feat(gen-owl): emit IRI-valued metadata as IRIs

docs/generators/owl.rst

@@ -67,6 +67,40 @@ Mapping
 
 .. note:: The current default settings for ``metaclasses`` and ``type-objects`` may change in the future
 
+Metadata values that are IRIs
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+Schema metadata and ``annotations`` become annotation triples on the ontology, class or
+property. Their values are literals, except for properties whose value is a resource by
+their own specification: the OWL ontology properties ``owl:versionIRI``,
+``owl:priorVersion``, ``owl:backwardCompatibleWith`` and ``owl:incompatibleWith``;
+``rdfs:seeAlso`` and ``rdfs:isDefinedBy``; the DCMI terms that relate a resource to
+another (``dcterms:license``, ``dcterms:conformsTo``, ``dcterms:references``,
+``dcterms:source``, ``dcterms:relation`` and its sub-properties); and
+``prov:wasDerivedFrom``, ``prov:wasRevisionOf`` and ``prov:hadPrimarySource``.
+
+A value of one of these is emitted as an IRI when it is an absolute IRI or a CURIE with a
+declared prefix; any other value stays a literal:
+
+.. code-block:: yaml
+
+    id: https://example.org/onto/v2
+    license: https://www.eclipse.org/legal/epl-2.0/
+    annotations:
+      owl:versionInfo: v2
+      owl:priorVersion: ex:onto/v1
+      prov:wasDerivedFrom: https://example.org/releases/tag/v2.0.0
+
+.. code-block:: turtle
+
+    <https://example.org/onto/v2> a owl:Ontology ;
+        owl:versionInfo "v2" ;
+        owl:priorVersion <https://example.org/onto/v1> ;
+        prov:wasDerivedFrom <https://example.org/releases/tag/v2.0.0> ;
+        dcterms:license <https://www.eclipse.org/legal/epl-2.0/> .
+
+``dcterms:identifier`` stays a literal: DCMI gives it the range ``rdfs:Literal``.
+
 Enums and PermissibleValues
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^
 

packages/linkml/src/linkml/generators/owlgen.py

@@ -2,6 +2,7 @@
 
 import logging
 import os
+import re
 from collections import defaultdict
 from collections.abc import Iterable, Sequence
 from copy import copy
@@ -54,6 +55,49 @@
 
 SWRL = rdflib.Namespace("http://www.w3.org/2003/11/swrl#")
 SWRLB = rdflib.Namespace("http://www.w3.org/2003/11/swrlb#")
+PROV = rdflib.Namespace("http://www.w3.org/ns/prov#")
+
+IRI_VALUED_METADATA_PROPERTIES: frozenset[URIRef] = frozenset(
+    {
+        # OWL 2 ontology properties and the version IRI relate an ontology to other
+        # ontologies (OWL 2 Structural Specification, sections 3.1 and 3.5).
+        OWL.versionIRI,
+        OWL.priorVersion,
+        OWL.backwardCompatibleWith,
+        OWL.incompatibleWith,
+        # rdfs:range rdfs:Resource, defined as pointing at a resource (RDF Schema 1.1, 5.4).
+        RDFS.seeAlso,
+        RDFS.isDefinedBy,
+        # DCMI Metadata Terms relating a resource to another resource.
+        DCTERMS.license,
+        DCTERMS.conformsTo,
+        DCTERMS.relation,
+        DCTERMS.references,
+        DCTERMS.isReferencedBy,
+        DCTERMS.hasVersion,
+        DCTERMS.isVersionOf,
+        DCTERMS.replaces,
+        DCTERMS.isReplacedBy,
+        DCTERMS.requires,
+        DCTERMS.isRequiredBy,
+        DCTERMS.source,
+        # rdfs:range prov:Entity (PROV-O).
+        PROV.wasDerivedFrom,
+        PROV.wasRevisionOf,
+        PROV.hadPrimarySource,
+    }
+)
+"""Metadata properties whose value is a resource by their own specification.
+
+A value of one of these properties that is an IRI, or a CURIE with a declared prefix, is
+emitted as an IRI node; any other value stays a literal. ``dcterms:identifier`` is not
+listed: DCMI gives it the range ``rdfs:Literal``.
+"""
+
+# An absolute IRI: an RFC 3986 scheme, a colon, and no character an IRI cannot contain
+# (RFC 3987, section 2.2). A CURIE has the same shape, so it is checked against the
+# declared prefixes first.
+_ABSOLUTE_IRI = re.compile(r"^[A-Za-z][A-Za-z0-9+.\-]*:[^\s<>\"{}|\\^`]+$")
 
