From 2f687f8254a651be87fb46f8d6e22b7e99b9fb8e Mon Sep 17 00:00:00 2001 From: Arsenios Chatzigeorgiou <49944135+arschat@users.noreply.github.com> Date: Wed, 10 Jul 2024 18:40:24 +0300 Subject: [PATCH 01/20] Added medical_tests module --- docs/jsonBrowser/module.md | 25 +++ docs/jsonBrowser/required_fields.md | 2 + docs/jsonBrowser/type.md | 1 + .../module/biomaterial/medical_tests.json | 161 ++++++++++++++++++ .../type/biomaterial/donor_organism.json | 6 + json_schema/update_log.csv | 1 + 6 files changed, 196 insertions(+) create mode 100644 json_schema/module/biomaterial/medical_tests.json diff --git a/docs/jsonBrowser/module.md b/docs/jsonBrowser/module.md index 14e14a97e..40157125f 100644 --- a/docs/jsonBrowser/module.md +++ b/docs/jsonBrowser/module.md @@ -426,6 +426,31 @@ mycoplasma_testing_results | Whether the biomaterial passed or failed the mycopl drug_treatment | Description of drugs added to the growth medium. | string | no | | Drug treatment | | 100 ug/mL ampicillin; 15 ug/mL tetracycline feeder_layer_type | Type of feeder layer cells on which biomaterial was grown. | string | no | | Feeder layer type | feeder-free, feeder-dependent, JK1 feeder cells, feeder-dependent, SNL 76/7 feeder cells, feeder-dependent, human marrow stromal cells, feeder-dependent, bovine embryonic fibroblast cells, feeder-dependent, mouse embryonic fibroblast cells, feeder-dependent, mouse fibroblast STO cells, feeder-dependent, mouse bone marrow stromal cells, feeder-dependent, mouse yolk sac-derived endothelial cells, feeder-dependent, human foreskin fibroblast cells, feeder-dependent, human newborn fibroblast cells, feeder-dependent, human fetal lung fibroblast cells, feeder-dependent, human uterine endometrial cells, feeder-dependent, human breast parenchymal cells, feeder-dependent, human embryonic fibroblast cells, feeder-dependent, human adipose stromal cells, feeder-dependent, human amniotic epithelial cells, feeder-dependent, human placental fibroblast cells, feeder-dependent, human umbilical cord stromal cells, feeder-dependent, human fetal muscle cells, feeder-dependent, human fetal skin cells, feeder-dependent, human fetal liver stromal cells, feeder-dependent, human fallopian tubal epithelial cells, feeder-dependent, human amniotic mesenchymal cells | feeder-free; feeder-dependent, mouse embryonic fibroblast cells +## Medical tests +_Information about the medical tests of a donor._ + +Location: module/biomaterial/medical_tests.json + +Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example +--- | --- | --- | --- | --- | --- | --- | --- +PFT_method | Indicate with which method, spirometry or plethysmography, the pulmonary function was accessed and whether DLCO/KCO testing was performed. | array | no | | Pulmonary Function Testing method | spirometry, plethysmography, DLCO_KCO_test | spirometry; plethysmography; DLCO_KCO_test +PFT_age | Indicate the age of the subject at the time point of pulmonary function parameter assessment in years, if known. | string | no | | Age at PFT | | 10; 34; 68 +PFT_time_point | Indicate at which date the pulmonary function parameters were recorded as DD/MM/YYYY if available. If this information is not shareable, please indicate 'not_shareable'. | string | no | | Date at PFT | | 14/11/2024; 31/01/2019; not_shareable +PFT_relative_time_point | If timepoint of sample collection (sample_collection_time_point) and/or timepoint of PFT recording (PFT_time_point) is not available, indicate how many days prior or after sample collection the pulmonary function parameters were assessed if available. | string | no | | Days between collection and PFT | | -5; 2; 0 +FEV1_predicted | Indicate the predicted Forced Expiratory Volume in 1 second (FEV1) in milliliters, based on patient age, sex, height, and ethnicity, if available. | string | no | | FEV1 predicted | | 3500; 4200; 2800 +FEV1_preBD | Indicate the measured FEV1 in milliliters before the administration of a bronchodilator if available. | string | no | | FEV1 before bronchodilator | | 3000; 3800; 2600 +FEV1_postBD | Indicate the measured FEV1 in milliliters after the administration of a bronchodilator if available. | string | no | | FEV1 after bronchodilator | | 3200; 4000; 2700 +FEV1_preBD_predicted_percent | Indicate the percentage of the predicted FEV1 achieved before bronchodilator administration if available. | string | no | | FEV1 percent of preBD to predicted | | 86; 90; 78 +FEV1_postBD_predicted_percent | Indicate the percentage of the predicted FEV1 achieved after bronchodilator administration if available. | string | no | | FEV1 percent of postBD to predicted | | 91; 95; 82 +FVC_predicted | Indicate the predicted Forced Vital Capacity (FVC) in milliliters, based on patient age, sex, height, and ethnicity, if available. | string | no | | FVC predicted | | 4500; 5000; 3800 +FVC_preBD | Indicate the measured FVC in milliliters before bronchodilator administration if available. | string | no | | FVC before bronchodilator | | 4000; 4800; 3600 +FVC_postBD | Indicate the measured FVC in milliliters after bronchodilator administration if available. | string | no | | FVC after bronchodilator | | 4200; 5000; 3700 +FVC_preBD_predicted_percent | Indicate the percentage of the predicted FVC achieved before bronchodilator administration if available. | string | no | | FVC percent of preBD to predicted | | 89; 96; 95 +FVC_postBD_predicted_percent | Indicate the percentage of the predicted FVC achieved after bronchodilator administration if available. | string | no | | FVC percent of postBD to predicted | | 93; 100; 97 +FEV1_FVC_ratio_preBD | Indicate the ratio of FEV1 to FVC before bronchodilator administration if available. | string | no | | FEV1 to FVC ratio before bronchodilator | | 0.75; 0.79; 0.72 +FEV1_FVC_ratio_postBD | Indicate the ratio of FEV1 to FVC after bronchodilator administration if available. | string | no | | FEV1 to FVC ratio after bronchodilator | | 0.76; 0.80; 0.73 +FRC_abs | Indicate the Functional Residual Capacity (FRC) in absolute milliliters if available. | string | no | | FRC absolute | | 3000; 3500; 2700 + ## Preservation and storage _Information relating to how a biomaterial was preserved and/or stored over a period of time._ diff --git a/docs/jsonBrowser/required_fields.md b/docs/jsonBrowser/required_fields.md index 9a69dd26c..4f2ca17ed 100644 --- a/docs/jsonBrowser/required_fields.md +++ b/docs/jsonBrowser/required_fields.md @@ -350,6 +350,8 @@ official_hca_publication | Has the publication been accepted as an official HCA _There are no required properties in schema Human-specific_ ### Growth conditions _There are no required properties in schema Growth conditions_ +### Medical tests +_There are no required properties in schema Medical tests_ ### Preservation and storage _There are no required properties in schema Preservation and storage_ ### Death diff --git a/docs/jsonBrowser/type.md b/docs/jsonBrowser/type.md index d1e61ebbd..93bb0082a 100644 --- a/docs/jsonBrowser/type.md +++ b/docs/jsonBrowser/type.md @@ -432,6 +432,7 @@ development_stage | A classification of the developmental stage of the organism. diseases | Short description of known disease(s) of the organism. | array | no | [See module disease_ontology](module.md#disease-ontology) | Known disease(s) | | death | Information about conditions of death of the organism. | object | no | [See module death](module.md#death) | Death conditions | | familial_relationships | Information about other organisms related to this organism. | array | no | [See module familial_relationship](module.md#familial-relationship) | Familial relationship | | +medical_tests | Information about the medical tests of the organism. | object | no | [See module medical_tests](module.md#medical-tests) | Medical tests | | medical_history | Information about the medical history of the organism. | object | no | [See module medical_history](module.md#medical-history) | Medical history | | gestational_age | Gestational age of pregnancy in Gestational age units measured from the last menstrual period. | string | no | | Gestational age | | 22; 8-9 gestational_age_unit | The unit in which Gestational age is expressed. | object | no | [See module time_unit_ontology](module.md#time-unit-ontology) | Gestational age unit | | diff --git a/json_schema/module/biomaterial/medical_tests.json b/json_schema/module/biomaterial/medical_tests.json new file mode 100644 index 000000000..d476d3098 --- /dev/null +++ b/json_schema/module/biomaterial/medical_tests.json @@ -0,0 +1,161 @@ +{ + "$schema": "http://json-schema.org/draft-07/schema#", + "description": "Information about the medical tests of a donor.", + "additionalProperties": false, + "title": "Medical tests", + "name": "medical_tests", + "type": "object", + "properties": { + "describedBy": { + "description": "The URL reference to the schema.", + "type": "string", + "pattern" : "^(http|https)://schema.(.*?)humancellatlas.org/module/biomaterial/(([0-9]{1,}.[0-9]{1,}.[0-9]{1,})|([a-zA-Z]*?))/medical_tests" + }, + "schema_version": { + "description": "The version number of the schema in major.minor.patch format.", + "type": "string", + "pattern": "^[0-9]{1,}.[0-9]{1,}.[0-9]{1,}$", + "example": "0.0.1" + }, + "PFT_method": { + "user_friendly": "Pulmonary Function Testing method", + "description": "Indicate with which method, spirometry or plethysmography, the pulmonary function was accessed and whether DLCO/KCO testing was performed.", + "type": "array", + "items": { + "type": "string", + "enum": ["spirometry", "plethysmography", "DLCO_KCO_test"] + }, + "example": "spirometry; plethysmography; DLCO_KCO_test", + "$comments": "pulmonary_function_parameter; lung" + }, + "PFT_age": { + "user_friendly": "Age at PFT", + "description": "Indicate the age of the subject at the time point of pulmonary function parameter assessment in years, if known.", + "type": "string", + "example": "10; 34; 68", + "pattern": "^[0-9]+$", + "$comments": "pulmonary_function_parameter; lung" + }, + "PFT_time_point": { + "user_friendly": "Date at PFT", + "description": "Indicate at which date the pulmonary function parameters were recorded as DD/MM/YYYY if available. If this information is not shareable, please indicate 'not_shareable'.", + "type": "string", + "example": "14/11/2024; 31/01/2019; not_shareable", + "pattern": "^((19|20)\\d\\d)([- \\.\\/][01]\\d){0,1}([- \\.\\/][0-3]\\d){0,1}$", + "$comments": "pulmonary_function_parameter; lung", + "guidelines": "If this information is not shareable, please indicate \\'not_shareable\\'." + }, + "PFT_relative_time_point": { + "user_friendly": "Days between collection and PFT", + "description": "If timepoint of sample collection (sample_collection_time_point) and/or timepoint of PFT recording (PFT_time_point) is not available, indicate how many days prior or after sample collection the pulmonary function parameters were assessed if available.", + "type": "string", + "example": "-5; 2; 0", + "pattern": "^[\\+\\-]?[0-9]+$", + "$comments": "pulmonary_function_parameter; lung" + }, + "FEV1_predicted": { + "user_friendly": "FEV1 predicted", + "description": "Indicate the predicted Forced Expiratory Volume in 1 second (FEV1) in milliliters, based on patient age, sex, height, and ethnicity, if available.", + "type": "string", + "example": "3500; 4200; 2800", + "pattern": "^[0-9]+$", + "$comments": "pulmonary_function_parameter; lung" + }, + "FEV1_preBD": { + "user_friendly": "FEV1 before bronchodilator", + "description": "Indicate the measured FEV1 in milliliters before the administration of a bronchodilator if available.", + "type": "string", + "example": "3000; 3800; 2600", + "pattern": "^[0-9]+$", + "$comments": "pulmonary_function_parameter; lung" + }, + "FEV1_postBD": { + "user_friendly": "FEV1 after bronchodilator", + "description": "Indicate the measured FEV1 in milliliters after the administration of a bronchodilator if available.", + "type": "string", + "example": "3200; 4000; 2700", + "pattern": "^[0-9]+$", + "$comments": "pulmonary_function_parameter; lung" + }, + "FEV1_preBD_predicted_percent": { + "user_friendly": "FEV1 percent of preBD to predicted", + "description": "Indicate the percentage of the predicted FEV1 achieved before bronchodilator administration if available.", + "type": "string", + "example": "86; 90; 78", + "pattern": "^[0-9]+$", + "$comments": "pulmonary_function_parameter; lung" + }, + "FEV1_postBD_predicted_percent": { + "user_friendly": "FEV1 percent of postBD to predicted", + "description": "Indicate the percentage of the predicted FEV1 achieved after bronchodilator administration if available.", + "type": "string", + "example": "91; 95; 82", + "pattern": "^[0-9]+$", + "$comments": "pulmonary_function_parameter; lung" + }, + "FVC_predicted": { + "user_friendly": "FVC predicted", + "description": "Indicate the predicted Forced Vital Capacity (FVC) in milliliters, based on patient age, sex, height, and ethnicity, if available.", + "type": "string", + "example": "4500; 5000; 3800", + "pattern": "^[0-9]+$", + "$comments": "pulmonary_function_parameter; lung" + }, + "FVC_preBD": { + "user_friendly": "FVC before bronchodilator", + "description": "Indicate the measured FVC in milliliters before bronchodilator administration if available.", + "type": "string", + "example": "4000; 4800; 3600", + "pattern": "^[0-9]+$", + "$comments": "pulmonary_function_parameter; lung" + }, + "FVC_postBD": { + "user_friendly": "FVC after bronchodilator", + "description": "Indicate the measured FVC in milliliters after bronchodilator administration if available.", + "type": "string", + "example": "4200; 5000; 3700", + "pattern": "^[0-9]+$", + "$comments": "pulmonary_function_parameter; lung" + }, + "FVC_preBD_predicted_percent": { + "user_friendly": "FVC percent of preBD to predicted", + "description": "Indicate the percentage of the predicted FVC achieved before bronchodilator administration if available.", + "type": "string", + "example": "89; 96; 95", + "pattern": "^[0-9]+$", + "$comments": "pulmonary_function_parameter; lung" + }, + "FVC_postBD_predicted_percent": { + "user_friendly": "FVC percent of postBD to predicted", + "description": "Indicate the percentage of the predicted FVC achieved after bronchodilator administration if available.", + "type": "string", + "example": "93; 100; 97", + "pattern": "^[0-9]+$", + "$comments": "pulmonary_function_parameter; lung" + }, + "FEV1_FVC_ratio_preBD": { + "user_friendly": "FEV1 to FVC ratio before bronchodilator", + "description": "Indicate the ratio of FEV1 to FVC before bronchodilator administration if available.", + "type": "string", + "example": "0.75; 0.79; 0.72", + "pattern": "^0\\.[0-9]+$", + "$comments": "pulmonary_function_parameter; lung" + }, + "FEV1_FVC_ratio_postBD": { + "user_friendly": "FEV1 to FVC ratio after bronchodilator", + "description": "Indicate the ratio of FEV1 to FVC after bronchodilator administration if available.", + "type": "string", + "example": "0.76; 0.80; 0.73", + "pattern": "^0\\.[0-9]+$", + "$comments": "pulmonary_function_parameter; lung" + }, + "FRC_abs": { + "user_friendly": "FRC absolute", + "description": "Indicate the Functional Residual Capacity (FRC) in absolute milliliters if available.", + "type": "string", + "example": "3000; 3500; 2700", + "pattern": "^[0-9]+$", + "$comments": "pulmonary_function_parameter; lung" + } + } +} diff --git a/json_schema/type/biomaterial/donor_organism.json b/json_schema/type/biomaterial/donor_organism.json index 6bab6b746..f53e4f72e 100644 --- a/json_schema/type/biomaterial/donor_organism.json +++ b/json_schema/type/biomaterial/donor_organism.json @@ -131,6 +131,12 @@ }, "user_friendly": "Familial relationship" }, + "medical_tests": { + "description": "Information about the medical tests of the organism.", + "type": "object", + "$ref": "module/biomaterial/medical_tests.json", + "user_friendly": "Medical tests" + }, "medical_history": { "description": "Information about the medical history of the organism.", "type": "object", diff --git a/json_schema/update_log.csv b/json_schema/update_log.csv index 3231ff199..8072702bb 100644 --- a/json_schema/update_log.csv +++ b/json_schema/update_log.csv @@ -1 +1,2 @@ Schema,Change type,Change message,Version,Date +/type/biomaterial/donor_organism.json,Add medical_tests module in donor_organism. Fixes #1562,, \ No newline at end of file From 639186bd28fad6db2c0a76152db95fe8d097825d Mon Sep 17 00:00:00 2001 From: Arsenios Chatzigeorgiou <49944135+arschat@users.noreply.github.com> Date: Mon, 15 Jul 2024 14:34:07 +0300 Subject: [PATCH 02/20] Changed the friendly name for pulmonary function testing fields --- docs/jsonBrowser/module.md | 6 +++--- json_schema/module/biomaterial/medical_tests.json | 6 +++--- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/docs/jsonBrowser/module.md b/docs/jsonBrowser/module.md index 40157125f..e4bd688bd 100644 --- a/docs/jsonBrowser/module.md +++ b/docs/jsonBrowser/module.md @@ -434,9 +434,9 @@ Location: module/biomaterial/medical_tests.json Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example --- | --- | --- | --- | --- | --- | --- | --- PFT_method | Indicate with which method, spirometry or plethysmography, the pulmonary function was accessed and whether DLCO/KCO testing was performed. | array | no | | Pulmonary Function Testing method | spirometry, plethysmography, DLCO_KCO_test | spirometry; plethysmography; DLCO_KCO_test -PFT_age | Indicate the age of the subject at the time point of pulmonary function parameter assessment in years, if known. | string | no | | Age at PFT | | 10; 34; 68 -PFT_time_point | Indicate at which date the pulmonary function parameters were recorded as DD/MM/YYYY if available. If this information is not shareable, please indicate 'not_shareable'. | string | no | | Date at PFT | | 14/11/2024; 31/01/2019; not_shareable -PFT_relative_time_point | If timepoint of sample collection (sample_collection_time_point) and/or timepoint of PFT recording (PFT_time_point) is not available, indicate how many days prior or after sample collection the pulmonary function parameters were assessed if available. | string | no | | Days between collection and PFT | | -5; 2; 0 +PFT_age | Indicate the age of the subject at the time point of pulmonary function parameter assessment in years, if known. | string | no | | Age at Pulmonary Function Test | | 10; 34; 68 +PFT_time_point | Indicate at which date the pulmonary function parameters were recorded as DD/MM/YYYY if available. If this information is not shareable, please indicate 'not_shareable'. | string | no | | Date at Pulmonary Function Test | | 14/11/2024; 31/01/2019; not_shareable +PFT_relative_time_point | If timepoint of sample collection (sample_collection_time_point) and/or timepoint of PFT recording (PFT_time_point) is not available, indicate how many days prior or after sample collection the pulmonary function parameters were assessed if available. | string | no | | Days between collection and Pulmonary Function Test | | -5; 2; 0 FEV1_predicted | Indicate the predicted Forced Expiratory Volume in 1 second (FEV1) in milliliters, based on patient age, sex, height, and ethnicity, if available. | string | no | | FEV1 predicted | | 3500; 4200; 2800 FEV1_preBD | Indicate the measured FEV1 in milliliters before the administration of a bronchodilator if available. | string | no | | FEV1 before bronchodilator | | 3000; 3800; 2600 FEV1_postBD | Indicate the measured FEV1 in milliliters after the administration of a bronchodilator if available. | string | no | | FEV1 after bronchodilator | | 3200; 4000; 2700 diff --git a/json_schema/module/biomaterial/medical_tests.json b/json_schema/module/biomaterial/medical_tests.json index d476d3098..13eae59e5 100644 --- a/json_schema/module/biomaterial/medical_tests.json +++ b/json_schema/module/biomaterial/medical_tests.json @@ -29,7 +29,7 @@ "$comments": "pulmonary_function_parameter; lung" }, "PFT_age": { - "user_friendly": "Age at PFT", + "user_friendly": "Age at Pulmonary Function Test", "description": "Indicate the age of the subject at the time point of pulmonary function parameter assessment in years, if known.", "type": "string", "example": "10; 34; 68", @@ -37,7 +37,7 @@ "$comments": "pulmonary_function_parameter; lung" }, "PFT_time_point": { - "user_friendly": "Date at PFT", + "user_friendly": "Date at Pulmonary Function Test", "description": "Indicate at which date the pulmonary function parameters were recorded as DD/MM/YYYY if available. If this information is not shareable, please indicate 'not_shareable'.", "type": "string", "example": "14/11/2024; 31/01/2019; not_shareable", @@ -46,7 +46,7 @@ "guidelines": "If this information is not shareable, please indicate \\'not_shareable\\'." }, "PFT_relative_time_point": { - "user_friendly": "Days between collection and PFT", + "user_friendly": "Days between collection and Pulmonary Function Test", "description": "If timepoint of sample collection (sample_collection_time_point) and/or timepoint of PFT recording (PFT_time_point) is not available, indicate how many days prior or after sample collection the pulmonary function parameters were assessed if available.", "type": "string", "example": "-5; 2; 0", From caa2e9a3a6cdb98b0f6a9ab2e23e16a3b708d2cf Mon Sep 17 00:00:00 2001 From: Arsenios Chatzigeorgiou <49944135+arschat@users.noreply.github.com> Date: Fri, 19 Jul 2024 16:24:23 +0100 Subject: [PATCH 03/20] Added missing fields --- docs/jsonBrowser/module.md | 41 +++-- .../module/biomaterial/medical_history.json | 2 +- .../module/biomaterial/medical_tests.json | 155 ++++++++++++++---- src/schema_linter.py | 2 +- 4 files changed, 152 insertions(+), 48 deletions(-) diff --git a/docs/jsonBrowser/module.md b/docs/jsonBrowser/module.md index e4bd688bd..6c64cd890 100644 --- a/docs/jsonBrowser/module.md +++ b/docs/jsonBrowser/module.md @@ -427,29 +427,38 @@ drug_treatment | Description of drugs added to the growth medium. | string | no feeder_layer_type | Type of feeder layer cells on which biomaterial was grown. | string | no | | Feeder layer type | feeder-free, feeder-dependent, JK1 feeder cells, feeder-dependent, SNL 76/7 feeder cells, feeder-dependent, human marrow stromal cells, feeder-dependent, bovine embryonic fibroblast cells, feeder-dependent, mouse embryonic fibroblast cells, feeder-dependent, mouse fibroblast STO cells, feeder-dependent, mouse bone marrow stromal cells, feeder-dependent, mouse yolk sac-derived endothelial cells, feeder-dependent, human foreskin fibroblast cells, feeder-dependent, human newborn fibroblast cells, feeder-dependent, human fetal lung fibroblast cells, feeder-dependent, human uterine endometrial cells, feeder-dependent, human breast parenchymal cells, feeder-dependent, human embryonic fibroblast cells, feeder-dependent, human adipose stromal cells, feeder-dependent, human amniotic epithelial cells, feeder-dependent, human placental fibroblast cells, feeder-dependent, human umbilical cord stromal cells, feeder-dependent, human fetal muscle cells, feeder-dependent, human fetal skin cells, feeder-dependent, human fetal liver stromal cells, feeder-dependent, human fallopian tubal epithelial cells, feeder-dependent, human amniotic mesenchymal cells | feeder-free; feeder-dependent, mouse embryonic fibroblast cells ## Medical tests -_Information about the medical tests of a donor._ +_Information about the medical tests performed on the individual._ Location: module/biomaterial/medical_tests.json Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example --- | --- | --- | --- | --- | --- | --- | --- PFT_method | Indicate with which method, spirometry or plethysmography, the pulmonary function was accessed and whether DLCO/KCO testing was performed. | array | no | | Pulmonary Function Testing method | spirometry, plethysmography, DLCO_KCO_test | spirometry; plethysmography; DLCO_KCO_test -PFT_age | Indicate the age of the subject at the time point of pulmonary function parameter assessment in years, if known. | string | no | | Age at Pulmonary Function Test | | 10; 34; 68 +PFT_age | Indicate the age of the subject at the time point of pulmonary function parameter assessment in years, if known. | number | no | | Age at Pulmonary Function Test | | 10; 34; 68 PFT_time_point | Indicate at which date the pulmonary function parameters were recorded as DD/MM/YYYY if available. If this information is not shareable, please indicate 'not_shareable'. | string | no | | Date at Pulmonary Function Test | | 14/11/2024; 31/01/2019; not_shareable PFT_relative_time_point | If timepoint of sample collection (sample_collection_time_point) and/or timepoint of PFT recording (PFT_time_point) is not available, indicate how many days prior or after sample collection the pulmonary function parameters were assessed if available. | string | no | | Days between collection and Pulmonary Function Test | | -5; 2; 0 -FEV1_predicted | Indicate the predicted Forced Expiratory Volume in 1 second (FEV1) in milliliters, based on patient age, sex, height, and ethnicity, if available. | string | no | | FEV1 predicted | | 3500; 4200; 2800 -FEV1_preBD | Indicate the measured FEV1 in milliliters before the administration of a bronchodilator if available. | string | no | | FEV1 before bronchodilator | | 3000; 3800; 2600 -FEV1_postBD | Indicate the measured FEV1 in milliliters after the administration of a bronchodilator if available. | string | no | | FEV1 after bronchodilator | | 3200; 4000; 2700 -FEV1_preBD_predicted_percent | Indicate the percentage of the predicted FEV1 achieved before bronchodilator administration if available. | string | no | | FEV1 percent of preBD to predicted | | 86; 90; 78 -FEV1_postBD_predicted_percent | Indicate the percentage of the predicted FEV1 achieved after bronchodilator administration if available. | string | no | | FEV1 percent of postBD to predicted | | 91; 95; 82 -FVC_predicted | Indicate the predicted Forced Vital Capacity (FVC) in milliliters, based on patient age, sex, height, and ethnicity, if available. | string | no | | FVC predicted | | 4500; 5000; 3800 -FVC_preBD | Indicate the measured FVC in milliliters before bronchodilator administration if available. | string | no | | FVC before bronchodilator | | 4000; 4800; 3600 -FVC_postBD | Indicate the measured FVC in milliliters after bronchodilator administration if available. | string | no | | FVC after bronchodilator | | 4200; 5000; 3700 -FVC_preBD_predicted_percent | Indicate the percentage of the predicted FVC achieved before bronchodilator administration if available. | string | no | | FVC percent of preBD to predicted | | 89; 96; 95 -FVC_postBD_predicted_percent | Indicate the percentage of the predicted FVC achieved after bronchodilator administration if available. | string | no | | FVC percent of postBD to predicted | | 93; 100; 97 -FEV1_FVC_ratio_preBD | Indicate the ratio of FEV1 to FVC before bronchodilator administration if available. | string | no | | FEV1 to FVC ratio before bronchodilator | | 0.75; 0.79; 0.72 -FEV1_FVC_ratio_postBD | Indicate the ratio of FEV1 to FVC after bronchodilator administration if available. | string | no | | FEV1 to FVC ratio after bronchodilator | | 0.76; 0.80; 0.73 -FRC_abs | Indicate the Functional Residual Capacity (FRC) in absolute milliliters if available. | string | no | | FRC absolute | | 3000; 3500; 2700 +FEV1_predicted | Indicate the predicted Forced Expiratory Volume in 1 second (FEV1) in milliliters, based on patient age, sex, height, and ethnicity, if available. | number | no | | FEV1 predicted | | 3500; 4200; 2800 +FEV1_preBD | Indicate the measured FEV1 in milliliters before the administration of a bronchodilator if available. | number | no | | FEV1 before bronchodilator | | 3000; 3800; 2600 +FEV1_postBD | Indicate the measured FEV1 in milliliters after the administration of a bronchodilator if available. | number | no | | FEV1 after bronchodilator | | 3200; 4000; 2700 +FEV1_preBD_predicted_percent | Indicate the percentage of the predicted FEV1 achieved before bronchodilator administration if available. | number | no | | FEV1 percent of preBD to predicted | | 86; 90; 78 +FEV1_postBD_predicted_percent | Indicate the percentage of the predicted FEV1 achieved after bronchodilator administration if available. | number | no | | FEV1 percent of postBD to predicted | | 91; 95; 82 +FVC_predicted | Indicate the predicted Forced Vital Capacity (FVC) in milliliters, based on patient age, sex, height, and ethnicity, if available. | number | no | | FVC predicted | | 4500; 5000; 3800 +FVC_preBD | Indicate the measured FVC in milliliters before bronchodilator administration if available. | number | no | | FVC before bronchodilator | | 4000; 4800; 3600 +FVC_postBD | Indicate the measured FVC in milliliters after bronchodilator administration if available. | number | no | | FVC after bronchodilator | | 4200; 5000; 3700 +FVC_preBD_predicted_percent | Indicate the percentage of the predicted FVC achieved before bronchodilator administration if available. | number | no | | FVC percent of preBD to predicted | | 89; 96; 95 +FVC_postBD_predicted_percent | Indicate the percentage of the predicted FVC achieved after bronchodilator administration if available. | number | no | | FVC percent of postBD to predicted | | 93; 100; 97 +FEV1_FVC_ratio_preBD | Indicate the ratio of FEV1 to FVC before bronchodilator administration if available. | number | no | | FEV1 to FVC ratio before bronchodilator | | 0.75; 0.79; 0.72 +FEV1_FVC_ratio_postBD | Indicate the ratio of FEV1 to FVC after bronchodilator administration if available. | number | no | | FEV1 to FVC ratio after bronchodilator | | 0.76; 0.80; 0.73 +FRC_abs | Indicate the Functional Residual Capacity (FRC) in absolute milliliters if available. | number | no | | FRC absolute | | 3000; 3500; 2700 +FRC_predicted_percent | Indicate the percentage of the predicted FRC, based on patient demographics, if available. | number | no | | FRC percent of predicted | | 95; 88; 102 +RV | Indicate the Residual Volume (RV) in milliliters if available. | number | no | | RV | | 1500; 1800; 1400 +RV_predicted_percent | Indicate the percentage of the predicted RV, based on patient demographics, if available. | number | no | | RV percent of predicted | | 80; 90; 85 +IC | Indicate the Inspiratory Capacity (IC) in milliliters if available. | number | no | | IC | | 3500; 4000; 3200 +IC_predicted_percent | Indicate the percentage of the predicted IC, based on patient demographics, if available. | number | no | | IC percent of predicted | | 92; 85; 97 +DLCO | Indicate the Diffusing Capacity of the Lung for Carbon Monoxide (DLCO) in milliliters if available. | number | no | | DLCO | | 25; 30; 22 +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 ## Preservation and storage _Information relating to how a biomaterial was preserved and/or stored over a period of time._ @@ -500,7 +509,7 @@ alcohol_history | Estimated amount of alcohol consumed per day. | string | no | medication | Medications the individual was taking at time of biomaterial collection. | string | no | | Medications | | Naproxen 500mg/day; Citalopram 20mg/day smoking_history | Estimated number of cigarettes smoked per day. | string | no | | Smoking history | | 20 cigarettes/day for 25 years, stopped 2000 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. -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 +test_results | Results from medical tests performed on the individual (free text). | string | no | | Test results | | lipid panel shows normal level of LDL (124 mg/dL); HIV, HBV, HCV: Negative 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 ## Cell morphology diff --git a/json_schema/module/biomaterial/medical_history.json b/json_schema/module/biomaterial/medical_history.json index 5382ca10a..b18601095 100644 --- a/json_schema/module/biomaterial/medical_history.json +++ b/json_schema/module/biomaterial/medical_history.json @@ -50,7 +50,7 @@ "example": "Should be one of: normal, fasting, or feeding tube removed." }, "test_results": { - "description": "Results from medical tests performed on the individual.", + "description": "Results from medical tests performed on the individual (free text).", "type": "string", "user_friendly": "Test results", "example": "lipid panel shows normal level of LDL (124 mg/dL); HIV, HBV, HCV: Negative" diff --git a/json_schema/module/biomaterial/medical_tests.json b/json_schema/module/biomaterial/medical_tests.json index 13eae59e5..9477ed9b5 100644 --- a/json_schema/module/biomaterial/medical_tests.json +++ b/json_schema/module/biomaterial/medical_tests.json @@ -1,6 +1,6 @@ { "$schema": "http://json-schema.org/draft-07/schema#", - "description": "Information about the medical tests of a donor.", + "description": "Information about the medical tests performed on the individual.", "additionalProperties": false, "title": "Medical tests", "name": "medical_tests", @@ -31,9 +31,10 @@ "PFT_age": { "user_friendly": "Age at Pulmonary Function Test", "description": "Indicate the age of the subject at the time point of pulmonary function parameter assessment in years, if known.", - "type": "string", + "type": "number", "example": "10; 34; 68", - "pattern": "^[0-9]+$", + "maximum": 150, + "minimum": 0, "$comments": "pulmonary_function_parameter; lung" }, "PFT_time_point": { @@ -41,7 +42,7 @@ "description": "Indicate at which date the pulmonary function parameters were recorded as DD/MM/YYYY if available. If this information is not shareable, please indicate 'not_shareable'.", "type": "string", "example": "14/11/2024; 31/01/2019; not_shareable", - "pattern": "^((19|20)\\d\\d)([- \\.\\/][01]\\d){0,1}([- \\.\\/][0-3]\\d){0,1}$", + "pattern": "^((0[1-9]|[12][0-9]|3[01])[- \\.\\/](0[1-9]|1[0-2])[- \\.\\/](19|20)\\d\\d|not_applicable)$", "$comments": "pulmonary_function_parameter; lung", "guidelines": "If this information is not shareable, please indicate \\'not_shareable\\'." }, @@ -56,105 +57,199 @@ "FEV1_predicted": { "user_friendly": "FEV1 predicted", "description": "Indicate the predicted Forced Expiratory Volume in 1 second (FEV1) in milliliters, based on patient age, sex, height, and ethnicity, if available.", - "type": "string", + "type": "number", "example": "3500; 4200; 2800", - "pattern": "^[0-9]+$", + "maximum": 15000, + "minimum": 0, "$comments": "pulmonary_function_parameter; lung" }, "FEV1_preBD": { "user_friendly": "FEV1 before bronchodilator", "description": "Indicate the measured FEV1 in milliliters before the administration of a bronchodilator if available.", - "type": "string", + "type": "number", "example": "3000; 3800; 2600", - "pattern": "^[0-9]+$", + "maximum": 15000, + "minimum": 0, "$comments": "pulmonary_function_parameter; lung" }, "FEV1_postBD": { "user_friendly": "FEV1 after bronchodilator", "description": "Indicate the measured FEV1 in milliliters after the administration of a bronchodilator if available.", - "type": "string", + "type": "number", "example": "3200; 4000; 2700", - "pattern": "^[0-9]+$", + "maximum": 15000, + "minimum": 0, "$comments": "pulmonary_function_parameter; lung" }, "FEV1_preBD_predicted_percent": { "user_friendly": "FEV1 percent of preBD to predicted", "description": "Indicate the percentage of the predicted FEV1 achieved before bronchodilator administration if available.", - "type": "string", + "type": "number", "example": "86; 90; 78", - "pattern": "^[0-9]+$", + "maximum": 200, + "minimum": 0, "$comments": "pulmonary_function_parameter; lung" }, "FEV1_postBD_predicted_percent": { "user_friendly": "FEV1 percent of postBD to predicted", "description": "Indicate the percentage of the predicted FEV1 achieved after bronchodilator administration if available.", - "type": "string", + "type": "number", "example": "91; 95; 82", - "pattern": "^[0-9]+$", + "maximum": 200, + "minimum": 0, "$comments": "pulmonary_function_parameter; lung" }, "FVC_predicted": { "user_friendly": "FVC predicted", "description": "Indicate the predicted Forced Vital Capacity (FVC) in milliliters, based on patient age, sex, height, and ethnicity, if available.", - "type": "string", + "type": "number", "example": "4500; 5000; 3800", - "pattern": "^[0-9]+$", + "maximum": 15000, + "minimum": 0, "$comments": "pulmonary_function_parameter; lung" }, "FVC_preBD": { "user_friendly": "FVC before bronchodilator", "description": "Indicate the measured FVC in milliliters before bronchodilator administration if available.", - "type": "string", + "type": "number", "example": "4000; 4800; 3600", - "pattern": "^[0-9]+$", + "maximum": 15000, + "minimum": 0, "$comments": "pulmonary_function_parameter; lung" }, "FVC_postBD": { "user_friendly": "FVC after bronchodilator", "description": "Indicate the measured FVC in milliliters after bronchodilator administration if available.", - "type": "string", + "type": "number", "example": "4200; 5000; 3700", - "pattern": "^[0-9]+$", + "maximum": 15000, + "minimum": 0, "$comments": "pulmonary_function_parameter; lung" }, "FVC_preBD_predicted_percent": { "user_friendly": "FVC percent of preBD to predicted", "description": "Indicate the percentage of the predicted FVC achieved before bronchodilator administration if available.", - "type": "string", + "type": "number", "example": "89; 96; 95", - "pattern": "^[0-9]+$", + "maximum": 200, + "minimum": 0, "$comments": "pulmonary_function_parameter; lung" }, "FVC_postBD_predicted_percent": { "user_friendly": "FVC percent of postBD to predicted", "description": "Indicate the percentage of the predicted FVC achieved after bronchodilator administration if available.", - "type": "string", + "type": "number", "example": "93; 100; 97", - "pattern": "^[0-9]+$", + "maximum": 200, + "minimum": 0, "$comments": "pulmonary_function_parameter; lung" }, "FEV1_FVC_ratio_preBD": { "user_friendly": "FEV1 to FVC ratio before bronchodilator", "description": "Indicate the ratio of FEV1 to FVC before bronchodilator administration if available.", - "type": "string", + "type": "number", "example": "0.75; 0.79; 0.72", - "pattern": "^0\\.[0-9]+$", + "maximum": 1, + "minimum": 0, "$comments": "pulmonary_function_parameter; lung" }, "FEV1_FVC_ratio_postBD": { "user_friendly": "FEV1 to FVC ratio after bronchodilator", "description": "Indicate the ratio of FEV1 to FVC after bronchodilator administration if available.", - "type": "string", + "type": "number", "example": "0.76; 0.80; 0.73", - "pattern": "^0\\.[0-9]+$", + "maximum": 1, + "minimum": 0, "$comments": "pulmonary_function_parameter; lung" }, "FRC_abs": { "user_friendly": "FRC absolute", "description": "Indicate the Functional Residual Capacity (FRC) in absolute milliliters if available.", - "type": "string", + "type": "number", "example": "3000; 3500; 2700", - "pattern": "^[0-9]+$", + "maximum": 15000, + "minimum": 0, + "$comments": "pulmonary_function_parameter; lung" + }, + "FRC_predicted_percent": { + "user_friendly": "FRC percent of predicted", + "description": "Indicate the percentage of the predicted FRC, based on patient demographics, if available.", + "type": "number", + "example": "95; 88; 102", + "maximum": 200, + "minimum": 0, + "$comments": "pulmonary_function_parameter; lung" + }, + "RV": { + "user_friendly": "RV", + "description": "Indicate the Residual Volume (RV) in milliliters if available.", + "type": "number", + "example": "1500; 1800; 1400", + "maximum": 15000, + "minimum": 0, + "$comments": "pulmonary_function_parameter; lung" + }, + "RV_predicted_percent": { + "user_friendly": "RV percent of predicted", + "description": "Indicate the percentage of the predicted RV, based on patient demographics, if available.", + "type": "number", + "example": "80; 90; 85", + "maximum": 200, + "minimum": 0, + "$comments": "pulmonary_function_parameter; lung" + }, + "IC": { + "user_friendly": "IC", + "description": "Indicate the Inspiratory Capacity (IC) in milliliters if available.", + "type": "number", + "example": "3500; 4000; 3200", + "maximum": 15000, + "minimum": 0, + "$comments": "pulmonary_function_parameter; lung" + }, + "IC_predicted_percent": { + "user_friendly": "IC percent of predicted", + "description": "Indicate the percentage of the predicted IC, based on patient demographics, if available.", + "type": "number", + "example": "92; 85; 97", + "maximum": 200, + "minimum": 0, + "$comments": "pulmonary_function_parameter; lung" + }, + "DLCO": { + "user_friendly": "DLCO", + "description": "Indicate the Diffusing Capacity of the Lung for Carbon Monoxide (DLCO) in milliliters if available.", + "type": "number", + "example": "25; 30; 22", + "maximum": 100, + "minimum": 5, + "$comments": "pulmonary_function_parameter; lung" + }, + "DLCO_predicted_percent": { + "user_friendly": "DLCO percent of predicted", + "description": "Indicate the percentage of the predicted DLCO, based on patient demographics, if available.", + "type": "number", + "example": "88; 95; 82", + "maximum": 15000, + "minimum": 0, + "$comments": "pulmonary_function_parameter; lung" + }, + "KCO": { + "user_friendly": "KCO", + "description": "Indicate the transfer coefficient of the lung for carbon monoxide (KCO) in mmol/min/kPa/L if available.", + "type": "number", + "example": "5; 6; 4.5", + "maximum": 15000, + "minimum": 0, + "$comments": "pulmonary_function_parameter; lung" + }, + "KCO_predicted_percent": { + "user_friendly": "KCO percent of predicted", + "description": "Indicate the percentage of the predicted KCO, based on patient demographics, if available.", + "type": "number", + "example": "90; 98; 85", + "maximum": 200, + "minimum": 0, "$comments": "pulmonary_function_parameter; lung" } } diff --git a/src/schema_linter.py b/src/schema_linter.py index 96edd6226..71dd75c92 100644 --- a/src/schema_linter.py +++ b/src/schema_linter.py @@ -32,7 +32,7 @@ # Property attributes -property_attributes = ['description', 'type', 'pattern', 'example', 'enum', '$ref', 'user_friendly', 'items', 'guidelines', 'format', 'comment', 'maximum', 'minimum', 'oneOf'] +property_attributes = ['description', 'type', 'pattern', 'example', 'enum', '$ref', 'user_friendly', 'items', 'guidelines', 'format', 'comment', 'maximum', 'minimum', 'oneOf', '$comments'] ontology_attributes = ['graph_restriction', 'ontologies', 'classes', 'relations', 'direct', 'include_self'] From 8432dd7ca7d9d0fe61cfa5f2af43bca83374403f Mon Sep 17 00:00:00 2001 From: Arsenios Chatzigeorgiou <49944135+arschat@users.noreply.github.com> Date: Fri, 19 Jul 2024 16:26:54 +0100 Subject: [PATCH 04/20] Remove free text label from previous test result field --- docs/jsonBrowser/module.md | 2 +- json_schema/module/biomaterial/medical_history.json | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/jsonBrowser/module.md b/docs/jsonBrowser/module.md index 6c64cd890..c3815cf12 100644 --- a/docs/jsonBrowser/module.md +++ b/docs/jsonBrowser/module.md @@ -509,7 +509,7 @@ alcohol_history | Estimated amount of alcohol consumed per day. | string | no | medication | Medications the individual was taking at time of biomaterial collection. | string | no | | Medications | | Naproxen 500mg/day; Citalopram 20mg/day smoking_history | Estimated number of cigarettes smoked per day. | string | no | | Smoking history | | 20 cigarettes/day for 25 years, stopped 2000 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. -test_results | Results from medical tests performed on the individual (free text). | string | no | | Test results | | lipid panel shows normal level of LDL (124 mg/dL); HIV, HBV, HCV: Negative +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 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 ## Cell morphology diff --git a/json_schema/module/biomaterial/medical_history.json b/json_schema/module/biomaterial/medical_history.json index b18601095..5382ca10a 100644 --- a/json_schema/module/biomaterial/medical_history.json +++ b/json_schema/module/biomaterial/medical_history.json @@ -50,7 +50,7 @@ "example": "Should be one of: normal, fasting, or feeding tube removed." }, "test_results": { - "description": "Results from medical tests performed on the individual (free text).", + "description": "Results from medical tests performed on the individual.", "type": "string", "user_friendly": "Test results", "example": "lipid panel shows normal level of LDL (124 mg/dL); HIV, HBV, HCV: Negative" From c1e69d026375a32ea1f6542e309ae9ebeace2491 Mon Sep 17 00:00:00 2001 From: Arsenios Chatzigeorgiou <49944135+arschat@users.noreply.github.com> Date: Mon, 22 Jul 2024 16:25:50 +0100 Subject: [PATCH 05/20] Change type to major --- json_schema/update_log.csv | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/json_schema/update_log.csv b/json_schema/update_log.csv index 8072702bb..5820278a4 100644 --- a/json_schema/update_log.csv +++ b/json_schema/update_log.csv @@ -1,2 +1,2 @@ Schema,Change type,Change message,Version,Date -/type/biomaterial/donor_organism.json,Add medical_tests module in donor_organism. Fixes #1562,, \ No newline at end of file +/type/biomaterial/donor_organism.json,major,Add medical_tests module in donor_organism. Fixes #1562,, \ No newline at end of file From 09ad25c96d55d14b3862ec6bc082cc5abc52d546 Mon Sep 17 00:00:00 2001 From: Arsenios Chatzigeorgiou <49944135+arschat@users.noreply.github.com> Date: Mon, 22 Jul 2024 16:47:18 +0100 Subject: [PATCH 06/20] Fix date to DCP format & typos --- docs/jsonBrowser/module.md | 6 +++--- json_schema/module/biomaterial/medical_tests.json | 12 ++++++------ 2 files changed, 9 insertions(+), 9 deletions(-) diff --git a/docs/jsonBrowser/module.md b/docs/jsonBrowser/module.md index c3815cf12..b597d1e82 100644 --- a/docs/jsonBrowser/module.md +++ b/docs/jsonBrowser/module.md @@ -433,9 +433,9 @@ Location: module/biomaterial/medical_tests.json Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example --- | --- | --- | --- | --- | --- | --- | --- -PFT_method | Indicate with which method, spirometry or plethysmography, the pulmonary function was accessed and whether DLCO/KCO testing was performed. | array | no | | Pulmonary Function Testing method | spirometry, plethysmography, DLCO_KCO_test | spirometry; plethysmography; DLCO_KCO_test -PFT_age | Indicate