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Add family hx table #29

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merged 4 commits into from
Mar 29, 2024
Merged

Add family hx table #29

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0fae80e
Merge branch 'main' of github.com:UW-GAC/primed_data_models into main
atk17 Dec 1, 2023
22094ff
add family hx table
atk17 Mar 29, 2024
8c0a801
Merge branch 'main' of github.com:UW-GAC/primed_data_models into main
atk17 Mar 29, 2024
b070d9c
Merge branch 'main' into add_family_hx_table
atk17 Mar 29, 2024
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208 changes: 207 additions & 1 deletion PRIMED_phenotype_data_model.json
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Original file line number Diff line number Diff line change
Expand Up @@ -117,7 +117,7 @@
"column": "domain",
"required": true,
"data_type": "enumeration",
"enumerations": ["pilot", "population_descriptor", "cmqt_flags", "cmqt_anthropometry", "cmqt_blood_pressure", "cmqt_lipids", "cmqt_hematology", "cmqt_glycemic", "cmqt_kidney_function", "diabetes_diabetes", "cvd_cad", "cancer_breast", "cancer_prostate"]
"enumerations": ["pilot", "population_descriptor", "cmqt_flags", "cmqt_anthropometry", "cmqt_blood_pressure", "cmqt_lipids", "cmqt_hematology", "cmqt_glycemic", "cmqt_kidney_function", "diabetes_diabetes", "cvd_cad", "cancer_breast", "cancer_prostate", "family_history"]
},
{
"column": "md5sum",
Expand Down Expand Up @@ -1438,6 +1438,212 @@
"notes": "Set to missing (either blank or NA) if individual is not deceased"
}
]
},
{
"table": "family_history",
"url": "https://docs.google.com/spreadsheets/d/1zFFNig5Ig24koPjhlrHEgqWk2Gan2fA4XWN3EdMaP_A/edit#gid=0",
"version": "1.0",
"columns": [
{
"column": "subject_id",
"primary_key": true,
"required": true,
"description": "the PRIMED subject id",
"data_type": "string",
"references": "> subject.subject_id",
"notes": "references subject_id in participant table"
},
{
"column": "age_at_obs",
"primary_key": true,
"required": true,
"description": "the age at which the observation or measurement for the phenotype(s) were taken",
"data_type": "float",
"examples": "56.2"
},
{
"column": "visit",
"description": "indicator of visit or time of observation",
"data_type": "string",
"examples": ["visit_2", "baseline", "median"],
"notes": "this can be any value that is used consistently within the study"
},
{
"column": "family_hx_cancer_breast_1",
"description": "Whether or not there is a family history of breast cancer",
"data_type": "enumeration",
"enumerations": ["0", "1"],
"notes": "0 = 'no' 1 = 'yes' Missing values can either be left blank or set to NA."
},
{
"column": "family_hx_cancer_breast_relatedness_1",
"description": "Degree of relatedness. If first and second degree available, prioritize first degree",
"data_type": "enumeration",
"enumerations": ["1st degree", "2nd degree", "unknown"],
"notes": "Missing values can either be left blank or set to NA."
},
{
"column": "family_hx_cancer_prostate",
"description": "Whether or not there is a family history of prostate cancer",
"data_type": "enumeration",
"enumerations": ["0", "1"],
"notes": "0 = 'no' 1 = 'yes' Missing values can either be left blank or set to NA."
},
{
"column": "family_hx_cancer_prostate_relatedness_1",
"description": "Degree of relatedness. If first and second degree available, prioritize first degree",
"data_type": "enumeration",
"enumerations": ["1st degree", "2nd degree", "unknown"],
"notes": "Missing values can either be left blank or set to NA."
},
{
"column": "family_hx_cancer_pancreatic",
"description": "Whether or not there is a family history of pancreatic cancer",
"data_type": "enumeration",
"enumerations": ["0", "1"],
"notes": "0 = 'no' 1 = 'yes' Missing values can either be left blank or set to NA."
},
{
"column": "family_hx_cancer_pancreatic_relatedness_1",
"description": "Degree of relatedness. If first and second degree available, prioritize first degree",
"data_type": "enumeration",
"enumerations": ["1st degree", "2nd degree", "unknown"],
"notes": "Missing values can either be left blank or set to NA."
},
{
"column": "family_hx_cancer_colorectal",
"description": "Whether of not there is a family history of colorectal cancer",
"data_type": "enumeration",
"enumerations": ["0", "1"],
"notes": "0 = 'no' 1 = 'yes' Missing values can either be left blank or set to NA."
},
{
"column": "family_hx_cancer_colorectal_relatedness_1",
"description": "Degree of relatedness. If first and second degree available, prioritize first degree",
"data_type": "enumeration",
"enumerations": ["1st degree", "2nd degree", "unknown"],
"notes": "Missing values can either be left blank or set to NA."
},
{
"column": "family_hx_cancer_lung",
"description": "Whether of not there is a family history of lung cancer",
