Add terms for endometrium

[dosumis]

Potential new terms for uterine muscle and epithelial cell types: https://www.nature.com/articles/s41588-021-00972-2

[ghost]

https://www.nature.com/articles/s41588-021-00972-2

@dosumis, thank you for the link. This paper derives cell types from in vitro organoids. Does this require any special considerations for curation?

[dosumis]

Hmmm - yes. We need to be careful about that. We need references for these type in vivo. IIRC there are other single cell studies on endometrium. Please take a look at CxG & maybe search pubmed. IIRC Sarah Teichman's group has published on this.

[ghost]

This may be a place to start: https://www.nature.com/articles/s41591-020-1040-z
Of note, cell types found in the endometrium will be especially impacted by cell state given the cyclical remodelling of the endometrium in several species.

[ghost]

After a cursory review of https://www.nature.com/articles/s41591-020-1040-z, here are some potential new cell types. Inviting feedback from @dosumis, @emquardokus and other interested parties.

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term from paper:
“stromal fibroblast”
-- appears to be same as CL:0002255 ‘stromal cell of endometrium’
action:
- suggested revisions in #1785 (DONE)

---

term from paper:
“endothelium”
-- assume the paper uses this term to refer to endothelial cells
-- main text does not appear to explore this cell type in depth (other than differentially expressed genes)
-- CL:2000091 ‘endometrial microvascular endothelial cell’ exists, but this may be a different cell type
action:
Optional: - seek additional references to support potential new term ‘endothelial cell of endometrium’

---

term from paper:
"macrophage"
-- main text does not appear to explore this cell type in depth (other than differentially expressed genes)
action:
Optional: - seek additional references to support potential new term ‘endometrial macrophage’

---

term from paper:
"lymphocyte"
-- main text does not appear to explore this cell type in depth (other than differentially expressed genes)
action:
Optional: - seek additional references to support potential new term ‘endometrial lymphocyte’

---

term from paper:
“ciliated epithelial cell”
action:
- add 3 new classes (#1843 - DONE):
‘endometrial ciliated epithelial cell’
with new child classes:
‘luminal endometrial ciliated epithelial cell’
‘glandular endometrial ciliated epithelial cell’

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term from paper:
“unciliated epithelial cell”
action:
- add 2 new classes:
‘endometrial unciliated epithelial cell’
with child classes:
‘luminal endometrial unciliated epithelial cell’ (new)
‘glandular endometrial unciliated epithelial cell’...
this may be same as CL:0009084 ‘epithelial cell of endometrial gland’ which may also be the same as CL:0002656 ‘glandular cell of endometrium’. If same, merge and relabel ‘glandular endometrial unciliated epithelial cell’

---

term from paper::
“smooth muscle cell”
action:
- confirm that this is present in endometrium and not the same as CL:0002366 'myometrial cell'. If new, add class ‘smooth muscle cell of endometrium’

[dosumis]

New epithelial cell types sound like a good place to start.

[github-actions]

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.

[dosumis]

@bvarner-ebi - how's progress on this? I think good to look at a range of papers. This one from Sarah Tiechman's group could also be a good source https://www.nature.com/articles/s41586-018-0698-6

[dosumis]

@bvarner-ebi @aleixpuigb to discuss whether appropriate to assign remaining work to Aleix - given importance to HubMap.

[aleixpuigb]

This one from Sarah Tiechman's group could also be a good source https://www.nature.com/articles/s41586-018-0698-6

We got feedback from the authors in the Female reproductive system jamboree and new cell types from this article will be added. Most likely there will be new tickets that will substitute this one, but will leave it open for the time being.