Thymus 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
Thymus	DN1 thymic pro-T cell	DN1 thymocytes	32
Thymus	immature T cell	DN4-DP in transition Cd69 negative rapidly div...	135
Thymus	immature T cell	DN4-DP in transition Cd69 negative thymocytes	540
Thymus	immature T cell	DN4-DP in transition Cd69 negative thyomcytes	39
Thymus	immature T cell	DN4-DP in transition Cd69 positive thymocytes	563
Thymus	professional antigen presenting cell	antigen presenting cell	40

Droplet free annotation table

tissue	cell_ontology_class	free_annotation	n_cells
Thymus	DN1 thymic pro-T cell	DN1 thymocytes	44
Thymus	immature T cell	DN3-DN4 thymocytes	33
Thymus	immature T cell	DN4-DP in transition Cd69 negative rapidly div...	219
Thymus	immature T cell	DN4-DP in transition Cd69 negative thymocytes	71
Thymus	immature T cell	DN4-DP in transition Cd69 positive thymocytes	187
Thymus	immature T cell	DN4-DP in transition Cd69_negative thymocytes	334
Thymus	immature T cell	DN4-DP transition Cd69 low thymocytes	227
Thymus	immature T cell	DN4-DP transition Cd69 negative rapidly dividi...	283
Thymus	professional antigen presenting cell	antigen presenting cells	31

Proposed annotations

@pknguyen1

FACS and Droplet

• double negative 1 (DN1) thymocyte synonym DN1 thymic pro-T cell
• DN4-DP in transition Cd69 negative rapidly dividing thymocyte is_a immature T cell
• DN4-DP in transition Cd69 positive rapidly dividing thymocyte is_a immature T cell
• DN4-DP in transition Cd69 negative is_a immature T cell
• DN4-DP in transition Cd69 positive is_a immature T cell

Droplet only

• DN3-DN4 thymocyte is_a immature T cell
• DN4-DP transition Cd69 low thymocyte is_a immature T cell
• DN4-DP transition Cd69 negative rapidly dividing thymocyte is_a immature T cell