"data_type": "enumeration",
"enumerations": ["0", "1"],
"notes": "0 = 'no' 1 = 'yes' Missing values can either be left blank or set to NA."
},
{
"column": "family_hx_cancer_lung_relatedness_1",
"description": "Degree of relatedness. If first and second degree available, prioritize first degree",
"data_type": "enumeration",
"enumerations": ["1st degree", "2nd degree", "unknown"],
"notes": "Missing values can either be left blank or set to NA."
},
{
"column": "family_hx_cancer_any",
"description": "Whether or not there is a family history of any time of cancer",
"data_type": "enumeration",
"enumerations": ["0", "1"],
"notes": "0 = 'no' 1 = 'yes' Missing values can either be left blank or set to NA."
},
{
"column": "family_hx_type2_diabetes",
"description": "Whether or not there is a family history of type 2 diabetes",
"data_type": "enumeration",
"enumerations": ["0", "1"],
"notes": "Missing values can either be left blank or set to NA."
},
{
"column": "family_hx_type2_diabetes_relatedness_1",
"description": "Degree of relatedness. If first and second degree available, prioritize first degree",
"data_type": "enumeration",
"enumerations": ["1st degree", "2nd degree", "unknown"],
"notes": "0 = 'no' 1 = 'yes' Missing values can either be left blank or set to NA."
},
{
"column": "family_hx_myocardial_infarction",
"description": "Whether or not there is a family history of myocardial infarction/heart attack",
"data_type": "enumeration",
"enumerations": ["0", "1"],
"notes": "Missing values can either be left blank or set to NA."
},
{
"column": "family_hx_myocardial_infarction_relatedness_1",
"description": "Degree of relatedness. If first and second degree available, prioritize first degree",
"data_type": "enumeration",
"enumerations": ["1st degree", "2nd degree", "unknown"],
"notes": "0 = 'no' 1 = 'yes' Missing values can either be left blank or set to NA."
},
{
"column": "family_hx_dementia",
"description": "Whether or not there is a family history of dementia (includes Alzheimer's, vascular, etc.)",
"data_type": "enumeration",
"enumerations": ["0", "1"],
"notes": "Missing values can either be left blank or set to NA."
},
{
"column": "family_hx_dementia_relatedness_1",
"description": "Degree of relatedness. If first and second degree available, prioritize first degree",
"data_type": "enumeration",
"enumerations": ["1st degree", "2nd degree", "unknown"],
"notes": "0 = 'no' 1 = 'yes' Missing values can either be left blank or set to NA."
},
{
"column": "family_hx_type1_diabetes",
"description": "Whether or not there is a family history of type 1 diabetes",
"data_type": "enumeration",
"enumerations": ["0", "1"],
"notes": "Missing values can either be left blank or set to NA."
},
{
"column": "family_hx_type1_diabetes_relatedness_1",
"description": "Degree of relatedness. If first and second degree available, prioritize first degree",
"data_type": "enumeration",
"enumerations": ["1st degree", "2nd degree", "unknown"],
"notes": "0 = 'no' 1 = 'yes' Missing values can either be left blank or set to NA."
},
{
"column": "family_hx_asthma",
"description": "Whether or not there is a family history of asthma",
"data_type": "enumeration",
"enumerations": ["0", "1"],
"notes": "Missing values can either be left blank or set to NA."
},
{
"column": "family_hx_asthma_relatedness_1",
"description": "Degree of relatedness. If first and second degree available, prioritize first degree",
"data_type": "enumeration",
"enumerations": ["1st degree", "2nd degree", "unknown"],
"notes": "0 = 'no' 1 = 'yes' Missing values can either be left blank or set to NA."
},
{
"column": "family_hx_stroke",
"description": "Whether or not there is a family history of stroke",
"data_type": "enumeration",
"enumerations": ["0", "1"],
"notes": "Missing values can either be left blank or set to NA."
},
{
"column": "family_hx_stroke_relatedness_1",
"description": "Degree of relatedness. If first and second degree available, prioritize first degree",
"data_type": "enumeration",
"enumerations": ["1st degree", "2nd degree", "unknown"],
"notes": "0 = 'no' 1 = 'yes' Missing values can either be left blank or set to NA."
},
{
"column": "family_hx_heart_failure",
"description": "Whether or not there is a family history of congestive heart failure",
"data_type": "enumeration",
"enumerations": ["0", "1"],
"notes": "Missing values can either be left blank or set to NA."
},
{
"column": "family_hx_heart_failure_relatedness_1",
"description": "Degree of relatedness. If first and second degree available, prioritize first degree",
"data_type": "enumeration",
"enumerations": ["1st degree", "2nd degree", "unknown"],
"notes": "0 = 'no' 1 = 'yes' Missing values can either be left blank or set to NA."
}
]
}
]
}
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