From 994c053a27249a92a980788aa4dc4d96db007554 Mon Sep 17 00:00:00 2001 From: idazucchi Date: Fri, 6 Feb 2026 12:37:18 +0000 Subject: [PATCH 01/64] Added diseases_history --- docs/jsonBrowser/module.md | 1 + json_schema/module/biomaterial/medical_history.json | 9 +++++++++ json_schema/update_log.csv | 1 + 3 files changed, 11 insertions(+) diff --git a/docs/jsonBrowser/module.md b/docs/jsonBrowser/module.md index edc1ea9bd..d8235eeec 100644 --- a/docs/jsonBrowser/module.md +++ b/docs/jsonBrowser/module.md @@ -588,6 +588,7 @@ nutritional_state | Nutritional state of individual at time of biomaterial colle diet_meat_consumption | Dietary patterns of donor - meat (chicken, seafood, fish, pork, lamb, beef, etc.) consumption versus meat-free diet - at time of sample collection. Fill yes if donor consumes meat or no if donor does not consumes meat. | boolean | no | | Meat consumption | | Should be one of: yes; no. reproductive_history | Reproductive history of the donor at the time of collection. | object | no | [See module reproductive_history](module.md#reproductive-history) | Reproductive history | | 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 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 diff --git a/json_schema/module/biomaterial/medical_history.json b/json_schema/module/biomaterial/medical_history.json index 552b0fdf0..33a0c6fc7 100644 --- a/json_schema/module/biomaterial/medical_history.json +++ b/json_schema/module/biomaterial/medical_history.json @@ -150,6 +150,15 @@ "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", diff --git a/json_schema/update_log.csv b/json_schema/update_log.csv index 3231ff199..3f13f97b3 100644 --- a/json_schema/update_log.csv +++ b/json_schema/update_log.csv @@ -1 +1,2 @@ Schema,Change type,Change message,Version,Date +module/biomaterial/medical_history,minor,"Added diseases_history" \ No newline at end of file From f55ebb4ea54bb68685a60ddc50ec8f6f82228374 Mon Sep 17 00:00:00 2001 From: idazucchi Date: Fri, 6 Feb 2026 12:48:16 +0000 Subject: [PATCH 02/64] Added device_treatment --- docs/jsonBrowser/module.md | 1 + .../module/biomaterial/medical_history.json | 17 +++++++++++++++++ json_schema/update_log.csv | 2 +- 3 files changed, 19 insertions(+), 1 deletion(-) diff --git a/docs/jsonBrowser/module.md b/docs/jsonBrowser/module.md index d8235eeec..98903b5a4 100644 --- a/docs/jsonBrowser/module.md +++ b/docs/jsonBrowser/module.md @@ -590,6 +590,7 @@ reproductive_history | Reproductive history of the donor at the time of collecti 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 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 diff --git a/json_schema/module/biomaterial/medical_history.json b/json_schema/module/biomaterial/medical_history.json index 33a0c6fc7..b6d33c8fb 100644 --- a/json_schema/module/biomaterial/medical_history.json +++ b/json_schema/module/biomaterial/medical_history.json @@ -165,6 +165,23 @@ "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"] + }, "previous_surgeries": { "description": "Previous surgeries the individual has undergone prior to biomaterial collection.", "type": "string", diff --git a/json_schema/update_log.csv b/json_schema/update_log.csv index 3f13f97b3..bc273cecc 100644 --- a/json_schema/update_log.csv +++ b/json_schema/update_log.csv @@ -1,2 +1,2 @@ Schema,Change type,Change message,Version,Date -module/biomaterial/medical_history,minor,"Added diseases_history" \ No newline at end of file +module/biomaterial/medical_history,minor,"Added diseases_history, device_treatment" \ No newline at end of file From 1340e85870a8237b1f851002b211e453d1d6e041 Mon Sep 17 00:00:00 2001 From: idazucchi Date: Fri, 6 Feb 2026 16:57:50 +0100 Subject: [PATCH 03/64] Added device_treatment --- docs/jsonBrowser/module.md | 151 ------------------ docs/jsonBrowser/required_fields.md | 33 ---- .../module/biomaterial/medical_history.json | 4 + 3 files changed, 4 insertions(+), 184 deletions(-) diff --git a/docs/jsonBrowser/module.md b/docs/jsonBrowser/module.md index 98903b5a4..7e7b545a6 100644 --- a/docs/jsonBrowser/module.md +++ b/docs/jsonBrowser/module.md @@ -566,154 +566,3 @@ parent | The individual's parent. | string | no | | Parent | | child | The individual's child. | string | no | | Child | | sibling | The individual's sibling. | string | no | | Sibling | | -## Medical history -_Information about the medical history of a donor._ - -Location: module/biomaterial/medical_history.json - -Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example ---- | --- | --- | --- | --- | --- | --- | --- -alcohol_status | Whether the individual is actively consuming, has formerly consumed or has never consumed alcohol beverages | string | no | | Alcohol status | active, former, never | Should be one of: active, former, never. -alcohol_type | Types of alcoholic beverages the donor consumed. | array | no | | Alcohol type | | beer; liquor; wine -alcohol_units | Alcohol consumption of donor in alcohol units per week (strength (ABV) x volume (ml) ÷ 1,000). | number | no | | Alcohol units | | 2.5; 15.2; 23 -alcohol_usage_duration | Number of years in which the donor consumed alcohol. | integer | no | | Alcohol usage duration | | 5 -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 -household_smoking_exposure | If the donor is exposed to passive smoking in their household or not (excluding if they are the ones smoking). | boolean | no | | Household smoking exposure | | Should be one of: yes; no. -vaping_status | Whether the individual is actively, was formerly or never vaped. | string | no | | Vaping status | active, former, never | Should be one of: active, former, never. -marijuana_inhaled_status | Whether the individual is actively, was formerly or never inhaled/smoked marijuana. | string | no | | Inhaled marijuana status | active, former, never | Should be one of: active, former, never. -nutritional_state | Nutritional state of individual at time of biomaterial collection. | string | no | | Nutritional state | normal, fasting, feeding tube removed | Should be one of: normal, fasting, or feeding tube removed. -diet_meat_consumption | Dietary patterns of donor - meat (chicken, seafood, fish, pork, lamb, beef, etc.) consumption versus meat-free diet - at time of sample collection. Fill yes if donor consumes meat or no if donor does not consumes meat. | boolean | no | | Meat consumption | | Should be one of: yes; no. -reproductive_history | Reproductive history of the donor at the time of collection. | object | no | [See module reproductive_history](module.md#reproductive-history) | Reproductive history | | -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 -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 - -## Residence -_Donor's residence location information._ - -Location: module/biomaterial/residence.json - -Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example ---- | --- | --- | --- | --- | --- | --- | --- -country_territory | Country or territory of donor's residence. | | no | | Country | Afghanistan, Albania, Algeria, American Samoa, Andorra, Angola, Anguilla, Antarctica, Antigua and Barbuda, Argentina, Armenia, Aruba, Ashmore and Cartier Islands, Australia, Austria, Azerbaijan, Bahamas, Bahrain, Baker Island, Bangladesh, Barbados, Bassas da India, Belarus, Belgium, Belize, Benin, Bermuda, Bhutan, Bolivia, Borneo, Bosnia and Herzegovina, Botswana, Bouvet Island, Brazil, British Virgin Islands, Brunei, Bulgaria, Burkina Faso, Burundi, Cambodia, Cameroon, Canada, Cape Verde, Cayman Islands, Central African Republic, Chad, Chile, China, Christmas Island, Clipperton Island, Cocos Islands, Colombia, Comoros, Cook Islands, Coral Sea Islands, Costa Rica, Cote d'Ivoire, Croatia, Cuba, Curacao, Cyprus, Czechia, Democratic Republic of the Congo, Denmark, Djibouti, Dominica, Dominican Republic, Ecuador, Egypt, El Salvador, Equatorial Guinea, Eritrea, Estonia, Eswatini, Ethiopia, Europa Island, Falkland Islands (Islas Malvinas), Faroe Islands, Fiji, Finland, France, French Guiana, French Polynesia, French Southern and Antarctic Lands, Gabon, Gambia, Gaza Strip, Georgia, Germany, Ghana, Gibraltar, Glorioso Islands, Greece, Greenland, Grenada, Guadeloupe, Guam, Guatemala, Guernsey, Guinea, Guinea-Bissau, Guyana, Haiti, Heard Island and McDonald Islands, Honduras, Hong Kong, Howland Island, Hungary, Iceland, India, Indonesia, Iran, Iraq, Ireland, Isle of Man, Israel, Italy, Jamaica, Jan Mayen, Japan, Jarvis Island, Jersey, Johnston Atoll, Jordan, Juan de Nova Island, Kazakhstan, Kenya, Kerguelen Archipelago, Kingman Reef, Kiribati, Kosovo, Kuwait, Kyrgyzstan, Laos, Latvia, Lebanon, Lesotho, Liberia, Libya, Liechtenstein, Line Islands, Lithuania, Luxembourg, Macau, Madagascar, Malawi, Malaysia, Maldives, Mali, Malta, Marshall Islands, Martinique, Mauritania, Mauritius, Mayotte, Mexico, Micronesia, Federated States of, Midway Islands, Moldova, Monaco, Mongolia, Montenegro, Montserrat, Morocco, Mozambique, Myanmar, Namibia, Nauru, Navassa Island, Nepal, Netherlands, New Caledonia, New Zealand, Nicaragua, Niger, Nigeria, Niue, Norfolk Island, North Korea, North Macedonia, Northern Mariana Islands, Norway, Oman, Pakistan, Palau, Palmyra Atoll, Panama, Papua New Guinea, Paracel Islands, Paraguay, Peru, Philippines, Pitcairn Islands, Poland, Portugal, Puerto Rico, Qatar, Republic of the Congo, Reunion, Romania, Russia, Rwanda, Saint Barthelemy, Saint Helena, Saint Kitts and Nevis, Saint Lucia, Saint Martin, Saint Pierre and Miquelon, Saint Vincent and the Grenadines, Samoa, San Marino, Sao Tome and Principe, Saudi Arabia, Senegal, Serbia, Seychelles, Sierra Leone, Singapore, Sint Maarten, Slovakia, Slovenia, Solomon Islands, Somalia, South Africa, South Georgia and the South Sandwich Islands, South Korea, South Sudan, Spain, Spratly Islands, Sri Lanka, State of Palestine, Sudan, Suriname, Svalbard, Sweden, Switzerland, Syria, Taiwan, Tajikistan, Tanzania, Thailand, Timor-Leste, Togo, Tokelau, Tonga, Trinidad and Tobago, Tromelin Island, Tunisia, Turkey, Turkmenistan, Turks and Caicos Islands, Tuvalu, Uganda, Ukraine, United Arab Emirates, United Kingdom, Uruguay, USA, Uzbekistan, Vanuatu, Venezuela, Viet Nam, Virgin Islands, Wake Island, Wallis and Futuna, West Bank, Western Sahara, Yemen, Zambia, Zimbabwe | Singapore; United Kingdom; Brazil; Australia; Nigeria -region | Region of donor's residence. | string | no | | Region | | Massachusetts; Catalonia; Ondo; Ontario -locality | Nearest city, town, or village to location of donor's residence. | string | no | | Locality | | Singapore; Cambridge; Boston; Kingston -duration | Duration of residence, in years, rounded up to the nearest whole number. | string | no | | Duration of residence | | 20; 37; 45-65 -area_type | Urban, suburban, or rural descriptor of residence. | string | no | | Area type of residence | urban, suburban, rural | urban; suburban; rural - -## Cell morphology -_Information relating to pathological and morphological features of cells._ - -Location: module/biomaterial/cell_morphology.json - -Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example ---- | --- | --- | --- | --- | --- | --- | --- -cell_morphology | General description of the morphology of cells. | string | no | | Cell morphology | | adherent cells; form single layer colonies -cell_size | Size of cells in Cell size unit. | string | no | | Cell size | | 15; 20-30 -cell_size_unit | The unit in which the Cell size is expressed. | object | no | [See module length_unit_ontology](module.md#length-unit-ontology) | Cell size unit | | -percent_cell_viability | Percent of cells determined to be viable. | number | no | | Percent cell viability | | 98.7 -cell_viability_method | The method by which cell viability was determined. | string | no | | Cell viability method | | Fluorescein diacetate hydrolysis; ATP test -cell_viability_result | Result of the cell viability test. | string | no | | Cell viability result | pass, fail | Should be one of: pass, fail -percent_necrosis | Percent of cells identified to be necrotic. | number | no | | Percent necrotic cells | | 10 - -## State of specimen -_State of specimen at time of collection._ - -Location: module/biomaterial/state_of_specimen.json - -Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example ---- | --- | --- | --- | --- | --- | --- | --- -autolysis_score | State of tissue breakdown due to self-digestion. | string | no | | Autolysis score | none, mild, moderate | Should be one of: none, mild, or moderate. -gross_description | Color, size, and other aspects of specimen as visible to naked eye. | string | no | | Gross description | | focal wedge shaped region of tan-orange discoloration; cystic -gross_images | List of filenames of photographs of specimen without magnification. | array | no | | Gross image | | my_gross_image_file.jpg -ischemic_temperature | Whether specimen experienced warm or cold ischemia. | string | no | | Ischemic temperature | warm, cold | Should be one of: warm, or cold. -ischemic_time | Duration of time, in seconds, between when the specimen stopped receiving oxygen and when it was preserved or processed. | integer | no | | Ischemic time | | 7200 -microscopic_description | How the specimen looks under the microscope and how it compares with normal cells. | string | no | | Microscopic description | | Mixture of different cell sizes apparent; Dead cells are quite faint on microscope -microscopic_images | List of filenames of photographs of specimen under microscope. | array | no | | Microscopic image | | my_microscopic_image_file.jpg -postmortem_interval | Duration of time between when death was declared and when the specimen was preserved or processed. | integer | no | | Post-mortem interval | | 2400 - -## Timecourse -_Information relating to a timecourse._ - -Location: module/biomaterial/timecourse.json - -Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example ---- | --- | --- | --- | --- | --- | --- | --- -value | The numerical value in Timecourse unit associated with a time interval used in the experiment. | string | yes | | Timecourse value | | 2; 5.5-10.5 -unit | The unit in which the Timecourse value is expressed. | object | yes | [See module time_unit_ontology](module.md#time-unit-ontology) | Timecourse unit | | -relevance | Relevance of the Timecourse value/unit to the experiment. | string | no | | Timecourse relevance | | Collection after tumor cells injected into the mammary gland; Time tissue underwent liberase digestion - -## Mouse-specific -_Information specific to an organism that is a mouse (Mus musculus)._ - -Location: module/biomaterial/mouse_specific.json - -Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example ---- | --- | --- | --- | --- | --- | --- | --- -strain | The name of the mouse strain. | array | no | [See module strain_ontology](module.md#strain-ontology) | Mouse strain | | - -## Purchased reagents -_Information describing purchased kits or reagents used in a protocol._ - -Location: module/process/purchased_reagents.json - -Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example ---- | --- | --- | --- | --- | --- | --- | --- -retail_name | The retail name of the kit/reagent. | string | no | | Retail name | | SureCell WTA 3' Library Prep Kit; CytoTune iPS 2.0 Sendai Reprogramming Kit -catalog_number | The catalog number of the kit/reagent. | string | no | | Catalog number | | 20014279 -manufacturer | The manufacturer of the kit/reagent. | string | no | | Manufacturer | | Illumina; ThermoFisher Scientific -lot_number | The batch or lot number of the kit/reagent. | string | no | | Batch/lot number | | 10001A -expiry_date | The date of expiration for the kit/reagent. | string | no | | Expiry date | | 2018-01-31; 2018-01 -kit_titer | Appropriate titer and volume recommendations found in kit/reagent Certificate of Analysis. | string | no | | Titer | | 3.0x10^7 - -## INSDC experiment -_Information relating to an INSDC experiment._ - -Location: module/process/sequencing/insdc_experiment.json - -Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example ---- | --- | --- | --- | --- | --- | --- | --- -insdc_experiment_accession | An International Nucleotide Sequence Database Collaboration (INSDC) experiment accession. | string | yes | | INSDC experiment accession | | SRX0000000 - -## Barcode -_Information about barcodes used in a protocol._ - -Location: module/process/sequencing/barcode.json - -Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example ---- | --- | --- | --- | --- | --- | --- | --- -barcode_read | The read in which the barcode is found. | string | yes | | Barcode-containing read | Read 1, Read 2, Read 3, Read 4, i7 Index, i5 Index | Should be one of: Read 1, Read 2, i7 Index, or i5 Index. -barcode_offset | The 0-based offset of start of barcode in read. | integer | yes | | Barcode offset | | 0 -barcode_length | Length of barcode in nucleotides. | integer | yes | | Barcode length | | 28 -white_list_file | Name of file containing legitimate barcode sequences. | string | no | | White list barcode file | | barcode_whitelist_file.txt - -## 10x-specific -_Information specific to 10x experiments._ - -Location: module/process/sequencing/10x.json - -Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example ---- | --- | --- | --- | --- | --- | --- | --- -fastq_method | Method used for the generation of fastq files from bcl files. | string | no | | Fastq creation method | | Cellranger mkfastq; bcl2fastq2 -fastq_method_version | Version of the program used for fastq generation. | string | no | | Fastq creation