From d971f5b0608b7c82cde638fd61ef98eb4a61a772 Mon Sep 17 00:00:00 2001 From: Sigfried Gold Date: Thu, 30 Jan 2025 14:32:54 -0500 Subject: [PATCH 1/4] nothing much --- resources/README.md | 2 +- resources/merged-TOPMed-harmonized-data-file/merge-files.py | 2 +- src/bdchm/schema/bdchm.yaml | 3 +++ 3 files changed, 5 insertions(+), 2 deletions(-) diff --git a/resources/README.md b/resources/README.md index 9e4aff9..33cfde6 100644 --- a/resources/README.md +++ b/resources/README.md @@ -15,7 +15,7 @@ ### External resources -* [copies-of-certain-files-from-gdrive/](copies-of-certain-files-from-gdrive/) +* [copies-of-certain-files-from-gdrive/](copies-of-source-files/) * [harmonized-variable-documentation](harmonized-variable-documentation) * Symbolic link to local clone of [UW-GAC/topmed-dcc-harmonized-phenotypes](https://github.com/UW-GAC/topmed-dcc-harmonized-phenotypes/tree/master/harmonized-variable-documentation). Clone that repo in the same directory as this repo, and the symlink should work. diff --git a/resources/merged-TOPMed-harmonized-data-file/merge-files.py b/resources/merged-TOPMed-harmonized-data-file/merge-files.py index 27368ca..04a536e 100644 --- a/resources/merged-TOPMed-harmonized-data-file/merge-files.py +++ b/resources/merged-TOPMed-harmonized-data-file/merge-files.py @@ -29,7 +29,7 @@ def extract_phv(text): merged_df = pd.merge( raw_to_harm, dbgap_vars, on='phv_number', - how='inner') + how='left') # Rename columns as needed (you can modify these names) column_mapping = { diff --git a/src/bdchm/schema/bdchm.yaml b/src/bdchm/schema/bdchm.yaml index b95823a..b962a45 100644 --- a/src/bdchm/schema/bdchm.yaml +++ b/src/bdchm/schema/bdchm.yaml @@ -97,6 +97,7 @@ classes: member_of_research_study: range: ResearchStudy description: A reference to the Study(s) of which this Participant is a member + comments: Shouldn't this be multivalued? age_at_enrollment: range: integer description: The age in days when the Participant enrolled on the ResearchStudy @@ -1430,6 +1431,8 @@ slots: range: Observation description: A set of one or more observations. multivalued: true + category: + range: string enums: From afa8b8ce6042d981c7064be3ed4f9410d9da5ed2 Mon Sep 17 00:00:00 2001 From: Sigfried Gold Date: Thu, 30 Jan 2025 17:19:10 -0500 Subject: [PATCH 2/4] got rid of all the symlinks and replaced references to them with relative paths not sure if everything will still work. i didn't test the python scripts. --- resources/README.md | 6 +- .../AHA_TABLES 1(Sheet1).csv | 160 ++ .../AHA_TABLES 1(Sheet2).csv | 1382 +++++++++++++++++ .../README.md | 0 .../biolincc_variables_all_studies.csv | 0 .../dbgap_variables_priority_cohorts.csv | 0 resources/harmonized-variable-documentation | 1 - .../find_harmonization_function_duplicates.py | 2 +- .../harmonization_documentation_generator.py | 2 +- .../harmonized-variable-source-documentation | 1 - .../topmed-variable-documentation.md | 1 - .../generate_mapping.py | 2 +- .../README.md | 21 +- .../dbgap_variables_priority_cohorts.csv | 1 - .../merge-files.py | 8 +- .../raw-to-harmonized-topmed-vars.csv | 1 - 16 files changed, 1555 insertions(+), 33 deletions(-) create mode 100644 resources/copies-of-external-source-files/AHA_TABLES 1(Sheet1).csv create mode 100644 resources/copies-of-external-source-files/AHA_TABLES 1(Sheet2).csv rename resources/{copies-of-certain-files-from-gdrive => copies-of-external-source-files}/README.md (100%) rename resources/{copies-of-certain-files-from-gdrive => copies-of-external-source-files}/biolincc_variables_all_studies.csv (100%) rename resources/{copies-of-certain-files-from-gdrive => copies-of-external-source-files}/dbgap_variables_priority_cohorts.csv (100%) delete mode 120000 resources/harmonized-variable-documentation delete mode 120000 resources/human-readable-harmonized-variable-documentation/harmonized-variable-source-documentation delete mode 120000 resources/human-readable-harmonized-variable-documentation/topmed-variable-documentation.md delete mode 120000 resources/merged-TOPMed-harmonized-data-file/dbgap_variables_priority_cohorts.csv delete mode 120000 resources/merged-TOPMed-harmonized-data-file/raw-to-harmonized-topmed-vars.csv diff --git a/resources/README.md b/resources/README.md index 33cfde6..6d9a8c9 100644 --- a/resources/README.md +++ b/resources/README.md @@ -8,14 +8,14 @@ -- Output * [human-readable-harmonized-variable-documentation/](human-readable-harmonized-variable-documentation/) - * [topmed-variable-documentation.md](human-readable-harmonized-variable-documentation/topmed-variable-documentation.md) + * [TopMED variable documentation](human-readable-harmonized-variable-documentation/generated-doc-pages/README.md) * [merged-TOPMed-harmonized-data-file](merged-TOPMed-harmonized-data-file/) ### External resources -* [copies-of-certain-files-from-gdrive/](copies-of-source-files/) -* [harmonized-variable-documentation](harmonized-variable-documentation) +* [copies-of-external-source-files](copies-of-source-files/) +* [harmonized-variable-documentation](../../../topmed-dcc-harmonized-phenotypes/harmonized-variable-documentation) * Symbolic link to local clone of [UW-GAC/topmed-dcc-harmonized-phenotypes](https://github.com/UW-GAC/topmed-dcc-harmonized-phenotypes/tree/master/harmonized-variable-documentation). Clone that repo in the same directory as this repo, and the symlink should work. diff --git a/resources/copies-of-external-source-files/AHA_TABLES 1(Sheet1).csv b/resources/copies-of-external-source-files/AHA_TABLES 1(Sheet1).csv new file mode 100644 index 0000000..5859e6f --- /dev/null +++ b/resources/copies-of-external-source-files/AHA_TABLES 1(Sheet1).csv @@ -0,0 +1,160 @@ +Harmonized Variable,Harmonized Variable Description,SNOMED CT ID,NINDS CDE ID,Studies Mapped,Missing Samples (%), +AFIB,"Atrial fibrillation (0=No, 1=Yes)",49436004,C17466; C52619,ARICFraminghamMESAREGARDS,1.26, +,,,,,, +AGE,Age,424144002,C00008,ARICFraminghamMESAREGARDS,1.3, +,,,,,, +ALCOHOL,Alcohol (servings per week),896811007,C56075,ARICFraminghamMESAREGARDS,0.46, +,,,,,, +ANYCHOLMED,"Taking cholesterol lowering medication (0=No, 1=Yes)",-,C58967,ARICFraminghamMESAREGARDS,1.24, +,,,,,, +ASPIRIN,"Taking aspirin (0=No, 1=Yes)",387458008,C10463,ARICFraminghamMESAREGARDS,1.24, +,,,,,, +BASE_CVD,Baseline CVD,-,-,ARICFraminghamMESA,0.65, +,,,,,, +BASE_STROKE,"Baseline Stroke/TIA(0=No, 1=TIA, 2=Stroke)",-,-,ARICFraminghamREGARDS,-, +,,,,,, +BG,Blood glucose (mg/dL) (fasting and non-fasting),-,-,Framingham,1.31, +,,,,,, +BMI,Body mass index (kg/m2),60621009,C11131,ARICFraminghamMESAREGARDS,1.28, +,,,,,, +CARSTEN,"Carotid stenosis (0=No, 1=Yes)",64586002,-,ARICFraminghamMESA,0.51, +,,,,,, +CENSDAY,Censor day,-,-,ARICFraminghamMESA,1.56, +,,,,,, +CREAT,Creatinine (mg/dL),15373003,C57972,ARICFraminghamMESAREGARDS,0.95, +,,,,,, +CURRSMK,"Current smoking status (0=No, 1=Yes)",77176002,C10473,ARICFraminghamMESAREGARDS,1.3, +,,,,,, +DAYS_SINCE_EXAM1,Time to event,-,-,Framingham,1.59, +,,,,,, +DEATH_IND,Death indicator,-,-,ARICFraminghamMESA,1.79, +,,,,,, +DEATH_IND_T2,-,-,-,MESA,1.45, +,,,,,, +DIAB,"Diabetes(0=No, 1=Yes)",73211009,C17480,ARICFraminghamMESAREGARDS,1.32, +,,,,,, +DIABP,-,271650006,C01507,ARICMESAREGARDS,1.25, +,,,,,, +DIABP1,"PHYSICIAN DIASTOLIC BLOOD PRESSURE, FIRST (MM HG)",-,-,Framingham,1.97, +,,,,,, +DIABP2,"PHYSICIAN DIASTOLIC BLOOD PRESSURE, SECOND (MM HG)",-,-,Framingham,1.24, +,,,,,, +EDUCLEV,"Education level (1=Less than High School, 2=High School, 3=Some College, 4=College)",276031006,C00012,ARICFraminghamMESAREGARDS,1.45, +,,,,,, +EVENT,Event code,-,-,Framingham,-, +,,,,,, +EVENT_DESC,Formatted value of EVENT,-,-,Framingham,-, +,,,,,, +EVENT_NAME_O,-,-,-,ARICMESA,-, +,,,,,, +EVENT_T2_O,-,-,-,ARICMESA,1.44, +,,,,,, +EVENT_VAL_C,-,-,-,ARICMESA,0.8, +,,,,,, +FAM_INCOME,Family income,224168007,-,ARICFraminghamMESAREGARDS,0.56, +,,,,,, +FASTING,-,-,-,REGARDS,-, +,,,,,, +FASTING_12HR,-,-,-,ARIC,0.66, +,,,,,, +FASTING_8HR,-,-,-,ARIC,0.66, +,,,,,, +FASTING_BG,Fasting blood glucose (>: 8 hours) (mg/dL),271062006,C54941,FraminghamMESA,1.53, +,,,,,, +FH_STROKE,"Family history of stroke, Mother or Father (0=No, 1=Yes)",443877004,C20253,ARICFraminghamMESAREGARDS,0.83, +,,,,,, +FRUITS,Fruits (servings per week),-,C10056,ARICFraminghamREGARDS,2.65, +,,,,,, +GENHLTH,"General Health (Exams 5-7, 4-category)",-,-,ARICFramingham,2.63, +,,,,,, +GENHLTH2,"General Health (Exams 8-9, 5-category)",-,-,ARICFraminghamMESAREGARDS,1.45, +,,,,,, +GLUCOSE,-,-,-,ARICREGARDS,0.33, +,,,,,, +HDL,HDL cholesterol (mg/dL),9422000,C18146,ARICFraminghamMESAREGARDS,1.3, +,,,,,, +HGT_CM,Height (centimeters),1153637007,C01522,ARICFraminghamMESAREGARDS,1.28, +,,,,,, +HRX,"Treated for hypertension (0=No, 1=Yes)",302192008,C58930,ARICFraminghamMESAREGARDS,1.31, +,,,,,, +HXCVD,History of cardiovascular disease,49601007,C21869; C17477; C17479,ARICFraminghamMESAREGARDS,1.12, +,,,,,, +HXHRTD,History of heart disease,56265001,C21869; C17477; C17479,ARICFraminghamMESAREGARDS,0.43, +,,,,,, +HXMI,History of MI(REGARDS model),22298006,C0450,ARICFraminghamMESAREGARDS,1.12, +,,,,,, +HXMI_SR,-,22298006,C0450,REGARDS,-, +,,,,,, +HXPAD,-,-,-,REGARDS,-, +,,,,,, +HXTIA,-,-,-,REGARDS,-, +,,,,,, +HYPT,-,-,-,MESA,1.25, +,,,,,, +ID_C,-,-,-,ARIC,-, +,,,,,, +INSULIN,"Taking insulin (0=No, 1=Yes)",67866001,C20268,ARICFraminghamMESAREGARDS,1.24, +,,,,,, +LDL,-,-,-,ARICMESAREGARDS,0.83, +,,,,,, +LVH,Left ventricular hypertrophy on ECG,55827005,C10735,ARICFraminghamMESAREGARDS,1.29, +,,,,,, +MESAID,-,-,-,MESA,-, +,,,,,, +NONSTATIN,"Taking non-statin medication (0=No, 1=Yes)",-,-,FraminghamMESA,1.24, +,,,,,, +PID,UNIQUE PARTICIPANT ID,-,-,Framingham,-, +,,,,,, +RACE_C,Race,103579009,C00030,ARICFraminghamMESAREGARDS,-, +,,,,,, +REGARDS_SUBJ_ID,-,-,-,REGARDS,-, +,,,,,, +SEX_C,Participant gender (character),-,-,ARICFraminghamMESAREGARDS,-, +,,,,,, +SEX_N,"Participant gender (1=Male, 0=Female)",-,-,ARICFraminghamMESAREGARDS,-, +,,,,,, +SODIUM,Sodium intake (mg/day),1148504005,C54943,ARICFraminghamREGARDS,-, +,,,,,, +STATE,Site location (state),398070004,-,ARICFraminghamMESAREGARDS,-, +,,,,,, +STATIN,"Taking statin medication (0=No, 1=Yes)",315053001,C54963,ARICFraminghamMESAREGARDS,1.24, +,,,,,, +STATNONSTAT,"Taking statin/non-statin combination (0=No, 1=Yes)",-,-,Framingham,-, +,,,,,, +STROKE,-,-,-,REGARDS,-, +,,,,,, +STROKE10,-,-,-,REGARDS,0.33, +,,,,,, +STROKE - ALL CAUSE,-,-,-,REGARDS,-, +,,,,,, +STROKE - HEMORRHAGIC,-,-,-,REGARDS,-, +,,,,,, +STROKE - ISCHEMIC,-,-,-,REGARDS,-, +,,,,,, +SYSBP,-,386536003,C01565,ARICMESAREGARDS,1.25, +,,,,,, +SYSBP1,"PHYSICIAN SYSTOLIC BLOOD PRESSURE, FIRST (MM HG)",-,-,Framingham,1.97, +,,,,,, +SYSBP2,"PHYSICIAN SYSTOLIC BLOOD PRESSURE, SECOND (MM HG)",-,-,Framingham,1.24, +,,,,,, +T2STROKE,-,-,-,REGARDS,0.33, +,,,,,, +T2STROKE10,-,-,-,REGARDS,0.33, +,,,,,, +T2STROKE10_YRS,-,-,-,REGARDS,0.33, +,,,,,, +T2STROKE_YRS,-,-,-,REGARDS,0.33, +,,,,,, +TC,Total cholesterol (mg/dL),121868005,C18168,ARICFraminghamMESAREGARDS,1.29, +,,,,,, +TRIG,Total Triglycerides (mg/dL),14740000,C18169,ARICFraminghamMESAREGARDS,1.29, +,,,,,, +VALVDIS,"Valvular heart disease (0=No, 1=Yes)",368009,C22435,FraminghamMESA,2.56, +,,,,,, +VEGETABLES,Vegetables (servings per week),401070008,C10056,ARICFraminghamREGARDS,2.64, +,,,,,, +VISDAY,Visit day (days since exam 1),-,-,ARICFraminghamMESA,1.52, +,,,,,, +VISIT,Visit,-,-,ARICFraminghamMESA,-, +,,,,,, +WGT,Weight (lbs),726527001,C01541,ARICFraminghamMESAREGARDS,, diff --git a/resources/copies-of-external-source-files/AHA_TABLES 1(Sheet2).csv b/resources/copies-of-external-source-files/AHA_TABLES 1(Sheet2).csv new file mode 100644 index 0000000..2dc99f1 --- /dev/null +++ b/resources/copies-of-external-source-files/AHA_TABLES 1(Sheet2).csv @@ -0,0 +1,1382 @@ +Harmonized Variable,Study Mapped,Variable Field Name,Variable Description,Missing Samples (%) +AFIB,ARIC,atrfib11.af,Atrial fibrillation,- +AFIB,ARIC,afincps13.afinc,Incident AF,2.1927486 +AFIB,ARIC,afincps13.ttaf,time to incident af,2.1927486 +AFIB,ARIC,atrfib21.af,Atrial fibrillation,- +AFIB,ARIC,afincps13.afinc,Incident AF,2.1927486 +AFIB,ARIC,afincps13.ttaf,time to incident af,2.1927486 +AFIB,ARIC,derive2_10.v2days,DAYS SINCE EXAM 1,- +AFIB,ARIC,atrfib31.af,Atrial fibrillation,- +AFIB,ARIC,afincps13.afinc,Incident AF,2.1927486 +AFIB,ARIC,afincps13.ttaf,time to incident af,2.1927486 +AFIB,ARIC,derive37.v3days,DAYS SINCE EXAM 1,- +AFIB,ARIC,atrfib41.af,Atrial fibrillation,- +AFIB,ARIC,afincps13.afinc,Incident AF,2.1927486 +AFIB,ARIC,afincps13.ttaf,time to incident af,2.1927486 +AFIB,ARIC,derive47.v4days,DAYS SINCE EXAM 1,- +AFIB,Framingham,ex1_1d_v3.a158,ATRIAL FIBRILLATION,0.040096231 +AFIB,Framingham,ex1_2d_v3.b269,D205-026-ATRIAL-FIBRILLATION,0.319829424 +AFIB,Framingham,ex1_3d_v1.c302,ATRIAL FIBRILLATION ON ECG,0.132908028 +AFIB,Framingham,ex1_4d_v1.d306,ECG-ATRIAL FIBRILLATION,0.128139416 +AFIB,Framingham,ex1_5d_v1.e589,ECG-RHYTHM,0.027114968 +AFIB,Framingham,ex1_6d_v1.f584,ECG-RHYTHM,- +AFIB,Framingham,ex1_7d_v2.g362,ECG - RHYTHM,0.086306099 +AFIB,Framingham,e_exam_ex08_1_0005d.h309,ECG - RHYTHM,0.033500838 +AFIB,Framingham,e_exam_ex09_1b_0844d.j364,ECG - RHYTHM,0.148864905 +AFIB,MESA,mesae1dres20220813.afib1c,ATRIAL FIBRILLATION / FLUTTER BY NOVACODE,0.719107719 +AFIB,MESA,mesaevaffu10_drepos_2015416.afib,Atrial Fibrillation Diagnosis (via ICD10 Code),- +AFIB,MESA,mesaevaffu10_drepos_2015416.afibtt,Atrial Fibrillation (via ICD10 Code): Time from Baseline to Diagnosis (Days),0.058702671 +AFIB,MESA,mesaevaffu10_drepos_2015416.afib,Atrial Fibrillation Diagnosis (via ICD10 Code),- +AFIB,MESA,mesaevaffu10_drepos_2015416.afibtt,Atrial Fibrillation (via ICD10 Code): Time from Baseline to Diagnosis (Days),0.058702671 +AFIB,MESA,mesae2dres06222012.e12dyc,"Time between exam visits, in days",8.526562959 +AFIB,MESA,mesaevaffu10_drepos_2015416.afib,Atrial Fibrillation Diagnosis (via ICD10 Code),- +AFIB,MESA,mesaevaffu10_drepos_2015416.afibtt,Atrial Fibrillation (via ICD10 Code): Time from Baseline to Diagnosis (Days),0.058702671 +AFIB,MESA,mesae3dres06222012.e13dyc,"Time between first and third visits, in days",12.72380393 +AFIB,MESA,mesaevaffu10_drepos_2015416.afib,Atrial Fibrillation Diagnosis (via ICD10 Code),- +AFIB,MESA,mesaevaffu10_drepos_2015416.afibtt,Atrial Fibrillation (via ICD10 Code): Time from Baseline to Diagnosis (Days),0.058702671 +AFIB,MESA,mesae4dres06222012.e14dyc,"Time between first and fourth visits, in days",14.61696507 +AFIB,MESA,mesae5_drepos_20220820.afib5c,ECG ATRIAL FIBRILLATION / FLUTTER,2.184054283 +AFIB,MESA,mesaevaffu10_drepos_2015416.afib,Atrial Fibrillation Diagnosis (via ICD10 Code),- +AFIB,MESA,mesaevaffu10_drepos_2015416.afibtt,Atrial Fibrillation (via ICD10 Code): Time from Baseline to Diagnosis (Days),0.058702671 +AFIB,MESA,mesae5_drepos_20220820.e15dyc,"TIME BETWEEN FIRST AND FIFTH VISITS, IN DAYS",- +AFIB,REGARDS,baseline_calculated_variables.AFIB_ECG,-,- +AFIB,REGARDS,baseline_calculated_variables.AFIB_SR,-,- +AGE,ARIC,derive13.v1age01,AGE AT VISIT 1,- +AGE,ARIC,derive2_10.v2age22,Age at Visit 2,- +AGE,ARIC,derive37.v3age31,Age at Visit 3,- +AGE,ARIC,derive47.v4age41,Age at Visit 4,- +AGE,ARIC,derive51.v5age52,Corrected Visit 5 age,- +AGE,Framingham,vr_wkthru_ex09_1_1001d.age1,"Age (years), Exam 1",- +AGE,Framingham,vr_wkthru_ex09_1_1001d.age2,"Age (years), Exam 2",24.77947073 +AGE,Framingham,vr_wkthru_ex09_1_1001d.age3,"Age (years), Exam 3",24.57898958 +AGE,Framingham,vr_wkthru_ex09_1_1001d.age4,"Age (years), Exam 4",21.77225341 +AGE,Framingham,vr_wkthru_ex09_1_1001d.age5,"Age (years), Exam 5",26.06255012 +AGE,Framingham,vr_wkthru_ex09_1_1001d.age6,"Age (years), Exam 6",31.61587811 +AGE,Framingham,vr_wkthru_ex09_1_1001d.age7,"Age (years), Exam 7",30.3127506 +AGE,Framingham,vr_wkthru_ex09_1_1001d.age8,"Age (years), Exam 8",40.1563753 +AGE,Framingham,vr_wkthru_ex09_1_1001d.age9,"Age (years), Exam 9",51.88452285 +AGE,MESA,mesae1dres20220813.age1c,AGE,- +AGE,MESA,mesae2dres06222012.age2c,AGE AT EXAM 2,8.526562959 +AGE,MESA,mesae3dres06222012.age3c,AGE AT EXAM3,12.72380393 +AGE,MESA,mesae4dres06222012.age4c,Age at exam 4,14.61696507 +AGE,MESA,mesae5_drepos_20220820.age5c,AGE AT EXAM 5,- +AGE,REGARDS,baseline_calculated_variables.AGE,-,- +ALCOHOL,ARIC,dtia.dtia90,DRINK ALCOHOLIC BEVERAGE Q90,- +ALCOHOL,ARIC,dtia.dtia96,NO OF GLASSES WINE CONSUMED P WK Q96,43.73831776 +ALCOHOL,ARIC,dtia.dtia97,NO OF CANS OF BEER CONSUMED P WK Q97,43.71161549 +ALCOHOL,ARIC,dtia.dtia98,NO OF HARD LIQUOR DRINKS PER WK Q98,43.76502003 +ALCOHOL,ARIC,phxb04.phxb14,EVER CONSUMED ALCOHOLIC BEVERAGES Q14,- +ALCOHOL,ARIC,phxb04.phxb15,DRINK ALCOHOL NOW Q15,- +ALCOHOL,ARIC,phxb04.phxb17a,USUAL # OF GLASSES WINE/WK Q17A,50.96950387 +ALCOHOL,ARIC,phxb04.phxb18a,USUAL # OF BEERS PER WEEK Q18A,50.99681384 +ALCOHOL,ARIC,phxb04.phxb19a,USUAL # OF HARD LIQUOR DRINKS/WK Q19A,50.99681384 +ALCOHOL,Framingham,ex1_3d_v1.c452,Total Alcohol Consumption,0.292397661 +ALCOHOL,Framingham,vr_ffreq_ex06_1_0506d.ffd114,BEER:(servings/week),0.886990802 +ALCOHOL,Framingham,vr_ffreq_ex06_1_0506d.ffd115,RED WINE:(servings/week),0.525624179 +ALCOHOL,Framingham,vr_ffreq_ex06_1_0506d.ffd116,WHITE WINE:(servings/week),0.591327201 +ALCOHOL,Framingham,vr_ffreq_ex06_1_0506d.ffd117,LIQUOR:(servings/week),0.229960578 +ALCOHOL,Framingham,vr_ffreq_ex08_1_0615d_v1.ffd114,BEER:(servings/week),1.115656378 +ALCOHOL,Framingham,vr_ffreq_ex08_1_0615d_v1.ffd115,RED WINE:(servings/week),0.483451097 +ALCOHOL,Framingham,vr_ffreq_ex08_1_0615d_v1.ffd116,WHITE WINE:(servings/week),0.520639643 +ALCOHOL,Framingham,vr_ffreq_ex08_1_0615d_v1.ffd117,LIQUOR:(servings/week),0.037188546 +ALCOHOL,MESA,mesae1dres20220813.alcwk1c,# DRINKS PER WEEK (CURRENT AND FORMER DRINKERS),21.44115057 +ALCOHOL,REGARDS,baseline_calculated_variables.ALC_DRINKS_WK,-,1.961368983 +ANYCHOLMED,ARIC,derive13.cholmdcode01,Cholesterol lowering medication w/in 2wks: Using 2004 Med Code -V1,0.759797387 +ANYCHOLMED,ARIC,derive2_10.cholmdcode21,Cholesterol lowering medication w/in 2wks: Using 2004 Med Code -V2,0.308710033 +ANYCHOLMED,ARIC,derive37.cholmdcode31,Cholesterol lowering medication w/in 2wks: Using 2004 Med Code -V3,0.205153455 +ANYCHOLMED,ARIC,derive47.cholmdcode41,Cholesterol lowering medication w/in 2wks: Using 2004 Med Code -V4,0.391442877 +ANYCHOLMED,ARIC,msr.msrf33e,Medication taken for high blood cholesterol,- +ANYCHOLMED,Framingham,ex1_5d_v1.e249,ANTI CHOLESTEROL DRUGS-OTHER,0.054229935 +ANYCHOLMED,Framingham,ex1_6d_v1.f209,MEDS - ANTI-CHOL -RESINS,0.029316916 +ANYCHOLMED,Framingham,ex1_6d_v1.f210,MEDS - ANTI-CHOL -NIACIN/NICOTINIC ACID,0.029316916 +ANYCHOLMED,Framingham,ex1_6d_v1.f211,MEDS - ANTI-CHOL -FIBRATES,0.029316916 +ANYCHOLMED,Framingham,ex1_5d_v1.e247,ANTI CHOLESTEROL DRUGS-FIBRATES,0.027114968 +ANYCHOLMED,Framingham,ex1_5d_v1.e248,ANTI CHOLESTEROL DRUGS-STATINS,0.027114968 +ANYCHOLMED,Framingham,ex1_1d_v3.a80,ANTI-CHOLESTEROL AGENTS,0.481154772 +ASPIRIN,ARIC,derive13.aspirincode01,"Used Aspirin-containing analgesics (at Visit 1) in last 2 weeks (0=No, 1=Yes), based on 2004 Med Code",0.866435617 +ASPIRIN,ARIC,derive2_10.aspirincode21,"Used Aspirin-containing analgesics (at Visit 2) in last 2 weeks (0=No, 1=Yes), based on 2004 Med Code",0.323410511 +ASPIRIN,ARIC,derive37.aspirincode31,"Used Aspirin-containing analgesics (at Visit 3) in last 2 weeks (0=No, 1=Yes), based on 2004 Med Code",0.262596422 +ASPIRIN,ARIC,derive47.aspirincode41,"Used Aspirin-containing analgesics (at Visit 4) in last 2 weeks (0=No, 1=Yes), based on 2004 Med Code",0.409649522 +ASPIRIN,ARIC,msr.msrf34,Aspirin taken in last 4 weeks,- +ASPIRIN,Framingham,ex1_5d_v1.e218,NUMBER OF ASPIRINS PER TIME INTERVAL,0.569414317 +ASPIRIN,Framingham,ex1_5d_v1.e219,TIME INTERVAL FOR ASPIRIN TAKEN,0.921908894 +ASPIRIN,Framingham,ex1_6d_v1.f181,NUMBER OF ASPIRINS TAKEN REGULARLY,0.35180299 +ASPIRIN,Framingham,ex1_6d_v1.f182,ASPIRIN FREQUENCY,0.322486075 +ASPIRIN,Framingham,ex1_7d_v2.g038,NUMBER OF ASPIRINS TAKEN REGULARLY,0.115074799 +ASPIRIN,Framingham,ex1_7d_v2.g039,ASPIRIN FREQUENCY,0.172612198 +ASPIRIN,Framingham,e_exam_ex08_1_0005d.h011,Number aspirins taken regularly,0.167504188 +ASPIRIN,Framingham,e_exam_ex08_1_0005d.h012,Aspirin Frequency per,0.201005025 +ASPIRIN,Framingham,vr_meds_ex08_1_0280d.atc_cod1,ATC CODE FOR MEDICATION OR FIRST DRUG IN COMPOUND,- +ASPIRIN,Framingham,vr_meds_ex08_1_0280d.atc_cod2,ATC CODE FOR SECOND DRUG IN COMPOUND,- +ASPIRIN,Framingham,vr_meds_ex08_1_0280d.atc_cod3,ATC CODE FOR THIRD DRUG IN COMPOUND,- +ASPIRIN,Framingham,vr_meds_ex08_1_0280d.atc_cod4,ATC CODE FOR FOURTH DRUG IN COMPOUND,- +ASPIRIN,Framingham,e_exam_ex09_1b_0844d.j011,"MEDS - ASPIR, # OF",0.558243394 +ASPIRIN,Framingham,e_exam_ex09_1b_0844d.j012,"MEDS - ASPIR, PER DY/WK/MO/YR",0.632675847 +ASPIRIN,Framingham,vr_meds_ex09_1b_0879d.atc_cod1,ATC code for medication or first drug in compound,- +ASPIRIN,Framingham,vr_meds_ex09_1b_0879d.atc_cod2,ATC code for medication or second drug in compound,- +ASPIRIN,Framingham,vr_meds_ex09_1b_0879d.atc_cod3,ATC code for medication or third drug in compound,- +ASPIRIN,Framingham,vr_meds_ex09_1b_0879d.atc_cod4,ATC code for medication or fourth drug in compound,- +ASPIRIN,MESA,mesae1dres20220813.asa1c,Aspirin from 280804 (anti-inflam agents),0.044027003 +ASPIRIN,MESA,mesae2dres06222012.asa2c,Aspirin from 280804 (anti-inflam agents),12.35691224 +ASPIRIN,MESA,mesae3dres06222012.asa3c,Aspirin from 280804 (anti-inflam agents),14.22072204 +ASPIRIN,MESA,mesae4dres06222012.asa4c,Aspirin from 280804 (anti-inflam agents),17.36131494 +ASPIRIN,MESA,mesae5_drepos_20220820.asa5c,ASPIRIN FROM 280804 (ANTI-INFLAM AGENTS),0.169635284 +ASPIRIN,REGARDS,baseline_calculated_variables.REG_ASA,-,- +BASE_CVD,ARIC,derive13.prvchd05,PREVALENT CORONARY HEART DISEASE,2.19941349 +BASE_CVD,ARIC,derive13.symchd03,SYMPTOMATIC CORONARY HEART DISEASE,1.073047187 +BASE_CVD,ARIC,derive13.roseic03,"ROSE INTERMITTENT CLAUDICATION, DEF. 3",0.299920021 +BASE_CVD,ARIC,derive13.prevhf01,Prevalent HF at Visit 1,1.832844575 +BASE_CVD,Framingham,vr_survcvd_2019_a_1334d.cvd,Cardiovascular Disease (CVD) status,- +BASE_CVD,Framingham,vr_survcvd_2019_a_1334d.cvddate,Date of Cardiovascular Disease (CVD) status,- +BASE_CVD,MESA,mesaevthr2015_drepos_20200330.prebase,Type of pre-baseline event,- +BASE_STROKE,ARIC,stroke01.stroke01,Stroke,- +BASE_STROKE,ARIC,stroke01.tia01,TIA,- +BASE_STROKE,Framingham,vr_svstk_2019_a_1335d.stroke,Stroke status,- +BASE_STROKE,Framingham,vr_svstk_2019_a_1335d.strokedate,Date of stroke,- +BASE_STROKE,Framingham,vr_svstktia_2019_a_1336d.stroke_tia,Stroke/TIA status,- +BASE_STROKE,Framingham,vr_svstktia_2019_a_1336d.stroketiadate,Date of stroke/TIA,- +BASE_STROKE,REGARDS,baseline_calculated_variables.STROKE_SR,-,- +BG,Framingham,vr_wkthru_ex09_1_1001d.bg1,"Blood glucose (mg/dL) (includes fasting and non-fasting), Exam 1",4.250200481 +BG,Framingham,vr_wkthru_ex09_1_1001d.bg2,"Blood glucose (mg/dL) (includes fasting and non-fasting), Exam 2",27.7265437 +BG,Framingham,vr_wkthru_ex09_1_1001d.bg3,"Blood glucose (mg/dL) (includes fasting and non-fasting), Exam 3",27.12510024 +BG,Framingham,vr_wkthru_ex09_1_1001d.bg4,"Blood glucose (mg/dL) (includes fasting and non-fasting), Exam 4",23.61668003 +BG,Framingham,vr_wkthru_ex09_1_1001d.bg5,"Blood glucose (mg/dL) (includes fasting and non-fasting), Exam 5",26.66399358 +BG,Framingham,vr_wkthru_ex09_1_1001d.bg6,"Blood glucose (mg/dL) (includes fasting and non-fasting), Exam 6",32.55813953 +BG,Framingham,vr_wkthru_ex09_1_1001d.bg7,"Blood glucose (mg/dL) (includes fasting and non-fasting), Exam 7",34.38251804 +BG,Framingham,vr_wkthru_ex09_1_1001d.bg8,"Blood glucose (mg/dL) (includes fasting and non-fasting), Exam 8",42.54210104 +BG,Framingham,vr_wkthru_ex09_1_1001d.bg9,"Blood glucose (mg/dL) (includes fasting and non-fasting), Exam 9",54.87169206 +BMI,ARIC,derive13.bmi01,BODY MASS INDEX IN KG/(M*M),0.159957345 +BMI,ARIC,derive2_10.bmi21,V2 body mass index in kg/m2,0.205806689 +BMI,ARIC,derive37.bmi32,Body Mass Index in kg/m**2,0.147710487 +BMI,ARIC,derive47.bmi41,Description not found,0.318616295 +BMI,ARIC,derive51.bm!51,-,- +BMI,Framingham,vr_wkthru_ex09_1_1001d.bmi1,"Body mass index (kg/m�), Exam 1",0.080192462 +BMI,Framingham,vr_wkthru_ex09_1_1001d.bmi2,"Body mass index (kg/m�), Exam 2",24.83961508 +BMI,Framingham,vr_wkthru_ex09_1_1001d.bmi3,"Body mass index (kg/m�), Exam 3",25.56134723 +BMI,Framingham,vr_wkthru_ex09_1_1001d.bmi4,"Body mass index (kg/m�), Exam 4",22.19326383 +BMI,Framingham,vr_wkthru_ex09_1_1001d.bmi5,"Body mass index (kg/m�), Exam 5",26.62389735 +BMI,Framingham,vr_wkthru_ex09_1_1001d.bmi6,"Body mass index (kg/m�), Exam 6",32.55813953 +BMI,Framingham,vr_wkthru_ex09_1_1001d.bmi7,"Body mass index (kg/m�), Exam 7",34.30232558 +BMI,Framingham,vr_wkthru_ex09_1_1001d.bmi8,"Body mass index (kg/m�), Exam 8",42.38171612 +BMI,Framingham,vr_wkthru_ex09_1_1001d.bmi9,"Body mass index (kg/m�), Exam 9",54.69125902 +BMI,MESA,mesae1dres20220813.bmi1c,BODY MASS INDEX (kg)/(m^2),- +BMI,MESA,mesae2dres06222012.bmi2c,BODY MASS INDEX (kg)/(m^2),8.555914294 +BMI,MESA,mesae3dres06222012.bmi3c,BODY MASS INDEX (kg)/(m^2),12.84120928 +BMI,MESA,mesae4dres06222012.bmi4c,BODY MASS INDEX (kg)/(m^2),16.31934253 +BMI,MESA,mesae5_drepos_20220820.bmi5c,BODY MASS INDEX (kg/m^2),1.569126378 +BMI,REGARDS,baseline_calculated_variables.BMI,-,0.722260875 +CARSTEN,ARIC,phea.phea10,CAROTID BRUITS? Q10,- +CARSTEN,ARIC,derive47.plaque42,Alt. Plaque in any site,40.6008193 +CARSTEN,Framingham,ex1_3d_v1.c361,CDI: LEFT CAROTID BRUIT,0.079744817 +CARSTEN,Framingham,ex1_3d_v1.c362,CDI: RIGHT CAROTID BRUIT,0.079744817 +CARSTEN,Framingham,ex1_6d_v1.f564,CAROTID BRUIT-LEFT,1.231310466 +CARSTEN,Framingham,ex1_6d_v1.f565,CAROTID BRUIT-RIGHT,1.260627382 +CARSTEN,Framingham,e_exam_ex08_1_0005d.h298,CAROTID BRUIT - LEFT,3.718592965 +CARSTEN,Framingham,e_exam_ex08_1_0005d.h299,CAROTID BRUIT - RIGHT,3.718592965 +CARSTEN,MESA,mesae1dres20220813.maxstn1c,"MAXIMUM CAROTID STENOSIS, GRADED",1.438215439 +CENSDAY,ARIC,incps18.fudth18,Follow Up Days to Death by 2018,- +CENSDAY,Framingham,vr_survdth_2019_a_1337d.datedth,Date of death,57.63052209 +CENSDAY,Framingham,vr_survdth_2019_a_1337d.lastcon,Date of last contact,42.36947791 +CENSDAY,MESA,mesaevthr2015_drepos_20200330.fuptt,Time until most recent follow-up (days),0.073378339 +CREAT,ARIC,chma.chma09,CREATININE (MG-DL) Q9,- +CREAT,ARIC,chmb.chmb08,CREATININE (mg per dL) DEC PT REQ Q8,- +CREAT,ARIC,chm.chm21,"Creatinine, Serum (mg/dL)",0.609652837 +CREAT,Framingham,vr_wkthru_ex09_1_1001d.creat2,"Creatinine (mg/dL), Exam 2",27.7265437 +CREAT,Framingham,vr_wkthru_ex09_1_1001d.creat5,"Creatinine (mg/dL), Exam 5",38.09141941 +CREAT,Framingham,vr_wkthru_ex09_1_1001d.creat6,"Creatinine (mg/dL), Exam 6",33.05934242 +CREAT,Framingham,vr_wkthru_ex09_1_1001d.creat7,"Creatinine (mg/dL), Exam 7",34.60304731 +CREAT,Framingham,vr_wkthru_ex09_1_1001d.creat8,"Creatinine (mg/dL), Exam 8",42.78267843 +CREAT,Framingham,vr_wkthru_ex09_1_1001d.creat9,"Creatinine (mg/dL), Exam 9",55.13231756 +CREAT,MESA,mesae1dres20220813.creatin1,CREATININE (mg/dl),0.366891694 +CREAT,MESA,mesae3dres06222012.creatin3,CREATININE (mg/dl),13.604344 +CREAT,MESA,mesae4dres06222012.creatin4,Creatinine (mg/dl),17.31728794 +CREAT,MESA,mesae5_drepos_20220820.creatnn5,CREATININE,95.41984733 +CREAT,REGARDS,baseline_calculated_variables.CREATININE_SERUM,-,4.323625882 +CURRSMK,ARIC,derive13.cursmk01,CURRENT CIGARETTE SMOKER,0.09997334 +CURRSMK,ARIC,derive2_10.cursmk21,Current Smoker Flag,0.242557883 +CURRSMK,ARIC,derive37.cursmk31,Current Smoker,0.303627113 +CURRSMK,ARIC,derive47.cursmk41,Current Cigarette Smoker,0.937642239 +CURRSMK,ARIC,derive51.cursmk52,V5 Current Cigarette Smoker,6.29005059 +CURRSMK,Framingham,vr_wkthru_ex09_1_1001d.currsmk1,"Current smoking status, Exam 1",0.320769848 +CURRSMK,Framingham,vr_wkthru_ex09_1_1001d.currsmk2,"Current smoking status, Exam 2",24.81956696 +CURRSMK,Framingham,vr_wkthru_ex09_1_1001d.currsmk3,"Current smoking status, Exam 3",24.61908581 +CURRSMK,Framingham,vr_wkthru_ex09_1_1001d.currsmk4,"Current smoking status, Exam 4",21.8925421 +CURRSMK,Framingham,vr_wkthru_ex09_1_1001d.currsmk5,"Current smoking status, Exam 5",26.12269447 +CURRSMK,Framingham,vr_wkthru_ex09_1_1001d.currsmk6,"Current smoking status, Exam 6",31.61587811 +CURRSMK,Framingham,vr_wkthru_ex09_1_1001d.currsmk7,"Current smoking status, Exam 7",30.35284683 +CURRSMK,Framingham,vr_wkthru_ex09_1_1001d.currsmk8,"Current smoking status, Exam 8",40.23656776 +CURRSMK,Framingham,vr_wkthru_ex09_1_1001d.currsmk9,"Current smoking status, Exam 9",52.04490778 +CURRSMK,MESA,mesae1dres20220813.cig1c,CIGARETTE SMOKING STATUS,0.32286469 +CURRSMK,MESA,mesae2dres06222012.cig2c,"Cigarrette Smoking Status, Exam 2",9.172292339 +CURRSMK,MESA,mesae3dres06222012.cig3c,"Cigarrette