diff --git a/changelog.md b/changelog.md index 5ceb6d72..876c26dc 100644 --- a/changelog.md +++ b/changelog.md @@ -7,6 +7,14 @@ and (starting with v4.0.0) this project adheres to [Semantic Versioning](http:// ## [Unreleased](https://github.com/HumanCellAtlas/metadata-schema/tree/staging) +### [module/biomaterial/disease_profile.json - v1.0.0] - 2024-09-30 +### Added +Added new disease profile module with COPD fields. Fixes#1572 + +### [type/biomaterial/donor_organism.json - v16.3.0] - 2024-09-30 +### Added +Added an optional disease profile field in the donor_organism. Fixes#1572 + ## [Released](https://github.com/HumanCellAtlas/metadata-schema/) ### [system/file_descriptor.json - v2.1.0] - 2024-09-24 diff --git a/docs/jsonBrowser/module.md b/docs/jsonBrowser/module.md index a0878882..8eefbf26 100644 --- a/docs/jsonBrowser/module.md +++ b/docs/jsonBrowser/module.md @@ -460,6 +460,20 @@ dlco_predicted_percent | Indicate the percentage of the predicted DLCO, based on kco | Indicate the transfer coefficient of the lung for carbon monoxide (KCO) in mmol/min/kPa/L if available. | number | no | | KCO | | 5; 6; 4.5 kco_predicted_percent | Indicate the percentage of the predicted KCO, based on patient demographics, if available. | number | no | | KCO percent of predicted | | 90; 98; 85 +## Disease profile +_Information about specific diseases profile of the individual._ + +Location: module/biomaterial/disease_profile.json + +Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example +--- | --- | --- | --- | --- | --- | --- | --- +copd_gold_stage | Indicating current GOLD stage (Global Initiative for Chronic Obstructive Lung Disease). | integer | no | | GOLD stage | 1, 2, 3, 4 | 1; 2; 3; 4 +copd_mmrc_grade | Indicate the Modified British Medical Research Council (mMRC) dyspnea scale grade. | integer | no | | mMRC grade | 0, 1, 2, 3, 4 | 0, 1; 2; 3; 4 +copd_cat_score | Indicate the COPD Assessment Test (CAT) score. | integer | no | | CAT score | | 2; 5; 37 +copd_gold_abe_assessment | Indicate the Global Initiative for Chronic Obstructive Lung Disease (GOLD) A, B, C, D assessment group if available. | string | no | | GOLD ABE assessment | A, B, E | A; B; E +copd_phenotype | Indicate the COPD disease phenotype(s) of donor. Please indicate all applicable phenotypes of donor. | array | no | | COPD phenotype | COPD not otherwise specified, COPD with emphysema, COPD with bronchitis, COPD with history of asthma, COPD with >300 eos in blood, COPD with allergy, COPD with Chronic Mucus Hypersecretion, COPD with frequent exacerbations | COPD with bronchitis; COPD with history of asthma; COPD with emphysema +copd_emphysema_percentage | Indicate the percentage of the lung that is affected by emphysema as judged based on non-invasive imaging, such as from a CT scan. | number | no | | Percentage of emphysema | | 30; 76; 92 + ## Preservation and storage _Information relating to how a biomaterial was preserved and/or stored over a period of time._ @@ -622,4 +636,3 @@ Property name | Description | Type | Required? | Object reference? | User friend plate_label | A label or name for the plate on which the well is located. | string | yes | | Plate label | | 2217 well_label | A label or name for the well in which the cell is located. | string | no | | Well label | | A1 well_quality | Quality of well if imaged before sequencing. | string | no | | Well quality | OK, control, 2-cell well, control, empty well, low quality cell | Should be one of: 'OK', 'control, 2-cell well', 'control, empty well', or 'low quality cell'. - diff --git a/docs/jsonBrowser/required_fields.md b/docs/jsonBrowser/required_fields.md index 4f2ca17e..6052fb77 100644 --- a/docs/jsonBrowser/required_fields.md +++ b/docs/jsonBrowser/required_fields.md @@ -352,6 +352,8 @@ _There are no required properties in schema Human-specific_ _There are no required properties in schema Growth conditions_ ### Medical tests _There are no required properties in schema Medical tests_ +### Disease profile +_There are no required properties in schema Disease profile_ ### Preservation and storage _There are no required properties in schema Preservation and storage_ ### Death diff --git a/docs/jsonBrowser/type.md b/docs/jsonBrowser/type.md index 1c02aed5..632af46f 100644 --- a/docs/jsonBrowser/type.md +++ b/docs/jsonBrowser/type.md @@ -434,6 +434,7 @@ diseases | Short description of known disease(s) of the organism. | array | no | death | Information about conditions of death of the organism. | object | no | [See module death](module.md#death) | Death conditions | | familial_relationships | Information about other organisms related to this organism. | array | no | [See module familial_relationship](module.md#familial-relationship) | Familial relationship | | medical_tests | Information about the medical tests of the organism. | object | no | [See module medical_tests](module.md#medical-tests) | Medical tests | | +disease_profile | Information about specific diseases profile of the individual. | object | no | [See module disease_profile](module.md#disease-profile) | Disease profile | | medical_history | Information about the medical history of the organism. | object | no | [See module medical_history](module.md#medical-history) | Medical history | | gestational_age | Gestational age