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Merge branch 'main' into update_cancer_tables
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@atk17
atk17 committed Nov 21, 2023
2 parents be9d670 + b98c124 commit 9c8d087
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Showing 6 changed files with 133 additions and 69 deletions.
5 changes: 3 additions & 2 deletions PRIMED_GSR_data_model.json
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@@ -1,7 +1,7 @@
{
"name": "PRIMED GSR Data Model",
"description": "Data model for Genomic Summary Results in the PRIMED consortium",
"version": "1.0",
"version": "1.1",
"tables": [
{
"table": "analysis",
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"column": "file_path",
"required": true,
"description": "File path in cloud storage",
"data_type": "string"
"data_type": "string",
"is_bucket_path": true
},
{
"column": "file_type",
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14 changes: 9 additions & 5 deletions PRIMED_genotype_data_model.json
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@@ -1,7 +1,7 @@
{
"name": "PRIMED Genotype Data Model",
"description": "Data model for genotype data in the PRIMED consortium",
"version": "1.2",
"version": "1.3",
"tables": [
{
"table": "subject",
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"column": "file_path",
"required": true,
"description": "absolute file path in cloud storage",
"data_type": "string"
"data_type": "string",
"is_bucket_path": true
},
{
"column": "file_type",
Expand Down Expand Up @@ -305,7 +306,8 @@
"column": "file_path",
"required": true,
"description": "absolute file path in cloud storage",
"data_type": "string"
"data_type": "string",
"is_bucket_path": true
},
{
"column": "file_type",
Expand Down Expand Up @@ -441,7 +443,8 @@
"column": "file_path",
"required": true,
"description": "absolute file path in cloud storage",
"data_type": "string"
"data_type": "string",
"is_bucket_path": true
},
{
"column": "file_type",
Expand Down Expand Up @@ -541,7 +544,8 @@
"column": "file_path",
"required": true,
"description": "absolute file path in cloud storage",
"data_type": "string"
"data_type": "string",
"is_bucket_path": true
},
{
"column": "file_type",
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66 changes: 58 additions & 8 deletions PRIMED_phenotype_data_model.json
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@@ -1,7 +1,7 @@
{
"name": "PRIMED Phenotype Data Model",
"description": "Data model for phenotype data in the PRIMED consortium",
"version": "1.2",
"version": "1.5",
"tables": [
{
"table": "subject",
Expand Down Expand Up @@ -57,6 +57,7 @@
{
"table": "population_descriptor",
"url": "https://docs.google.com/spreadsheets/d/1kpWz-6QfjMPVtm62fQwm4hoxzXhR0dnKxVt02fbx9ks/edit#gid=1733510035",
"version": "1.0",
"columns": [
{
"column": "population_descriptor_id",
Expand Down Expand Up @@ -128,13 +129,15 @@
"column": "file_path",
"required": true,
"description": "absolute file path in cloud storage",
"data_type": "string"
"data_type": "string",
"is_bucket_path": true
},
{
"column": "file_readme_path",
"required": true,
"description": "path to the README",
"data_type": "string"
"data_type": "string",
"is_bucket_path": true
},
{
"column": "n_subjects",
Expand Down Expand Up @@ -184,13 +187,15 @@
"column": "file_path",
"required": true,
"description": "absolute file path in cloud storage",
"data_type": "string"
