Marrow 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
Marrow	B cell	Cd3e+ Klrb1+ B cell	44
Marrow	late pro-B cell	Dntt+ late pro-B cell	117
Marrow	late pro-B cell	Dntt- late pro-B cell	189
Marrow	precursor B cell	pre-B cell (Philadelphia nomenclature)	517

Droplet free annotation table

tissue	cell_ontology_class	free_annotation	n_cells

Proposed annotations

@transcriptomics

FACS

• Cd3e+ Klrb1+ B cell is_a B cell
• Dntt+ late pro-B cell is_a late pro-B cell
• Dntt- late pro-B cell is_a late pro-B cell

[transcriptomics]

Hey @olgabot,

Dntt+ late pro-B cell is_a late pro-B cell
Dntt- late pro-B cell is_a late pro-B cell

The above two would be totally fine.

Marrow | precursor B cell | pre-B cell (Philadelphia nomenclature) | 517
This nomenclature already exists: CL_0000817. It is the first in the search results on ontobbe:
http://www.ontobee.org/search?ontology=&keywords=precursor+B+cell&submit=Search+terms
This is not a free annotation.

Cd3e+ Klrb1+ B cell is_a B cell

We actually do not know what those are-- they have marker signature of B, T, and NK cells. Can we rule out cross-contamination here?

[olgabot]

Thank you @transcriptomics!
Okay if we're not certain that the "Cd3e+ Klrb1+ B cell" group is certainly a new term, let's not do it. We can propose just the Dntt{+/-} terms. Could you give a few citations describing the Dntt+/- cells?
Thank you!
Warmest,
Olga