Merge pull request #937 from allyhawkins/allyhawkins/document-weird-t…

…erms

Document terms we aren't sure about in cell ontology

analyses/cell-type-consensus/references/README.md

@@ -16,3 +16,17 @@ To generate this file follow these steps:
 - Download the original reference file with `00-download-panglao-ref.sh`. 
 - Programmatically assign ontology lables with `01-prepare-cell-type-ontologies.sh`. 
 - Assign any ontology values manually by finding the most representive [cell type ontology (CL) identifier term](https://www.ebi.ac.uk/ols4/ontologies/cl). 
+
+There were a few terms that were assigned manually that did not have an obvious or exact match in the cell type ontology that should be noted: 
+
+- `Kidney progenitor cells` were assigned the [`CL:0000324` for metanephric mesenchyme stem cell](https://www.ebi.ac.uk/ols4/ontologies/cl/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FCL_0000324). 
+This term refers specifically to the stem cells that ultimately comprise the nephron, but does not account for the part of the kidney that is derived from ureteric bud cells. 
+- `Meningeal cells` were assigned to [`CL:0000708` for leptomeningeal cell](https://www.ebi.ac.uk/ols4/ontologies/cl/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FCL_0000708). 
+This was the closest term that covered general cell types found in the meninges. 
+- `Pancreatic progenitor cells` were assigned to [`CL:0002351` for progenitor cell of endocrine pancreas](https://www.ebi.ac.uk/ols4/ontologies/cl/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FCL_0002351). 
+This term only covers progenitor cells for the endocrine pancreas and does not cover the exocrine pancreas. 
+There were no terms that encompassed both other than `progenitor cell`. 
+- `Osteoclast precursor cells` were assigned to [`CL:0000576` for monocyte](https://www.ebi.ac.uk/ols4/ontologies/cl/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FCL_0000576).
+Monocytes differentiate into mononuclear osteoclasts which are then activated and become multinucleated osteoclasts. 
+Because monocytes are the "precursor" to the differentiated osteoclast, we chose to use this term. 
+- `NA` was used for `Undefined placental cells` and `Transient cells` as no clear cell type from the cell ontology was identified.