the age of the subject at the time point of pulmonary function parameter assessment in years, if known. | number | no | | Age at Pulmonary Function Test | | 10; 34; 68 -PFT_time_point | Indicate at which date the pulmonary function parameters were recorded as DD/MM/YYYY if available. If this information is not shareable, please indicate 'not_shareable'. | string | no | | Date at Pulmonary Function Test | | 14/11/2024; 31/01/2019; not_shareable +PFT_method | Indicate which Pulmonary Function Testing (PFT) method was used, spirometry or plethysmography, and whether DLCO/KCO testing was performed. | array | no | | Pulmonary Function Testing method | spirometry, plethysmography, DLCO_KCO_test | spirometry; plethysmography; DLCO_KCO_test +PFT_age | Indicate the age of the subject at the time point of Pulmonary Function Testing (PFT) in years, if known. | number | no | | Age at Pulmonary Function Test | | 10; 34; 68 +PFT_time_point | Indicate at which date the Pulmonary Function Testing (PFT) were recorded as YYYY-MM-DD if available. If this information is not shareable, please indicate 'not_shareable'. | string | no | | Date at Pulmonary Function Test | | 2024-11-14; 2019-01-31; not_shareable PFT_relative_time_point | If timepoint of sample collection (sample_collection_time_point) and/or timepoint of PFT recording (PFT_time_point) is not available, indicate how many days prior or after sample collection the pulmonary function parameters were assessed if available. | string | no | | Days between collection and Pulmonary Function Test | | -5; 2; 0 FEV1_predicted | Indicate the predicted Forced Expiratory Volume in 1 second (FEV1) in milliliters, based on patient age, sex, height, and ethnicity, if available. | number | no | | FEV1 predicted | | 3500; 4200; 2800 FEV1_preBD | Indicate the measured FEV1 in milliliters before the administration of a bronchodilator if available. | number | no | | FEV1 before bronchodilator | | 3000; 3800; 2600 diff --git a/json_schema/module/biomaterial/medical_tests.json b/json_schema/module/biomaterial/medical_tests.json index 9477ed9b5..b618d6bd3 100644 --- a/json_schema/module/biomaterial/medical_tests.json +++ b/json_schema/module/biomaterial/medical_tests.json @@ -19,7 +19,7 @@ }, "PFT_method": { "user_friendly": "Pulmonary Function Testing method", - "description": "Indicate with which method, spirometry or plethysmography, the pulmonary function was accessed and whether DLCO/KCO testing was performed.", + "description": "Indicate which Pulmonary Function Testing (PFT) method was used, spirometry or plethysmography, and whether DLCO/KCO testing was performed.", "type": "array", "items": { "type": "string", @@ -30,7 +30,7 @@ }, "PFT_age": { "user_friendly": "Age at Pulmonary Function Test", - "description": "Indicate the age of the subject at the time point of pulmonary function parameter assessment in years, if known.", + "description": "Indicate the age of the subject at the time point of Pulmonary Function Testing (PFT) in years, if known.", "type": "number", "example": "10; 34; 68", "maximum": 150, @@ -39,10 +39,10 @@ }, "PFT_time_point": { "user_friendly": "Date at Pulmonary Function Test", - "description": "Indicate at which date the pulmonary function parameters were recorded as DD/MM/YYYY if available. If this information is not shareable, please indicate 'not_shareable'.", + "description": "Indicate at which date the Pulmonary Function Testing (PFT) were recorded as YYYY-MM-DD if available. If this information is not shareable, please indicate 'not_shareable'.", "type": "string", - "example": "14/11/2024; 31/01/2019; not_shareable", - "pattern": "^((0[1-9]|[12][0-9]|3[01])[- \\.\\/](0[1-9]|1[0-2])[- \\.\\/](19|20)\\d\\d|not_applicable)$", + "example": "2024-11-14; 2019-01-31; not_shareable", + "pattern": "^((19|20)\\d\\d[- \\.\\/](0[1-9]|1[0-2])[- \\.\\/](0[1-9]|[12][0-9]|3[01])|not_shareable)$", "$comments": "pulmonary_function_parameter; lung", "guidelines": "If this information is not shareable, please indicate \\'not_shareable\\'." }, @@ -230,7 +230,7 @@ "description": "Indicate the percentage of the predicted DLCO, based on patient demographics, if available.", "type": "number", "example": "88; 95; 82", - "maximum": 15000, + "maximum": 200, "minimum": 0, "$comments": "pulmonary_function_parameter; lung" }, From cf0b2af7ed77156b527227b2475706452c39f276 Mon Sep 17 00:00:00 2001 From: Arsenios Chatzigeorgiou <49944135+arschat@users.noreply.github.com> Date: Tue, 23 Jul 2024 10:22:09 +0100 Subject: [PATCH 07/20] Fix PFT_method description & date pattern --- docs/jsonBrowser/module.md | 2 +- json_schema/module/biomaterial/medical_tests.json | 7 ++++--- 2 files changed, 5 insertions(+), 4 deletions(-) diff --git a/docs/jsonBrowser/module.md b/docs/jsonBrowser/module.md index b597d1e82..8fbd8bc57 100644 --- a/docs/jsonBrowser/module.md +++ b/docs/jsonBrowser/module.md @@ -433,7 +433,7 @@ Location: module/biomaterial/medical_tests.json Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example --- | --- | --- | --- | --- | --- | --- | --- -PFT_method | Indicate which Pulmonary Function Testing (PFT) method was used, spirometry or plethysmography, and whether DLCO/KCO testing was performed. | array | no | | Pulmonary Function Testing method | spirometry, plethysmography, DLCO_KCO_test | spirometry; plethysmography; DLCO_KCO_test +PFT_method | Indicate which Pulmonary Function Testings (PFTs) methods were performed. Please indicate all tests performed. | array | no | | Pulmonary Function Testing method | spirometry, plethysmography, DLCO_KCO_test | spirometry; plethysmography; DLCO_KCO_test PFT_age | Indicate the age of the subject at the time point of Pulmonary Function Testing (PFT) in years, if known. | number | no | | Age at Pulmonary Function Test | | 10; 34; 68 PFT_time_point | Indicate at which date the Pulmonary Function Testing (PFT) were recorded as YYYY-MM-DD if available. If this information is not shareable, please indicate 'not_shareable'. | string | no | | Date at Pulmonary Function Test | | 2024-11-14; 2019-01-31; not_shareable PFT_relative_time_point | If timepoint of sample collection (sample_collection_time_point) and/or timepoint of PFT recording (PFT_time_point) is not available, indicate how many days prior or after sample collection the pulmonary function parameters were assessed if available. | string | no | | Days between collection and Pulmonary Function Test | | -5; 2; 0 diff --git a/json_schema/module/biomaterial/medical_tests.json b/json_schema/module/biomaterial/medical_tests.json index b618d6bd3..6d0769add 100644 --- a/json_schema/module/biomaterial/medical_tests.json +++ b/json_schema/module/biomaterial/medical_tests.json @@ -19,14 +19,15 @@ }, "PFT_method": { "user_friendly": "Pulmonary Function Testing method", - "description": "Indicate which Pulmonary Function Testing (PFT) method was used, spirometry or plethysmography, and whether DLCO/KCO testing was performed.", + "description": "Indicate which Pulmonary Function Testings (PFTs) methods were performed. Please indicate all tests performed.", "type": "array", "items": { "type": "string", "enum": ["spirometry", "plethysmography", "DLCO_KCO_test"] }, "example": "spirometry; plethysmography; DLCO_KCO_test", - "$comments": "pulmonary_function_parameter; lung" + "$comments": "pulmonary_function_parameter; lung", + "guidelines": "Should be of spirometry, plethysmography and DLCO_KCO_test." }, "PFT_age": { "user_friendly": "Age at Pulmonary Function Test", @@ -42,7 +43,7 @@ "description": "Indicate at which date the Pulmonary Function Testing (PFT) were recorded as YYYY-MM-DD if available. If this information is not shareable, please indicate 'not_shareable'.", "type": "string", "example": "2024-11-14; 2019-01-31; not_shareable", - "pattern": "^((19|20)\\d\\d[- \\.\\/](0[1-9]|1[0-2])[- \\.\\/](0[1-9]|[12][0-9]|3[01])|not_shareable)$", + "pattern": "^(((19|20)\\d\\d){1}([- \\./][01]\\d){0,1}([- \\./][0-3]\\d){0,1}|not_shareable)$", "$comments": "pulmonary_function_parameter; lung", "guidelines": "If this information is not shareable, please indicate \\'not_shareable\\'." }, From f29b7bd9b027cd21f32334c59526d03404c41997 Mon Sep 17 00:00:00 2001 From: Arsenios Chatzigeorgiou <49944135+arschat@users.noreply.github.com> Date: Tue, 23 Jul 2024 10:23:57 +0100 Subject: [PATCH 08/20] Fix description in PFT_relative_time_point --- docs/jsonBrowser/module.md | 2 +- json_schema/module/biomaterial/medical_tests.json | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/jsonBrowser/module.md b/docs/jsonBrowser/module.md index 8fbd8bc57..e26a76d5f 100644 --- a/docs/jsonBrowser/module.md +++ b/docs/jsonBrowser/module.md @@ -436,7 +436,7 @@ Property name | Description | Type | Required? | Object reference? | User friend PFT_method | Indicate which Pulmonary Function Testings (PFTs) methods were performed. Please indicate all tests performed. | array | no | | Pulmonary Function Testing method | spirometry, plethysmography, DLCO_KCO_test | spirometry; plethysmography; DLCO_KCO_test PFT_age | Indicate the age of the subject at the time point of Pulmonary Function Testing (PFT) in years, if known. | number | no | | Age at Pulmonary Function Test | | 10; 34; 68 PFT_time_point | Indicate at which date the Pulmonary Function Testing (PFT) were recorded as YYYY-MM-DD if available. If this information is not shareable, please indicate 'not_shareable'. | string | no | | Date at Pulmonary Function Test | | 2024-11-14; 2019-01-31; not_shareable -PFT_relative_time_point | If timepoint of sample collection (sample_collection_time_point) and/or timepoint of PFT recording (PFT_time_point) is not available, indicate how many days prior or after sample collection the pulmonary function parameters were assessed if available. | string | no | | Days between collection and Pulmonary Function Test | | -5; 2; 0 +PFT_relative_time_point | If timepoint of sample collection (time of collection) and/or timepoint of PFT recording (PFT_time_point) is not available, indicate how many days prior or after sample collection the pulmonary function parameters were assessed if available. | string | no | | Days between collection and Pulmonary Function Test | | -5; 2; 0 FEV1_predicted | Indicate the predicted Forced Expiratory Volume in 1 second (FEV1) in milliliters, based on patient age, sex, height, and ethnicity, if available. | number | no | | FEV1 predicted | | 3500; 4200; 2800 FEV1_preBD | Indicate the measured FEV1 in milliliters before the administration of a bronchodilator if available. | number | no | | FEV1 before bronchodilator | | 3000; 3800; 2600 FEV1_postBD | Indicate the measured FEV1 in milliliters after the administration of a bronchodilator if available. | number | no | | FEV1 after bronchodilator | | 3200; 4000; 2700 diff --git a/json_schema/module/biomaterial/medical_tests.json b/json_schema/module/biomaterial/medical_tests.json index 6d0769add..0c7466248 100644 --- a/json_schema/module/biomaterial/medical_tests.json +++ b/json_schema/module/biomaterial/medical_tests.json @@ -49,7 +49,7 @@ }, "PFT_relative_time_point": { "user_friendly": "Days between collection and Pulmonary Function Test", - "description": "If timepoint of sample collection (sample_collection_time_point) and/or timepoint of PFT recording (PFT_time_point) is not available, indicate how many days prior or after sample collection the pulmonary function parameters were assessed if available.", + "description": "If timepoint of sample collection (time of collection) and/or timepoint of PFT recording (PFT_time_point) is not available, indicate how many days prior or after sample collection the pulmonary function parameters were assessed if available.", "type": "string", "example": "-5; 2; 0", "pattern": "^[\\+\\-]?[0-9]+$", From e568e7ff4a90e55c691c8190d15c8942c71460fd Mon Sep 17 00:00:00 2001 From: Arsenios Chatzigeorgiou <49944135+arschat@users.noreply.github.com> Date: Fri, 26 Jul 2024 10:58:54 +0100 Subject: [PATCH 09/20] Added guidelines for PFT_relative_time_point --- json_schema/module/biomaterial/medical_tests.json | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/json_schema/module/biomaterial/medical_tests.json b/json_schema/module/biomaterial/medical_tests.json index 0c7466248..a6fcdef5e 100644 --- a/json_schema/module/biomaterial/medical_tests.json +++ b/json_schema/module/biomaterial/medical_tests.json @@ -53,7 +53,9 @@ "type": "string", "example": "-5; 2; 0", "pattern": "^[\\+\\-]?[0-9]+$", - "$comments": "pulmonary_function_parameter; lung" + "$comments": "pulmonary_function_parameter; lung", + "guidelines": "If PFT recording was done before sample collection, then enter a negative day value. If PFT recording was done after sample collection, then enter a positive day value." + }, "FEV1_predicted": { "user_friendly": "FEV1 predicted", From 7bfa88630e136d3cbd3a9b587800d6d119ccfa2b Mon Sep 17 00:00:00 2001 From: Arsenios Chatzigeorgiou <49944135+arschat@users.noreply.github.com> Date: Mon, 29 Jul 2024 11:25:18 +0100 Subject: [PATCH 10/20] Added module creation log --- json_schema/update_log.csv | 3 ++- json_schema/versions.json | 1 + 2 files changed, 3 insertions(+), 1 deletion(-) diff --git a/json_schema/update_log.csv b/json_schema/update_log.csv index 5820278a4..27a9c79d9 100644 --- a/json_schema/update_log.csv +++ b/json_schema/update_log.csv @@ -1,2 +1,3 @@ Schema,Change type,Change message,Version,Date -/type/biomaterial/donor_organism.json,major,Add medical_tests module in donor_organism. Fixes #1562,, \ No newline at end of file +/type/biomaterial/donor_organism.json,minor,Added optional medical_tests module in donor_organism. Fixes #1562,, +/type/module/biomaterial/medical_tests.json,major,Added medical_tests module,, \ No newline at end of file diff --git a/json_schema/versions.json b/json_schema/versions.json index 124354590..141bac2a9 100644 --- a/json_schema/versions.json +++ b/json_schema/versions.json @@ -26,6 +26,7 @@ "growth_conditions": "6.4.2", "human_specific": "1.0.11", "medical_history": "5.2.8", + "medical_tests": "0.0.0", "mouse_specific": "1.0.8", "preservation_storage": "6.1.1", "state_of_specimen": "6.0.0", From d39e2cb22a5bc46ee3a95a33b7c92568bf011897 Mon Sep 17 00:00:00 2001 From: Arsenios Chatzigeorgiou <49944135+arschat@users.noreply.github.com> Date: Mon, 29 Jul 2024 11:33:59 +0100 Subject: [PATCH 11/20] Fix incorrect reserved keyword --- .../module/biomaterial/medical_tests.json | 52 +++++++++---------- src/schema_linter.py | 2 +- 2 files changed, 27 insertions(+), 27 deletions(-) diff --git a/json_schema/module/biomaterial/medical_tests.json b/json_schema/module/biomaterial/medical_tests.json index a6fcdef5e..864cfc5ba 100644 --- a/json_schema/module/biomaterial/medical_tests.json +++ b/json_schema/module/biomaterial/medical_tests.json @@ -26,7 +26,7 @@ "enum": ["spirometry", "plethysmography", "DLCO_KCO_test"] }, "example": "spirometry; plethysmography; DLCO_KCO_test", - "$comments": "pulmonary_function_parameter; lung", + "$comment": "pulmonary_function_parameter; lung", "guidelines": "Should be of spirometry, plethysmography and DLCO_KCO_test." }, "PFT_age": { @@ -36,7 +36,7 @@ "example": "10; 34; 68", "maximum": 150, "minimum": 0, - "$comments": "pulmonary_function_parameter; lung" + "$comment": "pulmonary_function_parameter; lung" }, "PFT_time_point": { "user_friendly": "Date at Pulmonary Function Test", @@ -44,7 +44,7 @@ "type": "string", "example": "2024-11-14; 2019-01-31; not_shareable", "pattern": "^(((19|20)\\d\\d){1}([- \\./][01]\\d){0,1}([- \\./][0-3]\\d){0,1}|not_shareable)$", - "$comments": "pulmonary_function_parameter; lung", + "$comment": "pulmonary_function_parameter; lung", "guidelines": "If this information is not shareable, please indicate \\'not_shareable\\'." }, "PFT_relative_time_point": { @@ -53,7 +53,7 @@ "type": "string", "example": "-5; 2; 0", "pattern": "^[\\+\\-]?