method version | | Cellranger 2.1.1; v2.20 -pooled_channels | The number of channels pooled within a sequencing lane. | number | no | | Pooled channels | | 4 -drop_uniformity | Whether drop uniformity was achieved as a result of visual inspection of emulsion after a 10x run. | boolean | no | | Drop uniformity | | Should be one of: yes, or no. - -## Plate-based sequencing -_Information specific to plate-based sequencing experiments._ - -Location: module/process/sequencing/plate_based_sequencing.json - -Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example ---- | --- | --- | --- | --- | --- | --- | --- -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 aefd876ee..3cae95aa7 100644 --- a/docs/jsonBrowser/required_fields.md +++ b/docs/jsonBrowser/required_fields.md @@ -376,36 +376,3 @@ Property name | Description | Type | Object reference? | User friendly name | Al cause_of_death | Conditions resulting in death. | string | | Cause of death | | Hypoxic brain damage; Sudden cardiac arrest ### Familial relationship _There are no required properties in schema Familial relationship_ -### Medical history -_There are no required properties in schema Medical history_ -### Residence -_There are no required properties in schema Residence_ -### Cell morphology -_There are no required properties in schema Cell morphology_ -### State of specimen -_There are no required properties in schema State of specimen_ -### Timecourse -Property name | Description | Type | Object reference? | User friendly name | Allowed values | Example ---- | --- | --- | --- | --- | --- | --- -value | The numerical value in Timecourse unit associated with a time interval used in the experiment. | string | | Timecourse value | | 2; 5.5-10.5 -unit | The unit in which the Timecourse value is expressed. | object | [See module time_unit_ontology](module.md#time-unit-ontology) | Timecourse unit | | -### Mouse-specific -_There are no required properties in schema Mouse-specific_ -### Purchased reagents -_There are no required properties in schema Purchased reagents_ -### INSDC experiment -Property name | Description | Type | Object reference? | User friendly name | Allowed values | Example ---- | --- | --- | --- | --- | --- | --- -insdc_experiment_accession | An International Nucleotide Sequence Database Collaboration (INSDC) experiment accession. | string | | INSDC experiment accession | | SRX0000000 -### Barcode -Property name | Description | Type | Object reference? | User friendly name | Allowed values | Example ---- | --- | --- | --- | --- | --- | --- -barcode_read | The read in which the barcode is found. | string | | Barcode-containing read | Read 1, Read 2, Read 3, Read 4, i7 Index, i5 Index | Should be one of: Read 1, Read 2, i7 Index, or i5 Index. -barcode_offset | The 0-based offset of start of barcode in read. | integer | | Barcode offset | | 0 -barcode_length | Length of barcode in nucleotides. | integer | | Barcode length | | 28 -### 10x-specific -_There are no required properties in schema 10x-specific_ -### Plate-based sequencing -Property name | Description | Type | Object reference? | User friendly name | Allowed values | Example ---- | --- | --- | --- | --- | --- | --- -plate_label | A label or name for the plate on which the well is located. | string | | Plate label | | 2217 diff --git a/json_schema/module/biomaterial/medical_history.json b/json_schema/module/biomaterial/medical_history.json index b6d33c8fb..5adf2d11c 100644 --- a/json_schema/module/biomaterial/medical_history.json +++ b/json_schema/module/biomaterial/medical_history.json @@ -181,6 +181,10 @@ "user_friendly": "Device Treatment", "example": "Should be one of: ECMO, IABP, Impella, LVAD, RVAD, PPM, ICD, CRT", "bionetworks": ["heart"] + }, + "user_friendly": "Device Treatment", + "example": "Should be one of: ECMO, IABP, Impella, LVAD, RVAD, PPM, ICD, CRT", + "bionetworks": ["heart"] }, "previous_surgeries": { "description": "Previous surgeries the individual has undergone prior to biomaterial collection.", From 26bdd4fe58f1ae214954aa583d245aa305d52326 Mon Sep 17 00:00:00 2001 From: idazucchi Date: Wed, 11 Feb 2026 10:34:36 +0100 Subject: [PATCH 04/64] Revert "Added device_treatment" This reverts commit 1340e85870a8237b1f851002b211e453d1d6e041. --- docs/jsonBrowser/module.md | 151 ++++++++++++++++++ docs/jsonBrowser/required_fields.md | 33 ++++ .../module/biomaterial/medical_history.json | 4 - 3 files changed, 184 insertions(+), 4 deletions(-) diff --git a/docs/jsonBrowser/module.md b/docs/jsonBrowser/module.md index 7e7b545a6..98903b5a4 100644 --- a/docs/jsonBrowser/module.md +++ b/docs/jsonBrowser/module.md @@ -566,3 +566,154 @@ parent | The individual's parent. | string | no | | Parent | | child | The individual's child. | string | no | | Child | | sibling | The individual's sibling. | string | no | | Sibling | | +## Medical history +_Information about the medical history of a donor._ + +Location: module/biomaterial/medical_history.json + +Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example +--- | --- | --- | --- | --- | --- | --- | --- +alcohol_status | Whether the individual is actively consuming, has formerly consumed or has never consumed alcohol beverages | string | no | | Alcohol status | active, former, never | Should be one of: active, former, never. +alcohol_type | Types of alcoholic beverages the donor consumed. | array | no | | Alcohol type | | beer; liquor; wine +alcohol_units | Alcohol consumption of donor in alcohol units per week (strength (ABV) x volume (ml) ÷ 1,000). | number | no | | Alcohol units | | 2.5; 15.2; 23 +alcohol_usage_duration | Number of years in which the donor consumed alcohol. | integer | no | | Alcohol usage duration | | 5 +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 +household_smoking_exposure | If the donor is exposed to passive smoking in their household or not (excluding if they are the ones smoking). | boolean | no | | Household smoking exposure | | Should be one of: yes; no. +vaping_status | Whether the individual is actively, was formerly or never vaped. | string | no | | Vaping status | active, former, never | Should be one of: active, former, never. +marijuana_inhaled_status | Whether the individual is actively, was formerly or never inhaled/smoked marijuana. | string | no | | Inhaled marijuana status | active, former, never | Should be one of: active, former, never. +nutritional_state | Nutritional state of individual at time of biomaterial collection. | string | no | | Nutritional state | normal, fasting, feeding tube removed | Should be one of: normal, fasting, or feeding tube removed. +diet_meat_consumption | Dietary patterns of donor - meat (chicken, seafood, fish, pork, lamb, beef, etc.) consumption versus meat-free diet - at time of sample collection. Fill yes if donor consumes meat or no if donor does not consumes meat. | boolean | no | | Meat consumption | | Should be one of: yes; no. +reproductive_history | Reproductive history of the donor at the time of collection. | object | no | [See module reproductive_history](module.md#reproductive-history) | Reproductive history | | +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 +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 + +## Residence +_Donor's residence location information._ + +Location: module/biomaterial/residence.json + +Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example +--- | --- | --- | --- | --- | --- | --- | --- +country_territory | Country or territory of donor's residence. | | no | | Country | Afghanistan, Albania, Algeria, American Samoa, Andorra, Angola, Anguilla, Antarctica, Antigua and Barbuda, Argentina, Armenia, Aruba, Ashmore and Cartier Islands, Australia, Austria, Azerbaijan, Bahamas, Bahrain, Baker Island, Bangladesh, Barbados, Bassas da India, Belarus, Belgium, Belize, Benin, Bermuda, Bhutan, Bolivia, Borneo, Bosnia and Herzegovina, Botswana, Bouvet Island, Brazil, British Virgin Islands, Brunei, Bulgaria, Burkina Faso, Burundi, Cambodia, Cameroon, Canada, Cape Verde, Cayman Islands, Central African Republic, Chad, Chile, China, Christmas Island, Clipperton Island, Cocos Islands, Colombia, Comoros, Cook Islands, Coral Sea Islands, Costa Rica, Cote d'Ivoire, Croatia, Cuba, Curacao, Cyprus, Czechia, Democratic Republic of the Congo, Denmark, Djibouti, Dominica, Dominican Republic, Ecuador, Egypt, El Salvador, Equatorial Guinea, Eritrea, Estonia, Eswatini, Ethiopia, Europa Island, Falkland Islands (Islas Malvinas), Faroe Islands, Fiji, Finland, France, French Guiana, French Polynesia, French Southern and Antarctic Lands, Gabon, Gambia, Gaza Strip, Georgia, Germany, Ghana, Gibraltar, Glorioso Islands, Greece, Greenland, Grenada, Guadeloupe, Guam, Guatemala, Guernsey, Guinea, Guinea-Bissau, Guyana, Haiti, Heard Island and McDonald Islands, Honduras, Hong Kong, Howland Island, Hungary, Iceland, India, Indonesia, Iran, Iraq, Ireland, Isle of Man, Israel, Italy, Jamaica, Jan Mayen, Japan, Jarvis Island, Jersey, Johnston Atoll, Jordan, Juan de Nova Island, Kazakhstan, Kenya, Kerguelen Archipelago, Kingman Reef, Kiribati, Kosovo, Kuwait, Kyrgyzstan, Laos, Latvia, Lebanon, Lesotho, Liberia, Libya, Liechtenstein, Line Islands, Lithuania, Luxembourg, Macau, Madagascar, Malawi, Malaysia, Maldives, Mali, Malta, Marshall Islands, Martinique, Mauritania, Mauritius, Mayotte, Mexico, Micronesia, Federated States of, Midway Islands, Moldova, Monaco, Mongolia, Montenegro, Montserrat, Morocco, Mozambique, Myanmar, Namibia, Nauru, Navassa Island, Nepal, Netherlands, New Caledonia, New Zealand, Nicaragua, Niger, Nigeria, Niue, Norfolk Island, North Korea, North Macedonia, Northern Mariana Islands, Norway, Oman, Pakistan, Palau, Palmyra Atoll, Panama, Papua New Guinea, Paracel Islands, Paraguay, Peru, Philippines, Pitcairn Islands, Poland, Portugal, Puerto Rico, Qatar, Republic of the Congo, Reunion, Romania, Russia, Rwanda, Saint Barthelemy, Saint Helena, Saint Kitts and Nevis, Saint Lucia, Saint Martin, Saint Pierre and Miquelon, Saint Vincent and the Grenadines, Samoa, San Marino, Sao Tome and Principe, Saudi Arabia, Senegal, Serbia, Seychelles, Sierra Leone, Singapore, Sint Maarten, Slovakia, Slovenia, Solomon Islands, Somalia, South Africa, South Georgia and the South Sandwich Islands, South Korea, South Sudan, Spain, Spratly Islands, Sri Lanka, State of Palestine, Sudan, Suriname, Svalbard, Sweden, Switzerland, Syria, Taiwan, Tajikistan, Tanzania, Thailand, Timor-Leste, Togo, Tokelau, Tonga, Trinidad and Tobago, Tromelin Island, Tunisia, Turkey, Turkmenistan, Turks and Caicos Islands, Tuvalu, Uganda, Ukraine, United Arab Emirates, United Kingdom, Uruguay, USA, Uzbekistan, Vanuatu, Venezuela, Viet Nam, Virgin Islands, Wake Island, Wallis and Futuna, West Bank, Western Sahara, Yemen, Zambia, Zimbabwe | Singapore; United Kingdom; Brazil; Australia; Nigeria +region | Region of donor's residence. | string | no | | Region | | Massachusetts; Catalonia; Ondo; Ontario +locality | Nearest city, town, or village to location of donor's residence. | string | no | | Locality | | Singapore; Cambridge; Boston; Kingston +duration | Duration of residence, in years, rounded up to the nearest whole number. | string | no | | Duration of residence | | 20; 37; 45-65 +area_type | Urban, suburban, or rural descriptor of residence. | string | no | | Area type of residence | urban, suburban, rural | urban; suburban; rural + +## Cell morphology +_Information relating to pathological and morphological features of cells._ + +Location: module/biomaterial/cell_morphology.json + +Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example +--- | --- | --- | --- | --- | --- | --- | --- +cell_morphology | General description of the morphology of cells. | string | no | | Cell morphology | | adherent cells; form single layer colonies +cell_size | Size of cells in Cell size unit. | string | no | | Cell size | | 15; 20-30 +cell_size_unit | The unit in which the Cell size is expressed. | object | no | [See module length_unit_ontology](module.md#length-unit-ontology) | Cell size unit | | +percent_cell_viability | Percent of cells determined to be viable. | number | no | | Percent cell viability | | 98.7 +cell_viability_method | The method by which cell viability was determined. | string | no | | Cell viability method | | Fluorescein diacetate hydrolysis; ATP test +cell_viability_result | Result of the cell viability test. | string | no | | Cell viability result | pass, fail | Should be one of: pass, fail +percent_necrosis | Percent of cells identified to be necrotic. | number | no | | Percent necrotic cells | | 10 + +## State of specimen +_State of specimen at time of collection._ + +Location: module/biomaterial/state_of_specimen.json + +Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example +--- | --- | --- | --- | --- | --- | --- | --- +autolysis_score | State of tissue breakdown due to self-digestion. | string | no | | Autolysis score | none, mild, moderate | Should be one of: none, mild, or moderate. +gross_description | Color, size, and other aspects of specimen as visible to naked eye. | string | no | | Gross description | | focal wedge shaped region of tan-orange discoloration; cystic +gross_images | List of filenames of photographs of specimen without magnification. | array | no | | Gross image | | my_gross_image_file.jpg +ischemic_temperature | Whether specimen experienced warm or cold ischemia. | string | no | | Ischemic temperature | warm, cold | Should be one of: warm, or cold. +ischemic_time | Duration of time, in seconds, between when the specimen stopped receiving oxygen and when it was preserved or processed. | integer | no | | Ischemic time | | 7200 +microscopic_description | How the specimen looks under the microscope and how it compares with normal cells. | string | no | | Microscopic description | | Mixture of different cell sizes apparent; Dead cells are quite faint on microscope +microscopic_images | List of filenames of photographs of specimen under microscope. | array | no | | Microscopic image | | my_microscopic_image_file.jpg +postmortem_interval | Duration of time between when death was declared and when the specimen was preserved or processed. | integer | no | | Post-mortem interval | | 2400 + +## Timecourse +_Information relating to a timecourse._ + +Location: module/biomaterial/timecourse.json + +Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example +--- | --- | --- | --- | --- | --- | --- | --- +value | The numerical value in Timecourse unit associated with a time interval used in the experiment. | string | yes | | Timecourse value | | 2; 5.5-10.5 +unit | The unit in which the Timecourse value is expressed. | object | yes | [See module time_unit_ontology](module.md#time-unit-ontology) | Timecourse unit | | +relevance | Relevance of the Timecourse value/unit to the experiment. | string | no | | Timecourse relevance | | Collection after tumor cells injected into the mammary gland; Time tissue underwent liberase digestion + +## Mouse-specific +_Information specific to an organism that is a mouse (Mus musculus)._ + +Location: module/biomaterial/mouse_specific.json + +Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example +--- | --- | --- | --- | --- | --- | --- | --- +strain | The name of the mouse strain. | array | no | [See module strain_ontology](module.md#strain-ontology) | Mouse strain | | + +## Purchased reagents +_Information describing purchased kits or reagents used in a protocol._ + +Location: module/process/purchased_reagents.json + +Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example +--- | --- | --- | --- | --- | --- | --- | --- +retail_name | The retail name of the kit/reagent. | string | no | | Retail name | | SureCell WTA 3' Library Prep Kit; CytoTune iPS 2.0 Sendai Reprogramming Kit +catalog_number | The catalog number of the kit/reagent. | string | no | | Catalog number | | 20014279 +manufacturer | The manufacturer of the kit/reagent. | string | no | | Manufacturer | | Illumina; ThermoFisher Scientific +lot_number | The batch or lot number of the kit/reagent. | string | no | | Batch/lot number | | 10001A +expiry_date | The date of expiration for the kit/reagent. | string | no | | Expiry date | | 2018-01-31; 2018-01 +kit_titer | Appropriate titer and volume recommendations found in kit/reagent Certificate of Analysis. | string | no | | Titer | | 3.0x10^7 + +## INSDC experiment +_Information relating to an INSDC experiment._ + +Location: module/process/sequencing/insdc_experiment.json + +Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example +--- | --- | --- | --- | --- | --- | --- | --- +insdc_experiment_accession | An International Nucleotide Sequence Database Collaboration (INSDC) experiment accession. | string | yes | | INSDC experiment accession | | SRX0000000 + +## Barcode +_Information about barcodes used in a protocol._ + +Location: module/process/sequencing/barcode.json + +Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example +--- | --- | --- | --- | --- | --- | --- | --- +barcode_read | The read in which the barcode is found. | string | yes | | Barcode-containing read | Read 1, Read 2, Read 3, Read 4, i7 Index, i5 Index | Should be one of: Read 1, Read 2, i7 Index, or i5 Index. +barcode_offset | The 0-based offset of start of barcode in read. | integer | yes | | Barcode offset | | 0 +barcode_length | Length of barcode in nucleotides. | integer | yes | | Barcode length | | 28 +white_list_file | Name of file containing legitimate barcode sequences. | string | no | | White list barcode file | | barcode_whitelist_file.txt + +## 10x-specific +_Information specific to 10x experiments._ + +Location: module/process/sequencing/10x.json + +Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example +--- | --- | --- | --- | --- | --- | --- | --- +fastq_method | Method used for the generation of fastq files from bcl files. | string | no | | Fastq creation method | | Cellranger mkfastq; bcl2fastq2 +fastq_method_version | Version of the program used for fastq generation. | string | no | | Fastq creation method version | | Cellranger 2.1.1; v2.20 +pooled_channels | The number of channels pooled within a sequencing lane. | number | no | | Pooled channels | | 4 +drop_uniformity | Whether drop uniformity was achieved as a result of visual inspection of emulsion after a 10x run. | boolean | no | | Drop uniformity | | Should be one of: yes, or no. + +## Plate-based sequencing +_Information specific to plate-based sequencing experiments._ + +Location: module/process/sequencing/plate_based_sequencing.json + +Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example +--- | --- | --- | --- | --- | --- | --- | --- +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 3cae95aa7..aefd876ee 100644 --- a/docs/jsonBrowser/required_fields.md +++ b/docs/jsonBrowser/required_fields.md @@ -376,3 +376,36 @@ Property name | Description | Type | Object reference? | User friendly name | Al cause_of_death | Conditions resulting in death. | string | | Cause of death | | Hypoxic brain damage; Sudden cardiac arrest ### Familial relationship _There are no required properties in schema Familial relationship_ +### Medical history +_There are no required properties in schema Medical history_ +### Residence +_There are no required properties in schema Residence_ +### Cell morphology +_There are no required properties in schema Cell morphology_ +### State of specimen +_There are no required properties in schema State of specimen_ +### Timecourse +Property name | Description | Type | Object reference? | User friendly name | Allowed values | Example +--- | --- | --- | --- | --- | --- | --- +value | The numerical value in Timecourse unit associated with a time interval used in the experiment. | string | | Timecourse value | | 2; 5.5-10.5 +unit | The unit in which the Timecourse value is expressed. | object | [See module time_unit_ontology](module.md#time-unit-ontology) | Timecourse unit | | +### Mouse-specific +_There are no required properties in schema Mouse-specific_ +### Purchased reagents +_There are no required properties in schema Purchased reagents_ +### INSDC experiment +Property name | Description | Type | Object reference? | User friendly name | Allowed values | Example +--- | --- | --- | --- | --- | --- | --- +insdc_experiment_accession | An International Nucleotide Sequence Database Collaboration (INSDC) experiment accession. | string | | INSDC experiment accession | | SRX0000000 +### Barcode +Property name | Description | Type | Object reference? | User friendly name | Allowed values | Example +--- | --- | --- | --- | --- | --- | --- +barcode_read | The read in which the barcode is found. | string | | Barcode-containing read | Read 1, Read 2, Read 3, Read 4, i7 Index, i5 Index | Should be one of: Read 1, Read 2, i7 Index, or i5 Index. +barcode_offset | The 0-based offset of start of barcode in read. | integer | | Barcode offset | | 0 +barcode_length | Length of barcode in nucleotides. | integer | | Barcode length | | 28 +### 10x-specific +_There are no required properties in schema 10x-specific_ +### Plate-based sequencing +Property name | Description | Type | Object reference? | User friendly name | Allowed values | Example +--- | --- | --- | --- | --- | --- | --- +plate_label | A label or name for the plate on which the well is located. | string | | Plate label | | 2217 diff --git a/json_schema/module/biomaterial/medical_history.json b/json_schema/module/biomaterial/medical_history.json index 5adf2d11c..b6d33c8fb 100644 --- a/json_schema/module/biomaterial/medical_history.json +++ b/json_schema/module/biomaterial/medical_history.json @@ -181,10 +181,6 @@ "user_friendly": "Device Treatment", "example": "Should be one of: ECMO, IABP, Impella, LVAD, RVAD, PPM, ICD, CRT", "bionetworks": ["heart"] - }, - "user_friendly": "Device Treatment", - "example": "Should be one of: ECMO, IABP, Impella, LVAD, RVAD, PPM, ICD, CRT", - "bionetworks": ["heart"] }, "previous_surgeries": { "description": "Previous surgeries the individual has undergone prior to biomaterial collection.", From d3f336992e37a5fd8fc267db29179774bc05735b Mon Sep 17 00:00:00 2001 From: idazucchi Date: Wed, 11 Feb 2026 10:55:48 +0100 Subject: [PATCH 05/64] Added cardioplegia --- docs/jsonBrowser/module.md | 1 + json_schema/module/biomaterial/medical_history.json | 8 ++++++++ json_schema/update_log.csv | 2 +- 3 files changed, 10 insertions(+), 1 deletion(-) diff --git a/docs/jsonBrowser/module.md b/docs/jsonBrowser/module.md index 98903b5a4..e67a6bf52 100644 --- a/docs/jsonBrowser/module.md +++ b/docs/jsonBrowser/module.md @@ -591,6 +591,7 @@ test_results | Results from medical tests performed on the individual. | string 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 diff --git a/json_schema/module/biomaterial/medical_history.json b/json_schema/module/biomaterial/medical_history.json index b6d33c8fb..8ebdbf673 100644 --- a/json_schema/module/biomaterial/medical_history.json +++ b/json_schema/module/biomaterial/medical_history.json @@ -182,6 +182,14 @@ "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/update_log.csv b/json_schema/update_log.csv index bc273cecc..63bf437a2 100644 --- a/json_schema/update_log.csv +++ b/json_schema/update_log.csv @@ -1,2 +1,2 @@ Schema,Change type,Change message,Version,Date -module/biomaterial/medical_history,minor,"Added diseases_history, device_treatment" \ No newline at end of file +module/biomaterial/medical_history,minor,"Added diseases_history, device_treatment, cardioplegia" \ No newline at end of file From 60330b78ccccf68f3fb5dc3993f31a580d364c24 Mon Sep 17 00:00:00 2001 From: idazucchi Date: Wed, 11 Feb 2026 11:34:23 +0100 Subject: [PATCH 06/64] Added mps_lvef --- docs/jsonBrowser/module.md | 1 + json_schema/module/biomaterial/medical_tests.json | 7 +++++++ json_schema/update_log.csv | 3 ++- 3 files changed, 10 insertions(+), 1 deletion(-) diff --git a/docs/jsonBrowser/module.md b/docs/jsonBrowser/module.md index e67a6bf52..bcfb56bad 100644 --- a/docs/jsonBrowser/module.md +++ b/docs/jsonBrowser/module.md @@ -487,6 +487,7 @@ 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 +mps_lvef | Left ventricular ejection fraction in percentage as measured by myocardial perfusion scintigraphy. | number | no | | Mps - LVEF | | 58; 60; 62 ## Collection institute _Information about collection institute location._ diff --git a/json_schema/module/biomaterial/medical_tests.json b/json_schema/module/biomaterial/medical_tests.json index 5359953cd..c207f67fc 100644 --- a/json_schema/module/biomaterial/medical_tests.json +++ b/json_schema/module/biomaterial/medical_tests.json @@ -254,6 +254,13 @@ "maximum": 200, "minimum": 0, "bionetworks": ["lung"] + }, + "mps_lvef": { + "user_friendly": "Mps - LVEF", + "description": "Left ventricular ejection fraction in percentage as measured by myocardial perfusion scintigraphy.", + "type": "number", + "example": "58; 60; 62", + "bionetworks": ["heart"] } } } diff --git a/json_schema/update_log.csv b/json_schema/update_log.csv index 63bf437a2..077c40d11 100644 --- a/json_schema/update_log.csv +++ b/json_schema/update_log.csv @@ -1,2 +1,3 @@ Schema,Change type,Change message,Version,Date -module/biomaterial/medical_history,minor,"Added diseases_history, device_treatment, cardioplegia" \ No newline at end of file +module/biomaterial/medical_history,minor,"Added diseases_history, device_treatment, cardioplegia" +module/biomaterial/medical_tests,minor,"Added mps_lvef" \ No newline at end of file From a6662e95e6b6cb5dba229a80c274ee725d2004c5 Mon Sep 17 00:00:00 2001 From: idazucchi Date: Wed, 11 Feb 2026 11:39:51 +0100 Subject: [PATCH 07/64] Added mps_inducible_ischaemic --- docs/jsonBrowser/module.md | 1 + json_schema/module/biomaterial/medical_tests.json | 7 +++++++ json_schema/update_log.csv | 2 +- 3 files changed, 9 insertions(+), 1 deletion(-) diff --git a/docs/jsonBrowser/module.md b/docs/jsonBrowser/module.md index bcfb56bad..9948d8f64 100644 --- a/docs/jsonBrowser/module.md +++ b/docs/jsonBrowser/module.md @@ -488,6 +488,7 @@ 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 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 ## Collection institute _Information about collection institute location._ diff --git a/json_schema/module/biomaterial/medical_tests.json b/json_schema/module/biomaterial/medical_tests.json index c207f67fc..daadf1882 100644 --- a/json_schema/module/biomaterial/medical_tests.json +++ b/json_schema/module/biomaterial/medical_tests.json @@ -261,6 +261,13 @@ "type": "number", "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", + "example": "0; 5; 12", + "bionetworks": ["heart"] } } } diff --git a/json_schema/update_log.csv b/json_schema/update_log.csv index 077c40d11..5604a4744 100644 --- a/json_schema/update_log.csv +++ b/json_schema/update_log.csv @@ -1,3 +1,3 @@ Schema,Change type,Change message,Version,Date module/biomaterial/medical_history,minor,"Added diseases_history, device_treatment, cardioplegia" -module/biomaterial/medical_tests,minor,"Added mps_lvef" \ No newline at end of file +module/biomaterial/medical_tests,minor,"Added mps_lvef, mps_inducible_ischaemic" \ No newline at end of file From de69e4a21f57abc12aa2b32b25004edbd5dd375e Mon Sep 17 00:00:00 2001 From: idazucchi Date: Wed, 11 Feb 2026 11:42:26 +0100 Subject: [PATCH 08/64] Added mps_scar --- docs/jsonBrowser/module.md | 1 + json_schema/module/biomaterial/medical_tests.json | 7 +++++++ json_schema/update_log.csv | 2 +- 3 files changed, 9 insertions(+), 1 deletion(-) diff --git a/docs/jsonBrowser/module.md b/docs/jsonBrowser/module.md index 9948d8f64..3842177bc 100644 --- a/docs/jsonBrowser/module.md +++ b/docs/jsonBrowser/module.md @@ -489,6 +489,7 @@ kco | Indicate the transfer coefficient of the lung for carbon monoxide (KCO) in 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 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 ## Collection institute _Information about collection institute location._ diff --git a/json_schema/module/biomaterial/medical_tests.json b/json_schema/module/biomaterial/medical_tests.json index daadf1882..8c76b392c 100644 --- a/json_schema/module/biomaterial/medical_tests.json +++ b/json_schema/module/biomaterial/medical_tests.json @@ -268,6 +268,13 @@ "type": "number", "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", + "example": "0; 3; 10", + "bionetworks": ["heart"] } } } diff --git a/json_schema/update_log.csv b/json_schema/update_log.csv index 5604a4744..6bedf06b0 100644 --- a/json_schema/update_log.csv +++ b/json_schema/update_log.csv @@ -1,3 +1,3 @@ Schema,Change type,Change message,Version,Date module/biomaterial/medical_history,minor,"Added diseases_history, device_treatment, cardioplegia" -module/biomaterial/medical_tests,minor,"Added mps_lvef, mps_inducible_ischaemic" \ No newline at end of file +module/biomaterial/medical_tests,minor,"Added mps_lvef, mps_inducible_ischaemic, mps_scar" \ No newline at end of file From 2fa97c7213ec5f5aa6bb746ccd5554cc5104921f Mon Sep 17 00:00:00 2001 From: idazucchi Date: Wed, 11 Feb 2026 11:46:33 +0100 Subject: [PATCH 09/64] Added mps_time_offset --- docs/jsonBrowser/module.md | 1 + json_schema/module/biomaterial/medical_tests.json | 7 +++++++ json_schema/update_log.csv | 2 +- 3 files changed, 9 insertions(+), 1 deletion(-) diff --git a/docs/jsonBrowser/module.md b/docs/jsonBrowser/module.md index 3842177bc..ed6579a7d 100644 --- a/docs/jsonBrowser/module.md +++ b/docs/jsonBrowser/module.md @@ -490,6 +490,7 @@ kco_predicted_percent | Indicate the percentage of the predicted KCO, based on p 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._ diff --git a/json_schema/module/biomaterial/medical_tests.json b/json_schema/module/biomaterial/medical_tests.json index 8c76b392c..361288734 100644 --- a/json_schema/module/biomaterial/medical_tests.json +++ b/json_schema/module/biomaterial/medical_tests.json @@ -275,6 +275,13 @@ "type": "number", "example": "0; 3; 10", "bionetworks": ["heart"] + }, + "mps_time_offset": { + "description": "Time between the test and the collection of the sample, in days.", + "type": "number", + "user_friendly": "Mps - Time Offset", + "example": "4; 20; 58", + "bionetworks": ["heart"] } } } diff --git a/json_schema/update_log.csv b/json_schema/update_log.csv index 6bedf06b0..55b3c5a76 100644 --- a/json_schema/update_log.csv +++ b/json_schema/update_log.csv @@ -1,3 +1,3 @@ Schema,Change type,Change message,Version,Date module/biomaterial/medical_history,minor,"Added diseases_history, device_treatment, cardioplegia" -module/biomaterial/medical_tests,minor,"Added mps_lvef, mps_inducible_ischaemic, mps_scar" \ No newline at end of file +module/biomaterial/medical_tests,minor,"Added mps_lvef, mps_inducible_ischaemic, mps_scar, mps_time_offset" \ No newline at end of file From 886fc853c5a41076016c3b5661527ee2bab476f5 Mon Sep 17 00:00:00 2001 From: idazucchi Date: Wed, 11 Feb 2026 12:00:27 +0100 Subject: [PATCH 10/64] Added ecg_heart_rate --- docs/jsonBrowser/module.md | 1 + json_schema/module/biomaterial/medical_tests.json | 7 +++++++ json_schema/update_log.csv | 2 +- 3 files changed, 9 insertions(+), 1 deletion(-) diff --git a/docs/jsonBrowser/module.md b/docs/jsonBrowser/module.md index ed6579a7d..f9da31265 100644 --- a/docs/jsonBrowser/module.md +++ b/docs/jsonBrowser/module.md @@ -487,6 +487,7 @@ 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 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 diff --git a/json_schema/module/biomaterial/medical_tests.json b/json_schema/module/biomaterial/medical_tests.json index 361288734..5f6ff0115 100644 --- a/json_schema/module/biomaterial/medical_tests.json +++ b/json_schema/module/biomaterial/medical_tests.json @@ -255,6 +255,13 @@ "minimum": 0, "bionetworks": ["lung"] }, + "ecg_heart_rate": { + "description": "Heart rate as measured by electrocardiogram in beats per minute.", + "type": "number", + "user_friendly": "Ecg - Heart Rate", + "example": "72; 65; 80", + "bionetworks": ["heart"] + }, "mps_lvef": { "user_friendly": "Mps - LVEF", "description": "Left ventricular ejection fraction in percentage as measured by myocardial perfusion scintigraphy.", diff --git a/json_schema/update_log.csv b/json_schema/update_log.csv index 55b3c5a76..426cf42ba 100644 --- a/json_schema/update_log.csv +++ b/json_schema/update_log.csv @@ -1,3 +1,3 @@ Schema,Change type,Change message,Version,Date 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" \ No newline at end of file +module/biomaterial/medical_tests,minor,"Added mps_lvef, mps_inducible_ischaemic, mps_scar, mps_time_offset, ecg_heart_rate" \ No newline at end of file From fb9c9445ba41f6205b578cfc8bb853637ac60276 Mon Sep 17 00:00:00 2001 From: idazucchi Date: Wed, 11 Feb 2026 12:06:15 +0100 Subject: [PATCH 11/64] Added ecg_heart_rhythm --- docs/jsonBrowser/module.md | 1 + json_schema/module/biomaterial/medical_tests.json | 7 +++++++ json_schema/update_log.csv | 2 +- 3 files changed, 9 insertions(+), 1 deletion(-) diff --git a/docs/jsonBrowser/module.md b/docs/jsonBrowser/module.md index f9da31265..a9f1f6ddb 100644 --- a/docs/jsonBrowser/module.md +++ b/docs/jsonBrowser/module.md @@ -488,6 +488,7 @@ 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 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 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 diff --git a/json_schema/module/biomaterial/medical_tests.json b/json_schema/module/biomaterial/medical_tests.json index 5f6ff0115..4c9895e80 100644 --- a/json_schema/module/biomaterial/medical_tests.json +++ b/json_schema/module/biomaterial/medical_tests.json @@ -262,6 +262,13 @@ "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"] + }, "mps_lvef": { "user_friendly": "Mps - LVEF", "description": "Left ventricular ejection fraction in percentage as measured by myocardial perfusion scintigraphy.", diff --git a/json_schema/update_log.csv b/json_schema/update_log.csv index 426cf42ba..85eeef684 100644 --- a/json_schema/update_log.csv +++ b/json_schema/update_log.csv @@ -1,3 +1,3 @@ Schema,Change type,Change message,Version,Date 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" \ No newline at end of file +module/biomaterial/medical_tests,minor,"Added mps_lvef, mps_inducible_ischaemic, mps_scar, mps_time_offset, ecg_heart_rate, ecg_heart_rhythm" \ No newline at end of file From 7ed241db380f2a834f2d936728b45b05ec175074 Mon Sep 17 00:00:00 2001 From: idazucchi Date: Wed, 11 Feb 2026 12:54:04 +0100 Subject: [PATCH 12/64] Added ecg_pr_interval_duration --- docs/jsonBrowser/module.md | 1 + json_schema/module/biomaterial/medical_tests.json | 7 +++++++ json_schema/update_log.csv | 2 +- 3 files changed, 9 insertions(+), 1 deletion(-) diff --git a/docs/jsonBrowser/module.md b/docs/jsonBrowser/module.md index a9f1f6ddb..e7adb5b14 100644 --- a/docs/jsonBrowser/module.md +++ b/docs/jsonBrowser/module.md @@ -489,6 +489,7 @@ kco | Indicate the transfer coefficient of the lung for carbon monoxide (KCO) in 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 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 diff --git