Smoking Status, Exam 3",13.34018198 +CURRSMK,MESA,mesae4dres06222012.cig4c,"Cigarette Smoking Status, Exam 4",15.58555914 +CURRSMK,MESA,mesae5_drepos_20220820.cig5c,"CIGARETTE SMOKING STATUS, EXAM 5",1.378286684 +CURRSMK,REGARDS,baseline_calculated_variables.SMOKE,-,- +DAYS_SINCE_EXAM1,Framingham,vr_soe_2020_a_1340d.date,DATE OF EVENT,0.016110843 +DAYS_SINCE_EXAM1,Framingham,vr_soe_2020_a_1340d.date,DATE OF EVENT,0.016110843 +DAYS_SINCE_EXAM1,Framingham,vr_soe_2020_a_1340d.date,DATE OF EVENT,0.016110843 +DAYS_SINCE_EXAM1,Framingham,vr_soe_2020_a_1340d.date,DATE OF EVENT,0.016110843 +DAYS_SINCE_EXAM1,Framingham,vr_soe_2020_a_1340d.date,DATE OF EVENT,0.016110843 +DEATH_IND,ARIC,incps18.dead18,Dead by 2018 from DTH/NDI/AFU,- +DEATH_IND,Framingham,vr_survdth_2019_a_1337d.datedth,Date of death,57.63052209 +DEATH_IND,MESA,mesaevthr2015_drepos_20200330.dth,Death,0.308189023 +DEATH_IND_T2,MESA,mesaevthr2015_drepos_20200330.dthtt,Time to All-Cause Death or End of Year 2015 (days),0.308189023 +DIAB,ARIC,derive37.diabts34,Diabetes Using Lower Cutpoint 126 mg/dL,0.623666503 +DIAB,ARIC,derive47.diabts42,Diabetes Using Lower Cutpoint 126 mg/dL,1.201638598 +DIAB,ARIC,derive51.diabts54,V5 Diabetes - Lower Cutpoint 126 mg/dL,3.591905565 +DIAB,Framingham,vr_diab_ex09_1_1002d.curr_diab1,"Diabetes Mellitus Status, Exam 1",4.731355253 +DIAB,Framingham,vr_diab_ex09_1_1002d.curr_diab2,"Diabetes Mellitus Status, Exam 2",27.96712109 +DIAB,Framingham,vr_diab_ex09_1_1002d.curr_diab3,"Diabetes Mellitus Status, Exam 3",27.12510024 +DIAB,Framingham,vr_diab_ex09_1_1002d.curr_diab4,"Diabetes Mellitus Status, Exam 4",23.65677626 +DIAB,Framingham,vr_diab_ex09_1_1002d.curr_diab5,"Diabetes Mellitus Status, Exam 5",26.64394547 +DIAB,Framingham,vr_diab_ex09_1_1002d.curr_diab6,"Diabetes Mellitus Status, Exam 6",32.47794707 +DIAB,Framingham,vr_diab_ex09_1_1002d.curr_diab7,"Diabetes Mellitus Status, Exam 7",33.9414595 +DIAB,Framingham,vr_diab_ex09_1_1002d.curr_diab8,"Diabetes Mellitus Status, Exam 8",42.26142743 +DIAB,Framingham,vr_diab_ex09_1_1002d.curr_diab9,"Diabetes Mellitus Status, Exam 9",54.83159583 +DIAB,MESA,mesae1dres20220813.dm031c,Exam 1 Diabetes mellitus by 2003 ADA fasting criteria algorithm,0.352216026 +DIAB,MESA,mesae2dres06222012.dm032c,Exam 2 Diabetes mellitus by 2003 ADA fasting criteria algorithm,9.186968007 +DIAB,MESA,mesae3dres06222012.dm033c,Exam 3 Diabetes mellitus by 2003 ADA fasting criteria algorithm,13.47226299 +DIAB,MESA,mesae4dres06222012.dm034c,Exam 4 Diabetes mellitus by 2003 ADA fasting criteria algorithm,16.90636924 +DIAB,MESA,mesae5_drepos_20220820.dm035c,DIABETES 2003 ADA FASTING CRITERIA,2.565733673 +DIAB,REGARDS,baseline_calculated_variables.DIABETES_SR,-,- +DIAB,REGARDS,baseline_calculated_variables.DIAB_SRMED_GLU,-,- +DIABP,ARIC,sbpa02.sbpa22,2ND AND 3RD DIASTOLIC BP AVERAGE Q22,0.079984003 +DIABP,ARIC,sbpb02.sbpb22,2ND AND 3RD DIASTOLIC BP AVERAGE Q22,0.029400956 +DIABP,ARIC,sbpc04_02.sbpc23,2ND AND 3RD DIASTOLIC BP AVERAGE Q23,0.024624477 +DIABP,ARIC,sbpd04_02.sbpd20,1ST AND 2ND DIASTOLIC BP AVERAGE Q20,0.109239873 +DIABP,ARIC,sbp.sbp15,AVG: Diastolic (mmHg),0.690817186 +DIABP,MESA,mesae1dres20220813.dbp1c,SEATED DIASTOLIC BLOOD PRESSURE (mmHg),0.044027003 +DIABP,MESA,mesae2dres06222012.dbp2c,Seated Diastolic Blood Pressure (mmHg),8.570589962 +DIABP,MESA,mesae3dres06222012.dbp3c,SEATED DIASTOLIC BLOOD PRESSURE (mmHg),12.88523628 +DIABP,MESA,mesae4dres06222012.dbp4c,Seated diastolic blood pressure (mmhg),16.3780452 +DIABP,MESA,mesae5_drepos_20220820.dbp5c,SEATED DIASTOLIC BLOOD PRESSURE (mmHg),1.335877863 +DIABP,REGARDS,baseline_calculated_variables.DBP,-,0.288241726 +DIABP1,Framingham,ex1_1d_v3.a56,"PHYSICIAN DIASTOLIC BLOOD PRESSURE, 1ST",0.180433039 +DIABP1,Framingham,ex1_2d_v3.b25,D201-050-DIAS-PHYS-FIRST,0.053304904 +DIABP1,Framingham,ex1_3d_v1.c185,FIRST DIASTOLIC BLOOD PRESSURE,0.079744817 +DIABP1,Framingham,ex1_4d_v1.d193,DIASTOLIC BP -PHYSICIAN - 1ST READING,0.051255766 +DIABP1,Framingham,ex1_5d_v1.e486,DIASTOLIC PRESSURE - 1ST MD READING,0.054229935 +DIABP1,Framingham,ex1_6d_v1.f477,PHYSICIAN BP-DIASTOLIC-1ST READING,0.087950748 +DIABP1,Framingham,ex1_7d_v2.g272,PHYSICIAN BP DIASTOLIC - 1ST READING,0.230149597 +DIABP1,Framingham,e_exam_ex08_1_0005d.h112,PHYSICIAN DIASTOLIC BP - 1ST READING,0.234505863 +DIABP1,Framingham,e_exam_ex09_1b_0844d.j118,"MDBP1 - DIASTOLIC 1, MMHG",0.111648679 +DIABP2,Framingham,ex1_1d_v3.a58,"PHYSICIAN DIASTOLIC BLOOD PRESSURE, 2ND",82.23736969 +DIABP2,Framingham,ex1_2d_v3.b27,D201-056-DIAS-PHYS-SECOND,0.13326226 +DIABP2,Framingham,ex1_3d_v1.c287,SECOND DIASTOLIC BLOOD PRESSURE,0.345560872 +DIABP2,Framingham,ex1_4d_v1.d289,DIASTOLIC BP -PHYSICIAN - 2ND READING,0.333162481 +DIABP2,Framingham,ex1_5d_v1.e582,DIASTOLIC PRESSURE - 2ND MD READING,0.10845987 +DIABP2,Framingham,ex1_6d_v1.f577,PHYSICIAN BP-2ND READING-DIASTOLIC,0.175901495 +DIABP2,Framingham,ex1_7d_v2.g355,PHYSICIAN BP DIASTOLIC - 2ND READING,0.201380898 +DIABP2,Framingham,e_exam_ex08_1_0005d.h234,PHYSICIAN DIASTOLIC BP - 2ND READING,0.234505863 +DIABP2,Framingham,e_exam_ex09_1b_0844d.j257,"MDBP2 - DIAST, MMHG",0.29772981 +EDUCLEV,ARIC,hom.hom54,HIGHEST EDUCATION COMPLETED Q54,0.14665689 +EDUCLEV,Framingham,ex1_2d_v3.b43,D201-099-YEARS-EDUCATION,0.159914712 +EDUCLEV,MESA,mesae1dres20220813.educ1,EDUCATION: HIGHEST LEVEL COMPLETED,0.337540358 +EDUCLEV,REGARDS,baseline_calculated_variables.ED_CAT,-,- +EVENT,Framingham,vr_soe_2020_a_1340d.event,EVENT NUMBER ON SEQUENCE OF EVENTS,- +EVENT,Framingham,vr_soe_2020_a_1340d.event,EVENT NUMBER ON SEQUENCE OF EVENTS,- +EVENT,Framingham,vr_soe_2020_a_1340d.event,EVENT NUMBER ON SEQUENCE OF EVENTS,- +EVENT,Framingham,vr_soe_2020_a_1340d.event,EVENT NUMBER ON SEQUENCE OF EVENTS,- +EVENT,Framingham,vr_soe_2020_a_1340d.event,EVENT NUMBER ON SEQUENCE OF EVENTS,- +EVENT_DESC,Framingham,vr_soe_2020_a_1340d.event,EVENT NUMBER ON SEQUENCE OF EVENTS,- +EVENT_DESC,Framingham,vr_soe_2020_a_1340d.event,EVENT NUMBER ON SEQUENCE OF EVENTS,- +EVENT_DESC,Framingham,vr_soe_2020_a_1340d.event,EVENT NUMBER ON SEQUENCE OF EVENTS,- +EVENT_DESC,Framingham,vr_soe_2020_a_1340d.event,EVENT NUMBER ON SEQUENCE OF EVENTS,- +EVENT_DESC,Framingham,vr_soe_2020_a_1340d.event,EVENT NUMBER ON SEQUENCE OF EVENTS,- +EVENT_T2_O,ARIC,incps18.fthem18,Follow-up HEM Strokes (days),- +EVENT_T2_O,ARIC,incps18.ft18chm,Follow-up CHM Strokes (days),- +EVENT_T2_O,ARIC,incps18.ftisc18,Follow-up ISC Strokes (days),- +EVENT_T2_O,ARIC,incps18.ft18dp,Follow-up DP Strokes (days),- +EVENT_T2_O,ARIC,incps18.ftdpp18,Follow-up DPP Strokes (days),- +EVENT_T2_O,MESA,mesaevthr2015_drepos_20200330.strktt,Time to Stroke or End of Year 2015 (days),0.4549457 +EVENT_T2_O,MESA,mesaevthr2015_drepos_20200330.fuptt,Time until most recent follow-up (days),0.073378339 +EVENT_T2_O,MESA,mesaevthr2015_drepos_20200330.strktt,Time to Stroke or End of Year 2015 (days),0.4549457 +EVENT_T2_O,MESA,mesaevthr2015_drepos_20200330.fuptt,Time until most recent follow-up (days),0.073378339 +EVENT_T2_O,MESA,mesaevthr2015_drepos_20200330.strktt,Time to Stroke or End of Year 2015 (days),0.4549457 +EVENT_T2_O,MESA,mesaevthr2015_drepos_20200330.fuptt,Time until most recent follow-up (days),0.073378339 +EVENT_T2_O,MESA,mesaevthr2015_drepos_20200330.strktt,Time to Stroke or End of Year 2015 (days),0.4549457 +EVENT_T2_O,MESA,mesaevthr2015_drepos_20200330.fuptt,Time until most recent follow-up (days),0.073378339 +EVENT_T2_O,MESA,mesaevthr2015_drepos_20200330.dthtt,Time to All-Cause Death or End of Year 2015 (days),0.308189023 +EVENT_T2_O,MESA,mesaevthr2015_drepos_20200330.fuptt,Time until most recent follow-up (days),0.073378339 +EVENT_VAL_C,ARIC,incps18.inhem18,Def/Prob Hemmorrhagic Inc. Stroke by Censoring Date,- +EVENT_VAL_C,ARIC,incps18.inchm18,Def/Prob Combined Hemm Inc. Stroke by Censoring Date,- +EVENT_VAL_C,ARIC,incps18.inisc18,Def/Prob Ischemic Inc. Stroke by Censoring Date,- +EVENT_VAL_C,ARIC,incps18.indp18,Def/Prob Incident Stroke by Censoring Date,- +EVENT_VAL_C,ARIC,incps18.indpp18,Def/Prob/Poss Inc. Stroke by Censoring Date,- +EVENT_VAL_C,MESA,mesaevthr2015_drepos_20200330.strk,Stroke,0.4549457 +EVENT_VAL_C,MESA,mesaevthr2015_drepos_20200330.strk,Stroke,0.4549457 +EVENT_VAL_C,MESA,mesaevthr2015_drepos_20200330.strktype,Stroke type,- +EVENT_VAL_C,MESA,mesaevthr2015_drepos_20200330.strk,Stroke,0.4549457 +EVENT_VAL_C,MESA,mesaevthr2015_drepos_20200330.strktype,Stroke type,- +EVENT_VAL_C,MESA,mesaevthr2015_drepos_20200330.strk,Stroke,0.4549457 +EVENT_VAL_C,MESA,mesaevthr2015_drepos_20200330.strktype,Stroke type,- +EVENT_VAL_C,MESA,mesaevthr2015_drepos_20200330.dth,Death,0.308189023 +EVENT_VAL_C,MESA,mesaevthr2015_drepos_20200330.dthtype,Death type,80.96565894 +FAM_INCOME,ARIC,hom.hom62,COMBINED FAMILY INCOME GROUP Q62,5.659622692 +FAM_INCOME,ARIC,sesa04.sesa6,HOUSEHOLD INCOME LAST YEAR Q6,- +FAM_INCOME,Framingham,q_psych_ex03_1_0167d.py125,Current total family income/yr before tx,20.96008931 +FAM_INCOME,MESA,mesae1dres20220813.income1,"TOTAL GROSS FAMILY INCOME, PAST 12 MONTHS",4.006457294 +FAM_INCOME,REGARDS,baseline_calculated_variables.INCOME,-,12.35794984 +FASTING,REGARDS,baseline_calculated_variables.FASTED,-,- +FASTING_12HR,ARIC,derive13.fast1202,FASTING TIME OF 12 HOURS OR MORE,0.459877366 +FASTING_12HR,ARIC,derive2_10.fast1223,"V2 Fast 12 Hrs or More, Definition 2",0.308710033 +FASTING_12HR,ARIC,derive37.fast1234,Fasting Time of 12 Hours or More,0.812407681 +FASTING_8HR,ARIC,derive13.fast0802,FASTING TIME OF 8 HOURS OR MORE,0.446547587 +FASTING_8HR,ARIC,derive2_10.fast0823,"V2 Fast 8 Hrs or More, Definition 2",0.301359794 +FASTING_8HR,ARIC,derive37.fast0834,Fasting Time of 8 Hours or More,0.812407681 +FASTING_BG,Framingham,vr_wkthru_ex09_1_1001d.fasting_bg3,"Fasting (>= 8 hours) blood glucose (mg/dL), Exam 3",29.17000802 +FASTING_BG,Framingham,vr_wkthru_ex09_1_1001d.fasting_bg4,"Fasting (>= 8 hours) blood glucose (mg/dL), Exam 4",26.98476343 +FASTING_BG,Framingham,vr_wkthru_ex09_1_1001d.fasting_bg5,"Fasting (>= 8 hours) blood glucose (mg/dL), Exam 5",27.5862069 +FASTING_BG,Framingham,vr_wkthru_ex09_1_1001d.fasting_bg6,"Fasting (>= 8 hours) blood glucose (mg/dL), Exam 6",33.72093023 +FASTING_BG,Framingham,vr_wkthru_ex09_1_1001d.fasting_bg7,"Fasting (>= 8 hours) blood glucose (mg/dL), Exam 7",35.56535686 +FASTING_BG,Framingham,vr_wkthru_ex09_1_1001d.fasting_bg8,"Fasting (>= 8 hours) blood glucose (mg/dL), Exam 8",43.68484362 +FASTING_BG,Framingham,vr_wkthru_ex09_1_1001d.fasting_bg9,"Fasting (>= 8 hours) blood glucose (mg/dL), Exam 9",55.87409783 +FASTING_BG,MESA,mesae1dres20220813.glucos1c,Exam 1 Fasting Glucose- Calibrated,0.366891694 +FASTING_BG,MESA,mesae2dres06222012.glucos2c,FASTING GLUCOSE (mg/dL) CALIBRATED,9.245670678 +FASTING_BG,MESA,mesae3dres06222012.glucos3c,FASTING GLUCOSE (mg/dL) CALIBRATED,13.604344 +FASTING_BG,MESA,mesae4dres06222012.glucos4c,Fasting Glucose (mg/dL) Calibrated,17.31728794 +FASTING_BG,MESA,mesae5_drepos_20220820.glucose5,FASTING GLUCOSE (mg/dl),2.735368957 +FH_STROKE,ARIC,derive13.momhistorystr,New Maternal History of Stroke,5.131964809 +FH_STROKE,ARIC,derive13.dadhistorystr,New Paternal History of Stroke,9.72407358 +FH_STROKE,Framingham,ex1_6d_v1.f692,FATHER-HAVE STROKE BEFORE AGE 65,12.28378775 +FH_STROKE,Framingham,ex1_6d_v1.f701,MOTHER-HAVE STROKE BEFORE AGE 65,11.6388156 +FH_STROKE,MESA,mesae1dres20220813.pstk1,FAMILY HISTORY OF STROKE: PARENT,0.058702671 +FH_STROKE,REGARDS,family_history.MOMSTROKE,-,- +FH_STROKE,REGARDS,family_history.DADSTROKE,-,- +FRUITS,ARIC,dtia.dtia09,CONSUMED APPLES OR PEARS Q9,- +FRUITS,ARIC,dtia.dtia10,CONSUMED ORANGES Q10,- +FRUITS,ARIC,dtia.dtia12,CONSUMED PEACHES APRICOTS PLUMS Q12,- +FRUITS,ARIC,dtia.dtia13,CONSUMED BANANAS Q13,- +FRUITS,ARIC,dtia.dtia14,CONSUMED OTHER FRUITS Q14,- +FRUITS,ARIC,dtic04.dtic9,CONSUMED APPLES OR PEARS Q9,- +FRUITS,ARIC,dtic04.dtic10,CONSUMED ORANGES Q10,- +FRUITS,ARIC,dtic04.dtic12,CONSUMED PEACHES APRICOTS PLUMS Q12,- +FRUITS,ARIC,dtic04.dtic13,CONSUMED BANANAS Q13,- +FRUITS,ARIC,dtic04.dtic14,CONSUMED OTHER FRUITS Q14,- +FRUITS,Framingham,q_ffreq_ex03_1_0302d.apple,FRESH APPLE OR PAIR,1.35209713 +FRUITS,Framingham,q_ffreq_ex03_1_0302d.orange,ORANGE OR TANGERINE,2.069536424 +FRUITS,Framingham,q_ffreq_ex03_1_0302d.grapfrut,HALF GRAPEFRUIT OR GLASS JUICE,1.90397351 +FRUITS,Framingham,q_ffreq_ex03_1_0302d.peaches,"PEACHES,APRICOTS,PLUMS OR NECTARINES",1.379690949 +FRUITS,Framingham,q_ffreq_ex03_1_0302d.bananas,BANANAS,1.07615894 +FRUITS,Framingham,q_ffreq_ex03_1_0302d.strawber,"FRESH,FROZEN OR CANNED STRAWBERRIES",1.62803532 +FRUITS,Framingham,q_ffreq_ex03_1_0302d.blackber,"BLACKBERRIES,BLUEBERRIES,RASPBERRIES",1.655629139 +FRUITS,Framingham,q_ffreq_ex03_1_0302d.melon,CANTELOUPE OR HONEYDEW MELON-SLICE,1.379690949 +FRUITS,Framingham,q_ffreq_ex03_1_0302d.watermel,SLICE OF WATERMELON,2.290286976 +FRUITS,Framingham,q_ffreq_ex03_1_0302d.pineappl,FRESH OR CANNED PINEAPPLE,1.766004415 +FRUITS,Framingham,q_ffreq_ex03_1_0302d.cherries,FRESH OR CANNED CHERRIES,1.931567329 +FRUITS,Framingham,q_ffreq_ex03_1_0302d.papayas,HALF CUP PAPAYAS,1.90397351 +FRUITS,Framingham,q_ffreq_ex03_1_0302d.avocados,ONE QUARTER OF AN AVOCADO,2.317880795 +FRUITS,Framingham,q_ffreq_ex03_1_0302d.prunes,HALF CUP RAISINS OR DRY APRICOTS,1.738410596 +FRUITS,Framingham,q_ffreq_ex03_1_0302d.dates,HALF CUP DATES OR FIGS,1.90397351 +FRUITS,Framingham,q_ffreq_ex03_1_0302d.raisins,SMALL PACK RAISINS OR GRAPES,1.600441501 +FRUITS,Framingham,vr_ffreq_ex06_1_0506d.ffd30,RAISINS:(servings/week),0.427069645 +FRUITS,Framingham,vr_ffreq_ex06_1_0506d.ffd31,PRUNES:(servings/week),0.919842313 +FRUITS,Framingham,vr_ffreq_ex06_1_0506d.ffd32,BANANAS:(servings/week),1.609724047 +FRUITS,Framingham,vr_ffreq_ex06_1_0506d.ffd33,CANTALOUPE:(servings/week),0.985545335 +FRUITS,Framingham,vr_ffreq_ex06_1_0506d.ffd34,WATERMELON:(servings/week),1.806833114 +FRUITS,Framingham,vr_ffreq_ex06_1_0506d.ffd35,"APPLES/PEARS, FRESH:(servings/week)",1.149802891 +FRUITS,Framingham,vr_ffreq_ex06_1_0506d.ffd37,ORANGES:(servings/week),1.741130092 +FRUITS,Framingham,vr_ffreq_ex06_1_0506d.ffd39,GRAPEFRUIT:(servings/week),1.281208936 +FRUITS,Framingham,vr_ffreq_ex06_1_0506d.ffd42,STRAWBERRIES:(servings/week),0.459921156 +FRUITS,Framingham,vr_ffreq_ex06_1_0506d.ffd43,BLUEBERRIES:(servings/week),0.427069645 +FRUITS,Framingham,vr_ffreq_ex06_1_0506d.ffd44,PEACHES:(servings/week),0.427069645 +FRUITS,Framingham,vr_ffreq_ex08_1_0615d_v1.ffd30,RAISINS:(servings/week),0.892525102 +FRUITS,Framingham,vr_ffreq_ex08_1_0615d_v1.ffd31,PRUNES:(servings/week),1.264410562 +FRUITS,Framingham,vr_ffreq_ex08_1_0615d_v1.ffd32,BANANAS:(servings/week),1.115656378 +FRUITS,Framingham,vr_ffreq_ex08_1_0615d_v1.ffd33,CANTALOUPE:(servings/week),1.301599108 +FRUITS,Framingham,vr_ffreq_ex08_1_0615d_v1.ffd34,WATERMELON:(servings/week),1.822238751 +FRUITS,Framingham,vr_ffreq_ex08_1_0615d_v1.ffd35,"APPLES/PEARS, FRESH:(servings/week)",1.338787653 +FRUITS,Framingham,vr_ffreq_ex08_1_0615d_v1.ffd37,ORANGES:(servings/week),1.375976199 +FRUITS,Framingham,vr_ffreq_ex08_1_0615d_v1.ffd39,GRAPEFRUIT:(servings/week),1.264410562 +FRUITS,Framingham,vr_ffreq_ex08_1_0615d_v1.ffd42,STRAWBERRIES:(servings/week),1.264410562 +FRUITS,Framingham,vr_ffreq_ex08_1_0615d_v1.ffd43,BLUEBERRIES:(servings/week),0.483451097 +FRUITS,Framingham,vr_ffreq_ex08_1_0615d_v1.ffd44,PEACHES:(servings/week),0.557828189 +FRUITS,REGARDS,ffq_analyzed.FRUITSRV,-,- +GENHLTH,ARIC,hom.hom09,HEALTH CONDITION Q9,- +GENHLTH,Framingham,ex1_5d_v1.e065,YOUR HEALTH NOW IN GENERAL,0.569414317 +GENHLTH,Framingham,ex1_6d_v1.f087,YOUR HEALTH NOW IN GENERAL,1.026092055 +GENHLTH,Framingham,ex1_7d_v2.g514,YOUR HEALTH NOW IN GENERAL,1.179516686 +GENHLTH2,ARIC,sfe.sfe1,Rate general health,- +GENHLTH2,Framingham,e_exam_ex08_1_0005d.h714,"IN GENERAL, HOW IS YOUR HEALTH",2.244556114 +GENHLTH2,Framingham,e_exam_ex09_1b_0844d.j890,SF-12 - HOW YOUR HLTH,4.242649795 +GENHLTH2,MESA,mesae2dres06222012.genhel2,IN GENERAL YOUR HEALTH IS,8.77604931 +GENHLTH2,REGARDS,baseline_calculated_variables.GEN_SR_HEALTH,-,- +GLUCOSE,ARIC,derive13.glucos01,DERIVED GLUCOSE VALUE in mg/dl,0.913089843 +GLUCOSE,ARIC,chmb.chmb07,GLUCOSE (mg per dL) DEC PT REQ Q7,- +GLUCOSE,ARIC,lipc04.lipc4a,GLUCOSE (VALUE IN MG/DL) Q4A,- +GLUCOSE,ARIC,lipd04.lipd4a,FASTING GLUCOSE (VALUE) Q4A,0.009175154 +GLUCOSE,ARIC,lip.lip23,Fasting Glucose (mg/dL),5.536742296 +GLUCOSE,REGARDS,baseline_calculated_variables.GLUCOSE,-,4.330252129 +HDL,ARIC,derive13.hdl01,RE-CALIBRATED HDL CHOL. in mg/dl,1.552919222 +HDL,ARIC,lipb.lipb03a,HDL CHOLESTREROL (VALUE) Q3A,0.317906255 +HDL,ARIC,lipc04.lipc3a,HDL CHOLESTEROL (VALUE IN MG/DL) Q3A,- +HDL,ARIC,lipd04.lipd3a,HDL CHOLESTEROL (VALUE) Q3A,0.009175154 +HDL,ARIC,lip.lip13,HDLC-Cholesterol (mg/dL),0.914324416 +HDL,Framingham,vr_wkthru_ex09_1_1001d.hdl1,"HDL cholesterol (mg/dL), Exam 1",2.08500401 +HDL,Framingham,vr_wkthru_ex09_1_1001d.hdl2,"HDL cholesterol (mg/dL), Exam 2",26.4234162 +HDL,Framingham,vr_wkthru_ex09_1_1001d.hdl3,"HDL cholesterol (mg/dL), Exam 3",27.34562951 +HDL,Framingham,vr_wkthru_ex09_1_1001d.hdl4,"HDL cholesterol (mg/dL), Exam 4",23.957498 +HDL,Framingham,vr_wkthru_ex09_1_1001d.hdl5,"HDL cholesterol (mg/dL), Exam 5",26.86447474 +HDL,Framingham,vr_wkthru_ex09_1_1001d.hdl6,"HDL cholesterol (mg/dL), Exam 6",32.73857257 +HDL,Framingham,vr_wkthru_ex09_1_1001d.hdl7,"HDL cholesterol (mg/dL), Exam 7",34.50280674 +HDL,Framingham,vr_wkthru_ex09_1_1001d.hdl8,"HDL cholesterol (mg/dL), Exam 8",42.54210104 +HDL,Framingham,vr_wkthru_ex09_1_1001d.hdl9,"HDL cholesterol (mg/dL), Exam 9",54.89174018 +HDL,MESA,mesae1dres20220813.hdl1,HDL CHOLESTROL (mg/dl),0.381567361 +HDL,MESA,mesae2dres06222012.hdl2,HDL CHOLESTEROL (mg/dl),9.260346346 +HDL,MESA,mesae3dres06222012.hdl3,HDL CHOLESTEROL (mg/dl),13.54564133 +HDL,MESA,mesae4dres06222012.hdl4,HDL Cholesterol (mg/dl),17.3319636 +HDL,MESA,mesae5_drepos_20220820.hdl5,HDL CHOLESTROL (mg/dl),2.86259542 +HDL,REGARDS,baseline_calculated_variables.HDL,-,4.813968128 +HGT_CM,ARIC,anta.anta01,STANDING HEIGHT TO NEAREST CM Q1,0.119968009 +HGT_CM,ARIC,antc04.antc1,STANDING HEIGHT TO NEAREST CM Q1,0.024640657 +HGT_CM,ARIC,antd05.antd1,Description not found,0.30040965 +HGT_CM,ARIC,ant.ant3,Standing height (cm),4.043807919 +HGT_CM,Framingham,vr_wkthru_ex09_1_1001d.hgt1,"Height (inches), Exam 1",0.080192462 +HGT_CM,Framingham,vr_wkthru_ex09_1_1001d.hgt2,"Height (inches), Exam 2",24.83961508 +HGT_CM,Framingham,vr_wkthru_ex09_1_1001d.hgt3,"Height (inches), Exam 3",25.50120289 +HGT_CM,Framingham,vr_wkthru_ex09_1_1001d.hgt4,"Height (inches), Exam 4",22.19326383 +HGT_CM,Framingham,vr_wkthru_ex09_1_1001d.hgt5,"Height (inches), Exam 5",26.58380112 +HGT_CM,Framingham,vr_wkthru_ex09_1_1001d.hgt6,"Height (inches), Exam 6",32.55813953 +HGT_CM,Framingham,vr_wkthru_ex09_1_1001d.hgt7,"Height (inches), Exam 7",34.30232558 +HGT_CM,Framingham,vr_wkthru_ex09_1_1001d.hgt8,"Height (inches), Exam 8",42.38171612 +HGT_CM,Framingham,vr_wkthru_ex09_1_1001d.hgt9,"Height (inches), Exam 9",54.69125902 +HGT_CM,MESA,mesae1dres20220813.htcm1,HEIGHT (cm),- +HRX,ARIC,derive13.hyptmd01,"HYPERTENSION LOWERING MED. USE, DEF. 1",0.579845375 +HRX,ARIC,derive2_10.hyptmd21,Hypertension Meds (Self reported),0.448364572 +HRX,ARIC,derive37.hyptmd31,"V3 HYPERTENSION MEDICATIONS, DEF. 1",0.607254226 +HRX,ARIC,derive47.hyptmd41,V4 Hypert Med in Past 2 Wks: Self-rptd,0.600819299 +HRX,ARIC,msr.msrf33d,Medication taken for high blodd pressure or hypertension,- +HRX,Framingham,vr_wkthru_ex09_1_1001d.hrx1,"Treated for hypertension, Exam 1",0.541299118 +HRX,Framingham,vr_wkthru_ex09_1_1001d.hrx2,"Treated for hypertension, Exam 2",24.83961508 +HRX,Framingham,vr_wkthru_ex09_1_1001d.hrx3,"Treated for hypertension, Exam 3",24.65918204 +HRX,Framingham,vr_wkthru_ex09_1_1001d.hrx4,"Treated for hypertension, Exam 4",21.93263833 +HRX,Framingham,vr_wkthru_ex09_1_1001d.hrx5,"Treated for hypertension, Exam 5",26.40336808 +HRX,Framingham,vr_wkthru_ex09_1_1001d.hrx6,"Treated for hypertension, Exam 6",31.85645549 +HRX,Framingham,vr_wkthru_ex09_1_1001d.hrx7,"Treated for hypertension, Exam 7",30.49318364 +HRX,Framingham,vr_wkthru_ex09_1_1001d.hrx8,"Treated for hypertension, Exam 8",40.21651965 +HRX,Framingham,vr_wkthru_ex09_1_1001d.hrx9,"Treated for hypertension, Exam 9",52.04490778 +HRX,MESA,mesae1dres20220813.htnmed1c,Hypertension Medication,0.044027003 +HRX,MESA,mesae2dres06222012.htnmed2c,Hypertension Medication,12.35691224 +HRX,MESA,mesae3dres06222012.htnmed3c,Any hypertension medication,14.22072204 +HRX,MESA,mesae4dres06222012.htnmed4c,Any hypertension medication,17.36131494 +HRX,MESA,mesae5_drepos_20220820.htnmed5c,ANY HYPERTENSION MEDICATION,0.169635284 +HRX,REGARDS,baseline_calculated_variables.HYPER_MEDS_SR_NOW,-,- +HXCVD,ARIC,derive13.roseic03,"ROSE INTERMITTENT CLAUDICATION, DEF. 3",0.299920021 +HXCVD,ARIC,derive13.prvchd05,PREVALENT CORONARY HEART DISEASE,2.19941349 +HXCVD,ARIC,derive13.rangna01,ROSE ANGINA,0.239936017 +HXCVD,ARIC,derive13.prevhf01,Prevalent HF at Visit 1,1.832844575 +HXCVD,ARIC,incps18.c7_futimehf,Follow-up time for INCHF18 in days,6.671554252 +HXCVD,ARIC,incps18.inchf18,Incident HF (from discharge codes),6.671554252 +HXCVD,ARIC,derive13.prevhf01,Prevalent HF at Visit 1,1.832844575 +HXCVD,ARIC,derive37.prvchd33,"Prevalent CHD at V3, definition 3",2.067946824 +HXCVD,ARIC,derive37.v3days,DAYS SINCE EXAM 1,- +HXCVD,ARIC,hhxc04.hhxc1,REPORT ROSE ANGINA IN AFU? Q1,- +HXCVD,ARIC,incps18.c7_futimehf,Follow-up time for INCHF18 in days,6.671554252 +HXCVD,ARIC,incps18.inchf18,Incident HF (from discharge codes),6.671554252 +HXCVD,ARIC,derive13.prevhf01,Prevalent HF at Visit 1,1.832844575 +HXCVD,ARIC,derive47.prvchd43,"Prevalent CHD at V4, definition 3",1.957214383 +HXCVD,ARIC,derive47.v4days,DAYS SINCE EXAM 1,- +HXCVD,ARIC,hhxd04.hhxd1,REPORT ROSE ANGINA IN AFU? Q1,- +HXCVD,ARIC,incps18.c7_futimehf,Follow-up time for INCHF18 in days,6.671554252 +HXCVD,ARIC,incps18.inchf18,Incident HF (from discharge codes),6.671554252 +HXCVD,Framingham,vr_survcvd_2019_a_1334d.cvd,Cardiovascular Disease (CVD) status,- +HXCVD,Framingham,vr_survcvd_2019_a_1334d.cvddate,Date of Cardiovascular Disease (CVD) status,- +HXCVD,Framingham,,-,- +HXCVD,Framingham,vr_soe_2020_a_1340d.date,DATE OF EVENT,0.016110843 +HXCVD,Framingham,vr_soe_2020_a_1340d.event,EVENT NUMBER ON SEQUENCE OF EVENTS,- +HXCVD,Framingham,vr_survcvd_2019_a_1334d.cvd,Cardiovascular Disease (CVD) status,- +HXCVD,Framingham,vr_survcvd_2019_a_1334d.cvddate,Date of Cardiovascular Disease (CVD) status,- +HXCVD,Framingham,vr_wkthru_ex09_1_1001d.date2,Date of Exam 2,24.77947073 +HXCVD,Framingham,vr_soe_2020_a_1340d.date,DATE OF EVENT,0.016110843 +HXCVD,Framingham,vr_soe_2020_a_1340d.event,EVENT NUMBER ON SEQUENCE OF EVENTS,- +HXCVD,Framingham,vr_survcvd_2019_a_1334d.cvd,Cardiovascular Disease (CVD) status,- +HXCVD,Framingham,vr_survcvd_2019_a_1334d.cvddate,Date of Cardiovascular Disease (CVD) status,- +HXCVD,Framingham,vr_wkthru_ex09_1_1001d.date3,Date of Exam 3,24.57898958 +HXCVD,Framingham,vr_soe_2020_a_1340d.date,DATE OF EVENT,0.016110843 +HXCVD,Framingham,vr_soe_2020_a_1340d.event,EVENT NUMBER ON SEQUENCE OF EVENTS,- +HXCVD,Framingham,vr_survcvd_2019_a_1334d.cvd,Cardiovascular Disease (CVD) status,- +HXCVD,Framingham,vr_survcvd_2019_a_1334d.cvddate,Date of Cardiovascular Disease (CVD) status,- +HXCVD,Framingham,vr_wkthru_ex09_1_1001d.date4,Date of Exam 4,21.77225341 +HXCVD,Framingham,vr_soe_2020_a_1340d.date,DATE OF EVENT,0.016110843 +HXCVD,Framingham,vr_soe_2020_a_1340d.event,EVENT NUMBER ON SEQUENCE OF EVENTS,- +HXCVD,Framingham,vr_survcvd_2019_a_1334d.cvd,Cardiovascular Disease (CVD) status,- +HXCVD,Framingham,vr_survcvd_2019_a_1334d.cvddate,Date of Cardiovascular Disease (CVD) status,- +HXCVD,Framingham,vr_wkthru_ex09_1_1001d.date5,Date of Exam 5,26.06255012 +HXCVD,Framingham,vr_soe_2020_a_1340d.date,DATE OF EVENT,0.016110843 +HXCVD,Framingham,vr_soe_2020_a_1340d.event,EVENT NUMBER ON SEQUENCE OF EVENTS,- +HXCVD,Framingham,vr_survcvd_2019_a_1334d.cvd,Cardiovascular Disease (CVD) status,- +HXCVD,Framingham,vr_survcvd_2019_a_1334d.cvddate,Date of Cardiovascular Disease (CVD) status,- +HXCVD,Framingham,vr_wkthru_ex09_1_1001d.date6,Date of Exam 6,31.61587811 +HXCVD,Framingham,vr_soe_2020_a_1340d.date,DATE OF EVENT,0.016110843 +HXCVD,Framingham,vr_soe_2020_a_1340d.event,EVENT NUMBER ON SEQUENCE OF EVENTS,- +HXCVD,Framingham,vr_survcvd_2019_a_1334d.cvd,Cardiovascular Disease (CVD) status,- +HXCVD,Framingham,vr_survcvd_2019_a_1334d.cvddate,Date of Cardiovascular Disease (CVD) status,- +HXCVD,Framingham,vr_wkthru_ex09_1_1001d.date7,Date of Exam 7,30.3127506 +HXCVD,Framingham,vr_soe_2020_a_1340d.date,DATE OF EVENT,0.016110843 +HXCVD,Framingham,vr_soe_2020_a_1340d.event,EVENT NUMBER ON SEQUENCE OF EVENTS,- +HXCVD,Framingham,vr_survcvd_2019_a_1334d.cvd,Cardiovascular Disease (CVD) status,- +HXCVD,Framingham,vr_survcvd_2019_a_1334d.cvddate,Date of Cardiovascular Disease (CVD) status,- +HXCVD,Framingham,vr_wkthru_ex09_1_1001d.date8,Date of Exam 8,40.1563753 +HXCVD,Framingham,vr_soe_2020_a_1340d.date,DATE OF EVENT,0.016110843 +HXCVD,Framingham,vr_soe_2020_a_1340d.event,EVENT NUMBER ON SEQUENCE OF EVENTS,- +HXCVD,Framingham,vr_survcvd_2019_a_1334d.cvd,Cardiovascular Disease (CVD) status,- +HXCVD,Framingham,vr_survcvd_2019_a_1334d.cvddate,Date of Cardiovascular Disease (CVD) status,- +HXCVD,Framingham,vr_wkthru_ex09_1_1001d.date9,Date of Exam 9,51.88452285 +HXCVD,Framingham,vr_soe_2020_a_1340d.date,DATE OF EVENT,0.016110843 +HXCVD,Framingham,vr_soe_2020_a_1340d.event,EVENT NUMBER ON SEQUENCE OF EVENTS,- +HXCVD,MESA,mesaevthr2015_drepos_20200330.mi,Myocardial Infarction (MI),0.440270032 +HXCVD,MESA,mesaevthr2015_drepos_20200330.mitt,Time to MI or End of Year 2015 (days),0.440270032 +HXCVD,MESA,mesaevthr2015_drepos_20200330.rca,Resuscitated Cardiac Arrest,0.4549457 +HXCVD,MESA,mesaevthr2015_drepos_20200330.rcatt,Time to RCA or End of Year 2015 (days),0.4549457 +HXCVD,MESA,mesaevthr2015_drepos_20200330.ang,Angina Pectoris,0.4549457 +HXCVD,MESA,mesaevthr2015_drepos_20200330.angtt,Time to Angina or End of Year 2015 (days),0.4549457 +HXCVD,MESA,mesaevthr2015_drepos_20200330.chf,Congestive Heart Failure (CHF),0.425594365 +HXCVD,MESA,mesaevthr2015_drepos_20200330.chftt,Time to CHF or End of Year 2015 (days),0.425594365 +HXCVD,MESA,mesaevthr2015_drepos_20200330.pvd,Peripheral Vascular Disease (PVD),0.513648371 +HXCVD,MESA,mesaevthr2015_drepos_20200330.pvdtt,Time to PVD or End of Year 2015 (days),0.4549457 +HXCVD,MESA,mesaevthr2015_drepos_20200330.prebase,Type of pre-baseline event,- +HXCVD,MESA,mesae1dres20220813.whoros1c,WHO ROSE Intermittent Claudication,9.054886997 +HXCVD,MESA,mesaevthr2015_drepos_20200330.mi,Myocardial Infarction (MI),0.440270032 +HXCVD,MESA,mesaevthr2015_drepos_20200330.mitt,Time to MI or End of Year 2015 (days),0.440270032 +HXCVD,MESA,mesaevthr2015_drepos_20200330.rca,Resuscitated Cardiac Arrest,0.4549457 +HXCVD,MESA,mesaevthr2015_drepos_20200330.rcatt,Time to RCA or End of Year 2015 (days),0.4549457 +HXCVD,MESA,mesaevthr2015_drepos_20200330.ang,Angina Pectoris,0.4549457 +HXCVD,MESA,mesaevthr2015_drepos_20200330.angtt,Time to Angina or End of Year 2015 (days),0.4549457 +HXCVD,MESA,mesaevthr2015_drepos_20200330.chf,Congestive Heart Failure (CHF),0.425594365 +HXCVD,MESA,mesaevthr2015_drepos_20200330.chftt,Time to CHF or End of Year 2015 (days),0.425594365 +HXCVD,MESA,mesaevthr2015_drepos_20200330.pvd,Peripheral Vascular Disease (PVD),0.513648371 +HXCVD,MESA,mesaevthr2015_drepos_20200330.pvdtt,Time to PVD or End of Year 2015 (days),0.4549457 +HXCVD,MESA,mesaevthr2015_drepos_20200330.prebase,Type of pre-baseline event,- +HXCVD,MESA,mesae2dres06222012.whoros2c,WHO ROSE Intermittent Claudication,14.26474905 +HXCVD,MESA,mesae2dres06222012.e12dyc,"Time between exam visits, in days",8.526562959 +HXCVD,MESA,mesaevthr2015_drepos_20200330.mi,Myocardial Infarction (MI),0.440270032 +HXCVD,MESA,mesaevthr2015_drepos_20200330.mitt,Time to MI or End of Year 2015 (days),0.440270032 +HXCVD,MESA,mesaevthr2015_drepos_20200330.rca,Resuscitated Cardiac Arrest,0.4549457 +HXCVD,MESA,mesaevthr2015_drepos_20200330.rcatt,Time to RCA or End of Year 2015 (days),0.4549457 +HXCVD,MESA,mesaevthr2015_drepos_20200330.ang,Angina Pectoris,0.4549457 +HXCVD,MESA,mesaevthr2015_drepos_20200330.angtt,Time to Angina or End of Year 2015 (days),0.4549457 +HXCVD,MESA,mesaevthr2015_drepos_20200330.chf,Congestive Heart Failure (CHF),0.425594365 +HXCVD,MESA,mesaevthr2015_drepos_20200330.chftt,Time to CHF or End of Year 2015 (days),0.425594365 +HXCVD,MESA,mesaevthr2015_drepos_20200330.pvd,Peripheral Vascular Disease (PVD),0.513648371 +HXCVD,MESA,mesaevthr2015_drepos_20200330.pvdtt,Time to PVD or End of Year 2015 (days),0.4549457 +HXCVD,MESA,mesaevthr2015_drepos_20200330.prebase,Type of