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Adds Adipose tier2 fields #1638
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b8ca334
extend body_mass_index validation to number ranges
idazucchi fdce2cd
add menstrual_cycle_stage
idazucchi 519b650
fix reproductive_history pattern
idazucchi 93fcea3
added new blood_test module
idazucchi 1d312d8
added androstenedione blood test
idazucchi 1b571c8
added dhea blood test
idazucchi 80e0b27
added estrogen blood test
idazucchi a49ef9f
added fasting_glucose blood test
idazucchi ce857c5
added fasting_insulin blood test
idazucchi 2714381
added free_fatty_acid blood test
idazucchi a147c2f
added haematocrit blood test
idazucchi 7fe06c1
added haemoglobin blood test
idazucchi 5b9be09
added hba1c blood test
idazucchi c0a6371
added hdl blood test
idazucchi c07d5d6
added homa_ir blood test
idazucchi bf95fa2
added ldl blood test
idazucchi b023f71
added platelet_count blood test
idazucchi fbe20fe
added shbg blood test
idazucchi 6255f42
added testosterone blood test
idazucchi 42611da
added triglycerides blood test
idazucchi 0245b5b
added white_blood_cell_count blood test
idazucchi b1ba63c
added bloodtest_time_offset blood test
idazucchi 96febde
added biopsy_procedure to collection protocol
idazucchi f84da97
added nuclei_yield to cell suspension
idazucchi be1bbc5
added fasting_time, previous_surgery
idazucchi 8f50781
added lifestyle module
idazucchi 0c66db3
remove previous_surgery
idazucchi 83a55a4
added physical_activity
idazucchi 11fade6
added waist_circumference, waist_hip_ratio
idazucchi fab7985
added time_to_laboratory
idazucchi 43b18e7
added processing_time
idazucchi 2b2dcb2
added experimental_condition
idazucchi a6a6dc5
fix json format
idazucchi ac7ea26
improve regex for processing_time
idazucchi 0a41472
Merge branch 'staging' into iz-adipose-tier2
idazucchi 95f9ab0
fix linting errors
idazucchi 92548ff
fix regex for body_mass_index, waist_circumference, waist_hip_ratio, …
idazucchi f2bd45a
added minium value for blood tests
idazucchi 39f4fc6
added minum value
idazucchi 569fff2
add number range to examples
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,337 @@ | ||
| { | ||
| "$schema": "http://json-schema.org/draft-07/schema#", | ||
| "description": "Blood test results of the donor.", | ||
| "additionalProperties": false, | ||
| "minProperties": 1, | ||
| "title": "Blood test", | ||
| "name": "blood_test", | ||
| "type": "object", | ||
| "properties": { | ||
| "describedBy": { | ||
| "description": "The URL reference to the schema.", | ||
| "type": "string", | ||
| "pattern" : "^(http|https)://schema.(.*?)humancellatlas.org/module/biomaterial/(([0-9]{1,}.[0-9]{1,}.[0-9]{1,})|([a-zA-Z]*?))/blood_test" | ||
| }, | ||
| "schema_version": { | ||
| "description": "The version number of the schema in major.minor.patch format.", | ||
| "type": "string", | ||
| "pattern": "^[0-9]{1,}.[0-9]{1,}.[0-9]{1,}$", | ||
| "example": "4.6.1" | ||
| }, | ||
| "androstenedione": { | ||
| "description": "Androstenedione in the last blood test of the donor before collection.", | ||
| "type": "number", | ||
| "user_friendly": "Androstenedione", | ||
| "example": "0.7; 3.4; 2.41", | ||
| "bionetworks": ["adipose"] | ||
| }, | ||
| "androstenedione_unit": { | ||
| "description": "Androstenedione unit.", | ||
| "type": "string", | ||
| "enum": [ | ||
| "ng/dL", | ||
| "nmol/L" | ||
| ], | ||
| "user_friendly": "Androstenedione unit", | ||
| "example": "ng/dL; nmol/L", | ||
| "guidelines": "Should be one of: ng/dL; nmol/L", | ||
| "bionetworks": ["adipose"] | ||
| }, | ||
| "dhea": { | ||