a/json_schema/module/biomaterial/medical_tests.json b/json_schema/module/biomaterial/medical_tests.json index 4c9895e80..d765a2573 100644 --- a/json_schema/module/biomaterial/medical_tests.json +++ b/json_schema/module/biomaterial/medical_tests.json @@ -269,6 +269,13 @@ "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", + "user_friendly": "Ecg - Pr Interval Duration", + "example": "160; 140; 180", + "bionetworks": ["heart"] + }, "mps_lvef": { "user_friendly": "Mps - LVEF", "description": "Left ventricular ejection fraction in percentage as measured by myocardial perfusion scintigraphy.", diff --git a/json_schema/update_log.csv b/json_schema/update_log.csv index 85eeef684..f67e32c6b 100644 --- a/json_schema/update_log.csv +++ b/json_schema/update_log.csv @@ -1,3 +1,3 @@ Schema,Change type,Change message,Version,Date 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" \ No newline at end of file +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" \ No newline at end of file From bd16b93148a386c281112d4487bc22cc99fe92f6 Mon Sep 17 00:00:00 2001 From: idazucchi Date: Wed, 11 Feb 2026 12:55:59 +0100 Subject: [PATCH 13/64] Added ecg_qrs_complex_duration --- docs/jsonBrowser/module.md | 1 + json_schema/module/biomaterial/medical_tests.json | 7 +++++++ json_schema/update_log.csv | 2 +- 3 files changed, 9 insertions(+), 1 deletion(-) diff --git a/docs/jsonBrowser/module.md b/docs/jsonBrowser/module.md index e7adb5b14..b88cfa564 100644 --- a/docs/jsonBrowser/module.md +++ b/docs/jsonBrowser/module.md @@ -490,6 +490,7 @@ kco_predicted_percent | Indicate the percentage of the predicted KCO, based on p 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 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 diff --git a/json_schema/module/biomaterial/medical_tests.json b/json_schema/module/biomaterial/medical_tests.json index d765a2573..0c6128d31 100644 --- a/json_schema/module/biomaterial/medical_tests.json +++ b/json_schema/module/biomaterial/medical_tests.json @@ -276,6 +276,13 @@ "example": "160; 140; 180", "bionetworks": ["heart"] }, + "ecg_qrs_complex_duration": { + "description": "QRS complex duration in ms as measured by electrocardiogram.", + "type": "number", + "user_friendly": "Ecg - QRS Complex Duration", + "example": "90; 100; 110", + "bionetworks": ["heart"] + }, "mps_lvef": { "user_friendly": "Mps - LVEF", "description": "Left ventricular ejection fraction in percentage as measured by myocardial perfusion scintigraphy.", diff --git a/json_schema/update_log.csv b/json_schema/update_log.csv index f67e32c6b..483efb965 100644 --- a/json_schema/update_log.csv +++ b/json_schema/update_log.csv @@ -1,3 +1,3 @@ Schema,Change type,Change message,Version,Date 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" \ No newline at end of file +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" \ No newline at end of file From 87dd7b34aa4968ca2760360beba4596c2b215ad4 Mon Sep 17 00:00:00 2001 From: idazucchi Date: Wed, 11 Feb 2026 12:00:02 +0000 Subject: [PATCH 14/64] Added ecg_lbbb_rbbb_ivcd --- docs/jsonBrowser/module.md | 1 + json_schema/module/biomaterial/medical_tests.json | 12 ++++++++++++ json_schema/update_log.csv | 2 +- 3 files changed, 14 insertions(+), 1 deletion(-) diff --git a/docs/jsonBrowser/module.md b/docs/jsonBrowser/module.md index b88cfa564..594b1961e 100644 --- a/docs/jsonBrowser/module.md +++ b/docs/jsonBrowser/module.md @@ -491,6 +491,7 @@ ecg_heart_rate | Heart rate as measured by electrocardiogram in beats per minute 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. 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 diff --git a/json_schema/module/biomaterial/medical_tests.json b/json_schema/module/biomaterial/medical_tests.json index 0c6128d31..72cdd873b 100644 --- a/json_schema/module/biomaterial/medical_tests.json +++ b/json_schema/module/biomaterial/medical_tests.json @@ -283,6 +283,18 @@ "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"] + }, "mps_lvef": { "user_friendly": "Mps - LVEF", "description": "Left ventricular ejection fraction in percentage as measured by myocardial perfusion scintigraphy.", diff --git a/json_schema/update_log.csv b/json_schema/update_log.csv index 483efb965..feaecaa4b 100644 --- a/json_schema/update_log.csv +++ b/json_schema/update_log.csv @@ -1,3 +1,3 @@ Schema,Change type,Change message,Version,Date 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" \ No newline at end of file +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" \ No newline at end of file From 4e5f1bdb88211aca68d8c03b64eb3c03a5aecd9d Mon Sep 17 00:00:00 2001 From: idazucchi Date: Wed, 11 Feb 2026 12:02:28 +0000 Subject: [PATCH 15/64] Added ecg_qt_interval_corrected --- docs/jsonBrowser/module.md | 1 + json_schema/module/biomaterial/medical_tests.json | 7 +++++++ json_schema/update_log.csv | 2 +- 3 files changed, 9 insertions(+), 1 deletion(-) diff --git a/docs/jsonBrowser/module.md b/docs/jsonBrowser/module.md index 594b1961e..889e20e98 100644 --- a/docs/jsonBrowser/module.md +++ b/docs/jsonBrowser/module.md @@ -492,6 +492,7 @@ ecg_heart_rhythm | Heart rhythm as measured by electrocardiogram. | string | no 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 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 diff --git a/json_schema/module/biomaterial/medical_tests.json b/json_schema/module/biomaterial/medical_tests.json index 72cdd873b..f0447d7a4 100644 --- a/json_schema/module/biomaterial/medical_tests.json +++ b/json_schema/module/biomaterial/medical_tests.json @@ -295,6 +295,13 @@ "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", + "user_friendly": "Ecg - QT Interval Corrected", + "example": "420; 410; 430", + "bionetworks": ["heart"] + }, "mps_lvef": { "user_friendly": "Mps - LVEF", "description": "Left ventricular ejection fraction in percentage as measured by myocardial perfusion scintigraphy.", diff --git a/json_schema/update_log.csv b/json_schema/update_log.csv index feaecaa4b..7a949b81c 100644 --- a/json_schema/update_log.csv +++ b/json_schema/update_log.csv @@ -1,3 +1,3 @@ Schema,Change type,Change message,Version,Date 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" \ No newline at end of file +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" \ No newline at end of file From 9403e4eda65c9d6a97e7d39f18bcb361120690cc Mon Sep 17 00:00:00 2001 From: idazucchi Date: Wed, 11 Feb 2026 12:05:11 +0000 Subject: [PATCH 16/64] Added ecg_time_offset --- docs/jsonBrowser/module.md | 1 + json_schema/module/biomaterial/medical_tests.json | 7 +++++++ json_schema/update_log.csv | 2 +- 3 files changed, 9 insertions(+), 1 deletion(-) diff --git a/docs/jsonBrowser/module.md b/docs/jsonBrowser/module.md index 889e20e98..ac9ada8f7 100644 --- a/docs/jsonBrowser/module.md +++ b/docs/jsonBrowser/module.md @@ -493,6 +493,7 @@ ecg_pr_interval_duration | PR interval duration in ms as measured by electrocard 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 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 diff --git a/json_schema/module/biomaterial/medical_tests.json b/json_schema/module/biomaterial/medical_tests.json index f0447d7a4..358dfa4b7 100644 --- a/json_schema/module/biomaterial/medical_tests.json +++ b/json_schema/module/biomaterial/medical_tests.json @@ -302,6 +302,13 @@ "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", + "user_friendly": "Ecg - 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.", diff --git a/json_schema/update_log.csv b/json_schema/update_log.csv index 7a949b81c..1afb3b71a 100644 --- a/json_schema/update_log.csv +++ b/json_schema/update_log.csv @@ -1,3 +1,3 @@ Schema,Change type,Change message,Version,Date 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" \ No newline at end of file +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" \ No newline at end of file From 4f150423a9650392cd2adb5fbf707bb0e1b728c9 Mon Sep 17 00:00:00 2001 From: idazucchi Date: Wed, 11 Feb 2026 15:34:16 +0000 Subject: [PATCH 17/64] added dots to readme --- README.md | 1 + 1 file changed, 1 insertion(+) diff --git a/README.md b/README.md index 7a4a69a67..c0428ade1 100644 --- a/README.md +++ b/README.md @@ -4,6 +4,7 @@ The Human Cell Atlas metadata-schema repo contains the schema specifications and supporting documentation for the HCA metadata standards. +... ## Table of Contents - [Documentation](#documentation) - [Metadata schemas and examples](#metadata-schemas-and-examples) From 5be6392da16b0fc09530383249f2c046f17887dd Mon Sep 17 00:00:00 2001 From: idazucchi Date: Wed, 11 Feb 2026 15:36:43 +0000 Subject: [PATCH 18/64] Revert "added dots to readme" This reverts commit 4f150423a9650392cd2adb5fbf707bb0e1b728c9. --- README.md | 1 - 1 file changed, 1 deletion(-) diff --git a/README.md b/README.md index c0428ade1..7a4a69a67 100644 --- a/README.md +++ b/README.md @@ -4,7 +4,6 @@ The Human Cell Atlas metadata-schema repo contains the schema specifications and supporting documentation for the HCA metadata standards. -... ## Table of Contents - [Documentation](#documentation) - [Metadata schemas and examples](#metadata-schemas-and-examples) From 9716db9a43d2bf9e65c04bc1f1afbaf0ef7173ae Mon Sep 17 00:00:00 2001 From: idazucchi Date: Tue, 17 Feb 2026 13:46:33 +0000 Subject: [PATCH 19/64] Added echo_aortic_stenosis --- docs/jsonBrowser/module.md | 1 + json_schema/module/biomaterial/medical_tests.json | 13 +++++++++++++ json_schema/update_log.csv | 2 +- 3 files changed, 15 insertions(+), 1 deletion(-) diff --git a/docs/jsonBrowser/module.md b/docs/jsonBrowser/module.md index a214e5d87..6480924cd 100644 --- a/docs/jsonBrowser/module.md +++ b/docs/jsonBrowser/module.md @@ -497,6 +497,7 @@ ecg_qrs_complex_duration | QRS complex duration in ms as measured by electrocard 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. 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 diff --git a/json_schema/module/biomaterial/medical_tests.json b/json_schema/module/biomaterial/medical_tests.json index 358dfa4b7..92e2777ee 100644 --- a/json_schema/module/biomaterial/medical_tests.json +++ b/json_schema/module/biomaterial/medical_tests.json @@ -309,6 +309,19 @@ "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"] + }, "mps_lvef": { "user_friendly": "Mps - LVEF", "description": "Left ventricular ejection fraction in percentage as measured by myocardial perfusion scintigraphy.", diff --git a/json_schema/update_log.csv b/json_schema/update_log.csv index 1afb3b71a..42b6ea55e 100644 --- a/json_schema/update_log.csv +++ b/json_schema/update_log.csv @@ -1,3 +1,3 @@ Schema,Change type,Change message,Version,Date 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" \ No newline at end of file +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" \ No newline at end of file From 5fe0b549e426bc92448ff9f2ed51274facafdf19 Mon Sep 17 00:00:00 2001 From: idazucchi Date: Tue, 17 Feb 2026 13:48:29 +0000 Subject: [PATCH 20/64] Added echo_aortic_regurgitation --- docs/jsonBrowser/module.md | 1 + json_schema/module/biomaterial/medical_tests.json | 13 +++++++++++++ json_schema/update_log.csv | 2 +- 3 files changed, 15 insertions(+), 1 deletion(-) diff --git a/docs/jsonBrowser/module.md b/docs/jsonBrowser/module.md index 6480924cd..fac44f4e4 100644 --- a/docs/jsonBrowser/module.md +++ b/docs/jsonBrowser/module.md @@ -498,6 +498,7 @@ ecg_lbbb_rbbb_ivcd | Bundle branch block and/or delayed atrioventricular conduct 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. 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 diff --git a/json_schema/module/biomaterial/medical_tests.json b/json_schema/module/biomaterial/medical_tests.json index 92e2777ee..c835fbad3 100644 --- a/json_schema/module/biomaterial/medical_tests.json +++ b/json_schema/module/biomaterial/medical_tests.json @@ -322,6 +322,19 @@ "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"] + }, "mps_lvef": { "user_friendly": "Mps - LVEF", "description": "Left ventricular ejection fraction in percentage as measured by myocardial perfusion scintigraphy.", diff --git a/json_schema/update_log.csv b/json_schema/update_log.csv index 42b6ea55e..7a81c2eee 100644 --- a/json_schema/update_log.csv +++ b/json_schema/update_log.csv @@ -1,3 +1,3 @@ Schema,Change type,Change message,Version,Date 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" \ No newline at end of file +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" \ No newline at end of file From 0812a0158946bcef640a947db1edb67a8f090fb0 Mon Sep 17 00:00:00 2001 From: idazucchi Date: Tue, 17 Feb 2026 13:50:32 +0000 Subject: [PATCH 21/64] Added echo_mitral_regurgitation --- docs/jsonBrowser/module.md | 1 + json_schema/module/biomaterial/medical_tests.json | 13 +++++++++++++ json_schema/update_log.csv | 2 +- 3 files changed, 15 insertions(+), 1 deletion(-) diff --git a/docs/jsonBrowser/module.md b/docs/jsonBrowser/module.md index fac44f4e4..636778b0b 100644 --- a/docs/jsonBrowser/module.md +++ b/docs/jsonBrowser/module.md @@ -499,6 +499,7 @@ ecg_qt_interval_corrected | Corrected QT interval in ms as measured by electroca 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. 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 diff --git a/json_schema/module/biomaterial/medical_tests.json b/json_schema/module/biomaterial/medical_tests.json index c835fbad3..e3b7b4bae 100644 --- a/json_schema/module/biomaterial/medical_tests.json +++ b/json_schema/module/biomaterial/medical_tests.json @@ -335,6 +335,19 @@ "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"] + }, "mps_lvef": { "user_friendly": "Mps - LVEF", "description": "Left ventricular ejection fraction in percentage as measured by myocardial perfusion scintigraphy.", diff --git a/json_schema/update_log.csv b/json_schema/update_log.csv index 7a81c2eee..5d6328e50 100644 --- a/json_schema/update_log.csv +++ b/json_schema/update_log.csv @@ -1,3 +1,3 @@ Schema,Change type,Change message,Version,Date 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" \ No newline at end of file +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" \ No newline at end of file From 89c21f534d1f40baedd5f767ab952fe6ca9e375e Mon Sep 17 00:00:00 2001 From: idazucchi Date: Tue, 17 Feb 2026 13:52:12 +0000 Subject: [PATCH 22/64] Added echo_mitral_stenosis --- docs/jsonBrowser/module.md | 1 + json_schema/module/biomaterial/medical_tests.json | 13 +++++++++++++ json_schema/update_log.csv | 2 +- 3 files changed, 15 insertions(+), 1 deletion(-) diff --git a/docs/jsonBrowser/module.md b/docs/jsonBrowser/module.md index 636778b0b..26f8bc7a7 100644 --- a/docs/jsonBrowser/module.md +++ b/docs/jsonBrowser/module.md @@ -500,6 +500,7 @@ ecg_time_offset | Time between the test and the collection of the sample, measur 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. 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 diff --git a/json_schema/module/biomaterial/medical_tests.json b/json_schema/module/biomaterial/medical_tests.json index e3b7b4bae..d89b60a23 100644 --- a/json_schema/module/biomaterial/medical_tests.json +++ b/json_schema/module/biomaterial/medical_tests.json @@ -348,6 +348,19 @@ "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"] + }, "mps_lvef": { "user_friendly": "Mps - LVEF", "description": "Left ventricular ejection fraction in percentage as measured by myocardial perfusion scintigraphy.", diff --git a/json_schema/update_log.csv b/json_schema/update_log.csv index 5d6328e50..d51cdb969 100644 --- a/json_schema/update_log.csv +++ b/json_schema/update_log.csv @@ -1,3 +1,3 @@ Schema,Change type,Change message,Version,Date 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" \ No newline at end of file +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" \ No newline at end of file From 05a768cee5979fd7f4ab8708ce618e10d2d0cb38 Mon Sep 17 00:00:00 2001 From: idazucchi Date: Tue, 17 Feb 2026 13:54:14 +0000 Subject: [PATCH 23/64] Added echo_tricuspid_regurgitation --- docs/jsonBrowser/module.md | 1 + json_schema/module/biomaterial/medical_tests.json | 13 +++++++++++++ json_schema/update_log.csv | 2 +- 3 files changed, 15 insertions(+), 1 deletion(-) diff --git a/docs/jsonBrowser/module.md b/docs/jsonBrowser/module.md index 26f8bc7a7..ff10b81d9 100644 --- a/docs/jsonBrowser/module.md +++ b/docs/jsonBrowser/module.md @@ -501,6 +501,7 @@ echo_aortic_stenosis | Aortic stenosis as measured by echocardiogram. | string | 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. 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 diff --git a/json_schema/module/biomaterial/medical_tests.json b/json_schema/module/biomaterial/medical_tests.json index d89b60a23..2df0a21b5 100644 --- a/json_schema/module/biomaterial/medical_tests.json +++ b/json_schema/module/biomaterial/medical_tests.json @@ -361,6 +361,19 @@ "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"] + }, "mps_lvef": { "user_friendly": "Mps - LVEF", "description": "Left ventricular ejection fraction in percentage as measured by myocardial perfusion scintigraphy.", diff --git a/json_schema/update_log.csv b/json_schema/update_log.csv index d51cdb969..ec437aaa8 100644 --- a/json_schema/update_log.csv +++ b/json_schema/update_log.csv @@ -1,3 +1,3 @@ Schema,Change type,Change message,Version,Date 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" \ No newline at end of file +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" \ No newline at end of file From 03ddcf4709ad2856c709262d357ed48d60bc2560 Mon Sep 17 00:00:00 2001 From: idazucchi Date: Tue, 17 Feb 2026 13:57:32 +0000 Subject: [PATCH 24/64] Added echo_estimated_rvsp --- docs/jsonBrowser/module.md | 1 + json_schema/module/biomaterial/medical_tests.json | 7 +++++++ json_schema/update_log.csv | 4 ++-- 3 files changed, 10 insertions(+), 2 deletions(-) diff --git a/docs/jsonBrowser/module.md b/docs/jsonBrowser/module.md index ff10b81d9..49f7214f0 100644 --- a/docs/jsonBrowser/module.md +++ b/docs/jsonBrowser/module.md @@ -502,6 +502,7 @@ echo_aortic_regurgitation | Aortic regurgitation as measured by echocardiogram. 