Mammary Gland 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
Mammary_Gland	luminal epithelial cell of mammary gland	luminal progenitor	411
Mammary_Gland	luminal epithelial cell of mammary gland	mature luminal cell	167

Droplet free annotation table

tissue	cell_ontology_class	free_annotation	n_cells
Mammary_Gland	luminal epithelial cell of mammary gland	luminal progenitor cell	243
Mammary_Gland	luminal epithelial cell of mammary gland	mature luminal cell	216

Proposed annotations

@sikandars

FACS and Droplet

• Luminal progenitor cell is_a luminal epithelial cell of mammary gland
• Mature luminal cell is_a luminal epithelial cell of mammary gland

[lindavan]

I see that the free_annotation for FACS is different from Droplet for the luminal progenitor cell, maybe it's a good idea to call both of them luminal progenitor cell?
Citations. For the distinction between the two luminal epithelial cell types based on the marker (CD14) we use (doi): https://doi.org/10.1128/MCB.05766-11 and https://doi.org/10.1186/bcr2560 and https://doi.org/10.1186/1471-2164-9-591 of these publications, https://doi.org/10.1128/MCB.05766-11 is the most important.
Let me know if this is sufficient or if you need something else.

EDIT: turned DOIs into URLs

[olgabot]

Ah you're right about the luminal progenitor cell! Good catch! I'll change it now.