of pregnancy in Gestational age units measured from the last menstrual period. | string | no | | Gestational age | | 22; 8-9 gestational_age_unit | The unit in which Gestational age is expressed. | object | no | [See module time_unit_ontology](module.md#time-unit-ontology) | Gestational age unit | | diff --git a/json_schema/module/biomaterial/disease_profile.json b/json_schema/module/biomaterial/disease_profile.json new file mode 100644 index 00000000..ceca6732 --- /dev/null +++ b/json_schema/module/biomaterial/disease_profile.json @@ -0,0 +1,82 @@ +{ + "$schema": "http://json-schema.org/draft-07/schema#", + "description": "Information about specific diseases profile of the individual.", + "additionalProperties": false, + "title": "Disease profile", + "name": "disease_profile", + "type": "object", + "minProperties": 1, + "properties": { + "describedBy": { + "description": "The URL reference to the schema.", + "type": "string", + "pattern" : "^(http|https)://schema.(.*?)humancellatlas.org/module/biomaterial/(([0-9]{1,}.[0-9]{1,}.[0-9]{1,})|([a-zA-Z]*?))/disease_profile" + }, + "schema_version": { + "description": "The version number of the schema in major.minor.patch format.", + "type": "string", + "pattern": "^[0-9]{1,}.[0-9]{1,}.[0-9]{1,}$", + "example": "0.0.1" + }, + "copd_gold_stage": { + "user_friendly": "GOLD stage", + "description": "Indicate the current GOLD stage (Global Initiative for Chronic Obstructive Lung Disease).", + "type": "integer", + "enum": [1, 2, 3, 4], + "example": "1; 2; 3; 4", + "bionetworks": ["lung"], + "guidelines": "Should be one of 1, 2, 3, 4" + }, + "copd_mmrc_grade": { + "user_friendly": "mMRC grade", + "description": "Indicate the Modified British Medical Research Council (mMRC) dyspnea scale grade.", + "type": "integer", + "enum": [0, 1, 2, 3, 4], + "example": "0, 1; 2; 3; 4", + "bionetworks": ["lung"], + "guidelines": "Should be one of 0, 1, 2, 3, 4" + }, + "copd_cat_score": { + "user_friendly": "CAT score", + "description": "Indicate the COPD Assessment Test (CAT) score.", + "type": "integer", + "minimum": 0, + "maximum": 40, + "example": "2; 5; 37", + "bionetworks": ["lung"], + "guidelines": "Should be between 0 and 40." + }, + "copd_gold_abe_assessment": { + "user_friendly": "GOLD ABE assessment", + "description": "Indicate the Global Initiative for Chronic Obstructive Lung Disease (GOLD) A, B, C, D assessment group if available.", + "type": "string", + "enum": ["A", "B", "E"], + "example": "A; B; E", + "bionetworks": ["lung"], + "guidelines": "Should be one of A, B, E" + + }, + "copd_phenotype": { + "user_friendly": "COPD phenotype", + "description": "Indicate the COPD disease phenotype(s) of donor. Please indicate all applicable phenotypes of donor.", + "type": "array", + "items": { + "type": "string", + "enum": ["COPD not otherwise specified", "COPD with emphysema", "COPD with bronchitis", + "COPD with history of asthma", "COPD with >300 eos in blood", "COPD with allergy", + "COPD with Chronic Mucus Hypersecretion", "COPD with frequent exacerbations"] + }, + "example": "COPD with bronchitis; COPD with history of asthma; COPD with emphysema", + "bionetworks": ["lung"], + "guidelines": "Should be one or more of: COPD not otherwise specified, COPD with emphysema, COPD with bronchitis, COPD with history of asthma, COPD with >300 eos in blood, COPD with allergy, COPD with Chronic Mucus Hypersecretion, COPD with frequent exacerbations" + }, + "copd_emphysema_percentage": { + "user_friendly": "Percentage of emphysema", + "description": "Indicate the percentage of the lung that is affected by emphysema as judged based on non-invasive imaging, such as from a CT scan.", + "type": "number", + "maximum": 150, + "minimum": 0, + "bionetworks": ["lung"] + } + } +} \ No newline at end of file diff --git a/json_schema/type/biomaterial/donor_organism.json b/json_schema/type/biomaterial/donor_organism.json index f53e4f72..8ba81c0f 100644 --- a/json_schema/type/biomaterial/donor_organism.json +++ b/json_schema/type/biomaterial/donor_organism.json @@ -137,6 +137,12 @@ "$ref": "module/biomaterial/medical_tests.json", "user_friendly": "Medical tests" }, + "disease_profile": { + "description": "Information about specific diseases profile of the individual.", + "type": "object", + "$ref": "module/biomaterial/disease_profile.json", + "user_friendly": "Disease profile" + }, "medical_history": { "description": "Information about the medical history of the organism.", "type": "object", diff --git a/json_schema/versions.json b/json_schema/versions.json index 5cec5fd9..e1db370b 100644 --- a/json_schema/versions.json +++ b/json_schema/versions.json @@ -1,5 +1,5 @@ { - "last_update_date": "2024-09-24T15:16:27Z", + "last_update_date": "2024-09-30T14:15:52Z", "version_numbers": { "core": { "biomaterial": { @@ -22,6 +22,7 @@ "biomaterial": { "cell_morphology": "6.1.7", "death": "5.5.1", + "disease_profile": "1.0.0", "familial_relationship": "6.0.3", "growth_conditions": "6.4.2", "human_specific": "1.0.11", @@ -92,7 +93,7 @@ "biomaterial": { "cell_line": "16.0.0", "cell_suspension": "14.0.0", - "donor_organism": "16.2.0", + "donor_organism": "16.3.0", "imaged_specimen": "3.5.0", "organoid": "11.5.0", "specimen_from_organism": "10.9.0" @@ -138,4 +139,4 @@ } } } -} \ No newline at end of file +}