Large Intestine 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
Large_Intestine	Brush cell of epithelium proper of large intes...	Tuft cell	63
Large_Intestine	enterocyte of epithelium of large intestine	Enterocyte (Distal)	191
Large_Intestine	enterocyte of epithelium of large intestine	Enterocyte (Proximal)	773
Large_Intestine	enteroendocrine cell	Chromaffin Cell	59
Large_Intestine	epithelial cell of large intestine	Lgr5+ amplifying undifferentiated cell (Distal)	106
Large_Intestine	epithelial cell of large intestine	Lgr5+ amplifying undifferentiated cell (Proximal)	172
Large_Intestine	epithelial cell of large intestine	Lgr5+ undifferentiated cell (Distal)	343
Large_Intestine	epithelial cell of large intestine	Lgr5+ undifferentiated cell (Proximal)	528
Large_Intestine	epithelial cell of large intestine	Lgr5- amplifying undifferentiated cell	576
Large_Intestine	epithelial cell of large intestine	Lgr5- undifferentiated cell	294
Large_Intestine	large intestine goblet cell	Goblet cell (Distal)	471
Large_Intestine	large intestine goblet cell	Goblet cell (Proximal)	264
Large_Intestine	large intestine goblet cell	Goblet cell, top of crypt (Distal)	98

Droplet free annotation table

tissue	cell_ontology_class	free_annotation	n_cells

Proposed annotations

@tisobe1

FACS

• tuft cell synonym Brush cell of epithelium proper of large intestine
• enterocyte (distal) is_a enterocyte of epithelium of large intestine
• enterocyte (proximal) is_a enterocyte of epithelium of large intestine
• chromaffin cell synonym enteroendocrine cell
• Lgr5+ amplifying undifferentiated cell is_a epithelial cell of large intestine
• Lgr5+ amplifying undifferentiated cell (Distal) is_a epithelial cell of large intestine
• Lgr5+ amplifying undifferentiated cell (Proximal) is_a epithelial cell of large intestine
• Lgr5+ undifferentiated cell is_a epithelial cell of large intestine
• Lgr5+ undifferentiated cell (Distal) is_a epithelial cell of large intestine
• Lgr5+ undifferentiated cell (Proximal) is_a epithelial cell of large intestine
• Goblet cell (Distal) is_a large intestine goblet cell
• Goblet cell (Proximal) is_a large intestine goblet cell
• Goblet cell, top of crypt (Distal) is_alarge intestine goblet cell

[tisobe1]

Hi Olga,
Thank you for working on cell ontology.
Distinguishments of proximal or distal colon from total colon have not been reported yet by single cell analysis at least, so I don't think we need to distinguish them for now.

[olgabot]

Thanks @tisobe1! So is this correct that we only need to propose these terms (below)? If so, could you provide 2-3 citations for each of them?
Much appreciated, thank you!
Warmest,
Olga

1. tuft cell is_a Brush cell of epithelium proper of large intestine
2. chromaffin cell is_a enteroendocrine cell
3. Lgr5+ amplifying undifferentiated cell is_a epithelial cell of large intestine
4. Lgr5+ undifferentiated cell is_a epithelial cell of large intestine

[tisobe1]

Hi Olga,
tuft cell 'synonym' Brush cell of epithelium proper of large intestine
chromaffin cell 'synonym' enteroendocrine cell
these 2 are not needed for submissions as a new cell types.
Best,
Taichi

[olgabot]

Great! Can you provide some citations to explain the relationships between the cell types?

1. tuft cell synonym Brush cell of epithelium proper of large intestine
2. chromaffin cell synonym enteroendocrine cell
3. Lgr5+ amplifying undifferentiated cell is_a epithelial cell of large intestine
4. Lgr5+ undifferentiated cell is_a epithelial cell of large intestine

[tisobe1]

Tuft cell is an alias of bush cell and chromatin cell is an alias of enteroendocrine cell. So I don't think we need to submit these two words this time. If we need to do, I will send the citations about these.
I suppose that we had several clusters of undifferentiated cells, Lgr5+ or Lgr5-, amplifying or non-amplifying. Not all the cells of Lgr5+ cluster express Lgr5. In such case, I don't know whether we need to submit this as new ontology or not. Can you give me your opinion.