diff --git a/.github/workflows/schema-tests.yml b/.github/workflows/schema-tests.yml
index 760844611..46ab94089 100644
--- a/.github/workflows/schema-tests.yml
+++ b/.github/workflows/schema-tests.yml
@@ -38,7 +38,7 @@ jobs:
- name: Use Node.js
uses: actions/setup-node@v3
with:
- node-version: '16.x'
+ node-version: '18.x'
cache: npm
cache-dependency-path: tests/package-lock.json
- run: npm ci
diff --git a/docs/jsonBrowser/module.md b/docs/jsonBrowser/module.md
index 6a7eb0967..55f1de83c 100644
--- a/docs/jsonBrowser/module.md
+++ b/docs/jsonBrowser/module.md
@@ -490,6 +490,50 @@ dlco | Indicate the Diffusing Capacity of the Lung for Carbon Monoxide (DLCO) in
dlco_predicted_percent | Indicate the percentage of the predicted DLCO, based on patient demographics, if available. | number | no | | DLCO percent of predicted | | 88; 95; 82
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
+ecg_heart_rate | Heart rate as measured by electrocardiogram in beats per minute. | number | no | | Ecg - Heart Rate | | 72; 65; 80
+ecg_heart_rhythm | Heart rhythm as measured by electrocardiogram. | string | no | | Ecg - Heart Rhythm | | sinus rhythm; atrial fibrillation; atrial flutter; atrial tachycardia
+ecg_pr_interval_duration | PR interval duration in ms as measured by electrocardiogram. It can be described as PQ interval duration in ECG description according to region. | number | no | | Ecg - Pr Interval Duration | | 160; 140; 180
+ecg_qrs_complex_duration | QRS complex duration in ms as measured by electrocardiogram. | number | no | | Ecg - QRS Complex Duration | | 90; 100; 110
+ecg_lbbb_rbbb_ivcd | Bundle branch block and/or delayed atrioventricular conduction as measured by electrocardiogram. LBBB - Left bundle branch block/ RBBB - right bundle branch block/ IVCD - intraventricular-conduction delay (QRSd >120ms not fulfilling LBBB or RBBB criteria). | string | no | | Ecg - LBBB RBBB IVCD | LBBB, RBBB, IVCD | Should be one of: LBBB, RBBB, IVCD.
+ecg_qt_interval_corrected | Corrected QT interval in ms as measured by electrocardiogram. | number | no | | Ecg - QT Interval Corrected | | 420; 410; 430
+ecg_time_offset | Time between the test and the collection of the sample, measured in days. | number | no | | Ecg - Time Offset | | 4; 20; 58
+echo_aortic_stenosis | Aortic stenosis as measured by echocardiogram. | string | no | | Echo - Aortic Stenosis | no, mild, mod, severe | Should be one of: no, mild, mod, severe.
+echo_aortic_regurgitation | Aortic regurgitation as measured by echocardiogram. | string | no | | Echo - Aortic Regurgitation | no, mild, mod, severe | Should be one of: no, mild, mod, severe.
+echo_mitral_regurgitation | Mitral regurgitation as measured by echocardiogram. | string | no | | Echo - Mitral Regurgitation | no, mild, mod, severe | Should be one of: no, mild, mod, severe.
+echo_mitral_stenosis | Mitral stenosis as measured by echocardiogram. | string | no | | Echo - Mitral Stenosis | no, mild, mod, severe | Should be one of: no, mild, mod, severe.
+echo_tricuspid_regurgitation | Tricuspid regurgitation as measured by echocardiogram. | string | no | | Echo - Tricuspid Regurgitation | no, mild, mod, severe | Should be one of: no, mild, mod, severe.
+echo_estimated_rvsp | Estimated right ventricular systolic pressure in mmHg as measured by echocardiogram. | number | no | | Echo - Estimated RVSP | | 25; 30; 35
+echo_lvedv | Left ventricular end-diastolic volume in ml as measured by echocardiogram. | number | no | | Echo - LVEDV | | 120; 110; 130
+echo_lvedv_indexed | Left ventricular end-diastolic volume indexed to body surface area in ml/m^2 (indexed to body surface area) as measured by echocardiogram. | number | no | | Echo - LVEDV Indexed | | 65; 70; 60
+echo_lvesv | Left ventricular end-systolic volume in ml as measured by echocardiogram. | number | no | | Echo - LVESV | | 50; 45; 55
+echo_lvesv_indexed | Left ventricular end-systolic volume indexed to body surface area in ml/m^2 (indexed to body surface area) as measured by echocardiogram. | number | no | | Echo - LVESV Indexed | | 25; 30; 28
+echo_lvef | Left ventricular ejection fraction as measured by echocardiogram. | number | no | | Echo - LVEF | | 55; 60; 65
+echo_lv_mass | Left ventricular mass in grams as measured by echocardiogram. | number | no | | Echo - LV Mass | | 150; 160; 140
+echo_lv_mass_indexed | Left ventricular mass indexed to body surface area in g/m^2 (indexed to body surface area) as measured by echocardiogram. | number | no | | Echo - LV Mass Indexed | | 75; 80; 70
+echo_rv_fac | Right Ventricular Fractional Area Change (RV FAC) in percentage as measured by echocardiogram. | number | no | | Echo - RV FAC | | 40; 45; 50
+echo_tapse | Tricuspid annular plane systolic excursion (TAPSE) in mm as measured by echocardiogram. | number | no | | Echo - TAPSE | | 20; 22; 18
+echo_lv_septum_thickness | Left ventricular septum thickness in mm as measured by echocardiogram. | number | no | | Echo - LV Septum Thickness | | 9; 10; 11
+echo_pw_thickness | Basal posterior LV wall thickness in mm as measured by echocardiogram. | number | no | | Echo - PW Thickness | | 9; 10; 11
+echo_la_dimension | Left atrial diameter in PLAX view in mm as measured by echocardiogram. | number | no | | Echo - LA Dimension | | 38; 36; 40
+echo_lav_indexed | Left atrial volume indexed to body surface area in ml/m^2 (left atrial volume indexed to body surface area) as measured by echocardiogram. | number | no | | Echo - LAV Indexed | | 28; 30; 32
+echo_time_offset | Time between the test and the collection of the sample, in days. | number | no | | Echo - Time Offset | | 4; 20; 58
+mri_lvedv | Left ventricular end-diastolic volume in ml as measured by MRI. | number | no | | Mri - LVEDV | | 140; 150; 130
+mri_lvedv_indexed | Left ventricular end-diastolic volume indexed to body surface area in ml/m^2 (indexed to body surface area) as measured by MRI. | number | no | | Mri - LVEDV Indexed | | 75; 70; 80
+mri_lvesv | Left ventricular end-systolic volume in ml as measured by MRI. | number | no | | Mri - LVESV | | 60; 55; 65
+mri_lvesv_indexed | Left ventricular end-systolic volume indexed to body surface area in ml/m^2 (indexed to body surface area) as measured by MRI. | number | no | | Mri - LVESV Indexed | | 30; 28; 32
+mri_lvef | Left ventricular ejection fraction measured by MRI. | number | no | | Mri - LVEF | | 55; 60; 58
+mri_lv_mass | Left ventricular mass in grams as measured by MRI. | number | no | | Mri - LV Mass | | 130; 120; 140
+mri_lv_mass_indexed | Left ventricular mass indexed to body surface area in g/m^2 (indexed to body surface area) as measured by MRI. | number | no | | Mri - LV Mass Indexed | | 65; 60; 70
+mri_rv_ejection_fraction | Right ventricular ejection fraction in percentage as measured by MRI. | number | no | | Mri - RV Ejection Fraction | | 50; 55; 60
+mri_mid_wall_lge | Late gadolinium enhancement (mid wall) as measured by MRI. | boolean | no | | Mri - Mid Wall LGE | | Should be one of: yes; no.
