obophenotype / cell-ontology

An ontology of cell types
https://obophenotype.github.io/cell-ontology/
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Some taxon constraints in CL are too tight for ZFA #2542

Closed gouttegd closed 1 month ago

gouttegd commented 1 month ago

Two CL terms have taxon constraints that are too tight and cause issues when ZFA is merged with Uberon and CL.

'B cell, CD-19 positive'

'B cell, CD-19 positive' is said to be mammal-specific (in_taxon some Mammalia). It’s actually part of the logical definition.

This makes, in turn, most of the B cells in CL (e.g. 'mature B cell', 'immature B cell', 'transitional stage B cell, etc.) mammal-specific.

But B cells (including mature and immature B cells, transitional stage B cell, etc.) exist beyond mammals, e.g. in zebrafish. Most ZFA terms for B cells are unsatisfiable in Uberon+CL+ZFA because of the restriction of 'B cell, CD-19 positive' to mammals.

'rod bipolar cell'

'rod bipolar cell is said to be mammal-specific (in_taxon some Mammalia).

But those cells apparently also exist in zebrafish, and the ZFA term for them is unsatisfiable in Uberon+CL+ZFA because of that restriction to mammals.

addiehl commented 1 month ago

We should probably drop the (in_taxon some Mammalia) for the B cell, CD19-positive. According to this article, CD19 is found on B cells in Zebrafish, and is thus most like a marker of B cells in most or all vertebrates.

Google Gemini offers up additional articles in support of CD19 on B cells in zebrafish. I have not had time to verify this information yet:

Scientific Articles Identifying CD19 as a B Cell Marker in Zebrafish

Here are a few scientific articles that have used CD19 as a marker for B cells in zebrafish:

  1. Page et al., 2013: This study characterized the development and behavior of IgM+ B cells in zebrafish. They utilized three fluorescent transgenic lines, including one expressing CD19, to define the existence of pro-B, immature/mature, and mature B cells in the kidney marrow.  

Title: "Zebrafish B cells exhibit a distinct developmental pattern and are highly plastic." Journal: Blood

  1. Lu et al., 2016: This research explored the role of B cells in zebrafish tumor immunity. They found that CD19+ B cells can express the death ligand FasL to directly induce cytotoxicity when stimulated by IL-17A.  

Title: "CD19+ B cells contribute to anti-tumor immunity in zebrafish through FasL-mediated cytotoxicity."   Journal: Frontiers in Immunology

  1. Hu et al., 2010: This study identified IgZ as a novel B cell marker in zebrafish. They also confirmed the expression of CD19 on B cells in different tissues.  

Title: "Identification of IgZ as a novel B cell marker and its expression in zebrafish immune tissues." Journal: Developmental and Comparative Immunology

  1. Tao et al., 2017: This research investigated the regulatory role of B cells in zebrafish inflammation. They found that CD19+ B cells can be negatively regulated by IL-10.

Title: "IL-10-producing B cells regulate inflammation in zebrafish." Journal: Journal of Immunology These articles provide valuable insights into the use of CD19 as a B cell marker in zebrafish and its role in various immune processes.

dosumis commented 1 month ago
image

Looks like recent work supports rod-bipolar pathway as more ancient than previously thought

image image

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10602083/

So I think OK to relax taxon constraints on this to.