Third group of cell ontology assignments

[allyhawkins]

Purpose/implementation Section

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

#887

What is the goal of this pull request?

Here I am adding in the third group of ontology labels for cell types.
As a heads up, this is the second to last PR with these label additions. The next one will be the last one since there are only ~25 labels left.

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

• I could not find a term for meningeal cells other than meningeal macrophage, which seemed too specific since there are multiple cell types in the meninges. The closest term for general cell types that are part of the meninges, was leptomeningeal cell. It looks like the leptomeninges is just part of the meninges but the only other option I could find was neural cell which seemed too broad.
• There was no general term for myocytes, just sub classes of myocytes so I used the parent term for the subclasses, which was cardiac muscle cell.
• I couldn't find a term for osteoclast precursor cells and from looking at some papers, it looks like there is not a ton known about exactly what characterizes an osteoclast precursor cell. One option would be to use a mononuclear osteoclast, which is a precursor to a fully activated osteoclast. Another option would be to use monocyte, since they differentiate into osteoclasts. I ended up using this term.
• The oxyphil cells are specific to the parathyroid gland in the Panglao reference, so I used oxyphil cell of parathyroid gland as the term.
• For pancreatic progenitor cells I used progenitor cell of endocrine pancreas, but this doesn't cover the exocrine pancreas. I couldn't find a term that encompasses both and the next best term was progenitor cell which seemed too broad.
• principal cells are from the Kidney in the Panglao reference, so I used renal principal cell.
• For pulmonary vascular smooth muscle cells I found smooth muscle cell of the pulmonary artery, but that is specific to the pulmonary artery and not other vasculature that is part of the pulmonary system. Additionally, these cells have smooth muscle listed as the organ in the panglao reference, so I ended up going with vascular associated smooth muscle cell.

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

Yes, one more PR for ontology terms.

[jaclyn-taroni]

One typo, and then a bunch of things I think we should write down, but I don't need to see this again.

[jaclyn-taroni]

I would capture this one in documentation (#924)

[jaclyn-taroni]

Flag for #924

[jaclyn-taroni]

Makes sense to me.

[jaclyn-taroni]

Flag for #924 -- I'm worried this one could actually get us into trouble!