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 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 diff --git a/json_schema/module/biomaterial/medical_tests.json b/json_schema/module/biomaterial/medical_tests.json index 2df0a21b5..33023c319 100644 --- a/json_schema/module/biomaterial/medical_tests.json +++ b/json_schema/module/biomaterial/medical_tests.json @@ -374,6 +374,13 @@ "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", + "user_friendly": "Echo - Estimated RVSP", + "example": "25; 30; 35", + "bionetworks": ["heart"] + }, "mps_lvef": { "user_friendly": "Mps - LVEF", "description": "Left ventricular ejection fraction in percentage as measured by myocardial perfusion scintigraphy.", diff --git a/json_schema/update_log.csv b/json_schema/update_log.csv index ec437aaa8..326ddf626 100644 --- a/json_schema/update_log.csv +++ b/json_schema/update_log.csv @@ -1,3 +1,3 @@ Schema,Change type,Change message,Version,Date -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" \ No newline at end of file +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",, \ No newline at end of file From 1c0d7764e45662eb0da3c39d3a69984f32687d02 Mon Sep 17 00:00:00 2001 From: idazucchi Date: Tue, 17 Feb 2026 15:02:06 +0000 Subject: [PATCH 25/64] Added echo_lvedv --- docs/jsonBrowser/module.md | 1 + json_schema/module/biomaterial/medical_tests.json | 7 +++++++ json_schema/update_log.csv | 2 +- 3 files changed, 9 insertions(+), 1 deletion(-) diff --git a/docs/jsonBrowser/module.md b/docs/jsonBrowser/module.md index 49f7214f0..6dbc19d09 100644 --- a/docs/jsonBrowser/module.md +++ b/docs/jsonBrowser/module.md @@ -503,6 +503,7 @@ echo_mitral_regurgitation | Mitral regurgitation as measured by echocardiogram. 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 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 diff --git a/json_schema/module/biomaterial/medical_tests.json b/json_schema/module/biomaterial/medical_tests.json index 33023c319..0448ba2b1 100644 --- a/json_schema/module/biomaterial/medical_tests.json +++ b/json_schema/module/biomaterial/medical_tests.json @@ -381,6 +381,13 @@ "example": "25; 30; 35", "bionetworks": ["heart"] }, + "echo_lvedv": { + "description": "Left ventricular end-diastolic volume in ml as measured by echocardiogram.", + "type": "number", + "user_friendly": "Echo - LVEDV", + "example": "120; 110; 130", + "bionetworks": ["heart"] + }, "mps_lvef": { "user_friendly": "Mps - LVEF", "description": "Left ventricular ejection fraction in percentage as measured by myocardial perfusion scintigraphy.", diff --git a/json_schema/update_log.csv b/json_schema/update_log.csv index 326ddf626..9028e8004 100644 --- a/json_schema/update_log.csv +++ b/json_schema/update_log.csv @@ -1,3 +1,3 @@ Schema,Change type,Change message,Version,Date 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",, \ No newline at end of file +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",, \ No newline at end of file From b05a5786134d425a2f1a12b608593a60dbf44945 Mon Sep 17 00:00:00 2001 From: idazucchi Date: Tue, 17 Feb 2026 15:03:45 +0000 Subject: [PATCH 26/64] Added echo_lvedv_indexed --- docs/jsonBrowser/module.md | 1 + json_schema/module/biomaterial/medical_tests.json | 7 +++++++ json_schema/update_log.csv | 2 +- 3 files changed, 9 insertions(+), 1 deletion(-) diff --git a/docs/jsonBrowser/module.md b/docs/jsonBrowser/module.md index 6dbc19d09..5cc51f490 100644 --- a/docs/jsonBrowser/module.md +++ b/docs/jsonBrowser/module.md @@ -504,6 +504,7 @@ echo_mitral_stenosis | Mitral stenosis as measured by echocardiogram. | string | 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 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 diff --git a/json_schema/module/biomaterial/medical_tests.json b/json_schema/module/biomaterial/medical_tests.json index 0448ba2b1..3b8be2c0b 100644 --- a/json_schema/module/biomaterial/medical_tests.json +++ b/json_schema/module/biomaterial/medical_tests.json @@ -388,6 +388,13 @@ "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", + "user_friendly": "Echo - LVEDV Indexed", + "example": "65; 70; 60", + "bionetworks": ["heart"] + }, "mps_lvef": { "user_friendly": "Mps - LVEF", "description": "Left ventricular ejection fraction in percentage as measured by myocardial perfusion scintigraphy.", diff --git a/json_schema/update_log.csv b/json_schema/update_log.csv index 9028e8004..86dda9531 100644 --- a/json_schema/update_log.csv +++ b/json_schema/update_log.csv @@ -1,3 +1,3 @@ Schema,Change type,Change message,Version,Date 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",, \ No newline at end of file +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",, \ No newline at end of file From 37a826f770242efdf90f33bd7ea56d58fd683820 Mon Sep 17 00:00:00 2001 From: idazucchi Date: Tue, 17 Feb 2026 15:07:11 +0000 Subject: [PATCH 27/64] Added echo_lvesv --- docs/jsonBrowser/module.md | 3 ++- json_schema/module/biomaterial/medical_tests.json | 9 ++++++++- json_schema/update_log.csv | 2 +- 3 files changed, 11 insertions(+), 3 deletions(-) diff --git a/docs/jsonBrowser/module.md b/docs/jsonBrowser/module.md index 5cc51f490..63aac9cb5 100644 --- a/docs/jsonBrowser/module.md +++ b/docs/jsonBrowser/module.md @@ -504,7 +504,8 @@ echo_mitral_stenosis | Mitral stenosis as measured by echocardiogram. | string | 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_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 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 diff --git a/json_schema/module/biomaterial/medical_tests.json b/json_schema/module/biomaterial/medical_tests.json index 3b8be2c0b..6578a0817 100644 --- a/json_schema/module/biomaterial/medical_tests.json +++ b/json_schema/module/biomaterial/medical_tests.json @@ -389,12 +389,19 @@ "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", + "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", "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", + "user_friendly": "Echo - LVESV", + "example": "50; 45; 55", + "bionetworks": ["heart"] + }, "mps_lvef": { "user_friendly": "Mps - LVEF", "description": "Left ventricular ejection fraction in percentage as measured by myocardial perfusion scintigraphy.", diff --git a/json_schema/update_log.csv b/json_schema/update_log.csv index 86dda9531..685f53660 100644 --- a/json_schema/update_log.csv +++ b/json_schema/update_log.csv @@ -1,3 +1,3 @@ Schema,Change type,Change message,Version,Date 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",, \ No newline at end of file +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",, \ No newline at end of file From 18a2775af63da71b7e89288cf311a2016303d5f2 Mon Sep 17 00:00:00 2001 From: idazucchi Date: Tue, 17 Feb 2026 15:09:03 +0000 Subject: [PATCH 28/64] Added echo_lvesv_indexed --- docs/jsonBrowser/module.md | 1 + json_schema/module/biomaterial/medical_tests.json | 7 +++++++ json_schema/update_log.csv | 2 +- 3 files changed, 9 insertions(+), 1 deletion(-) diff --git a/docs/jsonBrowser/module.md b/docs/jsonBrowser/module.md index 63aac9cb5..62787c16d 100644 --- a/docs/jsonBrowser/module.md +++ b/docs/jsonBrowser/module.md @@ -506,6 +506,7 @@ echo_estimated_rvsp | Estimated right ventricular systolic pressure in mmHg as m 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 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 diff --git a/json_schema/module/biomaterial/medical_tests.json b/json_schema/module/biomaterial/medical_tests.json index 6578a0817..74795418c 100644 --- a/json_schema/module/biomaterial/medical_tests.json +++ b/json_schema/module/biomaterial/medical_tests.json @@ -402,6 +402,13 @@ "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", + "user_friendly": "Echo - LVESV Indexed", + "example": "25; 30; 28", + "bionetworks": ["heart"] + }, "mps_lvef": { "user_friendly": "Mps - LVEF", "description": "Left ventricular ejection fraction in percentage as measured by myocardial perfusion scintigraphy.", diff --git a/json_schema/update_log.csv b/json_schema/update_log.csv index 685f53660..51dcf5fb9 100644 --- a/json_schema/update_log.csv +++ b/json_schema/update_log.csv @@ -1,3 +1,3 @@ Schema,Change type,Change message,Version,Date 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",, \ No newline at end of file +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",, \ No newline at end of file From 9f01a0a25ec4f0104b1f6b38d95ed52defa08de2 Mon Sep 17 00:00:00 2001 From: idazucchi Date: Tue, 17 Feb 2026 15:12:13 +0000 Subject: [PATCH 29/64] Added echo_lvef --- docs/jsonBrowser/module.md | 1 + json_schema/module/biomaterial/medical_tests.json | 7 +++++++ json_schema/update_log.csv | 2 +- 3 files changed, 9 insertions(+), 1 deletion(-) diff --git a/docs/jsonBrowser/module.md b/docs/jsonBrowser/module.md index 62787c16d..92d242afe 100644 --- a/docs/jsonBrowser/module.md +++ b/docs/jsonBrowser/module.md @@ -507,6 +507,7 @@ echo_lvedv | Left ventricular end-diastolic volume in ml as measured by echocard 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 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 diff --git a/json_schema/module/biomaterial/medical_tests.json b/json_schema/module/biomaterial/medical_tests.json index 74795418c..a0e2cf74c 100644 --- a/json_schema/module/biomaterial/medical_tests.json +++ b/json_schema/module/biomaterial/medical_tests.json @@ -409,6 +409,13 @@ "example": "25; 30; 28", "bionetworks": ["heart"] }, + "echo_lvef": { + "description": "Left ventricular ejection fraction as measured by echocardiogram.", + "type": "number", + "user_friendly": "Echo - LVEF", + "example": "55; 60; 65", + "bionetworks": ["heart"] + }, "mps_lvef": { "user_friendly": "Mps - LVEF", "description": "Left ventricular ejection fraction in percentage as measured by myocardial perfusion scintigraphy.", diff --git a/json_schema/update_log.csv b/json_schema/update_log.csv index 51dcf5fb9..1543c40e4 100644 --- a/json_schema/update_log.csv +++ b/json_schema/update_log.csv @@ -1,3 +1,3 @@ Schema,Change type,Change message,Version,Date 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",, \ No newline at end of file +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",, \ No newline at end of file From 5e5940f21b2a61a8d7c0f18351143250e5df0785 Mon Sep 17 00:00:00 2001 From: idazucchi Date: Tue, 17 Feb 2026 15:14:08 +0000 Subject: [PATCH 30/64] Added echo_lv_mass --- docs/jsonBrowser/module.md | 1 + json_schema/module/biomaterial/medical_tests.json | 7 +++++++ json_schema/update_log.csv | 2 +- 3 files changed, 9 insertions(+), 1 deletion(-) diff --git a/docs/jsonBrowser/module.md b/docs/jsonBrowser/module.md index 92d242afe..b690a4166 100644 --- a/docs/jsonBrowser/module.md +++ b/docs/jsonBrowser/module.md @@ -508,6 +508,7 @@ echo_lvedv_indexed | Left ventricular end-diastolic volume indexed to body surfa 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 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 diff --git a/json_schema/module/biomaterial/medical_tests.json b/json_schema/module/biomaterial/medical_tests.json index a0e2cf74c..fbe9ce049 100644 --- a/json_schema/module/biomaterial/medical_tests.json +++ b/json_schema/module/biomaterial/medical_tests.json @@ -416,6 +416,13 @@ "example": "55; 60; 65", "bionetworks": ["heart"] }, + "echo_lv_mass": { + "description": "Left ventricular mass in grams as measured by echocardiogram.", + "type": "number", + "user_friendly": "Echo - LV Mass", + "example": "150; 160; 140", + "bionetworks": ["heart"] + }, "mps_lvef": { "user_friendly": "Mps - LVEF", "description": "Left ventricular ejection fraction in percentage as measured by myocardial perfusion scintigraphy.", diff --git a/json_schema/update_log.csv b/json_schema/update_log.csv index 1543c40e4..6e110c97b 100644 --- a/json_schema/update_log.csv +++ b/json_schema/update_log.csv @@ -1,3 +1,3 @@ Schema,Change type,Change message,Version,Date 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",, \ No newline at end of file +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",, \ No newline at end of file From e0423101a1b27b0c6d6994b246cd93284ed3d869 Mon Sep 17 00:00:00 2001 From: idazucchi Date: Tue, 17 Feb 2026 15:15:49 +0000 Subject: [PATCH 31/64] Added echo_lv_mass_indexed --- docs/jsonBrowser/module.md | 1 + json_schema/module/biomaterial/medical_tests.json | 7 +++++++ json_schema/update_log.csv | 2 +- 3 files changed, 9 insertions(+), 1 deletion(-) diff --git a/docs/jsonBrowser/module.md b/docs/jsonBrowser/module.md index b690a4166..2596fb3d6 100644 --- a/docs/jsonBrowser/module.md +++ b/docs/jsonBrowser/module.md @@ -509,6 +509,7 @@ echo_lvesv | Left ventricular end-systolic volume in ml as measured by echocardi 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 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 diff --git a/json_schema/module/biomaterial/medical_tests.json b/json_schema/module/biomaterial/medical_tests.json index fbe9ce049..5ce096e30 100644 --- a/json_schema/module/biomaterial/medical_tests.json +++ b/json_schema/module/biomaterial/medical_tests.json @@ -423,6 +423,13 @@ "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", + "user_friendly": "Echo - LV Mass Indexed", + "example": "75; 80; 70", + "bionetworks": ["heart"] + }, "mps_lvef": { "user_friendly": "Mps - LVEF", "description": "Left ventricular ejection fraction in percentage as measured by myocardial perfusion scintigraphy.", diff --git a/json_schema/update_log.csv b/json_schema/update_log.csv index 6e110c97b..d6514a237 100644 --- a/json_schema/update_log.csv +++ b/json_schema/update_log.csv @@ -1,3 +1,3 @@ Schema,Change type,Change message,Version,Date 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",, \ No newline at end of file +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",, \ No newline at end of file From d7d05db9aa3aa41cc1a4fac69580ffb9bbe30c60 Mon Sep 17 00:00:00 2001 From: idazucchi Date: Tue, 17 Feb 2026 15:21:58 +0000 Subject: [PATCH 32/64] Added echo_rv_fac --- docs/jsonBrowser/module.md | 1 + json_schema/module/biomaterial/medical_tests.json | 7 +++++++ json_schema/update_log.csv | 2 +- 3 files changed, 9 insertions(+), 1 deletion(-) diff --git a/docs/jsonBrowser/module.md b/docs/jsonBrowser/module.md index 2596fb3d6..aec50156c 100644 --- a/docs/jsonBrowser/module.md +++ b/docs/jsonBrowser/module.md @@ -510,6 +510,7 @@ echo_lvesv_indexed | Left ventricular end-systolic volume indexed to body surfac 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 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 diff --git a/json_schema/module/biomaterial/medical_tests.json b/json_schema/module/biomaterial/medical_tests.json index 5ce096e30..41c074988 100644 --- a/json_schema/module/biomaterial/medical_tests.json +++ b/json_schema/module/biomaterial/medical_tests.json @@ -430,6 +430,13 @@ "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", + "user_friendly": "Echo - RV FAC", + "example": "40; 45; 50", + "bionetworks": ["heart"] + }, "mps_lvef": { "user_friendly": "Mps - LVEF", "description": "Left ventricular ejection fraction in percentage as measured by myocardial perfusion scintigraphy.", diff --git a/json_schema/update_log.csv b/json_schema/update_log.csv index d6514a237..f5847e701 100644 --- a/json_schema/update_log.csv +++ b/json_schema/update_log.csv @@ -1,3 +1,3 @@ Schema,Change type,Change message,Version,Date 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",, \ No newline at end of file +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",, \ No newline at end of file From 345d60af1e977bb1eee9a02ee2d062f105feff6f Mon Sep 17 00:00:00 2001 From: idazucchi Date: Tue, 17 Feb 2026 15:23:58 +0000 Subject: [PATCH 33/64] Added echo_tapse --- docs/jsonBrowser/module.md | 1 + json_schema/module/biomaterial/medical_tests.json | 7 +++++++ json_schema/update_log.csv | 2 +- 3 files changed, 9 insertions(+), 1 deletion(-) diff --git a/docs/jsonBrowser/module.md b/docs/jsonBrowser/module.md index aec50156c..1279258d1 100644 --- a/docs/jsonBrowser/module.md +++ b/docs/jsonBrowser/module.md @@ -511,6 +511,7 @@ echo_lvef | Left ventricular ejection fraction as measured by echocardiogram. | 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 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 diff --git a/json_schema/module/biomaterial/medical_tests.json b/json_schema/module/biomaterial/medical_tests.json index 41c074988..f136fbe42 100644 --- a/json_schema/module/biomaterial/medical_tests.json +++ b/json_schema/module/biomaterial/medical_tests.json @@ -437,6 +437,13 @@ "example": "40; 45; 50", "bionetworks": ["heart"] }, + "echo_tapse": { + "description": "Tricuspid annular plane systolic excursion (TAPSE) in mm as measured by echocardiogram.", + "type": "number", + "user_friendly": "Echo - TAPSE", + "example": "20; 22; 18", + "bionetworks": ["heart"] + }, "mps_lvef": { "user_friendly": "Mps - LVEF", "description": "Left ventricular ejection fraction in percentage as measured by myocardial perfusion scintigraphy.", diff --git a/json_schema/update_log.csv b/json_schema/update_log.csv index f5847e701..ce20fbc33 100644 --- a/json_schema/update_log.csv +++ b/json_schema/update_log.csv @@ -1,3 +1,3 @@ Schema,Change type,Change message,Version,Date 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",, \ No newline at end of file +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",, \ No newline at end of file From d73e5c7ed103d3384ba3a7647292e685b4b10007 Mon Sep 17 00:00:00 2001 From: idazucchi Date: Tue, 17 Feb 2026 15:53:25 +0000 Subject: [PATCH 34/64] Added echo_lv_septum_thickness --- docs/jsonBrowser/module.md | 1 + json_schema/module/biomaterial/medical_tests.json | 7 +++++++ json_schema/update_log.csv | 2 +- 3 files changed, 9 insertions(+), 1 deletion(-) diff --git a/docs/jsonBrowser/module.md b/docs/jsonBrowser/module.md index 1279258d1..615d0ffe2 100644 --- a/docs/jsonBrowser/module.md +++ b/docs/jsonBrowser/module.md @@ -512,6 +512,7 @@ echo_lv_mass | Left ventricular mass in grams as measured by echocardiogram. | n 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 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 diff --git a/json_schema/module/biomaterial/medical_tests.json b/json_schema/module/biomaterial/medical_tests.json index f136fbe42..d400df669 100644 --- a/json_schema/module/biomaterial/medical_tests.json +++ b/json_schema/module/biomaterial/medical_tests.json @@ -444,6 +444,13 @@ "example": "20; 22; 18", "bionetworks": ["heart"] }, + "echo_lv_septum_thickness": { + "description": "Left ventricular septum thickness in mm as measured by echocardiogram.", + "type": "number", + "user_friendly": "Echo - LV Septum Thickness", + "example": "9; 10; 11", + "bionetworks": ["heart"] + }, "mps_lvef": { "user_friendly": "Mps - LVEF", "description": "Left ventricular ejection fraction in percentage as measured by myocardial perfusion scintigraphy.", diff --git a/json_schema/update_log.csv b/json_schema/update_log.csv index ce20fbc33..287175c51 100644 --- a/json_schema/update_log.csv +++ b/json_schema/update_log.csv @@ -1,3 +1,3 @@ Schema,Change type,Change message,Version,Date 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",, \ No newline at end of file +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",, \ No newline at end of file From 1efa360324edf6cf059c9c8fea8c8dac16168314 Mon Sep 17 00:00:00 2001 From: idazucchi Date: Tue, 17 Feb 2026 15:54:44 +0000 Subject: [PATCH 35/64] Added echo_pw_thickness --- docs/jsonBrowser/module.md | 1 + json_schema/module/biomaterial/medical_tests.json | 7 +++++++ json_schema/update_log.csv | 2 +- 3 files changed, 9 insertions(+), 1 deletion(-) diff --git a/docs/jsonBrowser/module.md b/docs/jsonBrowser/module.md index 615d0ffe2..db602cd97 100644 --- a/docs/jsonBrowser/module.md +++ b/docs/jsonBrowser/module.md @@ -513,6 +513,7 @@ echo_lv_mass_indexed | Left ventricular mass indexed to body surface area in g/m 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 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 diff --git a/json_schema/module/biomaterial/medical_tests.json b/json_schema/module/biomaterial/medical_tests.json index d400df669..027dfcef5 100644 --- a/json_schema/module/biomaterial/medical_tests.json +++ b/json_schema/module/biomaterial/medical_tests.json @@ -451,6 +451,13 @@ "example": "9; 10; 11", "bionetworks": ["heart"] }, + "echo_pw_thickness": { + "description": "Basal posterior LV wall thickness in mm as measured by echocardiogram.", + "type": "number", + "user_friendly": "Echo - PW Thickness", + "example": "9; 10; 11", + "bionetworks": ["heart"] + }, "mps_lvef": { "user_friendly": "Mps - LVEF", "description": "Left ventricular ejection fraction in percentage as measured by myocardial perfusion scintigraphy.", diff --git a/json_schema/update_log.csv b/json_schema/update_log.csv index 287175c51..e32210cf6 100644 --- a/json_schema/update_log.csv +++ b/json_schema/update_log.csv @@ -1,3 +1,3 @@ Schema,Change type,Change message,Version,Date 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",, \ No newline at end of file +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",, \ No newline at end of file From aeba8a099be5ac550822029d0173a8154be4659e Mon Sep 17 00:00:00 2001 From: idazucchi Date: Tue, 17 Feb 2026 15:56:30 +0000 Subject: [PATCH 36/64] Added echo_la_dimension --- docs/jsonBrowser/module.md | 1 + json_schema/module/biomaterial/medical_tests.json | 7 +++++++ json_schema/update_log.csv | 2 +- 3 files changed, 9 insertions(+), 1 deletion(-) diff --git a/docs/jsonBrowser/module.md b/docs/jsonBrowser/module.md index db602cd97..a89ab6da0 100644 --- a/docs/jsonBrowser/module.md +++ b/docs/jsonBrowser/module.md @@ -514,6 +514,7 @@ echo_rv_fac | Right Ventricular Fractional Area Change (RV FAC) in percentage as 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 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 diff --git a/json_schema/module/biomaterial/medical_tests.json b/json_schema/module/biomaterial/medical_tests.json index 027dfcef5..f3bd24abc 100644 --- a/json_schema/module/biomaterial/medical_tests.json +++ b/json_schema/module/biomaterial/medical_tests.json @@ -458,6 +458,13 @@ "example": "9; 10; 11", "bionetworks": ["heart"] }, + "echo_la_dimension": { + "description": "Left atrial diameter in PLAX view in mm as measured by echocardiogram.", + "type": "number", + "user_friendly": "Echo - LA Dimension", + "example": "38; 36; 40", + "bionetworks": ["heart"] + }, "mps_lvef": { "user_friendly": "Mps - LVEF", "description": "Left ventricular ejection fraction in percentage as measured by myocardial perfusion scintigraphy.", diff --git a/json_schema/update_log.csv b/json_schema/update_log.csv index e32210cf6..e1b9d37f9 100644 --- a/json_schema/update_log.csv +++ b/json_schema/update_log.csv @@ -1,3 +1,3 @@ Schema,Change type,Change message,Version,Date 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",, \ No newline at end of file +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",, \ No newline at end of file From d811bc561387a374349f031029a3cce884a9c278 Mon Sep 17 00:00:00 2001 From: idazucchi Date: Tue, 17 Feb 2026 15:58:14 +0000 Subject: [PATCH 37/64] Added echo_lav_indexed --- docs/jsonBrowser/module.md | 1 + json_schema/module/biomaterial/medical_tests.json | 7 +++++++ json_schema/update_log.csv | 2 +- 3 files changed, 9 insertions(+), 1 deletion(-) diff --git a/docs/jsonBrowser/module.md b/docs/jsonBrowser/module.md index a89ab6da0..5b4ff18e4 100644 --- a/docs/jsonBrowser/module.md +++ b/docs/jsonBrowser/module.md @@ -515,6 +515,7 @@ echo_tapse | Tricuspid annular plane systolic excursion (TAPSE) in mm as measure 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 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 diff --git a/json_schema/module/biomaterial/medical_tests.json b/json_schema/module/biomaterial/medical_tests.json index f3bd24abc..7f4fac577 100644 --- a/json_schema/module/biomaterial/medical_tests.json +++ b/json_schema/module/biomaterial/medical_tests.json @@ -465,6 +465,13 @@ "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", + "user_friendly": "Echo - LAV Indexed", + "example": "28; 30; 32", + "bionetworks": ["heart"] + }, "mps_lvef": { "user_friendly": "Mps - LVEF", "description": "Left ventricular ejection fraction in percentage as measured by myocardial perfusion scintigraphy.", diff --git a/json_schema/update_log.csv b/json_schema/update_log.csv index e1b9d37f9..e46ee17d2 100644 --- a/json_schema/update_log.csv +++ b/json_schema/update_log.csv @@ -1,3 +1,3 @@ Schema,Change type,Change message,Version,Date 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",, \ No newline at end of file +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",, \ No newline at end of file From 554a6dab76d431d2f7de05d386cab4b5b47a820b Mon Sep 17 00:00:00 2001 From: idazucchi Date: Tue, 17 Feb 2026 16:00:06 +0000 Subject: [PATCH 38/64] Added echo_time_offset --- docs/jsonBrowser/module.md | 1 + json_schema/module/biomaterial/medical_tests.json | 7 +++++++ json_schema/update_log.csv | 2 +- 3 files changed, 9 insertions(+), 1 deletion(-) diff --git a/docs/jsonBrowser/module.md b/docs/jsonBrowser/module.md index 5b4ff18e4..607797b43 100644 --- a/docs/jsonBrowser/module.md +++ b/docs/jsonBrowser/module.md @@ -516,6 +516,7 @@ echo_lv_septum_thickness | Left ventricular septum thickness in mm as measured b 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 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 diff --git a/json_schema/module/biomaterial/medical_tests.json b/json_schema/module/biomaterial/medical_tests.json index 7f4fac577..757223725 100644 --- a/json_schema/module/biomaterial/medical_tests.json +++ b/json_schema/module/biomaterial/medical_tests.json @@ -472,6 +472,13 @@ "example": "28; 30; 32", "bionetworks": ["heart"] }, + "echo_time_offset": { + "description": "Time between the test and the collection of the sample, in days.", + "type": "number", + "user_friendly": "Echo - 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.", diff --git a/json_schema/update_log.csv b/json_schema/update_log.csv index e46ee17d2..6b4597df5 100644 --- a/json_schema/update_log.csv +++ b/json_schema/update_log.csv @@ -1,3 +1,3 @@ Schema,Change type,Change message,Version,Date 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",, \ No newline at end of file +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",, \ No newline at end of file From 741e1878ae9027322d273a50ddfd0cf42a3f0b81 Mon Sep 17 00:00:00 2001 From: idazucchi Date: Tue, 17 Feb 2026 16:06:47 +0000 Subject: [PATCH 39/64] Added mri_lvedv --- docs/jsonBrowser/module.md | 1 + json_schema/module/biomaterial/medical_tests.json | 7 +++++++ json_schema/update_log.csv | 2 +- 3 files changed, 9 insertions(+), 1 deletion(-) diff --git a/docs/jsonBrowser/module.md b/docs/jsonBrowser/module.md index 607797b43..87c905f22 100644 --- a/docs/jsonBrowser/module.md +++ b/docs/jsonBrowser/module.md @@ -517,6 +517,7 @@ echo_pw_thickness | Basal posterior LV wall thickness in mm as measured by echoc 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 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 diff --git a/json_schema/module/biomaterial/medical_tests.json b/json_schema/module/biomaterial/medical_tests.json index 757223725..9f6c115c0 100644 --- a/json_schema/module/biomaterial/medical_tests.json +++ b/json_schema/module/biomaterial/medical_tests.json @@ -479,6 +479,13 @@ "example": "4; 20; 58", "bionetworks": ["heart"] }, + "mri_lvedv": { + "description": "Left ventricular end-diastolic volume in ml as measured by MRI.", + "type": "number", + "user_friendly": "Mri - LVEDV", + "example": "140; 150; 130", + "bionetworks": ["heart"] + }, "mps_lvef": { "user_friendly": "Mps - LVEF", "description": "Left ventricular ejection fraction in percentage as measured by myocardial perfusion scintigraphy.", diff --git a/json_schema/update_log.csv b/json_schema/update_log.csv index 6b4597df5..98145bf51 100644 --- a/json_schema/update_log.csv +++ b/json_schema/update_log.csv @@ -1,3 +1,3 @@ Schema,Change type,Change message,Version,Date 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",, \ No newline at end of file +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",, \ No newline at end of file From e24679f65a33e780fc8ca90cc0c35fcecc263c66 Mon Sep 17 00:00:00 2001 From: idazucchi Date: Tue, 17 Feb 2026 16:08:56 +0000 Subject: [PATCH 40/64] Added mri_lvedv_indexed --- docs/jsonBrowser/module.md | 1 + json_schema/module/biomaterial/medical_tests.json | 7 +++++++ json_schema/update_log.csv | 2 +- 3 files changed, 9 insertions(+), 1 deletion(-) diff --git a/docs/jsonBrowser/module.md b/docs/jsonBrowser/module.md index 87c905f22..e3df5e36a 100644 --- a/docs/jsonBrowser/module.md +++ b/docs/jsonBrowser/module.md @@ -518,6 +518,7 @@ echo_la_dimension | Left atrial diameter in PLAX view in mm as measured by echoc 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 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 diff --git a/json_schema/module/biomaterial/medical_tests.json b/json_schema/module/biomaterial/medical_tests.json index 9f6c115c0..c2cc4d998 100644 --- a/json_schema/module/biomaterial/medical_tests.json +++ b/json_schema/module/biomaterial/medical_tests.json @@ -486,6 +486,13 @@ "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", + "user_friendly": "Mri - LVEDV Indexed", + "example": "75; 70; 80", + "bionetworks": ["heart"] + }, "mps_lvef": { "user_friendly": "Mps - LVEF", "description": "Left ventricular ejection fraction in percentage as measured by myocardial perfusion scintigraphy.", diff --git a/json_schema/update_log.csv b/json_schema/update_log.csv index 98145bf51..7569d9ee2 100644 --- a/json_schema/update_log.csv +++ b/json_schema/update_log.csv @@ -1,3 +1,3 @@ Schema,Change type,Change message,Version,Date 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",, \ No newline at end of file +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",, \ No newline at end of file From 48db7a8318d99e4856491fbf2a4b01c25bc25c02 Mon Sep 17 00:00:00 2001 From: idazucchi Date: Tue, 17 Feb 2026 16:10:34 +0000 Subject: [PATCH 41/64] Added mri_lvesv --- docs/jsonBrowser/module.md | 1 + json_schema/module/biomaterial/medical_tests.json | 7 +++++++ json_schema/update_log.csv | 2 +- 3 files changed, 9 insertions(+), 1 deletion(-) diff --git a/docs/jsonBrowser/module.md b/docs/jsonBrowser/module.md index e3df5e36a..ef590b73a 100644 --- a/docs/jsonBrowser/module.md +++ b/docs/jsonBrowser/module.md @@ -519,6 +519,7 @@ echo_lav_indexed | Left atrial volume indexed to body surface area in ml/m^2 (le 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 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 diff --git a/json_schema/module/biomaterial/medical_tests.json b/json_schema/module/biomaterial/medical_tests.json index c2cc4d998..eca3987c0 100644 --- a/json_schema/module/biomaterial/medical_tests.json +++ b/json_schema/module/biomaterial/medical_tests.json @@ -493,6 +493,13 @@ "example": "75; 70; 80", "bionetworks": ["heart"] }, + "mri_lvesv": { + "description": "Left ventricular end-systolic volume in ml as measured by MRI.", + "type": "number", + "user_friendly": "Mri - LVESV", + "example": "60; 55; 65", + "bionetworks": ["heart"] + }, "mps_lvef": { "user_friendly": "Mps - LVEF", "description": "Left ventricular ejection fraction in percentage as measured by myocardial perfusion scintigraphy.", diff --git a/json_schema/update_log.csv b/json_schema/update_log.csv index 7569d9ee2..25771c0f5 100644 --- a/json_schema/update_log.csv +++ b/json_schema/update_log.csv @@ -1,3 +1,3 @@ Schema,Change type,Change message,Version,Date 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",, \ No newline at end of file +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",, \ No newline at end of file From f923e2e72c7f93e76487d9fcf6a52bc9d1ee3def Mon Sep 17 00:00:00 2001 From: idazucchi Date: Tue, 17 Feb 2026 16:12:35 +0000 Subject: [PATCH 42/64] Added mri_lvesv_indexed --- docs/jsonBrowser/module.md | 1 + json_schema/module/biomaterial/medical_tests.json | 7 +++++++ json_schema/update_log.csv | 2 +- 3 files changed, 9 insertions(+), 1 deletion(-) diff --git a/docs/jsonBrowser/module.md b/docs/jsonBrowser/module.md index ef590b73a..173103b91 100644 --- a/docs/jsonBrowser/module.md +++ b/docs/jsonBrowser/module.md @@ -520,6 +520,7 @@ echo_time_offset | Time between the test and the collection of the sample, in da 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 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 diff --git a/json_schema/module/biomaterial/medical_tests.json b/json_schema/module/biomaterial/medical_tests.json index eca3987c0..e5c53b34e 100644 --- a/json_schema/module/biomaterial/medical_tests.json +++ b/json_schema/module/biomaterial/medical_tests.json @@ -500,6 +500,13 @@ "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", + "user_friendly": "Mri - LVESV Indexed", + "example": "30; 28; 32", + "bionetworks": ["heart"] + }, "mps_lvef": { "user_friendly": "Mps - LVEF", "description": "Left ventricular ejection fraction in percentage as measured by myocardial perfusion scintigraphy.", diff --git a/json_schema/update_log.csv b/json_schema/update_log.csv index 25771c0f5..017c7bfa3 100644 --- a/json_schema/update_log.csv +++ b/json_schema/update_log.csv @@ -1,3 +1,3 @@ Schema,Change type,Change message,Version,Date 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",, \ No newline at end of file +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",, \ No newline at end of file From 3c0ec1831d98d735638d702208a598bbd7543d72 Mon Sep 17 00:00:00 2001 From: idazucchi Date: Tue, 17 Feb 2026 16:15:19 +0000 Subject: [PATCH 43/64] Added mri_lvef --- docs/jsonBrowser/module.md | 1 + json_schema/module/biomaterial/medical_tests.json | 7 +++++++ json_schema/update_log.csv | 2 +- 3 files changed, 9 insertions(+), 1 deletion(-) diff --git a/docs/jsonBrowser/module.md b/docs/jsonBrowser/module.md index 173103b91..2615d479c 100644 --- a/docs/jsonBrowser/module.md +++ b/docs/jsonBrowser/module.md @@ -521,6 +521,7 @@ mri_lvedv | Left ventricular end-diastolic volume in ml as measured by MRI. | nu 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 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 diff --git a/json_schema/module/biomaterial/medical_tests.json b/json_schema/module/biomaterial/medical_tests.json index e5c53b34e..38171a830 100644 --- a/json_schema/module/biomaterial/medical_tests.json +++ b/json_schema/module/biomaterial/medical_tests.json @@ -507,6 +507,13 @@ "example": "30; 28; 32", "bionetworks": ["heart"] }, + "mri_lvef": { + "description": "Left ventricular ejection fraction measured