examples

Author: cmungall

linkml_model/model/schema/meta.yaml

@@ -2106,6 +2106,15 @@ slots:
     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
 

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

@@ -2,7 +2,14 @@ id: https://example.org/enum_bindings
 name: enum_bindings_example
 title: Enum Bindings Example
 description: |-
-  Example LinkML schema to demonstrate Enum bindings
+  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:
@@ -17,27 +24,59 @@ imports:
 classes:
 
   Concept:
+    description: A generic class for representing an element from a vocabulary or ontology.
     attributes:
       id:
         identifier: true
+        descrption: 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
@@ -48,5 +87,19 @@ enums:
       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: