Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Populate cell types under 'fenestrated' endothelial cell #2424

Open
2 of 6 tasks
dosumis opened this issue Jul 3, 2024 · 2 comments
Open
2 of 6 tasks

Populate cell types under 'fenestrated' endothelial cell #2424

dosumis opened this issue Jul 3, 2024 · 2 comments

Comments

@dosumis
Copy link
Contributor

dosumis commented Jul 3, 2024

There are many types of fenestrated endothelial cell, but we only have a couple of classes under this term ('fenestrated cell' ; CL_0000666 )

Some examples + papers to curate:
https://www.perplexity.ai/search/which-endothelial-cell-types-a-IMYlTiBZRi.MU99.CRfyHA

see also #2423

Tasks

  1. CL-classhierarchy logical definition text definition
    Caroline-99
  2. new term request
    Caroline-99
  3. new term request
    Caroline-99
  4. new term request
    Caroline-99
  5. new term request
    Caroline-99
  6. new term request
    Caroline-99
@dosumis dosumis changed the title Populate cell types under 'fenestrated' Populate cell types under 'fenestrated' endothelial cell Jul 7, 2024
@dosumis
Copy link
Contributor Author

dosumis commented Jul 8, 2024

Related issue:

GO has this term:

glomerular endothelium fenestra
http://purl.obolibrary.org/obo/GO_0036053

We should add a has_part relationship to this to the relevant CL term

Also - of the fenestrated capillary cells mentioned in the Perplexity response, we only have this one "peritubular capillary endothelial cell" - others will need to be new terms.

@dosumis
Copy link
Contributor Author

dosumis commented Aug 8, 2024

I think we should request a general term for endothelia cell fenestra from GO.

label: endothelial cell fenestra
def: A transcellular pore present in some types of endothelial cell, that facilitates efficient transfer of molecules across endothelia.

I think also possible to make more subclasses where there are clear differences in structure, e.g. - presence/absence fenstra diaphragm & presence/absence associated basal lamina, grouping into 'sieve plates' There are a few possiblilities for GO annotation - structural proteins of diaphragm and proteins that regulate formation and pore size.

See https://www.perplexity.ai/search/which-endothelial-cell-types-a-IMYlTiBZRi.MU99.CRfyHA
This looks like a good review https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2681366/

https://github.com/geneontology/go-ontology/issues/new?assignees=&labels=New+term+request&projects=&template=new-term-request.md&title=NTR%3A+%5Bproposed+new+term+label%5D

The GO terms can then be used to formally define and classify fenestrated endothelial cells.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Projects
Development

No branches or pull requests

2 participants