+mri_epicardial_lge | Late gadolinium enhancement (epicardial) as measured by MRI. | boolean | no | | Mri - Epicardial LGE | | Should be one of: yes; no.
+mri_infarct_pattern_lge | Late gadolinium enhancement (infarct pattern) as measured by MRI. | boolean | no | | Mri - Infarct Pattern LGE | | Should be one of: yes; no.
+mri_myocardial_oedema | Myocardial oedema as measured by MRI. | boolean | no | | Mri - Myocardial Oedema | | Should be one of: yes; no.
+mri_time_offset | Time between the test and the collection of the sample, in days. | number | no | | Mri - Time Offset | | 4; 20; 58
+mps_lvef | Left ventricular ejection fraction in percentage as measured by myocardial perfusion scintigraphy. | number | no | | Mps - LVEF | | 58; 60; 62
+mps_inducible_ischaemic | Left ventricular inducible ischemic percentage as measured by myocardial perfusion scintigraphy. | number | no | | Mps - Inducible Ischaemic | | 0; 5; 12
+mps_scar | Left ventricular scar percentage as measured by myocardial perfusion scintigraphy. | number | no | | Mps - Scar | | 0; 3; 10
+mps_time_offset | Time between the test and the collection of the sample, in days. | number | no | | Mps - Time Offset | | 4; 20; 58
## Collection institute
_Information about collection institute location._
@@ -552,6 +596,10 @@ Location: module/biomaterial/lifestyle.json
Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example
--- | --- | --- | --- | --- | --- | --- | ---
physical_activity | The habitual level of physical activity and regular physical activities. | string | no | | Physical activity | | active - football, tennis; sedentary
+substance_type | Any drug or substance the donor uses or used. | array | no | | Substance Type | marijuana, cocaine, heroin, methamphetamine, prescription drugs (non-medical use) | marijuana; cocaine; heroin; methamphetamine; prescription drugs (non-medical use)
+substance_frequency | Number of donor's substance usage per year. | number | no | | Substance Use Frequency | | 12; 50; 300
+substance_use_duration | Duration of donor's substance usage in years. | integer | no | | Duration Of Substance Use | | 4; 8; 20
+substance_duration_since_last_use | If donor is no longer using, specify the number of years since substance usage cessation, if available. | integer | no | | Duration Since Last Substance Use | | 1; 4; 20
## Death
_Information relating to the death of an organism._
@@ -603,7 +651,10 @@ diet_meat_consumption | Dietary patterns of donor - meat (chicken, seafood, fish
reproductive_history | Reproductive history of the donor at the time of collection. | object | no | [See module reproductive_history](module.md#reproductive-history) | Reproductive history | |
blood_test | Results from blood tests performed on the individual. | object | no | [See module blood_test](module.md#blood-test) | Blood tests | |
test_results | Results from medical tests performed on the individual. | string | no | | Test results | | lipid panel shows normal level of LDL (124 mg/dL); HIV, HBV, HCV: Negative
+diseases_history | Short description of known disease(s) that have previously affected the donor, but are not considered active now. | array | no | [See module disease_ontology](module.md#disease-ontology) | Diseases History | |
treatment | Treatments the individual has undergone prior to biomaterial collection. | string | no | | Treatments | | Patient treated with antibiotics for a urinary tract infection; Patient treated with chemotherapy (Epirubicin, cisplatin, capecitabine) to treat stomach cancer
+device_treatment | Device/interventional therapy 1 year before and/or at time of sample collection. | string | no | | Device Treatment | ECMO, IABP, Impella, LVAD, RVAD, PPM, ICD, CRT | Should be one of: ECMO, IABP, Impella, LVAD, RVAD, PPM, ICD, CRT
+cardioplegia | Cardioplegia applied right before or during time of biomaterial collection. | boolean | no | | Cardioplegia | | yes; no
previous_surgeries | Previous surgeries the individual has undergone prior to biomaterial collection. | string | no | | Previous surgeries | | Appendectomy; Coleostomy; Vaginoplasty; LASIK; Abdominal surgery
defined_diet | Whether the individual was following a defined diet at the time of biomaterial collection. | boolean | no | | Defined diet | | yes; no
diet_specific | Defined diet the donor was on at the time of biomaterial collection. | array | no | | Diet Specific | vegan, vegetarian, omnivore, gluten_free, fodmap, baby_formula, breastfeeding, elimination, keto, paleo | gluten_free; fodmap; baby_formula; breastfeeding; elimination; keto; paleo
@@ -646,9 +697,19 @@ testosterone | Testosterone in the last blood test of the donor before collectio
testosterone_unit | Testosterone unit. | string | no | | Testosterone unit | nmol/L, ng/dL | nmol/L; ng/dL
triglycerides | Triglycerides levels from the donor's last blood test after at least 9-12 hours of fasting, prior to the biopsy collection. | number | no | | Triglycerides | | 160; 133; 140
triglycerides_unit | Triglycerides unit. | string | no | | Triglycerides unit | mg/dL, mmol/L | mg/dL; mmol/L
+sodium | Sodium in the last blood test of the donor before collection. | number | no | | Sodium | | 138; 140; 142
+sodium_unit | Sodium unit. | string | no | | Sodium unit | mmol/L | mmol/L
+potassium | Potassium in the last blood test of the donor before collection. | number | no | | Potassium | | 4.0; 4.2; 3.8
+potassium_unit | Potassium unit. | string | no | | Potassium unit | mmol/L | mmol/L
+urea | Urea in the last blood test of the donor before collection. | number | no | | Urea | | 5.0; 5.5; 4.8
+urea_unit | Urea unit. | string | no | | Urea unit | mmol/L | mmol/L
