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fix: status's range is string instead of uriorcurie #263

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fix: status's range is string instead of uriorcurie #263

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8 changes: 5 additions & 3 deletions linkml_model/model/schema/meta.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -434,11 +434,13 @@ slots:
aliases:
- workflow status
domain: element
range: uriorcurie
range: string

@noelmcloughlin noelmcloughlin Jul 24, 2026 •
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Could we test this change against OWL generator?

While investigating linkml/linkml#3803 I tried this patch but found OwlSchemaGenerator.add_metadata() is silently dropping status annotation from OWL output due to this owlgen.py conditional

if metaslot_curie.startswith("linkml:"):
    # only mapped properties
    continue

This skips metaslots whose URI falls back to the native linkml: namespace - and after deleting slot_uri: bibo:status, the slot's URI becomes linkml:status, and every element's status value vanishes from the generated OWL.

https://github.com/linkml/linkml/blob/8e443f15faa4673acc3345923ea84199f73e7f50/packages/linkml/src/linkml/generators/owlgen.py#L379

@Silvanoc Silvanoc Jul 24, 2026

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@noelmcloughlin it might be related with issue linkml/linkml#3752. Please give the attached PR a try.

@noelmcloughlin noelmcloughlin Jul 24, 2026 •
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Seems different bug... let me clarify

this PR alone is problematic. After removing slot_uri: bibo:status, slot's URI becomes linkml:status, and every element (ArrayExpression, apply_to, range_expression, etc.) status value vanishes from generated OWL (on my branch, I confirmed zero "testing" occurrences in my output, versus ~32 bibo:testing triples using alternative uriocurie approach). So a sibling PR forowlgen.py is needed to address fallout

@Silvanoc Silvanoc Jul 24, 2026

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Hmm, this PR is not changing status itself, only its range. Since you have tried it out, I assume that the explanation is not precise, but the problematic effect exists.

I'll switch this PR to draft until I've clarified the situation and, it needed, provided the required sibling PR for owlgen.py.

@Silvanoc Silvanoc Jul 24, 2026 •
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@noelmcloughlin I've realized this issue trying to make SchemaView.expand_curie strict (trying to expand something that is neither a URI -no expansion needed- nor a CURIE -can be expanded) on PR linkml/linkml#3805 (specifically commit linkml/linkml@85fb0c9). Apparently this and that PRs are somehow coupled together.

@noelmcloughlin noelmcloughlin Jul 27, 2026

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yes, three lines in owlgen.py are coupled to this PR

if metaslot_curie.startswith("linkml:"):
    # only mapped properties
    continue

@Silvanoc Silvanoc Sep 4, 2026

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@noelmcloughlin Can you give me the link to a schema to reproduce the issue?

With the kitchen_sink.yaml schema I cannot see any difference on how this spot behaves after the change in the model. I'm printing out metaslot_curie and saving the output with and without the model change and I get exactly the same values.

@Silvanoc Silvanoc Sep 4, 2026

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The owlgen spot is about the slot URI, not about the value (what this patch changes), therefore I'm unsure if the diagnose is correct.

description: status of the element
slot_uri: bibo:status
close_mappings:
- bibo:status
examples:
- value: "bibo:draft"
- value: "testing"
- value: "unstable"
see_also:
- https://www.hl7.org/fhir/valueset-publication-status.html ## Draft, Active, Retired, Unknown
- https://www.hl7.org/fhir/versions.html#std-process ## Draft, Trial Use, Normative, Informative, Deprecated
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