Added alcohol consumption fields. Fix#1622

docs/jsonBrowser/module.md

@@ -552,7 +552,10 @@ Location: module/biomaterial/medical_history.json
 
 Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example 
 --- | --- | --- | --- | --- | --- | --- | --- 
-alcohol_history | Estimated amount of alcohol consumed per day. | string | no |  | Alcohol history |  | 3-6 alcohol units/day; 1 drink per day
+alcohol_status | Whether the individual is actively consuming, was formerly consuming or never consumed alcohol beverages | string | no |  | Alcohol status | active, former, never | Should be one of: active, former, never.
+alcohol_type | Types of alcoholic beverages the donor consumed. | array | no |  | Alcohol type |  | beer; liquor; wine
+alcohol_units | Alcohol consumption of donor in alcohol units per week (strength (ABV) x volume (ml) ÷ 1,000). | number | no |  | Alcohol units |  | 2.5; 15.2; 23
+alcohol_usage_duration | Number of years in which the donor consumed alcohol. | integer | no |  | Alcohol usage duration |  | 5
 medication | Medication(s) the individual was taking at time of biomaterial collection. | array | no | [See module  medication_ontology](module.md#medication-ontology) | Medication |  | 
 smoking_status | Whether the individual is actively, was formerly or never consumed smoking tobacco products like cigarettes, cigars, pipe etc. | string | no |  | Smoking status | active, former, never | Should be one of: active, former, never.
 smoking_pack_years | Estimated number of packs (20 cigarettes) smoked per day multiplied by the number of years the individual was smoking. | number | no |  | Smoking pack years |  | 4.55

json_schema/module/biomaterial/medical_history.json

@@ -17,12 +17,43 @@
             "pattern": "^[0-9]{1,}.[0-9]{1,}.[0-9]{1,}$",
             "example": "4.6.1"
         },
-        "alcohol_history": {
-            "description": "Estimated amount of alcohol consumed per day.",
+        "alcohol_status": {
+            "description": "Whether the individual is actively consuming, was formerly consuming or never consumed alcohol beverages",
             "type": "string",
-            "user_friendly": "Alcohol history",
-            "example": "3-6 alcohol units/day; 1 drink per day",
-            "guidelines": "Enter the amount consumed per day using units such as alcohol units (10mL or 8g of alcohol) or drinks (14g of alcohol)."
+            "enum": [
+                "active",
+                "former",
+                "never"
+            ],
+            "user_friendly": "Alcohol status",
+            "example": "Should be one of: active, former, never.",
+            "bionetworks": ["gut", "oral and craniofacial", "musculoskeletal", "liver"]
+        },
+        "alcohol_type": {
+            "description": "Types of alcoholic beverages the donor consumed.",
+            "type": "array",
+            "items": {
+                "type": "string"
+            },
+            "user_friendly": "Alcohol type",
+            "example": "beer; liquor; wine",
+            "bionetworks": ["gut", "oral and craniofacial", "musculoskeletal", "liver"]
+        },
+        "alcohol_units": {
+            "description": "Alcohol consumption of donor in alcohol units per week (strength (ABV) x volume (ml) ÷ 1,000).",
+            "type": "number",
+            "user_friendly": "Alcohol units",
+            "minimum": 0,
+            "example": "2.5; 15.2; 23",
+            "bionetworks": ["gut", "oral and craniofacial", "musculoskeletal", "liver", "heart"]
+        },
+        "alcohol_usage_duration": {
+            "description": "Number of years in which the donor consumed alcohol.",
+            "type": "integer",
+            "user_friendly": "Alcohol usage duration",
+            "minimum": 0,
+            "example": 5,
+            "bionetworks": ["gut", "oral and craniofacial", "musculoskeletal", "liver"]
         },
         "medication": {
             "description": "Medication(s) the individual was taking at time of biomaterial collection.",

json_schema/property_migrations.json

@@ -1,5 +1,12 @@
 {
     "migrations": [
+        {
+            "source_schema": "medical_history",
+            "property": "alcohol_history",
+            "effective_from": "9.0.0",
+            "reason": "Field standardization",
+            "type": "deprecated property"
+        },
         {
             "source_schema": "medical_history",
             "property": "smoking_history",

json_schema/update_log.csv

@@ -1 +1,3 @@
 Schema,Change type,Change message,Version,Date
+module/biomaterial/medical_history,minor,Added alcohol consumption details,,
+module/biomaterial/medical_history,major,Deprecate alcohol_history,,