| "description": "Dehydroepiandrosterone (DHEA) in the last blood test of the donor before collection.", | ||
| "type": "number", | ||
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||
| "user_friendly": "DHEA", | ||
| "example": "240; 3500; 1500", | ||
| "bionetworks": ["adipose"] | ||
| }, | ||
| "dhea_unit": { | ||
| "description": "DHEA unit.", | ||
| "type": "string", | ||
| "enum": [ | ||
| "ng/dL", | ||
| "nmol/L" | ||
| ], | ||
| "user_friendly": "DHEA unit", | ||
| "example": "ng/dL; nmol/L", | ||
| "guidelines": "Should be one of: ng/dL; nmol/L", | ||
| "bionetworks": ["adipose"] | ||
| }, | ||
| "estrogen": { | ||
| "description": "Estrogen in the last blood test of the donor before collection.", | ||
| "type": "number", | ||
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|
||
| "user_friendly": "Estrogen", | ||
| "example": "10; 150; 120", | ||
| "bionetworks": ["adipose"] | ||
| }, | ||
| "estrogen_unit": { | ||
| "description": "Estrogen unit.", | ||
| "type": "string", | ||
| "enum": [ | ||
| "pg/mL", | ||
| "pmol/L" | ||
| ], | ||
| "user_friendly": "Estrogen unit", | ||
| "example": "pg/mL; pmol/L", | ||
| "guidelines": "Should be one of: pg/mL; pmol/L", | ||
| "bionetworks": ["adipose"] | ||
| }, | ||
| "fasting_glucose": { | ||
| "description": "Fasting glucose levels from the donor's last blood test after at least 8 hours of fasting, prior to the biopsy collection.", | ||
| "type": "number", | ||
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||
| "user_friendly": "Fasting glucose", | ||
| "example": "70; 125; 90.2", | ||
| "bionetworks": ["adipose"] | ||
| }, | ||
| "fasting_glucose_unit": { | ||
| "description": "Fasting glucose unit.", | ||
| "type": "string", | ||
| "enum": [ | ||
| "mg/dL", | ||
| "mmol/L" | ||
| ], | ||
| "user_friendly": "Fasting glucose unit", | ||
| "example": "mg/dL; mmol/L", | ||
| "guidelines": "Should be one of: mg/dL; mmol/L", | ||
| "bionetworks": ["adipose"] | ||
| }, | ||
| "fasting_insulin": { | ||
| "description": "Fasting insulin levels from the donor's last blood test after at least 8 hours of fasting, prior to the biopsy collection.", | ||
| "type": "number", | ||
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|
||
| "user_friendly": "Fasting insulin", | ||
| "example": "2; 20; 14", | ||
| "bionetworks": ["adipose"] | ||
| }, | ||
| "fasting_insulin_unit": { | ||
| "description": "Fasting insulin unit.", | ||
| "type": "string", | ||
| "enum": [ | ||
| "μU/mL", | ||
| "pmol/L" | ||
| ], | ||
| "user_friendly": "Fasting insulin unit", | ||
| "example": "μU/mL; pmol/L", | ||
| "guidelines": "Should be one of: μU/mL; pmol/L", | ||
| "bionetworks": ["adipose"] | ||
| }, | ||
| "free_fatty_acid": { | ||
| "description": "Free Fatty Acid (FFA) in the last blood test of the donor before collection.", | ||
| "type": "number", | ||
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|
||
| "user_friendly": "FFA", | ||
| "example": "0.1; 0.6; 0.24", | ||
| "bionetworks": ["adipose"] | ||
| }, | ||
| "free_fatty_acid_unit": { | ||
| "description": "Free Fatty Acid (FFA) unit.", | ||
| "type": "string", | ||
| "enum": [ | ||
| "mmol/L" | ||
| ], | ||
| "user_friendly": "FFA unit", | ||
| "example": "mmol/L", | ||
| "guidelines": "Should be one of: mmol/L", | ||
| "bionetworks": ["adipose"] | ||
| }, | ||
| "haematocrit": { | ||
| "description": "Percentage of red blood cells in whole blood from the donor's last blood test prior to biopsy collection.", | ||
| "type": "number", | ||
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|
||
| "user_friendly": "Haematocrit", | ||
