czbiohub-sf/tabula-muris

Liver proposed new cell ontology terms

olgabot opened this issue · 3 comments

olgabot commented

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:

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

patsika commented

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 commented

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

patsika commented

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