CT Ontology issue

HIPC scRNA-seq Annotation Benchmark Challenge
1

The official ontology file `CT_Ontology_Spreadsheet_20260323.tsv` appears internally inconsistent around `Effector B`.

In the file, `Plasma Cell` and `Plasmablast` are children of `Effector B`. However, the provided definition for `Effector B` is: “A mature B cell that produces cytokines that can influence CD4 T cell differentiation.” This definition does not clearly describe antibody-secreting cells and is not a good parent-level summary for plasma cells or plasmablasts.

Also, ydT Cell → gd T Cell? I think the organizer confused gamma with y.

NK Cell is terminal, but isTerminalNode was FALSE.

2

Thanks for pointing out the incorrect “Effector B” definition and NK cell not being terminal. The CT Ontology Spreadsheet will be updated accordingly!

As for ydT, the y kind of looks like the gamma letter γ, so that is why we named it “ydT”. Thank you!!

3

Thanks! ydT should be corrected as gdT. No immunologist uses ydT, as you can see by a Google search, for example.

4

Thank you for the advice. We are modifying the ontology to replace “ydT Cell” with “gdT Cell”.

So teams that have already made progress do not need to change their workflow, since we will will accept “ydT Cell” and convert it to “gdT Cell” on our end automatically.

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