Merge pull request #1590 from HumanCellAtlas/ac-medication-ontology-I…

…ssue1589 Update medication field in medical_history module
HumanCellAtlas · Nov 6, 2024 · 281a87b · 281a87b
2 parents 1afba4d + 443cb24
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diff --git a/changelog.md b/changelog.md
@@ -7,6 +7,18 @@ and (starting with v4.0.0) this project adheres to [Semantic Versioning](http://
 
 ## [Unreleased](https://github.com/HumanCellAtlas/metadata-schema/tree/staging)
 
+### [module/biomaterial/medical_history.json - v7.0.0] - 2024-11-06
+### Changed
+Changed medication field type Fix#1589
+
+### [module/ontology/medication_ontology.json - v1.0.0] - 2024-11-06
+### Added
+Added medication ontology module Fix#1589
+
+### [type/biomaterial/donor_organism.json - v17.0.0] - 2024-11-06
+### Changed
+Changed medication field type Fix#1589
+
 ## [Released](https://github.com/HumanCellAtlas/metadata-schema/)
 
 ### [type/biomaterial/donor_organism.json - v16.4.0] - 2024-10-21

diff --git a/docs/jsonBrowser/module.md b/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._
 
@@ -365,7 +376,7 @@ Location: module/project/hca_bionetwork.json
 Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example 
 --- | --- | --- | --- | --- | --- | --- | --- 
 name | HCA Bionetwork the project is a part of (e.g. Kidney).  | string | no |  | Official HCA Bionetwork | Adipose, Breast, Development, Eye, Genetic Diversity, Gut, Heart, Immune, Kidney, Liver, Lung, Musculoskeletal, Nervous System, Oral & Craniofacial, Organoid, Pancreas, Reproduction, Skin | Kidney; Lung
-hca_tissue_atlas | A field describing if the project is part of a HCA Tissue Atlas (e.g. Brain Alzheimer Atlas).  | string | no |  | HCA Tissue Atlas | Adipose, Blood, Brain, Breast, Development, Eye, GDN, Gut, Heart, Immune, Kidney, Liver, Lung, MSK, ORCF, Organoid-Endoderm, Organoid-Neural, Pancreas Retina, Reproduction, Skin | Retina
+hca_tissue_atlas | A field describing if the project is part of a HCA Tissue Atlas (e.g. Brain Alzheimer Atlas).  | string | no |  | HCA Tissue Atlas | Adipose, Blood, Brain, Breast, Development, Eye, GDN, Gut, Heart, Immune, Kidney, Liver, Lung, MSK, ORCF, Organoid-Endoderm, Organoid-Neural, Pancreas, Retina, Reproduction, Skin | Retina
 hca_tissue_atlas_version | A field describing which version of the HCA Tissue Atlas is associated with the project (e.g. v1.0; v2.0) | string | no |  | Official HCA Tissue Atlas Version |  | v1.0; v2.0
 atlas_project | A field describing if this project is the HCA Tissue Atlas project which integrates data from other datasets. | boolean | no |  | Project Tissue Atlas Status |  | Yes; No
 
@@ -467,12 +478,12 @@ 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_gold_stage | Indicate the 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
+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 |  | 
 
 ## 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._
@@ -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'.
+
diff --git a/docs/jsonBrowser/required_fields.md b/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 
 --- | --- | --- | --- | --- | --- | --- 
@@ -353,7 +357,7 @@ _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_
+_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>

diff --git a/json_schema/module/biomaterial/medical_history.json b/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.",

diff --git a/json_schema/module/ontology/medication_ontology.json b/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"
+        }
+    }
+}
diff --git a/json_schema/versions.json b/json_schema/versions.json
@@ -1,5 +1,5 @@
 {
-    "last_update_date": "2024-10-21T12:21:40Z",
+    "last_update_date": "2024-11-06T17:01:14Z",
     "version_numbers": {
         "core": {
             "biomaterial": {
@@ -26,7 +26,7 @@
                 "familial_relationship": "6.0.3",
                 "growth_conditions": "6.4.2",
                 "human_specific": "1.0.11",
-                "medical_history": "6.0.0",
+                "medical_history": "7.0.0",
                 "medical_tests": "1.0.0",
                 "mouse_specific": "1.0.8",
                 "preservation_storage": "6.1.1",
@@ -50,6 +50,7 @@
                 "library_amplification_ontology": "1.2.5",
                 "library_construction_ontology": "1.2.5",
                 "mass_unit_ontology": "5.3.5",
+                "medication_ontology": "1.0.0",
                 "microscopy_ontology": "1.0.5",
                 "organ_ontology": "5.3.7",
                 "organ_part_ontology": "5.3.5",
@@ -93,7 +94,7 @@
             "biomaterial": {
                 "cell_line": "16.0.0",
                 "cell_suspension": "14.0.0",
-                "donor_organism": "16.4.0",
+                "donor_organism": "17.0.0",
                 "imaged_specimen": "3.5.0",
                 "organoid": "11.5.0",
                 "specimen_from_organism": "10.9.0"