+creatinine | Creatinine in the last blood test of the donor before collection. | number | no | | Creatinine | | 80; 85; 78
+creatinine_unit | Creatinine unit. | string | no | | Creatinine unit | micromol/L, mg/dL | micromol/L; mg/dL
+total_bilirubin | Total bilirubin in the last blood test of the donor before collection. | number | no | | Total bilirubin | | 12; 10; 14
+total_bilirubin_unit | Total bilirubin unit. | string | no | | Total bilirubin unit | micromol/L | micromol/L
white_blood_cell_count | Measurement of total white blood cells per unit volume of blood from the donor's last blood test prior to biopsy collection. | number | no | | White cell count | | 4.5; 11; 9.24
white_blood_cell_count_unit | White cell count unit. | string | no | | White cell count unit | 10^9/L, cells/μL | 10^9/L; cells/μL
-bloodtest_time_offset | Time between the test and the collection of the sample, in days. | number | no | | Blood test time offset | | 12; 42; 98
+blood_test_time_offset | Time between the test and the collection of the sample, in days. | number | no | | Blood test time offset | | 12; 42; 98
## Residence
_Donor's residence location information._
diff --git a/docs/jsonBrowser/type.md b/docs/jsonBrowser/type.md
index 0e30c1f96..7ab4bb916 100644
--- a/docs/jsonBrowser/type.md
+++ b/docs/jsonBrowser/type.md
@@ -226,8 +226,8 @@ schema_type | The type of the metadata schema entity. | string | yes | | | pro
provenance | Provenance information provided by the system. | object | no | [See provenance](.md#provenance) | | |
protocol_core | Core protocol-level information. | object | yes | [See core protocol_core](core.md#protocol-core) | Protocol core | |
method | Method used to collect the biomaterial. | object | yes | [See module process_type_ontology](module.md#process-type-ontology) | Collection method | |
-biopsy_procedure | Type of biopsy procedure used in the sample collection. | string | no | | Type of biopsy procedure | Bergstrom needle, Punch biopsy, Mercedes needle, dry aspiration, Mercedes needle, tumescent lidocaine “wet” aspiration | Bergstrom needle; Punch biopsy; Mercedes needle, dry aspiration; Mercedes needle, tumescent lidocaine “wet” aspiration
procedure | Procedure used to collect the specimen from the organism. | string | no | | Procedure | | colonoscopy; venipuncture; laparoscopic surgery
+biopsy_procedure | Type of biopsy procedure used in the sample collection. | string | no | | Type of biopsy procedure | Bergstrom needle, Punch biopsy, Mercedes needle, dry aspiration, Mercedes needle, tumescent lidocaine “wet” aspiration | Bergstrom needle; Punch biopsy; Mercedes needle, dry aspiration; Mercedes needle, tumescent lidocaine “wet” aspiration
reagents | A list of purchased reagents used in this protocol. | array | no | [See module purchased_reagents](module.md#purchased-reagents) | Protocol reagents | |
## Differentiation protocol
@@ -353,7 +353,8 @@ genus_species | The scientific binomial name for the species of the specimen. |
organ | The organ that the biomaterial came from. | object | yes | [See module organ_ontology](module.md#organ-ontology) | Organ | |
organ_parts | A term for a specific part of the organ that the biomaterial came from. | array | no | [See module organ_part_ontology](module.md#organ-part-ontology) | Organ part | |
radial_tissue_term | Layer(s) of the gut that was/were sampled. | array | no | | Radial tissue term | EPI, LP, MLN, MUILF, MUSC, PP, SMILF, SUB | EPI; LP; MLN; MUILF; MUSC; PP; SMILF; SUB
-transplant_organ | Was the specimen collected after extraction for organ transplantation? | boolean | no | | Transplant organ | | yes; no
+transplant_organ | Was the organ transplanted or explanted before biomaterial collection? | string | no | | Transplant organ | explanted organ, transplanted organ, no transplant | explanted organ; transplanted organ; no transplant.
+transplant_rejection_reason | If the organ was evaluated for transplantation but rejected give the reason for rejection. | string | no | | Transplant Rejection Reason | | Rejected because underlying malignant disease; not evaluated for transplantation
diseases | Short description of known disease(s) of the specimen. | array | no | [See module disease_ontology](module.md#disease-ontology) | Known disease(s) | |
adjacent_diseases | Short description of the disease(s) adjacent to the specimen's collection site (e.g. breast cancer). | array | no | [See module disease_ontology](module.md#disease-ontology) | Adjacent disease(s) | |
experimental_condition | Case of the sample used in the experiment context, it should include a description of the experimental conditions of the study. If disease case, specify the disease that was studied. | string | no | | Case Control definition | | healthy control; disease control; MAFLD disease case; gestational diabetes case
diff --git a/json_schema/module/biomaterial/blood_test.json b/json_schema/module/biomaterial/blood_test.json
index e26afb61f..d75c0cf3d 100644
--- a/json_schema/module/biomaterial/blood_test.json
+++ b/json_schema/module/biomaterial/blood_test.json
@@ -153,7 +153,7 @@
],
"user_friendly": "Haematocrit unit",
"example": "%",
- "guidelines": "Should be one of: %",
+ "guidelines": "Should be one of: percentage (%)",
"bionetworks": ["adipose"]
},
"haemoglobin": {
@@ -323,6 +323,102 @@
"guidelines": "Should be one of: mg/dL; mmol/L",
"bionetworks": ["adipose"]
},
+ "sodium": {
+ "description": "Sodium in the last blood test of the donor before collection.",
+ "type": "number",
+ "minimum": 0,
+ "user_friendly": "Sodium",
+ "example": "138; 140; 142",
+ "bionetworks": ["heart"]
+ },
+ "sodium_unit": {
