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obophenotype / cell-ontology

An ontology of cell types
https://obophenotype.github.io/cell-ontology/
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[NTR-HCA] 'immune cell'; superseded by editing synonym for leukocyte #1698

Closed ghost closed 2 years ago

ghost commented 2 years ago

Context: https://github.com/HumanCellAtlas/ontology/issues/120

Preferred term label immune cell

Synonyms (add reference(s), please) n/a

Definition (free text, with reference(s), please. PubMed ID format is PMID:XXXXXX) A cell that is part of the immune system and helps the body fight infections and other diseases. https://www.cancer.gov/publications/dictionaries/cancer-terms/def/immune-cell

Parent cell type term (check the hierarchy here https://www.ebi.ac.uk/ols/ontologies/cl) CL:0000988 'hematopoietic cell'

What is the anatomical structure that the cell is a part of? (check Uberon: https://www.ebi.ac.uk/ols/ontologies/uberon) 'immune system'

Your ORCID n/a

Additional notes or concerns Use case: Cell type ontology (HCA)

FYI @addiehl

addiehl commented 2 years ago

Looking at the source definition, I see that it contains the gloss "These include neutrophils, eosinophils, basophils, mast cells, monocytes, macrophages, dendritic cells, natural killer cells, and lymphocytes (B cells and T cells)." That is pretty much the same subtypes that the existing CL class 'leukocyte' has. How is 'immune cell' distinct from leukocyte?

I think that 'immune cell' should be added as a 'related synonym' to leukocyte. It's not an exact synonym, because there are non-leukocyte cells that play important roles in the functioning of the immune system (such as follicular dendritic cells, endothelial cells of the high-endothelial venues, platelets, and more), and these cells are important in the functioning of the immune system.

ghost commented 2 years ago

Per the comments above, "immune cell" will be changed from an exact synonym to a related synonym of the class leukocyte.