Add last group of cell type ontology IDs #928
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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.
salivary mucous cells
I usedsalivary gland glandular cell
since that includes mucous cells in the definition.satellite cells
, I usedskeletal muscle satellite cell
since the organ listed isskeletal muscle
in the Panglao reference.satellite glial cells
, I usedperineural satellite cell
. This paper defines satellite glial cells as:This matches the definition on OLS for perineural satellite cells.
Transient cells
I couldn't really find any match... I was gettingtransit 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 useNA
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.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.trophoblast cell
and then types of trophoblast cells but not stem or precursor cells. For both of these I ended up just using thetrophoblast 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.