diff --git a/changelog.md b/changelog.md
index 91659dee..8acf4103 100644
--- a/changelog.md
+++ b/changelog.md
@@ -9,6 +9,18 @@ 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 - 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
+
### [type/biomaterial/donor_organism.json - v16.4.0] - 2024-10-21
### Added
Added comorbidities field in the donor_organism Fix#1569
diff --git a/docs/jsonBrowser/module.md b/docs/jsonBrowser/module.md
index af2e62d8..eeb1db00 100644
--- 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 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 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
_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
index 7ba742ba..7346337f 100644
--- 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
+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
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
_There are no required properties in schema Medical tests_
### Disease profile
-_There are no required properties in schema 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/json_schema/module/biomaterial/medical_history.json b/json_schema/module/biomaterial/medical_history.json
index 224bc79e..112e5587 100644
--- 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": {
+ "$ref": "module/ontology/medication_ontology.json"
+ },
+ "user_friendly": "Medication"
},
"smoking_status": {
"description": "Whether the individual is actively, was formerly or never consumed smoking tobacco products like cigarettes, cigars, pipe etc.",
diff --git a/json_schema/module/ontology/medication_ontology.json b/json_schema/module/ontology/medication_ontology.json
new file mode 100644
index 00000000..646af56d
--- /dev/null
+++ b/json_schema/module/ontology/medication_ontology.json
@@ -0,0 +1,49 @@
+{
+ "$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"
+ }
+ }
+}
\ No newline at end of file
diff --git a/json_schema/versions.json b/json_schema/versions.json
index bcd03b5f..8e36fe0e 100644
--- 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"