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Fixes #2486 Fixes #2484 NTR- endocrine gland and pituitary gland capillary endothelial cell #2628

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merged 6 commits into from
Oct 10, 2024
Merged

Fixes #2486 Fixes #2484 NTR- endocrine gland and pituitary gland capillary endothelial cell #2628

merged 6 commits into from
Oct 10, 2024

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Caroline-99
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Fixes #2486 Fixes #2484

Added 2 new terms ( a grouping term and a subclass) with textual and logical defs and references

@Caroline-99
Fixes #2486 Fixes #2484
a41d599 
Added 2 new terms ( a grouping term and a subclass) with textual and logical defs and references
@Caroline-99 Caroline-99 linked an issue Oct 1, 2024 that may be closed by this pull request
[NTR] endocrine gland capillary endothelial cell #2484
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@Caroline-99 Caroline-99 self-assigned this Oct 1, 2024
@Caroline-99 Caroline-99 requested a review from AvolaAmg October 1, 2024 11:18
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#gogoeditdiff

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github-actions bot commented Oct 1, 2024 •
edited
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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/2024-10-10/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/2024-10-10/cl-simple.owl
  • Loaded from: file:/__w/cell-ontology/cell-ontology/src/ontology/cl-simple-pr.owl/cl-simple.owl

Ontology imports

Ontology annotations

endocrine gland capillary endothelial cell http://purl.obolibrary.org/obo/CL_4052015

Added

pituitary gland capillary endothelial cell http://purl.obolibrary.org/obo/CL_4052016

Added

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github-actions bot commented Oct 1, 2024 •
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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

endocrine gland capillary endothelial cell http://purl.obolibrary.org/obo/CL_4052015

Added

pituitary gland capillary endothelial cell http://purl.obolibrary.org/obo/CL_4052016

Added

dosumis
dosumis requested changes Oct 9, 2024
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src/ontology/cl-edit.owl Outdated

# Class: obo:CL_4052016 (pituitary gland capillary endothelial cell)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:10810312") Annotation(oboInOwl:hasDbXref "PMID:32910242") Annotation(oboInOwl:hasDbXref "PMID:4899902") obo:IAO_0000115 obo:CL_4052016 "A capillary endothelial cell that is part of the pituitary gland, particularly in the anterior pituitary. This cell is distinguished by its numerous fenestrations, which are covered by a single-layered diaphragm. The diaphragm features a dense ring-like structure, facilitating the passage of hormones and other substances essential for endocrine signalling.")
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Why particularly in the anterior pituitary - are there just more capillaries there? Name+ logical def defines as Any capillary endothelial cell of the pituitary gland, so needs to not be defining as subset. Please clarify or drop detail.

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I have changed the definition to make it more inclusive, as both the anterior and posterior lobes of the pituitary gland have fenestrated capillaries.

For the anterior lobe, I found a paper that provides detailed information about the fenestrations specifically within the capillary endothelial cells of the anterior pituitary in rats. I have included these information in the comments section but wasn't sure whether I should include it in the extended description instead

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#gogoeditdiff

@Caroline-99 Caroline-99 requested a review from dosumis October 10, 2024 09:38
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dosumis commented Oct 10, 2024

Looks good

Minor issue: I think better to drop the narrow synonym. I don't think useful as anyone looking for this is likely to find by general class name, which is identical apart from 'anterior'.

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Looks good

Minor issue: I think better to drop the narrow synonym. I don't think useful as anyone looking for this is likely to find by general class name, which is identical apart from 'anterior'.

yeah will remove it now

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#gogoeditdiff

@Caroline-99 Caroline-99 merged commit 7abc823 into master Oct 10, 2024
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@Caroline-99 Caroline-99 deleted the 2486-ntr-pituitary-gland-capillary-endothelial-cell branch October 10, 2024 14:10
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@dosumis dosumis dosumis approved these changes

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[NTR] pituitary gland capillary endothelial cell [NTR] endocrine gland capillary endothelial cell
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