Merge pull request #163 from linkml/implements-metaslot

Adding implements metaslot

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