Confirming mappings of single cell RN-seq defined cell types with ontology

[groliver]

Jonathan Barasch should weigh in on the up to date mappings of the sequencing derived ontology mappings. I was reviewing the 5-2018 release of KTAO vs the recent Science paper he is on, and they have additional abbreviations and proposed new cells we should probably include or map.

provisional mappings:
| 1 | Endo: endothelial, vascular and descending loop of Henle

| 1-1 | Endo: endothelial
http://purl.obolibrary.org/obo/CL_0000115
-- many different subtypes in the ontology

| 1-2 | Peri: vascular
?? pericyte http://purl.obolibrary.org/obo/CL_1001318
confirm mesangial and interstitial pericytes included in this class

| 1-3 | DLH: descending loop of Henle
http://purl.obolibrary.org/obo/CL_1001021

| 2 | Podo: podocyte
http://purl.obolibrary.org/obo/CL_1000451
http://purl.obolibrary.org/obo/CL_0000653

| 3 | PT: proximal tubule
http://purl.obolibrary.org/obo/CL_1000839

| 3-1 | S1 PCT: S1 segment of proximal tubule, proximal convoluted tubule
http://purl.obolibrary.org/obo/UBERON_0001287
http://purl.obolibrary.org/obo/UBERON_0005124

| 3-2 | S2: S2 segment of proximal tubule
http://purl.obolibrary.org/obo/UBERON_0004197
--NEED to add this

| 3-3 | S3 PST: S3 segment of proximal tubule, proximal straight tubule
http://purl.obolibrary.org/obo/UBERON_0001290

| 4 | LOH: loop of henle

http://purl.obolibrary.org/obo/UBERON_0001288
http://purl.obolibrary.org/obo/CL_1001109
http://purl.obolibrary.org/obo/CL_1001108
http://purl.obolibrary.org/obo/CL_1001107
http://purl.obolibrary.org/obo/CL_1001106

| 5 | DCT: distal convoluted tubule
http://purl.obolibrary.org/obo/UBERON_0005118
http://purl.obolibrary.org/obo/UBERON_0005120

| 6 | CD-PC: collecting duct principal cell
http://purl.obolibrary.org/obo/CL_1000550

| 7 | CD-IC: CD intercalated cell|collecting duct intercalated cell
http://purl.obolibrary.org/obo/CL_0005010
| 7-1 | A-IC: alpha intercalated cells|α-intercalated cells
http://purl.obolibrary.org/obo/CL_0005011
| 7-2 | B-IC: beta intercalated cells
http://purl.obolibrary.org/obo/CL_0002201
--Need to add

I don't see the remaining cells in the ontology
--Do we need to add new entries or links?

| 8 | CD-Trans: CD transient cell

| 9 | novel cell type 1
?? some type of proliferative or stem cell like PT cells
-- Do we need to add placeholder pending final publication describing?

| 10 | Fib: fibroblast
http://purl.obolibrary.org/obo/CL_0000057
| 11 | Macro: macrophage
http://purl.obolibrary.org/obo/CL_0000235
| 12 | Neutro: neutrophil
http://purl.obolibrary.org/obo/CL_0000096
| 13 | B lymphocyte
http://purl.obolibrary.org/obo/CL_0000236
| 14 | T lymphocyte
http://purl.obolibrary.org/obo/CL_0000084
| 15 | NK: natural killer cell.
http://purl.obolibrary.org/obo/CL_0000623

| 16 | novel cell type 2
-- Do we need to add placeholder pending final publication describing?

Summary proposed entities to add from NCBO
http://purl.obolibrary.org/obo/CL_0002201
http://purl.obolibrary.org/obo/UBERON_0004197

http://purl.obolibrary.org/obo/CL_0000057
http://purl.obolibrary.org/obo/CL_0000235
http://purl.obolibrary.org/obo/CL_0000096
http://purl.obolibrary.org/obo/CL_0000236
http://purl.obolibrary.org/obo/CL_0000084
http://purl.obolibrary.org/obo/CL_0000623

Summary proposed new entities
Collecting duct transient cell
novel cell type 1
novel cell type 2

[yongqunh]

The proposed terms have now been added to KTAO:

http://purl.obolibrary.org/obo/CL_0000096 # neutrophil
http://purl.obolibrary.org/obo/CL_0000236 #B lymphocyte
http://purl.obolibrary.org/obo/CL_0000084 # T lymphocyte
http://purl.obolibrary.org/obo/CL_0000623 #NK: natural killer cell.
http://purl.obolibrary.org/obo/UBERON_0004197 #S2: S2 segment of proximal tubule

In addition, added S1:
http://purl.obolibrary.org/obo/UBERON_0004196 # proximal convoluted tubule segment 1
and some other terms from UBERON.

Thanks.

[yongqunh]

Need to check if all commented terms have been addressed.