]

@jenjou Good catch—I believe that change was made while Bjoern was editing the template during the OBI call a couple weeks ago. I'll add a commit to change it to "single-cell RNA-Seq". Yes, please feel free to share this PR with the labs.

[jenjou]

Relaying some questions from my colleagues following their review:

• One term mentions "screening" whereas the others are "screen", should this be consistent?
• One term mentions "perturbation" whereas the others do not (just "CRISPR screen" instead of "CRISPR perturbation screen")
• For "in vitro CRISPR screening assay", would it make sense to restore the word "proliferation"? This may have been a miscommunication on my part.

Edit: one more question I missed.

• We have a lab that is knocking in mCherry to a target gene rather than using probes. We are wondering if that might merit adding another term similar to "in vitro CRISPR perturbation screen using FISH and flow cytometry", but rather than FISH, something like "in vitro CRISPR perturbation screen using fluorescence imaging-based reporter gene and flow cytometry" (referring to https://www.ebi.ac.uk/ols4/ontologies/obi/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FOBI_0002960?lang=en which seems to be the most similar term I can find.)

[sebastianduesing]

@jenjou Thanks for passing along your colleagues' feedback. Adding a term for "in vitro CRISPR perturbation screen using fluorescence imaging-based reporter gene and flow cytometry" is definitely doable. As for your first three points, my instinct is that those should be standardized, but I don't recall whether or not those phrasings were chosen for a specific reason when Bjoern was filling out the template, so I'll defer to his judgement here.

@bpeters42 Can I go ahead and make changes to address the terminology inconsistencies mentioned in Jennifer's comment? If so, do you have a preference on using "in vitro CRISPR perturbation screen assay" vs "in vitro CRISPR perturbation screening assay"?

[bpeters42]

Please go ahead and make changes, and I don't have preferences on the label ***@***.*** and her group should decide)

…

On Mon, Jul 22, 2024 at 1:04 PM Sebastian Duesing ***@***.***> wrote: @jenjou <https://github.com/jenjou> Thanks for passing along your colleagues' feedback. Adding a term for "in vitro CRISPR perturbation screen using fluorescence imaging-based reporter gene and flow cytometry" is definitely doable. As for your first three points, my instinct is that those should be standardized, but I don't recall whether or not those phrasings were chosen for a specific reason when Bjoern was filling out the template, so I'll defer to his judgement here. @bpeters42 <https://github.com/bpeters42> Can I go ahead and make changes to address the terminology inconsistencies mentioned in Jennifer's comment? If so, do you have a preference on using "in vitro CRISPR perturbation *screen* assay" vs "in vitro CRISPR perturbation *screening* assay"? — Reply to this email directly, view it on GitHub <#1796 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ADJX2IX66NEQTC3PW6WALOTZNVQTZAVCNFSM6AAAAABKTIT4S6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDENBTG4ZDCMBSGU> . You are receiving this because you were mentioned.Message ID: ***@***.***>

-- Bjoern Peters Professor La Jolla Institute for Immunology 9420 Athena Circle La Jolla, CA 92037, USA Tel: 858/752-6914 Fax: 858/752-6987 http://www.liai.org/pages/faculty-peters

[jenjou]

Hello, just wanted to provide some updates as we have had further internal discussion about the terms.

I think this is our preferred plan:

• Add "in vitro CRISPR screening assay" term, serving as a parent to the other 2 terms.
  • Need to address consistency of screen vs screening, "perturbation" or no "perturbation" in the term
• Add "in vitro CRISPR screen using single-cell RNA-seq"
  • Need to address consistency of screen vs screening, "perturbation" or no "perturbation" in the term
• Add "in vitro CRISPR perturbation screen using flow cytometry"
  • Removes "FISH" from the original request to make the term more generic (allows for different methods to cause fluorescence, or sorting by other parameters). Could allow future additions which are more specific for FISH or other methods.
  • Need to address consistency of screen vs screening, "perturbation" or no "perturbation" in the term

Please let me know if that would be reasonable to implement. Thank you!

[sebastianduesing]

Certainly. Does your group have a preference on "screen" vs "screening" or on "perturbation" vs no "perturbation" in the term label?

[jenjou]

Yes, I think our preference is for "screen" and omitting the word "perturbation". So that would correspond to each of the 3 terms like so:

• in vitro CRISPR screen assay
• in vitro CRISPR screen using single-cell RNA-seq
• in vitro CRISPR screen using flow cytometry

[sebastianduesing]

Got it, thanks for confirming! I'll make those changes tomorrow.

[jenjou]

Sorry for the back and forth -- but I think OBI:0003668 may not be actively needed on our end. Of course, if OBI thinks it still makes sense to have such a term, then we would have no objection to including it.

[sebastianduesing]

Got it, thanks for letting us know!