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Add Linked Open Vocabularies recommended ontology metadata #210

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What makes ontologies awesome is their reusability. To be reused an ontology needs to be discoverable and easily understandable through documentation (FAIR principles mention those requirements).

At Gaia-X we are working on making our LinkML generated ontology more discoverable and better documented through ontology metadata. The Linked Open Vocabularies project gives recommendations about how an ontology can be described through metadata by using well established vocabularies such as Dublin Core Terms, Creative Commons and OWL.

This pull request proposes a solution to integrate slots for this metadata in the schema definition to then use those slots in the LinkML generators.

@@ -497,14 +498,6 @@ slots:
in_subset:
- BasicSubset

publisher:
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we should probably deprecate this slot rather than delete.

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agreed

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It isn't deleted, you can find it at line 2632 😇

I didn't delete any existing attribute, I only modified them to add some information.

- https://creativecommons.org/ns
- https://lov.linkeddata.es/Recommendations_Vocabulary_Design.pdf

creator:
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should creator and contributor be multivalued?

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I had the exact same question while defining this but seemingly it's a single person according to Dublin Core:

image

I think it's possible to define multiple creators within an organization and reference it here 😊

@sierra-moxon sierra-moxon requested a review from cmungall January 6, 2025 17:33
@@ -49,6 +49,7 @@ prefixes:
qudt: http://qudt.org/schema/qudt/
cdisc: http://rdf.cdisc.org/mms#
SIO: http://semanticscience.org/resource/SIO_
cc: http://creativecommons.org/ns#
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Let's stick to established prefixes, e.g bioregistry

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I can't understand which part of this prefix is troublesome 😌

Is it the use of cc which is too short ?
Or is it that Creative Commons cannot be considered as an established prefix ?

- https://www.dublincore.org/specifications/dublin-core/dcmi-terms/#http://purl.org/dc/terms/creator
- https://lov.linkeddata.es/Recommendations_Vocabulary_Design.pdf

contributor:
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we already have contributors, which can be applied at any level (schema, element, ...)

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I added this to be compliant with the Linked Open Vocabularies standards but I imagine I can just change the behavior in the OWL generator to convert contributors to contributor ?

Then I'll have to find a way to manage multiple entries 🤔

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I suggest breaking this up into smaller PRs, and doing a careful alignment with what already exists - e.g. we already have contributors, so no need for contributor

@vincentkelleher vincentkelleher force-pushed the add_ontology_description_fields branch from 596755f to 1fb956b Compare January 7, 2025 10:01
@vincentkelleher vincentkelleher force-pushed the add_ontology_description_fields branch from 1fb956b to 434ec7d Compare January 7, 2025 10:11
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I suggest breaking this up into smaller PRs, and doing a careful alignment with what already exists - e.g. we already have contributors, so no need for contributor

What should be the granularity of those PRs ? One per attribute ?
I will have a closer look to see if I made some other alignment mistakes 👍

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3 participants