+ "description": "Sodium unit.",
+ "type": "string",
+ "enum": [
+ "mmol/L"
+ ],
+ "user_friendly": "Sodium unit",
+ "example": "mmol/L",
+ "guidelines": "Should be one of: mmol/L",
+ "bionetworks": ["heart"]
+ },
+ "potassium": {
+ "description": "Potassium in the last blood test of the donor before collection.",
+ "type": "number",
+ "user_friendly": "Potassium",
+ "minimum": 0,
+ "example": "4.0; 4.2; 3.8",
+ "bionetworks": ["heart"]
+ },
+ "potassium_unit": {
+ "description": "Potassium unit.",
+ "type": "string",
+ "enum": [
+ "mmol/L"
+ ],
+ "user_friendly": "Potassium unit",
+ "example": "mmol/L",
+ "guidelines": "Should be one of: mmol/L",
+ "bionetworks": ["heart"]
+ },
+ "urea": {
+ "description": "Urea in the last blood test of the donor before collection.",
+ "type": "number",
+ "minimum": 0,
+ "user_friendly": "Urea",
+ "example": "5.0; 5.5; 4.8",
+ "bionetworks": ["heart"]
+ },
+ "urea_unit": {
+ "description": "Urea unit.",
+ "type": "string",
+ "enum": [
+ "mmol/L"
+ ],
+ "user_friendly": "Urea unit",
+ "example": "mmol/L",
+ "guidelines": "Should be one of: mmol/L",
+ "bionetworks": ["heart"]
+ },
+ "creatinine": {
+ "description": "Creatinine in the last blood test of the donor before collection.",
+ "type": "number",
+ "minimum": 0,
+ "user_friendly": "Creatinine",
+ "example": "80; 85; 78",
+ "bionetworks": ["heart"]
+ },
+ "creatinine_unit": {
+ "description": "Creatinine unit.",
+ "type": "string",
+ "enum": [
+ "micromol/L",
+ "mg/dL"
+ ],
+ "user_friendly": "Creatinine unit",
+ "example": "micromol/L; mg/dL",
+ "guidelines": "Should be one of: micromol/L, mg/dL",
+ "bionetworks": ["heart"]
+ },
+ "total_bilirubin": {
+ "description": "Total bilirubin in the last blood test of the donor before collection.",
+ "type": "number",
+ "minimum": 0,
+ "user_friendly": "Total bilirubin",
+ "example": "12; 10; 14",
+ "bionetworks": ["heart"]
+ },
+ "total_bilirubin_unit": {
+ "description": "Total bilirubin unit.",
+ "type": "string",
+ "enum": [
+ "micromol/L"
+ ],
+ "user_friendly": "Total bilirubin unit",
+ "example": "micromol/L",
+ "guidelines": "Should be one of: micromol/L",
+ "bionetworks": ["heart"]
+ },
"white_blood_cell_count": {
"description": "Measurement of total white blood cells per unit volume of blood from the donor's last blood test prior to biopsy collection.",
"type": "number",
@@ -343,7 +439,7 @@
"guidelines": "Should be one of: 10^9/L; cells/μL",
"bionetworks": ["adipose"]
},
- "bloodtest_time_offset": {
+ "blood_test_time_offset": {
"description": "Time between the test and the collection of the sample, in days.",
"type": "number",
"minimum": 0,
diff --git a/json_schema/module/biomaterial/human_specific.json b/json_schema/module/biomaterial/human_specific.json
index 5f120db7d..4f91ac541 100644
--- a/json_schema/module/biomaterial/human_specific.json
+++ b/json_schema/module/biomaterial/human_specific.json
@@ -24,7 +24,7 @@
},
"body_mass_index": {
"description": "The body mass index of the donor.",
- "pattern": "(0|[1-9][0-9]*)(\\.(0|[0-9]*[1-9]))?(-(0|[1-9][0-9]*)(\\.(0|[0-9]*[1-9]))?)?$",
+ "pattern": "^(0|[1-9][0-9]*)(\\.(0|[0-9]*[1-9]))?(-(0|[1-9][0-9]*)(\\.(0|[0-9]*[1-9]))?)?$",
"type": "string",
"example": "36.4; 29-32 ",
"user_friendly": "Body mass index",
@@ -32,7 +32,7 @@
},
"waist_circumference": {
"description": "Waist circumference of the donor at the time of collection measured in cm.",
- "pattern": "(0|[1-9][0-9]*)(\\.(0|[0-9]*[1-9]))?(-(0|[1-9][0-9]*)(\\.(0|[0-9]*[1-9]))?)?$",
+ "pattern": "^(0|[1-9][0-9]*)(\\.(0|[0-9]*[1-9]))?(-(0|[1-9][0-9]*)(\\.(0|[0-9]*[1-9]))?)?$",
"type": "string",
"example": "60; 85-95; 153",
"user_friendly": "Waist circumference",
@@ -40,7 +40,7 @@
},
"waist_hip_ratio": {
"description": "Waist-hip ratio of the donor at the time of collection.",
- "pattern": "(0|[1-9][0-9]*)(\\.(0|[0-9]*[1-9]))?(-(0|[1-9][0-9]*)(\\.(0|[0-9]*[1-9]))?)?$",
+ "pattern": "^(0|[1-9][0-9]*)(\\.(0|[0-9]*[1-9]))?(-(0|[1-9][0-9]*)(\\.(0|[0-9]*[1-9]))?)?$",
"type": "string",
"example": "0.85; 0.85-0.91; 0.88",
"user_friendly": "Waist-hip ratio",
diff --git a/json_schema/module/biomaterial/lifestyle.json b/json_schema/module/biomaterial/lifestyle.json
index c8dc5893f..ef6e4d233 100644
--- a/json_schema/module/biomaterial/lifestyle.json
+++ b/json_schema/module/biomaterial/lifestyle.json
@@ -24,6 +24,48 @@
"user_friendly": "Physical activity",
"example": "active - football, tennis; sedentary",
"bionetworks": ["adipose","heart","musculoskeletal"]
+ },
+ "substance_type": {
+ "description": "Any drug or substance the donor uses or used.",
+ "type": "array",
+ "items": {
+ "type": "string",
+ "enum": [
+ "marijuana",
+ "cocaine",
+ "heroin",
+ "methamphetamine",
+ "prescription drugs (non-medical use)"
+ ]
+ },
+ "example": "marijuana; cocaine; heroin; methamphetamine; prescription drugs (non-medical use)",
+ "guidelines": "Should be one of: marijuana; cocaine; heroin; methamphetamine; prescription drugs (non-medical use).",
+ "user_friendly": "Substance Type",
+ "bionetworks": ["heart", "oral and craniofacial", "liver", "reproduction"]
+ },
+ "substance_frequency": {
+ "description": "Number of donor's substance usage per year.",
+ "type": "number",
+ "user_friendly": "Substance Use Frequency",
+ "minimum": 0,
+ "example": "12; 50; 300",
+ "bionetworks": ["heart", "oral and craniofacial", "liver", "reproduction"]
+ },
+ "substance_use_duration": {
+ "description": "Duration of donor's substance usage in years.",
+ "type": "integer",
+ "user_friendly": "Duration Of Substance Use",
+ "minimum": 0,
+ "example": "4; 8; 20",
+ "bionetworks": ["heart", "oral and craniofacial", "liver", "reproduction"]
+ },