[0-9]+$", - "$comments": "pulmonary_function_parameter; lung", + "$comment": "pulmonary_function_parameter; lung", "guidelines": "If PFT recording was done before sample collection, then enter a negative day value. If PFT recording was done after sample collection, then enter a positive day value." }, @@ -64,7 +64,7 @@ "example": "3500; 4200; 2800", "maximum": 15000, "minimum": 0, - "$comments": "pulmonary_function_parameter; lung" + "$comment": "pulmonary_function_parameter; lung" }, "FEV1_preBD": { "user_friendly": "FEV1 before bronchodilator", @@ -73,7 +73,7 @@ "example": "3000; 3800; 2600", "maximum": 15000, "minimum": 0, - "$comments": "pulmonary_function_parameter; lung" + "$comment": "pulmonary_function_parameter; lung" }, "FEV1_postBD": { "user_friendly": "FEV1 after bronchodilator", @@ -82,7 +82,7 @@ "example": "3200; 4000; 2700", "maximum": 15000, "minimum": 0, - "$comments": "pulmonary_function_parameter; lung" + "$comment": "pulmonary_function_parameter; lung" }, "FEV1_preBD_predicted_percent": { "user_friendly": "FEV1 percent of preBD to predicted", @@ -91,7 +91,7 @@ "example": "86; 90; 78", "maximum": 200, "minimum": 0, - "$comments": "pulmonary_function_parameter; lung" + "$comment": "pulmonary_function_parameter; lung" }, "FEV1_postBD_predicted_percent": { "user_friendly": "FEV1 percent of postBD to predicted", @@ -100,7 +100,7 @@ "example": "91; 95; 82", "maximum": 200, "minimum": 0, - "$comments": "pulmonary_function_parameter; lung" + "$comment": "pulmonary_function_parameter; lung" }, "FVC_predicted": { "user_friendly": "FVC predicted", @@ -109,7 +109,7 @@ "example": "4500; 5000; 3800", "maximum": 15000, "minimum": 0, - "$comments": "pulmonary_function_parameter; lung" + "$comment": "pulmonary_function_parameter; lung" }, "FVC_preBD": { "user_friendly": "FVC before bronchodilator", @@ -118,7 +118,7 @@ "example": "4000; 4800; 3600", "maximum": 15000, "minimum": 0, - "$comments": "pulmonary_function_parameter; lung" + "$comment": "pulmonary_function_parameter; lung" }, "FVC_postBD": { "user_friendly": "FVC after bronchodilator", @@ -127,7 +127,7 @@ "example": "4200; 5000; 3700", "maximum": 15000, "minimum": 0, - "$comments": "pulmonary_function_parameter; lung" + "$comment": "pulmonary_function_parameter; lung" }, "FVC_preBD_predicted_percent": { "user_friendly": "FVC percent of preBD to predicted", @@ -136,7 +136,7 @@ "example": "89; 96; 95", "maximum": 200, "minimum": 0, - "$comments": "pulmonary_function_parameter; lung" + "$comment": "pulmonary_function_parameter; lung" }, "FVC_postBD_predicted_percent": { "user_friendly": "FVC percent of postBD to predicted", @@ -145,7 +145,7 @@ "example": "93; 100; 97", "maximum": 200, "minimum": 0, - "$comments": "pulmonary_function_parameter; lung" + "$comment": "pulmonary_function_parameter; lung" }, "FEV1_FVC_ratio_preBD": { "user_friendly": "FEV1 to FVC ratio before bronchodilator", @@ -154,7 +154,7 @@ "example": "0.75; 0.79; 0.72", "maximum": 1, "minimum": 0, - "$comments": "pulmonary_function_parameter; lung" + "$comment": "pulmonary_function_parameter; lung" }, "FEV1_FVC_ratio_postBD": { "user_friendly": "FEV1 to FVC ratio after bronchodilator", @@ -163,7 +163,7 @@ "example": "0.76; 0.80; 0.73", "maximum": 1, "minimum": 0, - "$comments": "pulmonary_function_parameter; lung" + "$comment": "pulmonary_function_parameter; lung" }, "FRC_abs": { "user_friendly": "FRC absolute", @@ -172,7 +172,7 @@ "example": "3000; 3500; 2700", "maximum": 15000, "minimum": 0, - "$comments": "pulmonary_function_parameter; lung" + "$comment": "pulmonary_function_parameter; lung" }, "FRC_predicted_percent": { "user_friendly": "FRC percent of predicted", @@ -181,7 +181,7 @@ "example": "95; 88; 102", "maximum": 200, "minimum": 0, - "$comments": "pulmonary_function_parameter; lung" + "$comment": "pulmonary_function_parameter; lung" }, "RV": { "user_friendly": "RV", @@ -190,7 +190,7 @@ "example": "1500; 1800; 1400", "maximum": 15000, "minimum": 0, - "$comments": "pulmonary_function_parameter; lung" + "$comment": "pulmonary_function_parameter; lung" }, "RV_predicted_percent": { "user_friendly": "RV percent of predicted", @@ -199,7 +199,7 @@ "example": "80; 90; 85", "maximum": 200, "minimum": 0, - "$comments": "pulmonary_function_parameter; lung" + "$comment": "pulmonary_function_parameter; lung" }, "IC": { "user_friendly": "IC", @@ -208,7 +208,7 @@ "example": "3500; 4000; 3200", "maximum": 15000, "minimum": 0, - "$comments": "pulmonary_function_parameter; lung" + "$comment": "pulmonary_function_parameter; lung" }, "IC_predicted_percent": { "user_friendly": "IC percent of predicted", @@ -217,7 +217,7 @@ "example": "92; 85; 97", "maximum": 200, "minimum": 0, - "$comments": "pulmonary_function_parameter; lung" + "$comment": "pulmonary_function_parameter; lung" }, "DLCO": { "user_friendly": "DLCO", @@ -226,7 +226,7 @@ "example": "25; 30; 22", "maximum": 100, "minimum": 5, - "$comments": "pulmonary_function_parameter; lung" + "$comment": "pulmonary_function_parameter; lung" }, "DLCO_predicted_percent": { "user_friendly": "DLCO percent of predicted", @@ -235,7 +235,7 @@ "example": "88; 95; 82", "maximum": 200, "minimum": 0, - "$comments": "pulmonary_function_parameter; lung" + "$comment": "pulmonary_function_parameter; lung" }, "KCO": { "user_friendly": "KCO", @@ -244,7 +244,7 @@ "example": "5; 6; 4.5", "maximum": 15000, "minimum": 0, - "$comments": "pulmonary_function_parameter; lung" + "$comment": "pulmonary_function_parameter; lung" }, "KCO_predicted_percent": { "user_friendly": "KCO percent of predicted", @@ -253,7 +253,7 @@ "example": "90; 98; 85", "maximum": 200, "minimum": 0, - "$comments": "pulmonary_function_parameter; lung" + "$comment": "pulmonary_function_parameter; lung" } } } diff --git a/src/schema_linter.py b/src/schema_linter.py index 71dd75c92..0404e028b 100644 --- a/src/schema_linter.py +++ b/src/schema_linter.py @@ -32,7 +32,7 @@ # Property attributes -property_attributes = ['description', 'type', 'pattern', 'example', 'enum', '$ref', 'user_friendly', 'items', 'guidelines', 'format', 'comment', 'maximum', 'minimum', 'oneOf', '$comments'] +property_attributes = ['description', 'type', 'pattern', 'example', 'enum', '$ref', 'user_friendly', 'items', 'guidelines', 'format', 'comment', 'maximum', 'minimum', 'oneOf', '$comment'] ontology_attributes = ['graph_restriction', 'ontologies', 'classes', 'relations', 'direct', 'include_self'] From 418198cea6326787b93cf7ebea1a4101e33cc508 Mon Sep 17 00:00:00 2001 From: Arsenios Chatzigeorgiou <49944135+arschat@users.noreply.github.com> Date: Mon, 29 Jul 2024 11:38:18 +0100 Subject: [PATCH 12/20] Fix snake_case field names --- docs/jsonBrowser/module.md | 52 +++++++++---------- .../module/biomaterial/medical_tests.json | 52 +++++++++---------- 2 files changed, 52 insertions(+), 52 deletions(-) diff --git a/docs/jsonBrowser/module.md b/docs/jsonBrowser/module.md index e26a76d5f..8398eb236 100644 --- a/docs/jsonBrowser/module.md +++ b/docs/jsonBrowser/module.md @@ -433,32 +433,32 @@ Location: module/biomaterial/medical_tests.json Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example --- | --- | --- | --- | --- | --- | --- | --- -PFT_method | Indicate which Pulmonary Function Testings (PFTs) methods were performed. Please indicate all tests performed. | array | no | | Pulmonary Function Testing method | spirometry, plethysmography, DLCO_KCO_test | spirometry; plethysmography; DLCO_KCO_test -PFT_age | Indicate the age of the subject at the time point of Pulmonary Function Testing (PFT) in years, if known. | number | no | | Age at Pulmonary Function Test | | 10; 34; 68 -PFT_time_point | Indicate at which date the Pulmonary Function Testing (PFT) were recorded as YYYY-MM-DD if available. If this information is not shareable, please indicate 'not_shareable'. | string | no | | Date at Pulmonary Function Test | | 2024-11-14; 2019-01-31; not_shareable -PFT_relative_time_point | If timepoint of sample collection (time of collection) and/or timepoint of PFT recording (PFT_time_point) is not available, indicate how many days prior or after sample collection the pulmonary function parameters were assessed if available. | string | no | | Days between collection and Pulmonary Function Test | | -5; 2; 0 -FEV1_predicted | Indicate the predicted Forced Expiratory Volume in 1 second (FEV1) in milliliters, based on patient age, sex, height, and ethnicity, if available. | number | no | | FEV1 predicted | | 3500; 4200; 2800 -FEV1_preBD | Indicate the measured FEV1 in milliliters before the administration of a bronchodilator if available. | number | no | | FEV1 before bronchodilator | | 3000; 3800; 2600 -FEV1_postBD | Indicate the measured FEV1 in milliliters after the administration of a bronchodilator if available. | number | no | | FEV1 after bronchodilator | | 3200; 4000; 2700 -FEV1_preBD_predicted_percent | Indicate the percentage of the predicted FEV1 achieved before bronchodilator administration if available. | number | no | | FEV1 percent of preBD to predicted | | 86; 90; 78 -FEV1_postBD_predicted_percent | Indicate the percentage of the predicted FEV1 achieved after bronchodilator administration if available. | number | no | | FEV1 percent of postBD to predicted | | 91; 95; 82 -FVC_predicted | Indicate the predicted Forced Vital Capacity (FVC) in milliliters, based on patient age, sex, height, and ethnicity, if available. | number | no | | FVC predicted | | 4500; 5000; 3800 -FVC_preBD | Indicate the measured FVC in milliliters before bronchodilator administration if available. | number | no | | FVC before bronchodilator | | 4000; 4800; 3600 -FVC_postBD | Indicate the measured FVC in milliliters after bronchodilator administration if available. | number | no | | FVC after bronchodilator | | 4200; 5000; 3700 -FVC_preBD_predicted_percent | Indicate the percentage of the predicted FVC achieved before bronchodilator administration if available. | number | no | | FVC percent of preBD to predicted | | 89; 96; 95 -FVC_postBD_predicted_percent | Indicate the percentage of the predicted FVC achieved after bronchodilator administration if available. | number | no | | FVC percent of postBD to predicted | | 93; 100; 97 -FEV1_FVC_ratio_preBD | Indicate the ratio of FEV1 to FVC before bronchodilator administration if available. | number | no | | FEV1 to FVC ratio before bronchodilator | | 0.75; 0.79; 0.72 -FEV1_FVC_ratio_postBD | Indicate the ratio of FEV1 to FVC after bronchodilator administration if available. | number | no | | FEV1 to FVC ratio after bronchodilator | | 0.76; 0.80; 0.73 -FRC_abs | Indicate the Functional Residual Capacity (FRC) in absolute milliliters if available. | number | no | | FRC absolute | | 3000; 3500; 2700 -FRC_predicted_percent | Indicate the percentage of the predicted FRC, based on patient demographics, if available. | number | no | | FRC percent of predicted | | 95; 88; 102 -RV | Indicate the Residual Volume (RV) in milliliters if available. | number | no | | RV | | 1500; 1800; 1400 -RV_predicted_percent | Indicate the percentage of the predicted RV, based on patient demographics, if available. | number | no | | RV percent of predicted | | 80; 90; 85 -IC | Indicate the Inspiratory Capacity (IC) in milliliters if available. | number | no | | IC | | 3500; 4000; 3200 -IC_predicted_percent | Indicate the percentage of the predicted IC, based on patient demographics, if available. | number | no | | IC percent of predicted | | 92; 85; 97 -DLCO | Indicate the Diffusing Capacity of the Lung for Carbon Monoxide (DLCO) in milliliters if available. | number | no | | DLCO | | 25; 30; 22 -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 +pft_method | Indicate which Pulmonary Function Testings (PFTs) methods were performed. Please indicate all tests performed. | array | no | | Pulmonary Function Testing method | spirometry, plethysmography, DLCO_KCO_test | spirometry; plethysmography; DLCO_KCO_test +pft_age | Indicate the age of the subject at the time point of Pulmonary Function Testing (PFT) in years, if known. | number | no | | Age at Pulmonary Function Test | | 10; 34; 68 +pft_time_point | Indicate at which date the Pulmonary Function Testing (PFT) were recorded as YYYY-MM-DD if available. If this information is not shareable, please indicate 'not_shareable'. | string | no | | Date at Pulmonary Function Test | | 2024-11-14; 2019-01-31; not_shareable +pft_relative_time_point | If timepoint of sample collection (time of collection) and/or timepoint of PFT recording (PFT_time_point) is not available, indicate how many days prior or after sample collection the pulmonary function parameters were assessed if available. | string | no | | Days between collection and Pulmonary Function Test | | -5; 2; 0 +fev1_predicted | Indicate the predicted Forced Expiratory Volume in 1 second (FEV1) in milliliters, based on patient age, sex, height, and ethnicity, if available. | number | no | | FEV1 predicted | | 3500; 4200; 2800 +fev1_prebd | Indicate the measured FEV1 in milliliters before the administration of a bronchodilator if available. | number | no | | FEV1 before bronchodilator | | 3000; 3800; 2600 +fev1_postbd | Indicate the measured FEV1 in milliliters after the administration of a bronchodilator if available. | number | no | | FEV1 after bronchodilator | | 3200; 4000; 2700 +fev1_prebd_predicted_percent | Indicate the percentage of the predicted FEV1 achieved before bronchodilator administration if available. | number | no | | FEV1 percent of preBD to predicted | | 86; 90; 78 +fev1_postbd_predicted_percent | Indicate the percentage of the predicted FEV1 achieved after bronchodilator administration if available. | number | no | | FEV1 percent of postBD to predicted | | 91; 95; 82 +fvc_predicted | Indicate the predicted Forced Vital Capacity (FVC) in milliliters, based on patient age, sex, height, and ethnicity, if available. | number | no | | FVC predicted | | 4500; 5000; 3800 +fvc_prebd | Indicate the measured FVC in milliliters before bronchodilator administration if available. | number | no | | FVC before bronchodilator | | 4000; 4800; 3600 +fvc_postbd | Indicate the measured FVC in milliliters after bronchodilator administration if available. | number | no | | FVC after bronchodilator | | 4200; 5000; 3700 +fvc_prebd_predicted_percent | Indicate the percentage of the predicted FVC achieved before bronchodilator administration if available. | number | no | | FVC percent of preBD to predicted | | 89; 96; 95 +fvc_postbd_predicted_percent | Indicate the percentage of the predicted FVC achieved after bronchodilator administration if available. | number | no | | FVC percent of postBD to predicted | | 93; 100; 97 +fev1_fvc_ratio_prebd | Indicate the ratio of FEV1 to FVC before bronchodilator administration if available. | number | no | | FEV1 to FVC ratio before bronchodilator | | 0.75; 0.79; 0.72 +fev1_fvc_ratio_postbd | Indicate the ratio of FEV1 to FVC after bronchodilator administration if available. | number | no | | FEV1 to FVC ratio after bronchodilator | | 0.76; 0.80; 0.73 +frc_abs | Indicate the Functional Residual Capacity (FRC) in absolute milliliters if available. | number | no | | FRC absolute | | 3000; 3500; 2700 +frc_predicted_percent | Indicate the percentage of the predicted FRC, based on patient demographics, if available. | number | no | | FRC percent of predicted | | 95; 88; 102 +rv | Indicate the Residual Volume (RV) in milliliters if available. | number | no | | RV | | 1500; 1800; 1400 +rv_predicted_percent | Indicate the percentage of the predicted RV, based on patient demographics, if available. | number | no | | RV percent of predicted | | 80; 90; 85 +ic | Indicate the Inspiratory Capacity (IC) in milliliters if available. | number | no | | IC | | 3500; 4000; 3200 +ic_predicted_percent | Indicate the percentage of the predicted IC, based on patient demographics, if available. | number | no | | IC percent of predicted | | 92; 85; 97 +dlco | Indicate the Diffusing Capacity of the Lung for Carbon Monoxide (DLCO) in milliliters if available. | number | no | | DLCO | | 25; 30; 22 +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 ## Preservation and storage _Information relating to how a biomaterial was preserved and/or stored over a period of time._ diff --git a/json_schema/module/biomaterial/medical_tests.json b/json_schema/module/biomaterial/medical_tests.json index 864cfc5ba..bfcd17b06 100644 --- a/json_schema/module/biomaterial/medical_tests.json +++ b/json_schema/module/biomaterial/medical_tests.json @@ -17,7 +17,7 @@ "pattern": "^[0-9]{1,}.