Preferred design pattern for including marker genes in novel cell type names

[scheuerm]

Ou collaborators at UC Irvine have identified five putative fibroblast cell types in the ciliary body of the eye that appear to represent previously uncharacterized populations. Based on their marker gene expression, we have tentatively named them as follows:

CB_Fibro_BMP5+
CB_Fibro_GPC6+
CB_Fibro_CEMIP+
CB_Fibro_CHRM3+
CB_Fibro_CNTN4+

Is there a preferred standard syntax that we would recommend using for these situations?

[addiehl]

I think we should write out the full names as the main labels in CL and include your short names as exact synonyms. My recommended names are as follows:

BMP5-positive ciliary body fibroblast
GPC6-positive ciliary body fibroblast
CEMIP-positive ciliary body fibroblast
CHRM3-positive ciliary body fibroblast
CNTN4-positive ciliary body fibroblast

Do you think should have a common grouping term 'ciliary body fibroblast' or should these be direct children of 'fibroblast' (or is there another possible parent)?

We can also include additional exact synonyms of the form "BMP5+ ciliary body fibroblast" etc.

[scheuerm]

Thanks Alex. I agree with your naming convention recommendations and with the use of exact synonyms. Unless I hear otherwise in the next couple of days, that's what I'll recommend.

In terms of fibroblast vs ciliary body fibroblast as the parent, I'm kind of leaning toward fibroblast until we have evidence that all fibroblasts in the ciliary body have some common characteristic aside from location.

[dosumis]

Looks good. We should have some kind of taxon tag on these. If not in_taxon Hsap, then at least present_in_taxon Hsap.

Can we point to an HCA atlas on CAP or CxG for transcriptomic reference?