"data_type": "string",
"is_bucket_path": true
},
{
"column": "file_dd_path",
"required": true,
"description": "path to the data dictionary",
"data_type": "string"
"data_type": "string",
"is_bucket_path": true
},
{
"column": "n_subjects",
Expand All @@ -209,6 +214,7 @@
{
"table": "pilot",
"url": "https://docs.google.com/spreadsheets/d/1bo_I8_yOx0sXK9UcNAJ8b8DoKe8O3W4S9zzZG-y0thM/edit#gid=0",
"version": "1.0",
"columns": [
{
"column": "subject_id",
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{
"table": "cmqt_flags",
"url": "https://docs.google.com/spreadsheets/d/1vQE4gHvKQUOLPaRt1bpLLfNUFp2st9qOl56zD57gob0/edit#gid=0",
"version": "1.0",
"columns": [
{
"column": "subject_id",
Expand All @@ -299,7 +306,9 @@
"primary_key": true,
"required": true,
"description": "the age at which the observation or measurement for the phenotype(s) were taken",
"data_type": "float"
"data_type": "float",
"min": " 0",
"max": "89"
},
{
"column": "visit",
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{
"table": "cmqt_anthropometry",
"url": "https://docs.google.com/spreadsheets/d/1vQE4gHvKQUOLPaRt1bpLLfNUFp2st9qOl56zD57gob0/edit#gid=1206657525",
"version": "1.0",
"columns": [
{
"column": "subject_id",
Expand All @@ -444,6 +454,8 @@
"required": true,
"description": "the age at which the observation or measurement for the phenotype(s) were taken",
"data_type": "float",
"min": 0,
"max": 89,
"examples": "56.2"
},
{
Expand All @@ -457,18 +469,21 @@
"column": "height_1",
"description": "standing body height",
"data_type": "float",
"min": 0,
"examples": "165.1"
},
{
"column": "weight_1",
"description": "body weight at baseline",
"data_type": "float",
"min": 0,
"examples": "72.574"
},
{
"column": "bmi_1",
"description": "body mass index calculated",
"data_type": "float",
"min": 0,
"examples": "26.45"
},
{
Expand All @@ -481,6 +496,7 @@
{
"table": "cmqt_blood_pressure",
"url": "https://docs.google.com/spreadsheets/d/1vQE4gHvKQUOLPaRt1bpLLfNUFp2st9qOl56zD57gob0/edit#gid=455811479",
"version": "1.0",
"columns": [
{
"column": "subject_id",
Expand All @@ -497,6 +513,8 @@
"required": true,
"description": "the age at which the observation or measurement for the phenotype(s) were taken",
"data_type": "float",
"min": 0,
"max": 89,
"examples": "56.2"
},
{
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{
"table": "cmqt_lipids",
"url": "https://docs.google.com/spreadsheets/d/1vQE4gHvKQUOLPaRt1bpLLfNUFp2st9qOl56zD57gob0/edit#gid=1052869785",
"version": "1.0",
"columns": [
{
"column": "subject_id",
Expand All @@ -546,6 +565,8 @@
"required": true,
"description": "the age at which the observation or measurement for the phenotype(s) were taken",
"data_type": "float",
"min": 0,
"max": 89,
"examples": "56.2"
},
{
Expand Down Expand Up @@ -589,6 +610,7 @@
{
"table": "cmqt_hematology",
"url": "https://docs.google.com/spreadsheets/d/1vQE4gHvKQUOLPaRt1bpLLfNUFp2st9qOl56zD57gob0/edit#gid=1535206686",
"version": "1.0",
"columns": [
{
"column": "subject_id",
Expand All @@ -605,6 +627,8 @@
"required": true,
"description": "the age at which the observation or measurement for the phenotype(s) were taken",
"data_type": "float",
"min": 0,
"max": 89,
"examples": "56.2"
},
{
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{
"table": "cmqt_glycemic",
"url": "https://docs.google.com/spreadsheets/d/1vQE4gHvKQUOLPaRt1bpLLfNUFp2st9qOl56zD57gob0/edit#gid=2078107573",
"version": "1.0",
