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

Add last group of cell type ontology IDs #928

Merged

Conversation

allyhawkins
Copy link
Member

Purpose/implementation Section

Please link to the GitHub issue that this pull request addresses.

Closes #887

What is the goal of this pull request?

This is the last group of cell type ontology IDs that needs to be assigned.

Briefly describe the general approach you took to achieve this goal.

  • For salivary mucous cells I used salivary gland glandular cell since that includes mucous cells in the definition.
  • For the satellite cells, I used skeletal muscle satellite cell since the organ listed is skeletal muscle in the Panglao reference.
  • For satellite glial cells, I used perineural satellite cell. This paper defines satellite glial cells as:

Satellite glial cells (SGCs) closely envelop cell bodies of neurons in sensory, sympathetic and parasympathetic ganglia

This matches the definition on OLS for perineural satellite cells.

  • For the Transient cells I couldn't really find any match... I was getting transit amplifying cells on OLS but when I google transient cells it instead mentions white blood cells (but this is only in the AI summary and I couldn't find any actual information stating this). I also noticed that the organ for these cells is the kidney and when I searched for transient cells kidney I saw things about transitional cells instead. I felt like I didn't have enough information to assign an ID here so I thought we should use NA in this scenario. I think it's okay to have cell types with an unassigned ID if we don't feel we can confidently match it to an ID.
  • Related to the above point, there was a term Undefined placental cells that I also couldn't find. I think given these are "undefined" and not a specific placental cell then we should use NA here too. Searching for "placental cell" on OLS only shows "placental epithelial cell, placental pericyte, etc" and no general placental cell term.
  • For the trophoblast stem and precursor cells I was able to find a general term for trophoblast cell and then types of trophoblast cells but not stem or precursor cells. For both of these I ended up just using the trophoblast cell term.

If known, do you anticipate filing additional pull requests to complete this analysis module?

Yes, but no more ontology assignments! Next PR will be an exploratory notebook.

Copy link
Member

@jaclyn-taroni jaclyn-taroni left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

LGTM

@allyhawkins allyhawkins merged commit a13c576 into AlexsLemonade:main Dec 3, 2024
2 checks passed
@allyhawkins allyhawkins deleted the allyhawkins/panglao-ontologies-4 branch December 3, 2024 21:28
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

Successfully merging this pull request may close these issues.

Assign cell ontology identifiers to cell types in CellAssign reference
2 participants