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EBISPOT / efo

Github repo for the Experimental Factor Ontology (EFO)
https://www.ebi.ac.uk/efo/
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New term request for PhenoCycler #1630

Closed jychien closed 2 years ago

jychien commented 2 years ago

For new term requests, please provide the following information:

Preferred term label

PhenoCycler

Synonyms

CODEX, PhenoCycler-Fusion

Textual definition

A spatial discovery system from Akoya Biosciences where whole-slide staining of tissues using pre-designed or custom antibody panels are imaged through automated fluidics (PhenoCycler) and high-speed image acquisition (PhenoImager).

Suggested parent term

I've suggested to add "spatial proteomics" under "EFO:0001458 protein assay". This would be a child of "spatial proteomics".

Attribution

https://orcid.org/0000-0003-4389-9821

ghost commented 2 years ago

@jychien, after reviewing the link, it is not clear to me if 'PhenoCycler' is an exact synonym for 'PhenoCycler-Fusion' or if the former refers just to the instrument and the latter refers to the whole system. 'CODEX' seems to have referred to both and may include both hardware and software components.

From https://www.akoyabio.com/phenocycler/instrument/: "The PhenoCycler™ instrument (formerly CODEX®) is a cutting-edge fluidics control unit that integrates with the Fusion imaging platform to automate whole-slide staining and imaging."

From https://www.akoyabio.com/phenocycler/software/: "The PhenoCycler™ System (formerly CODEX®) provides unparalleled levels of highly multiplexed tissue imaging data."

Given your definition, does it make sense to set 'PhenoCycler-Fusion' as the preferred label and 'CODEX' and 'PhenoCycler' as narrow synonyms? Another option is to create a separate term for 'PhenoCycler' to represent the instrument and assert that 'PhenoCycler-Fusion' has_part 'PhenoCycler'- but I would need confirmation that that relationship is accurate. Could you advise?

jychien commented 2 years ago

@bvarner-ebi Thank you so much for the thorough review. After some discussion and browsing of the Akoya website, it seems as if PhenoCycler (CODEX) and PhenoImage (Phenoptics) enables automated whole-slide staining and imaging, respectively. And, together, they've been integrated to form PhenoCycler-Fusion.

Some additional link: https://www.biospace.com/article/releases/akoya-biosciences-announces-commercial-launch-of-phenocycler-fusion-the-fastest-single-cell-spatial-biology-system-/

ghost commented 2 years ago

Thank you for confirming, @jychien. Would you kindly provide your suggested textual definition and parent class for 'PhenoCycler'?

jychien commented 2 years ago

'PhenoCycler' textual definition: An automated fluidics system designed by Akoya Biosciences that uses oligonucleotide conjugated antibodies for tissue staining, followed by iterative cycles of applying fluorophore-conjugated reporter oligonucletides and gentle washing to generate multiplexed imaging data.

'PhenoCycler' parent term: This would be a child of "spatial proteomics".

I've also updated the 'PhenoCycler-Fusion' textual definition above (copy and pasted here): A spatial discovery system from Akoya Biosciences where whole-slide staining of tissues using pre-designed or custom antibody panels are imaged through automated fluidics (PhenoCycler) and high-speed image acquisition (PhenoImager).

ghost commented 2 years ago

@jychien, thank you for the clarifications! I am unable to add you as a reviewer to the PR, but please do have a look at #1662 and kindly advise if the modelling makes sense to you.

Please also note I realised that I used the wrong ID range when creating the term 'spatial proteomics' for #1629 and incorporated the fix in #1662.

ghost commented 2 years ago

@jychien, thank you again for your new term contributions. The following have been added to EFO:

EFO:0700001 PhenoCycler-Fusion EFO:0700002 PhenoCycler

If you require any edits, kindly advise so they can be applied before the next release.

jychien commented 2 years ago

@bvarner-ebi Thank you for adding the terms. We would like to make these terms more broad and remove references to Akoya Biosciences in the definitions. That way, any data resulting from CODEX before the existence of Akoya can still be associated with this term.

ghost commented 2 years ago

Hi @jychien,

Would the following edits address your needs?

EFO:0700002 PhenoCycler Current definition: An automated fluidics system designed by Akoya Biosciences that uses oligonucleotide conjugated antibodies for tissue staining, followed by iterative cycles of applying fluorophore-conjugated reporter oligonucletides and gentle washing to generate multiplexed imaging data. Proposed definition: An automated fluidics system that uses oligonucleotide conjugated antibodies for tissue staining, followed by iterative cycles of applying fluorophore-conjugated reporter oligonucletides and gentle washing to generate multiplexed imaging data.

EFO:0700001 PhenoCycler-Fusion Current definition: A spatial discovery system from Akoya Biosciences where whole-slide staining of tissues using pre-designed or custom antibody panels are imaged through automated fluidics (PhenoCycler) and high-speed image acquisition (PhenoImager). Proposed definition: A spatial discovery system where whole-slide staining of tissues using pre-designed or custom antibody panels are imaged through automated fluidics (PhenoCycler) and high-speed image acquisition (PhenoImager).

jychien commented 2 years ago

Thank you so much, @bvarner-ebi. Yes, the edits look good to me.

ghost commented 2 years ago

@jychien, the definitions have been updated in PR# #1699.