fix therapeutic agents and actions

ga4gh · Sep 10, 2023 · 375cb51 · 375cb51
1 parent ae3ad4b
commit 375cb51
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Showing 7 changed files with 10 additions and 196 deletions.
diff --git a/schema/core-source.yaml b/schema/core-source.yaml
@@ -225,11 +225,6 @@ $defs:
         const: TherapeuticAction
         default: TherapeuticAction
         description: MUST be "TherapeuticAction".
-      action:
-        description: The therapeutic action taken.
-        $ref: "#/$defs/MappableEntity"
-    required:
-      - action
 
   TherapeuticAgent:
     type: object
@@ -244,11 +239,6 @@ $defs:
         const: TherapeuticAgent
         default: TherapeuticAgent
         description: MUST be "TherapeuticAgent".
-      agent:
-        description: The therapeutic agent administered.
-        $ref: "#/$defs/MappableEntity"
-    required:
-      - agent
 
   CombinationTherapy:
     type: object
@@ -275,7 +265,7 @@ $defs:
             - $ref: "#/$defs/TherapeuticAgent"
         minItems: 2
     required:
-      - procedures
+      - components
 
   TherapeuticSubstituteGroup:
     type: object
@@ -300,7 +290,7 @@ $defs:
             - $ref: "#/$defs/TherapeuticAgent"
         minItems: 2
     required:
-      - procedures
+      - substitutes
 
   Gene:
     inherits: DomainEntity

diff --git a/schema/core.json b/schema/core.json
@@ -364,39 +364,9 @@
                "const": "TherapeuticAction",
                "default": "TherapeuticAction",
                "description": "MUST be \"TherapeuticAction\"."
-            },
-            "action": {
-               "description": "The therapeutic action taken.",
-               "oneOf": [
-                  {
-                     "$ref": "#/$defs/CombinationTherapy"
-                  },
-                  {
-                     "$ref": "#/$defs/Disease"
-                  },
-                  {
-                     "$ref": "#/$defs/Gene"
-                  },
-                  {
-                     "$ref": "#/$defs/Phenotype"
-                  },
-                  {
-                     "$ref": "#/$defs/TherapeuticAction"
-                  },
-                  {
-                     "$ref": "#/$defs/TherapeuticAgent"
-                  },
-                  {
-                     "$ref": "#/$defs/TherapeuticSubstituteGroup"
-                  },
-                  {
-                     "$ref": "#/$defs/TraitSet"
-                  }
-               ]
             }
          },
          "required": [
-            "action",
             "type"
          ],
          "additionalProperties": false
@@ -445,39 +415,9 @@
                "const": "TherapeuticAgent",
                "default": "TherapeuticAgent",
                "description": "MUST be \"TherapeuticAgent\"."
-            },
-            "agent": {
-               "description": "The therapeutic agent administered.",
-               "oneOf": [
-                  {
-                     "$ref": "#/$defs/CombinationTherapy"
-                  },
-                  {
-                     "$ref": "#/$defs/Disease"
-                  },
-                  {
-                     "$ref": "#/$defs/Gene"
-                  },
-                  {
-                     "$ref": "#/$defs/Phenotype"
-                  },
-                  {
-                     "$ref": "#/$defs/TherapeuticAction"
-                  },
-                  {
-                     "$ref": "#/$defs/TherapeuticAgent"
-                  },
-                  {
-                     "$ref": "#/$defs/TherapeuticSubstituteGroup"
-                  },
-                  {
-                     "$ref": "#/$defs/TraitSet"
-                  }
-               ]
             }
          },
          "required": [
-            "agent",
             "type"
          ],
          "additionalProperties": false
@@ -548,7 +488,7 @@
             }
          },
          "required": [
-            "procedures",
+            "components",
             "type"
          ],
          "additionalProperties": false
@@ -616,7 +556,7 @@
             }
          },
          "required": [
-            "procedures",
+            "substitutes",
             "type"
          ],
          "additionalProperties": false

diff --git a/schema/core.yaml b/schema/core.yaml
@@ -294,19 +294,7 @@ $defs:
         const: TherapeuticAction
         default: TherapeuticAction
         description: MUST be "TherapeuticAction".
-      action:
-        description: The therapeutic action taken.
-        oneOf:
-        - $ref: '#/$defs/CombinationTherapy'
-        - $ref: '#/$defs/Disease'
-        - $ref: '#/$defs/Gene'
-        - $ref: '#/$defs/Phenotype'
-        - $ref: '#/$defs/TherapeuticAction'
-        - $ref: '#/$defs/TherapeuticAgent'
-        - $ref: '#/$defs/TherapeuticSubstituteGroup'
-        - $ref: '#/$defs/TraitSet'
     required:
-    - action
     - type
     additionalProperties: false
   TherapeuticAgent:
@@ -348,19 +336,7 @@ $defs:
         const: TherapeuticAgent
         default: TherapeuticAgent
         description: MUST be "TherapeuticAgent".
-      agent:
-        description: The therapeutic agent administered.
-        oneOf:
-        - $ref: '#/$defs/CombinationTherapy'
-        - $ref: '#/$defs/Disease'
-        - $ref: '#/$defs/Gene'
-        - $ref: '#/$defs/Phenotype'
-        - $ref: '#/$defs/TherapeuticAction'
-        - $ref: '#/$defs/TherapeuticAgent'
-        - $ref: '#/$defs/TherapeuticSubstituteGroup'
-        - $ref: '#/$defs/TraitSet'
     required:
-    - agent
     - type
     additionalProperties: false
   CombinationTherapy:
@@ -414,7 +390,7 @@ $defs:
           - $ref: '#/$defs/TherapeuticAgent'
         minItems: 2
     required:
-    - procedures
+    - components
     - type
     additionalProperties: false
   TherapeuticSubstituteGroup:
@@ -467,7 +443,7 @@ $defs:
           - $ref: '#/$defs/TherapeuticAgent'
         minItems: 2
     required:
-    - procedures
+    - substitutes
     - type
     additionalProperties: false
   Gene:

