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obophenotype / cell-ontology

An ontology of cell types
https://obophenotype.github.io/cell-ontology/
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[NTR] hypoblast cell AND review of CL:0000352 epiblast cell ? #2133

Open ANiknejad opened 1 year ago

ANiknejad commented 1 year ago

Hello CL Team,

we need 'hypoblast cell' to capture the single-cell types from this recent paper https://pubmed.ncbi.nlm.nih.gov/37322291/

Looking at cells of epiblast, 'the other cell layers arising from the inner cell mass in the mammalian blastocyst, or from the blastula in reptiles and birds '/https://en.wikipedia.org/wiki/Epiblast), I see that 'epiblast cell' exists:

[Term] id: CL:0000352 name: epiblast cell def: "A cell of the outer layer of a blastula that gives rise to the ectoderm after gastrulation." [GOC:tfm, ISBN:0618947256] is_a: CL:0000052 ! totipotent stem cell

BUT it seems that 'epiblast cell' has a mammal-restricted definition regarding its fate, and that should be reported in CL:0000352 I guess, cf https://en.wikipedia.org/wiki/Epiblast: 'In mammalian embryogenesis, differentiation and segregation of cells composing the inner cell mass of the blastocyst yields two distinct layers—the epiblast ("primitive ectoderm") and the hypoblast ("primitive endoderm").'

Based on CL:0000352, I would propose:

[Term] id: CL:xxxxxxx name: hypoblast cell, mammalian def: "A cell of the inner layer of a blastocyst that gives rise to the endoderm after gastrulation[WP]." [Wikipedia:Hypoblast] is_a: CL:0000052 ! totipotent stem cell

Thank you very much for your kind attention.

Anne

ghost commented 1 year ago

@ANiknejad, thank you for this issue.

More time is required to investigate this request- if there is a specific use case, kindly advise. In the meantime, which Uberon term do you propose would be related to 'hypoblast cell'- 'hypoblast (generic)' or one of the subclasses?

ANiknejad commented 1 year ago

Thank you @bvarner-ebi

Epiblast cells and hypoblast cells are both part of the inner cell mass, https://discovery.lifemapsc.com/in-vivo-development/inner-cell-mass so I would say UBERON:0000087 (inner cell mass) may currently represent the more precise UBERON anatomical description for hypoblast cells

It exists the CL class CL:2000020 ! inner cell mass cell which currently may be used as the parent term for the missing hypoblast cell class.

github-actions[bot] commented 7 months ago

This issue has not seen any activity in the past 6 months; it will be closed automatically in one year from now if no action is taken.