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obophenotype / cell-ontology-training

Training session for the Cell Ontology
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[NTR] Add pulmonary ionocyte CL term #6

Open mshadbolt opened 4 years ago

mshadbolt commented 4 years ago

Note - please check that the term does not already exist (check OLS: https://www.ebi.ac.uk/ols/ontologies/cl)

Preferred term label: pulmonary ionocyte

Synonyms lung ionocyte

Definition (free text, please give PubMed ID in format PMID:XXXXXX) An ionocyte that is part of a lung which co-expresses FOXI1, multiple subunits of the vacuolar-type H+-ATPase (V-ATPase) and CFTR PMID:30069046

Parent cell type term (check the hierarchy here https://www.ebi.ac.uk/ols/ontologies/cl): epithelial cell of lung http://purl.obolibrary.org/obo/CL_0000082

What is the anatomical structure that the cell is a part of? Please check Uberon: https://www.ebi.ac.uk/ols/ontologies/uberon part of lung epithelium http://purl.obolibrary.org/obo/UBERON_0000115

Your nano-attribution (ORCID) https://orcid.org/0000-0001-7505-5418

Any additional notes or concerns I would like to add links to the genes expressed in the paper i.e. FOXI1 V-ATPase CFTR

dosumis commented 4 years ago

We already have this: http://purl.obolibrary.org/obo/CL_0017000

dosumis commented 4 years ago

definition "An ionocyte that is part of the lung epithelium. The cells from this type are major sources of the CFTR protein in human and mice."

dosumis commented 4 years ago

We could potentially add markers - although not directly to a species neutral term. I assume these are for human.

lubianat commented 4 years ago

That was actually my first CL cell type :) The original articles characterized the cell type both in mice and humans. In the original articles, they kind of mention the "CFTR gene" in a semi species neutral way, but I was not sure how to add the markers.

lubianat commented 4 years ago

I did not put "lung ionocyte" as a synonym, though, that could be readily updated (I think)

mshadbolt commented 4 years ago

Yeah I knew it was already in the ontology, I was just practicing adding a request for the training session. Though I do think it might be cool to add the marker genes if the evidence in the paper is considered good enough to do this.

I have kind of skimmed the paper and I think this cell type has specifically only been found in mice and human, but seems similar to the ionocytes in gills of fish. I wonder if there is any way of characterising that kind of relationship in the ontology?

mshadbolt commented 4 years ago

I did not put "lung ionocyte" as a synonym, though, that could be readily updated (I think)

I also kind of made that up as a synonym, just to practice, I don't know if anyone uses that as a synonym...