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

[dosumis]

• [NTR] Early enterocyte #2580

• Enterocyte - Late (APOA1, APOC3, APOB, GUCA2A, CDHR5)

• BEST4 enterocyte and subtypes #2465
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• [NTR]Epithelial stem cell of gut #2562 - -Not added anymore as 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

• [NTR] Lamina propria fibroblast (S1) #2565

• [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