Liver 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
Liver	endothelial cell of hepatic sinusoid	endothelial cell	182
Liver	natural killer cell	NK/NKT cells	39

### Droplet free annotation table

tissue	cell_ontology_class	free_annotation	n_cells
Liver	duct epithelial cell	bile duct epithelial cells	27
Liver	endothelial cell of hepatic sinusoid	endothelial cells	28
Liver	hepatocyte	midlobular female	234
Liver	hepatocyte	midlobular male	526
Liver	hepatocyte	pericentral female	274
Liver	hepatocyte	pericentral male	159
Liver	hepatocyte	periportal female	308
Liver	hepatocyte	periportal male	263
Liver	leukocyte	immune cells	26

Proposed annotations

@patsika @batson

FACS

(None)

Droplet

• [ ] bile duct epithelial cells is_a duct epithelial cell
• [ ] Periportal hepatocyte is_a hepatocyte
• [ ] Midlobular hepatocyte is_a hepatocyte
• [ ] Pericentral hepatocyte is_a hepatocyte

[patsika]

Hello from the Liver group,

endothelial cell synonym endothelial cell of hepatic sinusoid (endothelial cell is actually a more broad category that includes endothelial cells of the hepatic sinusoid and other endothelial cells)

NK and NKT cells is_a leukocyte "NK/NKT cells" is not one but two cell types, NK (natural killer) and NKT (natural killer t cells) NK and NKT cells both go under the category of leukocyte http://www.ontobee.org/ontology/CL?iri=http://purl.obolibrary.org/obo/CL_0000738

bile duct epithelial cells synonym intrahepatic bile duct epithelial cell (this term is more specific than the one we originally gave for the cell_ontology_class) http://www.ontobee.org/ontology/CL?iri=http://purl.obolibrary.org/obo/CL_0002538

Periportal hepatocyte synonym hepatocyte Midlobular hepatocyte synonym hepatocyte Pericentral hepatocyte synonym hepatocyte

(These three are types of hepatocytes, but aren't proven as different categories yet.)

[batson]

@patsika , does this mean that no additions to the cell ontology are warranted here?

[patsika]

@batson Yes, no new cell types need to be added to Cell Ontology.