Complete NTRs & edits required for mapping of Gut Cell Atlas terms

[dosumis]

• [NTR] Early enterocyte #2580

• Enterocyte - Late (APOA1, APOC3, APOB, GUCA2A, CDHR5) - decided this is same as enterocyte

• BEST4 enterocyte and subtypes #2465
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• [NTR]Epithelial stem cell of gut #2562 - -Not added anymore - the same as the existing term intestinal crypt stem call term

• [NTR] transit amplifying cell of gut #2563

• [NTR] intestinal villus capillary endothelial cell #2476 This is a specialised, fenestrated endothelial cell - check with experts whether this is appropriate mapping for their capillary cell.

• [NTR] intestinal subserosal fibroblast #2576

• [NTR] Mesenchymal lymphoid tissue organizer cell #2564

• Subepithelial fibroblasts and subclasses

• [NTR] intestinal enteroendocrine progenitor  #2586

• [NTR] follicle associated enterocyte #2587 - ticket is made but waiting for an uberon term follicle associated epithelium

• [NTR] intestinal enteroendocrine progenitor  #2586

• #2589

• [NTR] crypt support fibroblast (+ subclasses) #2558

• [NTR] intestinal fibroblastic reticular cell #2578

• [NTR] angiogenic pericyte #2517

• Immature Pericyte [NTR] Immature pericyte #2503

• Review mapping sheet for missing mappings

(almost all done - might be a few very recently added terms to map)

• Check for all cases where there is a validated CellGuide description

@Caroline-99 - work on simple script to lookup and report - matched_validated_descriptions_gut_atlas

• Review validated CellGuide descriptions for addition

check no contradiction with CL def

• Run GCA hierarchy through validator

(https://github.com/hubmapconsortium/validation-template) - requires reformatting. Try using ChatGPT to reformat. <-- stretch goal

[JABelfiore]

Following cell terms removed as they are not in the updated version of the GCA hierarchy

• Immune Organizing Fibroblast (mLN stroma)
• Crypt Support fibroblast [NTR] crypt support fibroblast (+ subclasses) #2558
• Villus Support fibroblast
• Immune Organizing Fibroblast (mLN stroma)

Following cell terms added from updated GCA hierarchy:

• [ ]Subepithelial fibroblasts (S2)
• [ ]Lamina propria fibroblasts (S1)
• [ ]Submucosal Fibroblasts (aka Crypt Support/Trophocytes/S3)
• [ ]Fibroblastic reticular cells

[Caroline-99]

There are 69 terms with a validated CellGuide description: matched_validated_descriptions_gut_atlas

[aleixpuigb]

Some of the cells are restricted in the intestinal compartment but contain the term 'gut' either in the label, the definition or both. The gut comprehends more structures than the intestine, such as the stomach or the esophagus, and the presence of intestinal cells in there might indicate pathology (e.g., Barret's esophagus). For example, transit amplifying cell of gut should be intestinal transit amplifying cell.
CC @emquardokus