Added disease_profile module to donor_organism. Fixes#1578

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<a name='Disease profile'></a>
+_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<a name='Preservation and storage'></a>
 _Information relating to how a biomaterial was preserved and/or stored over a period of time._
 
@@ -620,4 +634,3 @@ 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'.
-

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<a name='Medical tests'></a>
 _There are no required properties in schema Medical tests_
+### Disease profile<a name='Disease profile'></a>
+_There are no required properties in schema Disease profile_
 ### Preservation and storage<a name='Preservation and storage'></a>
 _There are no required properties in schema Preservation and storage_
 ### Death<a name='Death'></a>

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 |  | 

json_schema/module/biomaterial/disease_profile.json

@@ -0,0 +1,82 @@
+{
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "description": "Information about specific diseases profile of the individual.",
+    "additionalProperties": false,
+    "title": "Disease profile",
+    "name": "disease_profile",
+    "type": "object",
+    "minProperties": 1,
+    "properties": {
+        "describedBy":  {
+            "description": "The URL reference to the schema.",
+            "type": "string",
+            "pattern" : "^(http|https)://schema.(.*?)humancellatlas.org/module/biomaterial/(([0-9]{1,}.[0-9]{1,}.[0-9]{1,})|([a-zA-Z]*?))/medical_tests"
+        },
+        "schema_version": {
+            "description": "The version number of the schema in major.minor.patch format.",
+            "type": "string",
+            "pattern": "^[0-9]{1,}.[0-9]{1,}.[0-9]{1,}$",
+            "example": "0.0.1"
+        },
+        "copd_gold_stage": {
+            "user_friendly": "GOLD stage",
+            "description": "Indicating 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 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"]
+        }
+    }
+}

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",

json_schema/update_log.csv

@@ -1 +1,3 @@
 Schema,Change type,Change message,Version,Date
+module/biomaterial/disease_profile,major,"Added new disease profile module with COPD fields. Fixes#1572",,
+type/biomaterial/donor_organism,minor,"Added an optional disease profile field in the donor_organism. Fixes#1572"