Bladder proposed new cell ontology terms

[olgabot]

Hello! This discussion is to propose the free_annotation terms to the Cell Ontology so that future researchers may use your specific terms rather than the generic ones that you had to use. Below are your free_annotation terms and what I (@olgabot) thought the relationship was to the existing cell ontology term, whether it was brand new term and cell type, in which case I used is_a, or it was merely a synonym for a term that already existed in the cell ontology, in which case I used synonym.

Please comment below with what is the correct relationship between terms, or correct the term itself and I'll deal with the submission to the Cell Ontology group.

Thank you for your help! Warmest, Olga

For the annotations below, here is the format:

• [ ] free annotation relationship cell ontology class

Relationships could be either:

• is_a - means that the free annotation label is a new "cell type" to add to the cell ontology
• synonym - means that the free annotation label is not a new cell type, but another term for the same thing that already exists in the cell ontology

I wasn't always sure which relationship to use so please comment below and I will correct it.

Examples:

• [ ] Inhibitory neuron is_a neuron
• [ ] alveolar epithelial type 2 cells synonym type II pneumocyte

FACS and droplet free annotation tables in the "Details" below.

### FACS free annotation table

tissue	cell_ontology_class	free_annotation	n_cells
Bladder	bladder cell	Bladder mesenchymal cell	695
Bladder	bladder urothelial cell	Basal bladder epithelial cell	101
Bladder	bladder urothelial cell	Luminal bladder epithelial cell	582

### Droplet free annotation table

tissue	cell_ontology_class	free_annotation	n_cells
Bladder	bladder cell	Bladder mesenchymal cell	1203
Bladder	bladder urothelial cell	Basal bladder epithelial cell	498
Bladder	bladder urothelial cell	Luminal bladder epithelial cell	669
Bladder	leukocyte	Monocyte/Macrophage	73

Proposed annotations

@akershner @bkiss

FACS and Droplet

• [ ] Bladder mesenchymal cell is_a bladder cell
• [ ] Basal bladder epithelial cell is_a bladder urothelial cell
• [ ] Luminal bladder epithelial cellis_a bladder urothelial cell

[akershner]

Hi Olga,

Bladder mesenchymal cell is_a bladder cell ref: Lilly MA, Kulkulka NA, Firmiss PR, Ross MJ, Flum AS, Santos GBD, et al. (2015) The Murine Bladder Supports a Population of Stromal Sca-1+/CD34+/lin- Mesenchymal Stem Cells. PLoS ONE 10(11): e0141437.

Basal bladder epithelial cell is_a bladder urothelial cell refs: Hedgehog/Wnt feedback supports regenerative proliferation of epithelial stem cells in bladder Kunyoo Shin, John Lee, Nini Guo, James Kim, Agnes Lim, Lishu Qu, Indira U. Mysorekar & Philip A. Beachy Nature volume 472, pages 110–114 (07 April 2011)

KRT14 marks a subpopulation of bladder basal cells with pivotal role in regeneration and tumorigenesis. Papafotiou G, Paraskevopoulou V, Vasilaki E, Kanaki Z, Paschalidis N, Klinakis A. Nat Commun. 2016 Jun 20;7:11914

Retinoid signaling in progenitors controls specification and regeneration of the urothelium. Gandhi D, Molotkov A, Batourina E, Schneider K, Dan H, Reiley M, Laufer E, Metzger D, Liang F, Liao Y, Sun TT, Aronow B, Rosen R, Mauney J, Adam R, Rosselot C, Van Batavia J, McMahon A, McMahon J, Guo JJ, Mendelsohn C.

Luminal bladder epithelial cellis_a bladder urothelial cell ref: Retinoid signaling in progenitors controls specification and regeneration of the urothelium. Gandhi D, Molotkov A, Batourina E, Schneider K, Dan H, Reiley M, Laufer E, Metzger D, Liang F, Liao Y, Sun TT, Aronow B, Rosen R, Mauney J, Adam R, Rosselot C, Van Batavia J, McMahon A, McMahon J, Guo JJ, Mendelsohn C.

[olgabot]

Awesome, thank you!