[0-9]{1,}.[0-9]{1,}$", "example": "0.0.1" }, - "PFT_method": { + "pft_method": { "user_friendly": "Pulmonary Function Testing method", "description": "Indicate which Pulmonary Function Testings (PFTs) methods were performed. Please indicate all tests performed.", "type": "array", @@ -29,7 +29,7 @@ "$comment": "pulmonary_function_parameter; lung", "guidelines": "Should be of spirometry, plethysmography and DLCO_KCO_test." }, - "PFT_age": { + "pft_age": { "user_friendly": "Age at Pulmonary Function Test", "description": "Indicate the age of the subject at the time point of Pulmonary Function Testing (PFT) in years, if known.", "type": "number", @@ -38,7 +38,7 @@ "minimum": 0, "$comment": "pulmonary_function_parameter; lung" }, - "PFT_time_point": { + "pft_time_point": { "user_friendly": "Date at Pulmonary Function Test", "description": "Indicate at which date the Pulmonary Function Testing (PFT) were recorded as YYYY-MM-DD if available. If this information is not shareable, please indicate 'not_shareable'.", "type": "string", @@ -47,7 +47,7 @@ "$comment": "pulmonary_function_parameter; lung", "guidelines": "If this information is not shareable, please indicate \\'not_shareable\\'." }, - "PFT_relative_time_point": { + "pft_relative_time_point": { "user_friendly": "Days between collection and Pulmonary Function Test", "description": "If timepoint of sample collection (time of collection) and/or timepoint of PFT recording (PFT_time_point) is not available, indicate how many days prior or after sample collection the pulmonary function parameters were assessed if available.", "type": "string", @@ -57,7 +57,7 @@ "guidelines": "If PFT recording was done before sample collection, then enter a negative day value. If PFT recording was done after sample collection, then enter a positive day value." }, - "FEV1_predicted": { + "fev1_predicted": { "user_friendly": "FEV1 predicted", "description": "Indicate the predicted Forced Expiratory Volume in 1 second (FEV1) in milliliters, based on patient age, sex, height, and ethnicity, if available.", "type": "number", @@ -66,7 +66,7 @@ "minimum": 0, "$comment": "pulmonary_function_parameter; lung" }, - "FEV1_preBD": { + "fev1_prebd": { "user_friendly": "FEV1 before bronchodilator", "description": "Indicate the measured FEV1 in milliliters before the administration of a bronchodilator if available.", "type": "number", @@ -75,7 +75,7 @@ "minimum": 0, "$comment": "pulmonary_function_parameter; lung" }, - "FEV1_postBD": { + "fev1_postbd": { "user_friendly": "FEV1 after bronchodilator", "description": "Indicate the measured FEV1 in milliliters after the administration of a bronchodilator if available.", "type": "number", @@ -84,7 +84,7 @@ "minimum": 0, "$comment": "pulmonary_function_parameter; lung" }, - "FEV1_preBD_predicted_percent": { + "fev1_prebd_predicted_percent": { "user_friendly": "FEV1 percent of preBD to predicted", "description": "Indicate the percentage of the predicted FEV1 achieved before bronchodilator administration if available.", "type": "number", @@ -93,7 +93,7 @@ "minimum": 0, "$comment": "pulmonary_function_parameter; lung" }, - "FEV1_postBD_predicted_percent": { + "fev1_postbd_predicted_percent": { "user_friendly": "FEV1 percent of postBD to predicted", "description": "Indicate the percentage of the predicted FEV1 achieved after bronchodilator administration if available.", "type": "number", @@ -102,7 +102,7 @@ "minimum": 0, "$comment": "pulmonary_function_parameter; lung" }, - "FVC_predicted": { + "fvc_predicted": { "user_friendly": "FVC predicted", "description": "Indicate the predicted Forced Vital Capacity (FVC) in milliliters, based on patient age, sex, height, and ethnicity, if available.", "type": "number", @@ -111,7 +111,7 @@ "minimum": 0, "$comment": "pulmonary_function_parameter; lung" }, - "FVC_preBD": { + "fvc_prebd": { "user_friendly": "FVC before bronchodilator", "description": "Indicate the measured FVC in milliliters before bronchodilator administration if available.", "type": "number", @@ -120,7 +120,7 @@ "minimum": 0, "$comment": "pulmonary_function_parameter; lung" }, - "FVC_postBD": { + "fvc_postbd": { "user_friendly": "FVC after bronchodilator", "description": "Indicate the measured FVC in milliliters after bronchodilator administration if available.", "type": "number", @@ -129,7 +129,7 @@ "minimum": 0, "$comment": "pulmonary_function_parameter; lung" }, - "FVC_preBD_predicted_percent": { + "fvc_prebd_predicted_percent": { "user_friendly": "FVC percent of preBD to predicted", "description": "Indicate the percentage of the predicted FVC achieved before bronchodilator administration if available.", "type": "number", @@ -138,7 +138,7 @@ "minimum": 0, "$comment": "pulmonary_function_parameter; lung" }, - "FVC_postBD_predicted_percent": { + "fvc_postbd_predicted_percent": { "user_friendly": "FVC percent of postBD to predicted", "description": "Indicate the percentage of the predicted FVC achieved after bronchodilator administration if available.", "type": "number", @@ -147,7 +147,7 @@ "minimum": 0, "$comment": "pulmonary_function_parameter; lung" }, - "FEV1_FVC_ratio_preBD": { + "fev1_fvc_ratio_prebd": { "user_friendly": "FEV1 to FVC ratio before bronchodilator", "description": "Indicate the ratio of FEV1 to FVC before bronchodilator administration if available.", "type": "number", @@ -156,7 +156,7 @@ "minimum": 0, "$comment": "pulmonary_function_parameter; lung" }, - "FEV1_FVC_ratio_postBD": { + "fev1_fvc_ratio_postbd": { "user_friendly": "FEV1 to FVC ratio after bronchodilator", "description": "Indicate the ratio of FEV1 to FVC after bronchodilator administration if available.", "type": "number", @@ -165,7 +165,7 @@ "minimum": 0, "$comment": "pulmonary_function_parameter; lung" }, - "FRC_abs": { + "frc_abs": { "user_friendly": "FRC absolute", "description": "Indicate the Functional Residual Capacity (FRC) in absolute milliliters if available.", "type": "number", @@ -174,7 +174,7 @@ "minimum": 0, "$comment": "pulmonary_function_parameter; lung" }, - "FRC_predicted_percent": { + "frc_predicted_percent": { "user_friendly": "FRC percent of predicted", "description": "Indicate the percentage of the predicted FRC, based on patient demographics, if available.", "type": "number", @@ -183,7 +183,7 @@ "minimum": 0, "$comment": "pulmonary_function_parameter; lung" }, - "RV": { + "rv": { "user_friendly": "RV", "description": "Indicate the Residual Volume (RV) in milliliters if available.", "type": "number", @@ -192,7 +192,7 @@ "minimum": 0, "$comment": "pulmonary_function_parameter; lung" }, - "RV_predicted_percent": { + "rv_predicted_percent": { "user_friendly": "RV percent of predicted", "description": "Indicate the percentage of the predicted RV, based on patient demographics, if available.", "type": "number", @@ -201,7 +201,7 @@ "minimum": 0, "$comment": "pulmonary_function_parameter; lung" }, - "IC": { + "ic": { "user_friendly": "IC", "description": "Indicate the Inspiratory Capacity (IC) in milliliters if available.", "type": "number", @@ -210,7 +210,7 @@ "minimum": 0, "$comment": "pulmonary_function_parameter; lung" }, - "IC_predicted_percent": { + "ic_predicted_percent": { "user_friendly": "IC percent of predicted", "description": "Indicate the percentage of the predicted IC, based on patient demographics, if available.", "type": "number", @@ -219,7 +219,7 @@ "minimum": 0, "$comment": "pulmonary_function_parameter; lung" }, - "DLCO": { + "dlco": { "user_friendly": "DLCO", "description": "Indicate the Diffusing Capacity of the Lung for Carbon Monoxide (DLCO) in milliliters if available.", "type": "number", @@ -228,7 +228,7 @@ "minimum": 5, "$comment": "pulmonary_function_parameter; lung" }, - "DLCO_predicted_percent": { + "dlco_predicted_percent": { "user_friendly": "DLCO percent of predicted", "description": "Indicate the percentage of the predicted DLCO, based on patient demographics, if available.", "type": "number", @@ -237,7 +237,7 @@ "minimum": 0, "$comment": "pulmonary_function_parameter; lung" }, - "KCO": { + "kco": { "user_friendly": "KCO", "description": "Indicate the transfer coefficient of the lung for carbon monoxide (KCO) in mmol/min/kPa/L if available.", "type": "number", @@ -246,7 +246,7 @@ "minimum": 0, "$comment": "pulmonary_function_parameter; lung" }, - "KCO_predicted_percent": { + "kco_predicted_percent": { "user_friendly": "KCO percent of predicted", "description": "Indicate the percentage of the predicted KCO, based on patient demographics, if available.", "type": "number", From 93656415550a4cbe8f0ddc559d40bcdbb76bfb77 Mon Sep 17 00:00:00 2001 From: Arsenios Chatzigeorgiou <49944135+arschat@users.noreply.github.com> Date: Mon, 29 Jul 2024 11:43:19 +0100 Subject: [PATCH 13/20] Fix user_friendly bronchodilator abbreviation for consistency --- docs/jsonBrowser/module.md | 8 ++++---- json_schema/module/biomaterial/medical_tests.json | 8 ++++---- 2 files changed, 8 insertions(+), 8 deletions(-) diff --git a/docs/jsonBrowser/module.md b/docs/jsonBrowser/module.md index 8398eb236..a33f0e0b3 100644 --- a/docs/jsonBrowser/module.md +++ b/docs/jsonBrowser/module.md @@ -440,13 +440,13 @@ pft_relative_time_point | If timepoint of sample collection (time of collection) fev1_predicted | Indicate the predicted Forced Expiratory Volume in 1 second (FEV1) in milliliters, based on patient age, sex, height, and ethnicity, if available. | number | no | | FEV1 predicted | | 3500; 4200; 2800 fev1_prebd | Indicate the measured FEV1 in milliliters before the administration of a bronchodilator if available. | number | no | | FEV1 before bronchodilator | | 3000; 3800; 2600 fev1_postbd | Indicate the measured FEV1 in milliliters after the administration of a bronchodilator if available. | number | no | | FEV1 after bronchodilator | | 3200; 4000; 2700 -fev1_prebd_predicted_percent | Indicate the percentage of the predicted FEV1 achieved before bronchodilator administration if available. | number | no | | FEV1 percent of preBD to predicted | | 86; 90; 78 -fev1_postbd_predicted_percent | Indicate the percentage of the predicted FEV1 achieved after bronchodilator administration if available. | number | no | | FEV1 percent of postBD to predicted | | 91; 95; 82 +fev1_prebd_predicted_percent | Indicate the percentage of the predicted FEV1 achieved before bronchodilator administration if available. | number | no | | FEV1 before bronchodilator percent of predicted | | 86; 90; 78 +fev1_postbd_predicted_percent | Indicate the percentage of the predicted FEV1 achieved after bronchodilator administration if available. | number | no | | FEV1 after bronchodilator percent of predicted | | 91; 95; 82 fvc_predicted | Indicate the predicted Forced Vital Capacity (FVC) in milliliters, based on patient age, sex, height, and ethnicity, if available. | number | no | | FVC predicted | | 4500; 5000; 3800 fvc_prebd | Indicate the measured FVC in milliliters before bronchodilator administration if available. | number | no | | FVC before bronchodilator | | 4000; 4800; 3600 fvc_postbd | Indicate the measured FVC in milliliters after bronchodilator administration if available. | number | no | | FVC after bronchodilator | | 4200; 5000; 3700 -fvc_prebd_predicted_percent | Indicate the percentage of the predicted FVC achieved before bronchodilator administration if available. | number | no | | FVC percent of preBD to predicted | | 89; 96; 95 -fvc_postbd_predicted_percent | Indicate the percentage of the predicted FVC achieved after bronchodilator administration if available. | number | no | | FVC percent of postBD to predicted | | 93; 100; 97 +fvc_prebd_predicted_percent | Indicate the percentage of the predicted FVC achieved before bronchodilator administration if available. | number | no | | FVC before bronchodilator percent of predicted | | 89; 96; 95 +fvc_postbd_predicted_percent | Indicate the percentage of the predicted FVC achieved after bronchodilator administration if available. | number | no | | FVC after bronchodilator percent of predicted | | 93; 100; 97 fev1_fvc_ratio_prebd | Indicate the ratio of FEV1 to FVC before bronchodilator administration if available. | number | no | | FEV1 to FVC ratio before bronchodilator | | 0.75; 0.79; 0.72 fev1_fvc_ratio_postbd | Indicate the ratio of FEV1 to FVC after bronchodilator administration if available. | number | no | | FEV1 to FVC ratio after bronchodilator | | 0.76; 0.80; 0.73 frc_abs | Indicate the Functional Residual Capacity (FRC) in absolute milliliters if available. | number | no | | FRC absolute | | 3000; 3500; 2700 diff --git a/json_schema/module/biomaterial/medical_tests.json b/json_schema/module/biomaterial/medical_tests.json index bfcd17b06..ef5d49411 100644 --- a/json_schema/module/biomaterial/medical_tests.json +++ b/json_schema/module/biomaterial/medical_tests.json @@ -85,7 +85,7 @@ "$comment": "pulmonary_function_parameter; lung" }, "fev1_prebd_predicted_percent": { - "user_friendly": "FEV1 percent of preBD to predicted", + "user_friendly": "FEV1 before bronchodilator percent of predicted", "description": "Indicate the percentage of the predicted FEV1 achieved before bronchodilator administration if available.", "type": "number", "example": "86; 90; 78", @@ -94,7 +94,7 @@ "$comment": "pulmonary_function_parameter; lung" }, "fev1_postbd_predicted_percent": { - "user_friendly": "FEV1 percent of postBD to predicted", + "user_friendly": "FEV1 after bronchodilator percent of predicted", "description": "Indicate the percentage of the predicted FEV1 achieved after bronchodilator administration if available.", "type": "number", "example": "91; 95; 82", @@ -130,7 +130,7 @@ "$comment": "pulmonary_function_parameter; lung" }, "fvc_prebd_predicted_percent": { - "user_friendly": "FVC