From c1256585e80da7f3135d1dee50b896a8b9c9dfe8 Mon Sep 17 00:00:00 2001 From: Arsenios Chatzigeorgiou <49944135+arschat@users.noreply.github.com> Date: Mon, 18 Aug 2025 15:26:06 +0100 Subject: [PATCH 1/7] Added alcohol consumption fields and deprecated previous free-text alcohol_history --- docs/jsonBrowser/module.md | 5 ++- .../module/biomaterial/medical_history.json | 37 ++++++++++++++++--- json_schema/update_log.csv | 2 + 3 files changed, 38 insertions(+), 6 deletions(-) diff --git a/docs/jsonBrowser/module.md b/docs/jsonBrowser/module.md index f5c9748c2..2fb46933f 100644 --- a/docs/jsonBrowser/module.md +++ b/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 | Does the donor have drink/ drank/ never drank alcohol? | 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 the donor has used any 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 diff --git a/json_schema/module/biomaterial/medical_history.json b/json_schema/module/biomaterial/medical_history.json index 112e5587d..257760d43 100644 --- a/json_schema/module/biomaterial/medical_history.json +++ b/json_schema/module/biomaterial/medical_history.json @@ -17,12 +17,39 @@ "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": "Does the donor have drink/ drank/ never drank alcohol?", "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." + }, + "alcohol_type": { + "description": "Types of alcoholic beverages the donor consumed.", + "type": "array", + "items": { + "type": "string" + }, + "user_friendly": "Alcohol type", + "example": "beer; liquor; wine" + }, + "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" + }, + "alcohol_usage_duration": { + "description": "Number of years the donor has used any alcohol.", + "type": "integer", + "user_friendly": "Alcohol usage duration", + "minimum": 0, + "example": 5 }, "medication": { "description": "Medication(s) the individual was taking at time of biomaterial collection.", diff --git a/json_schema/update_log.csv b/json_schema/update_log.csv index 3231ff199..815bc099a 100644 --- a/json_schema/update_log.csv +++ b/json_schema/update_log.csv @@ -1 +1,3 @@ Schema,Change type,Change message,Version,Date +module/biomaterial/medical_history.json,major,Deprecate alcohol_history,, +module/biomaterial/medical_history.json,minor,Added alcohol consumption details,, \ No newline at end of file From e4146f4118c51f92c6dcb098975938962f9c0aa5 Mon Sep 17 00:00:00 2001 From: Arsenios Chatzigeorgiou <49944135+arschat@users.noreply.github.com> Date: Mon, 18 Aug 2025 15:53:41 +0100 Subject: [PATCH 2/7] Update update_log.csv --- json_schema/update_log.csv | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/json_schema/update_log.csv b/json_schema/update_log.csv index 815bc099a..6f7a0b142 100644 --- a/json_schema/update_log.csv +++ b/json_schema/update_log.csv @@ -1,3 +1,3 @@ Schema,Change type,Change message,Version,Date -module/biomaterial/medical_history.json,major,Deprecate alcohol_history,, -module/biomaterial/medical_history.json,minor,Added alcohol consumption details,, \ No newline at end of file +module/biomaterial/medical_history,minor,Added alcohol consumption details,, +module/biomaterial/medical_history,major,Deprecate alcohol_history,, \ No newline at end of file From 758262ebbf65becce225955925bad6737d6201fe Mon Sep 17 00:00:00 2001 From: Arsenios Chatzigeorgiou <49944135+arschat@users.noreply.github.com> Date: Mon, 18 Aug 2025 15:55:46 +0100 Subject: [PATCH 3/7] Added bionetwork attribute to alcohol consumption --- json_schema/module/biomaterial/medical_history.json | 12 ++++++++---- 1 file changed, 8 insertions(+), 4 deletions(-) diff --git a/json_schema/module/biomaterial/medical_history.json b/json_schema/module/biomaterial/medical_history.json index 257760d43..367f74f0a 100644 --- a/json_schema/module/biomaterial/medical_history.json +++ b/json_schema/module/biomaterial/medical_history.json @@ -26,7 +26,8 @@ "never" ], "user_friendly": "Alcohol status", - "example": "Should be one of: active, former, never." + "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.", @@ -35,21 +36,24 @@ "type": "string" }, "user_friendly": "Alcohol