"columns": [
{
"column": "subject_id",
Expand All @@ -710,6 +735,8 @@
"required": true,
"description": "the age at which the observation or measurement for the phenotype(s) were taken",
"data_type": "float",
"min": 0,
"max": 89,
"examples": "56.2"
},
{
Expand Down Expand Up @@ -744,6 +771,7 @@
{
"table": "cmqt_kidney_function",
"url": "https://docs.google.com/spreadsheets/d/1vQE4gHvKQUOLPaRt1bpLLfNUFp2st9qOl56zD57gob0/edit#gid=746527944",
"version": "1.0",
"columns": [
{
"column": "subject_id",
Expand All @@ -760,6 +788,8 @@
"required": true,
"description": "the age at which the observation or measurement for the phenotype(s) were taken",
"data_type": "float",
"min": 0,
"max": 89,
"examples": "56.2"
},
{
Expand All @@ -784,6 +814,7 @@
{
"table": "diabetes_diabetes",
"url": "https://docs.google.com/spreadsheets/d/1vQE4gHvKQUOLPaRt1bpLLfNUFp2st9qOl56zD57gob0/edit#gid=1891810958",
"version": "1.0",
"columns": [
{
"column": "subject_id",
Expand All @@ -800,6 +831,8 @@
"required": true,
"description": "the age at which the observation or measurement for the phenotype(s) were taken",
"data_type": "float",
"min": 0,
"max": 89,
"examples": "56.2"
},
{
Expand Down Expand Up @@ -828,6 +861,7 @@
{
"table": "cvd_cad",
"url": "https://docs.google.com/spreadsheets/d/1gchIrBIPt2s_3uVEloUK1c1Rst6IxnbBm7Zwps2k31I/edit#gid=253559161",
"version": "1.0",
"columns": [
{
"column": "subject_id",
Expand All @@ -844,6 +878,8 @@
"required": true,
"description": "the age at which the observation or measurement for the phenotype(s) were taken",
"data_type": "float",
"min": 0,
"max": 89,
"examples": "56.2"
},
{
Expand Down Expand Up @@ -872,6 +908,7 @@
{
"table": "cancer_breast",
"url": "https://docs.google.com/spreadsheets/d/1Gfj_EoPuYWhiNk7AaR6DOPjeTC7Nn06sF8qcoMGQ9KM/edit#gid=0",
"version": "1.0",
"columns": [
{
"column": "subject_id",
Expand All @@ -888,6 +925,8 @@
"required": true,
"description": "the age at which the observation or measurement for the phenotype(s) were taken",
"data_type": "float",
"min": 0,
"max": 89,
"examples": "56.2"
},
{
Expand Down Expand Up @@ -922,6 +961,8 @@
"column": "age_at_diagnosis_1",
"description": "age at which participant was diagnosed with breast cancer",
"data_type": "float",
"min": 0,
"max": 89,
"notes": "may be the same as age_at_obs or not"
},
{
Expand Down Expand Up @@ -1092,6 +1133,8 @@
"column": "age_at_natural_menopause_1",
"description": "age at which natural menopause occurred",
"data_type": "float",
"min": 0,
"max": 89,
"notes": "NA if menopause has not occurred"
},
{
Expand All @@ -1109,12 +1152,16 @@
{
"column": "age_at_first_birth_1",
"description": "age at which the first birth occurred",
"data_type": "float"
"data_type": "float",
"min": 0,
"max": 89
},
{
"column": "age_at_menarche_1",
"description": "age at which menarche occurred",
"data_type": "float"
"data_type": "float",
"min": 0,
"max": 89
},
{
"column": "deceased_1",
Expand All @@ -1134,13 +1181,16 @@
"column": "age_at_death_1",
"description": "age at death of individual",
"data_type": "float",
"min": 0,
"max": 89,
"notes": "Set to missing (either blank or NA) if individual is not deceased"
}
]
},
{
"table": "cancer_prostate",
"url": "https://docs.google.com/spreadsheets/d/1Gfj_EoPuYWhiNk7AaR6DOPjeTC7Nn06sF8qcoMGQ9KM/edit#gid=1811888649",
"version": "1.0",
"columns": [
{
"column": "subject_id",
Expand Down
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