+ "substance_duration_since_last_use": {
+ "description": "If donor is no longer using, specify the number of years since substance usage cessation, if available.",
+ "type": "integer",
+ "user_friendly": "Duration Since Last Substance Use",
+ "minimum": 0,
+ "example": "1; 4; 20",
+ "bionetworks": ["heart", "oral and craniofacial", "liver", "reproduction"]
}
}
}
diff --git a/json_schema/module/biomaterial/medical_history.json b/json_schema/module/biomaterial/medical_history.json
index cbd6fd55e..109d99bd6 100644
--- a/json_schema/module/biomaterial/medical_history.json
+++ b/json_schema/module/biomaterial/medical_history.json
@@ -163,12 +163,46 @@
"user_friendly": "Test results",
"example": "lipid panel shows normal level of LDL (124 mg/dL); HIV, HBV, HCV: Negative"
},
+ "diseases_history": {
+ "description": "Short description of known disease(s) that have previously affected the donor, but are not considered active now.",
+ "type": "array",
+ "items": {
+ "$ref": "module/ontology/disease_ontology.json"
+ },
+ "user_friendly": "Diseases History",
+ "bionetworks": ["heart", "oral and craniofacial"]
+ },
"treatment": {
"description": "Treatments the individual has undergone prior to biomaterial collection.",
"type": "string",
"user_friendly": "Treatments",
"example": "Patient treated with antibiotics for a urinary tract infection; Patient treated with chemotherapy (Epirubicin, cisplatin, capecitabine) to treat stomach cancer"
},
+ "device_treatment": {
+ "description": "Device/interventional therapy 1 year before and/or at time of sample collection.",
+ "type": "string",
+ "enum": [
+ "ECMO",
+ "IABP",
+ "Impella",
+ "LVAD",
+ "RVAD",
+ "PPM",
+ "ICD",
+ "CRT"
+ ],
+ "user_friendly": "Device Treatment",
+ "example": "Should be one of: ECMO, IABP, Impella, LVAD, RVAD, PPM, ICD, CRT",
+ "bionetworks": ["heart"]
+ },
+ "cardioplegia": {
+ "description": "Cardioplegia applied right before or during time of biomaterial collection.",
+ "type": "boolean",
+ "user_friendly": "Cardioplegia",
+ "guidelines": "Should be one of: yes, or no.",
+ "example": "yes; no",
+ "bionetworks": ["heart"]
+ },
"previous_surgeries": {
"description": "Previous surgeries the individual has undergone prior to biomaterial collection.",
"type": "string",
diff --git a/json_schema/module/biomaterial/medical_tests.json b/json_schema/module/biomaterial/medical_tests.json
index 5359953cd..af7aafe70 100644
--- a/json_schema/module/biomaterial/medical_tests.json
+++ b/json_schema/module/biomaterial/medical_tests.json
@@ -254,6 +254,382 @@
"maximum": 200,
"minimum": 0,
"bionetworks": ["lung"]
+ },
+ "ecg_heart_rate": {
+ "description": "Heart rate as measured by electrocardiogram in beats per minute.",
+ "type": "number",
+ "minimum": 0,
+ "user_friendly": "Ecg - Heart Rate",
+ "example": "72; 65; 80",
+ "bionetworks": ["heart"]
+ },
+ "ecg_heart_rhythm": {
+ "user_friendly": "Ecg - Heart Rhythm",
+ "description": "Heart rhythm as measured by electrocardiogram.",
+ "type": "string",
+ "example": "sinus rhythm; atrial fibrillation; atrial flutter; atrial tachycardia",
+ "bionetworks": ["heart"]
+ },
+ "ecg_pr_interval_duration": {
+ "description": "PR interval duration in ms as measured by electrocardiogram. It can be described as PQ interval duration in ECG description according to region.",
+ "type": "number",
+ "minimum": 0,
+ "user_friendly": "Ecg - Pr Interval Duration",
+ "example": "160; 140; 180",
+ "bionetworks": ["heart"]
+ },
+ "ecg_qrs_complex_duration": {
+ "description": "QRS complex duration in ms as measured by electrocardiogram.",
+ "type": "number",
+ "minimum": 0,
+ "user_friendly": "Ecg - QRS Complex Duration",
+ "example": "90; 100; 110",
+ "bionetworks": ["heart"]
+ },
+ "ecg_lbbb_rbbb_ivcd": {
+ "description": "Bundle branch block and/or delayed atrioventricular conduction as measured by electrocardiogram. LBBB - Left bundle branch block/ RBBB - right bundle branch block/ IVCD - intraventricular-conduction delay (QRSd >120ms not fulfilling LBBB or RBBB criteria).",
+ "type": "string",
+ "enum": [
+ "LBBB",
+ "RBBB",
+ "IVCD"
+ ],
+ "user_friendly": "Ecg - LBBB RBBB IVCD",
+ "example": "Should be one of: LBBB, RBBB, IVCD.",
+ "bionetworks": ["heart"]
+ },
+ "ecg_qt_interval_corrected": {
+ "description": "Corrected QT interval in ms as measured by electrocardiogram.",
+ "type": "number",
+ "minimum": 0,
+ "user_friendly": "Ecg - QT Interval Corrected",
+ "example": "420; 410; 430",
+ "bionetworks": ["heart"]
+ },
+ "ecg_time_offset": {
+ "description": "Time between the test and the collection of the sample, measured in days.",
+ "type": "number",
+ "minimum": 0,
+ "user_friendly": "Ecg - Time Offset",
+ "example": "4; 20; 58",
+ "bionetworks": ["heart"]
+ },
+ "echo_aortic_stenosis": {
+ "description": "Aortic stenosis as measured by echocardiogram.",
+ "type": "string",
+ "enum": [
+ "no",
+ "mild",
+ "mod",
+ "severe"
+ ],
+ "user_friendly": "Echo - Aortic Stenosis",
+ "example": "Should be one of: no, mild, mod, severe.",
+ "bionetworks": ["heart"]
+ },
+ "echo_aortic_regurgitation": {
+ "description": "Aortic regurgitation as measured by echocardiogram.",
+ "type": "string",
+ "enum": [
+ "no",
+ "mild",
+ "mod",
+ "severe"
+ ],
+ "user_friendly": "Echo - Aortic Regurgitation",
+ "example": "Should be one of: no, mild, mod, severe.",
+ "bionetworks": ["heart"]
+ },
+ "echo_mitral_regurgitation": {
+ "description": "Mitral regurgitation as measured by echocardiogram.",
+ "type": "string",
+ "enum": [
+ "no",
+ "mild",
+ "mod",
+ "severe"
+ ],
+ "user_friendly": "Echo - Mitral Regurgitation",
+ "example": "Should be one of: no, mild, mod, severe.",
+ "bionetworks": ["heart"]
+ },