| "example": "36; 54; 45", | ||
| "bionetworks": ["adipose"] | ||
| }, | ||
| "haematocrit_unit": { | ||
| "description": "Haematocrit unit.", | ||
| "type": "string", | ||
| "enum": [ | ||
| "percentage (%)" | ||
| ], | ||
| "user_friendly": "Haematocrit unit", | ||
| "example": "%", | ||
| "guidelines": "Should be one of: %", | ||
| "bionetworks": ["adipose"] | ||
| }, | ||
| "haemoglobin": { | ||
| "description": "Concentration of haemoglobin in whole blood from the donor's last blood test prior to biopsy collection.", | ||
| "type": "number", | ||
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|
||
| "user_friendly": "Haemoglobin", | ||
| "example": "12; 17.5; 14.2", | ||
| "bionetworks": ["adipose"] | ||
| }, | ||
| "haemoglobin_unit": { | ||
| "description": "Haemoglobin unit.", | ||
| "type": "string", | ||
| "enum": [ | ||
| "g/dL", | ||
| "mmol/L" | ||
| ], | ||
| "user_friendly": "Haemoglobin unit", | ||
| "example": "g/dL; mmol/L", | ||
| "guidelines": "Should be one of: g/dL; mmol/L", | ||
| "bionetworks": ["adipose"] | ||
| }, | ||
| "hba1c": { | ||
| "description": "Concentration of glycated hemoglobin (HbA1c) from the donor's last blood test prior to biopsy collection.", | ||
| "type": "number", | ||
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|
||
| "user_friendly": "HbA1c", | ||
| "example": "42; 58; 53.3", | ||
| "bionetworks": ["adipose"] | ||
| }, | ||
| "hba1c_unit": { | ||
| "description": "HbA1c unit.", | ||
| "type": "string", | ||
| "enum": [ | ||
| "mmol/mol", | ||
| "%" | ||
| ], | ||
| "user_friendly": "HbA1c unit", | ||
| "example": "mmol/mol; %", | ||
| "guidelines": "Should be one of: mmol/mol; %", | ||
| "bionetworks": ["adipose"] | ||
| }, | ||
| "hdl": { | ||
| "description": "High-density lipoprotein cholesterol (HDL) in the last blood test of the donor before collection.", | ||
| "type": "number", | ||
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|
||
| "user_friendly": "HDL", | ||
| "example": "40; 60; 92", | ||
| "bionetworks": ["adipose"] | ||
| }, | ||
| "hdl_unit": { | ||
| "description": "HDL unit.", | ||
| "type": "string", | ||
| "enum": [ | ||
| "mg/dL", | ||
| "mmol/L" | ||
| ], | ||
| "user_friendly": "HDL unit", | ||
| "example": "mg/dL; mmol/L", | ||
| "guidelines": "Should be one of: mg/dL; mmol/L", | ||
| "bionetworks": ["adipose"] | ||
| }, | ||
| "homa_ir": { | ||
| "description": "Homeostatic Model Assessment of Insulin Resistance (HOMA-IR) in the last blood test of the donor before collection.", | ||
| "type": "number", | ||
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||
| "user_friendly": "HOMA-IR", | ||
| "example": "0.4; 1.2; 0.94", | ||
| "bionetworks": ["adipose"] | ||
| }, | ||
| "ldl": { | ||
| "description": "Low-density lipoprotein cholesterol (LDL) in the last blood test of the donor before collection.", | ||
| "type": "number", | ||
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||
| "user_friendly": "LDL", | ||
| "example": "160; 133", | ||
| "bionetworks": ["adipose"] | ||
| }, | ||
| "ldl_unit": { | ||
| "description": "LDL unit.", | ||
| "type": "string", | ||
| "enum": [ | ||
| "mg/dL", | ||
| "mmol/L" | ||
| ], | ||
| "user_friendly": "LDL unit", | ||
| "example": "mg/dL; mmol/L", | ||
| "guidelines": "Should be one of: mg/dL; mmol/L", | ||
| "bionetworks": ["adipose"] | ||
| }, | ||
| "platelet_count": { | ||
| "description": "Measurement of platelets per unit volume of blood from the donor's last blood test prior to biopsy collection", | ||
| "type": "number", | ||
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| "user_friendly": "Platelet count", | ||