pre-baseline event,- +HXCVD,MESA,mesae3dres06222012.htnmed3c,Any hypertension medication,14.22072204 +HXCVD,MESA,mesae3dres06222012.e13dyc,"Time between first and third visits, in days",12.72380393 +HXCVD,MESA,mesaevthr2015_drepos_20200330.mi,Myocardial Infarction (MI),0.440270032 +HXCVD,MESA,mesaevthr2015_drepos_20200330.mitt,Time to MI or End of Year 2015 (days),0.440270032 +HXCVD,MESA,mesaevthr2015_drepos_20200330.rca,Resuscitated Cardiac Arrest,0.4549457 +HXCVD,MESA,mesaevthr2015_drepos_20200330.rcatt,Time to RCA or End of Year 2015 (days),0.4549457 +HXCVD,MESA,mesaevthr2015_drepos_20200330.ang,Angina Pectoris,0.4549457 +HXCVD,MESA,mesaevthr2015_drepos_20200330.angtt,Time to Angina or End of Year 2015 (days),0.4549457 +HXCVD,MESA,mesaevthr2015_drepos_20200330.chf,Congestive Heart Failure (CHF),0.425594365 +HXCVD,MESA,mesaevthr2015_drepos_20200330.chftt,Time to CHF or End of Year 2015 (days),0.425594365 +HXCVD,MESA,mesaevthr2015_drepos_20200330.pvd,Peripheral Vascular Disease (PVD),0.513648371 +HXCVD,MESA,mesaevthr2015_drepos_20200330.pvdtt,Time to PVD or End of Year 2015 (days),0.4549457 +HXCVD,MESA,mesaevthr2015_drepos_20200330.prebase,Type of pre-baseline event,- +HXCVD,MESA,mesae4dres06222012.whoros4c,WHO ROSE Intermittent Claudication,21.16231289 +HXCVD,MESA,mesae4dres06222012.e14dyc,"Time between first and fourth visits, in days",14.61696507 +HXCVD,MESA,mesaevthr2015_drepos_20200330.mi,Myocardial Infarction (MI),0.440270032 +HXCVD,MESA,mesaevthr2015_drepos_20200330.mitt,Time to MI or End of Year 2015 (days),0.440270032 +HXCVD,MESA,mesaevthr2015_drepos_20200330.rca,Resuscitated Cardiac Arrest,0.4549457 +HXCVD,MESA,mesaevthr2015_drepos_20200330.rcatt,Time to RCA or End of Year 2015 (days),0.4549457 +HXCVD,MESA,mesaevthr2015_drepos_20200330.ang,Angina Pectoris,0.4549457 +HXCVD,MESA,mesaevthr2015_drepos_20200330.angtt,Time to Angina or End of Year 2015 (days),0.4549457 +HXCVD,MESA,mesaevthr2015_drepos_20200330.chf,Congestive Heart Failure (CHF),0.425594365 +HXCVD,MESA,mesaevthr2015_drepos_20200330.chftt,Time to CHF or End of Year 2015 (days),0.425594365 +HXCVD,MESA,mesaevthr2015_drepos_20200330.pvd,Peripheral Vascular Disease (PVD),0.513648371 +HXCVD,MESA,mesaevthr2015_drepos_20200330.pvdtt,Time to PVD or End of Year 2015 (days),0.4549457 +HXCVD,MESA,mesaevthr2015_drepos_20200330.prebase,Type of pre-baseline event,- +HXCVD,MESA,mesae5_drepos_20220820.e15dyc,"TIME BETWEEN FIRST AND FIFTH VISITS, IN DAYS",- +HXCVD,REGARDS,baseline_calculated_variables.CAD_SR_ECG,-,- +HXCVD,REGARDS,baseline_calculated_variables.STROKE_SR,-,- +HXCVD,REGARDS,baseline_calculated_variables.TIA_SR,-,- +HXHRTD,ARIC,derive13.pad02,"PAD V1, Def 2 (same for both genders)",3.692348707 +HXHRTD,ARIC,derive13.rangna01,ROSE ANGINA,0.239936017 +HXHRTD,ARIC,derive13.prevhf01,Prevalent HF at Visit 1,1.832844575 +HXHRTD,ARIC,incps18.c7_futimehf,Follow-up time for INCHF18 in days,6.671554252 +HXHRTD,ARIC,incps18.inchf18,Incident HF (from discharge codes),6.671554252 +HXHRTD,ARIC,incps18.fuproc18,Follow up time for PROC18 (days),- +HXHRTD,ARIC,incps18.proc18,Cardiac Procedures,- +HXHRTD,ARIC,derive13.prevhf01,Prevalent HF at Visit 1,1.832844575 +HXHRTD,ARIC,derive37.pad32,"PAD V3, Def 2 (same for both genders)",65.00082061 +HXHRTD,ARIC,derive37.v3days,DAYS SINCE EXAM 1,- +HXHRTD,ARIC,hhxc04.hhxc1,REPORT ROSE ANGINA IN AFU? Q1,- +HXHRTD,ARIC,incps18.c7_futimehf,Follow-up time for INCHF18 in days,6.671554252 +HXHRTD,ARIC,incps18.inchf18,Incident HF (from discharge codes),6.671554252 +HXHRTD,ARIC,incps18.fuproc18,Follow up time for PROC18 (days),- +HXHRTD,ARIC,incps18.proc18,Cardiac Procedures,- +HXHRTD,ARIC,derive13.prevhf01,Prevalent HF at Visit 1,1.832844575 +HXHRTD,ARIC,derive47.pad42,"PAD V4, Def 2 (same for both genders)",44.86117433 +HXHRTD,ARIC,derive47.v4days,DAYS SINCE EXAM 1,- +HXHRTD,ARIC,hhxd04.hhxd1,REPORT ROSE ANGINA IN AFU? Q1,- +HXHRTD,ARIC,incps18.c7_futimehf,Follow-up time for INCHF18 in days,6.671554252 +HXHRTD,ARIC,incps18.inchf18,Incident HF (from discharge codes),6.671554252 +HXHRTD,ARIC,incps18.fuproc18,Follow up time for PROC18 (days),- +HXHRTD,ARIC,incps18.proc18,Cardiac Procedures,- +HXHRTD,Framingham,vr_survcvd_2019_a_1334d.cvd,Cardiovascular Disease (CVD) status,- +HXHRTD,Framingham,vr_survcvd_2019_a_1334d.cvddate,Date of Cardiovascular Disease (CVD) status,- +HXHRTD,Framingham,,-,- +HXHRTD,Framingham,vr_soe_2020_a_1340d.date,DATE OF EVENT,0.016110843 +HXHRTD,Framingham,vr_soe_2020_a_1340d.event,EVENT NUMBER ON SEQUENCE OF EVENTS,- +HXHRTD,Framingham,vr_cvdproc_2020_a_1313d.procdate,Date of cardiovascular procedure,- +HXHRTD,Framingham,vr_cvdproc_2020_a_1313d.procnum,PROCEDURE NUMBER,- +HXHRTD,Framingham,vr_survcvd_2019_a_1334d.cvd,Cardiovascular Disease (CVD) status,- +HXHRTD,Framingham,vr_survcvd_2019_a_1334d.cvddate,Date of Cardiovascular Disease (CVD) status,- +HXHRTD,Framingham,vr_wkthru_ex09_1_1001d.date2,Date of Exam 2,24.77947073 +HXHRTD,Framingham,vr_soe_2020_a_1340d.date,DATE OF EVENT,0.016110843 +HXHRTD,Framingham,vr_soe_2020_a_1340d.event,EVENT NUMBER ON SEQUENCE OF EVENTS,- +HXHRTD,Framingham,vr_cvdproc_2020_a_1313d.procdate,Date of cardiovascular procedure,- +HXHRTD,Framingham,vr_cvdproc_2020_a_1313d.procnum,PROCEDURE NUMBER,- +HXHRTD,Framingham,vr_survcvd_2019_a_1334d.cvd,Cardiovascular Disease (CVD) status,- +HXHRTD,Framingham,vr_survcvd_2019_a_1334d.cvddate,Date of Cardiovascular Disease (CVD) status,- +HXHRTD,Framingham,vr_wkthru_ex09_1_1001d.date3,Date of Exam 3,24.57898958 +HXHRTD,Framingham,vr_soe_2020_a_1340d.date,DATE OF EVENT,0.016110843 +HXHRTD,Framingham,vr_soe_2020_a_1340d.event,EVENT NUMBER ON SEQUENCE OF EVENTS,- +HXHRTD,Framingham,vr_cvdproc_2020_a_1313d.procdate,Date of cardiovascular procedure,- +HXHRTD,Framingham,vr_cvdproc_2020_a_1313d.procnum,PROCEDURE NUMBER,- +HXHRTD,Framingham,vr_survcvd_2019_a_1334d.cvd,Cardiovascular Disease (CVD) status,- +HXHRTD,Framingham,vr_survcvd_2019_a_1334d.cvddate,Date of Cardiovascular Disease (CVD) status,- +HXHRTD,Framingham,vr_wkthru_ex09_1_1001d.date4,Date of Exam 4,21.77225341 +HXHRTD,Framingham,vr_soe_2020_a_1340d.date,DATE OF EVENT,0.016110843 +HXHRTD,Framingham,vr_soe_2020_a_1340d.event,EVENT NUMBER ON SEQUENCE OF EVENTS,- +HXHRTD,Framingham,vr_cvdproc_2020_a_1313d.procdate,Date of cardiovascular procedure,- +HXHRTD,Framingham,vr_cvdproc_2020_a_1313d.procnum,PROCEDURE NUMBER,- +HXHRTD,Framingham,vr_survcvd_2019_a_1334d.cvd,Cardiovascular Disease (CVD) status,- +HXHRTD,Framingham,vr_survcvd_2019_a_1334d.cvddate,Date of Cardiovascular Disease (CVD) status,- +HXHRTD,Framingham,vr_wkthru_ex09_1_1001d.date5,Date of Exam 5,26.06255012 +HXHRTD,Framingham,vr_soe_2020_a_1340d.date,DATE OF EVENT,0.016110843 +HXHRTD,Framingham,vr_soe_2020_a_1340d.event,EVENT NUMBER ON SEQUENCE OF EVENTS,- +HXHRTD,Framingham,vr_cvdproc_2020_a_1313d.procdate,Date of cardiovascular procedure,- +HXHRTD,Framingham,vr_cvdproc_2020_a_1313d.procnum,PROCEDURE NUMBER,- +HXHRTD,Framingham,vr_survcvd_2019_a_1334d.cvd,Cardiovascular Disease (CVD) status,- +HXHRTD,Framingham,vr_survcvd_2019_a_1334d.cvddate,Date of Cardiovascular Disease (CVD) status,- +HXHRTD,Framingham,vr_wkthru_ex09_1_1001d.date6,Date of Exam 6,31.61587811 +HXHRTD,Framingham,vr_soe_2020_a_1340d.date,DATE OF EVENT,0.016110843 +HXHRTD,Framingham,vr_soe_2020_a_1340d.event,EVENT NUMBER ON SEQUENCE OF EVENTS,- +HXHRTD,Framingham,vr_cvdproc_2020_a_1313d.procdate,Date of cardiovascular procedure,- +HXHRTD,Framingham,vr_cvdproc_2020_a_1313d.procnum,PROCEDURE NUMBER,- +HXHRTD,Framingham,vr_survcvd_2019_a_1334d.cvd,Cardiovascular Disease (CVD) status,- +HXHRTD,Framingham,vr_survcvd_2019_a_1334d.cvddate,Date of Cardiovascular Disease (CVD) status,- +HXHRTD,Framingham,vr_wkthru_ex09_1_1001d.date7,Date of Exam 7,30.3127506 +HXHRTD,Framingham,vr_soe_2020_a_1340d.date,DATE OF EVENT,0.016110843 +HXHRTD,Framingham,vr_soe_2020_a_1340d.event,EVENT NUMBER ON SEQUENCE OF EVENTS,- +HXHRTD,Framingham,vr_cvdproc_2020_a_1313d.procdate,Date of cardiovascular procedure,- +HXHRTD,Framingham,vr_cvdproc_2020_a_1313d.procnum,PROCEDURE NUMBER,- +HXHRTD,Framingham,vr_survcvd_2019_a_1334d.cvd,Cardiovascular Disease (CVD) status,- +HXHRTD,Framingham,vr_survcvd_2019_a_1334d.cvddate,Date of Cardiovascular Disease (CVD) status,- +HXHRTD,Framingham,vr_wkthru_ex09_1_1001d.date8,Date of Exam 8,40.1563753 +HXHRTD,Framingham,vr_soe_2020_a_1340d.date,DATE OF EVENT,0.016110843 +HXHRTD,Framingham,vr_soe_2020_a_1340d.event,EVENT NUMBER ON SEQUENCE OF EVENTS,- +HXHRTD,Framingham,vr_cvdproc_2020_a_1313d.procdate,Date of cardiovascular procedure,- +HXHRTD,Framingham,vr_cvdproc_2020_a_1313d.procnum,PROCEDURE NUMBER,- +HXHRTD,Framingham,vr_survcvd_2019_a_1334d.cvd,Cardiovascular Disease (CVD) status,- +HXHRTD,Framingham,vr_survcvd_2019_a_1334d.cvddate,Date of Cardiovascular Disease (CVD) status,- +HXHRTD,Framingham,vr_wkthru_ex09_1_1001d.date9,Date of Exam 9,51.88452285 +HXHRTD,Framingham,vr_soe_2020_a_1340d.date,DATE OF EVENT,0.016110843 +HXHRTD,Framingham,vr_soe_2020_a_1340d.event,EVENT NUMBER ON SEQUENCE OF EVENTS,- +HXHRTD,Framingham,vr_cvdproc_2020_a_1313d.procdate,Date of cardiovascular procedure,- +HXHRTD,Framingham,vr_cvdproc_2020_a_1313d.procnum,PROCEDURE NUMBER,- +HXHRTD,MESA,mesaevthr2015_drepos_20200330.mi,Myocardial Infarction (MI),0.440270032 +HXHRTD,MESA,mesaevthr2015_drepos_20200330.mitt,Time to MI or End of Year 2015 (days),0.440270032 +HXHRTD,MESA,mesaevthr2015_drepos_20200330.rca,Resuscitated Cardiac Arrest,0.4549457 +HXHRTD,MESA,mesaevthr2015_drepos_20200330.rcatt,Time to RCA or End of Year 2015 (days),0.4549457 +HXHRTD,MESA,mesaevthr2015_drepos_20200330.ang,Angina Pectoris,0.4549457 +HXHRTD,MESA,mesaevthr2015_drepos_20200330.angtt,Time to Angina or End of Year 2015 (days),0.4549457 +HXHRTD,MESA,mesaevthr2015_drepos_20200330.chf,Congestive Heart Failure (CHF),0.425594365 +HXHRTD,MESA,mesaevthr2015_drepos_20200330.chftt,Time to CHF or End of Year 2015 (days),0.425594365 +HXHRTD,MESA,mesaevthr2015_drepos_20200330.pvd,Peripheral Vascular Disease (PVD),0.513648371 +HXHRTD,MESA,mesaevthr2015_drepos_20200330.pvdtt,Time to PVD or End of Year 2015 (days),0.4549457 +HXHRTD,MESA,mesaevthr2015_drepos_20200330.cbg,Coronary Bypass Graft (CBG),0.4549457 +HXHRTD,MESA,mesaevthr2015_drepos_20200330.cbgtt,Time to CBG or End of Year 2015 (days),0.4549457 +HXHRTD,MESA,mesaevthr2015_drepos_20200330.ptca,"PTCA, Cor. Stent, or Cor. Atherectomy",0.440270032 +HXHRTD,MESA,mesaevthr2015_drepos_20200330.ptcatt,Time to PTCA or End of Year 2015 (days),0.440270032 +HXHRTD,MESA,mesaevthr2015_drepos_20200330.revc,Coronary Revascularization,0.440270032 +HXHRTD,MESA,mesaevthr2015_drepos_20200330.revctt,Time to Cor. Revasc. or End of Year 2015 (days),0.440270032 +HXHRTD,MESA,mesaevthr2015_drepos_20200330.prebase,Type of pre-baseline event,- +HXHRTD,MESA,mesaevthr2015_drepos_20200330.mi,Myocardial Infarction (MI),0.440270032 +HXHRTD,MESA,mesaevthr2015_drepos_20200330.mitt,Time to MI or End of Year 2015 (days),0.440270032 +HXHRTD,MESA,mesaevthr2015_drepos_20200330.rca,Resuscitated Cardiac Arrest,0.4549457 +HXHRTD,MESA,mesaevthr2015_drepos_20200330.rcatt,Time to RCA or End of Year 2015 (days),0.4549457 +HXHRTD,MESA,mesaevthr2015_drepos_20200330.ang,Angina Pectoris,0.4549457 +HXHRTD,MESA,mesaevthr2015_drepos_20200330.angtt,Time to Angina or End of Year 2015 (days),0.4549457 +HXHRTD,MESA,mesaevthr2015_drepos_20200330.chf,Congestive Heart Failure (CHF),0.425594365 +HXHRTD,MESA,mesaevthr2015_drepos_20200330.chftt,Time to CHF or End of Year 2015 (days),0.425594365 +HXHRTD,MESA,mesaevthr2015_drepos_20200330.pvd,Peripheral Vascular Disease (PVD),0.513648371 +HXHRTD,MESA,mesaevthr2015_drepos_20200330.pvdtt,Time to PVD or End of Year 2015 (days),0.4549457 +HXHRTD,MESA,mesaevthr2015_drepos_20200330.cbg,Coronary Bypass Graft (CBG),0.4549457 +HXHRTD,MESA,mesaevthr2015_drepos_20200330.cbgtt,Time to CBG or End of Year 2015 (days),0.4549457 +HXHRTD,MESA,mesaevthr2015_drepos_20200330.ptca,"PTCA, Cor. Stent, or Cor. Atherectomy",0.440270032 +HXHRTD,MESA,mesaevthr2015_drepos_20200330.ptcatt,Time to PTCA or End of Year 2015 (days),0.440270032 +HXHRTD,MESA,mesaevthr2015_drepos_20200330.revc,Coronary Revascularization,0.440270032 +HXHRTD,MESA,mesaevthr2015_drepos_20200330.revctt,Time to Cor. Revasc. or End of Year 2015 (days),0.440270032 +HXHRTD,MESA,mesaevthr2015_drepos_20200330.prebase,Type of pre-baseline event,- +HXHRTD,MESA,mesae2dres06222012.e12dyc,"Time between exam visits, in days",8.526562959 +HXHRTD,MESA,mesaevthr2015_drepos_20200330.mi,Myocardial Infarction (MI),0.440270032 +HXHRTD,MESA,mesaevthr2015_drepos_20200330.mitt,Time to MI or End of Year 2015 (days),0.440270032 +HXHRTD,MESA,mesaevthr2015_drepos_20200330.rca,Resuscitated Cardiac Arrest,0.4549457 +HXHRTD,MESA,mesaevthr2015_drepos_20200330.rcatt,Time to RCA or End of Year 2015 (days),0.4549457 +HXHRTD,MESA,mesaevthr2015_drepos_20200330.ang,Angina Pectoris,0.4549457 +HXHRTD,MESA,mesaevthr2015_drepos_20200330.angtt,Time to Angina or End of Year 2015 (days),0.4549457 +HXHRTD,MESA,mesaevthr2015_drepos_20200330.chf,Congestive Heart Failure (CHF),0.425594365 +HXHRTD,MESA,mesae4dres06222012.e14dyc,"Time between first and fourth visits, in days",14.61696507 +HXHRTD,MESA,mesaevthr2015_drepos_20200330.chftt,Time to CHF or End of Year 2015 (days),0.425594365 +HXHRTD,MESA,mesaevthr2015_drepos_20200330.pvd,Peripheral Vascular Disease (PVD),0.513648371 +HXHRTD,MESA,mesaevthr2015_drepos_20200330.pvdtt,Time to PVD or End of Year 2015 (days),0.4549457 +HXHRTD,MESA,mesaevthr2015_drepos_20200330.cbg,Coronary Bypass Graft (CBG),0.4549457 +HXHRTD,MESA,mesaevthr2015_drepos_20200330.cbgtt,Time to CBG or End of Year 2015 (days),0.4549457 +HXHRTD,MESA,mesaevthr2015_drepos_20200330.ptca,"PTCA, Cor. Stent, or Cor. Atherectomy",0.440270032 +HXHRTD,MESA,mesaevthr2015_drepos_20200330.ptcatt,Time to PTCA or End of Year 2015 (days),0.440270032 +HXHRTD,MESA,mesaevthr2015_drepos_20200330.revc,Coronary Revascularization,0.440270032 +HXHRTD,MESA,mesaevthr2015_drepos_20200330.revctt,Time to Cor. Revasc. or End of Year 2015 (days),0.440270032 +HXHRTD,MESA,mesaevthr2015_drepos_20200330.prebase,Type of pre-baseline event,- +HXHRTD,MESA,mesae3dres06222012.e13dyc,"Time between first and third visits, in days",12.72380393 +HXHRTD,MESA,mesaevthr2015_drepos_20200330.mi,Myocardial Infarction (MI),0.440270032 +HXHRTD,MESA,mesaevthr2015_drepos_20200330.mitt,Time to MI or End of Year 2015 (days),0.440270032 +HXHRTD,MESA,mesaevthr2015_drepos_20200330.rca,Resuscitated Cardiac Arrest,0.4549457 +HXHRTD,MESA,mesaevthr2015_drepos_20200330.mi,Myocardial Infarction (MI),0.440270032 +HXHRTD,MESA,mesaevthr2015_drepos_20200330.rcatt,Time to RCA or End of Year 2015 (days),0.4549457 +HXHRTD,MESA,mesaevthr2015_drepos_20200330.ang,Angina Pectoris,0.4549457 +HXHRTD,MESA,mesaevthr2015_drepos_20200330.angtt,Time to Angina or End of Year 2015 (days),0.4549457 +HXHRTD,MESA,mesaevthr2015_drepos_20200330.chf,Congestive Heart Failure (CHF),0.425594365 +HXHRTD,MESA,mesaevthr2015_drepos_20200330.chftt,Time to CHF or End of Year 2015 (days),0.425594365 +HXHRTD,MESA,mesaevthr2015_drepos_20200330.pvd,Peripheral Vascular Disease (PVD),0.513648371 +HXHRTD,MESA,mesaevthr2015_drepos_20200330.pvdtt,Time to PVD or End of Year 2015 (days),0.4549457 +HXHRTD,MESA,mesaevthr2015_drepos_20200330.cbg,Coronary Bypass Graft (CBG),0.4549457 +HXHRTD,MESA,mesaevthr2015_drepos_20200330.cbgtt,Time to CBG or End of Year 2015 (days),0.4549457 +HXHRTD,MESA,mesaevthr2015_drepos_20200330.ptca,"PTCA, Cor. Stent, or Cor. Atherectomy",0.440270032 +HXHRTD,MESA,mesaevthr2015_drepos_20200330.ptcatt,Time to PTCA or End of Year 2015 (days),0.440270032 +HXHRTD,MESA,mesaevthr2015_drepos_20200330.revc,Coronary Revascularization,0.440270032 +HXHRTD,MESA,mesaevthr2015_drepos_20200330.revctt,Time to Cor. Revasc. or End of Year 2015 (days),0.440270032 +HXHRTD,MESA,mesaevthr2015_drepos_20200330.prebase,Type of pre-baseline event,- +HXHRTD,MESA,mesaevthr2015_drepos_20200330.mitt,Time to MI or End of Year 2015 (days),0.440270032 +HXHRTD,MESA,mesaevthr2015_drepos_20200330.rca,Resuscitated Cardiac Arrest,0.4549457 +HXHRTD,MESA,mesaevthr2015_drepos_20200330.rcatt,Time to RCA or End of Year 2015 (days),0.4549457 +HXHRTD,MESA,mesaevthr2015_drepos_20200330.ang,Angina Pectoris,0.4549457 +HXHRTD,MESA,mesaevthr2015_drepos_20200330.angtt,Time to Angina or End of Year 2015 (days),0.4549457 +HXHRTD,MESA,mesaevthr2015_drepos_20200330.chf,Congestive Heart Failure (CHF),0.425594365 +HXHRTD,MESA,mesaevthr2015_drepos_20200330.chftt,Time to CHF or End of Year 2015 (days),0.425594365 +HXHRTD,MESA,mesaevthr2015_drepos_20200330.pvd,Peripheral Vascular Disease (PVD),0.513648371 +HXHRTD,MESA,mesaevthr2015_drepos_20200330.pvdtt,Time to PVD or End of Year 2015 (days),0.4549457 +HXHRTD,MESA,mesaevthr2015_drepos_20200330.cbg,Coronary Bypass Graft (CBG),0.4549457 +HXHRTD,MESA,mesaevthr2015_drepos_20200330.cbgtt,Time to CBG or End of Year 2015 (days),0.4549457 +HXHRTD,MESA,mesaevthr2015_drepos_20200330.ptca,"PTCA, Cor. Stent, or Cor. Atherectomy",0.440270032 +HXHRTD,MESA,mesaevthr2015_drepos_20200330.ptcatt,Time to PTCA or End of Year 2015 (days),0.440270032 +HXHRTD,MESA,mesaevthr2015_drepos_20200330.revc,Coronary Revascularization,0.440270032 +HXHRTD,MESA,mesaevthr2015_drepos_20200330.revctt,Time to Cor. Revasc. or End of Year 2015 (days),0.440270032 +HXHRTD,MESA,mesaevthr2015_drepos_20200330.prebase,Type of pre-baseline event,- +HXHRTD,MESA,mesae5_drepos_20220820.e15dyc,"TIME BETWEEN FIRST AND FIFTH VISITS, IN DAYS",- +HXHRTD,REGARDS,baseline_calculated_variables.CAD_SR_ECG,-,- +HXMI,ARIC,derive13.mddxmi02,MD DIAGNOSED MYOCARDIAL INFARCTION,0.359904026 +HXMI,ARIC,derive13.hxofmi02,HISTORY OF MYOCARDIAL INFARCTION,0.366568915 +HXMI,ARIC,incps18.fumi18,Follow up time for MI18 (days),- +HXMI,ARIC,incps18.fuinc18,Follow up time for INC_BY18 (days),- +HXMI,ARIC,incps18.mi18,MI by Censoring Date,- +HXMI,ARIC,incps18.inc18,MI/FATCHD by Censoring Date,- +HXMI,ARIC,derive2_10.mddxmi21,V2 MD Diagnosed Myocardial Infarction,- +HXMI,ARIC,derive2_10.hxofmi21,V2 History of Myocardial Infarction,- +HXMI,ARIC,derive2_10.v2days,DAYS SINCE EXAM 1,- +HXMI,ARIC,incps18.fumi18,Follow up time for MI18 (days),- +HXMI,ARIC,incps18.fuinc18,Follow up time for INC_BY18 (days),- +HXMI,ARIC,incps18.mi18,MI by Censoring Date,- +HXMI,ARIC,incps18.inc18,MI/FATCHD by Censoring Date,- +HXMI,ARIC,derive37.mddxmi31,V3 MD Diagnosed Myocardial Infarction,- +HXMI,ARIC,derive37.hxofmi31,V3 History of Myocardial Infarction,0.008206138 +HXMI,ARIC,derive37.v3days,DAYS SINCE EXAM 1,- +HXMI,ARIC,incps18.fumi18,Follow up time for MI18 (days),- +HXMI,ARIC,incps18.fuinc18,Follow up time for INC_BY18 (days),- +HXMI,ARIC,incps18.mi18,MI by Censoring Date,- +HXMI,ARIC,incps18.inc18,MI/FATCHD by Censoring Date,- +HXMI,ARIC,derive47.mddxmi41,V4 MD Diagnosed Myocardial Infarction,- +HXMI,ARIC,derive47.hxofmi41,V4 History of Myocardial Infarction,- +HXMI,ARIC,derive47.v4days,DAYS SINCE EXAM 1,- +HXMI,ARIC,incps18.fumi18,Follow up time for MI18 (days),- +HXMI,ARIC,incps18.fuinc18,Follow up time for INC_BY18 (days),- +HXMI,ARIC,incps18.mi18,MI by Censoring Date,- +HXMI,ARIC,incps18.inc18,MI/FATCHD by Censoring Date,- +HXMI,Framingham,vr_soe_2020_a_1340d.date,DATE OF EVENT,0.016110843 +HXMI,Framingham,vr_soe_2020_a_1340d.event,EVENT NUMBER ON SEQUENCE OF EVENTS,- +HXMI,Framingham,,-,- +HXMI,Framingham,vr_soe_2020_a_1340d.date,DATE OF EVENT,0.016110843 +HXMI,Framingham,vr_soe_2020_a_1340d.event,EVENT NUMBER ON SEQUENCE OF EVENTS,- +HXMI,Framingham,vr_wkthru_ex09_1_1001d.date2,Date of Exam 2,24.77947073 +HXMI,Framingham,vr_soe_2020_a_1340d.date,DATE OF EVENT,0.016110843 +HXMI,Framingham,vr_soe_2020_a_1340d.event,EVENT NUMBER ON SEQUENCE OF EVENTS,- +HXMI,Framingham,vr_wkthru_ex09_1_1001d.date3,Date of Exam 3,24.57898958 +HXMI,Framingham,vr_soe_2020_a_1340d.date,DATE OF EVENT,0.016110843 +HXMI,Framingham,vr_soe_2020_a_1340d.event,EVENT NUMBER ON SEQUENCE OF EVENTS,- +HXMI,Framingham,vr_wkthru_ex09_1_1001d.date4,Date of Exam 4,21.77225341 +HXMI,Framingham,vr_soe_2020_a_1340d.date,DATE OF EVENT,0.016110843 +HXMI,Framingham,vr_soe_2020_a_1340d.event,EVENT NUMBER ON SEQUENCE OF EVENTS,- +HXMI,Framingham,vr_wkthru_ex09_1_1001d.date5,Date of Exam 5,26.06255012 +HXMI,Framingham,vr_soe_2020_a_1340d.date,DATE OF EVENT,0.016110843 +HXMI,Framingham,vr_soe_2020_a_1340d.event,EVENT NUMBER ON SEQUENCE OF EVENTS,- +HXMI,Framingham,vr_wkthru_ex09_1_1001d.date6,Date of Exam 6,31.61587811 +HXMI,Framingham,vr_soe_2020_a_1340d.date,DATE OF EVENT,0.016110843 +HXMI,Framingham,vr_soe_2020_a_1340d.event,EVENT NUMBER ON SEQUENCE OF EVENTS,- +HXMI,Framingham,vr_wkthru_ex09_1_1001d.date7,Date of Exam 7,30.3127506 +HXMI,Framingham,vr_soe_2020_a_1340d.date,DATE OF EVENT,0.016110843 +HXMI,Framingham,vr_soe_2020_a_1340d.event,EVENT NUMBER ON SEQUENCE OF EVENTS,- +HXMI,Framingham,vr_wkthru_ex09_1_1001d.date8,Date of Exam 8,40.1563753 +HXMI,Framingham,vr_soe_2020_a_1340d.date,DATE OF EVENT,0.016110843 +HXMI,Framingham,vr_soe_2020_a_1340d.event,EVENT NUMBER ON SEQUENCE OF EVENTS,- +HXMI,Framingham,vr_wkthru_ex09_1_1001d.date9,Date of Exam 9,51.88452285 +HXMI,MESA,mesaevthr2015_drepos_20200330.mi,Myocardial Infarction (MI),0.440270032 +HXMI,MESA,mesaevthr2015_drepos_20200330.mitt,Time to MI or End of Year 2015 (days),0.440270032 +HXMI,MESA,mesaevthr2015_drepos_20200330.mi,Myocardial Infarction (MI),0.440270032 +HXMI,MESA,mesaevthr2015_drepos_20200330.mitt,Time to MI or End of Year 2015 (days),0.440270032 +HXMI,MESA,mesae2dres06222012.e12dyc,"Time between exam visits, in days",8.526562959 +HXMI,MESA,mesaevthr2015_drepos_20200330.mi,Myocardial Infarction (MI),0.440270032 +HXMI,MESA,mesaevthr2015_drepos_20200330.mitt,Time to MI or End of Year 2015 (days),0.440270032 +HXMI,MESA,mesae3dres06222012.e13dyc,"Time between first and third visits, in days",12.72380393 +HXMI,MESA,mesaevthr2015_drepos_20200330.mi,Myocardial Infarction (MI),0.440270032 +HXMI,MESA,mesaevthr2015_drepos_20200330.mitt,Time to MI or End of Year 2015 (days),0.440270032 +HXMI,MESA,mesae4dres06222012.e14dyc,"Time between first and fourth visits, in days",14.61696507 +HXMI,MESA,mesaevthr2015_drepos_20200330.mi,Myocardial Infarction (MI),0.440270032 +HXMI,MESA,mesaevthr2015_drepos_20200330.mitt,Time to MI or End of Year 2015 (days),0.440270032 +HXMI,MESA,mesae5_drepos_20220820.e15dyc,"TIME BETWEEN FIRST AND FIFTH VISITS, IN DAYS",- +HXMI,REGARDS,baseline_calculated_variables.MI_SR_ECG,-,- +HXMI_SR,REGARDS,baseline_calculated_variables.MI_SR,-,- +HXPAD,REGARDS,baseline_calculated_variables.PAD_AMPUTATION,-,- +HXPAD,REGARDS,baseline_calculated_variables.PAD_SURGERY,-,- +HXPAD,REGARDS,baseline_calculated_variables.DVT_SR,-,- +HXTIA,REGARDS,baseline_calculated_variables.TIA_SR,-,- +HYPT,MESA,mesae1dres20220813.htn1c,Hypertension by JNC VI (1997) criteria,- +HYPT,MESA,mesae2dres06222012.htn2c,"Hypertension by JNC VI (1997) criteria, Exam 2",9.451130026 +HYPT,MESA,mesae3dres06222012.htn3c,"Hypertension by JNC VI (1997) criteria, Exam 3",13.42823598 +HYPT,MESA,mesae4dres06222012.htn4c,"Hypertension by JNC VI (1997) criteria, Exam 4",16.40739654 +HYPT,MESA,mesae5_drepos_20220820.htn5c,"HYPERTENSION BY JNC VI (1997) CRITERIA, EXAM 5",1.335877863 +ID_C,ARIC,derive13.id_c,Scrambled Cohort Visit ID,- +ID_C,ARIC,derive2_10.id_c,Scrambled Cohort Visit ID,- +ID_C,ARIC,derive37.id_c,Scrambled Cohort Visit ID,- +ID_C,ARIC,derive47.id_c,Scrambled Cohort Visit ID,- +ID_C,ARIC,derive51.id_c,Scrambled Cohort Visit ID,- +INSULIN,ARIC,msrcod07.msra04aa,MEDICATION & CONCENTRATION Q4M01A,- +INSULIN,ARIC,msrcod07.msra04ba,MEDICATION & CONCENTRATION Q4M02A,- +INSULIN,ARIC,msrcod07.msra04ca,MEDICATION & CONCENTRATION Q4M03A,- +INSULIN,ARIC,msrcod07.msra04da,MEDICATION & CONCENTRATION Q4M04A,- +INSULIN,ARIC,msrcod07.msra04ea,MEDICATION & CONCENTRATION Q4M05A,- +INSULIN,ARIC,msrcod07.msra04fa,MEDICATION & CONCENTRATION Q4M06A,- +INSULIN,ARIC,msrcod07.msra04ga,MEDICATION & CONCENTRATION Q4M07A,- +INSULIN,ARIC,msrcod07.msra04ha,MEDICATION & CONCENTRATION Q4M08A,- +INSULIN,ARIC,msrcod07.msra04ia,MEDICATION & CONCENTRATION Q4M09A,- +INSULIN,ARIC,msrcod07.msra04ja,MEDICATION & CONCENTRATION Q4M10A,- +INSULIN,ARIC,msrcod07.msra04ka,MEDICATION & CONCENTRATION Q4M11A,- +INSULIN,ARIC,msrcod07.msra04la,MEDICATION & CONCENTRATION Q4M12A,- +INSULIN,ARIC,msrcod07.msra04ma,MEDICATION & CONCENTRATION Q4M13A,- +INSULIN,ARIC,msrcod07.msra04na,MEDICATION & CONCENTRATION Q4M14A,- +INSULIN,ARIC,msrcod07.msra04oa,MEDICATION & CONCENTRATION Q4M15A,- +INSULIN,ARIC,msrcod07.msra04pa,MEDICATION & CONCENTRATION Q4M16A,- +INSULIN,ARIC,msrcod07.msra04qa,MEDICATION & CONCENTRATION Q4M17A,- +INSULIN,ARIC,msrcod26.msrb04a,MEDICATION NAME & CONCENTRATION Q4A,- +INSULIN,ARIC,msrcod26.msrb05a,MEDICATION NAME & CONCENTRATION Q5A,- +INSULIN,ARIC,msrcod26.msrb06a,MEDICATION NAME & CONCENTRATION Q6A,- +INSULIN,ARIC,msrcod26.msrb07a,MEDICATION NAME & CONCENTRATION Q7A,- +INSULIN,ARIC,msrcod26.msrb08a,MEDICATION NAME & CONCENTRATION Q8A,- +INSULIN,ARIC,msrcod26.msrb09a,MEDICATION NAME & CONCENTRATION Q9A,- +INSULIN,ARIC,msrcod26.msrb10a,MEDICATION NAME & CONCENTRATION Q10A,- +INSULIN,ARIC,msrcod26.msrb11a,MEDICATION NAME & CONCENTRATION Q11A,- +INSULIN,ARIC,msrcod26.msrb12a,MEDICATION NAME & CONCENTRATION Q12A,- +INSULIN,ARIC,msrcod26.msrb13a,MEDICATION NAME & CONCENTRATION Q13A,- +INSULIN,ARIC,msrcod26.msrb14a,MEDICATION NAME & CONCENTRATION Q14A,- +INSULIN,ARIC,msrcod26.msrb15a,MEDICATION NAME & CONCENTRATION Q15A,- +INSULIN,ARIC,msrcod26.msrb16a,MEDICATION NAME & CONCENTRATION Q16A,- +INSULIN,ARIC,msrcod26.msrb17a,MEDICATION NAME & CONCENTRATION Q17A,- +INSULIN,ARIC,msrcod26.msrb18a,MEDICATION NAME & CONCENTRATION Q18A,- +INSULIN,ARIC,msrcod26.msrb19a,MEDICATION NAME & CONCENTRATION Q19A,- +INSULIN,ARIC,msrcod26.msrb20a,MEDICATION NAME & CONCENTRATION Q20A,- +INSULIN,ARIC,msrc04.msrc4a,MEDICATION A NAME & CONCENTATION Q4A,- +INSULIN,ARIC,msrc04.msrc5a,MEDICATION B NAME & CONCENTRATION Q5A,- +INSULIN,ARIC,msrc04.msrc6a,MEDICATION C NAME & CONCENTRATION Q6A,- +INSULIN,ARIC,msrc04.msrc7a,MEDICATION D NAME & CONCENTRATION Q7A,- +INSULIN,ARIC,msrc04.msrc8a,MEDICATION E NAME & CONCENTRATION Q8A,- +INSULIN,ARIC,msrc04.msrc9a,MEDICATION F NAME & CONCENTRATION Q9A,- +INSULIN,ARIC,msrc04.msrc10a,MEDICATION G NAME & CONCENTRATION Q10A,- +INSULIN,ARIC,msrc04.msrc11a,MEDICATION H NAME & CONCENTRATION Q11A,- +INSULIN,ARIC,msrc04.msrc12a,MEDICATION I NAME & CONCENTRATION Q12A,- +INSULIN,ARIC,msrc04.msrc13a,MEDICATION J NAME & CONCENTRATION Q13A,- +INSULIN,ARIC,msrc04.msrc14a,MEDICATION K NAME & CONCENTRATION Q14A,- +INSULIN,ARIC,msrc04.msrc15a,MEDICATION L NAME & CONCENTRATION Q15A,- +INSULIN,ARIC,msrc04.msrc16a,MEDICATION M NAME & CONCENTRATION Q16A,- +INSULIN,ARIC,msrc04.msrc17a,MEDICATION N NAME & CONCENTRATION Q17A,- +INSULIN,ARIC,msrc04.msrc80a,-,- +INSULIN,ARIC,msrc04.msrc19a,MEDICATION P NAME & CONCENTRATION Q19A,- +INSULIN,ARIC,msrc04.msrc20a,MEDICATION Q NAME & CONCENTRATION Q20A,- +INSULIN,ARIC,msrd04.msrd4a,MEDICATION A NAME Q4A,- +INSULIN,ARIC,msrd04.msrd5a,MEDICATION B NAME Q5A,- +INSULIN,ARIC,msrd04.msrd6a,MEDICATION C NAME Q6A,- +INSULIN,ARIC,msrd04.msrd7a,MEDICATION D NAME Q7A,- +INSULIN,ARIC,msrd04.msrd8a,MEDICATION E NAME Q8A,- +INSULIN,ARIC,msrd04.msrd9a,MEDICATION F NAME Q9A,- +INSULIN,ARIC,msrd04.msrd10a,MEDICATION G NAME Q10A,- +INSULIN,ARIC,msrd04.msrd11a,MEDICATION H NAME Q11A,- +INSULIN,ARIC,msrd04.msrd12a,MEDICATION I NAME Q12A,- +INSULIN,ARIC,msrd04.msrd13a,MEDICATION J NAME Q13A,- +INSULIN,ARIC,msrd04.msrd14a,MEDICATION K NAME Q14A,- +INSULIN,ARIC,msrd04.msrd15a,MEDICATION L NAME Q15A,- +INSULIN,ARIC,msrd04.msrd16a,MEDICATION M NAME Q16A,- +INSULIN,ARIC,msrd04.msrd17a,MEDICATION N NAME Q17A,- +INSULIN,ARIC,msrd04.msrd18a,MEDICATION O NAME Q18A,- +INSULIN,ARIC,msrd04.msrd19a,MEDICATION P NAME Q19A,- +INSULIN,ARIC,msrd04.msrd20a,MEDICATION Q NAME Q20A,- +INSULIN,ARIC,msrcod51.msrcod5a,Med 1: Scanned UPC med name,- +INSULIN,ARIC,msrcod51.msrcod6a,Med 2: Scanned UPC med name,- +INSULIN,ARIC,msrcod51.msrcod7a,Med 3: Scanned UPC med name,- +INSULIN,ARIC,msrcod51.msrcod8a,Med 4: Scanned UPC med name,- +INSULIN,ARIC,msrcod51.msrcod9a,Med 5: Scanned UPC med name,- +INSULIN,ARIC,msrcod51.msrcod10a,Med 6: Scanned UPC med name,- +INSULIN,ARIC,msrcod51.msrcod11a,Med 7: Scanned UPC med name,- +INSULIN,ARIC,msrcod51.msrcod12a,Med 8: Scanned UPC med name,- +INSULIN,ARIC,msrcod51.msrcod13a,Med 9: Scanned UPC med name,- +INSULIN,ARIC,msrcod51.msrcod14a,Med 10: Scanned UPC med name,- +INSULIN,ARIC,msrcod51.msrcod15a,Med 11: Scanned UPC med name,- +INSULIN,ARIC,msrcod51.msrcod16a,Med 12: Scanned UPC med name,- +INSULIN,ARIC,msrcod51.msrcod17a,Med 13: Scanned UPC med name,- +INSULIN,ARIC,msrcod51.msrcod18a,Med 14: Scanned