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Develop to Master Branch #870

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shanmukhkalasamudram wants to merge 9 commits into
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develop
Open

Develop to Master Branch #870
shanmukhkalasamudram wants to merge 9 commits into
masterfrom
develop

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@shanmukhkalasamudram

@shanmukhkalasamudram shanmukhkalasamudram commented May 15, 2026

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johnbeve and others added 5 commits April 7, 2026 10:26
@johnbeve
updating version info to align with 2.1 release
a051575
@shanmukhkalasamudram
Rebuild merged file to Develop Branch(#861) (#864)
9a8b27c 
* rebuild merged file (#861)

* fix: rebuild CommonCoreOntologiesMerged with 11 modules only
@johnbeve
Add files via upload
af9c38e
@johnbeve
Update README.md (#869)
48827b4
@johnbeve
Cco purls (#873)
d9b266a 
* Update README.md

* purl testing continued

* Rename index.html to index.html

* Update index.html

* Update README.md

* Update README.md

* purl'ish testing

* temp

* rename trickery

* renaming

* Create readme.md

* Add files via upload

* deleted first try html index

* added ttls

* Create ont00000958.ttl

* Create c.ttl

* Rename c.ttl to .ttl

* Rename .ttl to index.html

* Rename src/cco-iris/index.html to src/cco-iris/.ttl/index.html

* Update and rename src/cco-iris/.ttl/index.html to src/cco-iris/w.ttl

* Rename w.ttl to .ttl

* testing new iris

* All the IRIs

---------

Co-authored-by: Mark Jensen <mpjensen@buffalo.edu>
@shanmukhkalasamudram shanmukhkalasamudram mentioned this pull request May 21, 2026
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@mark-jensen

mark-jensen commented Jun 5, 2026

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@johnbeve @shanmukhkalasamudram Something is amiss. In the email I received I was directed to review #871, but that is only correcting something in this commit. Can you direct me to where you have all the new files generated? I don't think the ones in this commit are those.

Based on the contents of this commit:
Did you use the most recent version (2.1) of the ontologies to generate the individual fils for each element? The reason I ask is that the ontology files, 11 modules plus Merged and All Core, are all annotated at v2.0. Please confirm that you are using the most recent version to generate all the element-specific files.

In CCO Merged v2.1, this branch, I see 1914 CCO-unique element IRIs. So, adding the 13 ontology IRIs, that = 1927 IRIs that need to resolved.

re workflow: All of the IRIs, minus the 11 core modules, are derived products based don those core files, and should only be generated once the core 11 are ready for release.

@shanmukhkalasamudram

shanmukhkalasamudram commented Jun 5, 2026

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@mark-jensen — sorry for the mix-up. #871 only resolves the CommonCoreOntologiesMerged.ttl
merge conflict; it does not contain the regenerated files. All the newly generated IRI
files are in a separate PR:

#881

On your specific points:

@shanmukhkalasamudram
Regenerate CCO IRI resolution files from v2.1 (#881)
0d93da8 
- Stamp TimeOntology & UnitsOfMeasureOntology at Version 2.1 (2026-04-04);
  the 2.1 version bump had skipped these two modules.
- Refresh the 13 ontology-IRI resolver files (11 modules + Merged + AllCore)
  in src/cco-iris/ from current 2.1 sources (were frozen at 2.0).
- Regenerate the 1,914 per-element IRI snippets from the merged ontology:
  480 content updates, 33 new terms (ont00002000+).
- Enhance generate_cco_iris.py to normalize the OWL API version tag (removes
  ~1,401 cosmetic-only diffs) and report NEW / content-CHANGED files to the log.

Out of scope (flagged for Mark): 114 non-core resolver files left untouched --
109 extension-derived (Barcode etc.) + 5 retired terms.

Co-authored-by: Shanmukh <shanmukhkalasamudram@Shanmukhs-MBP.lan>
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3 participants

@shanmukhkalasamudram @mark-jensen @johnbeve