diff --git a/schema/defs/core/TherapeuticAction.rst b/schema/defs/core/TherapeuticAction.rst
@@ -44,7 +44,3 @@ Some TherapeuticAction attributes are inherited from :ref:`DomainEntity`.
           - string
           - 1..1
           - MUST be "TherapeuticAction".
-       *  - action
-          - :ref:`MappableEntity`
-          - 1..1
-          - The therapeutic action taken.
diff --git a/schema/defs/core/TherapeuticAgent.rst b/schema/defs/core/TherapeuticAgent.rst
@@ -44,7 +44,3 @@ Some TherapeuticAgent attributes are inherited from :ref:`DomainEntity`.
           - string
           - 1..1
           - MUST be "TherapeuticAgent".
-       *  - agent
-          - :ref:`MappableEntity`
-          - 1..1
-          - The therapeutic agent administered.
diff --git a/schema/merged.json b/schema/merged.json
@@ -1216,39 +1216,9 @@
                "const": "TherapeuticAction",
                "default": "TherapeuticAction",
                "description": "MUST be \"TherapeuticAction\"."
-            },
-            "action": {
-               "description": "The therapeutic action taken.",
-               "oneOf": [
-                  {
-                     "$ref": "#/$defs/CombinationTherapy"
-                  },
-                  {
-                     "$ref": "#/$defs/Disease"
-                  },
-                  {
-                     "$ref": "#/$defs/Gene"
-                  },
-                  {
-                     "$ref": "#/$defs/Phenotype"
-                  },
-                  {
-                     "$ref": "#/$defs/TherapeuticAction"
-                  },
-                  {
-                     "$ref": "#/$defs/TherapeuticAgent"
-                  },
-                  {
-                     "$ref": "#/$defs/TherapeuticSubstituteGroup"
-                  },
-                  {
-                     "$ref": "#/$defs/TraitSet"
-                  }
-               ]
             }
          },
          "required": [
-            "action",
             "type"
          ],
          "additionalProperties": false
@@ -1297,39 +1267,9 @@
                "const": "TherapeuticAgent",
                "default": "TherapeuticAgent",
                "description": "MUST be \"TherapeuticAgent\"."
-            },
-            "agent": {
-               "description": "The therapeutic agent administered.",
-               "oneOf": [
-                  {
-                     "$ref": "#/$defs/CombinationTherapy"
-                  },
-                  {
-                     "$ref": "#/$defs/Disease"
-                  },
-                  {
-                     "$ref": "#/$defs/Gene"
-                  },
-                  {
-                     "$ref": "#/$defs/Phenotype"
-                  },
-                  {
-                     "$ref": "#/$defs/TherapeuticAction"
-                  },
-                  {
-                     "$ref": "#/$defs/TherapeuticAgent"
-                  },
-                  {
-                     "$ref": "#/$defs/TherapeuticSubstituteGroup"
-                  },
-                  {
-                     "$ref": "#/$defs/TraitSet"
-                  }
-               ]
             }
          },
          "required": [
-            "agent",
             "type"
          ],
          "additionalProperties": false
@@ -1400,7 +1340,7 @@
             }
          },
          "required": [
-            "procedures",
+            "components",
             "type"
          ],
          "additionalProperties": false
@@ -1468,7 +1408,7 @@
             }
          },
          "required": [
-            "procedures",
+            "substitutes",
             "type"
          ],
          "additionalProperties": false

diff --git a/schema/merged.yaml b/schema/merged.yaml
@@ -948,19 +948,7 @@ $defs:
         const: TherapeuticAction
         default: TherapeuticAction
         description: MUST be "TherapeuticAction".
-      action:
-        description: The therapeutic action taken.
-        oneOf:
-        - $ref: '#/$defs/CombinationTherapy'
-        - $ref: '#/$defs/Disease'
-        - $ref: '#/$defs/Gene'
-        - $ref: '#/$defs/Phenotype'
-        - $ref: '#/$defs/TherapeuticAction'
-        - $ref: '#/$defs/TherapeuticAgent'
-        - $ref: '#/$defs/TherapeuticSubstituteGroup'
-        - $ref: '#/$defs/TraitSet'
     required:
-    - action
     - type
     additionalProperties: false
   TherapeuticAgent:
@@ -1002,19 +990,7 @@ $defs:
         const: TherapeuticAgent
         default: TherapeuticAgent
         description: MUST be "TherapeuticAgent".
-      agent:
-        description: The therapeutic agent administered.
-        oneOf:
-        - $ref: '#/$defs/CombinationTherapy'
-        - $ref: '#/$defs/Disease'
-        - $ref: '#/$defs/Gene'
-        - $ref: '#/$defs/Phenotype'
-        - $ref: '#/$defs/TherapeuticAction'
-        - $ref: '#/$defs/TherapeuticAgent'
-        - $ref: '#/$defs/TherapeuticSubstituteGroup'
-        - $ref: '#/$defs/TraitSet'
     required:
-    - agent
     - type
     additionalProperties: false
   CombinationTherapy:
@@ -1068,7 +1044,7 @@ $defs:
           - $ref: '#/$defs/TherapeuticAgent'
         minItems: 2
     required:
-    - procedures
+    - components
     - type
     additionalProperties: false
   TherapeuticSubstituteGroup:
@@ -1121,7 +1097,7 @@ $defs:
           - $ref: '#/$defs/TherapeuticAgent'
         minItems: 2
     required:
-    - procedures
+    - substitutes
     - type
     additionalProperties: false
   Gene: