diff --git a/PRIMED_phenotype_data_model.json b/PRIMED_phenotype_data_model.json index e53d6a5..97f1e12 100755 --- a/PRIMED_phenotype_data_model.json +++ b/PRIMED_phenotype_data_model.json @@ -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"] + "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"] }, { "column": "md5sum", @@ -897,8 +897,8 @@ "notes": "0 = 'no' 1 = 'yes' Missing values can either be left blank or set to NA." }, { - "column": "cad_ehr_1", - "description": "ehr-defined variable", + "column": "cad_emerge_1", + "description": "indicator of coronary artery disease event occurrence using the emerge ehr-based definition", "data_type": "enumeration", "enumerations": ["0", "1"], "notes": "0 = 'no' 1 = 'yes' Missing values can either be left blank or set to NA." @@ -937,8 +937,22 @@ "notes": "this can be any value that is used consistently within the study" }, { - "column": "breast_cancer_status_1", - "description": "whether or not the participant had breast cancer", + "column": "breast_cancer_status_emerge_1", + "description": "whether or not the participant had breast cancer using the eMERGE EHR-based definition and instructions", + "data_type": "enumeration", + "enumerations": ["0", "1"], + "notes": "0 = 'no' 1 = 'yes' Missing values can either be left blank or set to NA." + }, + { + "column": "breast_cancer_status_registry_1", + "description": "whether or not the participant had breast cancer as reported in a registry", + "data_type": "enumeration", + "enumerations": ["0", "1"], + "notes": "0 = 'no' 1 = 'yes' Missing values can either be left blank or set to NA." + }, + { + "column": "breast_cancer_status_survey_1", + "description": "whether or not the participant had breast cancer as reported in a survey or self-report", "data_type": "enumeration", "enumerations": ["0", "1"], "notes": "0 = 'no' 1 = 'yes' Missing values can either be left blank or set to NA." @@ -1040,7 +1054,7 @@ "enumerations": ["MX", "M0", "M1"] }, { - "column": "stage_system", + "column": "stage_system_1", "description": "definition of staging system used (e.g., SEER, AJCC) and time period (e.g., year), if applicable", "data_type": "string", "examples": ["AJCC 2003", "SEER 1999"], @@ -1203,8 +1217,22 @@ "notes": "this can be any value that is used consistently within the study" }, { - "column": "prostate_cancer_status_1", - "description": "whether or not the participant had prostate cancer", + "column": "prostate_cancer_status_emerge_1", + "description": "whether or not the participant had prostate cancer using the eMERGE EHR-based definition and instructions", + "data_type": "enumeration", + "enumerations": ["0", "1"], + "notes": "0 = 'no' 1 = 'yes' Missing values can either be left blank or set to NA." + }, + { + "column": "prostate_cancer_status_registry_1", + "description": "whether or not the participant had prostate cancer as reported in a registry", + "data_type": "enumeration", + "enumerations": ["0", "1"], + "notes": "0 = 'no' 1 = 'yes' Missing values can either be left blank or set to NA." + }, + { + "column": "prostate_cancer_status_survey_1", + "description": "whether or not the participant had prostate cancer as reported in a survey or self-report", "data_type": "enumeration", "enumerations": ["0", "1"], "notes": "0 = 'no' 1 = 'yes' Missing values can either be left blank or set to NA." @@ -1216,7 +1244,7 @@ "notes": "may be the same as age_at_obs or not" }, { - "column": "year_at_diagnosis", + "column": "year_at_diagnosis_1", "description": "year participant was diagnosed", "data_type": "integer", "examples": "1999" @@ -1280,7 +1308,7 @@ "enumerations": ["MX", "M0", "M1"] }, { - "column": "stage_system", + "column": "stage_system_1", "description": "definition of staging system (e.g., SEER, AJCC) and time period (e.g., year), if applicable", "data_type": "string", "examples": ["AJCC 2003", "SEER 1999"], @@ -1307,6 +1335,11 @@ "enumerations": ["2", "3", "4", "5", "6", "7", "8", "9", "10"], "notes": "missing values can either be left blank or set to NA" }, + { + "column": "psa_1", + "description": "psa score at current visit", + "data_type": "float" + }, { "column": "psa_at_diagnosis_1", "description": "psa score at diagnosis of prostate cancer",