Merge pull request #193 from linkml/enum-bindings

Adding enum bindings

Author: cmungall

linkml_model/model/schema/meta.yaml

@@ -616,7 +616,6 @@ slots:
       - BasicSubset
 
   pv_formula:
-    domain: enum_expression
     range: pv_formula_options
     description: >-
       Defines the specific formula to be used to generate the permissible values.
@@ -1541,7 +1540,7 @@ slots:
     domain: slot_definition
     range: presence_enum
     inherited: true
-    description: if true then a value must be present (for lists there must be at least one value). If false then a value must be absent (for lists, must be empty)
+    description: if PRESENT then a value must be present (for lists there must be at least one value). If ABSENT then a value must be absent (for lists, must be empty)
     comments:
       - if set to true this has the same effect as required=true. In contrast, required=false allows a value to be present
     status: unstable
@@ -2096,6 +2095,42 @@ slots:
     in_subset:
       - SpecificationSubset
 
+  bindings:
+    domain: element
+    range: enum_binding
+    multivalued: true
+    inlined: true
+    status: testing
+    description: >-
+      A collection of enum bindings that specify how a slot can be bound to a permissible value
+      from an enumeration.
+
+      LinkML provides enums to allow string values to be restricted to one of a set of permissible
+      values (specified statically or dynamically).
+
+      Enum bindings allow enums to be bound to any object, including complex nested objects. For
+      example, given a (generic) class Concept with slots id and label, it may be desirable to restrict the
+      values the id takes on in a given context. For example, a HumanSample class may have a slot for
+      representing sample site, with a range of concept, but the values of that slot may be restricted to
+      concepts from a particular branch of an anatomy ontology.
+    in_subset:
+      - SpecificationSubset
+
+  binds_value_of:
+    domain: enum_binding
+    range: string
+    description: >-
+      A path to a slot that is being bound to a permissible value from an enumeration.
+    in_subset:
+      - SpecificationSubset
+
+  obligation_level:
+    range: obligation_level_enum
+    description: >-
+      The level of obligation or recommendation strength for a metadata element
+    in_subset:
+      - SpecificationSubset
+
 
   # -----------------------------------
   # Slots for type definition
@@ -2518,6 +2553,7 @@ classes:
       - generation_date
       - slot_names_unique
       - settings
+      - bindings
     see_also:
       - https://en.wikipedia.org/wiki/Data_dictionary
     close_mappings:
@@ -2671,6 +2707,24 @@ classes:
     slots:
       - enum_uri
 
+  enum_binding:
+    description: >-
+      A binding of a slot or a class to a permissible value from an enumeration.
+    slots:
+      - range
+      - obligation_level
+      - binds_value_of
+      - pv_formula
+    slot_usage:
+      range:
+        range: enum_definition
+    in_subset:
+      - SpecificationSubset
+    mixins:
+      - extensible
+      - annotatable
+      - common_metadata
+
   match_query:
     description: >-
       A query that is used on an enum expression to dynamically obtain a set of permissivle values via a query that 
@@ -2770,6 +2824,7 @@ classes:
       - range
       - range_expression
       - enum_range
+      - bindings
       - required
       - recommended
       - inlined
@@ -3194,3 +3249,28 @@ enums:
         meaning: skos:broaderMatch
       NARROW_SYNONYM:
         meaning: skos:narrowerMatch
+
+  obligation_level_enum:
+    rank: 10
+    description: >-
+      The level of obligation or recommendation strength for a metadata element
+    permissible_values:
+      REQUIRED:
+        description: >-
+          The metadata element is required to be present in the model
+      RECOMMENDED:
+        aliases:
+          - ENCOURAGED
+        description: >-
+          The metadata element is recommended to be present in the model
+      OPTIONAL:
+        description: >-
+          The metadata element is optional to be present in the model
+      EXAMPLE:
+        description: >-
+          The metadata element is an example of how to use the model
+      DISCOURAGED:
+        description: >-
+          The metadata element is allowed but discouraged to be present in the model
+    in_subset:
+      - SpecificationSubset

tests/input/examples/schema_definition-enum_bindings-1.yaml

@@ -0,0 +1,105 @@
+id: https://example.org/enum_bindings
+name: enum_bindings_example
+title: Enum Bindings Example
+description: |-
+  Example LinkML schema to demonstrate Enum bindings.
+
+  Here we define a generic Sample class which has a range indicating
+  the material type of the sample. In an environmental context this
+  could be soil, seawater, etc. In a medical context it may be human
+  tissue.
+
+  In both cases we want to use a generic Concept class
+license: MIT
+
+prefixes:
+  linkml: https://w3id.org/linkml/
+  example: https://example.org/
+
+default_prefix: example
+
+imports:
+  - linkml:types
+
+classes:
+
+  Concept:
+    description: A generic class for representing an element from a vocabulary or ontology.
+    attributes:
+      id:
+        identifier: true
+        description: CURIE/identifier for the concept. E.g. ENVO:1234567
+      name:
+        description: human-readable label of the concept. E.g. "blood"
+      vocabulary:
+        description: E.g. UBERON, PO, ENVO, NCIT
+
+
+  Sample:
+    description: Abstract grouping for different sample types
+    abstract: true
+    attributes:
+      name:
+        description: E.g. my blood sample
+      sample_material_type:
+        description: The material type for the sample - depending on the type of sample, could be tissue (e.g. blood, muscle) or environmental (rock, soil, ...)
+        range: Concept
+            
+  EnvironmentalMaterialSample:
+    description: A sample taken from the environment
+    slot_usage:
+      sample_material_type:
+        description: Environmental material type
+        bindings:
+          - binds_value_of: id
+            range: ENVOMaterialEnum
+            obligation_level: RECOMMENDED
+            description: Material type from the ENVO ontology
+
+  HumanSampleSample:
+    description: A sample taken from a human subject
+    slot_usage:
+      sample_material_type:
+        description: Tissue material type
+        bindings:
+          - binds_value_of: id
+            range: AnatomyMaterialEnum
+            obligation_level: RECOMMENDED
+            description: Material type from an anatomy ontology
+
+  AlternateHumanSampleSample:
+    description: A sample taken from a human subject (alternative example for illustrative purposes)
+    slot_usage:
+      sample_material_type:
+        description: Does not constrain the ID that is used, but restricts the vocabulary field to a fixed enum
+        bindings:
+          - binds_value_of: vocabulary
+            range: HumanSampleVocabularyEnum
+            obligation_level: RECOMMENDED
+
+enums:
+  ENVOMaterialEnum:
+    description: Material type from the ENVO ontology
+    reachable_from:
+      source_ontology: obo:envo
+      source_nodes:
+        - ENVO:00010483  ## environmental material
+      is_direct: false
+      relationship_types:
+        - rdfs:subClassOf
+  AnatomyMaterialEnum:
+    description: Material type from the UBERON anatomy ontology
+    reachable_from:
+      source_ontology: obo:uberon
+      source_nodes:
+        - UBERON:0000465 ## material anatomical entity
+      is_direct: false
+      relationship_types:
+        - rdfs:subClassOf
+  HumanSampleVocabularyEnum:
+    permissible_values:
+      UBERON:
+      FMA:
+      NCIT:
+
+