type", - "example": "beer; liquor; wine" + "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" + "example": "2.5; 15.2; 23", + "bionetworks": ["gut", "oral and craniofacial", "musculoskeletal", "liver", "heart"] }, "alcohol_usage_duration": { "description": "Number of years the donor has used any alcohol.", "type": "integer", "user_friendly": "Alcohol usage duration", "minimum": 0, - "example": 5 + "example": 5, + "bionetworks": ["gut", "oral and craniofacial", "musculoskeletal", "liver"] }, "medication": { "description": "Medication(s) the individual was taking at time of biomaterial collection.", From bcc81e66a11ef236e2f0a33e7c664621ccdd4503 Mon Sep 17 00:00:00 2001 From: Arsenios Chatzigeorgiou <49944135+arschat@users.noreply.github.com> Date: Mon, 1 Sep 2025 09:59:21 +0100 Subject: [PATCH 4/7] Update json_schema/module/biomaterial/medical_history.json Co-authored-by: idazucchi <45209056+idazucchi@users.noreply.github.com> --- json_schema/module/biomaterial/medical_history.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/json_schema/module/biomaterial/medical_history.json b/json_schema/module/biomaterial/medical_history.json index 257760d43..c87226241 100644 --- a/json_schema/module/biomaterial/medical_history.json +++ b/json_schema/module/biomaterial/medical_history.json @@ -18,7 +18,7 @@ "example": "4.6.1" }, "alcohol_status": { - "description": "Does the donor have drink/ drank/ never drank alcohol?", + "description": "Whether the individual is actively consuming, was formerly consuming or never consumed alcohol beverages", "type": "string", "enum": [ "active", From ecff85f4d3e491f64058c4ee8a3d7b6e1c08a0e9 Mon Sep 17 00:00:00 2001 From: Arsenios Chatzigeorgiou <49944135+arschat@users.noreply.github.com> Date: Mon, 1 Sep 2025 09:59:43 +0100 Subject: [PATCH 5/7] Update json_schema/module/biomaterial/medical_history.json Co-authored-by: idazucchi <45209056+idazucchi@users.noreply.github.com> --- json_schema/module/biomaterial/medical_history.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/json_schema/module/biomaterial/medical_history.json b/json_schema/module/biomaterial/medical_history.json index c87226241..266623460 100644 --- a/json_schema/module/biomaterial/medical_history.json +++ b/json_schema/module/biomaterial/medical_history.json @@ -45,7 +45,7 @@ "example": "2.5; 15.2; 23" }, "alcohol_usage_duration": { - "description": "Number of years the donor has used any alcohol.", + "description": "Number of years in which the donor consumed alcohol.", "type": "integer", "user_friendly": "Alcohol usage duration", "minimum": 0, From 4778d2959a2f333a0afb0d690bb2c67cac38d3d9 Mon Sep 17 00:00:00 2001 From: Arsenios Chatzigeorgiou <49944135+arschat@users.noreply.github.com> Date: Mon, 1 Sep 2025 10:03:10 +0100 Subject: [PATCH 6/7] Apply alcohol consumption description changes in docs --- docs/jsonBrowser/module.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/jsonBrowser/module.md b/docs/jsonBrowser/module.md index 2fb46933f..45fa17e5f 100644 --- a/docs/jsonBrowser/module.md +++ b/docs/jsonBrowser/module.md @@ -552,10 +552,10 @@ Location: module/biomaterial/medical_history.json Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example --- | --- | --- | --- | --- | --- | --- | --- -alcohol_status | Does the donor have drink/ drank/ never drank alcohol? | string | no | | Alcohol status | active, former, never | Should be one of: active, former, never. +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 the donor has used any alcohol. | integer | no | | Alcohol usage duration | | 5 +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 From 871577feb8ea5cda9f514776db3d6d468702236f Mon Sep 17 00:00:00 2001 From: Arsenios Chatzigeorgiou <49944135+arschat@users.noreply.github.com> Date: Mon, 1 Sep 2025 10:51:11 +0100 Subject: [PATCH 7/7] Update property_migrations.json --- json_schema/property_migrations.json | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/json_schema/property_migrations.json b/json_schema/property_migrations.json index aab24f8b2..f8986b273 100644 --- a/json_schema/property_migrations.json +++ b/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",