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Fix merge conflicts for the "Stomatogastric ganglion crab lobster" #1

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gouttegd
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This PR resolves the existing conflicts on the original PR submitted to CL.

Once it will have been merged here, on the CL side we will be able to merge the resulting, fixed PR.

JABelfiore and others added 30 commits January 31, 2025 14:18
* Def and refs

* edited parent term

* definition amend and partonomy update

* plural -> singular

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Co-authored-by: CEastwood <116108977+Caroline-99@users.noreply.github.com>
…te (#2653)

* Obsolete neuronal brush cells and adjust logical definition of tanycyte

Fixes #2514 #2634

* Update cl-edit.owl

* Update merged_import.owl

* Update cl-edit.owl

Fixed incomplete obsoletion

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Co-authored-by: CEastwood <116108977+Caroline-99@users.noreply.github.com>
Co-authored-by: dosumis <dosumis@gmail.com>
Co-authored-by: Caroline Eastwood <ce12@sanger.ac.uk>
* defs, refs, uberon import

stomach smooth muscle inner oblique layer imported from uberon

* refresh merged_import.owl

* ref update, equiv class updayte

* ref removed

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Co-authored-by: CEastwood <116108977+Caroline-99@users.noreply.github.com>
Fixes #2863
Moved the disclaimer to the end of the extended description with brackets
Fixes #2929
- Improved Intestinal tuft cell textual definition
- Added references

The term 'cytospinule' has been added to GO and will be linked to this term once available.
* Fixes #2931

* Update cl-edit.owl

* Update cl-edit.owl

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Co-authored-by: Caroline Eastwood <ce12@sanger.ac.uk>
Co-authored-by: CEastwood <116108977+Caroline-99@users.noreply.github.com>
* def and refs

* partonomy added

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Co-authored-by: CEastwood <116108977+Caroline-99@users.noreply.github.com>
* Fixes #2925 Conjunctiva goblet cell

Fixes #2925
- Improved textual and logical definition
- Added references

* updated definition and synonym
Fixes #2939

- Fixed textual definition and added a reference
- Cleaned up logical def
- Changed the main label for concistency
* Fixes #2904 - NTR subclasses of nasal tuft cell

- Added two terms tuft cell of olfactory epithelium and tuft cell of nasal cavity respiratory epithelium.

-Fixed logical definition of olfactory epithelial cell and basal cell of olfactory epithelium.

* Update cl-edit.owl
* def and refs

* partonomy added

* changed synonym type to related and abbreviations

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Co-authored-by: JABelfiore <jb69@sanger.ac.uk>
Co-authored-by: Jasmine Belfiore <166385424+JABelfiore@users.noreply.github.com>
Co-authored-by: CEastwood <116108977+Caroline-99@users.noreply.github.com>
Fixes #2955
- NTR tuft cell of stomach

Co-authored-by: Aleix Puig <94959119+aleixpuigb@users.noreply.github.com>
Fixes #2850

Imported dendriole and linked it to unipolar brush cell
* Fixes #2953 NTR-tuft cell of salivary gland

Fixes #2953

NTR-tuft cell of salivary gland

* updates the label, fixed the logical def and removed synonym

* Update cl-edit.owl
We remove a bunch of rules in the custom Makefile that were intended to
generate some custom diffs. Those rules are never called from amywhere,
so the diffs are only generated when they are explicitly called by a
user on the command line -- which means they are probably never used at
all, especially now that we are producing and *publishing* more complete
diffs on every release.

closes #2641
Fixes #2957

NTR-tuft cell of auditory tube
* Fixes #2671 - Squamous epithelial cell and subclasses

Fixes #2671 -

Squamous epithelial cell and subclasses

* Update cl-edit.owl

* updated periderm cells logical def
* Fixes #2959 - NTR tuft cell of urethra

Fixes #2959

- NTR tuft cell of urethra
- Links to GO term - 'capable of' some 'positive regulation of smooth muscle contraction involved in micturition'

* updated definition and added a comment
* Fixes #2974 follicular cell ovary classification

fixes #2974

Changed the logical definition of follicular cell of ovary.

* Update cl-edit.owl
Fixes #2976
Changed logical definition of luteal cell - removed SubclassOf "stromal cell of ovary"
* def and refs

* doi to PMID

* second sentence removed

* 2nd sentence removed

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Co-authored-by: CEastwood <116108977+Caroline-99@users.noreply.github.com>
* Fixes #2980 - early and late luteal cell

Fixes #2980

- Added new terms - early and late luteal cells

* Update cl-edit.owl
* def and refs

* added myenteric to name

* name update

* name change, space added, synonym added

* synonym ref added

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Co-authored-by: CEastwood <116108977+Caroline-99@users.noreply.github.com>
* def and refs

* added synonym

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Co-authored-by: CEastwood <116108977+Caroline-99@users.noreply.github.com>
* dogiel type I mesenteric neuron

* typo fix

* inline refs, typo, removed 2nd sentence

* logical def updated

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Co-authored-by: David Osumi-Sutherland <dosumis@gmail.com>
Caroline-99 and others added 4 commits March 7, 2025 15:43
* Fixes #2978 - steroidogenic stromal cell of ovary

Added a new term steroidogenic stromal cell of ovary.

* Update cl-edit.owl
* def and refs

* synonym added

* doi lowercase

* doi to PMID

* changed to related synonym

* added  abbreviation property type
* merge mucous neck cell
* improved def
* redundancies removed (inference checked)

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Co-authored-by: CEastwood <116108977+Caroline-99@users.noreply.github.com>
Co-authored-by: David Osumi-Sutherland <dosumis@gmail.com>
@stevewds
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Thank you!

@stevewds stevewds merged commit 2ff203f into Waltham-Data-Science:stomatogastric_ganglion_crab_lobster Mar 13, 2025
@gouttegd gouttegd deleted the stomatogastric_ganglion_crab_lobster_fixed branch March 13, 2025 09:40
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7 participants