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Obsolete the NMDC environmental context value set properties and remove the membership template - #1682
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…ve the membership template The 17 subset properties ENVO_03605010 to ENVO_03605026 were released in 2025-02-05 and 2026-10-23, so they are deprecated with an obsolete label rather than deleted. The template robot_templates/nmdc_env_context_subset_membership.owl that asserted 673 ENVO classes into those subsets is removed together with the Makefile rules and catalog entry that built and imported it: it was generated in https://github.com/microbiomedata/submission-schema from a released envo.owl and copied back here, so each side depended on the other's release, and the value sets include terms from ontologies other than ENVO. They are maintained in that repository only. Part of #1675 and #1642
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🟢 Approval recommended
The retirement preserves published property identifiers and consistently removes the membership sources and their build and import references.
No open issues 🎉
What changed in this PR
Retires ENVO’s NMDC environmental context value sets while preserving their published identifiers. Value-set maintenance remains in the NMDC submission schema, removing the circular release dependency.
Changes:
- Marks all 17 annotation properties obsolete, preserves their existing metadata, and adds migration notes.
- Deletes the membership template and generated OWL module.
- Removes the module’s build rules, ontology import, and catalog mapping.
| File | Description |
|---|---|
src/envo/robot_templates/nmdc_env_context_subset_membership.tsv |
Removes the subset membership template. |
src/envo/robot_templates/nmdc_env_context_subset_membership.owl |
Removes the generated membership module. |
src/envo/Makefile |
Removes membership generation targets and source dependency. |
src/envo/envo-edit.owl |
Obsoletes 17 properties and removes the membership import. |
src/envo/catalog-v001.xml |
Removes the deleted module’s import mapping. |
Review effort: Balanced
This was referenced Oct 26, 2026
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This retires the NMDC environmental context value sets from ENVO. The 17 subset annotation properties ENVO:03605010 to ENVO:03605026 keep their identifiers and are marked obsolete, because they were published in the 2025-02-05 and 2026-10-23 releases. The template that asserted 673 ENVO classes into those subsets is removed, together with the Makefile rules and the catalog entry that built and imported it.
Part of #1675
The value sets were generated in https://github.com/microbiomedata/submission-schema from a released envo.owl and copied back into ENVO to be merged into the next release, so each side depended on the other's release. They also include terms from other ontologies, 26 Plant Ontology classes in the plant-associated medium set alone, which an ENVO subset cannot carry. I maintain them on the NMDC side, and from now on they live there only. The first issue below asked for the subsets to be restored after the 2025-08-19 release lost them; the restore brought them back, and this pull request records the decision to retire them instead.
Each property keeps its comment and seeAlso, gains
owl:deprecated true, an "obsolete" label prefix and an editor note pointing at the submission schema, and loses its sub-property axioms. The ODK CI target passes locally, and because every labelled ENVO identifier survives, the check proposed in the second pull request below passes as well.