percent of preBD to predicted", + "user_friendly": "FVC before bronchodilator percent of predicted", "description": "Indicate the percentage of the predicted FVC achieved before bronchodilator administration if available.", "type": "number", "example": "89; 96; 95", @@ -139,7 +139,7 @@ "$comment": "pulmonary_function_parameter; lung" }, "fvc_postbd_predicted_percent": { - "user_friendly": "FVC percent of postBD to predicted", + "user_friendly": "FVC after bronchodilator percent of predicted", "description": "Indicate the percentage of the predicted FVC achieved after bronchodilator administration if available.", "type": "number", "example": "93; 100; 97", From fcb3e7ea4ee79ca998e6ea9c0df08117e6397271 Mon Sep 17 00:00:00 2001 From: Arsenios Chatzigeorgiou <49944135+arschat@users.noreply.github.com> Date: Mon, 29 Jul 2024 16:20:19 +0100 Subject: [PATCH 14/20] Add rule to restrict empty module --- json_schema/module/biomaterial/medical_tests.json | 1 + src/schema_linter.py | 2 +- 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/json_schema/module/biomaterial/medical_tests.json b/json_schema/module/biomaterial/medical_tests.json index ef5d49411..d219275f3 100644 --- a/json_schema/module/biomaterial/medical_tests.json +++ b/json_schema/module/biomaterial/medical_tests.json @@ -5,6 +5,7 @@ "title": "Medical tests", "name": "medical_tests", "type": "object", + "minProperties": 1, "properties": { "describedBy": { "description": "The URL reference to the schema.", diff --git a/src/schema_linter.py b/src/schema_linter.py index 0404e028b..c82d06f7e 100644 --- a/src/schema_linter.py +++ b/src/schema_linter.py @@ -16,7 +16,7 @@ required_schema_fields = ['$schema', 'description', 'additionalProperties', 'title', 'name', 'type', 'properties'] -allowed_schema_fields = ['$schema', 'description', 'additionalProperties', 'required', 'title', 'name', 'type', 'properties', 'definitions', 'dependencies', 'if', 'then', 'else'] +allowed_schema_fields = ['$schema', 'description', 'additionalProperties', 'required', 'title', 'name', 'type', 'properties', 'definitions', 'dependencies', 'if', 'then', 'else', 'minProperties'] # Properties From 986903a1d4121e3f93ef80a5d3df44f88bcd7e19 Mon Sep 17 00:00:00 2001 From: Arsenios Chatzigeorgiou <49944135+arschat@users.noreply.github.com> Date: Tue, 30 Jul 2024 10:11:28 +0100 Subject: [PATCH 15/20] Fix pft_relative_time_point type to integer --- docs/jsonBrowser/module.md | 2 +- json_schema/module/biomaterial/medical_tests.json | 7 +++---- 2 files changed, 4 insertions(+), 5 deletions(-) diff --git a/docs/jsonBrowser/module.md b/docs/jsonBrowser/module.md index a33f0e0b3..44d0a60b7 100644 --- a/docs/jsonBrowser/module.md +++ b/docs/jsonBrowser/module.md @@ -436,7 +436,7 @@ Property name | Description | Type | Required? | Object reference? | User friend pft_method | Indicate which Pulmonary Function Testings (PFTs) methods were performed. Please indicate all tests performed. | array | no | | Pulmonary Function Testing method | spirometry, plethysmography, DLCO_KCO_test | spirometry; plethysmography; DLCO_KCO_test pft_age | Indicate the age of the subject at the time point of Pulmonary Function Testing (PFT) in years, if known. | number | no | | Age at Pulmonary Function Test | | 10; 34; 68 pft_time_point | Indicate at which date the Pulmonary Function Testing (PFT) were recorded as YYYY-MM-DD if available. If this information is not shareable, please indicate 'not_shareable'. | string | no | | Date at Pulmonary Function Test | | 2024-11-14; 2019-01-31; not_shareable -pft_relative_time_point | If timepoint of sample collection (time of collection) and/or timepoint of PFT recording (PFT_time_point) is not available, indicate how many days prior or after sample collection the pulmonary function parameters were assessed if available. | string | no | | Days between collection and Pulmonary Function Test | | -5; 2; 0 +pft_relative_time_point | If timepoint of sample collection (time of collection) and/or timepoint of PFT recording (pft_time_point) is not available, indicate how many days prior or after sample collection the pulmonary function parameters were assessed if available. | integer | no | | Days between collection and Pulmonary Function Test | | -5; 2; 0 fev1_predicted | Indicate the predicted Forced Expiratory Volume in 1 second (FEV1) in milliliters, based on patient age, sex, height, and ethnicity, if available. | number | no | | FEV1 predicted | | 3500; 4200; 2800 fev1_prebd | Indicate the measured FEV1 in milliliters before the administration of a bronchodilator if available. | number | no | | FEV1 before bronchodilator | | 3000; 3800; 2600 fev1_postbd | Indicate the measured FEV1 in milliliters after the administration of a bronchodilator if available. | number | no | | FEV1 after bronchodilator | | 3200; 4000; 2700 diff --git a/json_schema/module/biomaterial/medical_tests.json b/json_schema/module/biomaterial/medical_tests.json index d219275f3..bad11dce0 100644 --- a/json_schema/module/biomaterial/medical_tests.json +++ b/json_schema/module/biomaterial/medical_tests.json @@ -50,12 +50,11 @@ }, "pft_relative_time_point": { "user_friendly": "Days between collection and Pulmonary Function Test", - "description": "If timepoint of sample collection (time of collection) and/or timepoint of PFT recording (PFT_time_point) is not available, indicate how many days prior or after sample collection the pulmonary function parameters were assessed if available.", - "type": "string", + "description": "If timepoint of sample collection (time of collection) and/or timepoint of PFT recording (pft_time_point) is not available, indicate how many days prior or after sample collection the pulmonary function parameters were assessed if available.", + "type": "integer", "example": "-5; 2; 0", - "pattern": "^[\\+\\-]?[0-9]+$", "$comment": "pulmonary_function_parameter; lung", - "guidelines": "If PFT recording was done before sample collection, then enter a negative day value. If PFT recording was done after sample collection, then enter a positive day value." + "guidelines": "If PFT recording was done before sample collection, then enter a negative day value. If PFT recording was done after sample collection, then enter an unsigned positive day value." }, "fev1_predicted": { From b6b02fdd8d98ac6716decd6e5875f27c9de58078 Mon Sep 17 00:00:00 2001 From: Arsenios Chatzigeorgiou <49944135+arschat@users.noreply.github.com> Date: Thu, 1 Aug 2024 10:18:37 +0100 Subject: [PATCH 16/20] Change $comment keyword to bionetwork --- .../module/biomaterial/medical_tests.json | 52 +++++++++---------- src/schema_linter.py | 2 +- 2 files changed, 27 insertions(+), 27 deletions(-) diff --git a/json_schema/module/biomaterial/medical_tests.json b/json_schema/module/biomaterial/medical_tests.json index bad11dce0..1cf200855 100644 --- a/json_schema/module/biomaterial/medical_tests.json +++ b/json_schema/module/biomaterial/medical_tests.json @@ -27,7 +27,7 @@ "enum": ["spirometry", "plethysmography", "DLCO_KCO_test"] }, "example": "spirometry; plethysmography; DLCO_KCO_test", - "$comment": "pulmonary_function_parameter; lung", + "bionetwork": "lung", "guidelines": "Should be of spirometry, plethysmography and DLCO_KCO_test." }, "pft_age": { @@ -37,7 +37,7 @@ "example": "10; 34; 68", "maximum": 150, "minimum": 0, - "$comment": "pulmonary_function_parameter; lung" + "bionetwork": "lung" }, "pft_time_point": { "user_friendly": "Date at Pulmonary Function Test", @@ -45,7 +45,7 @@ "type": "string", "example": "2024-11-14; 2019-01-31; not_shareable", "pattern": "^(((19|20)\\d\\d){1}([- \\./][01]\\d){0,1}([- \\./][0-3]\\d){0,1}|not_shareable)$", - "$comment": "pulmonary_function_parameter; lung", + "bionetwork": "lung", "guidelines": "If this information is not shareable, please indicate \\'not_shareable\\'." }, "pft_relative_time_point": { @@ -53,7 +53,7 @@ "description": "If timepoint of sample collection (time of collection) and/or timepoint of PFT recording (pft_time_point) is not available, indicate how many days prior or after sample collection the pulmonary function parameters were assessed if available.", "type": "integer", "example": "-5; 2; 0", - "$comment": "pulmonary_function_parameter; lung", + "bionetwork": "lung", "guidelines": "If PFT recording was done before sample collection, then enter a negative day value. If PFT recording was done after sample collection, then enter an unsigned positive day value." }, @@ -64,7 +64,7 @@ "example": "3500; 4200; 2800", "maximum": 15000, "minimum": 0, - "$comment": "pulmonary_function_parameter; lung" + "bionetwork": "lung" }, "fev1_prebd": { "user_friendly": "FEV1 before bronchodilator", @@ -73,7 +73,7 @@ "example": "3000; 3800; 2600", "maximum": 15000, "minimum": 0, - "$comment": "pulmonary_function_parameter; lung" + "bionetwork": "lung" }, "fev1_postbd": { "user_friendly": "FEV1 after bronchodilator", @@ -82,7 +82,7 @@ "example": "3200; 4000; 2700", "maximum": 15000, "minimum": 0, - "$comment": "pulmonary_function_parameter; lung" + "bionetwork": "lung" }, "fev1_prebd_predicted_percent": { "user_friendly": "FEV1 before bronchodilator percent of predicted", @@ -91,7 +91,7 @@ "example": "86; 90; 78", "maximum": 200, "minimum": 0, - "$comment": "pulmonary_function_parameter; lung" + "bionetwork": "lung" }, "fev1_postbd_predicted_percent": { "user_friendly": "FEV1 after bronchodilator percent of predicted", @@ -100,7 +100,7 @@ "example": "91; 95; 82", "maximum": 200, "minimum": 0, - "$comment": "pulmonary_function_parameter; lung" + "bionetwork": "lung" }, "fvc_predicted": { "user_friendly": "FVC predicted", @@ -109,7 +109,7 @@ "example": "4500; 5000; 3800", "maximum": 15000, "minimum": 0, - "$comment": "pulmonary_function_parameter; lung" + "bionetwork": "lung" }, "fvc_prebd": { "user_friendly": "FVC before bronchodilator", @@ -118,7 +118,7 @@ "example": "4000; 4800; 3600", "maximum": 15000, "minimum": 0, - "$comment": "pulmonary_function_parameter; lung" + "bionetwork": "lung" }, "fvc_postbd": { "user_friendly": "FVC after bronchodilator", @@ -127,7 +127,7 @@ "example": "4200; 5000; 3700", "maximum": 15000, "minimum": 0, - "$comment": "pulmonary_function_parameter; lung" + "bionetwork": "lung" }, "fvc_prebd_predicted_percent": { "user_friendly": "FVC before bronchodilator percent of predicted", @@ -136,7 +136,7 @@ "example": "89; 96; 95", "maximum": 200, "minimum": 0, - "$comment": "pulmonary_function_parameter; lung" + "bionetwork": "lung" }, "fvc_postbd_predicted_percent": { "user_friendly": "FVC after bronchodilator percent of predicted", @@ -145,7 +145,7 @@ "example": "93; 100; 97", "maximum": 200, "minimum": 0, - "$comment": "pulmonary_function_parameter; lung" + "bionetwork": "lung" }, "fev1_fvc_ratio_prebd": { "user_friendly": "FEV1 to FVC ratio before bronchodilator", @@ -154,7 +154,7 @@ "example": "0.75; 0.79; 0.72", "maximum": 1, "minimum": 0, - "$comment": "pulmonary_function_parameter; lung" + "bionetwork": "lung" }, "fev1_fvc_ratio_postbd": { "user_friendly": "FEV1 to FVC ratio after bronchodilator", @@ -163,7 +163,7 @@ "example": "0.76; 0.80; 0.73", "maximum": 1, "minimum": 0, - "$comment": "pulmonary_function_parameter; lung" + "bionetwork": "lung" }, "frc_abs": { "user_friendly": "FRC absolute", @@ -172,7 +172,7 @@ "example": "3000; 3500; 2700", "maximum": 15000, "minimum": 0, - "$comment": "pulmonary_function_parameter; lung" + "bionetwork": "lung" }, "frc_predicted_percent": { "user_friendly": "FRC percent of predicted", @@ -181,7 +181,7 @@ "example": "95; 88; 102", "maximum": 200, "minimum": 0, - "$comment": "pulmonary_function_parameter; lung" + "bionetwork": "lung" }, "rv": { "user_friendly": "RV", @@ -190,7 +190,7 @@ "example": "1500; 1800; 1400", "maximum": 15000, "minimum": 0, - "$comment": "pulmonary_function_parameter; lung" + "bionetwork": "lung" }, "rv_predicted_percent": { "user_friendly": "RV percent of predicted", @@ -199,7 +199,7 @@ "example": "80; 90; 85", "maximum": 200, "minimum": 0, - "$comment": "pulmonary_function_parameter; lung" + "bionetwork": "lung" }, "ic": { "user_friendly": "IC", @@ -208,7 +208,7 @@ "example": "3500; 4000; 3200", "maximum": 15000, "minimum": 0, - "$comment": "pulmonary_function_parameter; lung" + "bionetwork": "lung" }, "ic_predicted_percent": { "user_friendly": "IC percent of predicted", @@ -217,7 +217,7 @@ "example": "92; 85; 97", "maximum": 200, "minimum": 0, - "$comment": "pulmonary_function_parameter; lung" + "bionetwork": "lung" }, "dlco": { "user_friendly": "DLCO", @@ -226,7 +226,7 @@ "example": "25; 30; 22", "maximum": 100, "minimum": 5, - "$comment": "pulmonary_function_parameter; lung" + "bionetwork": "lung" }, "dlco_predicted_percent": { "user_friendly": "DLCO percent of predicted", @@ -235,7 +235,7 @@ "example": "88; 95; 82", "maximum": 200, "minimum": 0, - "$comment": "pulmonary_function_parameter; lung" + "bionetwork": "lung" }, "kco": { "user_friendly": "KCO", @@ -244,7 +244,7 @@ "example": "5; 6; 4.5", "maximum": 15000, "minimum": 0, - "$comment": "pulmonary_function_parameter; lung" + "bionetwork": "lung" }, "kco_predicted_percent": { "user_friendly": "KCO percent of predicted", @@ -253,7 +253,7 @@ "example": "90; 98; 85", "maximum": 200, "minimum": 0, - "$comment": "pulmonary_function_parameter; lung" + "bionetwork": "lung" } } } diff --git a/src/schema_linter.py b/src/schema_linter.py index c82d06f7e..9793d6bae 100644 --- a/src/schema_linter.py +++ b/src/schema_linter.py @@ -32,7 +32,7 @@ # Property attributes -property_attributes = ['description', 'type', 'pattern', 'example', 'enum', '$ref', 'user_friendly', 'items', 'guidelines', 'format', 'comment', 'maximum', 'minimum', 'oneOf', '$comment'] +property_attributes = ['description', 'type', 'pattern', 'example', 'enum', '$ref', 'user_friendly', 'items', 'guidelines', 'format', 'comment', 'maximum', 'minimum', 'oneOf', 'bionetwork'] ontology_attributes = ['graph_restriction', 'ontologies', 'classes', 'relations', 'direct', 'include_self'] From 61b26092e98444b24b287b6a94401ad95c00338c Mon Sep 17 00:00:00 2001 From: Arsenios Chatzigeorgiou <49944135+arschat@users.noreply.github.com> Date: Wed, 7 Aug 2024 11:00:27 +0100 Subject: [PATCH 17/20] Changing bionetwork attribute to array --- .../module/biomaterial/medical_tests.json | 52 +++++++++---------- 1 file changed, 26 insertions(+), 26 deletions(-) diff --git a/json_schema/module/biomaterial/medical_tests.json b/json_schema/module/biomaterial/medical_tests.json index 1cf200855..1fbf70fcc 100644 --- a/json_schema/module/biomaterial/medical_tests.json +++ b/json_schema/module/biomaterial/medical_tests.json @@ -27,7 +27,7 @@ "enum": ["spirometry", "plethysmography", "DLCO_KCO_test"] }, "example": "spirometry; plethysmography; DLCO_KCO_test", - "bionetwork": "lung", + "bionetwork": ["lung"], "guidelines": "Should be of spirometry, plethysmography and DLCO_KCO_test." }, "pft_age": { @@ -37,7 +37,7 @@ "example": "10; 34; 68", "maximum": 150, "minimum": 0, - "bionetwork": "lung" + "bionetwork": ["lung"] }, "pft_time_point": { "user_friendly": "Date at Pulmonary Function Test", @@ -45,7 +45,7 @@ "type": "string", "example": "2024-11-14; 2019-01-31; not_shareable", "pattern": "^(((19|20)\\d\\d){1}([- \\./][01]\\d){0,1}([- \\./][0-3]\\d){0,1}|not_shareable)$", - "bionetwork": "lung", + "bionetwork": ["lung"], "guidelines": "If this information is not shareable, please