+ "echo_mitral_stenosis": {
+ "description": "Mitral stenosis as measured by echocardiogram.",
+ "type": "string",
+ "enum": [
+ "no",
+ "mild",
+ "mod",
+ "severe"
+ ],
+ "user_friendly": "Echo - Mitral Stenosis",
+ "example": "Should be one of: no, mild, mod, severe.",
+ "bionetworks": ["heart"]
+ },
+ "echo_tricuspid_regurgitation": {
+ "description": "Tricuspid regurgitation as measured by echocardiogram.",
+ "type": "string",
+ "enum": [
+ "no",
+ "mild",
+ "mod",
+ "severe"
+ ],
+ "user_friendly": "Echo - Tricuspid Regurgitation",
+ "example": "Should be one of: no, mild, mod, severe.",
+ "bionetworks": ["heart"]
+ },
+ "echo_estimated_rvsp": {
+ "description": "Estimated right ventricular systolic pressure in mmHg as measured by echocardiogram.",
+ "type": "number",
+ "minimum": 0,
+ "user_friendly": "Echo - Estimated RVSP",
+ "example": "25; 30; 35",
+ "bionetworks": ["heart"]
+ },
+ "echo_lvedv": {
+ "description": "Left ventricular end-diastolic volume in ml as measured by echocardiogram.",
+ "type": "number",
+ "minimum": 0,
+ "user_friendly": "Echo - LVEDV",
+ "example": "120; 110; 130",
+ "bionetworks": ["heart"]
+ },
+ "echo_lvedv_indexed": {
+ "description": "Left ventricular end-diastolic volume indexed to body surface area in ml/m^2 (indexed to body surface area) as measured by echocardiogram.",
+ "type": "number",
+ "minimum": 0,
+ "user_friendly": "Echo - LVEDV Indexed",
+ "example": "65; 70; 60",
+ "bionetworks": ["heart"]
+ },
+ "echo_lvesv": {
+ "description": "Left ventricular end-systolic volume in ml as measured by echocardiogram.",
+ "type": "number",
+ "minimum": 0,
+ "user_friendly": "Echo - LVESV",
+ "example": "50; 45; 55",
+ "bionetworks": ["heart"]
+ },
+ "echo_lvesv_indexed": {
+ "description": "Left ventricular end-systolic volume indexed to body surface area in ml/m^2 (indexed to body surface area) as measured by echocardiogram.",
+ "type": "number",
+ "minimum": 0,
+ "user_friendly": "Echo - LVESV Indexed",
+ "example": "25; 30; 28",
+ "bionetworks": ["heart"]
+ },
+ "echo_lvef": {
+ "description": "Left ventricular ejection fraction as measured by echocardiogram.",
+ "type": "number",
+ "minimum": 0,
+ "user_friendly": "Echo - LVEF",
+ "example": "55; 60; 65",
+ "bionetworks": ["heart"]
+ },
+ "echo_lv_mass": {
+ "description": "Left ventricular mass in grams as measured by echocardiogram.",
+ "type": "number",
+ "minimum": 0,
+ "user_friendly": "Echo - LV Mass",
+ "example": "150; 160; 140",
+ "bionetworks": ["heart"]
+ },
+ "echo_lv_mass_indexed": {
+ "description": "Left ventricular mass indexed to body surface area in g/m^2 (indexed to body surface area) as measured by echocardiogram.",
+ "type": "number",
+ "minimum": 0,
+ "user_friendly": "Echo - LV Mass Indexed",
+ "example": "75; 80; 70",
+ "bionetworks": ["heart"]
+ },
+ "echo_rv_fac": {
+ "description": "Right Ventricular Fractional Area Change (RV FAC) in percentage as measured by echocardiogram.",
+ "type": "number",
+ "minimum": 0,
+ "user_friendly": "Echo - RV FAC",
+ "example": "40; 45; 50",
+ "bionetworks": ["heart"]
+ },
+ "echo_tapse": {
+ "description": "Tricuspid annular plane systolic excursion (TAPSE) in mm as measured by echocardiogram.",
+ "type": "number",
+ "minimum": 0,
+ "user_friendly": "Echo - TAPSE",
+ "example": "20; 22; 18",
+ "bionetworks": ["heart"]
+ },
+ "echo_lv_septum_thickness": {
+ "description": "Left ventricular septum thickness in mm as measured by echocardiogram.",
+ "type": "number",
+ "minimum": 0,
+ "user_friendly": "Echo - LV Septum Thickness",
+ "example": "9; 10; 11",
+ "bionetworks": ["heart"]
+ },
+ "echo_pw_thickness": {
+ "description": "Basal posterior LV wall thickness in mm as measured by echocardiogram.",
+ "type": "number",
+ "minimum": 0,
+ "user_friendly": "Echo - PW Thickness",
+ "example": "9; 10; 11",
+ "bionetworks": ["heart"]
+ },
+ "echo_la_dimension": {
+ "description": "Left atrial diameter in PLAX view in mm as measured by echocardiogram.",
+ "type": "number",
+ "minimum": 0,
+ "user_friendly": "Echo - LA Dimension",
+ "example": "38; 36; 40",
+ "bionetworks": ["heart"]
+ },
+ "echo_lav_indexed": {
+ "description": "Left atrial volume indexed to body surface area in ml/m^2 (left atrial volume indexed to body surface area) as measured by echocardiogram.",
+ "type": "number",
+ "minimum": 0,
+ "user_friendly": "Echo - LAV Indexed",
+ "example": "28; 30; 32",
+ "bionetworks": ["heart"]
+ },
+ "echo_time_offset": {
+ "description": "Time between the test and the collection of the sample, in days.",
+ "type": "number",
+ "minimum": 0,
+ "user_friendly": "Echo - Time Offset",
+ "example": "4; 20; 58",
+ "bionetworks": ["heart"]
+ },
+ "mri_lvedv": {
+ "description": "Left ventricular end-diastolic volume in ml as measured by MRI.",
+ "type": "number",
+ "minimum": 0,
+ "user_friendly": "Mri - LVEDV",
+ "example": "140; 150; 130",
+ "bionetworks": ["heart"]
+ },
+ "mri_lvedv_indexed": {
+ "description": "Left ventricular end-diastolic volume indexed to body surface area in ml/m^2 (indexed to body surface area) as measured by MRI.",
+ "type": "number",
+ "minimum": 0,
+ "user_friendly": "Mri - LVEDV Indexed",
+ "example": "75; 70; 80",
+ "bionetworks": ["heart"]
+ },
+ "mri_lvesv": {
+ "description": "Left ventricular end-systolic volume in ml as measured by MRI.",
+ "type": "number",
+ "minimum": 0,
+ "user_friendly": "Mri - LVESV",
+ "example": "60; 55; 65",
+ "bionetworks": ["heart"]
+ },
+ "mri_lvesv_indexed": {
+ "description": "Left ventricular end-systolic volume indexed to body surface area in ml/m^2 (indexed to body surface area) as measured by MRI.",
+ "type": "number",
+ "minimum": 0,
+ "user_friendly": "Mri - LVESV Indexed",