 
 @unique
@@ -396,6 +440,9 @@ def add_metadata(self, e: Definition | PermissibleValue, uri: URIRef) -> None:
                         obj = URIRef(v)
                     elif metaslot_range == "uriorcurie":
                         obj = URIRef(this_sv.expand_curie(v))
+                    elif (iri := self._metadata_iri(metaslot_uri, v)) is not None:
+                        # e.g. license and conforms_to: strings in the metamodel, resources by their property
+                        obj = iri
                     elif metaslot_range in self._LANGUAGE_TAGGABLE_RANGES and lang:
                         obj = Literal(v, lang=lang)
                     else:
@@ -435,12 +482,31 @@ def add_metadata(self, e: Definition | PermissibleValue, uri: URIRef) -> None:
                 if k_uri == k:
                     k_uri = None
             if k_uri:
-                if isinstance(v.value, str):
+                if (iri := self._metadata_iri(URIRef(k_uri), v.value)) is not None:
+                    obj = iri
+                elif isinstance(v.value, str):
                     obj = self._literal(v.value, e)
                 else:
                     obj = Literal(v.value)
                 self.graph.add((uri, URIRef(k_uri), obj))
 
+    def _metadata_iri(self, prop: URIRef, value: Any) -> URIRef | None:
+        """The IRI *value* denotes, if *prop* takes resources and *value* is an IRI or CURIE.
+
+        Only the properties in :data:`IRI_VALUED_METADATA_PROPERTIES` take resources by their
+        specification. A CURIE is expanded when its prefix is declared; any other value that
+        is a syntactically valid absolute IRI is used as it is. Returns ``None`` otherwise, and
+        the value is emitted as a literal, as for every other property.
+        """
+        if prop not in IRI_VALUED_METADATA_PROPERTIES or not isinstance(value, str):
+            return None
+        if not _ABSOLUTE_IRI.match(value):
+            return None
+        prefix = value.split(":", 1)[0]
+        if prefix in self.schemaview.namespaces():
+            return URIRef(self.schemaview.expand_curie(value))
+        return URIRef(value)
+
     def add_class(self, cls: ClassDefinition) -> None:
         """
         Each ClassDefinition is represented as an OWL class.

tests/linkml/test_base/__snapshots__/meta.owl

@@ -1502,7 +1502,7 @@ linkml:imported_from a owl:ObjectProperty,
 linkml:in_language a owl:ObjectProperty,
         linkml:SlotDefinition ;
     rdfs:label "in_language" ;
-    dcterms:conformsTo "https://www.rfc-editor.org/rfc/bcp/bcp47.txt" ;
+    dcterms:conformsTo <https://www.rfc-editor.org/rfc/bcp/bcp47.txt> ;
     rdfs:range linkml:String ;
     skos:definition "the primary language used in the sources" ;
     skos:inScheme linkml:meta ;
@@ -4785,7 +4785,7 @@ linkml:ClassDefinition a owl:Class,
 
 linkml:meta a owl:Ontology ;
     rdfs:label "meta" ;
-    dcterms:license "https://creativecommons.org/publicdomain/zero/1.0/" ;
+    dcterms:license <https://creativecommons.org/publicdomain/zero/1.0/> ;
     dcterms:title "LinkML Schema Metamodel" ;
     skos:definition """The metamodel for schemas defined using the Linked Data Modeling Language framework.
 