by MRI.", + "type": "number", + "user_friendly": "Mri - LVEF", + "example": "55; 60; 58", + "bionetworks": ["heart"] + }, "mps_lvef": { "user_friendly": "Mps - LVEF", "description": "Left ventricular ejection fraction in percentage as measured by myocardial perfusion scintigraphy.", diff --git a/json_schema/update_log.csv b/json_schema/update_log.csv index 017c7bfa3..626ce64bf 100644 --- a/json_schema/update_log.csv +++ b/json_schema/update_log.csv @@ -1,3 +1,3 @@ Schema,Change type,Change message,Version,Date 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",, \ No newline at end of file +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",, \ No newline at end of file From f14ebf2350a9d44dbee275d36a127035d52f4b1a Mon Sep 17 00:00:00 2001 From: idazucchi Date: Tue, 17 Feb 2026 16:17:09 +0000 Subject: [PATCH 44/64] Added mri_lv_mass --- docs/jsonBrowser/module.md | 1 + json_schema/module/biomaterial/medical_tests.json | 7 +++++++ json_schema/update_log.csv | 2 +- 3 files changed, 9 insertions(+), 1 deletion(-) diff --git a/docs/jsonBrowser/module.md b/docs/jsonBrowser/module.md index 2615d479c..e0d3f1fb4 100644 --- a/docs/jsonBrowser/module.md +++ b/docs/jsonBrowser/module.md @@ -522,6 +522,7 @@ mri_lvedv_indexed | Left ventricular end-diastolic volume indexed to body surfac 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 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 diff --git a/json_schema/module/biomaterial/medical_tests.json b/json_schema/module/biomaterial/medical_tests.json index 38171a830..1ccafebd0 100644 --- a/json_schema/module/biomaterial/medical_tests.json +++ b/json_schema/module/biomaterial/medical_tests.json @@ -514,6 +514,13 @@ "example": "55; 60; 58", "bionetworks": ["heart"] }, + "mri_lv_mass": { + "description": "Left ventricular mass in grams as measured by MRI.", + "type": "number", + "user_friendly": "Mri - LV Mass", + "example": "130; 120; 140", + "bionetworks": ["heart"] + }, "mps_lvef": { "user_friendly": "Mps - LVEF", "description": "Left ventricular ejection fraction in percentage as measured by myocardial perfusion scintigraphy.", diff --git a/json_schema/update_log.csv b/json_schema/update_log.csv index 626ce64bf..822f16773 100644 --- a/json_schema/update_log.csv +++ b/json_schema/update_log.csv @@ -1,3 +1,3 @@ Schema,Change type,Change message,Version,Date 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",, \ No newline at end of file +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",, \ No newline at end of file From 5be586ec8aa10d7ee97a3911f8501c3ce2154663 Mon Sep 17 00:00:00 2001 From: idazucchi Date: Tue, 17 Feb 2026 16:19:14 +0000 Subject: [PATCH 45/64] Added mri_lv_mass_indexed --- docs/jsonBrowser/module.md | 1 + json_schema/module/biomaterial/medical_tests.json | 7 +++++++ json_schema/update_log.csv | 2 +- 3 files changed, 9 insertions(+), 1 deletion(-) diff --git a/docs/jsonBrowser/module.md b/docs/jsonBrowser/module.md index e0d3f1fb4..c7bc2366a 100644 --- a/docs/jsonBrowser/module.md +++ b/docs/jsonBrowser/module.md @@ -523,6 +523,7 @@ mri_lvesv | Left ventricular end-systolic volume in ml as measured by MRI. | num 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 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 diff --git a/json_schema/module/biomaterial/medical_tests.json b/json_schema/module/biomaterial/medical_tests.json index 1ccafebd0..7287484e2 100644 --- a/json_schema/module/biomaterial/medical_tests.json +++ b/json_schema/module/biomaterial/medical_tests.json @@ -521,6 +521,13 @@ "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", + "user_friendly": "Mri - LV Mass Indexed", + "example": "65; 60; 70", + "bionetworks": ["heart"] + }, "mps_lvef": { "user_friendly": "Mps - LVEF", "description": "Left ventricular ejection fraction in percentage as measured by myocardial perfusion scintigraphy.", diff --git a/json_schema/update_log.csv b/json_schema/update_log.csv index 822f16773..e1aa62691 100644 --- a/json_schema/update_log.csv +++ b/json_schema/update_log.csv @@ -1,3 +1,3 @@ Schema,Change type,Change message,Version,Date 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",, \ No newline at end of file +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",, \ No newline at end of file From d57232a0a782b966ac1e48bba02396f495e0d1d3 Mon Sep 17 00:00:00 2001 From: idazucchi Date: Tue, 17 Feb 2026 16:22:42 +0000 Subject: [PATCH 46/64] Added mri_rv_ejection_fraction --- docs/jsonBrowser/module.md | 1 + json_schema/module/biomaterial/medical_tests.json | 7 +++++++ json_schema/update_log.csv | 2 +- 3 files changed, 9 insertions(+), 1 deletion(-) diff --git a/docs/jsonBrowser/module.md b/docs/jsonBrowser/module.md index c7bc2366a..165462d39 100644 --- a/docs/jsonBrowser/module.md +++ b/docs/jsonBrowser/module.md @@ -524,6 +524,7 @@ mri_lvesv_indexed | Left ventricular end-systolic volume indexed to body surface 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 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 diff --git a/json_schema/module/biomaterial/medical_tests.json b/json_schema/module/biomaterial/medical_tests.json index 7287484e2..6f620c197 100644 --- a/json_schema/module/biomaterial/medical_tests.json +++ b/json_schema/module/biomaterial/medical_tests.json @@ -528,6 +528,13 @@ "example": "65; 60; 70", "bionetworks": ["heart"] }, + "mri_rv_ejection_fraction": { + "description": "Right ventricular ejection fraction in percentage as measured by MRI.", + "type": "number", + "user_friendly": "Mri - RV Ejection Fraction", + "example": "50; 55; 60", + "bionetworks": ["heart"] + }, "mps_lvef": { "user_friendly": "Mps - LVEF", "description": "Left ventricular ejection fraction in percentage as measured by myocardial perfusion scintigraphy.", diff --git a/json_schema/update_log.csv b/json_schema/update_log.csv index e1aa62691..54bfaeb95 100644 --- a/json_schema/update_log.csv +++ b/json_schema/update_log.csv @@ -1,3 +1,3 @@ Schema,Change type,Change message,Version,Date 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",, \ No newline at end of file +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",, \ No newline at end of file From fe27d9fa6dad3afa7e3ddad6fef24bef8c6a4fed Mon Sep 17 00:00:00 2001 From: idazucchi Date: Tue, 17 Feb 2026 16:26:13 +0000 Subject: [PATCH 47/64] Added mri_mid_wall_lge --- docs/jsonBrowser/module.md | 1 + json_schema/module/biomaterial/medical_tests.json | 7 +++++++ json_schema/update_log.csv | 2 +- 3 files changed, 9 insertions(+), 1 deletion(-) diff --git a/docs/jsonBrowser/module.md b/docs/jsonBrowser/module.md index 165462d39..026a3596f 100644 --- a/docs/jsonBrowser/module.md +++ b/docs/jsonBrowser/module.md @@ -525,6 +525,7 @@ mri_lvef | Left ventricular ejection fraction measured by MRI. | number | no | 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. 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 diff --git a/json_schema/module/biomaterial/medical_tests.json b/json_schema/module/biomaterial/medical_tests.json index 6f620c197..dc3ae15e4 100644 --- a/json_schema/module/biomaterial/medical_tests.json +++ b/json_schema/module/biomaterial/medical_tests.json @@ -535,6 +535,13 @@ "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"] + }, "mps_lvef": { "user_friendly": "Mps - LVEF", "description": "Left ventricular ejection fraction in percentage as measured by myocardial perfusion scintigraphy.", diff --git a/json_schema/update_log.csv b/json_schema/update_log.csv index 54bfaeb95..827883ec3 100644 --- a/json_schema/update_log.csv +++ b/json_schema/update_log.csv @@ -1,3 +1,3 @@ Schema,Change type,Change message,Version,Date 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",, \ No newline at end of file +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",, \ No newline at end of file From 6ff3fca43bc68aa56f6c314d4c7b6bc332653d3b Mon Sep 17 00:00:00 2001 From: idazucchi Date: Tue, 17 Feb 2026 17:03:58 +0000 Subject: [PATCH 48/64] Added mri_epicardial_lge --- docs/jsonBrowser/module.md | 1 + json_schema/module/biomaterial/medical_tests.json | 7 +++++++ json_schema/update_log.csv | 2 +- 3 files changed, 9 insertions(+), 1 deletion(-) diff --git a/docs/jsonBrowser/module.md b/docs/jsonBrowser/module.md index 026a3596f..8378dcea2 100644 --- a/docs/jsonBrowser/module.md +++ b/docs/jsonBrowser/module.md @@ -526,6 +526,7 @@ mri_lv_mass | Left ventricular mass in grams as measured by MRI. | number | no | 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. 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 diff --git a/json_schema/module/biomaterial/medical_tests.json b/json_schema/module/biomaterial/medical_tests.json index dc3ae15e4..34b5a634a 100644 --- a/json_schema/module/biomaterial/medical_tests.json +++ b/json_schema/module/biomaterial/medical_tests.json @@ -542,6 +542,13 @@ "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"] + }, "mps_lvef": { "user_friendly": "Mps - LVEF", "description": "Left ventricular ejection fraction in percentage as measured by myocardial perfusion scintigraphy.", diff --git a/json_schema/update_log.csv b/json_schema/update_log.csv index 827883ec3..61bd75b50 100644 --- a/json_schema/update_log.csv +++ b/json_schema/update_log.csv @@ -1,3 +1,3 @@ Schema,Change type,Change message,Version,Date 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",, \ No newline at end of file +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",, \ No newline at end of file From d1eb72bc8181708ae764dcd9179e71a0b2566ff1 Mon Sep 17 00:00:00 2001 From: idazucchi Date: Tue, 17 Feb 2026 17:06:31 +0000 Subject: [PATCH 49/64] Added mri_infarct_pattern_lge --- docs/jsonBrowser/module.md | 1 + json_schema/module/biomaterial/medical_tests.json | 7 +++++++ json_schema/update_log.csv | 2 +- 3 files changed, 9 insertions(+), 1 deletion(-) diff --git a/docs/jsonBrowser/module.md b/docs/jsonBrowser/module.md index 8378dcea2..61aba126e 100644 --- a/docs/jsonBrowser/module.md +++ b/docs/jsonBrowser/module.md @@ -527,6 +527,7 @@ mri_lv_mass_indexed | Left ventricular mass indexed to body surface area in g/m^ 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. 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 diff --git a/json_schema/module/biomaterial/medical_tests.json b/json_schema/module/biomaterial/medical_tests.json index 34b5a634a..1d02aeb12 100644 --- a/json_schema/module/biomaterial/medical_tests.json +++ b/json_schema/module/biomaterial/medical_tests.json @@ -549,6 +549,13 @@ "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"] + }, "mps_lvef": { "user_friendly": "Mps - LVEF", "description": "Left ventricular ejection fraction in percentage as measured by myocardial perfusion scintigraphy.", diff --git a/json_schema/update_log.csv b/json_schema/update_log.csv index 61bd75b50..f2d0fcbee 100644 --- a/json_schema/update_log.csv +++ b/json_schema/update_log.csv @@ -1,3 +1,3 @@ Schema,Change type,Change message,Version,Date 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",, \ No newline at end of file +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",, \ No newline at end of file From b2614dd4c8780e9c3da218c46c3728fc6a027ea6 Mon Sep 17 00:00:00 2001 From: idazucchi Date: Tue, 17 Feb 2026 17:07:42 +0000 Subject: [PATCH 50/64] Added mri_myocardial_oedema --- docs/jsonBrowser/module.md | 1 + json_schema/module/biomaterial/medical_tests.json | 7 +++++++ json_schema/update_log.csv | 2 +- 3 files changed, 9 insertions(+), 1 deletion(-) diff --git a/docs/jsonBrowser/module.md b/docs/jsonBrowser/module.md index 61aba126e..88531fe05 100644 --- a/docs/jsonBrowser/module.md +++ b/docs/jsonBrowser/module.md @@ -528,6 +528,7 @@ mri_rv_ejection_fraction | Right ventricular ejection fraction in percentage as 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. 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 diff --git a/json_schema/module/biomaterial/medical_tests.json b/json_schema/module/biomaterial/medical_tests.json index 1d02aeb12..6b21d4649 100644 --- a/json_schema/module/biomaterial/medical_tests.json +++ b/json_schema/module/biomaterial/medical_tests.json @@ -556,6 +556,13 @@ "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"] + }, "mps_lvef": { "user_friendly": "Mps - LVEF", "description": "Left ventricular ejection fraction in percentage as measured by myocardial perfusion scintigraphy.", diff --git a/json_schema/update_log.csv b/json_schema/update_log.csv index f2d0fcbee..1c40ce03d 100644 --- a/json_schema/update_log.csv +++ b/json_schema/update_log.csv @@ -1,3 +1,3 @@ Schema,Change type,Change message,Version,Date 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",, \ No newline at end of file +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",, \ No newline at end of file From 4f84a2d3506dceec9f401ba05daa41b0dd1a26ae Mon Sep 17 00:00:00 2001 From: idazucchi Date: Tue, 17 Feb 2026 17:08:56 +0000 Subject: [PATCH 51/64] Added mri_time_offset --- docs/jsonBrowser/module.md | 1 + json_schema/module/biomaterial/medical_tests.json | 7 +++++++ json_schema/update_log.csv | 2 +- 3 files changed, 9 insertions(+), 1 deletion(-) diff --git a/docs/jsonBrowser/module.md b/docs/jsonBrowser/module.md index 88531fe05..c772f5a15 100644 --- a/docs/jsonBrowser/module.md +++ b/docs/jsonBrowser/module.md @@ -529,6 +529,7 @@ mri_mid_wall_lge | Late gadolinium enhancement (mid wall) as measured by MRI. | 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 diff --git a/json_schema/module/biomaterial/medical_tests.json b/json_schema/module/biomaterial/medical_tests.json index 6b21d4649..a91e8f1bc 100644 --- a/json_schema/module/biomaterial/medical_tests.json +++ b/json_schema/module/biomaterial/medical_tests.json @@ -563,6 +563,13 @@ "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", + "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.", diff --git a/json_schema/update_log.csv b/json_schema/update_log.csv index 1c40ce03d..62e7f66f7 100644 --- a/json_schema/update_log.csv +++ b/json_schema/update_log.csv @@ -1,3 +1,3 @@ Schema,Change type,Change message,Version,Date 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",, \ No newline at end of file +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",, \ No newline at end of file From 20ab01abde038fa97583a73ae5c21ef632d30cee Mon Sep 17 00:00:00 2001 From: idazucchi Date: Tue, 17 Feb 2026 17:20:07 +0000 Subject: [PATCH 52/64] Added sodium blood test --- docs/jsonBrowser/module.md | 2 ++ json_schema/module/biomaterial/blood_test.json | 18 ++++++++++++++++++ json_schema/update_log.csv | 3 ++- 3 files changed, 22 insertions(+), 1 deletion(-) diff --git a/docs/jsonBrowser/module.md b/docs/jsonBrowser/module.md index c772f5a15..9ed5c3149 100644 --- a/docs/jsonBrowser/module.md +++ b/docs/jsonBrowser/module.md @@ -693,6 +693,8 @@ 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 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 diff --git a/json_schema/module/biomaterial/blood_test.json b/json_schema/module/biomaterial/blood_test.json index 21dd09717..3fd168ec4 100644 --- a/json_schema/module/biomaterial/blood_test.json +++ b/json_schema/module/biomaterial/blood_test.json @@ -307,6 +307,24 @@ "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", + "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"] + }, "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", diff --git a/json_schema/update_log.csv b/json_schema/update_log.csv index 62e7f66f7..f7480c206 100644 --- a/json_schema/update_log.csv +++ b/json_schema/update_log.csv @@ -1,3 +1,4 @@ Schema,Change type,Change message,Version,Date 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",, \ No newline at end of file +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",, \ No newline at end of file From 1cea71f83bf1816feab72ffdcfdef00edcdb00d2 Mon Sep 17 00:00:00 2001 From: idazucchi Date: Tue, 17 Feb 2026 17:24:08 +0000 Subject: [PATCH 53/64] Added potassium blood test --- docs/jsonBrowser/module.md | 2 ++ json_schema/module/biomaterial/blood_test.json | 18 ++++++++++++++++++ json_schema/update_log.csv | 2 +- 3 files changed, 21 insertions(+), 1 deletion(-) diff --git a/docs/jsonBrowser/module.md b/docs/jsonBrowser/module.md index 9ed5c3149..4173c6fd5 100644 --- a/docs/jsonBrowser/module.md +++ b/docs/jsonBrowser/module.md @@ -695,6 +695,8 @@ triglycerides | Triglycerides levels from the donor's last blood test after at l 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 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 diff --git a/json_schema/module/biomaterial/blood_test.json b/json_schema/module/biomaterial/blood_test.json index 3fd168ec4..40cf3e4f8 100644 --- a/json_schema/module/biomaterial/blood_test.json +++ b/json_schema/module/biomaterial/blood_test.json @@ -325,6 +325,24 @@ "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", + "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"] + }, "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", diff --git a/json_schema/update_log.csv b/json_schema/update_log.csv index f7480c206..2f4d365f3 100644 --- a/json_schema/update_log.csv +++ b/json_schema/update_log.csv @@ -1,4 +1,4 @@ Schema,Change type,Change message,Version,Date 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",, \ No newline at end of file +module/biomaterial/blood_test,minor,"Added sodium, sodium_unit, potassium, potassium_unit",, \ No newline at end of file From 208a0f38af5ea2fb57c2d8d53801b6ecb4452cfd Mon Sep 17 00:00:00 2001 From: idazucchi Date: Tue, 17 Feb 2026 17:29:22 +0000 Subject: [PATCH 54/64] Added urea blood test --- docs/jsonBrowser/module.md | 2 ++ json_schema/module/biomaterial/blood_test.json | 18 ++++++++++++++++++ json_schema/update_log.csv | 2 +- 3 files changed, 21 insertions(+), 1 deletion(-) diff --git a/docs/jsonBrowser/module.md b/docs/jsonBrowser/module.md index 4173c6fd5..e5664b77a 100644 --- a/docs/jsonBrowser/module.md +++ b/docs/jsonBrowser/module.md @@ -697,6 +697,8 @@ sodium | Sodium in the last blood test of the donor before collection. | number 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 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 diff --git a/json_schema/module/biomaterial/blood_test.json b/json_schema/module/biomaterial/blood_test.json index 40cf3e4f8..b777690fc 100644 --- a/json_schema/module/biomaterial/blood_test.json +++ b/json_schema/module/biomaterial/blood_test.json @@ -343,6 +343,24 @@ "guidelines": "Should be one of: mmol/L", "bionetworks": ["heart"] }, + "urea": { + "description": "Urea in the last blood test of the donor before collection.", + "type": "number", + "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"] + }, "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", diff --git a/json_schema/update_log.csv b/json_schema/update_log.csv index 2f4d365f3..51e274855 100644 --- a/json_schema/update_log.csv +++ b/json_schema/update_log.csv @@ -1,4 +1,4 @@ Schema,Change type,Change message,Version,Date 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",, \ No newline at end of file +module/biomaterial/blood_test,minor,"Added sodium, sodium_unit, potassium, potassium_unit, urea, urea_unit",, \ No newline at end of file From aaba0f602c1240e509e905451254ef2e0d8048ef Mon Sep 17 00:00:00 2001 From: idazucchi Date: Tue, 17 Feb 2026 17:32:07 +0000 Subject: [PATCH 55/64] Added creatinine blood test --- docs/jsonBrowser/module.md | 2 ++ .../module/biomaterial/blood_test.json | 19 +++++++++++++++++++ json_schema/update_log.csv | 2 +- 3 files changed, 22 insertions(+), 1 deletion(-) diff --git a/docs/jsonBrowser/module.md b/docs/jsonBrowser/module.md index e5664b77a..6de232159 100644 --- a/docs/jsonBrowser/module.md +++ b/docs/jsonBrowser/module.md @@ -699,6 +699,8 @@ potassium | Potassium in the last blood test of the donor before collection. | n 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 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 diff --git a/json_schema/module/biomaterial/blood_test.json b/json_schema/module/biomaterial/blood_test.json index b777690fc..135c164dc 100644 --- a/json_schema/module/biomaterial/blood_test.json +++ b/json_schema/module/biomaterial/blood_test.json @@ -361,6 +361,25 @@ "guidelines": "Should be one of: mmol/L", "bionetworks": ["heart"] }, + "creatinine": { + "description": "Creatinine in the last blood test of the donor before collection.", + "type": "number", + "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"] + }, "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", diff --git a/json_schema/update_log.csv b/json_schema/update_log.csv index 51e274855..2f6e8c643 100644 --- a/json_schema/update_log.csv +++ b/json_schema/update_log.csv @@ -1,4 +1,4 @@ Schema,Change type,Change message,Version,Date 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",, \ No newline at end of file +module/biomaterial/blood_test,minor,"Added sodium, sodium_unit, potassium, potassium_unit, urea, urea_unit, creatinine, creatinine_unit",, \ No newline at end of file From 56710fde5c4a94338ba701fc0d6b440d3a613ad5 Mon Sep 17 00:00:00 2001 From: idazucchi Date: Tue, 17 Feb 2026 17:35:04 +0000 Subject: [PATCH 56/64] Added total_bilirubin blood test --- docs/jsonBrowser/module.md | 2 ++ json_schema/module/biomaterial/blood_test.json | 18 ++++++++++++++++++ json_schema/update_log.csv | 2 +- 3 files changed, 21 insertions(+), 1 deletion(-) diff --git a/docs/jsonBrowser/module.md b/docs/jsonBrowser/module.md index 6de232159..38fdd1d6a 100644 --- a/docs/jsonBrowser/module.md +++ b/docs/jsonBrowser/module.md @@ -701,6 +701,8 @@ urea | Urea in the last blood test of the donor before collection. | number | no 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 diff --git a/json_schema/module/biomaterial/blood_test.json b/json_schema/module/biomaterial/blood_test.json index 135c164dc..ae4512a0b 100644 --- a/json_schema/module/biomaterial/blood_test.json +++ b/json_schema/module/biomaterial/blood_test.json @@ -380,6 +380,24 @@ "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", + "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", diff --git a/json_schema/update_log.csv b/json_schema/update_log.csv index 2f6e8c643..8f137f559 100644 --- a/json_schema/update_log.csv +++ b/json_schema/update_log.csv @@ -1,4 +1,4 @@ Schema,Change type,Change message,Version,Date 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",, \ No newline at end of file +module/biomaterial/blood_test,minor,"Added sodium, sodium_unit, potassium, potassium_unit, urea, urea_unit, creatinine, creatinine_unit, total_bilirubin, total_bilirubin_unit",, \ No newline at end of file From 981eafddccc4c4b1b70b0a5cfb1dd8b1e201603c Mon Sep 17 00:00:00 2001 From: idazucchi Date: Tue, 17 Feb 2026 18:25:38 +0000 Subject: [PATCH 57/64] update project test files --- tests/schema_test_files/project/test_fail_project_0.json | 7 ++++--- tests/schema_test_files/project/test_pass_project_0.json | 7 ++++--- 2 files changed, 8 insertions(+), 6 deletions(-) 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 From 72ee25dd02bcc022d1cc3c234d15f4cfb2548450 Mon Sep 17 00:00:00 2001 From: idazucchi Date: Wed, 18 Feb 2026 09:36:52 +0000 Subject: [PATCH 58/64] Added substance use fields --- docs/jsonBrowser/module.md | 4 ++ json_schema/module/biomaterial/lifestyle.json | 42 +++++++++++++++++++ json_schema/update_log.csv | 3 +- 3 files changed, 48 insertions(+), 1 deletion(-) diff --git a/docs/jsonBrowser/module.md b/docs/jsonBrowser/module.md index 38fdd1d6a..982749b6a 100644 --- a/docs/jsonBrowser/module.md +++ b/docs/jsonBrowser/module.md @@ -596,6 +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._ 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/update_log.csv b/json_schema/update_log.csv index 8f137f559..edf354aca 100644 --- a/json_schema/update_log.csv +++ b/json_schema/update_log.csv @@ -1,4 +1,5 @@ Schema,Change type,Change message,Version,Date 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",, \ No newline at end of file +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",, \ No newline at end of file From e8d84b94f665629ae6f8891d9372c114584f406d Mon Sep 17 00:00:00 2001 From: idazucchi Date: Wed, 18 Feb 2026 15:43:27 +0000 Subject: [PATCH 59/64] Expanded transplant fields --- docs/jsonBrowser/type.md | 3 ++- .../biomaterial/specimen_from_organism.json | 19 +++++++++++++++---- json_schema/update_log.csv | 3 ++- 3 files changed, 19 insertions(+), 6 deletions(-) diff --git a/docs/jsonBrowser/type.md b/docs/jsonBrowser/type.md index 33b8167c6..aec9f6943 100644 --- a/docs/jsonBrowser/type.md +++ b/docs/jsonBrowser/type.md @@ -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) | | adjacent_disease_location | A term for the specific location of the adjacent disease. | object | no | [See module organ_ontology](module.md#organ-ontology) | Adjacent disease location | | diff --git a/json_schema/type/biomaterial/specimen_from_organism.json b/json_schema/type/biomaterial/specimen_from_organism.json index c8a731d22..2c4c0eba0 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.", diff --git a/json_schema/update_log.csv b/json_schema/update_log.csv index edf354aca..ba9080594 100644 --- a/json_schema/update_log.csv +++ b/json_schema/update_log.csv @@ -2,4 +2,5 @@ Schema,Change type,Change message,Version,Date 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",, \ No newline at end of file +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",, \ No newline at end of file From 92341b3ce078188e367dfb05dd82198754c11b80 Mon Sep 17 00:00:00 2001 From: idazucchi Date: Thu, 5 Mar 2026 15:01:18 +0000 Subject: [PATCH 60/64] fix linting comments --- docs/jsonBrowser/module.md | 12 ++++++------ json_schema/module/biomaterial/blood_test.json | 14 +++++++------- json_schema/module/biomaterial/human_specific.json | 6 +++--- .../type/biomaterial/specimen_from_organism.json | 2 +- .../collection_protocol.json | 2 +- 5 files changed, 18 insertions(+), 18 deletions(-) diff --git a/docs/jsonBrowser/module.md b/docs/jsonBrowser/module.md index 982749b6a..10df64c1f 100644 --- a/docs/jsonBrowser/module.md +++ b/docs/jsonBrowser/module.md @@ -699,17 +699,17 @@ triglycerides | Triglycerides levels from the donor's last blood test after at l 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 | 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 | 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 +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/json_schema/module/biomaterial/blood_test.json b/json_schema/module/biomaterial/blood_test.json index ae4512a0b..dd219d011 100644 --- a/json_schema/module/biomaterial/blood_test.json +++ b/json_schema/module/biomaterial/blood_test.json @@ -146,7 +146,7 @@ ], "user_friendly": "Haematocrit unit", "example": "%", - "guidelines": "Should be one of: %", + "guidelines": "Should be one of: percentage (%)", "bionetworks": ["adipose"] }, "haemoglobin": { @@ -329,7 +329,7 @@ "description": "Potassium in the last blood test of the donor before collection.", "type": "number", "user_friendly": "Potassium", - "example": "4.0, 4.2, 3.8", + "example": "4.0; 4.2; 3.8", "bionetworks": ["heart"] }, "potassium_unit": { @@ -347,7 +347,7 @@ "description": "Urea in the last blood test of the donor before collection.", "type": "number", "user_friendly": "Urea", - "example": "5.0, 5.5, 4.8", + "example": "5.0; 5.5; 4.8", "bionetworks": ["heart"] }, "urea_unit": { @@ -365,7 +365,7 @@ "description": "Creatinine in the last blood test of the donor before collection.", "type": "number", "user_friendly": "Creatinine", - "example": "80, 85, 78", + "example": "80; 85; 78", "bionetworks": ["heart"] }, "creatinine_unit": { @@ -376,7 +376,7 @@ "mg/dL" ], "user_friendly": "Creatinine unit", - "example": "micromol/L, mg/dL", + "example": "micromol/L; mg/dL", "guidelines": "Should be one of: micromol/L, mg/dL", "bionetworks": ["heart"] }, @@ -384,7 +384,7 @@ "description": "Total bilirubin in the last blood test of the donor before collection.", "type": "number", "user_friendly": "Total bilirubin", - "example": "12, 10, 14", + "example": "12; 10; 14", "bionetworks": ["heart"] }, "total_bilirubin_unit": { @@ -417,7 +417,7 @@ "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", "user_friendly": "Blood test time offset", diff --git a/json_schema/module/biomaterial/human_specific.json b/json_schema/module/biomaterial/human_specific.json index fe9cf4b02..91e701b99 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]))?)?$", "type": "string", "example": "60; 95; 153", "user_friendly": "Waist circumference", @@ -40,7 +40,7 @@ }, "waist_hip_ratio": { "description": "Waist-hip ratio of the donor at the time of collection.", - "pattern": "(0|[1-9][0-9]*)(\\.(0|[0-9]*[1-9]))?(-(0|[1-9][0-9]*)(\\.(0|[0-9]*[1-9]))?)?$", + "pattern": "^(0|[1-9][0-9]*)(\\.(0|[0-9]*[1-9]))?(-(0|[1-9][0-9]*)(\\.(0|[0-9]*[1-9]))?)?$", "type": "string", "example": "0.85; 0.91; 0.88", "user_friendly": "Waist-hip ratio", diff --git a/json_schema/type/biomaterial/specimen_from_organism.json b/json_schema/type/biomaterial/specimen_from_organism.json index 7eeeff90d..3f0ebf7a4 100644 --- a/json_schema/type/biomaterial/specimen_from_organism.json +++ b/json_schema/type/biomaterial/specimen_from_organism.json @@ -172,7 +172,7 @@ }, "time_to_laboratory": { "description": "Transit time in hours between tissue collection and tissue processing, meaning either storage in the laboratory or processing for sequencing.", - "pattern": "(0|[1-9][0-9]*)(\\.(0|[0-9]*[1-9]))?(-(0|[1-9][0-9]*)(\\.(0|[0-9]*[1-9]))?)?$", + "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; 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 8bc49b52c..d9b6817d9 100644 --- a/json_schema/type/protocol/biomaterial_collection/collection_protocol.json +++ b/json_schema/type/protocol/biomaterial_collection/collection_protocol.json @@ -65,7 +65,7 @@ ], "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", + "guidelines": "Should be one of: Bergstrom needle; Punch biopsy; Mercedes needle, dry aspiration; Mercedes needle, tumescent lidocaine “wet” aspiration.", "bionetworks": ["adipose"] }, "reagents": { From 9b058c43bdbc317961471c3aa9ea8a50c746036a Mon Sep 17 00:00:00 2001 From: Amnon Khen Date: Fri, 6 Mar 2026 15:28:00 +0000 Subject: [PATCH 61/64] Apply suggestion from @Copilot - use vscode market place rather than cursor's Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> --- tests/README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) 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) From ce939afaf2b654701abec1aa1a1cdc103ad30ab8 Mon Sep 17 00:00:00 2001 From: Amnon Khen Date: Fri, 6 Mar 2026 15:29:08 +0000 Subject: [PATCH 62/64] Update .github/workflows/schema-tests.yml to use node 18 --- .github/workflows/schema-tests.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) 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 From 2970f43335c7f5718cddb215dc35cee19af029a4 Mon Sep 17 00:00:00 2001 From: idazucchi Date: Fri, 10 Apr 2026 13:24:01 +0100 Subject: [PATCH 63/64] added regex fix to update log --- json_schema/update_log.csv | 2 ++ 1 file changed, 2 insertions(+) diff --git a/json_schema/update_log.csv b/json_schema/update_log.csv index 6f688b9bf..c1991c0f0 100644 --- a/json_schema/update_log.csv +++ b/json_schema/update_log.csv @@ -1,4 +1,6 @@ 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",, From 61f5f5d4a96f69d2febb3abf33b386bbce730ba3 Mon Sep 17 00:00:00 2001 From: idazucchi Date: Fri, 10 Apr 2026 13:53:05 +0100 Subject: [PATCH 64/64] added minimum value --- .../module/biomaterial/blood_test.json | 5 +++ .../module/biomaterial/medical_tests.json | 33 +++++++++++++++++++ 2 files changed, 38 insertions(+) diff --git a/json_schema/module/biomaterial/blood_test.json b/json_schema/module/biomaterial/blood_test.json index 50897317c..d75c0cf3d 100644 --- a/json_schema/module/biomaterial/blood_test.json +++ b/json_schema/module/biomaterial/blood_test.json @@ -326,6 +326,7 @@ "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"] @@ -345,6 +346,7 @@ "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"] }, @@ -362,6 +364,7 @@ "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"] @@ -380,6 +383,7 @@ "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"] @@ -399,6 +403,7 @@ "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"] diff --git a/json_schema/module/biomaterial/medical_tests.json b/json_schema/module/biomaterial/medical_tests.json index a91e8f1bc..af7aafe70 100644 --- a/json_schema/module/biomaterial/medical_tests.json +++ b/json_schema/module/biomaterial/medical_tests.json @@ -258,6 +258,7 @@ "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"] @@ -272,6 +273,7 @@ "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"] @@ -279,6 +281,7 @@ "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"] @@ -298,6 +301,7 @@ "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"] @@ -305,6 +309,7 @@ "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"] @@ -377,6 +382,7 @@ "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"] @@ -384,6 +390,7 @@ "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"] @@ -391,6 +398,7 @@ "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"] @@ -398,6 +406,7 @@ "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"] @@ -405,6 +414,7 @@ "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"] @@ -412,6 +422,7 @@ "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"] @@ -419,6 +430,7 @@ "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"] @@ -426,6 +438,7 @@ "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"] @@ -433,6 +446,7 @@ "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"] @@ -440,6 +454,7 @@ "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"] @@ -447,6 +462,7 @@ "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"] @@ -454,6 +470,7 @@ "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"] @@ -461,6 +478,7 @@ "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"] @@ -468,6 +486,7 @@ "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"] @@ -475,6 +494,7 @@ "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"] @@ -482,6 +502,7 @@ "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"] @@ -489,6 +510,7 @@ "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"] @@ -496,6 +518,7 @@ "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"] @@ -503,6 +526,7 @@ "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"] @@ -510,6 +534,7 @@ "mri_lvef": { "description": "Left ventricular ejection fraction measured by MRI.", "type": "number", + "minimum": 0, "user_friendly": "Mri - LVEF", "example": "55; 60; 58", "bionetworks": ["heart"] @@ -517,6 +542,7 @@ "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"] @@ -524,6 +550,7 @@ "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"] @@ -531,6 +558,7 @@ "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"] @@ -566,6 +594,7 @@ "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"] @@ -574,6 +603,7 @@ "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"] }, @@ -581,6 +611,7 @@ "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"] }, @@ -588,12 +619,14 @@ "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"]