| "example": "240; 124; 110", | ||
| "bionetworks": ["adipose"] | ||
| }, | ||
| "platelet_count_unit": { | ||
| "description": "Platelet count unit.", | ||
| "type": "string", | ||
| "enum": [ | ||
| "10^9/L", | ||
| "cells/μL" | ||
| ], | ||
| "user_friendly": "Platelet count unit", | ||
| "example": "10^9/L; cells/μL", | ||
| "guidelines": "Should be one of: 10^9/L; cells/μL", | ||
| "bionetworks": ["adipose"] | ||
| }, | ||
| "shbg": { | ||
| "description": "Sex hormone binding globulin (SHBG) in the last blood test of the donor before collection.", | ||
| "type": "number", | ||
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|
||
| "user_friendly": "SHBG", | ||
| "example": "10; 140; 72", | ||
| "bionetworks": ["adipose"] | ||
| }, | ||
| "shbg_unit": { | ||
| "description": "SHBG unit.", | ||
| "type": "string", | ||
| "enum": [ | ||
| "nmol/L" | ||
| ], | ||
| "user_friendly": "SHBG unit", | ||
| "example": "nmol/L", | ||
| "guidelines": "Should be one of: nmol/L", | ||
| "bionetworks": ["adipose"] | ||
| }, | ||
| "testosterone": { | ||
| "description": "Testosterone in the last blood test of the donor before collection.", | ||
| "type": "number", | ||
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||
| "user_friendly": "Testosterone", | ||
| "example": "15; 1000; 420", | ||
| "bionetworks": ["adipose"] | ||
| }, | ||
| "testosterone_unit": { | ||
| "description": "Testosterone unit.", | ||
| "type": "string", | ||
| "enum": [ | ||
| "nmol/L", | ||
| "ng/dL" | ||
| ], | ||
| "user_friendly": "Testosterone unit", | ||
| "example": "nmol/L; ng/dL", | ||
| "guidelines": "Should be one of: nmol/L; ng/dL", | ||
| "bionetworks": ["adipose"] | ||
| }, | ||
| "triglycerides": { | ||
| "description": "Triglycerides levels from the donor's last blood test after at least 9-12 hours of fasting, prior to the biopsy collection.", | ||
| "type": "number", | ||
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| "user_friendly": "Triglycerides", | ||
| "example": "160; 133; 140", | ||
| "bionetworks": ["adipose"] | ||
| }, | ||
| "triglycerides_unit": { | ||
| "description": "Triglycerides unit.", | ||
| "type": "string", | ||
| "enum": [ | ||
| "mg/dL", | ||
| "mmol/L" | ||
| ], | ||
| "user_friendly": "Triglycerides unit", | ||
| "example": "mg/dL; mmol/L", | ||
| "guidelines": "Should be one of: mg/dL; mmol/L", | ||
| "bionetworks": ["adipose"] | ||
| }, | ||
| "white_blood_cell_count": { | ||
| "description": "Measurement of total white blood cells per unit volume of blood from the donor's last blood test prior to biopsy collection.", | ||
| "type": "number", | ||
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| "user_friendly": "White cell count", | ||
| "example": "4.5; 11; 9.24", | ||
| "bionetworks": ["adipose"] | ||
| }, | ||
| "white_blood_cell_count_unit": { | ||
| "description": "White cell count unit.", | ||
| "type": "string", | ||
| "enum": [ | ||
| "10^9/L", | ||
| "cells/μL" | ||
| ], | ||
| "user_friendly": "White cell count unit", | ||
| "example": "10^9/L; cells/μL", | ||
| "guidelines": "Should be one of: 10^9/L; cells/μL", | ||
| "bionetworks": ["adipose"] | ||
| }, | ||
| "bloodtest_time_offset": { | ||
| "description": "Time between the test and the collection of the sample, in days.", | ||
| "type": "number", | ||
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| "user_friendly": "Blood test time offset", | ||
| "example": "12; 42; 98", | ||
| "bionetworks": ["adipose"] | ||
| } | ||
| } | ||
| } | ||
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