Add medication ontology

docs/jsonBrowser/module.md

@@ -214,6 +214,17 @@ text | The name of the strain to which the organism belongs. | string | yes |  |
 ontology | An ontology term identifier in the form prefix:accession. | string | no |  | Strain ontology ID |  | EFO:0004472; EFO:0000602
 ontology_label | The preferred label for the ontology term referred to in the ontology field. This may differ from the user-supplied value in the text field. | string | no |  | Strain ontology label |  | C57BL/6; BALB/c
 
+## Medication ontology<a name='Medication ontology'></a>
+_A term that may be associated with a medication-related ontology term._
+
+Location: module/ontology/medication_ontology.json
+
+Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example 
+--- | --- | --- | --- | --- | --- | --- | --- 
+text | Medication(s) the individual was taking at time of biomaterial collection. | string | yes |  | Medication |  | bisoprolol; paracetamol; loratadine
+ontology | An ontology term identifier in the form prefix:accession. | string | no |  | Medication ontology ID |  | CHEBI:3127; CHEBI:46195; CHEBI:6538
+ontology_label | The preferred label for the ontology term referred to in the ontology field. This may differ from the user-supplied value in the text field. | string | no |  | Medication ontology label |  | bisoprolol; paracetamol; loratadine
+
 ## File format ontology<a name='File format ontology'></a>
 _A term that may be associated with a file format-related ontology term._
 
@@ -520,7 +531,7 @@ 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
-medication | Medications the individual was taking at time of biomaterial collection. | string | no |  | Medications |  | Naproxen 500mg/day; Citalopram 20mg/day
+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
 years_since_smoking_cessation | If smoking status is 'former', specify the number of years since smoking cessation. | integer | no |  | Years since smoking cessation |  | 12
@@ -636,3 +647,4 @@ 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

@@ -280,6 +280,10 @@ text | The text for the term as the user provides it. | string |  | Disease |  |
 Property name | Description | Type | Object reference? | User friendly name | Allowed values | Example 
 --- | --- | --- | --- | --- | --- | --- 
 text | The name of the strain to which the organism belongs. | string |  | Strain |  | C57BL/6; BALB/c
+### Medication ontology<a name='Medication ontology'></a>
+Property name | Description | Type | Object reference? | User friendly name | Allowed values | Example 
+--- | --- | --- | --- | --- | --- | --- 
+text | Medication(s) the individual was taking at time of biomaterial collection. | string |  | Medication |  | bisoprolol; paracetamol; loratadine
 ### File format ontology<a name='File format ontology'></a>
 Property name | Description | Type | Object reference? | User friendly name | Allowed values | Example 
 --- | --- | --- | --- | --- | --- | --- 

json_schema/module/biomaterial/medical_history.json

@@ -25,11 +25,12 @@
             "guidelines": "Enter the amount consumed per day using units such as alcohol units (10mL or 8g of alcohol) or drinks (14g of alcohol)."
         },
         "medication": {
-            "description": "Medications the individual was taking at time of biomaterial collection.",
-            "type": "string",
-            "user_friendly": "Medications",
-            "example": "Naproxen 500mg/day; Citalopram 20mg/day",
-            "guidelines": "Enter the medication and dosage. Separate multiple medications with commas."
+            "description": "Medication(s) the individual was taking at time of biomaterial collection.",
+            "type": "array",
+            "items": {
+                "$ref": "module/ontology/medication_ontology.json"
+            },
+            "user_friendly": "Medication"
         },
         "smoking_status": {
             "description": "Whether the individual is actively, was formerly or never consumed smoking tobacco products like cigarettes, cigars, pipe etc.",

json_schema/module/ontology/medication_ontology.json

@@ -0,0 +1,49 @@
+{
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "description": "A term that may be associated with a medication-related ontology term.",
+    "additionalProperties": false,
+    "required": [
+        "text"
+    ],
+    "title": "Medication ontology",
+    "name": "medication_ontology",
+    "type": "object",
+    "properties": {
+        "describedBy" : {
+            "description": "The URL reference to the schema.",
+            "pattern" : "^(http|https)://schema.(.*?)humancellatlas.org/module/ontology/(([0-9]{1,}.[0-9]{1,}.[0-9]{1,})|([a-zA-Z]*?))/medication_ontology",
+            "type": "string"
+        },
+        "schema_version": {
+            "description": "Version number in major.minor.patch format.",
+            "type": "string",
+            "pattern": "^[0-9]{1,}.[0-9]{1,}.[0-9]{1,}$",
+            "example": "4.6.1"
+        },
+        "text": {
+            "description": "Medication(s) the individual was taking at time of biomaterial collection.",
+            "type": "string",
+            "user_friendly": "Medication",
+            "example": "bisoprolol; paracetamol; loratadine"
+        },
+        "ontology": {
+            "description": "An ontology term identifier in the form prefix:accession.",
+            "type": "string",
+            "graph_restriction":  {
+                "ontologies" : ["obo:dron"],
+                "classes": ["BFO:0000040"],
+                "relations": ["rdfs:subClassOf"],
+                "direct": false,
+                "include_self": false
+            },
+            "user_friendly": "Medication ontology ID",
+            "example": "CHEBI:3127; CHEBI:46195; CHEBI:6538"
+        },
+        "ontology_label": {
+            "description": "The preferred label for the ontology term referred to in the ontology field. This may differ from the user-supplied value in the text field.",
+            "type": "string",
+            "user_friendly": "Medication ontology label",
+            "example": "bisoprolol; paracetamol; loratadine"
+        }
+    }
+}

json_schema/update_log.csv

@@ -1 +1,3 @@
 Schema,Change type,Change message,Version,Date
+module/biomaterial/medical_history,major,"Update medication field with ontology Fix#1589",,
+module/ontology/medication_ontology,major,"Created medication ontology module Fix#1589",,

json_schema/versions.json

@@ -50,6 +50,7 @@
                 "library_amplification_ontology": "1.2.5",
                 "library_construction_ontology": "1.2.5",
                 "mass_unit_ontology": "5.3.5",
+                "medication_ontology": "0.0.0",
                 "microscopy_ontology": "1.0.5",
                 "organ_ontology": "5.3.7",
                 "organ_part_ontology": "5.3.5",