extending the Phenopackets schema

bycon/schemas/models/json/bycon-database-schemas/pgxIndividual.json

@@ -50,8 +50,8 @@
                 }
             ]
         },
-        "vitalStatus": {
-            "$ref": "../common/vitalStatus.json"
+        "VitalStatus": {
+            "$ref": "../common/VitalStatus.json"
         },
         "geoLocation": {
             "$ref": "../common/GeoLocation.json"

bycon/schemas/models/json/bycon-model/common/Interpretation.json

@@ -0,0 +1,56 @@
+{
+    "$schema": "https://json-schema.org/draft/2020-12/schema",
+    "title": "Interpretation",
+    "description": "This object intends to represent the interpretation of a genomic analysis, such as the report from a diagnostic laboratory. Source: Phenopackets v2 <https://phenopacket-schema.readthedocs.io/en/latest/interpretation.html#interpretation>",
+    "type": "object",
+    "properties": {
+        "id": {
+            "description": "Interpretation identifier.",
+            "type": "string",
+            "examples": [
+                "CONSORTIUM:0000123456"
+            ]
+        },
+        "progressStatus": {
+            "type": "string",
+            "enum": [
+                "UNKNOWN_PROGRESS",
+                "IN_PROGRESS",
+                "COMPLETED",
+                "SOLVED",
+                "UNSOLVED"
+            ]
+        },
+        "diagnosis": {
+            "$ref": "#/$defs/Diagnosis"
+        },
+        "summary": {
+            "type": "string",
+            "description": "Additional data about this interpretation, e.g. free text summary."
+        }
+    },
+    "$defs": {
+        "Diagnosis": {
+            "properties": {
+                "disease": {
+                    "$ref": "ontologyTerm.json"
+                },
+                "genomicInterpretations": {
+                    "type": "array",
+                    "items": {
+                        "description": "TODO: Define class \"GenomicInterpretation\".",
+                        "type": "object"
+                    }
+                }
+            },
+            "required": [
+                "disease"
+            ]
+        }
+    },
+    "required": [
+        "id",
+        "progressStatus"
+    ],
+    "additionalProperties": true
+}

bycon/schemas/models/json/bycon-model/common/pedigree.json

@@ -10,7 +10,7 @@
             "example": "Pedigree1001"
         },
         "disease": {
-            "$ref": "../common/disease.json"
+            "$ref": "disease.json"
         },
         "numSubjects": {
             "description": "Total number of subjects in pedigree.",

bycon/schemas/models/json/bycon-model/common/vitalStatus.json

@@ -1,6 +1,6 @@
 {
     "$schema": "https://json-schema.org/draft/2020-12/schema",
-    "$id": "https://progenetix.org/services/schemas/vitalStatus/v2021-12-02",
+    "$id": "https://progenetix.org/services/schemas/VitalStatus/v2021-12-02",
     "title": "VitalStatus",
     "description": "This element can be used to report whether the individual is living or dead at the timepoint when the phenopacket was created (or if the status is unknown). Source: Phenopackets v2, with modifications",
     "type": "object",

bycon/schemas/models/json/bycon-model/phenopackets/defaultSchema.json

@@ -50,13 +50,14 @@
         "interpretations": {
             "type": "array",
             "items": {
-                "$ref": "Interpretation.json"
+                "$ref": "../common/Interpretation.json"
             }
         },
         "medicalActions": {
             "type": "array",
             "items": {
-                "$ref": "MedicalAction.json"
+                "description": "TODO: Define class \"MedicalAction\". <https://phenopacket-schema.readthedocs.io/en/latest/medical-action.html#medicalaction>",
+                "type": "object"
             }
         }
     }

bycon/schemas/models/src/bycon-database-schemas/pgxIndividual.yaml

@@ -40,8 +40,8 @@ properties:
         notes: HapMap individual
       - id: 022f39e9-57ee-4b2b-8b3a-8929e3d69a37
         notes: TCGA case_id
-  vitalStatus:
-    $ref: ../common/vitalStatus.yaml
+  VitalStatus:
+    $ref: ../common/VitalStatus.yaml
   geoLocation:
     $ref: ../common/GeoLocation.yaml
   ancestries:

bycon/schemas/models/src/bycon-model/common/Interpretation.yaml

@@ -0,0 +1,44 @@
+$schema: https://json-schema.org/draft/2020-12/schema
+title: Interpretation
+description: >-
+  This object intends to represent the interpretation of a genomic analysis, such
+  as the report from a diagnostic laboratory.
+  Source: Phenopackets v2 <https://phenopacket-schema.readthedocs.io/en/latest/interpretation.html#interpretation>
+type: object
+properties:
+  id:
+    description: Interpretation identifier.
+    type: string
+    examples:
+      - CONSORTIUM:0000123456
+  progressStatus:
+    type: string
+    enum:
+      - UNKNOWN_PROGRESS
+      - IN_PROGRESS
+      - COMPLETED
+      - SOLVED
+      - UNSOLVED
+  diagnosis:
+    $ref: '#/$defs/Diagnosis'
+  summary:
+    type: string
+    description: >-
+      Additional data about this interpretation, e.g. free text summary.
+$defs:
+  Diagnosis:
+    properties:
+      disease:
+        $ref: ontologyTerm.yaml
+      genomicInterpretations:
+        type: array
+        items:
+          description: >-
+            TODO: Define class "GenomicInterpretation".
+          type: object
+    required:
+      - disease
+required:
+  - id
+  - progressStatus
+additionalProperties: true

bycon/schemas/models/src/bycon-model/common/pedigree.yaml

@@ -8,7 +8,7 @@ properties:
     type: string
     example: Pedigree1001
   disease:
-    $ref: ../common/disease.yaml
+    $ref: disease.yaml
   numSubjects:
     description: Total number of subjects in pedigree.
     type: integer

bycon/schemas/models/src/bycon-model/common/vitalStatus.yaml

@@ -1,5 +1,5 @@
 $schema: https://json-schema.org/draft/2020-12/schema
-$id: https://progenetix.org/services/schemas/vitalStatus/v2021-12-02
+$id: https://progenetix.org/services/schemas/VitalStatus/v2021-12-02
 title: VitalStatus
 description: >-
   This element can be used to report whether the individual is living or dead

bycon/schemas/models/src/bycon-model/phenopackets/defaultSchema.yaml

@@ -42,10 +42,13 @@ properties:
   interpretations:
     type: array
     items:
-      $ref: Interpretation.yaml
+      $ref: ../common/Interpretation.yaml
   medicalActions:
     type: array
     items:
-      $ref: MedicalAction.yaml
+      description: >-
+        TODO: Define class "MedicalAction".
+        <https://phenopacket-schema.readthedocs.io/en/latest/medical-action.html#medicalaction>
+      type: object