Merge pull request #147 from linkml/fix-examples

fixing normalization errors

Author: cmungall

examples/dynamic-enums-example.yaml

@@ -71,9 +71,9 @@ enums:
       relationship_types:
         - rdfs:subClassOf
     minus:
-      permissible_values:
-        root_node:
-          meaning: MONDO:0000001 ## disease or disorder
+      - permissible_values:
+          root_node:
+            meaning: MONDO:0000001 ## disease or disorder
 
   HumanDisease:
     description: Extends the Disease value set, including NCIT neoplasms, excluding non-human diseases
@@ -107,8 +107,8 @@ enums:
             - loinc:LP43571-6
           is_direct: true
     minus:
-      concepts:
-        - LOINC:5932-9
+      - concepts:
+          - LOINC:5932-9
 
   HCAExample:
     see_also:
@@ -123,8 +123,8 @@ enums:
           relationship_types:
             - rdfs:subClassOf
     minus:
-      concepts:
-        - LOINC:5932-9
+      - concepts:
+          - LOINC:5932-9
 
   BodyPartEnum:
     reachable_from:

examples/rules-example.yaml

@@ -165,7 +165,7 @@ classes:
         slot_conditions:
           encodes:
             none_of:
-              range: Protein
+              - range: Protein
   ProteinCodingGene:
     is_a: Gene
     classification_rules:

examples/structured_alias.yaml

@@ -41,8 +41,8 @@ slots:
     inherited: true
     symmetric: true
     annotations:
-      tag: biolink:canonical_predicate
-      value: true
+      - tag: biolink:canonical_predicate
+        value: true
     exact_mappings:
       - skos:relatedMatch
       - UMLS:related_to
@@ -57,12 +57,12 @@ slots:
       - RO:0002084
     aliases: ['similar to']
     structured_aliases:
-      - alias_name: mapped_to
-        alias_type: close
+      - literal_form: mapped_to
+        predicate: RELATED_SYNONYM
         source: infores:mesh
-      - alias_name: higher_than
-        alias_type: narrow
+      - literal_form: higher_than
+        predicate: NARROW_SYNONYM
         source: infores:semmeddb
-      - alias_name: related_to
-        alias_type: exact
-        source: infores:bte
+      - literal_form: related_to
+        predicate: EXACT_SYNONYM
+        source: infores:bte

linkml_model/model/schema/meta.yaml

@@ -1754,7 +1754,7 @@ slots:
     range: slot_definition
     description: If s transitive_form_of d, then (1) s holds whenever d holds (2) s is transitive (3) d holds whenever s holds and there are no intermediates, and s is not reflexive
     comments:
-      - Example: ancestor_of is the transitive_form_of parent_of
+      - "Example: ancestor_of is the transitive_form_of parent_of"
     in_subset:
       - SpecificationSubset
 
@@ -2100,8 +2100,8 @@ slots:
     slot_uri: sh:group
     range_expression:
       slot_conditions:
-        - is_grouping_slot:
-            equals_expression: True
+        is_grouping_slot:
+          equals_expression: "True"
     in_subset:
       - SpecificationSubset
       - BasicSubset
@@ -2382,6 +2382,7 @@ classes:
       - value set
       - term set
       - Terminology Value Set
+      - answer list
     description: an element whose instances must be drawn from a specified set of permissible values
     is_a: definition
     mixins:
@@ -2829,10 +2830,14 @@ enums:
     description: >-
       The formula used to generate the set of permissible values from the code_set values
     permissible_values:
-      CODE: The permissible values are the set of possible codes in the code set
-      CURIE: The permissible values are the set of CURIES in the code set
-      URI: The permissible values are the set of code URIs in the code set
-      FHIR_CODING: The permissible values are the set of FHIR coding elements derived from the code set
+      CODE:
+        description: The permissible values are the set of possible codes in the code set
+      CURIE:
+        description: The permissible values are the set of CURIES in the code set
+      URI:
+        description: The permissible values are the set of code URIs in the code set
+      FHIR_CODING:
+        description: The permissible values are the set of FHIR coding elements derived from the code set
     in_subset:
       - SpecificationSubset
       - BasicSubset