+ "example": "30; 28; 32",
+ "bionetworks": ["heart"]
+ },
+ "mri_lvef": {
+ "description": "Left ventricular ejection fraction measured by MRI.",
+ "type": "number",
+ "minimum": 0,
+ "user_friendly": "Mri - LVEF",
+ "example": "55; 60; 58",
+ "bionetworks": ["heart"]
+ },
+ "mri_lv_mass": {
+ "description": "Left ventricular mass in grams as measured by MRI.",
+ "type": "number",
+ "minimum": 0,
+ "user_friendly": "Mri - LV Mass",
+ "example": "130; 120; 140",
+ "bionetworks": ["heart"]
+ },
+ "mri_lv_mass_indexed": {
+ "description": "Left ventricular mass indexed to body surface area in g/m^2 (indexed to body surface area) as measured by MRI.",
+ "type": "number",
+ "minimum": 0,
+ "user_friendly": "Mri - LV Mass Indexed",
+ "example": "65; 60; 70",
+ "bionetworks": ["heart"]
+ },
+ "mri_rv_ejection_fraction": {
+ "description": "Right ventricular ejection fraction in percentage as measured by MRI.",
+ "type": "number",
+ "minimum": 0,
+ "user_friendly": "Mri - RV Ejection Fraction",
+ "example": "50; 55; 60",
+ "bionetworks": ["heart"]
+ },
+ "mri_mid_wall_lge": {
+ "description": "Late gadolinium enhancement (mid wall) as measured by MRI.",
+ "type": "boolean",
+ "user_friendly": "Mri - Mid Wall LGE",
+ "example": "Should be one of: yes; no.",
+ "bionetworks": ["heart"]
+ },
+ "mri_epicardial_lge": {
+ "description": "Late gadolinium enhancement (epicardial) as measured by MRI.",
+ "type": "boolean",
+ "user_friendly": "Mri - Epicardial LGE",
+ "example": "Should be one of: yes; no.",
+ "bionetworks": ["heart"]
+ },
+ "mri_infarct_pattern_lge": {
+ "description": "Late gadolinium enhancement (infarct pattern) as measured by MRI.",
+ "type": "boolean",
+ "user_friendly": "Mri - Infarct Pattern LGE",
+ "example": "Should be one of: yes; no.",
+ "bionetworks": ["heart"]
+ },
+ "mri_myocardial_oedema": {
+ "description": "Myocardial oedema as measured by MRI.",
+ "type": "boolean",
+ "user_friendly": "Mri - Myocardial Oedema",
+ "example": "Should be one of: yes; no.",
+ "bionetworks": ["heart"]
+ },
+ "mri_time_offset": {
+ "description": "Time between the test and the collection of the sample, in days.",
+ "type": "number",
+ "minimum": 0,
+ "user_friendly": "Mri - Time Offset",
+ "example": "4; 20; 58",
+ "bionetworks": ["heart"]
+ },
+ "mps_lvef": {
+ "user_friendly": "Mps - LVEF",
+ "description": "Left ventricular ejection fraction in percentage as measured by myocardial perfusion scintigraphy.",
+ "type": "number",
+ "minimum": 0,
+ "example": "58; 60; 62",
+ "bionetworks": ["heart"]
+ },
+ "mps_inducible_ischaemic": {
+ "user_friendly": "Mps - Inducible Ischaemic",
+ "description": "Left ventricular inducible ischemic percentage as measured by myocardial perfusion scintigraphy.",
+ "type": "number",
+ "minimum": 0,
+ "example": "0; 5; 12",
+ "bionetworks": ["heart"]
+ },
+ "mps_scar": {
+ "user_friendly": "Mps - Scar",
+ "description": "Left ventricular scar percentage as measured by myocardial perfusion scintigraphy.",
+ "type": "number",
+ "minimum": 0,
+ "example": "0; 3; 10",
+ "bionetworks": ["heart"]
+ },
+ "mps_time_offset": {
+ "description": "Time between the test and the collection of the sample, in days.",
+ "type": "number",
+ "minimum": 0,
+ "user_friendly": "Mps - Time Offset",
+ "example": "4; 20; 58",
+ "bionetworks": ["heart"]
}
}
}
diff --git a/json_schema/type/biomaterial/specimen_from_organism.json b/json_schema/type/biomaterial/specimen_from_organism.json
index 720324aca..d356685e7 100644
--- a/json_schema/type/biomaterial/specimen_from_organism.json
+++ b/json_schema/type/biomaterial/specimen_from_organism.json
@@ -87,11 +87,22 @@
"bionetworks": ["gut"]
},
"transplant_organ": {
- "description": "Was the specimen collected after extraction for organ transplantation?",
- "type": "boolean",
+ "description": "Was the organ transplanted or explanted before biomaterial collection?",
+ "type": "string",
+ "enum": [
+ "explanted organ", "transplanted organ","no transplant"
+ ],
+ "example": "explanted organ; transplanted organ; no transplant.",
+ "guidelines": "Should be one of: explanted organ; transplanted organ; no transplant.",
"user_friendly": "Transplant organ",
- "guidelines": "Should be one of: yes, or no.",
- "example": "yes; no"
+ "bionetworks": ["heart"]
+ },
+ "transplant_rejection_reason": {
+ "description": "If the organ was evaluated for transplantation but rejected give the reason for rejection.",
+ "type": "string",
+ "user_friendly": "Transplant Rejection Reason",
+ "example": "Rejected because underlying malignant disease; not evaluated for transplantation",
+ "bionetworks": ["heart"]
},
"diseases": {
"description": "Short description of known disease(s) of the specimen.",
@@ -161,7 +172,7 @@
},
"time_to_laboratory": {
"description": "Transit time in hours between tissue collection and tissue processing, meaning either storage in the laboratory or processing for sequencing.",
- "pattern": "(0|[1-9][0-9]*)(\\.(0|[0-9]*[1-9]))?(-(0|[1-9][0-9]*)(\\.(0|[0-9]*[1-9]))?)?$",
+ "pattern": "^(0|[1-9][0-9]*)(\\.(0|[0-9]*[1-9]))?(-(0|[1-9][0-9]*)(\\.(0|[0-9]*[1-9]))?)?$",
"type": "string",
"example": "2; 4-5; 8",
"user_friendly": "Time to laboratory",
diff --git a/json_schema/type/protocol/biomaterial_collection/collection_protocol.json b/json_schema/type/protocol/biomaterial_collection/collection_protocol.json
index 3efe6c63c..d9b6817d9 100644
--- a/json_schema/type/protocol/biomaterial_collection/collection_protocol.json
+++ b/json_schema/type/protocol/biomaterial_collection/collection_protocol.json
@@ -47,20 +47,6 @@
"$ref": "module/ontology/process_type_ontology.json",
"user_friendly": "Collection method"
