diff --git a/changelog.md b/changelog.md index 1cfdbd35..2d1994cd 100644 --- a/changelog.md +++ b/changelog.md @@ -9,6 +9,19 @@ and (starting with v4.0.0) this project adheres to [Semantic Versioning](http:// ## [Released](https://github.com/HumanCellAtlas/metadata-schema/) + +### [module/biomaterial/medical_history.json - v5.3.0] - 2024-09-16 +### Added +Added optional smoking related fields in medical_history module. Fix #1565 + +### [module/biomaterial/medical_history.json - v6.0.0] - 2024-09-16 +### Removed +Removed smoking_history in medical_history module. Fix #1565 + +### [type/biomaterial/donor_organism.json - v16.2.0] - 2024-09-16 +### Added +Added optional smoking related fields in medical_history module. Fix #1565 + ### [module/ontology/file_content_ontology.json - v2.0.0] - 2024-08-28 ### Fixed Fixed class from data:0006 to EDAM:0006. Fixes #1571 diff --git a/docs/jsonBrowser/module.md b/docs/jsonBrowser/module.md index 34bf8f76..a0878882 100644 --- a/docs/jsonBrowser/module.md +++ b/docs/jsonBrowser/module.md @@ -507,7 +507,9 @@ Property name | Description | Type | Required? | Object reference? | User friend --- | --- | --- | --- | --- | --- | --- | --- alcohol_history | Estimated amount of alcohol consumed per day. | string | no | | Alcohol history | | 3-6 alcohol units/day; 1 drink per day medication | Medications the individual was taking at time of biomaterial collection. | string | no | | Medications | | Naproxen 500mg/day; Citalopram 20mg/day -smoking_history | Estimated number of cigarettes smoked per day. | string | no | | Smoking history | | 20 cigarettes/day for 25 years, stopped 2000 +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 +years_since_smoking_cessation | If smoking status is 'former', specify the number of years since smoking cessation. | integer | no | | Years since smoking cessation | | 12 nutritional_state | Nutritional state of individual at time of biomaterial collection. | string | no | | Nutritional state | normal, fasting, feeding tube removed | Should be one of: normal, fasting, or feeding tube removed. test_results | Results from medical tests performed on the individual. | string | no | | Test results | | lipid panel shows normal level of LDL (124 mg/dL); HIV, HBV, HCV: Negative treatment | Treatments the individual has undergone prior to biomaterial collection. | string | no | | Treatments | | Patient treated with antibiotics for a urinary tract infection; Patient treated with chemotherapy (Epirubicin, cisplatin, capecitabine) to treat stomach cancer diff --git a/json_schema/module/biomaterial/medical_history.json b/json_schema/module/biomaterial/medical_history.json index 5382ca10..224bc79e 100644 --- a/json_schema/module/biomaterial/medical_history.json +++ b/json_schema/module/biomaterial/medical_history.json @@ -31,12 +31,30 @@ "example": "Naproxen 500mg/day; Citalopram 20mg/day", "guidelines": "Enter the medication and dosage. Separate multiple medications with commas." }, - "smoking_history": { - "description": "Estimated number of cigarettes smoked per day.", + "smoking_status": { + "description": "Whether the individual is actively, was formerly or never consumed smoking tobacco products like cigarettes, cigars, pipe etc.", "type": "string", - "user_friendly": "Smoking history", - "example": "20 cigarettes/day for 25 years, stopped 2000", - "guidelines": "Enter an estimated number of cigarettes smoked per day and for how many years." + "enum": [ + "active", + "former", + "never" + ], + "user_friendly": "Smoking status", + "example": "Should be one of: active, former, never." + }, + "smoking_pack_years": { + "description": "Estimated number of packs (20 cigarettes) smoked per day multiplied by the number of years the individual was smoking.", + "type": "number", + "user_friendly": "Smoking pack years", + "minimum": 0, + "example": 4.55 + }, + "years_since_smoking_cessation": { + "description": "If smoking status is 'former', specify the number of years since smoking cessation.", + "type": "integer", + "user_friendly": "Years since smoking cessation", + "minimum": 0, + "example": 12 }, "nutritional_state": { "description": "Nutritional state of individual at time of biomaterial collection.", @@ -61,5 +79,43 @@ "user_friendly": "Treatments", "example": "Patient treated with antibiotics for a urinary tract infection; Patient treated with chemotherapy (Epirubicin, cisplatin, capecitabine) to treat stomach cancer" } - } + }, + "allOf": + [ + { + "if": { + "properties": { + "smoking_status": { + "const": "active" + } + } + }, + "then": { + "properties": { + "years_since_smoking_cessation": { + "maximum": 0 + } + } + } + }, + { + "if": { + "properties": { + "smoking_status": { + "const": "never" + } + } + }, + "then": { + "properties": { + "years_since_smoking_cessation": { + "type": "null" + }, + "smoking_pack_years": { + "maximum": 0 + } + } + } + } + ] } diff --git a/json_schema/property_migrations.json b/json_schema/property_migrations.json index fbdfbdd2..aab24f8b 100644 --- a/json_schema/property_migrations.json +++ b/json_schema/property_migrations.json @@ -1,5 +1,12 @@ { "migrations": [ + { + "source_schema": "medical_history", + "property": "smoking_history", + "effective_from": "6.0.0", + "reason": "Field standardization", + "type": "deprecated property" + }, { "source_schema": "project", "property": "data_use_restriction", diff --git a/json_schema/versions.json b/json_schema/versions.json index f48261af..27bebe93 100644 --- a/json_schema/versions.json +++ b/json_schema/versions.json @@ -1,5 +1,5 @@ { - "last_update_date": "2024-08-28T14:24:32Z", + "last_update_date": "2024-09-16T14:52:03Z", "version_numbers": { "core": { "biomaterial": { @@ -25,7 +25,7 @@ "familial_relationship": "6.0.3", "growth_conditions": "6.4.2", "human_specific": "1.0.11", - "medical_history": "5.2.8", + "medical_history": "6.0.0", "medical_tests": "1.0.0", "mouse_specific": "1.0.8", "preservation_storage": "6.1.1", @@ -92,7 +92,7 @@ "biomaterial": { "cell_line": "16.0.0", "cell_suspension": "14.0.0", - "donor_organism": "16.1.0", + "donor_organism": "16.2.0", "imaged_specimen": "3.5.0", "organoid": "11.5.0", "specimen_from_organism": "10.9.0"