Lung 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
Lung	NA	lung neuroendocrine cells and unknown cells	40
Lung	ciliated columnar cell of tracheobronchial tree	multiciliated cells	25
Lung	classical monocyte	invading monocytes	90
Lung	epithelial cell of lung	alveolar epithelial type 1 cells, alveolar epi...	113
Lung	leukocyte	mast cells and unknown immune cells	35
Lung	monocyte	circulating monocytes	65
Lung	myeloid cell	dendritic cells, alveolar macrophages, and int...	85

Droplet free annotation table

tissue	cell_ontology_class	free_annotation	n_cells
Lung	ciliated columnar cell of tracheobronchial tree	multiciliated cells	49
Lung	classical monocyte	invading monocytes	161
Lung	myeloid cell	dendritic cells and interstital macrophages	87
Lung	non-classical monocyte	circulating monocytes	220
Lung	type II pneumocyte	alveolar epithelial type 2 cells	89

Proposed annotations

@ktravaglini

FACS and Droplet

• multiciliated cells is_a ciliated columnar cell of tracheobronchial tree
• invading monocytes is_a classical monocyte
• circulating monocytes is_a monocyte

Droplet only

• circulating monocytes is_a non-classical monocyte
• alveolar epithelial type 2 cells synonym type II pneumocyte