},
- "biopsy_procedure": {
- "description": "Type of biopsy procedure used in the sample collection.",
- "type": "string",
- "enum": [
- "Bergstrom needle",
- "Punch biopsy",
- "Mercedes needle, dry aspiration",
- "Mercedes needle, tumescent lidocaine “wet” aspiration"
- ],
- "user_friendly": "Type of biopsy procedure",
- "example": "Bergstrom needle; Punch biopsy; Mercedes needle, dry aspiration; Mercedes needle, tumescent lidocaine “wet” aspiration",
- "guidelines": "Should be one of: Bergstrom needle; Punch biopsy; Mercedes needle, dry aspiration; Mercedes needle, tumescent lidocaine “wet” aspiration",
- "bionetworks": ["adipose"]
- },
"procedure": {
"description": "Procedure used to collect the specimen from the organism.",
"type": "string",
@@ -68,6 +54,20 @@
"example": "colonoscopy; venipuncture; laparoscopic surgery",
"bionetworks": ["gut"]
},
+ "biopsy_procedure": {
+ "description": "Type of biopsy procedure used in the sample collection.",
+ "type": "string",
+ "enum": [
+ "Bergstrom needle",
+ "Punch biopsy",
+ "Mercedes needle, dry aspiration",
+ "Mercedes needle, tumescent lidocaine “wet” aspiration"
+ ],
+ "user_friendly": "Type of biopsy procedure",
+ "example": "Bergstrom needle; Punch biopsy; Mercedes needle, dry aspiration; Mercedes needle, tumescent lidocaine “wet” aspiration",
+ "guidelines": "Should be one of: Bergstrom needle; Punch biopsy; Mercedes needle, dry aspiration; Mercedes needle, tumescent lidocaine “wet” aspiration.",
+ "bionetworks": ["adipose"]
+ },
"reagents": {
"description": "A list of purchased reagents used in this protocol.",
"type": "array",
diff --git a/json_schema/update_log.csv b/json_schema/update_log.csv
index 3231ff199..c1991c0f0 100644
--- a/json_schema/update_log.csv
+++ b/json_schema/update_log.csv
@@ -1 +1,8 @@
Schema,Change type,Change message,Version,Date
+module/biomaterial/human_specific,patch,"Fixed the regex for body_mass_index, waist_circumference, waist_hip_ratio",,
+type/biomaterial/specimen_from_organism,patch,"Fixed the regex for time_to_laboratory",,
+module/biomaterial/medical_history,minor,"Added diseases_history, device_treatment, cardioplegia",,
+module/biomaterial/medical_tests,minor,"Added mps_lvef, mps_inducible_ischaemic, mps_scar, mps_time_offset, ecg_heart_rate, ecg_heart_rhythm, ecg_pr_interval_duration, ecg_qrs_complex_duration, ecg_lbbb_rbbb_ivcd, ecg_qt_interval_corrected, ecg_time_offset, echo_aortic_stenosis, echo_aortic_regurgitation, echo_mitral_regurgitation, echo_mitral_stenosis, echo_tricuspid_regurgitation, echo_estimated_rvsp, echo_lvedv, echo_lvedv_indexed, echo_lvesv, echo_lvesv_indexed, echo_lvef, echo_lv_mass, echo_lv_mass_indexed, echo_rv_fac, echo_tapse, echo_lv_septum_thickness, echo_pw_thickness, echo_la_dimension, echo_lav_indexed, echo_time_offset, mri_lvedv, mri_lvedv_indexed, mri_lvesv, mri_lvesv_indexed, mri_lvef, mri_lv_mass, mri_lv_mass_indexed, mri_rv_ejection_fraction, mri_mid_wall_lge, mri_epicardial_lge, mri_infarct_pattern_lge, mri_myocardial_oedema, mri_time_offset",,
+module/biomaterial/blood_test,minor,"Added sodium, sodium_unit, potassium, potassium_unit, urea, urea_unit, creatinine, creatinine_unit, total_bilirubin, total_bilirubin_unit",,
+module/biomaterial/lifestyle,minor,"Added substance_type, substance_frequency, substance_use_duration, substance_duration_since_last_use",,
+type/biomaterial/specimen_from_organism,major,"Changed the type of transplant_organ from boolean to enum and added transplant_rejection_reason",,
diff --git a/tests/README.md b/tests/README.md
index 427597407..0c03fb77e 100644
--- a/tests/README.md
+++ b/tests/README.md
@@ -26,4 +26,4 @@ npm test
### Running in vs code
-The tests are visible in the "Testing" sidebar after installing [Mocha Test Explorer](https://marketplace.cursorapi.com/items/?itemName=hbenl.vscode-mocha-test-adapter)
+The tests are visible in the "Testing" sidebar after installing [Mocha Test Explorer](https://marketplace.visualstudio.com/items?itemName=hbenl.vscode-mocha-test-adapter)
diff --git a/tests/schema_test_files/project/test_fail_project_0.json b/tests/schema_test_files/project/test_fail_project_0.json
index 1e532b843..09612b2cc 100644
--- a/tests/schema_test_files/project/test_fail_project_0.json
+++ b/tests/schema_test_files/project/test_fail_project_0.json
@@ -1,6 +1,6 @@
{
- "describedBy": "https://schema.dev.data.humancellatlas.org/type/project/5.1.0/project",
- "schema_version": "5.1.0",
+ "describedBy": "https://schema.dev.data.humancellatlas.org/type/project/20.0.0/project",
+ "schema_version": "20.0.0",
"schema_type": "project",
"project_core": {
"project_title": "Project 1",
@@ -19,5 +19,6 @@
"grant_id": "BB/P0000001/1",
"organization": "Biotechnology and Biological Sciences Research Council (BBSRC)"
}
- ]
+ ],
+ "data_use_restriction" : "NRES"
}
\ No newline at end of file
diff --git a/tests/schema_test_files/project/test_pass_project_0.json b/tests/schema_test_files/project/test_pass_project_0.json
index 042ac794b..ad7237c3b 100644
--- a/tests/schema_test_files/project/test_pass_project_0.json
+++ b/tests/schema_test_files/project/test_pass_project_0.json
@@ -1,6 +1,6 @@
{
- "describedBy": "https://schema.dev.data.humancellatlas.org/type/project/14.1.0/project",
- "schema_version": "14.1.0",
+ "describedBy": "https://schema.dev.data.humancellatlas.org/type/project/20.0.0/project",
+ "schema_version": "20.0.0",
"schema_type": "project",
"project_core": {
"project_short_name": "P1",
@@ -20,5 +20,6 @@
"grant_id": "BB/P0000001/1",
"organization": "Biotechnology and Biological Sciences Research Council (BBSRC)"
}
- ]
+ ],
+ "data_use_restriction" : "NRES"
}
\ No newline at end of file