[NTR] New Term Request: aerocyte

[lubianat]

Preferred term label
aerocyte

Synonyms (add reference(s), please)
aerocyte capillary endothelial cell, aerocyte capillary EC, aCap - EDNRB+

Definition (free text, with reference(s), please. PubMed ID format is PMID:XXXXXX)

The Tabula Sapiens: A multiple-organ, single-cell transcriptomic atlas of humans
PMID:35549404

and also
https://pubmed.ncbi.nlm.nih.gov/33057196

Parent cell type term (check the hierarchy here Cell Ontology CL)
Superclasses: lung endothelial cell, capillary endothelial cell
CL IDs: CL_0002144

Anatomical structure where the cell type is found (check Uberon for anatomical structures: Uberon Ontology)
Locations: lung
Uberon IDs: UBERON_0002048

Your ORCID

Additional notes or concerns
This request draft was autogenerated from Wikidata. For more details, see the Wikidata item or the source script.

[lubianat]

There is one or two bugs in there, but I am playing around with this kind of auto-generation of an NTR ticket from Wikidata.

It is missing a definition (need manual generation or fancy LLM stuff) and an ORCID (user-specific).

It also failed to locate the likely CL synonym alveolar capillary type 2 endothelial cell
https://www.ebi.ac.uk/ols4/ontologies/cl/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FCL_4028003

[lubianat]

The original term by @JoshuaFortriede was added in PR

• add new terms for alveolar capillary cells and pulmonary capillary endothelial cell #1318
  and very similar to
• Capillary 2 cell [NTR] #1056

In any case, perhaps "aerocyte" should be the main label, as it is explicitly used as the name of the cell type in the paper, what do you think?

[gpryhuber]

Just noting that the aerocyte / aCAP / alveolar capillary type 2 endothelial cell was published as distinct from gCAP/ general (pulmonary) capillary endothelial cell/ alveolar capillary type 1 endothelial cell. The capillary 1 and capillary 2 assignment was made in https://doi.org/10.1016/j.devcel.2021.11.007.
If we use "aerocyte" as the main label for the synonym alveolar capillary type 2 endothelial cell then the logic would be to use "general" in the leading term for the other alveolar capillary type but I think that would be confusing as "general" could be taken to mean non-specific. It is true that doi:10.1126/science.abl4896 suggests that the gCap transcriptome is more similar to capillary endothelial cells in other tissues so maybe to refer to them as "general" is okay? To try to avoid the confusion, when entering these two cell types into CL, we used the https://doi.org/10.1016/j.devcel.2021.11.007 convention of alveolar capillary type 1 endothelial cell with synonym gCAP and alveolar capillary type 2 endothelial cell with synonym aCAP and aerocyte. As long as we keep the synonyms, either choice of main label would likely be okay. Thanks for working on this. Of note, we have a cross-consortium lung endothelial cell task force that should be addressing this as domain experts.

[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.

[gpryhuber]

The endothelial cell working group prefers to keep alveolar capillary type 1 cell (CAP1) and alveolar capillary type 2 cell (CAP2) as this is not dissimilar from the alveolar epithelial type 1 (AT1) and alveolar epithelial type 2 (AT2) convention. Unlike "aerocyte" and "general capillary," these terms CAP1 and CAP2, is in line with nomenclature from other compartments (i.e. AT1 and AT2) and don't infer function for which data is still inadequate.