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fenestrated capillary endothelial cells updates #2475

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merged 10 commits into from
Aug 16, 2024
Merged

fenestrated capillary endothelial cells updates #2475

merged 10 commits into from
Aug 16, 2024

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Caroline-99
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@Caroline-99 Caroline-99 commented Aug 6, 2024 •
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Updated logical and textual defs for peritubular capillary endothelial cells and subclasses

  • added logical defs
  • updated the textual defs and included references
  • added extra description in the comments section

Updated glomerular endothelial cell defs

  • linked to GO term GO:0036053
  • added extra description in the comments section
  • added references

@Caroline-99
updated logical and textual defs
2e882c7 
updated logical and textual defs for peritubular capillary endothelial cells and subclasses
-added logical defs
-Updated the textual defs and included references
-added extra description in the comments section
@Caroline-99 Caroline-99 linked an issue Aug 6, 2024 that may be closed by this pull request
Revise glomerular and peritubular capillary endothelial cell classification and defs #2474
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@Caroline-99
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Caroline-99 commented Aug 6, 2024 •
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This could be a separate ticket but I think glomerular endothelial cell should be merged into glomerular capillary endothelial cell as they both refer to the exact same cell type ( same specialized endothelial cells found in the glomerular capillaries of the kidney). And glomerular endothelial cell could be added as a synonym?

@Caroline-99 Caroline-99 self-assigned this Aug 6, 2024
@aleixpuigb
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#gogoeditdiff

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github-actions bot commented Aug 9, 2024

Your branch is 1 commit/s behind, please update your branch.

@aleixpuigb
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#gogoeditdiff

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github-actions bot commented Aug 9, 2024

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/2024-08-09/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/2024-08-09/cl-simple.owl
  • Loaded from: file:/__w/cell-ontology/cell-ontology/src/ontology/cl-simple-pr.owl/cl-simple.owl

Ontology imports

Ontology annotations

glomerular endothelial cell http://purl.obolibrary.org/obo/CL_0002188

Added

  • glomerular endothelial cell comment "Glomerular endothelial cells have 60-80 nm fenestrations typically lacking diaphragms in adults but present during embryonic development. Some studies found diaphragms in 2-6% of mature rat glomerular capillaries. Their presence may depend on fixation techniques, developmental stage, or dynamic cell changes. Additionally, these cells help maintain the structural integrity of glomerular capillaries through interactions with the basement membrane and podocytes."

kidney cortex peritubular capillary cell http://purl.obolibrary.org/obo/CL_1001124

Removed

Added

kidney outer medulla peritubular capillary cell http://purl.obolibrary.org/obo/CL_1001123

Removed

Added

peritubular capillary endothelial cell http://purl.obolibrary.org/obo/CL_1001033

Removed

Added

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github-actions bot commented Aug 9, 2024

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

GO_0036053 http://purl.obolibrary.org/obo/GO_0036053

Added

glomerular endothelial cell http://purl.obolibrary.org/obo/CL_0002188

Added

kidney cortex peritubular capillary cell http://purl.obolibrary.org/obo/CL_1001124

Added

kidney outer medulla peritubular capillary cell http://purl.obolibrary.org/obo/CL_1001123

Removed

Added

peritubular capillary endothelial cell http://purl.obolibrary.org/obo/CL_1001033

Removed

Added

aleixpuigb
aleixpuigb reviewed Aug 13, 2024
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I would suggest to use 'that is part of' instead of 'found in'.

@Caroline-99
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I would suggest to use 'that is part of' instead of 'found in'.

Done

aleixpuigb
aleixpuigb requested changes Aug 15, 2024
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Please, see inline comments

src/ontology/cl-edit.owl Outdated Show resolved Hide resolved
src/ontology/cl-edit.owl Show resolved Hide resolved
aleixpuigb and others added 2 commits August 15, 2024 15:40
@aleixpuigb
Merge branch 'master' into 2474-fenestrated-capillary-endothelial-cells
a2e40ed
@Caroline-99
text defs updated
43fcd8f 
-Text definitions updated and a definition for kidney capillary endothelial cell is added
@Caroline-99
Update go_terms.txt
ca41283 
glomerular glomerular endothelium fenestra has been added to go_terms.txt import file
@Caroline-99 Caroline-99 merged commit 24b8d90 into master Aug 16, 2024
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@Caroline-99 Caroline-99 deleted the 2474-fenestrated-capillary-endothelial-cells branch August 16, 2024 09:16
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@aleixpuigb aleixpuigb aleixpuigb approved these changes

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Revise glomerular and peritubular capillary endothelial cell classification and defs
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