UPC med name,- +INSULIN,ARIC,msrcod51.msrcod19a,Med 15: Scanned UPC med name,- +INSULIN,ARIC,msrcod51.msrcod20a,Med 16: Scanned UPC med name,- +INSULIN,ARIC,msrcod51.msrcod21a,Med 17: Scanned UPC med name,- +INSULIN,ARIC,msrcod51.msrcod22a,Med 18: Scanned UPC med name,- +INSULIN,ARIC,msrcod51.msrcod23a,Med 19: Scanned UPC med name,- +INSULIN,ARIC,msrcod51.msrcod24a,Med 20: Scanned UPC med name,- +INSULIN,ARIC,msrcod51.msrcod25a,Med 21: Scanned UPC med name,- +INSULIN,ARIC,msrcod51.msrcod26a,Med 22: Scanned UPC med name,- +INSULIN,ARIC,msrcod51.msrcod27a,Med 23: Scanned UPC med name,- +INSULIN,ARIC,msrcod51.msrcod28a,Med 24: Scanned UPC med name,- +INSULIN,ARIC,msrcod51.msrcod29a,Med 25: Scanned UPC med name,- +INSULIN,Framingham,ex1_5d_v1.e254,INSULIN,0.027114968 +INSULIN,Framingham,ex1_2d_v3.b68,D202-23-INSULIN,0.026652452 +INSULIN,Framingham,ex1_3d_v1.c29,INSULIN,- +INSULIN,Framingham,ex1_4d_v1.d035,INSULIN,0.230650948 +INSULIN,Framingham,ex1_6d_v1.f218,MEDS - INSULIN,0.205218411 +INSULIN,Framingham,ex1_7d_v2.g050,MEDS - INSULIN,0.057537399 +INSULIN,Framingham,vr_meds_ex08_1_0280d.atc_cod1,ATC CODE FOR MEDICATION OR FIRST DRUG IN COMPOUND,- +INSULIN,Framingham,vr_meds_ex08_1_0280d.atc_cod2,ATC CODE FOR SECOND DRUG IN COMPOUND,- +INSULIN,Framingham,vr_meds_ex08_1_0280d.atc_cod3,ATC CODE FOR THIRD DRUG IN COMPOUND,- +INSULIN,Framingham,vr_meds_ex08_1_0280d.atc_cod4,ATC CODE FOR FOURTH DRUG IN COMPOUND,- +INSULIN,Framingham,vr_meds_ex09_1b_0879d.atc_cod1,ATC code for medication or first drug in compound,- +INSULIN,Framingham,vr_meds_ex09_1b_0879d.atc_cod2,ATC code for medication or second drug in compound,- +INSULIN,Framingham,vr_meds_ex09_1b_0879d.atc_cod3,ATC code for medication or third drug in compound,- +INSULIN,Framingham,vr_meds_ex09_1b_0879d.atc_cod4,ATC code for medication or fourth drug in compound,- +INSULIN,MESA,mesae1dres20220813.insln1c,Insulins,0.044027003 +INSULIN,MESA,mesae2dres06222012.insln2c,Insulins,12.35691224 +INSULIN,MESA,mesae3dres06222012.insln3c,Insulins,14.22072204 +INSULIN,MESA,mesae4dres06222012.insln4c,Insulins,17.36131494 +INSULIN,MESA,mesae5_drepos_20220820.insln5c,INSULINS,0.169635284 +INSULIN,REGARDS,baseline_calculated_variables.DIABETES_MEDS_SR_INSULIN,-,- +LDL,ARIC,derive13.ldl02,RE-CALIBRATED LDL CHOL. in mg/dl,3.005865103 +LDL,ARIC,derive2_10.ldl22,V2 re-calculated LDL-C in mg/dL,2.396177876 +LDL,ARIC,derive37.ldl32,Re-Calibrated LDL Cholesterol in mg/dL,2.04332841 +LDL,ARIC,derive47.ldl41,V4 Recalculated LDL Cholesterol,2.403277196 +LDL,ARIC,lip.lip18,LDLCC-Cholesterol calculated (mg/dL),1.557737894 +LDL,MESA,mesae1dres20220813.ldl1,LDL CHOLESTEROL (mg/dl),1.658350455 +LDL,MESA,mesae2dres06222012.ldl2,LDL CHOLESTEROL (mg/dl),10.27296742 +LDL,MESA,mesae3dres06222012.ldl3,LDL CHOLESTEROL (mg/dl),14.73437041 +LDL,MESA,mesae4dres06222012.ldl4,LDL Cholesterol (mg/dl),18.153801 +LDL,MESA,mesae5_drepos_20220820.ldl5,LDL CHOLESTEROL (mg/dl),3.329092451 +LDL,REGARDS,baseline_calculated_variables.LDL,-,6.145843687 +LVH,ARIC,derive13.clvh01,LVH present by cornell definition,- +LVH,ARIC,derive2_10.clvh21,LVH present by cornell definition,- +LVH,ARIC,derive37.clvh31,LVH present by cornell definition,- +LVH,ARIC,derive47.clvh41,LVH present by cornell definition,- +LVH,Framingham,vr_wkthru_ex09_1_1001d.dlvh1,"Definite left ventricular hypertrophy, Exam 1",0.040096231 +LVH,Framingham,vr_wkthru_ex09_1_1001d.dlvh2,"Definite left ventricular hypertrophy, Exam 2",25.02004812 +LVH,Framingham,vr_wkthru_ex09_1_1001d.dlvh3,"Definite left ventricular hypertrophy, Exam 3",24.67923015 +LVH,Framingham,vr_wkthru_ex09_1_1001d.dlvh4,"Definite left ventricular hypertrophy, Exam 4",22.45388933 +LVH,Framingham,vr_wkthru_ex09_1_1001d.dlvh5,"Definite left ventricular hypertrophy, Exam 5",27.36567763 +LVH,Framingham,vr_wkthru_ex09_1_1001d.dlvh6,"Definite left ventricular hypertrophy, Exam 6",32.59823577 +LVH,Framingham,vr_wkthru_ex09_1_1001d.dlvh7,"Definite left ventricular hypertrophy, Exam 7",31.77626303 +LVH,Framingham,vr_wkthru_ex09_1_1001d.dlvh8,"Definite left ventricular hypertrophy, Exam 8",42.16118685 +LVH,Framingham,vr_wkthru_ex09_1_1001d.dlvh9,"Definite left ventricular hypertrophy, Exam 9",53.8893344 +LVH,MESA,mesae1dres20220813.ecglvh1c,LEFT VENTRICULAR HYPERTROPHY BY NOVACODE,0.719107719 +LVH,MESA,mesae5_drepos_20220820.ecglvh5c,ECG LEFT VENTRICULAR HYPERTROPHY BY NOVACODE,2.184054283 +LVH,REGARDS,baseline_calculated_variables.LVH_12,-,- +MESAID,MESA,mesae1dres20220813.mesaid,MESA Participant Identification Number,- +MESAID,MESA,mesae2dres06222012.mesaid,MESA Participant Identification Number,- +MESAID,MESA,mesae3dres06222012.mesaid,MESA Participant Identification Number,- +MESAID,MESA,mesae4dres06222012.mesaid,MESA Participant Identification Number,- +MESAID,MESA,mesae5_drepos_20220820.mesaid,MESA PARTICIPANT IDENTIFICATION NUMBER,- +NONSTATIN,Framingham,ex1_1d_v3.a80,ANTI-CHOLESTEROL AGENTS,0.481154772 +NONSTATIN,Framingham,ex1_2d_v3.b61,D202-016-ANTI-CHOLESTEROL,0.053304904 +NONSTATIN,Framingham,ex1_3d_v1.c26,ANTI CHOLESTEROL DRUGS,0.026581606 +NONSTATIN,Framingham,ex1_4d_v1.d030,ANTI CHOLESTEROL DRUGS,0.230650948 +NONSTATIN,Framingham,ex1_5d_v1.e245,ANTI CHOLESTEROL DRUGS-RESINS,0.027114968 +NONSTATIN,Framingham,ex1_5d_v1.e246,ANTI CHOLESTEROL DRUGS-NIACIN,0.027114968 +NONSTATIN,Framingham,ex1_5d_v1.e247,ANTI CHOLESTEROL DRUGS-FIBRATES,0.027114968 +NONSTATIN,Framingham,ex1_5d_v1.e249,ANTI CHOLESTEROL DRUGS-OTHER,0.054229935 +NONSTATIN,Framingham,ex1_6d_v1.f209,MEDS - ANTI-CHOL -RESINS,0.029316916 +NONSTATIN,Framingham,ex1_6d_v1.f210,MEDS - ANTI-CHOL -NIACIN/NICOTINIC ACID,0.029316916 +NONSTATIN,Framingham,ex1_6d_v1.f211,MEDS - ANTI-CHOL -FIBRATES,0.029316916 +NONSTATIN,Framingham,ex1_6d_v1.f213,MEDS - ANTI-CHOL -OTHER,0.029316916 +NONSTATIN,Framingham,ex1_7d_v2.g041,MEDS - ANTI-CHOL - RESINS,0.115074799 +NONSTATIN,Framingham,ex1_7d_v2.g042,MEDS - ANTI-CHOL - NIACIN/NICOTINIC ACID,0.115074799 +NONSTATIN,Framingham,ex1_7d_v2.g043,MEDS - ANTI-CHOL - FIBRATES,0.115074799 +NONSTATIN,Framingham,ex1_7d_v2.g045,MEDS - ANTI-CHOL - OTHER,0.115074799 +NONSTATIN,Framingham,vr_meds_ex08_1_0280d.atc_cod1,ATC CODE FOR MEDICATION OR FIRST DRUG IN COMPOUND,- +NONSTATIN,Framingham,vr_meds_ex08_1_0280d.atc_cod2,ATC CODE FOR SECOND DRUG IN COMPOUND,- +NONSTATIN,Framingham,vr_meds_ex08_1_0280d.atc_cod3,ATC CODE FOR THIRD DRUG IN COMPOUND,- +NONSTATIN,Framingham,vr_meds_ex08_1_0280d.atc_cod4,ATC CODE FOR FOURTH DRUG IN COMPOUND,- +NONSTATIN,Framingham,vr_meds_ex09_1b_0879d.atc_cod1,ATC code for medication or first drug in compound,- +NONSTATIN,Framingham,vr_meds_ex09_1b_0879d.atc_cod2,ATC code for medication or second drug in compound,- +NONSTATIN,Framingham,vr_meds_ex09_1b_0879d.atc_cod3,ATC code for medication or third drug in compound,- +NONSTATIN,Framingham,vr_meds_ex09_1b_0879d.atc_cod4,ATC code for medication or fourth drug in compound,- +NONSTATIN,MESA,mesae1dres20220813.basq1c,Bile-acid sequestrants,0.044027003 +NONSTATIN,MESA,mesae1dres20220813.fibr1c,Fibrates,0.044027003 +NONSTATIN,MESA,mesae1dres20220813.mlpd1c,Miscellaneous lipid-lowering drugs,0.044027003 +NONSTATIN,MESA,mesae1dres20220813.niac1c,Niacin and nictotinic acid,0.044027003 +NONSTATIN,MESA,mesae1dres20220813.prob1c,Probucol,0.044027003 +NONSTATIN,MESA,mesae2dres06222012.basq2c,Bile-acid sequestrants,12.35691224 +NONSTATIN,MESA,mesae2dres06222012.fibr2c,Fibrates,12.35691224 +NONSTATIN,MESA,mesae2dres06222012.mlpd2c,Miscellaneous lipid-lowering drugs,12.35691224 +NONSTATIN,MESA,mesae2dres06222012.niac2c,Niacin and nictotinic acid,12.35691224 +NONSTATIN,MESA,mesae2dres06222012.prob2c,Probucol,12.35691224 +NONSTATIN,MESA,mesae3dres06222012.basq3c,Bile-acid sequestrants,14.22072204 +NONSTATIN,MESA,mesae3dres06222012.fibr3c,Fibrates,14.22072204 +NONSTATIN,MESA,mesae3dres06222012.mlpd3c,Miscellaneous lipid-lowering drugs,14.22072204 +NONSTATIN,MESA,mesae3dres06222012.niac3c,Niacin and nictotinic acid,14.22072204 +NONSTATIN,MESA,mesae3dres06222012.prob3c,Probucol,14.22072204 +NONSTATIN,MESA,mesae3dres06222012.basq4c,-,- +NONSTATIN,MESA,mesae4dres06222012.fibr4c,Fibrates,17.36131494 +NONSTATIN,MESA,mesae4dres06222012.mlpd4c,Miscellaneous lipid-lowering drugs,17.36131494 +NONSTATIN,MESA,mesae4dres06222012.niac4c,Niacin and nictotinic acid,17.36131494 +NONSTATIN,MESA,mesae4dres06222012.prob4c,Probucol,17.36131494 +NONSTATIN,MESA,mesae5_drepos_20220820.basq5c,BILE-ACID SEQUESTRANTS,0.169635284 +NONSTATIN,MESA,mesae5_drepos_20220820.fibr5c,FIBRATES,0.169635284 +NONSTATIN,MESA,mesae5_drepos_20220820.mlpd5c,MISCELLANEOUS LIPID-LOWERING DRUGS,0.169635284 +NONSTATIN,MESA,mesae5_drepos_20220820.niac5c,NIACIN AND NICTOTINIC ACID,0.169635284 +NONSTATIN,MESA,mesae5_drepos_20220820.prob5c,PROBUCOL,0.169635284 +PID,Framingham,vr_wkthru_ex09_1_1001d.pid,COHORT GENERAL EXAM DATA RANDOM ID,- +PID,Framingham,vr_wkthru_ex09_1_1001d.pid,COHORT GENERAL EXAM DATA RANDOM ID,- +PID,Framingham,vr_wkthru_ex09_1_1001d.pid,COHORT GENERAL EXAM DATA RANDOM ID,- +PID,Framingham,vr_wkthru_ex09_1_1001d.pid,COHORT GENERAL EXAM DATA RANDOM ID,- +PID,Framingham,vr_wkthru_ex09_1_1001d.pid,COHORT GENERAL EXAM DATA RANDOM ID,- +PID,Framingham,vr_wkthru_ex09_1_1001d.pid,COHORT GENERAL EXAM DATA RANDOM ID,- +PID,Framingham,vr_wkthru_ex09_1_1001d.pid,COHORT GENERAL EXAM DATA RANDOM ID,- +PID,Framingham,vr_wkthru_ex09_1_1001d.pid,COHORT GENERAL EXAM DATA RANDOM ID,- +PID,Framingham,vr_wkthru_ex09_1_1001d.pid,COHORT GENERAL EXAM DATA RANDOM ID,- +RACE_C,ARIC,derive13.racegrp,RACE (from FTRA23),- +RACE_C,ARIC,derive13.racegrp,RACE (from FTRA23),- +RACE_C,ARIC,derive13.racegrp,RACE (from FTRA23),- +RACE_C,ARIC,derive13.racegrp,RACE (from FTRA23),- +RACE_C,ARIC,derive13.racegrp,RACE (from FTRA23),- +RACE_C,MESA,mesae1dres20220813.race1c,RACE,- +RACE_C,MESA,mesae1dres20220813.race1c,RACE,- +RACE_C,MESA,mesae1dres20220813.race1c,RACE,- +RACE_C,MESA,mesae1dres20220813.race1c,RACE,- +RACE_C,MESA,mesae1dres20220813.race1c,RACE,- +RACE_C,REGARDS,baseline_calculated_variables.RACE,-,- +REGARDS_SUBJ_ID,REGARDS,baseline_calculated_variables.ID,-,- +SEX_C,ARIC,derive13.gender,SEX (from FTRA22),- +SEX_C,ARIC,derive2_10.gender,SEX (from FTRA22),- +SEX_C,ARIC,derive47.gender,SEX (from FTRA22),- +SEX_C,Framingham,vr_dates_2019_a_1175d.sex,\x91Participant gender\x92,- +SEX_C,Framingham,vr_dates_2019_a_1175d.sex,\x91Participant gender\x92,- +SEX_C,Framingham,vr_dates_2019_a_1175d.sex,\x91Participant gender\x92,- +SEX_C,Framingham,vr_dates_2019_a_1175d.sex,\x91Participant gender\x92,- +SEX_C,Framingham,vr_dates_2019_a_1175d.sex,\x91Participant gender\x92,- +SEX_C,Framingham,vr_dates_2019_a_1175d.sex,\x91Participant gender\x92,- +SEX_C,Framingham,vr_dates_2019_a_1175d.sex,\x91Participant gender\x92,- +SEX_C,Framingham,vr_dates_2019_a_1175d.sex,\x91Participant gender\x92,- +SEX_C,Framingham,vr_dates_2019_a_1175d.sex,\x91Participant gender\x92,- +SEX_C,MESA,mesae1dres20220813.gender1,gender,- +SEX_C,MESA,mesae2dres06222012.gender2,-,- +SEX_C,MESA,mesae3dres06222012.gender3,-,- +SEX_C,MESA,mesae4dres06222012.gender4,-,- +SEX_C,MESA,mesae5_drepos_20220820.gender5,-,- +SEX_C,REGARDS,baseline_calculated_variables.GENDER,-,- +SEX_N,ARIC,derive47.gender,SEX (from FTRA22),- +SEX_N,ARIC,derive13.gender,SEX (from FTRA22),- +SEX_N,ARIC,derive2_10.gender,SEX (from FTRA22),- +SEX_N,Framingham,vr_dates_2019_a_1175d.sex,\x91Participant gender\x92,- +SEX_N,Framingham,vr_dates_2019_a_1175d.sex,\x91Participant gender\x92,- +SEX_N,Framingham,vr_dates_2019_a_1175d.sex,\x91Participant gender\x92,- +SEX_N,Framingham,vr_dates_2019_a_1175d.sex,\x91Participant gender\x92,- +SEX_N,Framingham,vr_dates_2019_a_1175d.sex,\x91Participant gender\x92,- +SEX_N,Framingham,vr_dates_2019_a_1175d.sex,\x91Participant gender\x92,- +SEX_N,Framingham,vr_dates_2019_a_1175d.sex,\x91Participant gender\x92,- +SEX_N,Framingham,vr_dates_2019_a_1175d.sex,\x91Participant gender\x92,- +SEX_N,Framingham,vr_dates_2019_a_1175d.sex,\x91Participant gender\x92,- +SEX_N,MESA,mesae1dres20220813.gender1,gender,- +SEX_N,MESA,mesae2dres06222012.gender2,-,- +SEX_N,MESA,mesae3dres06222012.gender3,-,- +SEX_N,MESA,mesae4dres06222012.gender4,-,- +SEX_N,MESA,mesae5_drepos_20220820.gender5,-,- +SEX_N,REGARDS,baseline_calculated_variables.GENDER,-,- +SODIUM,ARIC,anut2.sodi,sodium (mg),- +SODIUM,ARIC,nutv3.sodi,sodium (mg),- +SODIUM,Framingham,vr_ffreq_ex06_1_0506d.nut_sodium,SODIUM (mg),- +SODIUM,Framingham,vr_ffreq_ex08_1_0615d_v1.nut_sodium,Sodium mg,- +SODIUM,REGARDS,ffq_analyzed.SODIUM,-,- +STATE,ARIC,derive13.centerid,Description not found,- +STATE,ARIC,derive13.centerid,Description not found,- +STATE,MESA,mesa_site_drepos_20181106.site1c,Exam 1: Site,- +STATE,REGARDS,baseline_calculated_variables.STATE,-,- +STATIN,ARIC,derive13.statincode01,"Used Statin (at Visit 1) last 2weeks (0=No, 1=Yes) based on 2004 Med Code",0.766462277 +STATIN,ARIC,derive2_10.statincode21,"Used Statin (at Visit 2) last 2weeks (0=No, 1=Yes) based on 2004 Med Code",0.323410511 +STATIN,ARIC,derive37.statincode31,"Used Statin (at Visit 3) last 2weeks (0=No, 1=Yes) based on 2004 Med Code",0.254390284 +STATIN,ARIC,derive47.statincode41,"Used Statin (at Visit 4) last 2weeks (0=No, 1=Yes) based on 2004 Med Code",0.400546199 +STATIN,ARIC,msrcod51.code5a2,Med 1: Therapeutic Class Code,- +STATIN,ARIC,msrcod51.code6a2,Med 2: Therapeutic Class Code,- +STATIN,ARIC,msrcod51.code7a2,Med 3: Therapeutic Class Code,- +STATIN,ARIC,msrcod51.code8a2,Med 4: Therapeutic Class Code,- +STATIN,ARIC,msrcod51.code9a2,Med 5: Therapeutic Class Code,- +STATIN,ARIC,msrcod51.code10a2,Med 6: Therapeutic Class Code,- +STATIN,ARIC,msrcod51.code11a2,Med 7: Therapeutic Class Code,- +STATIN,ARIC,msrcod51.code12a2,Med 8: Therapeutic Class Code,- +STATIN,ARIC,msrcod51.code13a2,Med 9: Therapeutic Class Code,- +STATIN,ARIC,msrcod51.code14a2,Med 10: Therapeutic Class Code,- +STATIN,ARIC,msrcod51.code15a2,Med 11: Therapeutic Class Code,- +STATIN,ARIC,msrcod51.code16a2,Med 12: Therapeutic Class Code,- +STATIN,ARIC,msrcod51.code17a2,Med 13: Therapeutic Class Code,- +STATIN,ARIC,msrcod51.code18a2,Med 14: Therapeutic Class Code,- +STATIN,ARIC,msrcod51.code19a2,Med 15: Therapeutic Class Code,- +STATIN,ARIC,msrcod51.code20a2,Med 16: Therapeutic Class Code,- +STATIN,ARIC,msrcod51.code21a2,Med 17: Therapeutic Class Code,- +STATIN,ARIC,msrcod51.code22a2,Med 18: Therapeutic Class Code,- +STATIN,ARIC,msrcod51.code23a2,Med 19: Therapeutic Class Code,- +STATIN,ARIC,msrcod51.code24a2,Med 20: Therapeutic Class Code,- +STATIN,ARIC,msrcod51.code25a2,Med 21: Therapeutic Class Code,- +STATIN,ARIC,msrcod51.code26a2,Med 22: Therapeutic Class Code,- +STATIN,ARIC,msrcod51.code27a2,Med 23: Therapeutic Class Code,- +STATIN,ARIC,msrcod51.code28a2,Med 24: Therapeutic Class Code,- +STATIN,ARIC,msrcod51.code29a2,Med 25: Therapeutic Class Code,- +STATIN,Framingham,ex1_5d_v1.e248,ANTI CHOLESTEROL DRUGS-STATINS,0.027114968 +STATIN,Framingham,ex1_6d_v1.f212,MEDS - ANTI-CHOL -STATINS,0.029316916 +STATIN,Framingham,ex1_7d_v2.g044,MEDS - ANTI-CHOL - STATINS,0.086306099 +STATIN,Framingham,vr_meds_ex08_1_0280d.atc_cod1,ATC CODE FOR MEDICATION OR FIRST DRUG IN COMPOUND,- +STATIN,Framingham,vr_meds_ex08_1_0280d.atc_cod2,ATC CODE FOR SECOND DRUG IN COMPOUND,- +STATIN,Framingham,vr_meds_ex08_1_0280d.atc_cod3,ATC CODE FOR THIRD DRUG IN COMPOUND,- +STATIN,Framingham,vr_meds_ex08_1_0280d.atc_cod4,ATC CODE FOR FOURTH DRUG IN COMPOUND,- +STATIN,Framingham,vr_meds_ex09_1b_0879d.atc_cod1,ATC code for medication or first drug in compound,- +STATIN,Framingham,vr_meds_ex09_1b_0879d.atc_cod2,ATC code for medication or second drug in compound,- +STATIN,Framingham,vr_meds_ex09_1b_0879d.atc_cod3,ATC code for medication or third drug in compound,- +STATIN,Framingham,vr_meds_ex09_1b_0879d.atc_cod4,ATC code for medication or fourth drug in compound,- +STATIN,MESA,mesae1dres20220813.sttn1c,HMG CoA reducatace inhibitors (statins),0.044027003 +STATIN,MESA,mesae2dres06222012.sttn2c,HMG CoA reducatace inhibitors (statins),12.35691224 +STATIN,MESA,mesae3dres06222012.sttn3c,HMG CoA reducatace inhibitors (statins),14.22072204 +STATIN,MESA,mesae4dres06222012.sttn4c,HMG CoA reducatace inhibitors (statins),17.36131494 +STATIN,MESA,mesae5_drepos_20220820.sttn5c,HMG COA REDUCATACE INHIBITORS (STATINS),0.169635284 +STATIN,REGARDS,baseline_meds.MEDS_STATIN,-,- +STATNONSTAT,Framingham,vr_meds_ex08_1_0280d.atc_cod1,ATC CODE FOR MEDICATION OR FIRST DRUG IN COMPOUND,- +STATNONSTAT,Framingham,vr_meds_ex08_1_0280d.atc_cod2,ATC CODE FOR SECOND DRUG IN COMPOUND,- +STATNONSTAT,Framingham,vr_meds_ex09_1b_0879d.atc_cod1,ATC code for medication or first drug in compound,- +STATNONSTAT,Framingham,vr_meds_ex09_1b_0879d.atc_cod2,ATC code for medication or second drug in compound,- +STROKE,REGARDS,stroke_outcome.STROKE19,-,- +STROKE10,REGARDS,stroke_outcome.STROKE19,-,- +STROKE10,REGARDS,stroke_outcome.STROKE19DT,-,- +STROKE10,REGARDS,baseline_calculated_variables.INHOMEDATE,-,0.046383726 +STROKE - ALL CAUSE,REGARDS,stroke_outcome.STROKE19,-,- +STROKE - ALL CAUSE,REGARDS,stroke_outcome.STROKE19DT,-,- +STROKE - HEMORRHAGIC,REGARDS,stroke_outcome.HEMORRHAGIC19,-,- +STROKE - HEMORRHAGIC,REGARDS,stroke_outcome.HEMORRHAGIC19DT,-,- +STROKE - ISCHEMIC,REGARDS,stroke_outcome.ISCHEMIC19,-,- +STROKE - ISCHEMIC,REGARDS,stroke_outcome.ISCHEMIC19DT,-,- +SYSBP,ARIC,sbpa02.sbpa21,2ND AND 3RD SYSTOLIC BP AVERAGE Q21,0.079984003 +SYSBP,ARIC,sbpb02.sbpb21,2ND AND 3RD SYSTOLIC BP AVERAGE Q21,0.036751194 +SYSBP,ARIC,sbpc04_02.sbpc22,2ND AND 3RD SYSTOLIC BP AVERAGE Q22,0.024624477 +SYSBP,ARIC,sbpd04_02.sbpc19,-,- +SYSBP,ARIC,sbp.sbp14,AVG: Systolic (mmHg),0.690817186 +SYSBP,MESA,mesae1dres20220813.sbp1c,SEATED SYSTOLIC BLOOD PRESSURE (mmHg),0.044027003 +SYSBP,MESA,mesae2dres06222012.sbp2c,Seated Systolic Blood Pressure (mmHg),8.570589962 +SYSBP,MESA,mesae3dres06222012.sbp3c,SEATED SYSTOLIC BLOOD PRESSURE (mmHg),12.88523628 +SYSBP,MESA,mesae4dres06222012.sbp4c,Seated systolic blood pressure (mmhg),16.3780452 +SYSBP,MESA,mesae5_drepos_20220820.sbp5c,SEATED SYSTOLIC BLOOD PRESSURE (mmHg),1.335877863 +SYSBP,REGARDS,baseline_calculated_variables.SBP,-,0.284928602 +SYSBP1,Framingham,ex1_1d_v3.a55,"PHYSICIAN SYSTOLIC BLOOD PRESSURE, 1ST",0.180433039 +SYSBP1,Framingham,ex1_2d_v3.b24,D201-047-SYS-PHYS-FIRST,0.026652452 +SYSBP1,Framingham,ex1_3d_v1.c184,FIRST SYSTOLIC BLOOD PRESSURE,0.053163211 +SYSBP1,Framingham,ex1_4d_v1.d192,SYSTOLIC BP - PHYSICIAN - 1ST READING,- +SYSBP1,Framingham,ex1_5d_v1.e485,SYSTOLIC PRESSURE - 1ST MD READING,0.054229935 +SYSBP1,Framingham,ex1_6d_v1.f476,PHYSICIAN BP-SYSTOLIC-1ST READING,0.058633832 +SYSBP1,Framingham,ex1_7d_v2.g271,PHYSICIAN BP SYSTOLIC - 1ST READING,0.115074799 +SYSBP1,Framingham,e_exam_ex08_1_0005d.h111,PHYSICIAN SYSTOLIC BP - 1ST READING,0.13400335 +SYSBP1,Framingham,e_exam_ex09_1b_0844d.j116,"MDBP1 - SYSTOLIC1, MMHG",0.111648679 +SYSBP2,Framingham,ex1_1d_v3.a57,"PHYSICIAN SYSTOLIC BLOOD PRESSURE, 2ND",82.23736969 +SYSBP2,Framingham,ex1_2d_v3.b26,D201-053-SYS-PHYS-SECOND,0.106609808 +SYSBP2,Framingham,ex1_3d_v1.c286,SECOND SYSTOLIC BLOOD PRESSURE,0.372142477 +SYSBP2,Framingham,ex1_4d_v1.d288,SYSTOLIC BP - PHYSICIAN - 2ND READING,0.281906715 +SYSBP2,Framingham,ex1_5d_v1.e581,SYSTOLIC PRESSURE - 2ND MD READING,0.081344902 +SYSBP2,Framingham,ex1_6d_v1.f576,PHYSICIAN BP-2ND READING-SYSTOLIC,0.146584579 +SYSBP2,Framingham,ex1_7d_v2.g354,PHYSICIAN BP SYSTOLIC - 2ND READING,0.143843498 +SYSBP2,Framingham,e_exam_ex08_1_0005d.h233,PHYSICIAN SYSTOLIC BP - 2ND READING,0.201005025 +SYSBP2,Framingham,e_exam_ex09_1b_0844d.j255,"MDBP2 - SYST, MMHG",0.29772981 +T2STROKE,REGARDS,stroke_outcome.STROKE19DT,-,- +T2STROKE,REGARDS,baseline_calculated_variables.INHOMEDATE,-,0.046383726 +T2STROKE10,REGARDS,stroke_outcome.STROKE19,-,- +T2STROKE10,REGARDS,stroke_outcome.STROKE19DT,-,- +T2STROKE10,REGARDS,baseline_calculated_variables.INHOMEDATE,-,0.046383726 +T2STROKE10_YRS,REGARDS,stroke_outcome.STROKE19,-,- +T2STROKE10_YRS,REGARDS,stroke_outcome.STROKE19DT,-,- +T2STROKE10_YRS,REGARDS,baseline_calculated_variables.INHOMEDATE,-,0.046383726 +T2STROKE_YRS,REGARDS,stroke_outcome.STROKE19DT,-,- +T2STROKE_YRS,REGARDS,baseline_calculated_variables.INHOMEDATE,-,0.046383726 +TC,ARIC,lipa.lipa01,TOTAL CHOLESTEROL (MG-DL),0.020308692 +TC,ARIC,lipb.lipb01a,CHOLESTEROL (VALUE) Q1A,0.014786337 +TC,ARIC,lipc04.lipc1a,CHOLESTEROL (VALUE IN MG/DL) Q1A,- +TC,ARIC,lipd04.lipd1a,CHOLESTEROL (VALUE) Q1A,0.009175154 +TC,ARIC,lip.lip3,Total Cholesterol (mg/dL),0.914324416 +TC,Framingham,vr_wkthru_ex09_1_1001d.tc1,"Total cholesterol (mg/dL), Exam 1",1.744186047 +TC,Framingham,vr_wkthru_ex09_1_1001d.tc2,"Total cholesterol (mg/dL), Exam 2",26.4234162 +TC,Framingham,vr_wkthru_ex09_1_1001d.tc3,"Total cholesterol (mg/dL), Exam 3",27.08500401 +TC,Framingham,vr_wkthru_ex09_1_1001d.tc4,"Total cholesterol (mg/dL), Exam 4",23.61668003 +TC,Framingham,vr_wkthru_ex09_1_1001d.tc5,"Total cholesterol (mg/dL), Exam 5",26.62389735 +TC,Framingham,vr_wkthru_ex09_1_1001d.tc6,"Total cholesterol (mg/dL), Exam 6",32.55813953 +TC,Framingham,vr_wkthru_ex09_1_1001d.tc7,"Total cholesterol (mg/dL), Exam 7",34.38251804 +TC,Framingham,vr_wkthru_ex09_1_1001d.tc8,"Total cholesterol (mg/dL), Exam 8",42.52205293 +TC,Framingham,vr_wkthru_ex09_1_1001d.tc9,"Total cholesterol (mg/dL), Exam 9",54.87169206 +TC,MESA,mesae1dres20220813.chol1,TOTAL CHOLESTEROL (mg/dl),0.337540358 +TC,MESA,mesae2dres06222012.chol2,TOTAL CHOLESTEROL (mg/dl),9.23099501 +TC,MESA,mesae3dres06222012.chol3,TOTAL CHOLESTEROL (mg/dl),13.53096566 +TC,MESA,mesae4dres06222012.chol4,Total Cholesterol (mg/dl),17.31728794 +TC,MESA,mesae5_drepos_20220820.chol5,TOTAL CHOLESTEROL (mg/dl),2.841391009 +TC,REGARDS,baseline_calculated_variables.CHOLEST,-,4.316999636 +TRIG,ARIC,lipa.lipa02,TOTAL TRIGLYCERIDES (MG-DL),- +TRIG,ARIC,lipb.lipb02a,TRIGLYCERIDE (VALUE) Q2A,0.029572675 +TRIG,ARIC,lipc04.lipc2a,TRIGLYCERIDE (VALUE IN MG/DL) Q2A,- +TRIG,ARIC,lipd04.lipd2a,TRIGLYCERIDE (VALUE) Q2A,0.009175154 +TRIG,ARIC,lip.lip8,Total Triglycerides (mg/dL),0.914324416 +TRIG,Framingham,vr_wkthru_ex09_1_1001d.trig1,"Triglycerides (mg/dL), Exam 1",1.784282278 +TRIG,Framingham,vr_wkthru_ex09_1_1001d.trig2,"Triglycerides (mg/dL), Exam 2",26.4234162 +TRIG,Framingham,vr_wkthru_ex09_1_1001d.trig3,"Triglycerides (mg/dL), Exam 3",27.10505213 +TRIG,Framingham,vr_wkthru_ex09_1_1001d.trig4,"Triglycerides (mg/dL), Exam 4",23.65677626 +TRIG,Framingham,vr_wkthru_ex09_1_1001d.trig5,"Triglycerides (mg/dL), Exam 5",26.62389735 +TRIG,Framingham,vr_wkthru_ex09_1_1001d.trig6,"Triglycerides (mg/dL), Exam 6",32.55813953 +TRIG,Framingham,vr_wkthru_ex09_1_1001d.trig7,"Triglycerides (mg/dL), Exam 7",34.38251804 +TRIG,Framingham,vr_wkthru_ex09_1_1001d.trig8,"Triglycerides (mg/dL), Exam 8",42.52205293 +TRIG,Framingham,vr_wkthru_ex09_1_1001d.trig9,"Triglycerides (mg/dL), Exam 9",54.87169206 +TRIG,MESA,mesae1dres20220813.trig1,TRIGLYCERIDES (mg/dl),0.337540358 +TRIG,MESA,mesae2dres06222012.trig2,TRIGLYCERIDES (mg/dl),9.23099501 +TRIG,MESA,mesae3dres06222012.trig3,TRIGLYCERIDES (mg/dl),13.53096566 +TRIG,MESA,mesae4dres06222012.trig4,Triglycerides (mg/dl),17.31728794 +TRIG,MESA,mesae5_drepos_20220820.trig5,TRIGLYCERIDES (mg/dl),2.841391009 +TRIG,REGARDS,baseline_calculated_variables.TRIGLY,-,4.346817745 +VALVDIS,Framingham,ex1_3d_v1.c339,CDI: RHEUMATIC HEART DISEASE,0.053163211 +VALVDIS,Framingham,ex1_3d_v1.c340,CDI: AORTIC VALVE DISEASE,0.079744817 +VALVDIS,Framingham,ex1_3d_v1.c341,CDI: MITRAL VALVE DISEASE,0.053163211 +VALVDIS,Framingham,ex1_6d_v1.f617,CDI-RHEUMATIC HEART DISEASE,1.34857813 +VALVDIS,Framingham,ex1_6d_v1.f618,CDI-AORTIC VALVE DISEASE,1.34857813 +VALVDIS,Framingham,ex1_6d_v1.f619,CDI-MITRAL VALVE DISEASE,1.377895045 +VALVDIS,Framingham,e_exam_ex08_1_0005d.h339,CDI - RHEUMATIC HEART DISEASE,0.201005025 +VALVDIS,Framingham,e_exam_ex08_1_0005d.h340,CDI - AORTIC VALVE DISEASE,0.167504188 +VALVDIS,Framingham,e_exam_ex08_1_0005d.h341,CDI - MITRAL VALVE DISEASE,0.167504188 +VALVDIS,MESA,mesae1dres20220813.rheuhv1,RHEUMATIC HEART DISEASE: SELF-REPORT,0.014675668 +VEGETABLES,ARIC,dtia.dtia15,CONSUMED STRING OR GREEN BEANS Q15,- +VEGETABLES,ARIC,dtia.dtia16,CONSUMED BROCCOLI Q16,- +VEGETABLES,ARIC,dtia.dtia17,"CABBAGE, CAULIFLWR,BUS SPROUT Q17",- +VEGETABLES,ARIC,dtia.dtia18,CONSUMED CARROTS Q18,- +VEGETABLES,ARIC,dtia.dtia19,CONSUMED CORN Q19,- +VEGETABLES,ARIC,dtia.dtia20,"SPINACH, COLLARDS, GREENS Q20",- +VEGETABLES,ARIC,dtia.dtia21,CONSUMED PEAS OR LIMA BEANS Q21,- +VEGETABLES,ARIC,dtia.dtia22,CONSUMED DARK YELLOW SQUASH Q22,- +VEGETABLES,ARIC,dtia.dtia23,CONSUMED SWEET POTATOES Q23,- +VEGETABLES,ARIC,dtia.dtia24,CONSUMED BEANS OR LENTILS Q24,- +VEGETABLES,ARIC,dtia.dtia25,CONSUMED TOMATOES Q25,- +VEGETABLES,ARIC,dtic04.dtic15,CONSUMED STRING OR GREEN BEANS Q15,- +VEGETABLES,ARIC,dtic04.dtic16,CONSUMED BROCCOLI Q16,- +VEGETABLES,ARIC,dtic04.dtic17,"CABBAGE, CAULIFLWR, BRUS SPROUTS Q17",- +VEGETABLES,ARIC,dtic04.dtic18,CONSUMED CARROTS Q18,- +VEGETABLES,ARIC,dtic04.dtic19,CONSUMED CORN Q19,- +VEGETABLES,ARIC,dtic04.dtic20,"SPINACH, COLLARDS, GREENS Q20",- +VEGETABLES,ARIC,dtic04.dtic21,CONSUMED PEAS OR LIMA BEANS Q21,- +VEGETABLES,ARIC,dtic04.dtic22,CONSUMED DARK YELLOW SQUASH Q22,- +VEGETABLES,ARIC,dtic04.dtic23,CONSUMED SWEET POTATOES Q23,- +VEGETABLES,ARIC,dtic04.dtic24,CONSUMED BEANS OR LENTILS Q24,- +VEGETABLES,ARIC,dtic04.dtic25,CONSUMED TOMATOES Q25,- +VEGETABLES,Framingham,q_ffreq_ex03_1_0302d.greenben,GREEN STRING BEANS OR ASPARAGUS,1.434878587 +VEGETABLES,Framingham,q_ffreq_ex03_1_0302d.broccoli,HALF CUP BROCCOLI,1.379690949 +VEGETABLES,Framingham,q_ffreq_ex03_1_0302d.cabbage,CABBAGE COLE SLAW OR SAUERKRAUT,1.655629139 +VEGETABLES,Framingham,q_ffreq_ex03_1_0302d.caulflwr,CAULIFLOWER-HALF CUP,1.710816777 +VEGETABLES,Framingham,q_ffreq_ex03_1_0302d.bruselsp,HALF CUP BRUSSEL SPROUTS,1.62803532 +VEGETABLES,Framingham,q_ffreq_ex03_1_0302d.carrots,ONE WHOLE OR HALF CUP COOKED,0.965783665 +VEGETABLES,Framingham,q_ffreq_ex03_1_0302d.corn,EAR OR HALF CUP FROZEN,1.62803532 +VEGETABLES,Framingham,q_ffreq_ex03_1_0302d.spinach,HALF CUP SPINACH RAW OR COOKED,1.62803532 +VEGETABLES,Framingham,q_ffreq_ex03_1_0302d.peppers,GREEN OR RED PEPPERS-HALF CUP,2.317880795 +VEGETABLES,Framingham,q_ffreq_ex03_1_0302d.kale,"KALE,MUSTARD,CHARD,BEET OR OTHER GREENS",2.786975717 +VEGETABLES,Framingham,q_ffreq_ex03_1_0302d.iceberg,CUP OF ICEBERG OR HEAD LETTUCE,1.490066225 +VEGETABLES,Framingham,q_ffreq_ex03_1_0302d.romaine,"ESCAROLE,ROMAINE,WATERCRESS LEAFLETTUCE",2.73178808 +VEGETABLES,Framingham,q_ffreq_ex03_1_0302d.peas,"PEAS,LIMA BEANS OR PEA PODS",1.766004415 +VEGETABLES,Framingham,q_ffreq_ex03_1_0302d.wintersq,YELLOW WINTER SQUASH OR PUMPKINS,1.766004415 +VEGETABLES,Framingham,q_ffreq_ex03_1_0302d.zucchini,"EGGPLANT,ZUCCHINI,OTHER SUMMER SQUASH",1.710816777 +VEGETABLES,Framingham,q_ffreq_ex03_1_0302d.yams,HALF CUP YAMS OR SWEET POTATOES,2.262693157 +VEGETABLES,Framingham,q_ffreq_ex03_1_0302d.tomatoes,ONE TOMATO OR HALF CUP,1.407284768 +VEGETABLES,Framingham,q_ffreq_ex03_1_0302d.lentils,"LENTILS, CHICK PEAS, KIDNEY,PINTO BEANS",2.124724062 +VEGETABLES,Framingham,vr_ffreq_ex06_1_0506d.ffd45,TOMATOES:(servings/week),0.262812089 +VEGETABLES,Framingham,vr_ffreq_ex06_1_0506d.ffd50,STRING BEANS:(servings/week),0.361366623 +VEGETABLES,Framingham,vr_ffreq_ex06_1_0506d.ffd51,BROCCOLI:(servings/week),0.821287779 +VEGETABLES,Framingham,vr_ffreq_ex06_1_0506d.ffd52,CABBAGE/COLE SLAW:(servings/week),0.295663601 +VEGETABLES,Framingham,vr_ffreq_ex06_1_0506d.ffd53,CAULIFLOWER:(servings/week),0.55847569 +VEGETABLES,Framingham,vr_ffreq_ex06_1_0506d.ffd54,BRUSSELS SPROUTS:(servings/week),0.624178712 +VEGETABLES,Framingham,vr_ffreq_ex06_1_0506d.ffd55,"CARROTS, RAW:(servings/week)",1.248357424 +VEGETABLES,Framingham,vr_ffreq_ex06_1_0506d.ffd56,"CARROTS, COOKED:(servings/week)",0.788436268 +VEGETABLES,Framingham,vr_ffreq_ex06_1_0506d.ffd57,CORN:(servings/week),1.018396846 +VEGETABLES,Framingham,vr_ffreq_ex06_1_0506d.ffd58,PEAS/LIMA BEANS:(servings/week),0.459921156 +VEGETABLES,Framingham,vr_ffreq_ex06_1_0506d.ffd59,MIXED VEGETABLES:(servings/week),0.722733246 +VEGETABLES,Framingham,vr_ffreq_ex06_1_0506d.ffd60,BEANS/LENTILS:(servings/week),0.85413929 +VEGETABLES,Framingham,vr_ffreq_ex06_1_0506d.ffd61,WINTER SQUASH:(servings/week),0.919842313 +VEGETABLES,Framingham,vr_ffreq_ex06_1_0506d.ffd62,SUMMER SQUASH:(servings/week),0.492772668 +VEGETABLES,Framingham,vr_ffreq_ex06_1_0506d.ffd63,YAMS/SWEET POTATOES:(servings/week),0.164257556 +VEGETABLES,Framingham,vr_ffreq_ex06_1_0506d.ffd64,"SPINACH, COOKED:(servings/week)",0.328515112 +VEGETABLES,Framingham,vr_ffreq_ex06_1_0506d.ffd65,"SPANACH, RAW:(servings/week)",0.788436268 +VEGETABLES,Framingham,vr_ffreq_ex06_1_0506d.ffd66,KALE/MUSTARD/CHARD:(servings/week),0.85413929 +VEGETABLES,Framingham,vr_ffreq_ex06_1_0506d.ffd67,ICEBERG/HEAD LETTUCE:(servings/week),0.886990802 +VEGETABLES,Framingham,vr_ffreq_ex06_1_0506d.ffd68,ROMAINE/LEAF LETTUCE:(servings/week),0.657030223 +VEGETABLES,Framingham,vr_ffreq_ex06_1_0506d.ffd69,CELERY:(servings/week),0.657030223 +VEGETABLES,Framingham,vr_ffreq_ex06_1_0506d.ffd70,BEETS:(servings/week),0.328515112 +VEGETABLES,Framingham,vr_ffreq_ex08_1_0615d_v1.ffd45,TOMATOES:(servings/week),0.483451097 +VEGETABLES,Framingham,vr_ffreq_ex08_1_0615d_v1.ffd50,STRING BEANS:(servings/week),0.929713648 +VEGETABLES,Framingham,vr_ffreq_ex08_1_0615d_v1.ffd51,BROCCOLI:(servings/week),0.892525102 +VEGETABLES,Framingham,vr_ffreq_ex08_1_0615d_v1.ffd52,CABBAGE/COLE SLAW:(servings/week),0.409074005 +VEGETABLES,Framingham,vr_ffreq_ex08_1_0615d_v1.ffd53,CAULIFLOWER:(servings/week),0.520639643 +VEGETABLES,Framingham,vr_ffreq_ex08_1_0615d_v1.ffd54,BRUSSELS SPROUTS:(servings/week),0.669393827 +VEGETABLES,Framingham,vr_ffreq_ex08_1_0615d_v1.ffd55,"CARROTS, RAW:(servings/week)",1.375976199 +VEGETABLES,Framingham,vr_ffreq_ex08_1_0615d_v1.ffd56,"CARROTS, COOKED:(servings/week)",1.375976199 +VEGETABLES,Framingham,vr_ffreq_ex08_1_0615d_v1.ffd57,CORN:(servings/week),1.413164745 +VEGETABLES,Framingham,vr_ffreq_ex08_1_0615d_v1.ffd58,PEAS/LIMA BEANS:(servings/week),0.520639643 +VEGETABLES,Framingham,vr_ffreq_ex08_1_0615d_v1.ffd59,MIXED VEGETABLES:(servings/week),1.487541837 +VEGETABLES,Framingham,vr_ffreq_ex08_1_0615d_v1.ffd60,BEANS/LENTILS:(servings/week),0.557828189 +VEGETABLES,Framingham,vr_ffreq_ex08_1_0615d_v1.ffd61,WINTER SQUASH:(servings/week),1.227222016 +VEGETABLES,Framingham,vr_ffreq_ex08_1_0615d_v1.ffd62,SUMMER SQUASH:(servings/week),0.260319822 +VEGETABLES,Framingham,vr_ffreq_ex08_1_0615d_v1.ffd63,YAMS/SWEET POTATOES:(servings/week),0.148754184 +VEGETABLES,Framingham,vr_ffreq_ex08_1_0615d_v1.ffd64,"SPINACH, COOKED:(servings/week)",0.855336556 +VEGETABLES,Framingham,vr_ffreq_ex08_1_0615d_v1.ffd65,"SPANACH, RAW:(servings/week)",0.855336556 +VEGETABLES,Framingham,vr_ffreq_ex08_1_0615d_v1.ffd66,KALE/MUSTARD/CHARD:(servings/week),1.450353291 +VEGETABLES,Framingham,vr_ffreq_ex08_1_0615d_v1.ffd67,ICEBERG/HEAD LETTUCE:(servings/week),1.338787653 +VEGETABLES,Framingham,vr_ffreq_ex08_1_0615d_v1.ffd68,ROMAINE/LEAF LETTUCE:(servings/week),0.706582373 +VEGETABLES,Framingham,vr_ffreq_ex08_1_0615d_v1.ffd69,CELERY:(servings/week),0.595016735 +VEGETABLES,Framingham,vr_ffreq_ex08_1_0615d_v1.ffd70,BEETS:(servings/week),0.446262551 +VEGETABLES,REGARDS,ffq_analyzed.VEGSRV,-,- +VISDAY,ARIC,derive2_10.v2days,DAYS SINCE EXAM 1,- +VISDAY,ARIC,derive37.v3days,DAYS SINCE EXAM 1,- +VISDAY,ARIC,derive47.v4days,DAYS SINCE EXAM 1,- +VISDAY,ARIC,derive51.v5date51_days,"Visit 5 Date, NCS Stage 1 - days from visit 1",- +VISDAY,Framingham,vr_wkthru_ex09_1_1001d.date2,Date of Exam 2,24.77947073 +VISDAY,Framingham,vr_wkthru_ex09_1_1001d.date3,Date of Exam 3,24.57898958 +VISDAY,Framingham,vr_wkthru_ex09_1_1001d.date4,Date of Exam 4,21.77225341 +VISDAY,Framingham,vr_wkthru_ex09_1_1001d.date5,Date of Exam 5,26.06255012 +VISDAY,Framingham,vr_wkthru_ex09_1_1001d.date6,Date of Exam 6,31.61587811 +VISDAY,Framingham,vr_wkthru_ex09_1_1001d.date7,Date of Exam 7,30.3127506 +VISDAY,Framingham,vr_wkthru_ex09_1_1001d.date8,Date of Exam 8,40.1563753 +VISDAY,Framingham,vr_wkthru_ex09_1_1001d.date9,Date of Exam 9,51.88452285 +VISDAY,MESA,mesae2dres06222012.e12dyc,"Time between exam visits, in days",8.526562959 +VISDAY,MESA,mesae3dres06222012.e13dyc,"Time between first and third visits, in days",12.72380393 +VISDAY,MESA,mesae4dres06222012.e14dyc,"Time between first and fourth visits, in days",14.61696507 +VISDAY,MESA,mesae5_drepos_20220820.e15dyc,"TIME BETWEEN FIRST AND FIFTH VISITS, IN DAYS",- +WGT,ARIC,anta.anta04,WEIGHT TO THE NEAREST LB Q4,0.159957345 +WGT,ARIC,antb.antb01,WEIGHT TO NEAREST LB Q1,0.154355017 +WGT,ARIC,antc04.antc2,WEIGHT TO NEAREST LB Q2,0.057494867 +WGT,ARIC,antd05.antd2,WEIGHT TO NEAREST LB Q2,0.282203004 +WGT,ARIC,ant.ant4,Weight (kg),1.48272957 +WGT,Framingham,vr_wkthru_ex09_1_1001d.wgt1,"Weight (pounds), Exam 1",- +WGT,Framingham,vr_wkthru_ex09_1_1001d.wgt2,"Weight (pounds), Exam 2",24.77947073 +WGT,Framingham,vr_wkthru_ex09_1_1001d.wgt3,"Weight (pounds), Exam 3",25.32076985 +WGT,Framingham,vr_wkthru_ex09_1_1001d.wgt4,"Weight (pounds), Exam 4",21.97273456 +WGT,Framingham,vr_wkthru_ex09_1_1001d.wgt5,"Weight (pounds), Exam 5",26.40336808 +WGT,Framingham,vr_wkthru_ex09_1_1001d.wgt6,"Weight (pounds), Exam 6",31.97674419 +WGT,Framingham,vr_wkthru_ex09_1_1001d.wgt7,"Weight (pounds), Exam 7",30.93424218 +WGT,Framingham,vr_wkthru_ex09_1_1001d.wgt8,"Weight (pounds), Exam 8",40.29671211 +WGT,Framingham,vr_wkthru_ex09_1_1001d.wgt9,"Weight (pounds), Exam 9",51.88452285 +WGT,MESA,mesae1dres20220813.wtlb1,WEIGHT (lbs),- +WGT,MESA,mesae2dres06222012.wtlb2,WEIGHT (lbs),8.555914294 +WGT,MESA,mesae3dres06222012.wtlb3,WEIGHT (lbs),12.84120928 +WGT,MESA,mesae4dres06222012.wtlb4,WEIGHT (lbs),16.30466686 +WGT,MESA,mesae5_drepos_20220820.wtlb5,WEIGHT (lbs),1.547921968 +WGT,REGARDS,baseline_calculated_variables.WEIGHT_KG,-,0.351191068 diff --git a/resources/copies-of-certain-files-from-gdrive/README.md b/resources/copies-of-external-source-files/README.md similarity index 100% rename from resources/copies-of-certain-files-from-gdrive/README.md rename to resources/copies-of-external-source-files/README.md diff --git a/resources/copies-of-certain-files-from-gdrive/biolincc_variables_all_studies.csv b/resources/copies-of-external-source-files/biolincc_variables_all_studies.csv similarity index 100% rename from resources/copies-of-certain-files-from-gdrive/biolincc_variables_all_studies.csv rename to resources/copies-of-external-source-files/biolincc_variables_all_studies.csv diff --git a/resources/copies-of-certain-files-from-gdrive/dbgap_variables_priority_cohorts.csv b/resources/copies-of-external-source-files/dbgap_variables_priority_cohorts.csv similarity index 100% rename from resources/copies-of-certain-files-from-gdrive/dbgap_variables_priority_cohorts.csv rename to resources/copies-of-external-source-files/dbgap_variables_priority_cohorts.csv diff --git a/resources/harmonized-variable-documentation b/resources/harmonized-variable-documentation deleted file mode 120000 index 4e9d69c..0000000 --- a/resources/harmonized-variable-documentation +++ /dev/null @@ -1 +0,0 @@ -../../topmed-dcc-harmonized-phenotypes/harmonized-variable-documentation \ No newline at end of file diff --git a/resources/human-readable-harmonized-variable-documentation/find_harmonization_function_duplicates.py b/resources/human-readable-harmonized-variable-documentation/find_harmonization_function_duplicates.py index 0aedb8d..f8e74f1 100644 --- a/resources/human-readable-harmonized-variable-documentation/find_harmonization_function_duplicates.py +++ b/resources/human-readable-harmonized-variable-documentation/find_harmonization_function_duplicates.py @@ -101,7 +101,7 @@ def analyze_functions(functions_data, duplicate_groups): def main(): - input_dir = "harmonized-variable-source-documentation" + input_dir = "../../../topmed-dcc-harmonized-phenotypes/harmonized-variable-documentation" # Get functions and analyze functions_data, duplicate_groups = get_harmonization_functions(input_dir) diff --git a/resources/human-readable-harmonized-variable-documentation/harmonization_documentation_generator.py b/resources/human-readable-harmonized-variable-documentation/harmonization_documentation_generator.py index 1089934..261af74 100644 --- a/resources/human-readable-harmonized-variable-documentation/harmonization_documentation_generator.py +++ b/resources/human-readable-harmonized-variable-documentation/harmonization_documentation_generator.py @@ -278,7 +278,7 @@ def generate_markdown(root_dir, output_dir, output_index): def main(): - input_dir = "harmonized-variable-source-documentation" + input_dir = "../../../topmed-dcc-harmonized-phenotypes/harmonized-variable-documentation" output_index = "README.md" output_dir = "generated-doc-pages" diff --git a/resources/human-readable-harmonized-variable-documentation/harmonized-variable-source-documentation b/resources/human-readable-harmonized-variable-documentation/harmonized-variable-source-documentation deleted file mode 120000 index e3229ce..0000000 --- a/resources/human-readable-harmonized-variable-documentation/harmonized-variable-source-documentation +++ /dev/null @@ -1 +0,0 @@ -../harmonized-variable-documentation \ No newline at end of file diff --git a/resources/human-readable-harmonized-variable-documentation/topmed-variable-documentation.md b/resources/human-readable-harmonized-variable-documentation/topmed-variable-documentation.md deleted file mode 120000 index c7fc55e..0000000 --- a/resources/human-readable-harmonized-variable-documentation/topmed-variable-documentation.md +++ /dev/null @@ -1 +0,0 @@ -generated-doc-pages/README.md \ No newline at end of file diff --git a/resources/map-topmed-raw-to-harmonized/generate_mapping.py b/resources/map-topmed-raw-to-harmonized/generate_mapping.py index 8413438..6411056 100644 --- a/resources/map-topmed-raw-to-harmonized/generate_mapping.py +++ b/resources/map-topmed-raw-to-harmonized/generate_mapping.py @@ -69,7 +69,7 @@ def write_csv(mappings, output_file): def main(): # Define input directory and output file - input_dir = "../harmonized-variable-documentation" + input_dir = "../../../topmed-dcc-harmonized-phenotypes/harmonized-variable-documentation" output_file = "raw-to-harmonized-topmed-vars.csv" # Process JSON files and get mappings diff --git a/resources/merged-TOPMed-harmonized-data-file/README.md b/resources/merged-TOPMed-harmonized-data-file/README.md index 71e7e09..ece0067 100644 --- a/resources/merged-TOPMed-harmonized-data-file/README.md +++ b/resources/merged-TOPMed-harmonized-data-file/README.md @@ -1,28 +1,13 @@ ### Generating a TOPMed harmonized data file by merging -* [raw-to-harmonized-topmed-vars.csv](raw-to-harmonized-topmed-vars.csv) and -* [dbgap_variables_priority_cohorts.csv](dbgap_variables_priority_cohorts.csv) +* [raw-to-harmonized-topmed-vars.csv](../map-topmed-raw-to-harmonized/raw-to-harmonized-topmed-vars.csv) and +* [dbgap_variables_priority_cohorts.csv](../copies-of-external-source-files/dbgap_variables_priority_cohorts.csv) using the PHS and PHV ID’s (Exclude the version numbers if needed). - -#### First findings - -Extracted just phv values (without version) into - - * [phv-names-dbgap](phv-names-dbgap) (170,729 values) - * [phv-names-raw-to-harmonized](phv-names-raw-to-harmonized) (2,289 values, 1,162 distinct) - -The two files had only 773 values in common. - - Sorted them and ran - - comm -12 phv-names-raw-to-harmonized phv-names-dbgap | wc -l - 773 - #### Filtered raw-to-harmonized to only include priority cohorts (i.e., ARIC,CARDIA,CHS,COPDGene,FHS,HCHS_SOL,JHS,MESA,WHI) Command for getting phv values common to both files: - comm -12 <(cat dbgap_variables_priority_cohorts.csv | sed 's/^.*\(phv[0-1]*\)/\1/' | sed 's/\..*//' | sort -u) <(cat raw-to-harmonized-topmed-vars.csv | sed 's/^.*\(phv[0-1]*\)/\1/' | sed 's/\..*//' | sort -u) + comm -12 <(cat ../copies-of-external-source-files/dbgap_variables_priority_cohorts.csv | sed 's/^.*\(phv[0-1]*\)/\1/' | sed 's/\..*//' | sort -u) <(cat ../map-topmed-raw-to-harmonized/raw-to-harmonized-topmed-vars.csv | sed 's/^.*\(phv[0-1]*\)/\1/' | sed 's/\..*//' | sort -u) diff --git a/resources/merged-TOPMed-harmonized-data-file/dbgap_variables_priority_cohorts.csv b/resources/merged-TOPMed-harmonized-data-file/dbgap_variables_priority_cohorts.csv deleted file mode 120000 index 64cbd38..0000000 --- a/resources/merged-TOPMed-harmonized-data-file/dbgap_variables_priority_cohorts.csv +++ /dev/null @@ -1 +0,0 @@ -../copies-of-certain-files-from-gdrive/dbgap_variables_priority_cohorts.csv \ No newline at end of file diff --git a/resources/merged-TOPMed-harmonized-data-file/merge-files.py b/resources/merged-TOPMed-harmonized-data-file/merge-files.py index 04a536e..254ad59 100644 --- a/resources/merged-TOPMed-harmonized-data-file/merge-files.py +++ b/resources/merged-TOPMed-harmonized-data-file/merge-files.py @@ -9,8 +9,8 @@ def extract_phv(text): # Read the CSVs -dbgap_vars = pd.read_csv('dbgap_variables_priority_cohorts.csv') -raw_to_harm = pd.read_csv('raw-to-harmonized-topmed-vars.csv') +dbgap_vars = pd.read_csv('../copies-of-external-source-files/dbgap_variables_priority_cohorts.csv') +raw_to_harm = pd.read_csv('../map-topmed-raw-to-harmonized/raw-to-harmonized-topmed-vars.csv') # Extract PHV numbers from the 'Variable accession' column dbgap_vars['phv_number'] = dbgap_vars['Variable accession'].apply(extract_phv) @@ -20,10 +20,10 @@ def extract_phv(text): # Verify uniqueness of PHV numbers in both dataframes if len(dbgap_vars['phv_number'].unique()) != len(dbgap_vars['phv_number']): - print("Warning: Duplicate PHV numbers found in dbgap_variables_priority_cohorts.csv") + print("Warning: Duplicate PHV numbers found in ../copies-of-external-source-files/dbgap_variables_priority_cohorts.csv") # if len(raw_to_harm['phv_number'].unique()) != len(raw_to_harm['phv_number']): -# print("Warning: Duplicate PHV numbers found in raw-to-harmonized-topmed-vars.csv") +# print("Warning: Duplicate PHV numbers found in ../map-topmed-raw-to-harmonized/raw-to-harmonized-topmed-vars.csv") # Merge dataframes on PHV number merged_df = pd.merge( raw_to_harm, diff --git a/resources/merged-TOPMed-harmonized-data-file/raw-to-harmonized-topmed-vars.csv b/resources/merged-TOPMed-harmonized-data-file/raw-to-harmonized-topmed-vars.csv deleted file mode 120000 index 4e279ce..0000000 --- a/resources/merged-TOPMed-harmonized-data-file/raw-to-harmonized-topmed-vars.csv +++ /dev/null @@ -1 +0,0 @@ -../map-topmed-raw-to-harmonized/raw-to-harmonized-topmed-vars.csv \ No newline at end of file From 37f7b550599cb57d5f15eb3846e3859793c8010f Mon Sep 17 00:00:00 2001 From: Sigfried Gold Date: Mon, 3 Feb 2025 15:43:23 -0500 Subject: [PATCH 3/4] Added PIC-SURE permissible values to input vars for TopMED docs Wanted to import a couple functions from files which required setting stuff up as modules. Haven't changed - to _ in all dir names, but changed the ones I needed to. And had to change paths because resources is now the working directory. Not sure it all works at the moment. --- poetry.lock | 10 +- resources/README.md | 4 +- resources/__init__.py | 0 .../AHA_TABLES 1(Sheet1).csv | 79 - .../AHA_TABLES 1(Sheet2).csv | 0 .../README.md | 0 .../biolincc_variables_all_studies.csv | 0 .../dbgap_variables_priority_cohorts.csv | 0 .../__init__.py | 0 .../find_harmonization_function_duplicates.py | 12 +- .../generated-doc-pages/README.md | 5 +- .../generated-doc-pages/atherosclerosis.md | 506 ++++- .../atherosclerosis_events_incident.md | 540 +++++- .../atherosclerosis_events_prior.md | 564 +++++- .../baseline_common_covariates.md | 834 +++++++-- .../generated-doc-pages/blood_cell_count.md | 1628 ++++++++++++++--- .../generated-doc-pages/blood_pressure.md | 796 ++++++-- .../generated-doc-pages/demographic.md | 300 ++- .../generated-doc-pages/inflammation.md | 480 ++++- .../generated-doc-pages/lipids.md | 454 ++++- .../generated-doc-pages/sleep.md | 130 +- .../generated-doc-pages/vte.md | 76 +- .../harmonization_documentation_generator.py | 56 +- .../picsure_data_dict.py | 134 ++ .../generate_mapping.py | 4 +- .../merge-files.py | 75 - .../README.md | 6 +- .../__init__.py | 0 .../common-phv-values.txt | 0 .../merge_files.py | 97 + .../merged_variables.csv | 0 .../raw_to_harm_only.csv | 177 ++ 32 files changed, 5670 insertions(+), 1297 deletions(-) create mode 100644 resources/__init__.py rename resources/{copies-of-external-source-files => copies_of_external_source_files}/AHA_TABLES 1(Sheet1).csv (90%) rename resources/{copies-of-external-source-files => copies_of_external_source_files}/AHA_TABLES 1(Sheet2).csv (100%) rename resources/{copies-of-external-source-files => copies_of_external_source_files}/README.md (100%) rename resources/{copies-of-external-source-files => copies_of_external_source_files}/biolincc_variables_all_studies.csv (100%) rename resources/{copies-of-external-source-files => copies_of_external_source_files}/dbgap_variables_priority_cohorts.csv (100%) create mode 100644 resources/human-readable-harmonized-variable-documentation/__init__.py create mode 100644 resources/human-readable-harmonized-variable-documentation/picsure_data_dict.py delete mode 100644 resources/merged-TOPMed-harmonized-data-file/merge-files.py rename resources/{merged-TOPMed-harmonized-data-file => merged_TOPMed_harmonized_data_file}/README.md (70%) create mode 100644 resources/merged_TOPMed_harmonized_data_file/__init__.py rename resources/{merged-TOPMed-harmonized-data-file => merged_TOPMed_harmonized_data_file}/common-phv-values.txt (100%) create mode 100644 resources/merged_TOPMed_harmonized_data_file/merge_files.py rename resources/{merged-TOPMed-harmonized-data-file => merged_TOPMed_harmonized_data_file}/merged_variables.csv (100%) create mode 100644 resources/merged_TOPMed_harmonized_data_file/raw_to_harm_only.csv diff --git a/poetry.lock b/poetry.lock index 73ce56b..6cea906 100644 --- a/poetry.lock +++ b/poetry.lock @@ -936,7 +936,7 @@ jsonschema = {version = ">=4.0.0", extras = ["format"]} linkml-dataops = "*" linkml-runtime = ">=1.7.0" openpyxl = "*" -parse = "*" +picsure_dd_parse = "*" prefixcommons = ">=0.1.7" prefixmaps = ">=0.1.3" pydantic = ">=1.0.0,<3.0.0" @@ -1255,14 +1255,14 @@ files = [ ] [[package]] -name = "parse" +name = "picsure_dd_parse" version = "1.20.1" -description = "parse() is the opposite of format()" +description = "picsure_dd_parse() is the opposite of format()" optional = false python-versions = "*" files = [ - {file = "parse-1.20.1-py2.py3-none-any.whl", hash = "sha256:76ddd5214255ae711db4c512be636151fbabaa948c6f30115aecc440422ca82c"}, - {file = "parse-1.20.1.tar.gz", hash = "sha256:09002ca350ad42e76629995f71f7b518670bcf93548bdde3684fd55d2be51975"}, + {file = "picsure_dd_parse-1.20.1-py2.py3-none-any.whl", hash = "sha256:76ddd5214255ae711db4c512be636151fbabaa948c6f30115aecc440422ca82c"}, + {file = "picsure_dd_parse-1.20.1.tar.gz", hash = "sha256:09002ca350ad42e76629995f71f7b518670bcf93548bdde3684fd55d2be51975"}, ] [[package]] diff --git a/resources/README.md b/resources/README.md index 6d9a8c9..5ae5620 100644 --- a/resources/README.md +++ b/resources/README.md @@ -10,12 +10,12 @@ * [human-readable-harmonized-variable-documentation/](human-readable-harmonized-variable-documentation/) * [TopMED variable documentation](human-readable-harmonized-variable-documentation/generated-doc-pages/README.md) -* [merged-TOPMed-harmonized-data-file](merged-TOPMed-harmonized-data-file/) +* [merged_TOPMed_harmonized_data_file](merged_TOPMed_harmonized_data_file/) ### External resources -* [copies-of-external-source-files](copies-of-source-files/) +* [copies_of_external_source_files](copies_of_source_files/) * [harmonized-variable-documentation](../../../topmed-dcc-harmonized-phenotypes/harmonized-variable-documentation) * Symbolic link to local clone of [UW-GAC/topmed-dcc-harmonized-phenotypes](https://github.com/UW-GAC/topmed-dcc-harmonized-phenotypes/tree/master/harmonized-variable-documentation). Clone that repo in the same directory as this repo, and the symlink should work. diff --git a/resources/__init__.py b/resources/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/resources/copies-of-external-source-files/AHA_TABLES 1(Sheet1).csv b/resources/copies_of_external_source_files/AHA_TABLES 1(Sheet1).csv similarity index 90% rename from resources/copies-of-external-source-files/AHA_TABLES 1(Sheet1).csv rename to resources/copies_of_external_source_files/AHA_TABLES 1(Sheet1).csv index 5859e6f..27e1715 100644 --- a/resources/copies-of-external-source-files/AHA_TABLES 1(Sheet1).csv +++ b/resources/copies_of_external_source_files/AHA_TABLES 1(Sheet1).csv @@ -1,160 +1,81 @@ Harmonized Variable,Harmonized Variable Description,SNOMED CT ID,NINDS CDE ID,Studies Mapped,Missing Samples (%), AFIB,"Atrial fibrillation (0=No, 1=Yes)",49436004,C17466; C52619,ARICFraminghamMESAREGARDS,1.26, -,,,,,, AGE,Age,424144002,C00008,ARICFraminghamMESAREGARDS,1.3, -,,,,,, ALCOHOL,Alcohol (servings per week),896811007,C56075,ARICFraminghamMESAREGARDS,0.46, -,,,,,, ANYCHOLMED,"Taking cholesterol lowering medication (0=No, 1=Yes)",-,C58967,ARICFraminghamMESAREGARDS,1.24, -,,,,,, ASPIRIN,"Taking aspirin (0=No, 1=Yes)",387458008,C10463,ARICFraminghamMESAREGARDS,1.24, -,,,,,, BASE_CVD,Baseline CVD,-,-,ARICFraminghamMESA,0.65, -,,,,,, BASE_STROKE,"Baseline Stroke/TIA(0=No, 1=TIA, 2=Stroke)",-,-,ARICFraminghamREGARDS,-, -,,,,,, BG,Blood glucose (mg/dL) (fasting and non-fasting),-,-,Framingham,1.31, -,,,,,, BMI,Body mass index (kg/m2),60621009,C11131,ARICFraminghamMESAREGARDS,1.28, -,,,,,, CARSTEN,"Carotid stenosis (0=No, 1=Yes)",64586002,-,ARICFraminghamMESA,0.51, -,,,,,, CENSDAY,Censor day,-,-,ARICFraminghamMESA,1.56, -,,,,,, CREAT,Creatinine (mg/dL),15373003,C57972,ARICFraminghamMESAREGARDS,0.95, -,,,,,, CURRSMK,"Current smoking status (0=No, 1=Yes)",77176002,C10473,ARICFraminghamMESAREGARDS,1.3, -,,,,,, DAYS_SINCE_EXAM1,Time to event,-,-,Framingham,1.59, -,,,,,, DEATH_IND,Death indicator,-,-,ARICFraminghamMESA,1.79, -,,,,,, DEATH_IND_T2,-,-,-,MESA,1.45, -,,,,,, DIAB,"Diabetes(0=No, 1=Yes)",73211009,C17480,ARICFraminghamMESAREGARDS,1.32, -,,,,,, DIABP,-,271650006,C01507,ARICMESAREGARDS,1.25, -,,,,,, DIABP1,"PHYSICIAN DIASTOLIC BLOOD PRESSURE, FIRST (MM HG)",-,-,Framingham,1.97, -,,,,,, DIABP2,"PHYSICIAN DIASTOLIC BLOOD PRESSURE, SECOND (MM HG)",-,-,Framingham,1.24, -,,,,,, EDUCLEV,"Education level (1=Less than High School, 2=High School, 3=Some College, 4=College)",276031006,C00012,ARICFraminghamMESAREGARDS,1.45, -,,,,,, EVENT,Event code,-,-,Framingham,-, -,,,,,, EVENT_DESC,Formatted value of EVENT,-,-,Framingham,-, -,,,,,, EVENT_NAME_O,-,-,-,ARICMESA,-, -,,,,,, EVENT_T2_O,-,-,-,ARICMESA,1.44, -,,,,,, EVENT_VAL_C,-,-,-,ARICMESA,0.8, -,,,,,, FAM_INCOME,Family income,224168007,-,ARICFraminghamMESAREGARDS,0.56, -,,,,,, FASTING,-,-,-,REGARDS,-, -,,,,,, FASTING_12HR,-,-,-,ARIC,0.66, -,,,,,, FASTING_8HR,-,-,-,ARIC,0.66, -,,,,,, FASTING_BG,Fasting blood glucose (>: 8 hours) (mg/dL),271062006,C54941,FraminghamMESA,1.53, -,,,,,, FH_STROKE,"Family history of stroke, Mother or Father (0=No, 1=Yes)",443877004,C20253,ARICFraminghamMESAREGARDS,0.83, -,,,,,, FRUITS,Fruits (servings per week),-,C10056,ARICFraminghamREGARDS,2.65, -,,,,,, GENHLTH,"General Health (Exams 5-7, 4-category)",-,-,ARICFramingham,2.63, -,,,,,, GENHLTH2,"General Health (Exams 8-9, 5-category)",-,-,ARICFraminghamMESAREGARDS,1.45, -,,,,,, GLUCOSE,-,-,-,ARICREGARDS,0.33, -,,,,,, HDL,HDL cholesterol (mg/dL),9422000,C18146,ARICFraminghamMESAREGARDS,1.3, -,,,,,, HGT_CM,Height (centimeters),1153637007,C01522,ARICFraminghamMESAREGARDS,1.28, -,,,,,, HRX,"Treated for hypertension (0=No, 1=Yes)",302192008,C58930,ARICFraminghamMESAREGARDS,1.31, -,,,,,, HXCVD,History of cardiovascular disease,49601007,C21869; C17477; C17479,ARICFraminghamMESAREGARDS,1.12, -,,,,,, HXHRTD,History of heart disease,56265001,C21869; C17477; C17479,ARICFraminghamMESAREGARDS,0.43, -,,,,,, HXMI,History of MI(REGARDS model),22298006,C0450,ARICFraminghamMESAREGARDS,1.12, -,,,,,, HXMI_SR,-,22298006,C0450,REGARDS,-, -,,,,,, HXPAD,-,-,-,REGARDS,-, -,,,,,, HXTIA,-,-,-,REGARDS,-, -,,,,,, HYPT,-,-,-,MESA,1.25, -,,,,,, ID_C,-,-,-,ARIC,-, -,,,,,, INSULIN,"Taking insulin (0=No, 1=Yes)",67866001,C20268,ARICFraminghamMESAREGARDS,1.24, -,,,,,, LDL,-,-,-,ARICMESAREGARDS,0.83, -,,,,,, LVH,Left ventricular hypertrophy on ECG,55827005,C10735,ARICFraminghamMESAREGARDS,1.29, -,,,,,, MESAID,-,-,-,MESA,-, -,,,,,, NONSTATIN,"Taking non-statin medication (0=No, 1=Yes)",-,-,FraminghamMESA,1.24, -,,,,,, PID,UNIQUE PARTICIPANT ID,-,-,Framingham,-, -,,,,,, RACE_C,Race,103579009,C00030,ARICFraminghamMESAREGARDS,-, -,,,,,, REGARDS_SUBJ_ID,-,-,-,REGARDS,-, -,,,,,, SEX_C,Participant gender (character),-,-,ARICFraminghamMESAREGARDS,-, -,,,,,, SEX_N,"Participant gender (1=Male, 0=Female)",-,-,ARICFraminghamMESAREGARDS,-, -,,,,,, SODIUM,Sodium intake (mg/day),1148504005,C54943,ARICFraminghamREGARDS,-, -,,,,,, STATE,Site location (state),398070004,-,ARICFraminghamMESAREGARDS,-, -,,,,,, STATIN,"Taking statin medication (0=No, 1=Yes)",315053001,C54963,ARICFraminghamMESAREGARDS,1.24, -,,,,,, STATNONSTAT,"Taking statin/non-statin combination (0=No, 1=Yes)",-,-,Framingham,-, -,,,,,, STROKE,-,-,-,REGARDS,-, -,,,,,, STROKE10,-,-,-,REGARDS,0.33, -,,,,,, STROKE - ALL CAUSE,-,-,-,REGARDS,-, -,,,,,, STROKE - HEMORRHAGIC,-,-,-,REGARDS,-, -,,,,,, STROKE - ISCHEMIC,-,-,-,REGARDS,-, -,,,,,, SYSBP,-,386536003,C01565,ARICMESAREGARDS,1.25, -,,,,,, SYSBP1,"PHYSICIAN SYSTOLIC BLOOD PRESSURE, FIRST (MM HG)",-,-,Framingham,1.97, -,,,,,, SYSBP2,"PHYSICIAN SYSTOLIC BLOOD PRESSURE, SECOND (MM HG)",-,-,Framingham,1.24, -,,,,,, T2STROKE,-,-,-,REGARDS,0.33, -,,,,,, T2STROKE10,-,-,-,REGARDS,0.33, -,,,,,, T2STROKE10_YRS,-,-,-,REGARDS,0.33, -,,,,,, T2STROKE_YRS,-,-,-,REGARDS,0.33, -,,,,,, TC,Total cholesterol (mg/dL),121868005,C18168,ARICFraminghamMESAREGARDS,1.29, -,,,,,, TRIG,Total Triglycerides (mg/dL),14740000,C18169,ARICFraminghamMESAREGARDS,1.29, -,,,,,, VALVDIS,"Valvular heart disease (0=No, 1=Yes)",368009,C22435,FraminghamMESA,2.56, -,,,,,, VEGETABLES,Vegetables (servings per week),401070008,C10056,ARICFraminghamREGARDS,2.64, -,,,,,, VISDAY,Visit day (days since exam 1),-,-,ARICFraminghamMESA,1.52, -,,,,,, VISIT,Visit,-,-,ARICFraminghamMESA,-, -,,,,,, WGT,Weight (lbs),726527001,C01541,ARICFraminghamMESAREGARDS,, diff --git a/resources/copies-of-external-source-files/AHA_TABLES 1(Sheet2).csv b/resources/copies_of_external_source_files/AHA_TABLES 1(Sheet2).csv similarity index 100% rename from resources/copies-of-external-source-files/AHA_TABLES 1(Sheet2).csv rename to resources/copies_of_external_source_files/AHA_TABLES 1(Sheet2).csv diff --git a/resources/copies-of-external-source-files/README.md b/resources/copies_of_external_source_files/README.md similarity index 100% rename from resources/copies-of-external-source-files/README.md rename to resources/copies_of_external_source_files/README.md diff --git a/resources/copies-of-external-source-files/biolincc_variables_all_studies.csv b/resources/copies_of_external_source_files/biolincc_variables_all_studies.csv similarity index 100% rename from resources/copies-of-external-source-files/biolincc_variables_all_studies.csv rename to resources/copies_of_external_source_files/biolincc_variables_all_studies.csv diff --git a/resources/copies-of-external-source-files/dbgap_variables_priority_cohorts.csv b/resources/copies_of_external_source_files/dbgap_variables_priority_cohorts.csv similarity index 100% rename from resources/copies-of-external-source-files/dbgap_variables_priority_cohorts.csv rename to resources/copies_of_external_source_files/dbgap_variables_priority_cohorts.csv diff --git a/resources/human-readable-harmonized-variable-documentation/__init__.py b/resources/human-readable-harmonized-variable-documentation/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/resources/human-readable-harmonized-variable-documentation/find_harmonization_function_duplicates.py b/resources/human-readable-harmonized-variable-documentation/find_harmonization_function_duplicates.py index f8e74f1..b1b5161 100644 --- a/resources/human-readable-harmonized-variable-documentation/find_harmonization_function_duplicates.py +++ b/resources/human-readable-harmonized-variable-documentation/find_harmonization_function_duplicates.py @@ -3,7 +3,10 @@ from collections import defaultdict import hashlib - +""" +The main point of this script was to identify whether any function appeared +more than once in the JSON files. None do. +""" def get_harmonization_functions(root_dir): """ Extract all harmonization functions from JSON files and identify duplicates. @@ -60,8 +63,7 @@ def get_harmonization_functions(root_dir): # Filter to only duplicate groups (more than one function) duplicate_groups = { - h: files for h, files in func_hash_to_info.items() - if len(files) > 1 + h: files for h, files in func_hash_to_info.items() if len(files) > 1 } return functions_data, duplicate_groups @@ -101,7 +103,7 @@ def analyze_functions(functions_data, duplicate_groups): def main(): - input_dir = "../../../topmed-dcc-harmonized-phenotypes/harmonized-variable-documentation" + input_dir = "./topmed-dcc-harmonized-phenotypes/harmonized-variable-documentation" # Get functions and analyze functions_data, duplicate_groups = get_harmonization_functions(input_dir) @@ -109,4 +111,4 @@ def main(): if __name__ == "__main__": - main() \ No newline at end of file + main() diff --git a/resources/human-readable-harmonized-variable-documentation/generated-doc-pages/README.md b/resources/human-readable-harmonized-variable-documentation/generated-doc-pages/README.md index 17e8576..8fd6369 100644 --- a/resources/human-readable-harmonized-variable-documentation/generated-doc-pages/README.md +++ b/resources/human-readable-harmonized-variable-documentation/generated-doc-pages/README.md @@ -1,5 +1,4 @@ # TOPMed Variable Documentation -### [List of component variables](#component_vars) ## Contents * [atherosclerosis](atherosclerosis.md) * [atherosclerosis_events_incident](atherosclerosis_events_incident.md) @@ -13,6 +12,10 @@ * [sleep](sleep.md) * [vte](vte.md) +934 of 1,110 input study variables have dbGap metadata + +670 of 1,110 input study variables have PIC-SURE metadata + diff --git a/resources/human-readable-harmonized-variable-documentation/generated-doc-pages/atherosclerosis.md b/resources/human-readable-harmonized-variable-documentation/generated-doc-pages/atherosclerosis.md index 6d0cb59..b5641bc 100644 --- a/resources/human-readable-harmonized-variable-documentation/generated-doc-pages/atherosclerosis.md +++ b/resources/human-readable-harmonized-variable-documentation/generated-doc-pages/atherosclerosis.md @@ -41,8 +41,16 @@ * ### atherosclerosis/cac_score_1 -- **CHS Cardiovascular Health Study (CHS) Cohort: an NHLBI-funded observational study of risk factors for cardiovascular disease in adults 65 years or older**: * 2 component_study_variables - * _phs000287.v6.pht001459.v1.phv00100691.v1_. dbGap Name: **CACSCORE**, Desc: **Coronary Artery Calcification by electron beam CYT scan**, Table: **CHS_CAC**. - * _phs000287.v6.pht001475.v1.phv00102583.v1_. dbGap Name: **AGEY11**, Desc: **AGE AT YEAR 11**, Table: **YR11**. + * _phs000287.v6.pht001459.v1.phv00100691.v1_ + * dbGap name: **CACSCORE** + * dbGap desc: **Coronary Artery Calcification by electron beam CYT scan** + * dbGap table: **CHS_CAC** + * No permissible values listed in PIC-SURE data dictionary + * _phs000287.v6.pht001475.v1.phv00102583.v1_ + * dbGap name: **AGEY11** + * dbGap desc: **AGE AT YEAR 11** + * dbGap table: **YR11** + * No permissible values listed in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -74,8 +82,14 @@ * ### atherosclerosis/cac_score_1 -- **JHS Jackson Heart Study (JHS) Cohort**: * 2 component_study_variables - * _phs000286.v5.pht001948.v1.phv00126002.v1_. dbGap Name: **CSTA24**, Desc: **24. Agatston Score All Coronary (does not include others)**, Table: **csta**. - * _phs000286.v5.pht001949.v1.phv00126009.v1_. No dbGap metadata available. + * _phs000286.v5.pht001948.v1.phv00126002.v1_ + * dbGap name: **CSTA24** + * dbGap desc: **24. Agatston Score All Coronary (does not include others)** + * dbGap table: **csta** + * varId _phv00126002_ not found in PIC-SURE data dictionary + * _phs000286.v5.pht001949.v1.phv00126009.v1_ + * No dbGap metadata available + * varId _phv00126009_ not found in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -130,9 +144,21 @@ * ### atherosclerosis/cac_volume_1 -- **FHS Framingham Cohort**: * 3 component_study_variables - * _phs000007.v29.pht003099.v4.phv00177930.v4_. dbGap Name: **age1**, Desc: **Age at Exam 1**, Table: **vr_dates_2019_a_1175s**. - * _phs000007.v29.pht005161.v1.phv00257671.v1_. dbGap Name: **CAC_V**, Desc: **Coronary artery calcium volume**, Table: **t_ctthrcac_2011_m_0682s**. - * _phs000007.v29.pht005161.v1.phv00257672.v1_. dbGap Name: **scan_date**, Desc: **CT scan date**, Table: **t_ctthrcac_2011_m_0682s**. + * _phs000007.v29.pht003099.v4.phv00177930.v4_ + * dbGap name: **age1** + * dbGap desc: **Age at Exam 1** + * dbGap table: **vr_dates_2019_a_1175s** + * No permissible values listed in PIC-SURE data dictionary + * _phs000007.v29.pht005161.v1.phv00257671.v1_ + * dbGap name: **CAC_V** + * dbGap desc: **Coronary artery calcium volume** + * dbGap table: **t_ctthrcac_2011_m_0682s** + * No permissible values listed in PIC-SURE data dictionary + * _phs000007.v29.pht005161.v1.phv00257672.v1_ + * dbGap name: **scan_date** + * dbGap desc: **CT scan date** + * dbGap table: **t_ctthrcac_2011_m_0682s** + * No permissible values listed in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -209,8 +235,16 @@ * ### atherosclerosis/carotid_plaque_1 -- **ARIC Atherosclerosis Risk in Communities (ARIC) Cohort**: * 2 component_study_variables - * _phs000280.v3.pht004063.v1.phv00204712.v1_. dbGap Name: **V1AGE01**, Desc: **Age at visit 1 [Cohort. Visit 1]**, Table: **DERIVE13**. - * _phs000280.v3.pht004063.v1.phv00204791.v1_. dbGap Name: **PLAQUE01**, Desc: **Plaque (with or without shadowing) in any carotid site [Cohort. Visit 1]**, Table: **DERIVE13**. + * _phs000280.v3.pht004063.v1.phv00204712.v1_ + * dbGap name: **V1AGE01** + * dbGap desc: **Age at visit 1 [Cohort. Visit 1]** + * dbGap table: **DERIVE13** + * varId _phv00204712_ not found in PIC-SURE data dictionary + * _phs000280.v3.pht004063.v1.phv00204791.v1_ + * dbGap name: **PLAQUE01** + * dbGap desc: **Plaque (with or without shadowing) in any carotid site [Cohort. Visit 1]** + * dbGap table: **DERIVE13** + * varId _phv00204791_ not found in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -237,12 +271,36 @@ * ### atherosclerosis/carotid_plaque_1 -- **CHS Cardiovascular Health Study (CHS) Cohort: an NHLBI-funded observational study of risk factors for cardiovascular disease in adults 65 years or older**: * 6 component_study_variables - * _phs000287.v6.pht001452.v1.phv00100290.v1_. dbGap Name: **PERSTAT**, Desc: **COHORT**, Table: **BASEBOTH**. - * _phs000287.v6.pht001452.v1.phv00100487.v1_. dbGap Name: **AGEBL**, Desc: **CALCULATED AGE AT BASELINE**, Table: **BASEBOTH**. - * _phs000287.v6.pht001473.v1.phv00101306.v1_. dbGap Name: **LMRPH141**, Desc: **YEAR 5 LESION MORPHOLOGY, RT SIDE**, Table: **ULTRAYR5**. - * _phs000287.v6.pht001473.v1.phv00101307.v1_. dbGap Name: **LMRPH241**, Desc: **YEAR 5 LESION MORPHOLOGY, LFT SIDE**, Table: **ULTRAYR5**. - * _phs000287.v6.pht001473.v1.phv00101317.v1_. dbGap Name: **LMRPH155**, Desc: **BL REREAD LESION MORPHOLOGY, RT SIDE**, Table: **ULTRAYR5**. - * _phs000287.v6.pht001473.v1.phv00101318.v1_. dbGap Name: **LMRPH255**, Desc: **BL REREAD LESION MORPHOLOGY, LFT SIDE**, Table: **ULTRAYR5**. + * _phs000287.v6.pht001452.v1.phv00100290.v1_ + * dbGap name: **PERSTAT** + * dbGap desc: **COHORT** + * dbGap table: **BASEBOTH** + * PIC-SURE permissible values: NEW COHORT, OLD COHORT + * _phs000287.v6.pht001452.v1.phv00100487.v1_ + * dbGap name: **AGEBL** + * dbGap desc: **CALCULATED AGE AT BASELINE** + * dbGap table: **BASEBOTH** + * No permissible values listed in PIC-SURE data dictionary + * _phs000287.v6.pht001473.v1.phv00101306.v1_ + * dbGap name: **LMRPH141** + * dbGap desc: **YEAR 5 LESION MORPHOLOGY, RT SIDE** + * dbGap table: **ULTRAYR5** + * No permissible values listed in PIC-SURE data dictionary + * _phs000287.v6.pht001473.v1.phv00101307.v1_ + * dbGap name: **LMRPH241** + * dbGap desc: **YEAR 5 LESION MORPHOLOGY, LFT SIDE** + * dbGap table: **ULTRAYR5** + * No permissible values listed in PIC-SURE data dictionary + * _phs000287.v6.pht001473.v1.phv00101317.v1_ + * dbGap name: **LMRPH155** + * dbGap desc: **BL REREAD LESION MORPHOLOGY, RT SIDE** + * dbGap table: **ULTRAYR5** + * No permissible values listed in PIC-SURE data dictionary + * _phs000287.v6.pht001473.v1.phv00101318.v1_ + * dbGap name: **LMRPH255** + * dbGap desc: **BL REREAD LESION MORPHOLOGY, LFT SIDE** + * dbGap table: **ULTRAYR5** + * No permissible values listed in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -307,8 +365,12 @@ * ### atherosclerosis/carotid_plaque_1 -- **JHS Jackson Heart Study (JHS) Cohort**: * 2 component_study_variables - * _phs000286.v5.pht001949.v1.phv00126009.v1_. No dbGap metadata available. - * _phs000286.v5.pht001978.v1.phv00128573.v1_. No dbGap metadata available. + * _phs000286.v5.pht001949.v1.phv00126009.v1_ + * No dbGap metadata available + * varId _phv00126009_ not found in PIC-SURE data dictionary + * _phs000286.v5.pht001978.v1.phv00128573.v1_ + * No dbGap metadata available + * varId _phv00128573_ not found in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -336,11 +398,31 @@ * ### atherosclerosis/carotid_plaque_1 -- **MESA Multi-Ethnic Study of Atherosclerosis (MESA) Cohort**: * 5 component_study_variables - * _phs000209.v13.pht001111.v4.phv00082639.v2_. dbGap Name: **age1c**, Desc: **AGE**, Table: **MESA_AirNRExamMain**. - * _phs000209.v13.pht001116.v10.phv00084442.v3_. dbGap Name: **age1c**, Desc: **AGE**, Table: **MESA_Exam1Main**. - * _phs000209.v13.pht001116.v10.phv00084797.v2_. dbGap Name: **rmorph1**, Desc: **RIGHT MORPHOLOGY**, Table: **MESA_Exam1Main**. - * _phs000209.v13.pht001116.v10.phv00084802.v2_. dbGap Name: **lmorph1**, Desc: **LEFT MORPHOLOGY**, Table: **MESA_Exam1Main**. - * _phs000209.v13.pht001121.v3.phv00087071.v1_. dbGap Name: **agefc**, Desc: **AGE**, Table: **MESA_FamilyExamMain**. + * _phs000209.v13.pht001111.v4.phv00082639.v2_ + * dbGap name: **age1c** + * dbGap desc: **AGE** + * dbGap table: **MESA_AirNRExamMain** + * No permissible values listed in PIC-SURE data dictionary + * _phs000209.v13.pht001116.v10.phv00084442.v3_ + * dbGap name: **age1c** + * dbGap desc: **AGE** + * dbGap table: **MESA_Exam1Main** + * No permissible values listed in PIC-SURE data dictionary + * _phs000209.v13.pht001116.v10.phv00084797.v2_ + * dbGap name: **rmorph1** + * dbGap desc: **RIGHT MORPHOLOGY** + * dbGap table: **MESA_Exam1Main** + * PIC-SURE permissible values: CANNOT TELL, HETEROGENEOUS, HOMOGENEOUS, NO LESION + * _phs000209.v13.pht001116.v10.phv00084802.v2_ + * dbGap name: **lmorph1** + * dbGap desc: **LEFT MORPHOLOGY** + * dbGap table: **MESA_Exam1Main** + * PIC-SURE permissible values: CANNOT TELL, HETEROGENEOUS, HOMOGENEOUS, NO LESION + * _phs000209.v13.pht001121.v3.phv00087071.v1_ + * dbGap name: **agefc** + * dbGap desc: **AGE** + * dbGap table: **MESA_FamilyExamMain** + * No permissible values listed in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -409,12 +491,36 @@ * ### atherosclerosis/carotid_stenosis_1 -- **CHS Cardiovascular Health Study (CHS) Cohort: an NHLBI-funded observational study of risk factors for cardiovascular disease in adults 65 years or older**: * 6 component_study_variables - * _phs000287.v6.pht001452.v1.phv00100290.v1_. dbGap Name: **PERSTAT**, Desc: **COHORT**, Table: **BASEBOTH**. - * _phs000287.v6.pht001452.v1.phv00100487.v1_. dbGap Name: **AGEBL**, Desc: **CALCULATED AGE AT BASELINE**, Table: **BASEBOTH**. - * _phs000287.v6.pht001473.v1.phv00101302.v1_. dbGap Name: **PSTEN141**, Desc: **YEAR 5 PERCENT STENOSIS, RT SIDE**, Table: **ULTRAYR5**. - * _phs000287.v6.pht001473.v1.phv00101303.v1_. dbGap Name: **PSTEN241**, Desc: **YEAR 5 PERCENT STENOSIS, LFT SIDE**, Table: **ULTRAYR5**. - * _phs000287.v6.pht001473.v1.phv00101313.v1_. dbGap Name: **PSTEN155**, Desc: **BL REREAD PERCENT STENOSIS, RT SIDE**, Table: **ULTRAYR5**. - * _phs000287.v6.pht001473.v1.phv00101314.v1_. dbGap Name: **PSTEN255**, Desc: **BL REREAD PERCENT STENOSIS, LFT SIDE**, Table: **ULTRAYR5**. + * _phs000287.v6.pht001452.v1.phv00100290.v1_ + * dbGap name: **PERSTAT** + * dbGap desc: **COHORT** + * dbGap table: **BASEBOTH** + * PIC-SURE permissible values: NEW COHORT, OLD COHORT + * _phs000287.v6.pht001452.v1.phv00100487.v1_ + * dbGap name: **AGEBL** + * dbGap desc: **CALCULATED AGE AT BASELINE** + * dbGap table: **BASEBOTH** + * No permissible values listed in PIC-SURE data dictionary + * _phs000287.v6.pht001473.v1.phv00101302.v1_ + * dbGap name: **PSTEN141** + * dbGap desc: **YEAR 5 PERCENT STENOSIS, RT SIDE** + * dbGap table: **ULTRAYR5** + * No permissible values listed in PIC-SURE data dictionary + * _phs000287.v6.pht001473.v1.phv00101303.v1_ + * dbGap name: **PSTEN241** + * dbGap desc: **YEAR 5 PERCENT STENOSIS, LFT SIDE** + * dbGap table: **ULTRAYR5** + * No permissible values listed in PIC-SURE data dictionary + * _phs000287.v6.pht001473.v1.phv00101313.v1_ + * dbGap name: **PSTEN155** + * dbGap desc: **BL REREAD PERCENT STENOSIS, RT SIDE** + * dbGap table: **ULTRAYR5** + * No permissible values listed in PIC-SURE data dictionary + * _phs000287.v6.pht001473.v1.phv00101314.v1_ + * dbGap name: **PSTEN255** + * dbGap desc: **BL REREAD PERCENT STENOSIS, LFT SIDE** + * dbGap table: **ULTRAYR5** + * No permissible values listed in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -505,9 +611,21 @@ * ### atherosclerosis/carotid_stenosis_1 -- **FHS Framingham Cohort**: * 3 component_study_variables - * _phs000007.v29.pht000083.v6.phv00021700.v5_. dbGap Name: **R_STENO**, Desc: **PERCENT STENOSIS ON THE RIGHT**, Table: **carotid1_6s**. - * _phs000007.v29.pht000083.v6.phv00021702.v5_. dbGap Name: **L_STENO**, Desc: **PERCENT STENOSIS ON THE LEFT**, Table: **carotid1_6s**. - * _phs000007.v29.pht003099.v4.phv00177940.v4_. dbGap Name: **age6**, Desc: **Age at Exam 6**, Table: **vr_dates_2019_a_1175s**. + * _phs000007.v29.pht000083.v6.phv00021700.v5_ + * dbGap name: **R_STENO** + * dbGap desc: **PERCENT STENOSIS ON THE RIGHT** + * dbGap table: **carotid1_6s** + * PIC-SURE permissible values: 1-24 %, 100 %, 25-49 %, 50-74 %, 75-99 %, NONE + * _phs000007.v29.pht000083.v6.phv00021702.v5_ + * dbGap name: **L_STENO** + * dbGap desc: **PERCENT STENOSIS ON THE LEFT** + * dbGap table: **carotid1_6s** + * PIC-SURE permissible values: 1-24 %, 100 %, 25-49 %, 50-74 %, 75-99 %, NONE + * _phs000007.v29.pht003099.v4.phv00177940.v4_ + * dbGap name: **age6** + * dbGap desc: **Age at Exam 6** + * dbGap table: **vr_dates_2019_a_1175s** + * No permissible values listed in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -533,11 +651,31 @@ * ### atherosclerosis/carotid_stenosis_1 -- **MESA Multi-Ethnic Study of Atherosclerosis (MESA) Cohort**: * 5 component_study_variables - * _phs000209.v13.pht001111.v4.phv00082639.v2_. dbGap Name: **age1c**, Desc: **AGE**, Table: **MESA_AirNRExamMain**. - * _phs000209.v13.pht001116.v10.phv00084442.v3_. dbGap Name: **age1c**, Desc: **AGE**, Table: **MESA_Exam1Main**. - * _phs000209.v13.pht001116.v10.phv00084798.v2_. dbGap Name: **rsten1**, Desc: **RIGHT STENOSIS**, Table: **MESA_Exam1Main**. - * _phs000209.v13.pht001116.v10.phv00084803.v2_. dbGap Name: **lsten1**, Desc: **LEFT STENOSIS**, Table: **MESA_Exam1Main**. - * _phs000209.v13.pht001121.v3.phv00087071.v1_. dbGap Name: **agefc**, Desc: **AGE**, Table: **MESA_FamilyExamMain**. + * _phs000209.v13.pht001111.v4.phv00082639.v2_ + * dbGap name: **age1c** + * dbGap desc: **AGE** + * dbGap table: **MESA_AirNRExamMain** + * No permissible values listed in PIC-SURE data dictionary + * _phs000209.v13.pht001116.v10.phv00084442.v3_ + * dbGap name: **age1c** + * dbGap desc: **AGE** + * dbGap table: **MESA_Exam1Main** + * No permissible values listed in PIC-SURE data dictionary + * _phs000209.v13.pht001116.v10.phv00084798.v2_ + * dbGap name: **rsten1** + * dbGap desc: **RIGHT STENOSIS** + * dbGap table: **MESA_Exam1Main** + * PIC-SURE permissible values: 1 - 24%, 100%, 25 - 49%, 50 - 74%, 75 - 99%, BAD IMAGE/NORMAL DOPPLER, CAN'T TELL, NO LESION + * _phs000209.v13.pht001116.v10.phv00084803.v2_ + * dbGap name: **lsten1** + * dbGap desc: **LEFT STENOSIS** + * dbGap table: **MESA_Exam1Main** + * PIC-SURE permissible values: 1 - 24%, 100%, 25 - 49%, 50 - 74%, 75 - 99%, BAD IMAGE/NORMAL DOPPLER, CAN'T TELL, NO LESION + * _phs000209.v13.pht001121.v3.phv00087071.v1_ + * dbGap name: **agefc** + * dbGap desc: **AGE** + * dbGap table: **MESA_FamilyExamMain** + * No permissible values listed in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -596,13 +734,41 @@ * ### atherosclerosis/cimt_1 -- **ARIC Atherosclerosis Risk in Communities (ARIC) Cohort**: * 7 component_study_variables - * _phs000280.v3.pht004063.v1.phv00204712.v1_. dbGap Name: **V1AGE01**, Desc: **Age at visit 1 [Cohort. Visit 1]**, Table: **DERIVE13**. - * _phs000280.v3.pht004207.v1.phv00211095.v1_. dbGap Name: **LOPAAV45**, Desc: **Average far wall width, left common carotid: optimal angle [Ultrasound Derived Data. UBMD4. Visit 1]**, Table: **UBMD4**. - * _phs000280.v3.pht004207.v1.phv00211096.v1_. dbGap Name: **LANAAV45**, Desc: **Average far wall width, left common carotid: anterior angle [Ultrasound Derived Data. UBMD4. Visit 1]**, Table: **UBMD4**. - * _phs000280.v3.pht004207.v1.phv00211097.v1_. dbGap Name: **LPOAAV45**, Desc: **Average far wall width, left common carotid: posterior angle [Ultrasound Derived Data. UBMD4. Visit 1]**, Table: **UBMD4**. - * _phs000280.v3.pht004207.v1.phv00211101.v1_. dbGap Name: **ROPAAV45**, Desc: **Average far wall width, right common carotid: optimal angle [Ultrasound Derived Data. UBMD4. Visit 1]**, Table: **UBMD4**. - * _phs000280.v3.pht004207.v1.phv00211102.v1_. dbGap Name: **RANAAV45**, Desc: **Average far wall width, right common carotid: anterior angle [Ultrasound Derived Data. UBMD4. Visit 1]**, Table: **UBMD4**. - * _phs000280.v3.pht004207.v1.phv00211103.v1_. dbGap Name: **RPOAAV45**, Desc: **Average far wall width, right common carotid: posterior angle [Ultrasound Derived Data. UBMD4. Visit 1]**, Table: **UBMD4**. + * _phs000280.v3.pht004063.v1.phv00204712.v1_ + * dbGap name: **V1AGE01** + * dbGap desc: **Age at visit 1 [Cohort. Visit 1]** + * dbGap table: **DERIVE13** + * varId _phv00204712_ not found in PIC-SURE data dictionary + * _phs000280.v3.pht004207.v1.phv00211095.v1_ + * dbGap name: **LOPAAV45** + * dbGap desc: **Average far wall width, left common carotid: optimal angle [Ultrasound Derived Data. UBMD4. Visit 1]** + * dbGap table: **UBMD4** + * varId _phv00211095_ not found in PIC-SURE data dictionary + * _phs000280.v3.pht004207.v1.phv00211096.v1_ + * dbGap name: **LANAAV45** + * dbGap desc: **Average far wall width, left common carotid: anterior angle [Ultrasound Derived Data. UBMD4. Visit 1]** + * dbGap table: **UBMD4** + * varId _phv00211096_ not found in PIC-SURE data dictionary + * _phs000280.v3.pht004207.v1.phv00211097.v1_ + * dbGap name: **LPOAAV45** + * dbGap desc: **Average far wall width, left common carotid: posterior angle [Ultrasound Derived Data. UBMD4. Visit 1]** + * dbGap table: **UBMD4** + * varId _phv00211097_ not found in PIC-SURE data dictionary + * _phs000280.v3.pht004207.v1.phv00211101.v1_ + * dbGap name: **ROPAAV45** + * dbGap desc: **Average far wall width, right common carotid: optimal angle [Ultrasound Derived Data. UBMD4. Visit 1]** + * dbGap table: **UBMD4** + * varId _phv00211101_ not found in PIC-SURE data dictionary + * _phs000280.v3.pht004207.v1.phv00211102.v1_ + * dbGap name: **RANAAV45** + * dbGap desc: **Average far wall width, right common carotid: anterior angle [Ultrasound Derived Data. UBMD4. Visit 1]** + * dbGap table: **UBMD4** + * varId _phv00211102_ not found in PIC-SURE data dictionary + * _phs000280.v3.pht004207.v1.phv00211103.v1_ + * dbGap name: **RPOAAV45** + * dbGap desc: **Average far wall width, right common carotid: posterior angle [Ultrasound Derived Data. UBMD4. Visit 1]** + * dbGap table: **UBMD4** + * varId _phv00211103_ not found in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -649,8 +815,16 @@ * ### atherosclerosis/cimt_1 -- **CHS Cardiovascular Health Study (CHS) Cohort: an NHLBI-funded observational study of risk factors for cardiovascular disease in adults 65 years or older**: * 2 component_study_variables - * _phs000287.v6.pht001452.v1.phv00100487.v1_. dbGap Name: **AGEBL**, Desc: **CALCULATED AGE AT BASELINE**, Table: **BASEBOTH**. - * _phs000287.v6.pht001468.v1.phv00100864.v1_. dbGap Name: **CCA_FWME**, Desc: **Mean of the mean far wall intima media t (var=CCA_FWME)**, Table: **IMT_POLACK**. + * _phs000287.v6.pht001452.v1.phv00100487.v1_ + * dbGap name: **AGEBL** + * dbGap desc: **CALCULATED AGE AT BASELINE** + * dbGap table: **BASEBOTH** + * No permissible values listed in PIC-SURE data dictionary + * _phs000287.v6.pht001468.v1.phv00100864.v1_ + * dbGap name: **CCA_FWME** + * dbGap desc: **Mean of the mean far wall intima media t (var=CCA_FWME)** + * dbGap table: **IMT_POLACK** + * No permissible values listed in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -674,8 +848,16 @@ * ### atherosclerosis/cimt_1 -- **FHS Framingham Cohort**: * 2 component_study_variables - * _phs000007.v29.pht000907.v5.phv00076366.v4_. dbGap Name: **cca_fw_mean_imt**, Desc: **Mean of the mean common carotid IMT far wall of both sides**, Table: **imtcarotid1_6s**. - * _phs000007.v29.pht003099.v4.phv00177940.v4_. dbGap Name: **age6**, Desc: **Age at Exam 6**, Table: **vr_dates_2019_a_1175s**. + * _phs000007.v29.pht000907.v5.phv00076366.v4_ + * dbGap name: **cca_fw_mean_imt** + * dbGap desc: **Mean of the mean common carotid IMT far wall of both sides** + * dbGap table: **imtcarotid1_6s** + * No permissible values listed in PIC-SURE data dictionary + * _phs000007.v29.pht003099.v4.phv00177940.v4_ + * dbGap name: **age6** + * dbGap desc: **Age at Exam 6** + * dbGap table: **vr_dates_2019_a_1175s** + * No permissible values listed in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -696,13 +878,27 @@ * ### atherosclerosis/cimt_1 -- **JHS Jackson Heart Study (JHS) Cohort**: * 7 component_study_variables - * _phs000286.v5.pht001949.v1.phv00126009.v1_. No dbGap metadata available. - * _phs000286.v5.pht001978.v1.phv00128531.v1_. No dbGap metadata available. - * _phs000286.v5.pht001978.v1.phv00128532.v1_. No dbGap metadata available. - * _phs000286.v5.pht001978.v1.phv00128533.v1_. No dbGap metadata available. - * _phs000286.v5.pht001978.v1.phv00128534.v1_. No dbGap metadata available. - * _phs000286.v5.pht001978.v1.phv00128535.v1_. No dbGap metadata available. - * _phs000286.v5.pht001978.v1.phv00128536.v1_. No dbGap metadata available. + * _phs000286.v5.pht001949.v1.phv00126009.v1_ + * No dbGap metadata available + * varId _phv00126009_ not found in PIC-SURE data dictionary + * _phs000286.v5.pht001978.v1.phv00128531.v1_ + * No dbGap metadata available + * varId _phv00128531_ not found in PIC-SURE data dictionary + * _phs000286.v5.pht001978.v1.phv00128532.v1_ + * No dbGap metadata available + * varId _phv00128532_ not found in PIC-SURE data dictionary + * _phs000286.v5.pht001978.v1.phv00128533.v1_ + * No dbGap metadata available + * varId _phv00128533_ not found in PIC-SURE data dictionary + * _phs000286.v5.pht001978.v1.phv00128534.v1_ + * No dbGap metadata available + * varId _phv00128534_ not found in PIC-SURE data dictionary + * _phs000286.v5.pht001978.v1.phv00128535.v1_ + * No dbGap metadata available + * varId _phv00128535_ not found in PIC-SURE data dictionary + * _phs000286.v5.pht001978.v1.phv00128536.v1_ + * No dbGap metadata available + * varId _phv00128536_ not found in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -789,19 +985,71 @@ * ### atherosclerosis/cimt_2 -- **ARIC Atherosclerosis Risk in Communities (ARIC) Cohort**: * 13 component_study_variables - * _phs000280.v3.pht004063.v1.phv00204712.v1_. dbGap Name: **V1AGE01**, Desc: **Age at visit 1 [Cohort. Visit 1]**, Table: **DERIVE13**. - * _phs000280.v3.pht004207.v1.phv00211053.v1_. dbGap Name: **LOPAMX23**, Desc: **Maximum near wall width, left common carotid: optimal angle [Ultrasound Derived Data. UBMD4. Visit 1]**, Table: **UBMD4**. - * _phs000280.v3.pht004207.v1.phv00211054.v1_. dbGap Name: **LANAMX23**, Desc: **Maximum near wall width, left common carotid: anterior angle [Ultrasound Derived Data. UBMD4. Visit 1]**, Table: **UBMD4**. - * _phs000280.v3.pht004207.v1.phv00211055.v1_. dbGap Name: **LPOAMX23**, Desc: **Maximum near wall width, left common carotid: posterior angle [Ultrasound Derived Data. UBMD4. Visit 1]**, Table: **UBMD4**. - * _phs000280.v3.pht004207.v1.phv00211059.v1_. dbGap Name: **ROPAMX23**, Desc: **Maximum near wall width, right common carotid: optimal angle [Ultrasound Derived Data. UBMD4. Visit 1]**, Table: **UBMD4**. - * _phs000280.v3.pht004207.v1.phv00211060.v1_. dbGap Name: **RANAMX23**, Desc: **Maximum near wall width, right common carotid: anterior angle [Ultrasound Derived Data. UBMD4. Visit 1]**, Table: **UBMD4**. - * _phs000280.v3.pht004207.v1.phv00211061.v1_. dbGap Name: **RPOAMX23**, Desc: **Maximum near wall width, right common carotid: posterior angle [Ultrasound Derived Data. UBMD4. Visit 1]**, Table: **UBMD4**. - * _phs000280.v3.pht004207.v1.phv00211081.v1_. dbGap Name: **LOPAMX45**, Desc: **Maximum far wall width, left common carotid: optimal angle [Ultrasound Derived Data. UBMD4. Visit 1]**, Table: **UBMD4**. - * _phs000280.v3.pht004207.v1.phv00211082.v1_. dbGap Name: **LANAMX45**, Desc: **Maximum far wall width, left common carotid: anterior angle [Ultrasound Derived Data. UBMD4. Visit 1]**, Table: **UBMD4**. - * _phs000280.v3.pht004207.v1.phv00211083.v1_. dbGap Name: **LPOAMX45**, Desc: **Maximum far wall width, left common carotid: posterior angle [Ultrasound Derived Data. UBMD4. Visit 1]**, Table: **UBMD4**. - * _phs000280.v3.pht004207.v1.phv00211087.v1_. dbGap Name: **ROPAMX45**, Desc: **Maximum far wall width, right common carotid: optimal angle [Ultrasound Derived Data. UBMD4. Visit 1]**, Table: **UBMD4**. - * _phs000280.v3.pht004207.v1.phv00211088.v1_. dbGap Name: **RANAMX45**, Desc: **Maximum far wall width, right common carotid: anterior angle [Ultrasound Derived Data. UBMD4. Visit 1]**, Table: **UBMD4**. - * _phs000280.v3.pht004207.v1.phv00211089.v1_. dbGap Name: **RPOAMX45**, Desc: **Maximum far wall width, right common carotid: posterior angle [Ultrasound Derived Data. UBMD4. Visit 1]**, Table: **UBMD4**. + * _phs000280.v3.pht004063.v1.phv00204712.v1_ + * dbGap name: **V1AGE01** + * dbGap desc: **Age at visit 1 [Cohort. Visit 1]** + * dbGap table: **DERIVE13** + * varId _phv00204712_ not found in PIC-SURE data dictionary + * _phs000280.v3.pht004207.v1.phv00211053.v1_ + * dbGap name: **LOPAMX23** + * dbGap desc: **Maximum near wall width, left common carotid: optimal angle [Ultrasound Derived Data. UBMD4. Visit 1]** + * dbGap table: **UBMD4** + * varId _phv00211053_ not found in PIC-SURE data dictionary + * _phs000280.v3.pht004207.v1.phv00211054.v1_ + * dbGap name: **LANAMX23** + * dbGap desc: **Maximum near wall width, left common carotid: anterior angle [Ultrasound Derived Data. UBMD4. Visit 1]** + * dbGap table: **UBMD4** + * varId _phv00211054_ not found in PIC-SURE data dictionary + * _phs000280.v3.pht004207.v1.phv00211055.v1_ + * dbGap name: **LPOAMX23** + * dbGap desc: **Maximum near wall width, left common carotid: posterior angle [Ultrasound Derived Data. UBMD4. Visit 1]** + * dbGap table: **UBMD4** + * varId _phv00211055_ not found in PIC-SURE data dictionary + * _phs000280.v3.pht004207.v1.phv00211059.v1_ + * dbGap name: **ROPAMX23** + * dbGap desc: **Maximum near wall width, right common carotid: optimal angle [Ultrasound Derived Data. UBMD4. Visit 1]** + * dbGap table: **UBMD4** + * varId _phv00211059_ not found in PIC-SURE data dictionary + * _phs000280.v3.pht004207.v1.phv00211060.v1_ + * dbGap name: **RANAMX23** + * dbGap desc: **Maximum near wall width, right common carotid: anterior angle [Ultrasound Derived Data. UBMD4. Visit 1]** + * dbGap table: **UBMD4** + * varId _phv00211060_ not found in PIC-SURE data dictionary + * _phs000280.v3.pht004207.v1.phv00211061.v1_ + * dbGap name: **RPOAMX23** + * dbGap desc: **Maximum near wall width, right common carotid: posterior angle [Ultrasound Derived Data. UBMD4. Visit 1]** + * dbGap table: **UBMD4** + * varId _phv00211061_ not found in PIC-SURE data dictionary + * _phs000280.v3.pht004207.v1.phv00211081.v1_ + * dbGap name: **LOPAMX45** + * dbGap desc: **Maximum far wall width, left common carotid: optimal angle [Ultrasound Derived Data. UBMD4. Visit 1]** + * dbGap table: **UBMD4** + * varId _phv00211081_ not found in PIC-SURE data dictionary + * _phs000280.v3.pht004207.v1.phv00211082.v1_ + * dbGap name: **LANAMX45** + * dbGap desc: **Maximum far wall width, left common carotid: anterior angle [Ultrasound Derived Data. UBMD4. Visit 1]** + * dbGap table: **UBMD4** + * varId _phv00211082_ not found in PIC-SURE data dictionary + * _phs000280.v3.pht004207.v1.phv00211083.v1_ + * dbGap name: **LPOAMX45** + * dbGap desc: **Maximum far wall width, left common carotid: posterior angle [Ultrasound Derived Data. UBMD4. Visit 1]** + * dbGap table: **UBMD4** + * varId _phv00211083_ not found in PIC-SURE data dictionary + * _phs000280.v3.pht004207.v1.phv00211087.v1_ + * dbGap name: **ROPAMX45** + * dbGap desc: **Maximum far wall width, right common carotid: optimal angle [Ultrasound Derived Data. UBMD4. Visit 1]** + * dbGap table: **UBMD4** + * varId _phv00211087_ not found in PIC-SURE data dictionary + * _phs000280.v3.pht004207.v1.phv00211088.v1_ + * dbGap name: **RANAMX45** + * dbGap desc: **Maximum far wall width, right common carotid: anterior angle [Ultrasound Derived Data. UBMD4. Visit 