Add Linked Open Vocabularies recommended ontology metadata #210

vincentkelleher · 2024-12-24T10:07:42Z

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.

sierra-moxon · 2025-01-06T17:26:55Z

linkml_model/model/schema/meta.yaml

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

-  publisher:


we should probably deprecate this slot rather than delete.

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.

linkml_model/model/schema/meta.yaml

sierra-moxon · 2025-01-06T17:33:23Z

linkml_model/model/schema/meta.yaml

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


should creator and contributor be multivalued?

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

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

I think they should both be multivalued. conceptually that does not translate to one property assertion with multiple values, but multiple property assertions, like

?schema dc:creator orcid:123 ; dc:creator orcid:124 .

That said, I think this is redundant with contributors see comment below.

cmungall · 2025-01-06T17:54:28Z

linkml_model/model/schema/meta.yaml

@@ -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#


Let's stick to established prefixes, e.g bioregistry

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 ?

The prefix is standard: https://bioregistry.io/registry/cc

The expansion as far as I can see should be https?

linkml_model/model/schema/meta.yaml

cmungall · 2025-01-06T17:56:17Z

linkml_model/model/schema/meta.yaml

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


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

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 🤔

can just change the behavior in the OWL generator to convert contributors to contributor ?

Isnt this as easy as asserting slot_uri: dc:contributor? Need to check with @sierra-moxon to be sure.

cmungall

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

Signed-off-by: Vincent Kelleher <vincent.kelleher@gaia-x.eu>

vincentkelleher · 2025-01-07T10:17:00Z

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 👍

vincentkelleher · 2025-02-20T09:22:20Z

Just a little bump to have your opinion on the questions above 😇

matentzn

I didnt look into redundancy but I think the proposed properties are useful. I have a little issue with anarchy in the ranges of the proposed properties, but I guess everyone can decided by themselves of they want to use stronger URIs (@sierra-moxon any idea what the rdf representation of a string typed literal that looks like a URI will look like? probably a string, right?)

matentzn · 2025-02-21T19:00:35Z

linkml_model/model/schema/meta.yaml

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


I think they should both be multivalued. conceptually that does not translate to one property assertion with multiple values, but multiple property assertions, like

?schema dc:creator orcid:123 ; dc:creator orcid:124 .

That said, I think this is redundant with contributors see comment below.

matentzn · 2025-02-21T19:02:38Z

linkml_model/model/schema/meta.yaml

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


can just change the behavior in the OWL generator to convert contributors to contributor ?

Isnt this as easy as asserting slot_uri: dc:contributor? Need to check with @sierra-moxon to be sure.

matentzn · 2025-02-21T19:03:26Z

linkml_model/prefixmap/meta.yaml

@@ -4,7 +4,9 @@
   "OIO": "http://www.geneontology.org/formats/oboInOwl#",
   "SIO": "http://semanticscience.org/resource/SIO_",
   "bibo": "http://purl.org/ontology/bibo/",
+   "cc": "http://creativecommons.org/ns#",


matentzn · 2025-02-21T19:06:25Z

linkml_model/model/schema/meta.yaml

+      Recommended practice is to identify the contributor with a URI. 
+      If this is not possible or feasible, a literal value that identifies the publisher may be provided.
+    domain: schema_definition
+    range: string


not so keen on this, but I guess I will lose this battle.. (why not uriorcurie)?

matentzn · 2025-02-21T19:08:08Z

linkml_model/model/schema/meta.yaml

+      Recommended practice is to refer to a rights statement with a URI. 
+      If this is not possible or feasible, a literal value (name, label, or short text) may be provided.
+    domain: schema_definition
+    range: string


again, it would really help if we could get people that go all the way to developing a LinkML schema to use URIs for licenses, contributors and creators etc.

sierra-moxon reviewed Jan 6, 2025

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sierra-moxon requested a review from cmungall January 6, 2025 17:33

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vincentkelleher force-pushed the add_ontology_description_fields branch from 596755f to 1fb956b Compare January 7, 2025 10:01

add Linked Open Vocabularies recommended ontology metadata

434ec7d

Signed-off-by: Vincent Kelleher <vincent.kelleher@gaia-x.eu>

vincentkelleher force-pushed the add_ontology_description_fields branch from 1fb956b to 434ec7d Compare January 7, 2025 10:11

vincentkelleher requested review from sierra-moxon and cmungall January 14, 2025 13:23

matentzn reviewed Feb 21, 2025

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Add Linked Open Vocabularies recommended ontology metadata #210

Add Linked Open Vocabularies recommended ontology metadata #210

vincentkelleher commented Dec 24, 2024

sierra-moxon Jan 6, 2025

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Add Linked Open Vocabularies recommended ontology metadata #210

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vincentkelleher commented Dec 24, 2024

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