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NTR mesenchymal lymphoid tissue organizer cell #2610

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NTR mesenchymal lymphoid tissue organizer cell #2610

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JABelfiore
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definition, synonyms and refs added

@JABelfiore JABelfiore linked an issue Sep 24, 2024 that may be closed by this pull request
[NTR] Mesenchymal lymphoid tissue organizer cell #2564
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@JABelfiore JABelfiore self-assigned this Sep 24, 2024
@JABelfiore JABelfiore marked this pull request as ready for review September 24, 2024 15:26
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dosumis commented Sep 25, 2024

#gogoeditdiff

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Here's a diff of how these changes impact the classified ontology (on -simple file):

Ontology comparison

Left

  • Ontology IRI: http://purl.obolibrary.org/obo/cl/cl-simple.owl
  • Version IRI: http://purl.obolibrary.org/obo/cl/releases/2024-09-25/cl-simple.owl
  • Loaded from: file:/__w/cell-ontology/cell-ontology/src/ontology/cl-simple-master.owl/cl-simple.owl

Right

  • Ontology IRI: http://purl.obolibrary.org/obo/cl/cl-simple.owl
  • Version IRI: http://purl.obolibrary.org/obo/cl/releases/2024-09-25/cl-simple.owl
  • Loaded from: file:/__w/cell-ontology/cell-ontology/src/ontology/cl-simple-pr.owl/cl-simple.owl

Ontology imports

Ontology annotations

mesenchymal lymphoid tissue organizer cell http://purl.obolibrary.org/obo/CL_4047022

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Here's a diff of your edit file (unreasoned)

Ontology comparison

Left

  • Ontology IRI: http://purl.obolibrary.org/obo/cl.owl
  • Version IRI: None
  • Loaded from: file:/__w/cell-ontology/cell-ontology/master/src/ontology/cl-edit.owl

Right

  • Ontology IRI: http://purl.obolibrary.org/obo/cl.owl
  • Version IRI: None
  • Loaded from: file:/__w/cell-ontology/cell-ontology/branch/src/ontology/cl-edit.owl

Ontology imports

Ontology annotations

mesenchymal lymphoid tissue organizer cell http://purl.obolibrary.org/obo/CL_4047022

Added

dosumis
dosumis requested changes Sep 25, 2024
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I think more discussion needed on this one. Looks like we should have a general cell type + maybe one for fetal gut (based on Elementaite). Needs ref that supports adult. I think assertions are complex enough that it would be much better if we could add minirefs in text defs so that users and future editors know exactly which refs to go to to check assertions.

src/ontology/cl-edit.owl
@@ -32490,6 +32491,16 @@ AnnotationAssertion(terms:date obo:CL_4047012 "2024-09-06T08:41:39Z"^^xsd:dateTi
AnnotationAssertion(rdfs:label obo:CL_4047012 "angiogenic pericyte"@en)
SubClassOf(obo:CL_4047012 obo:CL_0000669)

# Class: obo:CL_4047022 (mesenchymal lymphoid tissue organizer cell)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:31201308") Annotation(oboInOwl:hasDbXref "PMID:34497389") obo:IAO_0000115 obo:CL_4047022 "A stromal cell found in the adult gut that plays a crucial role in the formation and maintenance of gut-associated lymphoid tissues (GALTs). This cell is characterized by it's ability to interact with lymphoid tissue inducer (LTi) cells, express lymphotoxin beta receptor (LTβR) and vascular cell adhesion molecule (VCAM), produce chemokines and cytokines for immune cell recruitment and positioning, and contribute to the structural organization of lymphoid tissues within the intestinal environment. mLTo cells are distinguished from other stromal cells by their specific function in orchestrating the development and maintenance of organized lymphoid structures in the gut, which are essential for intestinal immune responses and homeostasis.")
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"PMID:31201308" not a relevant paper. Typo?

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@dosumis dosumis dosumis requested changes

@AvolaAmg AvolaAmg Awaiting requested review from AvolaAmg

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[NTR] Mesenchymal lymphoid tissue organizer cell
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