1]** + * dbGap table: **UBMD4** + * varId _phv00211088_ not found in PIC-SURE data dictionary + * _phs000280.v3.pht004207.v1.phv00211089.v1_ + * dbGap name: **RPOAMX45** + * dbGap desc: **Maximum far wall width, right common carotid: posterior angle [Ultrasound Derived Data. UBMD4. Visit 1]** + * dbGap table: **UBMD4** + * varId _phv00211089_ not found in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -866,16 +1114,56 @@ * ### atherosclerosis/cimt_2 -- **CHS Cardiovascular Health Study (CHS) Cohort: an NHLBI-funded observational study of risk factors for cardiovascular disease in adults 65 years or older**: * 10 component_study_variables - * _phs000287.v6.pht001452.v1.phv00100290.v1_. dbGap Name: **PERSTAT**, Desc: **COHORT**, Table: **BASEBOTH**. - * _phs000287.v6.pht001452.v1.phv00100487.v1_. dbGap Name: **AGEBL**, Desc: **CALCULATED AGE AT BASELINE**, Table: **BASEBOTH**. - * _phs000287.v6.pht001473.v1.phv00101238.v1_. dbGap Name: **NMAX155**, Desc: **BL REREAD NEAR WALL MAX, R. COMMON**, Table: **ULTRAYR5**. - * _phs000287.v6.pht001473.v1.phv00101239.v1_. dbGap Name: **FMAX155**, Desc: **BL REREAD FAR WALL MAX, R. COMMON**, Table: **ULTRAYR5**. - * _phs000287.v6.pht001473.v1.phv00101250.v1_. dbGap Name: **NMAX555**, Desc: **BL REREAD NEAR WALL MAX, L. COMMON**, Table: **ULTRAYR5**. - * _phs000287.v6.pht001473.v1.phv00101251.v1_. dbGap Name: **FMAX555**, Desc: **BL REREAD FAR WALL MAX, L. COMMON**, Table: **ULTRAYR5**. - * _phs000287.v6.pht001473.v1.phv00101264.v1_. dbGap Name: **NMAX141**, Desc: **YEAR 5 NEAR WALL MAX, R. COMMON**, Table: **ULTRAYR5**. - * _phs000287.v6.pht001473.v1.phv00101265.v1_. dbGap Name: **FMAX141**, Desc: **YEAR 5 FAR WALL MAX, R. COMMON**, Table: **ULTRAYR5**. - * _phs000287.v6.pht001473.v1.phv00101276.v1_. dbGap Name: **NMAX541**, Desc: **YEAR 5 NEAR WALL MAX, L. COMMON**, Table: **ULTRAYR5**. - * _phs000287.v6.pht001473.v1.phv00101277.v1_. dbGap Name: **FMAX541**, Desc: **YEAR 5 FAR WALL MAX, L. COMMON**, Table: **ULTRAYR5**. + * _phs000287.v6.pht001452.v1.phv00100290.v1_ + * dbGap name: **PERSTAT** + * dbGap desc: **COHORT** + * dbGap table: **BASEBOTH** + * PIC-SURE permissible values: NEW COHORT, OLD COHORT + * _phs000287.v6.pht001452.v1.phv00100487.v1_ + * dbGap name: **AGEBL** + * dbGap desc: **CALCULATED AGE AT BASELINE** + * dbGap table: **BASEBOTH** + * No permissible values listed in PIC-SURE data dictionary + * _phs000287.v6.pht001473.v1.phv00101238.v1_ + * dbGap name: **NMAX155** + * dbGap desc: **BL REREAD NEAR WALL MAX, R. COMMON** + * dbGap table: **ULTRAYR5** + * No permissible values listed in PIC-SURE data dictionary + * _phs000287.v6.pht001473.v1.phv00101239.v1_ + * dbGap name: **FMAX155** + * dbGap desc: **BL REREAD FAR WALL MAX, R. COMMON** + * dbGap table: **ULTRAYR5** + * No permissible values listed in PIC-SURE data dictionary + * _phs000287.v6.pht001473.v1.phv00101250.v1_ + * dbGap name: **NMAX555** + * dbGap desc: **BL REREAD NEAR WALL MAX, L. COMMON** + * dbGap table: **ULTRAYR5** + * No permissible values listed in PIC-SURE data dictionary + * _phs000287.v6.pht001473.v1.phv00101251.v1_ + * dbGap name: **FMAX555** + * dbGap desc: **BL REREAD FAR WALL MAX, L. COMMON** + * dbGap table: **ULTRAYR5** + * No permissible values listed in PIC-SURE data dictionary + * _phs000287.v6.pht001473.v1.phv00101264.v1_ + * dbGap name: **NMAX141** + * dbGap desc: **YEAR 5 NEAR WALL MAX, R. COMMON** + * dbGap table: **ULTRAYR5** + * No permissible values listed in PIC-SURE data dictionary + * _phs000287.v6.pht001473.v1.phv00101265.v1_ + * dbGap name: **FMAX141** + * dbGap desc: **YEAR 5 FAR WALL MAX, R. COMMON** + * dbGap table: **ULTRAYR5** + * No permissible values listed in PIC-SURE data dictionary + * _phs000287.v6.pht001473.v1.phv00101276.v1_ + * dbGap name: **NMAX541** + * dbGap desc: **YEAR 5 NEAR WALL MAX, L. COMMON** + * dbGap table: **ULTRAYR5** + * No permissible values listed in PIC-SURE data dictionary + * _phs000287.v6.pht001473.v1.phv00101277.v1_ + * dbGap name: **FMAX541** + * dbGap desc: **YEAR 5 FAR WALL MAX, L. COMMON** + * dbGap table: **ULTRAYR5** + * No permissible values listed in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -941,8 +1229,16 @@ * ### atherosclerosis/cimt_2 -- **FHS Framingham Cohort**: * 2 component_study_variables - * _phs000007.v29.pht000083.v6.phv00021728.v5_. dbGap Name: **CCD_MEMX**, Desc: **MEAN OF MAX IMT FOR BOTH LEFT AND RIGHT COMMON CAROTID ARTERIES IN DIASTOLE (MM)**, Table: **carotid1_6s**. - * _phs000007.v29.pht003099.v4.phv00177940.v4_. dbGap Name: **age6**, Desc: **Age at Exam 6**, Table: **vr_dates_2019_a_1175s**. + * _phs000007.v29.pht000083.v6.phv00021728.v5_ + * dbGap name: **CCD_MEMX** + * dbGap desc: **MEAN OF MAX IMT FOR BOTH LEFT AND RIGHT COMMON CAROTID ARTERIES IN DIASTOLE (MM)** + * dbGap table: **carotid1_6s** + * No permissible values listed in PIC-SURE data dictionary + * _phs000007.v29.pht003099.v4.phv00177940.v4_ + * dbGap name: **age6** + * dbGap desc: **Age at Exam 6** + * dbGap table: **vr_dates_2019_a_1175s** + * No permissible values listed in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -960,19 +1256,45 @@ * ### atherosclerosis/cimt_2 -- **JHS Jackson Heart Study (JHS) Cohort**: * 13 component_study_variables - * _phs000286.v5.pht001949.v1.phv00126009.v1_. No dbGap metadata available. - * _phs000286.v5.pht001978.v1.phv00128541.v1_. No dbGap metadata available. - * _phs000286.v5.pht001978.v1.phv00128542.v1_. No dbGap metadata available. - * _phs000286.v5.pht001978.v1.phv00128543.v1_. No dbGap metadata available. - * _phs000286.v5.pht001978.v1.phv00128544.v1_. No dbGap metadata available. - * _phs000286.v5.pht001978.v1.phv00128545.v1_. No dbGap metadata available. - * _phs000286.v5.pht001978.v1.phv00128546.v1_. No dbGap metadata available. - * _phs000286.v5.pht001978.v1.phv00128561.v1_. No dbGap metadata available. - * _phs000286.v5.pht001978.v1.phv00128562.v1_. No dbGap metadata available. - * _phs000286.v5.pht001978.v1.phv00128563.v1_. No dbGap metadata available. - * _phs000286.v5.pht001978.v1.phv00128564.v1_. No dbGap metadata available. - * _phs000286.v5.pht001978.v1.phv00128565.v1_. No dbGap metadata available. - * _phs000286.v5.pht001978.v1.phv00128566.v1_. No dbGap metadata available. + * _phs000286.v5.pht001949.v1.phv00126009.v1_ + * No dbGap metadata available + * varId _phv00126009_ not found in PIC-SURE data dictionary + * _phs000286.v5.pht001978.v1.phv00128541.v1_ + * No dbGap metadata available + * varId _phv00128541_ not found in PIC-SURE data dictionary + * _phs000286.v5.pht001978.v1.phv00128542.v1_ + * No dbGap metadata available + * varId _phv00128542_ not found in PIC-SURE data dictionary + * _phs000286.v5.pht001978.v1.phv00128543.v1_ + * No dbGap metadata available + * varId _phv00128543_ not found in PIC-SURE data dictionary + * _phs000286.v5.pht001978.v1.phv00128544.v1_ + * No dbGap metadata available + * varId _phv00128544_ not found in PIC-SURE data dictionary + * _phs000286.v5.pht001978.v1.phv00128545.v1_ + * No dbGap metadata available + * varId _phv00128545_ not found in PIC-SURE data dictionary + * _phs000286.v5.pht001978.v1.phv00128546.v1_ + * No dbGap metadata available + * varId _phv00128546_ not found in PIC-SURE data dictionary + * _phs000286.v5.pht001978.v1.phv00128561.v1_ + * No dbGap metadata available + * varId _phv00128561_ not found in PIC-SURE data dictionary + * _phs000286.v5.pht001978.v1.phv00128562.v1_ + * No dbGap metadata available + * varId _phv00128562_ not found in PIC-SURE data dictionary + * _phs000286.v5.pht001978.v1.phv00128563.v1_ + * No dbGap metadata available + * varId _phv00128563_ not found in PIC-SURE data dictionary + * _phs000286.v5.pht001978.v1.phv00128564.v1_ + * No dbGap metadata available + * varId _phv00128564_ not found in PIC-SURE data dictionary + * _phs000286.v5.pht001978.v1.phv00128565.v1_ + * No dbGap metadata available + * varId _phv00128565_ not found in PIC-SURE data dictionary + * _phs000286.v5.pht001978.v1.phv00128566.v1_ + * No dbGap metadata available + * varId _phv00128566_ not found in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ diff --git a/resources/human-readable-harmonized-variable-documentation/generated-doc-pages/atherosclerosis_events_incident.md b/resources/human-readable-harmonized-variable-documentation/generated-doc-pages/atherosclerosis_events_incident.md index 3ee2fe6..edaa2b4 100644 --- a/resources/human-readable-harmonized-variable-documentation/generated-doc-pages/atherosclerosis_events_incident.md +++ b/resources/human-readable-harmonized-variable-documentation/generated-doc-pages/atherosclerosis_events_incident.md @@ -35,11 +35,31 @@ * ### atherosclerosis_events_incident/angina_incident_1 -- **FHS Framingham Cohort**: * 5 component_study_variables - * _phs000007.v30.pht000309.v13.phv00036469.v12_. dbGap Name: **EVENT**, Desc: **Event Number**, Table: **vr_soe_2020_a_1340s**. - * _phs000007.v30.pht000309.v13.phv00036471.v12_. dbGap Name: **DATE**, Desc: **Date of Event**, Table: **vr_soe_2020_a_1340s**. - * _phs000007.v30.pht003099.v5.phv00177930.v5_. dbGap Name: **age1**, Desc: **Age at Exam 1**, Table: **vr_dates_2019_a_1175s**. - * _phs000007.v30.pht003316.v7.phv00190817.v7_. dbGap Name: **cvd**, Desc: **Cardiovascular Disease (CVD) status**, Table: **vr_survcvd_2019_a_1334s**. - * _phs000007.v30.pht003316.v7.phv00190823.v7_. dbGap Name: **cvddate**, Desc: **Date of Cardiovascular Disease (CVD) status**, Table: **vr_survcvd_2019_a_1334s**. + * _phs000007.v30.pht000309.v13.phv00036469.v12_ + * dbGap name: **EVENT** + * dbGap desc: **Event Number** + * dbGap table: **vr_soe_2020_a_1340s** + * PIC-SURE permissible values: ABI (Atherothrombotic Infarction of brain), AP, first episode only, Acute MI by autopsy, previously coded as 1 or 2, CHF, hospitalized, CHF, not hospitalized, diagnosed on basis of on exam or MD notes, CHF, questionable CHF at exam 1, CI, definite by both history and ECG, CVA, definite CVA, type unknown, Cerebral embolism, Death, CHD sudden, within 1 hour, Death, CHD, 1-23 hours, non sudden, Death, CHD, 24-47 hours, non sudden, Death, CHD, 48 hours or more, non sudden, Death, CVA, Death, Cancer, Death, cause unknown, Death, other CVD, Death, other causes, Definite CVA at exam 1, but questionable type, IC, first episode only, IC, questionable IC at exam 1, Intracerebral hemorrhage, MI recognized, with diagnostic ECG, MI recognized, without diagnostic ECG, with autopsy evidence, new event (see also code 9), MI recognized, without diagnostic ECG, with enzymes and history, MI unrecognized, not silent, MI unrecognized, silent, Other CVA, Questionable CVA at exam 1, Questionable MI at exam 1, Subarachnoid hemorrhage, TIA (Transient Ischemic Attack) only the 1st TIA is coded, TIA with positive imaging + * _phs000007.v30.pht000309.v13.phv00036471.v12_ + * dbGap name: **DATE** + * dbGap desc: **Date of Event** + * dbGap table: **vr_soe_2020_a_1340s** + * No permissible values listed in PIC-SURE data dictionary + * _phs000007.v30.pht003099.v5.phv00177930.v5_ + * dbGap name: **age1** + * dbGap desc: **Age at Exam 1** + * dbGap table: **vr_dates_2019_a_1175s** + * No permissible values listed in PIC-SURE data dictionary + * _phs000007.v30.pht003316.v7.phv00190817.v7_ + * dbGap name: **cvd** + * dbGap desc: **Cardiovascular Disease (CVD) status** + * dbGap table: **vr_survcvd_2019_a_1334s** + * PIC-SURE permissible values: No, Yes + * _phs000007.v30.pht003316.v7.phv00190823.v7_ + * dbGap name: **cvddate** + * dbGap desc: **Date of Cardiovascular Disease (CVD) status** + * dbGap table: **vr_survcvd_2019_a_1334s** + * No permissible values listed in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -126,13 +146,41 @@ * ### atherosclerosis_events_incident/angina_incident_1 -- **WHI Women's Health Initiative**: * 7 component_study_variables - * _phs000200.v11.pht000998.v6.phv00078436.v6_. dbGap Name: **F2DAYS**, Desc: **F2 Days since randomization**, Table: **f2_rel1**. - * _phs000200.v11.pht000998.v6.phv00078437.v6_. dbGap Name: **AGE**, Desc: **Age at screening**, Table: **f2_rel1**. - * _phs000200.v11.pht003395.v3.phv00192302.v3_. dbGap Name: **EXT2MRC**, Desc: **Extension 2 MRC Participant**, Table: **ext_rel2**. - * _phs000200.v11.pht003407.v3.phv00193145.v3_. dbGap Name: **ANGINA**, Desc: **Angina**, Table: **outc_ct_os_rel4**. - * _phs000200.v11.pht003407.v3.phv00193146.v3_. dbGap Name: **ANGINADY**, Desc: **Days enrollment to Angina**, Table: **outc_ct_os_rel4**. - * _phs000200.v11.pht003407.v3.phv00193504.v3_. dbGap Name: **ENDEXT1DY**, Desc: **Days enrollment to end of Ext1 followup**, Table: **outc_ct_os_rel4**. - * _phs000200.v11.pht003407.v3.phv00193505.v3_. dbGap Name: **ENDFOLLOWDY**, Desc: **Days enrollment to end of followup**, Table: **outc_ct_os_rel4**. + * _phs000200.v11.pht000998.v6.phv00078436.v6_ + * dbGap name: **F2DAYS** + * dbGap desc: **F2 Days since randomization** + * dbGap table: **f2_rel1** + * No permissible values listed in PIC-SURE data dictionary + * _phs000200.v11.pht000998.v6.phv00078437.v6_ + * dbGap name: **AGE** + * dbGap desc: **Age at screening** + * dbGap table: **f2_rel1** + * No permissible values listed in PIC-SURE data dictionary + * _phs000200.v11.pht003395.v3.phv00192302.v3_ + * dbGap name: **EXT2MRC** + * dbGap desc: **Extension 2 MRC Participant** + * dbGap table: **ext_rel2** + * PIC-SURE permissible values: No, Yes + * _phs000200.v11.pht003407.v3.phv00193145.v3_ + * dbGap name: **ANGINA** + * dbGap desc: **Angina** + * dbGap table: **outc_ct_os_rel4** + * PIC-SURE permissible values: No, Yes + * _phs000200.v11.pht003407.v3.phv00193146.v3_ + * dbGap name: **ANGINADY** + * dbGap desc: **Days enrollment to Angina** + * dbGap table: **outc_ct_os_rel4** + * No permissible values listed in PIC-SURE data dictionary + * _phs000200.v11.pht003407.v3.phv00193504.v3_ + * dbGap name: **ENDEXT1DY** + * dbGap desc: **Days enrollment to end of Ext1 followup** + * dbGap table: **outc_ct_os_rel4** + * No permissible values listed in PIC-SURE data dictionary + * _phs000200.v11.pht003407.v3.phv00193505.v3_ + * dbGap name: **ENDFOLLOWDY** + * dbGap desc: **Days enrollment to end of followup** + * dbGap table: **outc_ct_os_rel4** + * No permissible values listed in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -181,11 +229,31 @@ * ### atherosclerosis_events_incident/cabg_incident_1 -- **FHS Framingham Cohort**: * 5 component_study_variables - * _phs000007.v30.pht000389.v10.phv00054697.v8_. dbGap Name: **procdate**, Desc: **Date of cardiovascular procedure**, Table: **vr_cvdproc_2020_a_1313s**. - * _phs000007.v30.pht000389.v10.phv00163410.v7_. dbGap Name: **vessel**, Desc: **Coronary Artery Bypass Graft (CABG) - Number of vessels bypassed - PROCNUM = 141**, Table: **vr_cvdproc_2020_a_1313s**. - * _phs000007.v30.pht003099.v5.phv00177930.v5_. dbGap Name: **age1**, Desc: **Age at Exam 1**, Table: **vr_dates_2019_a_1175s**. - * _phs000007.v30.pht003316.v7.phv00190817.v7_. dbGap Name: **cvd**, Desc: **Cardiovascular Disease (CVD) status**, Table: **vr_survcvd_2019_a_1334s**. - * _phs000007.v30.pht003316.v7.phv00190823.v7_. dbGap Name: **cvddate**, Desc: **Date of Cardiovascular Disease (CVD) status**, Table: **vr_survcvd_2019_a_1334s**. + * _phs000007.v30.pht000389.v10.phv00054697.v8_ + * dbGap name: **procdate** + * dbGap desc: **Date of cardiovascular procedure** + * dbGap table: **vr_cvdproc_2020_a_1313s** + * No permissible values listed in PIC-SURE data dictionary + * _phs000007.v30.pht000389.v10.phv00163410.v7_ + * dbGap name: **vessel** + * dbGap desc: **Coronary Artery Bypass Graft (CABG) - Number of vessels bypassed - PROCNUM = 141** + * dbGap table: **vr_cvdproc_2020_a_1313s** + * PIC-SURE permissible values: CABG Procedure not done, Five (5) vessels bypassed, Four (4) vessels bypassed, One (1) vessel bypassed, Seven (7) vessels bypassed, Six (6) vessels bypassed, Three (3) vessels bypassed, Two (2) vessels bypassed + * _phs000007.v30.pht003099.v5.phv00177930.v5_ + * dbGap name: **age1** + * dbGap desc: **Age at Exam 1** + * dbGap table: **vr_dates_2019_a_1175s** + * No permissible values listed in PIC-SURE data dictionary + * _phs000007.v30.pht003316.v7.phv00190817.v7_ + * dbGap name: **cvd** + * dbGap desc: **Cardiovascular Disease (CVD) status** + * dbGap table: **vr_survcvd_2019_a_1334s** + * PIC-SURE permissible values: No, Yes + * _phs000007.v30.pht003316.v7.phv00190823.v7_ + * dbGap name: **cvddate** + * dbGap desc: **Date of Cardiovascular Disease (CVD) status** + * dbGap table: **vr_survcvd_2019_a_1334s** + * No permissible values listed in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -263,13 +331,41 @@ * ### atherosclerosis_events_incident/cabg_incident_1 -- **WHI Women's Health Initiative**: * 7 component_study_variables - * _phs000200.v11.pht000998.v6.phv00078436.v6_. dbGap Name: **F2DAYS**, Desc: **F2 Days since randomization**, Table: **f2_rel1**. - * _phs000200.v11.pht000998.v6.phv00078437.v6_. dbGap Name: **AGE**, Desc: **Age at screening**, Table: **f2_rel1**. - * _phs000200.v11.pht003395.v3.phv00192302.v3_. dbGap Name: **EXT2MRC**, Desc: **Extension 2 MRC Participant**, Table: **ext_rel2**. - * _phs000200.v11.pht003407.v3.phv00193157.v3_. dbGap Name: **CABG**, Desc: **CABG**, Table: **outc_ct_os_rel4**. - * _phs000200.v11.pht003407.v3.phv00193158.v3_. dbGap Name: **CABGDY**, Desc: **Days enrollment to CABG**, Table: **outc_ct_os_rel4**. - * _phs000200.v11.pht003407.v3.phv00193504.v3_. dbGap Name: **ENDEXT1DY**, Desc: **Days enrollment to end of Ext1 followup**, Table: **outc_ct_os_rel4**. - * _phs000200.v11.pht003407.v3.phv00193505.v3_. dbGap Name: **ENDFOLLOWDY**, Desc: **Days enrollment to end of followup**, Table: **outc_ct_os_rel4**. + * _phs000200.v11.pht000998.v6.phv00078436.v6_ + * dbGap name: **F2DAYS** + * dbGap desc: **F2 Days since randomization** + * dbGap table: **f2_rel1** + * No permissible values listed in PIC-SURE data dictionary + * _phs000200.v11.pht000998.v6.phv00078437.v6_ + * dbGap name: **AGE** + * dbGap desc: **Age at screening** + * dbGap table: **f2_rel1** + * No permissible values listed in PIC-SURE data dictionary + * _phs000200.v11.pht003395.v3.phv00192302.v3_ + * dbGap name: **EXT2MRC** + * dbGap desc: **Extension 2 MRC Participant** + * dbGap table: **ext_rel2** + * PIC-SURE permissible values: No, Yes + * _phs000200.v11.pht003407.v3.phv00193157.v3_ + * dbGap name: **CABG** + * dbGap desc: **CABG** + * dbGap table: **outc_ct_os_rel4** + * PIC-SURE permissible values: No, Yes + * _phs000200.v11.pht003407.v3.phv00193158.v3_ + * dbGap name: **CABGDY** + * dbGap desc: **Days enrollment to CABG** + * dbGap table: **outc_ct_os_rel4** + * No permissible values listed in PIC-SURE data dictionary + * _phs000200.v11.pht003407.v3.phv00193504.v3_ + * dbGap name: **ENDEXT1DY** + * dbGap desc: **Days enrollment to end of Ext1 followup** + * dbGap table: **outc_ct_os_rel4** + * No permissible values listed in PIC-SURE data dictionary + * _phs000200.v11.pht003407.v3.phv00193505.v3_ + * dbGap name: **ENDFOLLOWDY** + * dbGap desc: **Days enrollment to end of followup** + * dbGap table: **outc_ct_os_rel4** + * No permissible values listed in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -313,7 +409,11 @@ * ### atherosclerosis_events_incident/cad_followup_start_age_1 -- **FHS Framingham Cohort**: * 1 component_study_variables - * _phs000007.v30.pht003099.v5.phv00177930.v5_. dbGap Name: **age1**, Desc: **Age at Exam 1**, Table: **vr_dates_2019_a_1175s**. + * _phs000007.v30.pht003099.v5.phv00177930.v5_ + * dbGap name: **age1** + * dbGap desc: **Age at Exam 1** + * dbGap table: **vr_dates_2019_a_1175s** + * No permissible values listed in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -329,7 +429,11 @@ * ### atherosclerosis_events_incident/cad_followup_start_age_1 -- **WHI Women's Health Initiative**: * 1 component_study_variables - * _phs000200.v11.pht000998.v6.phv00078437.v6_. dbGap Name: **AGE**, Desc: **Age at screening**, Table: **f2_rel1**. + * _phs000200.v11.pht000998.v6.phv00078437.v6_ + * dbGap name: **AGE** + * dbGap desc: **Age at screening** + * dbGap table: **f2_rel1** + * No permissible values listed in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -362,11 +466,31 @@ * ### atherosclerosis_events_incident/chd_death_definite_1 -- **FHS Framingham Cohort**: * 5 component_study_variables - * _phs000007.v30.pht000309.v13.phv00036469.v12_. dbGap Name: **EVENT**, Desc: **Event Number**, Table: **vr_soe_2020_a_1340s**. - * _phs000007.v30.pht000309.v13.phv00036471.v12_. dbGap Name: **DATE**, Desc: **Date of Event**, Table: **vr_soe_2020_a_1340s**. - * _phs000007.v30.pht003099.v5.phv00177930.v5_. dbGap Name: **age1**, Desc: **Age at Exam 1**, Table: **vr_dates_2019_a_1175s**. - * _phs000007.v30.pht003316.v7.phv00190817.v7_. dbGap Name: **cvd**, Desc: **Cardiovascular Disease (CVD) status**, Table: **vr_survcvd_2019_a_1334s**. - * _phs000007.v30.pht003316.v7.phv00190823.v7_. dbGap Name: **cvddate**, Desc: **Date of Cardiovascular Disease (CVD) status**, Table: **vr_survcvd_2019_a_1334s**. + * _phs000007.v30.pht000309.v13.phv00036469.v12_ + * dbGap name: **EVENT** + * dbGap desc: **Event Number** + * dbGap table: **vr_soe_2020_a_1340s** + * PIC-SURE permissible values: ABI (Atherothrombotic Infarction of brain), AP, first episode only, Acute MI by autopsy, previously coded as 1 or 2, CHF, hospitalized, CHF, not hospitalized, diagnosed on basis of on exam or MD notes, CHF, questionable CHF at exam 1, CI, definite by both history and ECG, CVA, definite CVA, type unknown, Cerebral embolism, Death, CHD sudden, within 1 hour, Death, CHD, 1-23 hours, non sudden, Death, CHD, 24-47 hours, non sudden, Death, CHD, 48 hours or more, non sudden, Death, CVA, Death, Cancer, Death, cause unknown, Death, other CVD, Death, other causes, Definite CVA at exam 1, but questionable type, IC, first episode only, IC, questionable IC at exam 1, Intracerebral hemorrhage, MI recognized, with diagnostic ECG, MI recognized, without diagnostic ECG, with autopsy evidence, new event (see also code 9), MI recognized, without diagnostic ECG, with enzymes and history, MI unrecognized, not silent, MI unrecognized, silent, Other CVA, Questionable CVA at exam 1, Questionable MI at exam 1, Subarachnoid hemorrhage, TIA (Transient Ischemic Attack) only the 1st TIA is coded, TIA with positive imaging + * _phs000007.v30.pht000309.v13.phv00036471.v12_ + * dbGap name: **DATE** + * dbGap desc: **Date of Event** + * dbGap table: **vr_soe_2020_a_1340s** + * No permissible values listed in PIC-SURE data dictionary + * _phs000007.v30.pht003099.v5.phv00177930.v5_ + * dbGap name: **age1** + * dbGap desc: **Age at Exam 1** + * dbGap table: **vr_dates_2019_a_1175s** + * No permissible values listed in PIC-SURE data dictionary + * _phs000007.v30.pht003316.v7.phv00190817.v7_ + * dbGap name: **cvd** + * dbGap desc: **Cardiovascular Disease (CVD) status** + * dbGap table: **vr_survcvd_2019_a_1334s** + * PIC-SURE permissible values: No, Yes + * _phs000007.v30.pht003316.v7.phv00190823.v7_ + * dbGap name: **cvddate** + * dbGap desc: **Date of Cardiovascular Disease (CVD) status** + * dbGap table: **vr_survcvd_2019_a_1334s** + * No permissible values listed in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -466,14 +590,46 @@ * ### atherosclerosis_events_incident/chd_death_definite_1 -- **WHI Women's Health Initiative**: * 8 component_study_variables - * _phs000200.v11.pht000998.v6.phv00078436.v6_. dbGap Name: **F2DAYS**, Desc: **F2 Days since randomization**, Table: **f2_rel1**. - * _phs000200.v11.pht000998.v6.phv00078437.v6_. dbGap Name: **AGE**, Desc: **Age at screening**, Table: **f2_rel1**. - * _phs000200.v11.pht003395.v3.phv00192302.v3_. dbGap Name: **EXT2MRC**, Desc: **Extension 2 MRC Participant**, Table: **ext_rel2**. - * _phs000200.v11.pht003407.v3.phv00193498.v3_. dbGap Name: **DEATHDY**, Desc: **Days enrollment to Death**, Table: **outc_ct_os_rel4**. - * _phs000200.v11.pht003407.v3.phv00193504.v3_. dbGap Name: **ENDEXT1DY**, Desc: **Days enrollment to end of Ext1 followup**, Table: **outc_ct_os_rel4**. - * _phs000200.v11.pht003407.v3.phv00193505.v3_. dbGap Name: **ENDFOLLOWDY**, Desc: **Days enrollment to end of followup**, Table: **outc_ct_os_rel4**. - * _phs000200.v11.pht003409.v3.phv00193531.v2_. dbGap Name: **DEATH**, Desc: **Death**, Table: **outc_death_rel5**. - * _phs000200.v11.pht003409.v3.phv00193532.v2_. dbGap Name: **DEATHCAUSE**, Desc: **Cause of Death**, Table: **outc_death_rel5**. + * _phs000200.v11.pht000998.v6.phv00078436.v6_ + * dbGap name: **F2DAYS** + * dbGap desc: **F2 Days since randomization** + * dbGap table: **f2_rel1** + * No permissible values listed in PIC-SURE data dictionary + * _phs000200.v11.pht000998.v6.phv00078437.v6_ + * dbGap name: **AGE** + * dbGap desc: **Age at screening** + * dbGap table: **f2_rel1** + * No permissible values listed in PIC-SURE data dictionary + * _phs000200.v11.pht003395.v3.phv00192302.v3_ + * dbGap name: **EXT2MRC** + * dbGap desc: **Extension 2 MRC Participant** + * dbGap table: **ext_rel2** + * PIC-SURE permissible values: No, Yes + * _phs000200.v11.pht003407.v3.phv00193498.v3_ + * dbGap name: **DEATHDY** + * dbGap desc: **Days enrollment to Death** + * dbGap table: **outc_ct_os_rel4** + * No permissible values listed in PIC-SURE data dictionary + * _phs000200.v11.pht003407.v3.phv00193504.v3_ + * dbGap name: **ENDEXT1DY** + * dbGap desc: **Days enrollment to end of Ext1 followup** + * dbGap table: **outc_ct_os_rel4** + * No permissible values listed in PIC-SURE data dictionary + * _phs000200.v11.pht003407.v3.phv00193505.v3_ + * dbGap name: **ENDFOLLOWDY** + * dbGap desc: **Days enrollment to end of followup** + * dbGap table: **outc_ct_os_rel4** + * No permissible values listed in PIC-SURE data dictionary + * _phs000200.v11.pht003409.v3.phv00193531.v2_ + * dbGap name: **DEATH** + * dbGap desc: **Death** + * dbGap table: **outc_death_rel5** + * PIC-SURE permissible values: Yes + * _phs000200.v11.pht003409.v3.phv00193532.v2_ + * dbGap name: **DEATHCAUSE** + * dbGap desc: **Cause of Death** + * dbGap table: **outc_death_rel5** + * PIC-SURE permissible values: ALS, Accessory Sinus Cancer, Accident, Adrenal Gland Cancer, Alzheimers, Anus Cancer, Appendix Cancer, Biliary Tract Cancer, Bladder Cancer, Bone-Limb Cancer, Bone-Non Limb Cancer, Brain Cancer, Breast Cancer, COPD, Central Nervous System Cancer, Cerebrovascular, Cervix Cancer, Colon Cancer, Connective Tissue Cancer, Definite CHD, Dementia NOS, Endocrine Glands Cancer, Endometrial Cancer, Esophagus Cancer, Eye and Adnexa Cancer, Gallbladder Cancer, Genital Organ Cancer, Gum Cancer, Heart Cancer, Hepatic Cirrhosis, Homicide, Hypopharynx Cancer, Kidney Cancer, Known Other Cause, Larynx Cancer, Leukemia, Liver Cancer, Lung Cancer, Lymph Node Cancer, Lymphoma (NHL only), Lymphoma, Hodgkins, Melanoma, Meninges Cancer, Multiple Myeloma, Nasal Cavity Mid Ear Cancer, Nasopharynx Cancer, Oral (Mouth) Cancer, Oropharynx Cancer, Other Cancer Death, Other Cardiovascular, Other Digestive Cancer, Other Injury, Other Lip Cancer, Ovarian Cancer, Palate Cancer, Pancreas, Parkinson's, Parotid Gland,Stensens Cancer, Peritoneum Cancer, Pneumonia, Possible CHD, Pulmonary Embolism, Pulmonary Fibrosis, Rectosigmoid Cancer, Rectum Cancer, Renal Failure, Renal Pelvis Cancer, Salivary Glands Cancer, Sepsis, Small Intestine Cancer, Stomach Cancer, Suicide, Thymus Cancer, Thyroid Cancer, Tongue Cancer, Tonsil Cancer, Unknown Cancer Site, Unknown Cardiovascular, Unknown Cause, Unknown Cause (Not yet adj), Ureter Cancer, Urinary Organs Cancer, Uterine Cancer, Vagina Cancer, Vulva Cancer * **Function:** ```r harmonize <- function(phen_list){ @@ -516,11 +672,31 @@ * ### atherosclerosis_events_incident/chd_death_probable_1 -- **FHS Framingham Cohort**: * 5 component_study_variables - * _phs000007.v30.pht000309.v13.phv00036469.v12_. dbGap Name: **EVENT**, Desc: **Event Number**, Table: **vr_soe_2020_a_1340s**. - * _phs000007.v30.pht000309.v13.phv00036471.v12_. dbGap Name: **DATE**, Desc: **Date of Event**, Table: **vr_soe_2020_a_1340s**. - * _phs000007.v30.pht003099.v5.phv00177930.v5_. dbGap Name: **age1**, Desc: **Age at Exam 1**, Table: **vr_dates_2019_a_1175s**. - * _phs000007.v30.pht003316.v7.phv00190817.v7_. dbGap Name: **cvd**, Desc: **Cardiovascular Disease (CVD) status**, Table: **vr_survcvd_2019_a_1334s**. - * _phs000007.v30.pht003316.v7.phv00190823.v7_. dbGap Name: **cvddate**, Desc: **Date of Cardiovascular Disease (CVD) status**, Table: **vr_survcvd_2019_a_1334s**. + * _phs000007.v30.pht000309.v13.phv00036469.v12_ + * dbGap name: **EVENT** + * dbGap desc: **Event Number** + * dbGap table: **vr_soe_2020_a_1340s** + * PIC-SURE permissible values: ABI (Atherothrombotic