indicate \\'not_shareable\\'." }, "pft_relative_time_point": { @@ -53,7 +53,7 @@ "description": "If timepoint of sample collection (time of collection) and/or timepoint of PFT recording (pft_time_point) is not available, indicate how many days prior or after sample collection the pulmonary function parameters were assessed if available.", "type": "integer", "example": "-5; 2; 0", - "bionetwork": "lung", + "bionetwork": ["lung"], "guidelines": "If PFT recording was done before sample collection, then enter a negative day value. If PFT recording was done after sample collection, then enter an unsigned positive day value." }, @@ -64,7 +64,7 @@ "example": "3500; 4200; 2800", "maximum": 15000, "minimum": 0, - "bionetwork": "lung" + "bionetwork": ["lung"] }, "fev1_prebd": { "user_friendly": "FEV1 before bronchodilator", @@ -73,7 +73,7 @@ "example": "3000; 3800; 2600", "maximum": 15000, "minimum": 0, - "bionetwork": "lung" + "bionetwork": ["lung"] }, "fev1_postbd": { "user_friendly": "FEV1 after bronchodilator", @@ -82,7 +82,7 @@ "example": "3200; 4000; 2700", "maximum": 15000, "minimum": 0, - "bionetwork": "lung" + "bionetwork": ["lung"] }, "fev1_prebd_predicted_percent": { "user_friendly": "FEV1 before bronchodilator percent of predicted", @@ -91,7 +91,7 @@ "example": "86; 90; 78", "maximum": 200, "minimum": 0, - "bionetwork": "lung" + "bionetwork": ["lung"] }, "fev1_postbd_predicted_percent": { "user_friendly": "FEV1 after bronchodilator percent of predicted", @@ -100,7 +100,7 @@ "example": "91; 95; 82", "maximum": 200, "minimum": 0, - "bionetwork": "lung" + "bionetwork": ["lung"] }, "fvc_predicted": { "user_friendly": "FVC predicted", @@ -109,7 +109,7 @@ "example": "4500; 5000; 3800", "maximum": 15000, "minimum": 0, - "bionetwork": "lung" + "bionetwork": ["lung"] }, "fvc_prebd": { "user_friendly": "FVC before bronchodilator", @@ -118,7 +118,7 @@ "example": "4000; 4800; 3600", "maximum": 15000, "minimum": 0, - "bionetwork": "lung" + "bionetwork": ["lung"] }, "fvc_postbd": { "user_friendly": "FVC after bronchodilator", @@ -127,7 +127,7 @@ "example": "4200; 5000; 3700", "maximum": 15000, "minimum": 0, - "bionetwork": "lung" + "bionetwork": ["lung"] }, "fvc_prebd_predicted_percent": { "user_friendly": "FVC before bronchodilator percent of predicted", @@ -136,7 +136,7 @@ "example": "89; 96; 95", "maximum": 200, "minimum": 0, - "bionetwork": "lung" + "bionetwork": ["lung"] }, "fvc_postbd_predicted_percent": { "user_friendly": "FVC after bronchodilator percent of predicted", @@ -145,7 +145,7 @@ "example": "93; 100; 97", "maximum": 200, "minimum": 0, - "bionetwork": "lung" + "bionetwork": ["lung"] }, "fev1_fvc_ratio_prebd": { "user_friendly": "FEV1 to FVC ratio before bronchodilator", @@ -154,7 +154,7 @@ "example": "0.75; 0.79; 0.72", "maximum": 1, "minimum": 0, - "bionetwork": "lung" + "bionetwork": ["lung"] }, "fev1_fvc_ratio_postbd": { "user_friendly": "FEV1 to FVC ratio after bronchodilator", @@ -163,7 +163,7 @@ "example": "0.76; 0.80; 0.73", "maximum": 1, "minimum": 0, - "bionetwork": "lung" + "bionetwork": ["lung"] }, "frc_abs": { "user_friendly": "FRC absolute", @@ -172,7 +172,7 @@ "example": "3000; 3500; 2700", "maximum": 15000, "minimum": 0, - "bionetwork": "lung" + "bionetwork": ["lung"] }, "frc_predicted_percent": { "user_friendly": "FRC percent of predicted", @@ -181,7 +181,7 @@ "example": "95; 88; 102", "maximum": 200, "minimum": 0, - "bionetwork": "lung" + "bionetwork": ["lung"] }, "rv": { "user_friendly": "RV", @@ -190,7 +190,7 @@ "example": "1500; 1800; 1400", "maximum": 15000, "minimum": 0, - "bionetwork": "lung" + "bionetwork": ["lung"] }, "rv_predicted_percent": { "user_friendly": "RV percent of predicted", @@ -199,7 +199,7 @@ "example": "80; 90; 85", "maximum": 200, "minimum": 0, - "bionetwork": "lung" + "bionetwork": ["lung"] }, "ic": { "user_friendly": "IC", @@ -208,7 +208,7 @@ "example": "3500; 4000; 3200", "maximum": 15000, "minimum": 0, - "bionetwork": "lung" + "bionetwork": ["lung"] }, "ic_predicted_percent": { "user_friendly": "IC percent of predicted", @@ -217,7 +217,7 @@ "example": "92; 85; 97", "maximum": 200, "minimum": 0, - "bionetwork": "lung" + "bionetwork": ["lung"] }, "dlco": { "user_friendly": "DLCO", @@ -226,7 +226,7 @@ "example": "25; 30; 22", "maximum": 100, "minimum": 5, - "bionetwork": "lung" + "bionetwork": ["lung"] }, "dlco_predicted_percent": { "user_friendly": "DLCO percent of predicted", @@ -235,7 +235,7 @@ "example": "88; 95; 82", "maximum": 200, "minimum": 0, - "bionetwork": "lung" + "bionetwork": ["lung"] }, "kco": { "user_friendly": "KCO", @@ -244,7 +244,7 @@ "example": "5; 6; 4.5", "maximum": 15000, "minimum": 0, - "bionetwork": "lung" + "bionetwork": ["lung"] }, "kco_predicted_percent": { "user_friendly": "KCO percent of predicted", @@ -253,7 +253,7 @@ "example": "90; 98; 85", "maximum": 200, "minimum": 0, - "bionetwork": "lung" + "bionetwork": ["lung"] } } } From e6209ef9631cf67999fcbfef4a23d0a8727c67e1 Mon Sep 17 00:00:00 2001 From: Arsenios Chatzigeorgiou <49944135+arschat@users.noreply.github.com> Date: Wed, 7 Aug 2024 11:03:36 +0100 Subject: [PATCH 18/20] Change bionetwork attribute to plural "bionetworks" --- .../module/biomaterial/medical_tests.json | 52 +++++++++---------- src/schema_linter.py | 2 +- 2 files changed, 27 insertions(+), 27 deletions(-) diff --git a/json_schema/module/biomaterial/medical_tests.json b/json_schema/module/biomaterial/medical_tests.json index 1fbf70fcc..5359953cd 100644 --- a/json_schema/module/biomaterial/medical_tests.json +++ b/json_schema/module/biomaterial/medical_tests.json @@ -27,7 +27,7 @@ "enum": ["spirometry", "plethysmography", "DLCO_KCO_test"] }, "example": "spirometry; plethysmography; DLCO_KCO_test", - "bionetwork": ["lung"], + "bionetworks": ["lung"], "guidelines": "Should be of spirometry, plethysmography and DLCO_KCO_test." }, "pft_age": { @@ -37,7 +37,7 @@ "example": "10; 34; 68", "maximum": 150, "minimum": 0, - "bionetwork": ["lung"] + "bionetworks": ["lung"] }, "pft_time_point": { "user_friendly": "Date at Pulmonary Function Test", @@ -45,7 +45,7 @@ "type": "string", "example": "2024-11-14; 2019-01-31; not_shareable", "pattern": "^(((19|20)\\d\\d){1}([- \\./][01]\\d){0,1}([- \\./][0-3]\\d){0,1}|not_shareable)$", - "bionetwork": ["lung"], + "bionetworks": ["lung"], "guidelines": "If this information is not shareable, please indicate \\'not_shareable\\'." }, "pft_relative_time_point": { @@ -53,7 +53,7 @@ "description": "If timepoint of sample collection (time of collection) and/or timepoint of PFT recording (pft_time_point) is not available, indicate how many days prior or after sample collection the pulmonary function parameters were assessed if available.", "type": "integer", "example": "-5; 2; 0", - "bionetwork": ["lung"], + "bionetworks": ["lung"], "guidelines": "If PFT recording was done before sample collection, then enter a negative day value. If PFT recording was done after sample collection, then enter an unsigned positive day value." }, @@ -64,7 +64,7 @@ "example": "3500; 4200; 2800", "maximum": 15000, "minimum": 0, - "bionetwork": ["lung"] + "bionetworks": ["lung"] }, "fev1_prebd": { "user_friendly": "FEV1 before bronchodilator", @@ -73,7 +73,7 @@ "example": "3000; 3800; 2600", "maximum": 15000, "minimum": 0, - "bionetwork": ["lung"] + "bionetworks": ["lung"] }, "fev1_postbd": { "user_friendly": "FEV1 after bronchodilator", @@ -82,7 +82,7 @@ "example": "3200; 4000; 2700", "maximum": 15000, "minimum": 0, - "bionetwork": ["lung"] + "bionetworks": ["lung"] }, "fev1_prebd_predicted_percent": { "user_friendly": "FEV1 before bronchodilator percent of predicted", @@ -91,7 +91,7 @@ "example": "86; 90; 78", "maximum": 200, "minimum": 0, - "bionetwork": ["lung"] + "bionetworks": ["lung"] }, "fev1_postbd_predicted_percent": { "user_friendly": "FEV1 after bronchodilator percent of predicted", @@ -100,7 +100,7 @@ "example": "91; 95; 82", "maximum": 200, "minimum": 0, - "bionetwork": ["lung"] + "bionetworks": ["lung"] }, "fvc_predicted": { "user_friendly": "FVC predicted", @@ -109,7 +109,7 @@ "example": "4500; 5000; 3800", "maximum": 15000, "minimum": 0, - "bionetwork": ["lung"] + "bionetworks": ["lung"] }, "fvc_prebd": { "user_friendly": "FVC before bronchodilator", @@ -118,7 +118,7 @@ "example": "4000; 4800; 3600", "maximum": 15000, "minimum": 0, - "bionetwork": ["lung"] + "bionetworks": ["lung"] }, "fvc_postbd": { "user_friendly": "FVC after bronchodilator", @@ -127,7 +127,7 @@ "example": "4200; 5000; 3700", "maximum": 15000, "minimum": 0, - "bionetwork": ["lung"] + "bionetworks": ["lung"] }, "fvc_prebd_predicted_percent": { "user_friendly": "FVC before bronchodilator percent of predicted", @@ -136,7 +136,7 @@ "example": "89; 96; 95", "maximum": 200, "minimum": 0, - "bionetwork": ["lung"] + "bionetworks": ["lung"] }, "fvc_postbd_predicted_percent": { "user_friendly": "FVC after bronchodilator percent of predicted", @@ -145,7 +145,7 @@ "example": "93; 100; 97", "maximum": 200, "minimum": 0, - "bionetwork": ["lung"] + "bionetworks": ["lung"] }, "fev1_fvc_ratio_prebd": { "user_friendly": "FEV1 to FVC ratio before bronchodilator", @@ -154,7 +154,7 @@ "example": "0.75; 0.79; 0.72", "maximum": 1, "minimum": 0, - "bionetwork": ["lung"] + "bionetworks": ["lung"] }, "fev1_fvc_ratio_postbd": { "user_friendly": "FEV1 to FVC ratio after bronchodilator", @@ -163,7 +163,7 @@ "example": "0.76; 0.80; 0.73", "maximum": 1, "minimum": 0, - "bionetwork": ["lung"] + "bionetworks": ["lung"] }, "frc_abs": { "user_friendly": "FRC absolute", @@ -172,7 +172,7 @@ "example": "3000; 3500; 2700", "maximum": 15000, "minimum": 0, - "bionetwork": ["lung"] + "bionetworks": ["lung"] }, "frc_predicted_percent": { "user_friendly": "FRC percent of predicted", @@ -181,7 +181,7 @@ "example": "95; 88; 102", "maximum": 200, "minimum": 0, - "bionetwork": ["lung"] + "bionetworks": ["lung"] }, "rv": { "user_friendly": "RV", @@ -190,7 +190,7 @@ "example": "1500; 1800; 1400", "maximum": 15000, "minimum": 0, - "bionetwork": ["lung"] + "bionetworks": ["lung"] }, "rv_predicted_percent": { "user_friendly": "RV percent of predicted", @@ -199,7 +199,7 @@ "example": "80; 90; 85", "maximum": 200, "minimum": 0, - "bionetwork": ["lung"] + "bionetworks": ["lung"] }, "ic": { "user_friendly": "IC", @@ -208,7 +208,7 @@ "example": "3500; 4000; 3200", "maximum": 15000, "minimum": 0, - "bionetwork": ["lung"] + "bionetworks": ["lung"] }, "ic_predicted_percent": { "user_friendly": "IC percent of predicted", @@ -217,7 +217,7 @@ "example": "92; 85; 97", "maximum": 200, "minimum": 0, - "bionetwork": ["lung"] + "bionetworks": ["lung"] }, "dlco": { "user_friendly": "DLCO", @@ -226,7 +226,7 @@ "example": "25; 30; 22", "maximum": 100, "minimum": 5, - "bionetwork": ["lung"] + "bionetworks": ["lung"] }, "dlco_predicted_percent": { "user_friendly": "DLCO percent of predicted", @@ -235,7 +235,7 @@ "example": "88; 95; 82", "maximum": 200, "minimum": 0, - "bionetwork": ["lung"] + "bionetworks": ["lung"] }, "kco": { "user_friendly": "KCO", @@ -244,7 +244,7 @@ "example": "5; 6; 4.5", "maximum": 15000, "minimum": 0, - "bionetwork": ["lung"] + "bionetworks": ["lung"] }, "kco_predicted_percent": { "user_friendly": "KCO percent of predicted", @@ -253,7 +253,7 @@ "example": "90; 98; 85", "maximum": 200, "minimum": 0, - "bionetwork": ["lung"] + "bionetworks": ["lung"] } } } diff --git a/src/schema_linter.py b/src/schema_linter.py index 9793d6bae..5772657e9 100644 --- a/src/schema_linter.py +++ b/src/schema_linter.py @@ -32,7 +32,7 @@ # Property attributes -property_attributes = ['description', 'type', 'pattern', 'example', 'enum', '$ref', 'user_friendly', 'items', 'guidelines', 'format', 'comment', 'maximum', 'minimum', 'oneOf', 'bionetwork'] +property_attributes = ['description', 'type', 'pattern', 'example', 'enum', '$ref', 'user_friendly', 'items', 'guidelines', 'format', 'comment', 'maximum', 'minimum', 'oneOf', 'bionetworks'] ontology_attributes = ['graph_restriction', 'ontologies', 'classes', 'relations', 'direct', 'include_self'] From c667772b8001fff7340c7a12a41b1716eb449d86 Mon Sep 17 00:00:00 2001 From: Arsenios Chatzigeorgiou <49944135+arschat@users.noreply.github.com> Date: Tue, 13 Aug 2024 12:08:34 +0100 Subject: [PATCH 19/20] Ran release_prepare.py script. --- changelog.md | 8 ++++++++ json_schema/update_log.csv | 2 -- json_schema/versions.json | 6 +++--- 3 files changed, 11 insertions(+), 5 deletions(-) diff --git a/changelog.md b/changelog.md index 87b5e0d0a..50d133ca8 100644 --- a/changelog.md +++ b/changelog.md @@ -7,6 +7,14 @@ and (starting with v4.0.0) this project adheres to [Semantic Versioning](http:// ## [Unreleased](https://github.com/HumanCellAtlas/metadata-schema/tree/staging) +### [module/biomaterial/medical_tests.json - v1.0.0] - 2024-08-13 +### Added +Added medical_tests module + +### [type/biomaterial/donor_organism.json - v16.1.0] - 2024-08-13 +### Added +Added optional medical_tests module in donor_organism. Fixes #1562 + ## [Released](https://github.com/HumanCellAtlas/metadata-schema/) ### [type/file/sequence_file.json - v9.6.0] - 2024-07-15 diff --git a/json_schema/update_log.csv b/json_schema/update_log.csv index 27a9c79d9..3231ff199 100644 --- a/json_schema/update_log.csv +++ b/json_schema/update_log.csv @@ -1,3 +1 @@ Schema,Change type,Change message,Version,Date -/type/biomaterial/donor_organism.json,minor,Added optional medical_tests module in donor_organism. Fixes #1562,, -/type/module/biomaterial/medical_tests.json,major,Added medical_tests module,, \ No newline at end of file diff --git a/json_schema/versions.json b/json_schema/versions.json index b52e66c00..f09972241 100644 --- a/json_schema/versions.json +++ b/json_schema/versions.json @@ -1,5 +1,5 @@ { - "last_update_date": "2024-07-15T12:34:46Z", + "last_update_date": "2024-08-13T12:07:03Z", "version_numbers": { "core": { "biomaterial": { @@ -26,7 +26,7 @@ "growth_conditions": "6.4.2", "human_specific": "1.0.11", "medical_history": "5.2.8", - "medical_tests": "0.0.0", + "medical_tests": "1.0.0", "mouse_specific": "1.0.8", "preservation_storage": "6.1.1", "state_of_specimen": "6.0.0", @@ -92,7 +92,7 @@ "biomaterial": { "cell_line": "16.0.0", "cell_suspension": "14.0.0", - "donor_organism": "16.0.0", + "donor_organism": "16.1.0", "imaged_specimen": "3.5.0", "organoid": "11.5.0", "specimen_from_organism": "10.9.0" From bb5d805c925213bcce3b72984baac140976a2bfd Mon Sep 17 00:00:00 2001 From: Arsenios Chatzigeorgiou <49944135+arschat@users.noreply.github.com> Date: Tue, 13 Aug 2024 12:13:20 +0100 Subject: [PATCH 20/20] Release from staging to master 2024-08-13. --- changelog.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/changelog.md b/changelog.md index 50d133ca8..3b2f0a46c 100644 --- a/changelog.md +++ b/changelog.md @@ -7,6 +7,8 @@ and (starting with v4.0.0) this project adheres to [Semantic Versioning](http:// ## [Unreleased](https://github.com/HumanCellAtlas/metadata-schema/tree/staging) +## [Released](https://github.com/HumanCellAtlas/metadata-schema/) + ### [module/biomaterial/medical_tests.json - v1.0.0] - 2024-08-13 ### Added Added medical_tests module @@ -15,8 +17,6 @@ Added medical_tests module ### Added Added optional medical_tests module in donor_organism. Fixes #1562 -## [Released](https://github.com/HumanCellAtlas/metadata-schema/) - ### [type/file/sequence_file.json - v9.6.0] - 2024-07-15 ### Added Added sequencing_run_batch field in the sequencing_file - Fixes#1557