Merge pull request #163 from linkml/implements-metaslot

Adding implements metaslot

Author: cmungall

linkml_model/model/docs/specification/05validation.md

@@ -240,6 +240,68 @@ here `T.uri` is used to determine the type:
 
 ## Inference of new values
 
+## Schema Validation
+
+A LinkML schema is a LinkML instance that conforms to the LinkML metamodel. As such, it can be validated
+in the same way as any other LinkML instance.
+
+### Metamodel refinement using annotations
+
+#### Background
+
+The LinkML model provides a fixed set of metamodel slots which can be applied to any schema element.
+Any schema that assigns slot values not in the metamodel is invalid.
+
+Sometimes it is useful to attach additional information to elements in a schema, this is called
+schema *extension*. Alternatively, it may be useful to be able to make the metamodel more restrictive
+in some contexts; for example, making the `description` metamodel slot `required` rather than `recommended`.
+
+The LinkML metamodel can be effectively extended through the use of `annotation` slot assignments.
+Annotations are `tag`-`value` pairs.
+
+As an example, if we want to add a metamodel slot `review` intended to store a review of a schema element.
+
+```yaml
+classes:
+  Person:
+    annotations:
+      review: A very useful class that is well defined
+      ...
+```
+
+#### Annotation validation
+
+By default, all annotation tags and values are valid. 
+
+LinkML 1.6 introduces the ability to validate annotation tags and values.
+
+This is done by adding an `instantiates` slot-value assignment onto any schema element. The range of
+the `instantiates` slot is a `uriorcurie` that references a class that serves as a metamodel extension class.
+
+If a schema element instantiates at least one class then *all* annotations are validated.
+
+For example:
+
+```yaml
+classes:
+  Person:
+    instantiates:
+     - mymetamodel:Reviewable
+    annotations:
+      review: A very useful class that is well defined
+      ...
+```
+
+The `Reviewable` class is defined as follows:
+
+```yaml
+classes:
+  Reviewable:
+    class_uri: mymetamodel:Reviewable
+    slots:
+      description: an expert review of a schema element
+      review: string
+```
 
 
 

linkml_model/model/schema/meta.yaml

@@ -186,6 +186,13 @@ slots:
       into the schema for the implementing element. However, the referenced schema may be used to check
       conformance of the implementing element.
     multivalued: true
+
+  instantiates:
+    domain: element
+    range: uriorcurie
+    description: >-
+      An element in another schema which this element instantiates.
+    multivalued: true
 
   categories:
     range: uriorcurie
@@ -1518,7 +1525,6 @@ slots:
     range: integer
     inherited: true
     description: the minimum number of entries for a multivalued slot
-    status: testing
     in_subset:
       - SpecificationSubset
 
@@ -1527,7 +1533,6 @@ slots:
     range: integer
     inherited: true
     description: the maximum number of entries for a multivalued slot
-    status: testing
     in_subset:
       - SpecificationSubset
 
@@ -2371,6 +2376,8 @@ classes:
       - modified_by
       - status
       - rank
+      - categories
+      - keywords
     in_subset:
       - BasicSubset
 
@@ -2392,6 +2399,7 @@ classes:
       - local_names
       - conforms_to
       - implements
+      - instantiates
     see_also:
       - https://en.wikipedia.org/wiki/Data_element
     in_subset:
@@ -2432,8 +2440,6 @@ classes:
       - generation_date
       - slot_names_unique
       - settings
-      - categories
-      - keywords
     see_also:
       - https://en.wikipedia.org/wiki/Data_dictionary
     close_mappings:

tests/input/examples/schema_definition-implements.yaml

@@ -0,0 +1,53 @@
+id: https://w3id.org/linkml/examples/enums
+title: Dynamic Enums Example
+name: dynamicenums-example
+description: This demonstrates the use of dynamic enums
+license: https://creativecommons.org/publicdomain/zero/1.0/
+
+prefixes:
+  linkml: https://w3id.org/linkml/
+  linkml.measurements: https://w3id.org/linkml/measurements
+  ex: https://w3id.org/linkml/examples/enums/
+  sh: https://w3id.org/shacl/
+  bioregistry: https://bioregistry.io/registry/
+  MONDO: http://purl.obolibrary.org/obo/MONDO_
+  NCIT: http://purl.obolibrary.org/obo/NCIT_
+  loinc: http://loinc.org/
+
+default_prefix: ex
+default_range: string
+
+default_curi_maps:
+    - semweb_context
+
+emit_prefixes:
+  - linkml
+  - rdf
+  - rdfs
+  - xsd
+  - owl
+
+imports:
+  - linkml:types
+
+  
+#==================================
+# Classes                         #
+#==================================
+
+classes:
+  Measurement:
+    description: a measurement
+    implements:
+      - linkml.measurements:Measurement
+    attributes:
+      value:
+        range: float
+        description: the numeric value
+        implements:
+          - linkml.measurements:value
+      unit:
+        range: string
+        description: the unit
+        implements:
+          - linkml.measurements:unit