tests/linkml/test_biolink_model/__snapshots__/biolink.owl.ttl

@@ -79,7 +79,7 @@ os:SomeSomeInterpretation a owl:Class , biolink:LogicalInterpretationEnum ;
 	rdfs:label "some_some" ;
 	rdfs:subClassOf biolink:LogicalInterpretationEnum ;
 	skos:definition "A modifier on a triple that causes the triple to be interpreted as a some-some statement" .
-<https://w3id.org/biolink/biolink-model> dct:license "https://creativecommons.org/publicdomain/zero/1.0/" ;
+<https://w3id.org/biolink/biolink-model> dct:license <https://creativecommons.org/publicdomain/zero/1.0/> ;
 	pav:version "4.2.5" ;
 	a owl:Ontology ;
 	rdfs:label "Biolink-Model" ;

tests/linkml/test_generators/test_owlgen.py

@@ -1232,3 +1232,68 @@ def test_complement_of_union_of_mixed_none_filters_silently():
     # Should succeed and return a BNode (the complement expression).
     assert result is not None
     assert isinstance(result, BNode)
+
+
+_IRI_METADATA_SCHEMA = """
+id: https://example.org/onto/v2
+name: iri_metadata
+license: https://www.eclipse.org/legal/epl-2.0/
+conforms_to: https://example.org/onto/v2/shapes
+see_also:
+  - https://example.org/docs
+prefixes:
+  linkml: https://w3id.org/linkml/
+  ex: https://example.org/
+  owl: http://www.w3.org/2002/07/owl#
+  prov: http://www.w3.org/ns/prov#
+  dcterms: http://purl.org/dc/terms/
+default_prefix: ex
+imports:
+  - linkml:types
+annotations:
+  owl:versionInfo: v2
+  owl:versionIRI: https://example.org/onto/v2
+  owl:priorVersion: ex:onto/v1
+  prov:wasDerivedFrom: https://example.org/releases/tag/v2.0.0
+  dcterms:references: https://example.org/other
+  dcterms:identifier: https://example.org/onto
+  dcterms:creator: The Example Team
+classes:
+  Thing:
+    annotations:
+      dcterms:license: Not an IRI, just text
+"""
+
+
+def test_iri_valued_metadata_is_emitted_as_iris():
+    """Annotations and metadata of properties that take resources are IRIs when their value is one."""
+    g = Graph()
+    g.parse(data=OwlSchemaGenerator(_IRI_METADATA_SCHEMA, metaclasses=False).serialize(), format="turtle")
+    onto = URIRef("https://example.org/onto/v2")
+    DCT = Namespace("http://purl.org/dc/terms/")
+    PROV = Namespace("http://www.w3.org/ns/prov#")
+
+    assert g.value(onto, OWL.versionIRI) == onto
+    # a CURIE with a declared prefix is expanded
+    assert g.value(onto, OWL.priorVersion) == URIRef("https://example.org/onto/v1")
+    assert g.value(onto, PROV.wasDerivedFrom) == URIRef("https://example.org/releases/tag/v2.0.0")
+    assert g.value(onto, DCT.references) == URIRef("https://example.org/other")
+    # string-ranged metamodel slots whose property takes resources
+    assert g.value(onto, DCT.license) == URIRef("https://www.eclipse.org/legal/epl-2.0/")
+    assert g.value(onto, DCT.conformsTo) == URIRef("https://example.org/onto/v2/shapes")
+    assert g.value(onto, RDFS.seeAlso) == URIRef("https://example.org/docs")
+
+
+def test_literal_valued_metadata_stays_literal():
+    """Other properties, and values that are not IRIs, keep their literals."""
+    g = Graph()
+    g.parse(data=OwlSchemaGenerator(_IRI_METADATA_SCHEMA, metaclasses=False).serialize(), format="turtle")
+    onto = URIRef("https://example.org/onto/v2")
+    DCT = Namespace("http://purl.org/dc/terms/")
+
+    assert g.value(onto, OWL.versionInfo) == Literal("v2")
+    # DCMI gives dcterms:identifier the range rdfs:Literal
+    assert g.value(onto, DCT.identifier) == Literal("https://example.org/onto")
+    assert g.value(onto, DCT.creator) == Literal("The Example Team")
+    # a property that takes resources, with a value that is not an IRI
+    assert g.value(URIRef("https://example.org/Thing"), DCT.license) == Literal("Not an IRI, just text")