Infarction of brain), AP, first episode only, Acute MI by autopsy, previously coded as 1 or 2, CHF, hospitalized, CHF, not hospitalized, diagnosed on basis of on exam or MD notes, CHF, questionable CHF at exam 1, CI, definite by both history and ECG, CVA, definite CVA, type unknown, Cerebral embolism, Death, CHD sudden, within 1 hour, Death, CHD, 1-23 hours, non sudden, Death, CHD, 24-47 hours, non sudden, Death, CHD, 48 hours or more, non sudden, Death, CVA, Death, Cancer, Death, cause unknown, Death, other CVD, Death, other causes, Definite CVA at exam 1, but questionable type, IC, first episode only, IC, questionable IC at exam 1, Intracerebral hemorrhage, MI recognized, with diagnostic ECG, MI recognized, without diagnostic ECG, with autopsy evidence, new event (see also code 9), MI recognized, without diagnostic ECG, with enzymes and history, MI unrecognized, not silent, MI unrecognized, silent, Other CVA, Questionable CVA at exam 1, Questionable MI at exam 1, Subarachnoid hemorrhage, TIA (Transient Ischemic Attack) only the 1st TIA is coded, TIA with positive imaging + * _phs000007.v30.pht000309.v13.phv00036471.v12_ + * dbGap name: **DATE** + * dbGap desc: **Date of Event** + * dbGap table: **vr_soe_2020_a_1340s** + * No permissible values listed in PIC-SURE data dictionary + * _phs000007.v30.pht003099.v5.phv00177930.v5_ + * dbGap name: **age1** + * dbGap desc: **Age at Exam 1** + * dbGap table: **vr_dates_2019_a_1175s** + * No permissible values listed in PIC-SURE data dictionary + * _phs000007.v30.pht003316.v7.phv00190817.v7_ + * dbGap name: **cvd** + * dbGap desc: **Cardiovascular Disease (CVD) status** + * dbGap table: **vr_survcvd_2019_a_1334s** + * PIC-SURE permissible values: No, Yes + * _phs000007.v30.pht003316.v7.phv00190823.v7_ + * dbGap name: **cvddate** + * dbGap desc: **Date of Cardiovascular Disease (CVD) status** + * dbGap table: **vr_survcvd_2019_a_1334s** + * No permissible values listed in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -620,14 +796,46 @@ * ### atherosclerosis_events_incident/chd_death_probable_1 -- **WHI Women's Health Initiative**: * 8 component_study_variables - * _phs000200.v11.pht000998.v6.phv00078436.v6_. dbGap Name: **F2DAYS**, Desc: **F2 Days since randomization**, Table: **f2_rel1**. - * _phs000200.v11.pht000998.v6.phv00078437.v6_. dbGap Name: **AGE**, Desc: **Age at screening**, Table: **f2_rel1**. - * _phs000200.v11.pht003395.v3.phv00192302.v3_. dbGap Name: **EXT2MRC**, Desc: **Extension 2 MRC Participant**, Table: **ext_rel2**. - * _phs000200.v11.pht003407.v3.phv00193498.v3_. dbGap Name: **DEATHDY**, Desc: **Days enrollment to Death**, Table: **outc_ct_os_rel4**. - * _phs000200.v11.pht003407.v3.phv00193504.v3_. dbGap Name: **ENDEXT1DY**, Desc: **Days enrollment to end of Ext1 followup**, Table: **outc_ct_os_rel4**. - * _phs000200.v11.pht003407.v3.phv00193505.v3_. dbGap Name: **ENDFOLLOWDY**, Desc: **Days enrollment to end of followup**, Table: **outc_ct_os_rel4**. - * _phs000200.v11.pht003409.v3.phv00193531.v2_. dbGap Name: **DEATH**, Desc: **Death**, Table: **outc_death_rel5**. - * _phs000200.v11.pht003409.v3.phv00193532.v2_. dbGap Name: **DEATHCAUSE**, Desc: **Cause of Death**, Table: **outc_death_rel5**. + * _phs000200.v11.pht000998.v6.phv00078436.v6_ + * dbGap name: **F2DAYS** + * dbGap desc: **F2 Days since randomization** + * dbGap table: **f2_rel1** + * No permissible values listed in PIC-SURE data dictionary + * _phs000200.v11.pht000998.v6.phv00078437.v6_ + * dbGap name: **AGE** + * dbGap desc: **Age at screening** + * dbGap table: **f2_rel1** + * No permissible values listed in PIC-SURE data dictionary + * _phs000200.v11.pht003395.v3.phv00192302.v3_ + * dbGap name: **EXT2MRC** + * dbGap desc: **Extension 2 MRC Participant** + * dbGap table: **ext_rel2** + * PIC-SURE permissible values: No, Yes + * _phs000200.v11.pht003407.v3.phv00193498.v3_ + * dbGap name: **DEATHDY** + * dbGap desc: **Days enrollment to Death** + * dbGap table: **outc_ct_os_rel4** + * No permissible values listed in PIC-SURE data dictionary + * _phs000200.v11.pht003407.v3.phv00193504.v3_ + * dbGap name: **ENDEXT1DY** + * dbGap desc: **Days enrollment to end of Ext1 followup** + * dbGap table: **outc_ct_os_rel4** + * No permissible values listed in PIC-SURE data dictionary + * _phs000200.v11.pht003407.v3.phv00193505.v3_ + * dbGap name: **ENDFOLLOWDY** + * dbGap desc: **Days enrollment to end of followup** + * dbGap table: **outc_ct_os_rel4** + * No permissible values listed in PIC-SURE data dictionary + * _phs000200.v11.pht003409.v3.phv00193531.v2_ + * dbGap name: **DEATH** + * dbGap desc: **Death** + * dbGap table: **outc_death_rel5** + * PIC-SURE permissible values: Yes + * _phs000200.v11.pht003409.v3.phv00193532.v2_ + * dbGap name: **DEATHCAUSE** + * dbGap desc: **Cause of Death** + * dbGap table: **outc_death_rel5** + * PIC-SURE permissible values: ALS, Accessory Sinus Cancer, Accident, Adrenal Gland Cancer, Alzheimers, Anus Cancer, Appendix Cancer, Biliary Tract Cancer, Bladder Cancer, Bone-Limb Cancer, Bone-Non Limb Cancer, Brain Cancer, Breast Cancer, COPD, Central Nervous System Cancer, Cerebrovascular, Cervix Cancer, Colon Cancer, Connective Tissue Cancer, Definite CHD, Dementia NOS, Endocrine Glands Cancer, Endometrial Cancer, Esophagus Cancer, Eye and Adnexa Cancer, Gallbladder Cancer, Genital Organ Cancer, Gum Cancer, Heart Cancer, Hepatic Cirrhosis, Homicide, Hypopharynx Cancer, Kidney Cancer, Known Other Cause, Larynx Cancer, Leukemia, Liver Cancer, Lung Cancer, Lymph Node Cancer, Lymphoma (NHL only), Lymphoma, Hodgkins, Melanoma, Meninges Cancer, Multiple Myeloma, Nasal Cavity Mid Ear Cancer, Nasopharynx Cancer, Oral (Mouth) Cancer, Oropharynx Cancer, Other Cancer Death, Other Cardiovascular, Other Digestive Cancer, Other Injury, Other Lip Cancer, Ovarian Cancer, Palate Cancer, Pancreas, Parkinson's, Parotid Gland,Stensens Cancer, Peritoneum Cancer, Pneumonia, Possible CHD, Pulmonary Embolism, Pulmonary Fibrosis, Rectosigmoid Cancer, Rectum Cancer, Renal Failure, Renal Pelvis Cancer, Salivary Glands Cancer, Sepsis, Small Intestine Cancer, Stomach Cancer, Suicide, Thymus Cancer, Thyroid Cancer, Tongue Cancer, Tonsil Cancer, Unknown Cancer Site, Unknown Cardiovascular, Unknown Cause, Unknown Cause (Not yet adj), Ureter Cancer, Urinary Organs Cancer, Uterine Cancer, Vagina Cancer, Vulva Cancer * **Function:** ```r harmonize <- function(phen_list){ @@ -667,13 +875,41 @@ * ### atherosclerosis_events_incident/coronary_angioplasty_incident_1 -- **WHI Women's Health Initiative**: * 7 component_study_variables - * _phs000200.v11.pht000998.v6.phv00078436.v6_. dbGap Name: **F2DAYS**, Desc: **F2 Days since randomization**, Table: **f2_rel1**. - * _phs000200.v11.pht000998.v6.phv00078437.v6_. dbGap Name: **AGE**, Desc: **Age at screening**, Table: **f2_rel1**. - * _phs000200.v11.pht003395.v3.phv00192302.v3_. dbGap Name: **EXT2MRC**, Desc: **Extension 2 MRC Participant**, Table: **ext_rel2**. - * _phs000200.v11.pht003407.v3.phv00193199.v3_. dbGap Name: **PTCA**, Desc: **PTCA**, Table: **outc_ct_os_rel4**. - * _phs000200.v11.pht003407.v3.phv00193200.v3_. dbGap Name: **PTCADY**, Desc: **Days enrollment to PTCA**, Table: **outc_ct_os_rel4**. - * _phs000200.v11.pht003407.v3.phv00193504.v3_. dbGap Name: **ENDEXT1DY**, Desc: **Days enrollment to end of Ext1 followup**, Table: **outc_ct_os_rel4**. - * _phs000200.v11.pht003407.v3.phv00193505.v3_. dbGap Name: **ENDFOLLOWDY**, Desc: **Days enrollment to end of followup**, Table: **outc_ct_os_rel4**. + * _phs000200.v11.pht000998.v6.phv00078436.v6_ + * dbGap name: **F2DAYS** + * dbGap desc: **F2 Days since randomization** + * dbGap table: **f2_rel1** + * No permissible values listed in PIC-SURE data dictionary + * _phs000200.v11.pht000998.v6.phv00078437.v6_ + * dbGap name: **AGE** + * dbGap desc: **Age at screening** + * dbGap table: **f2_rel1** + * No permissible values listed in PIC-SURE data dictionary + * _phs000200.v11.pht003395.v3.phv00192302.v3_ + * dbGap name: **EXT2MRC** + * dbGap desc: **Extension 2 MRC Participant** + * dbGap table: **ext_rel2** + * PIC-SURE permissible values: No, Yes + * _phs000200.v11.pht003407.v3.phv00193199.v3_ + * dbGap name: **PTCA** + * dbGap desc: **PTCA** + * dbGap table: **outc_ct_os_rel4** + * PIC-SURE permissible values: No, Yes + * _phs000200.v11.pht003407.v3.phv00193200.v3_ + * dbGap name: **PTCADY** + * dbGap desc: **Days enrollment to PTCA** + * dbGap table: **outc_ct_os_rel4** + * No permissible values listed in PIC-SURE data dictionary + * _phs000200.v11.pht003407.v3.phv00193504.v3_ + * dbGap name: **ENDEXT1DY** + * dbGap desc: **Days enrollment to end of Ext1 followup** + * dbGap table: **outc_ct_os_rel4** + * No permissible values listed in PIC-SURE data dictionary + * _phs000200.v11.pht003407.v3.phv00193505.v3_ + * dbGap name: **ENDFOLLOWDY** + * dbGap desc: **Days enrollment to end of followup** + * dbGap table: **outc_ct_os_rel4** + * No permissible values listed in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -719,11 +955,31 @@ * ### atherosclerosis_events_incident/mi_incident_1 -- **FHS Framingham Cohort**: * 5 component_study_variables - * _phs000007.v30.pht000309.v13.phv00036469.v12_. dbGap Name: **EVENT**, Desc: **Event Number**, Table: **vr_soe_2020_a_1340s**. - * _phs000007.v30.pht000309.v13.phv00036471.v12_. dbGap Name: **DATE**, Desc: **Date of Event**, Table: **vr_soe_2020_a_1340s**. - * _phs000007.v30.pht003099.v5.phv00177930.v5_. dbGap Name: **age1**, Desc: **Age at Exam 1**, Table: **vr_dates_2019_a_1175s**. - * _phs000007.v30.pht003316.v7.phv00190817.v7_. dbGap Name: **cvd**, Desc: **Cardiovascular Disease (CVD) status**, Table: **vr_survcvd_2019_a_1334s**. - * _phs000007.v30.pht003316.v7.phv00190823.v7_. dbGap Name: **cvddate**, Desc: **Date of Cardiovascular Disease (CVD) status**, Table: **vr_survcvd_2019_a_1334s**. + * _phs000007.v30.pht000309.v13.phv00036469.v12_ + * dbGap name: **EVENT** + * dbGap desc: **Event Number** + * dbGap table: **vr_soe_2020_a_1340s** + * PIC-SURE permissible values: ABI (Atherothrombotic Infarction of brain), AP, first episode only, Acute MI by autopsy, previously coded as 1 or 2, CHF, hospitalized, CHF, not hospitalized, diagnosed on basis of on exam or MD notes, CHF, questionable CHF at exam 1, CI, definite by both history and ECG, CVA, definite CVA, type unknown, Cerebral embolism, Death, CHD sudden, within 1 hour, Death, CHD, 1-23 hours, non sudden, Death, CHD, 24-47 hours, non sudden, Death, CHD, 48 hours or more, non sudden, Death, CVA, Death, Cancer, Death, cause unknown, Death, other CVD, Death, other causes, Definite CVA at exam 1, but questionable type, IC, first episode only, IC, questionable IC at exam 1, Intracerebral hemorrhage, MI recognized, with diagnostic ECG, MI recognized, without diagnostic ECG, with autopsy evidence, new event (see also code 9), MI recognized, without diagnostic ECG, with enzymes and history, MI unrecognized, not silent, MI unrecognized, silent, Other CVA, Questionable CVA at exam 1, Questionable MI at exam 1, Subarachnoid hemorrhage, TIA (Transient Ischemic Attack) only the 1st TIA is coded, TIA with positive imaging + * _phs000007.v30.pht000309.v13.phv00036471.v12_ + * dbGap name: **DATE** + * dbGap desc: **Date of Event** + * dbGap table: **vr_soe_2020_a_1340s** + * No permissible values listed in PIC-SURE data dictionary + * _phs000007.v30.pht003099.v5.phv00177930.v5_ + * dbGap name: **age1** + * dbGap desc: **Age at Exam 1** + * dbGap table: **vr_dates_2019_a_1175s** + * No permissible values listed in PIC-SURE data dictionary + * _phs000007.v30.pht003316.v7.phv00190817.v7_ + * dbGap name: **cvd** + * dbGap desc: **Cardiovascular Disease (CVD) status** + * dbGap table: **vr_survcvd_2019_a_1334s** + * PIC-SURE permissible values: No, Yes + * _phs000007.v30.pht003316.v7.phv00190823.v7_ + * dbGap name: **cvddate** + * dbGap desc: **Date of Cardiovascular Disease (CVD) status** + * dbGap table: **vr_survcvd_2019_a_1334s** + * No permissible values listed in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -810,13 +1066,41 @@ * ### atherosclerosis_events_incident/mi_incident_1 -- **WHI Women's Health Initiative**: * 7 component_study_variables - * _phs000200.v11.pht000998.v6.phv00078436.v6_. dbGap Name: **F2DAYS**, Desc: **F2 Days since randomization**, Table: **f2_rel1**. - * _phs000200.v11.pht000998.v6.phv00078437.v6_. dbGap Name: **AGE**, Desc: **Age at screening**, Table: **f2_rel1**. - * _phs000200.v11.pht003395.v3.phv00192302.v3_. dbGap Name: **EXT2MRC**, Desc: **Extension 2 MRC Participant**, Table: **ext_rel2**. - * _phs000200.v11.pht003407.v3.phv00193169.v3_. dbGap Name: **MI**, Desc: **Clinical MI**, Table: **outc_ct_os_rel4**. - * _phs000200.v11.pht003407.v3.phv00193170.v3_. dbGap Name: **MIDY**, Desc: **Days enrollment to Clinical MI**, Table: **outc_ct_os_rel4**. - * _phs000200.v11.pht003407.v3.phv00193504.v3_. dbGap Name: **ENDEXT1DY**, Desc: **Days enrollment to end of Ext1 followup**, Table: **outc_ct_os_rel4**. - * _phs000200.v11.pht003407.v3.phv00193505.v3_. dbGap Name: **ENDFOLLOWDY**, Desc: **Days enrollment to end of followup**, Table: **outc_ct_os_rel4**. + * _phs000200.v11.pht000998.v6.phv00078436.v6_ + * dbGap name: **F2DAYS** + * dbGap desc: **F2 Days since randomization** + * dbGap table: **f2_rel1** + * No permissible values listed in PIC-SURE data dictionary + * _phs000200.v11.pht000998.v6.phv00078437.v6_ + * dbGap name: **AGE** + * dbGap desc: **Age at screening** + * dbGap table: **f2_rel1** + * No permissible values listed in PIC-SURE data dictionary + * _phs000200.v11.pht003395.v3.phv00192302.v3_ + * dbGap name: **EXT2MRC** + * dbGap desc: **Extension 2 MRC Participant** + * dbGap table: **ext_rel2** + * PIC-SURE permissible values: No, Yes + * _phs000200.v11.pht003407.v3.phv00193169.v3_ + * dbGap name: **MI** + * dbGap desc: **Clinical MI** + * dbGap table: **outc_ct_os_rel4** + * PIC-SURE permissible values: No, Yes + * _phs000200.v11.pht003407.v3.phv00193170.v3_ + * dbGap name: **MIDY** + * dbGap desc: **Days enrollment to Clinical MI** + * dbGap table: **outc_ct_os_rel4** + * No permissible values listed in PIC-SURE data dictionary + * _phs000200.v11.pht003407.v3.phv00193504.v3_ + * dbGap name: **ENDEXT1DY** + * dbGap desc: **Days enrollment to end of Ext1 followup** + * dbGap table: **outc_ct_os_rel4** + * No permissible values listed in PIC-SURE data dictionary + * _phs000200.v11.pht003407.v3.phv00193505.v3_ + * dbGap name: **ENDFOLLOWDY** + * dbGap desc: **Days enrollment to end of followup** + * dbGap table: **outc_ct_os_rel4** + * No permissible values listed in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -866,11 +1150,31 @@ * ### atherosclerosis_events_incident/pad_incident_1 -- **FHS Framingham Cohort**: * 5 component_study_variables - * _phs000007.v30.pht000309.v13.phv00036469.v12_. dbGap Name: **EVENT**, Desc: **Event Number**, Table: **vr_soe_2020_a_1340s**. - * _phs000007.v30.pht000309.v13.phv00036471.v12_. dbGap Name: **DATE**, Desc: **Date of Event**, Table: **vr_soe_2020_a_1340s**. - * _phs000007.v30.pht003099.v5.phv00177930.v5_. dbGap Name: **age1**, Desc: **Age at Exam 1**, Table: **vr_dates_2019_a_1175s**. - * _phs000007.v30.pht003316.v7.phv00190817.v7_. dbGap Name: **cvd**, Desc: **Cardiovascular Disease (CVD) status**, Table: **vr_survcvd_2019_a_1334s**. - * _phs000007.v30.pht003316.v7.phv00190823.v7_. dbGap Name: **cvddate**, Desc: **Date of Cardiovascular Disease (CVD) status**, Table: **vr_survcvd_2019_a_1334s**. + * _phs000007.v30.pht000309.v13.phv00036469.v12_ + * dbGap name: **EVENT** + * dbGap desc: **Event Number** + * dbGap table: **vr_soe_2020_a_1340s** + * PIC-SURE permissible values: ABI (Atherothrombotic Infarction of brain), AP, first episode only, Acute MI by autopsy, previously coded as 1 or 2, CHF, hospitalized, CHF, not hospitalized, diagnosed on basis of on exam or MD notes, CHF, questionable CHF at exam 1, CI, definite by both history and ECG, CVA, definite CVA, type unknown, Cerebral embolism, Death, CHD sudden, within 1 hour, Death, CHD, 1-23 hours, non sudden, Death, CHD, 24-47 hours, non sudden, Death, CHD, 48 hours or more, non sudden, Death, CVA, Death, Cancer, Death, cause unknown, Death, other CVD, Death, other causes, Definite CVA at exam 1, but questionable type, IC, first episode only, IC, questionable IC at exam 1, Intracerebral hemorrhage, MI recognized, with diagnostic ECG, MI recognized, without diagnostic ECG, with autopsy evidence, new event (see also code 9), MI recognized, without diagnostic ECG, with enzymes and history, MI unrecognized, not silent, MI unrecognized, silent, Other CVA, Questionable CVA at exam 1, Questionable MI at exam 1, Subarachnoid hemorrhage, TIA (Transient Ischemic Attack) only the 1st TIA is coded, TIA with positive imaging + * _phs000007.v30.pht000309.v13.phv00036471.v12_ + * dbGap name: **DATE** + * dbGap desc: **Date of Event** + * dbGap table: **vr_soe_2020_a_1340s** + * No permissible values listed in PIC-SURE data dictionary + * _phs000007.v30.pht003099.v5.phv00177930.v5_ + * dbGap name: **age1** + * dbGap desc: **Age at Exam 1** + * dbGap table: **vr_dates_2019_a_1175s** + * No permissible values listed in PIC-SURE data dictionary + * _phs000007.v30.pht003316.v7.phv00190817.v7_ + * dbGap name: **cvd** + * dbGap desc: **Cardiovascular Disease (CVD) status** + * dbGap table: **vr_survcvd_2019_a_1334s** + * PIC-SURE permissible values: No, Yes + * _phs000007.v30.pht003316.v7.phv00190823.v7_ + * dbGap name: **cvddate** + * dbGap desc: **Date of Cardiovascular Disease (CVD) status** + * dbGap table: **vr_survcvd_2019_a_1334s** + * No permissible values listed in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -959,20 +1263,76 @@ * ### atherosclerosis_events_incident/pad_incident_1 -- **WHI Women's Health Initiative**: * 14 component_study_variables - * _phs000200.v11.pht000998.v6.phv00078436.v6_. dbGap Name: **F2DAYS**, Desc: **F2 Days since randomization**, Table: **f2_rel1**. - * _phs000200.v11.pht000998.v6.phv00078437.v6_. dbGap Name: **AGE**, Desc: **Age at screening**, Table: **f2_rel1**. - * _phs000200.v11.pht003395.v3.phv00192302.v3_. dbGap Name: **EXT2MRC**, Desc: **Extension 2 MRC Participant**, Table: **ext_rel2**. - * _phs000200.v11.pht003406.v3.phv00193101.v3_. dbGap Name: **PADDX**, Desc: **PAD diagnosis**, Table: **outc_cardio_rel4**. - * _phs000200.v11.pht003406.v3.phv00193102.v3_. dbGap Name: **PADPLAQ**, Desc: **Ultrasonography or angiography**, Table: **outc_cardio_rel4**. - * _phs000200.v11.pht003406.v3.phv00193103.v3_. dbGap Name: **PADABDOP**, Desc: **No Doppler pulse in vessels**, Table: **outc_cardio_rel4**. - * _phs000200.v11.pht003406.v3.phv00193104.v3_. dbGap Name: **PADEXER**, Desc: **Positive exercise test**, Table: **outc_cardio_rel4**. - * _phs000200.v11.pht003406.v3.phv00193105.v3_. dbGap Name: **PADSURG**, Desc: **Surgery, angioplasty or thromb**, Table: **outc_cardio_rel4**. - * _phs000200.v11.pht003406.v3.phv00193106.v3_. dbGap Name: **PADAMP**, Desc: **PAD Amputation of one or more toes**, Table: **outc_cardio_rel4**. - * _phs000200.v11.pht003406.v3.phv00193107.v3_. dbGap Name: **PADLEG**, Desc: **Exertional leg pain**, Table: **outc_cardio_rel4**. - * _phs000200.v11.pht003407.v3.phv00193190.v3_. dbGap Name: **PERIPH**, Desc: **PAD**, Table: **outc_ct_os_rel4**. - * _phs000200.v11.pht003407.v3.phv00193191.v3_. dbGap Name: **PERIPHDY**, Desc: **Days enrollment to PAD**, Table: **outc_ct_os_rel4**. - * _phs000200.v11.pht003407.v3.phv00193504.v3_. dbGap Name: **ENDEXT1DY**, Desc: **Days enrollment to end of Ext1 followup**, Table: **outc_ct_os_rel4**. - * _phs000200.v11.pht003407.v3.phv00193505.v3_. dbGap Name: **ENDFOLLOWDY**, Desc: **Days enrollment to end of followup**, Table: **outc_ct_os_rel4**. + * _phs000200.v11.pht000998.v6.phv00078436.v6_ + * dbGap name: **F2DAYS** + * dbGap desc: **F2 Days since randomization** + * dbGap table: **f2_rel1** + * No permissible values listed in PIC-SURE data dictionary + * _phs000200.v11.pht000998.v6.phv00078437.v6_ + * dbGap name: **AGE** + * dbGap desc: **Age at screening** + * dbGap table: **f2_rel1** + * No permissible values listed in PIC-SURE data dictionary + * _phs000200.v11.pht003395.v3.phv00192302.v3_ + * dbGap name: **EXT2MRC** + * dbGap desc: **Extension 2 MRC Participant** + * dbGap table: **ext_rel2** + * PIC-SURE permissible values: No, Yes + * _phs000200.v11.pht003406.v3.phv00193101.v3_ + * dbGap name: **PADDX** + * dbGap desc: **PAD diagnosis** + * dbGap table: **outc_cardio_rel4** + * PIC-SURE permissible values: Abdominal aortic anuerysm (AAA), Arterial embolism and/or thrombosis of the lower extremities, Atherosclerosis of arteries of the lower extremities, Lower extremity claudication + * _phs000200.v11.pht003406.v3.phv00193102.v3_ + * dbGap name: **PADPLAQ** + * dbGap desc: **Ultrasonography or angiography** + * dbGap table: **outc_cardio_rel4** + * PIC-SURE permissible values: No, Yes + * _phs000200.v11.pht003406.v3.phv00193103.v3_ + * dbGap name: **PADABDOP** + * dbGap desc: **No Doppler pulse in vessels** + * dbGap table: **outc_cardio_rel4** + * PIC-SURE permissible values: No, Yes + * _phs000200.v11.pht003406.v3.phv00193104.v3_ + * dbGap name: **PADEXER** + * dbGap desc: **Positive exercise test** + * dbGap table: **outc_cardio_rel4** + * PIC-SURE permissible values: No, Yes + * _phs000200.v11.pht003406.v3.phv00193105.v3_ + * dbGap name: **PADSURG** + * dbGap desc: **Surgery, angioplasty or thromb** + * dbGap table: **outc_cardio_rel4** + * PIC-SURE permissible values: No, Yes + * _phs000200.v11.pht003406.v3.phv00193106.v3_ + * dbGap name: **PADAMP** + * dbGap desc: **PAD Amputation of one or more toes** + * dbGap table: **outc_cardio_rel4** + * PIC-SURE permissible values: No, Yes + * _phs000200.v11.pht003406.v3.phv00193107.v3_ + * dbGap name: **PADLEG** + * dbGap desc: **Exertional leg pain** + * dbGap table: **outc_cardio_rel4** + * PIC-SURE permissible values: No, Yes + * _phs000200.v11.pht003407.v3.phv00193190.v3_ + * dbGap name: **PERIPH** + * dbGap desc: **PAD** + * dbGap table: **outc_ct_os_rel4** + * PIC-SURE permissible values: No, Yes + * _phs000200.v11.pht003407.v3.phv00193191.v3_ + * dbGap name: **PERIPHDY** + * dbGap desc: **Days enrollment to PAD** + * dbGap table: **outc_ct_os_rel4** + * No permissible values listed in PIC-SURE data dictionary + * _phs000200.v11.pht003407.v3.phv00193504.v3_ + * dbGap name: **ENDEXT1DY** + * dbGap desc: **Days enrollment to end of Ext1 followup** + * dbGap table: **outc_ct_os_rel4** + * No permissible values listed in PIC-SURE data dictionary + * _phs000200.v11.pht003407.v3.phv00193505.v3_ + * dbGap name: **ENDFOLLOWDY** + * dbGap desc: **Days enrollment to end of followup** + * dbGap table: **outc_ct_os_rel4** + * No permissible values listed in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ diff --git a/resources/human-readable-harmonized-variable-documentation/generated-doc-pages/atherosclerosis_events_prior.md b/resources/human-readable-harmonized-variable-documentation/generated-doc-pages/atherosclerosis_events_prior.md index 53c09c8..29e1205 100644 --- a/resources/human-readable-harmonized-variable-documentation/generated-doc-pages/atherosclerosis_events_prior.md +++ b/resources/human-readable-harmonized-variable-documentation/generated-doc-pages/atherosclerosis_events_prior.md @@ -48,8 +48,16 @@ * ### atherosclerosis_events_prior/angina_prior_1 -- **CHS Cardiovascular Health Study (CHS) Cohort: an NHLBI-funded observational study of risk factors for cardiovascular disease in adults 65 years or older**: * 2 component_study_variables - * _phs000287.v6.pht001452.v1.phv00100487.v1_. dbGap Name: **AGEBL**, Desc: **CALCULATED AGE AT BASELINE**, Table: **BASEBOTH**. - * _phs000287.v6.pht001452.v1.phv00100504.v1_. dbGap Name: **ANBLMOD**, Desc: **ANG MODIFIED BL STAT**, Table: **BASEBOTH**. + * _phs000287.v6.pht001452.v1.phv00100487.v1_ + * dbGap name: **AGEBL** + * dbGap desc: **CALCULATED AGE AT BASELINE** + * dbGap table: **BASEBOTH** + * No permissible values listed in PIC-SURE data dictionary + * _phs000287.v6.pht001452.v1.phv00100504.v1_ + * dbGap name: **ANBLMOD** + * dbGap desc: **ANG MODIFIED BL STAT** + * dbGap table: **BASEBOTH** + * PIC-SURE permissible values: Incident, Prevalent * **Function:** ```r harmonize <- function(phen_list){ @@ -64,8 +72,12 @@ * ### atherosclerosis_events_prior/angina_prior_1 -- **COPDGene **: * 2 component_study_variables - * _phs000179.v5.pht002239.v4.phv00159608.v4_. No dbGap metadata available. - * _phs000179.v5.pht002239.v4.phv00159836.v4_. No dbGap metadata available. + * _phs000179.v5.pht002239.v4.phv00159608.v4_ + * No dbGap metadata available + * PIC-SURE permissible values: No, Yes + * _phs000179.v5.pht002239.v4.phv00159836.v4_ + * No dbGap metadata available + * No permissible values listed in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -88,11 +100,31 @@ * ### atherosclerosis_events_prior/angina_prior_1 -- **FHS Framingham Cohort**: * 5 component_study_variables - * _phs000007.v30.pht000309.v13.phv00036469.v12_. dbGap Name: **EVENT**, Desc: **Event Number**, Table: **vr_soe_2020_a_1340s**. - * _phs000007.v30.pht000309.v13.phv00036471.v12_. dbGap Name: **DATE**, Desc: **Date of Event**, Table: **vr_soe_2020_a_1340s**. - * _phs000007.v30.pht003099.v5.phv00177930.v5_. dbGap Name: **age1**, Desc: **Age at Exam 1**, Table: **vr_dates_2019_a_1175s**. - * _phs000007.v30.pht003316.v7.phv00190817.v7_. dbGap Name: **cvd**, Desc: **Cardiovascular Disease (CVD) status**, Table: **vr_survcvd_2019_a_1334s**. - * _phs000007.v30.pht003316.v7.phv00190823.v7_. dbGap Name: **cvddate**, Desc: **Date of Cardiovascular Disease (CVD) status**, Table: **vr_survcvd_2019_a_1334s**. + * _phs000007.v30.pht000309.v13.phv00036469.v12_ + * dbGap name: **EVENT** + * dbGap desc: **Event Number** + * dbGap table: **vr_soe_2020_a_1340s** + * PIC-SURE permissible values: ABI (Atherothrombotic Infarction of brain), AP, first episode only, Acute MI by autopsy, previously coded as 1 or 2, CHF, hospitalized, CHF, not hospitalized, diagnosed on basis of on exam or MD notes, CHF, questionable CHF at exam 1, CI, definite by both history and ECG, CVA, definite CVA, type unknown, Cerebral embolism, Death, CHD sudden, within 1 hour, Death, CHD, 1-23 hours, non sudden, Death, CHD, 24-47 hours, non sudden, Death, CHD, 48 hours or more, non sudden, Death, CVA, Death, Cancer, Death, cause unknown, Death, other CVD, Death, other causes, Definite CVA at exam 1, but questionable type, IC, first episode only, IC, questionable IC at exam 1, Intracerebral hemorrhage, MI recognized, with diagnostic ECG, MI recognized, without diagnostic ECG, with autopsy evidence, new event (see also code 9), MI recognized, without diagnostic ECG, with enzymes and history, MI unrecognized, not silent, MI unrecognized, silent, Other CVA, Questionable CVA at exam 1, Questionable MI at exam 1, Subarachnoid hemorrhage, TIA (Transient Ischemic Attack) only the 1st TIA is coded, TIA with positive imaging + * _phs000007.v30.pht000309.v13.phv00036471.v12_ + * dbGap name: **DATE** + * dbGap desc: **Date of Event** + * dbGap table: **vr_soe_2020_a_1340s** + * No permissible values listed in PIC-SURE data dictionary + * _phs000007.v30.pht003099.v5.phv00177930.v5_ + * dbGap name: **age1** + * dbGap desc: **Age at Exam 1** + * dbGap table: **vr_dates_2019_a_1175s** + * No permissible values listed in PIC-SURE data dictionary + * _phs000007.v30.pht003316.v7.phv00190817.v7_ + * dbGap name: **cvd** + * dbGap desc: **Cardiovascular Disease (CVD) status** + * dbGap table: **vr_survcvd_2019_a_1334s** + * PIC-SURE permissible values: No, Yes + * _phs000007.v30.pht003316.v7.phv00190823.v7_ + * dbGap name: **cvddate** + * dbGap desc: **Date of Cardiovascular Disease (CVD) status** + * dbGap table: **vr_survcvd_2019_a_1334s** + * No permissible values listed in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -180,7 +212,11 @@ * ### atherosclerosis_events_prior/angina_prior_1 -- **MESA Multi-Ethnic Study of Atherosclerosis (MESA) Cohort**: * 1 component_study_variables - * _phs000209.v13.pht001116.v10.phv00084442.v3_. dbGap Name: **age1c**, Desc: **AGE**, Table: **MESA_Exam1Main**. + * _phs000209.v13.pht001116.v10.phv00084442.v3_ + * dbGap name: **age1c** + * dbGap desc: **AGE** + * dbGap table: **MESA_Exam1Main** + * No permissible values listed in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -193,10 +229,26 @@ * ### atherosclerosis_events_prior/angina_prior_1 -- **WHI Women's Health Initiative**: * 4 component_study_variables - * _phs000200.v11.pht000998.v6.phv00078436.v6_. dbGap Name: **F2DAYS**, Desc: **F2 Days since randomization**, Table: **f2_rel1**. - * _phs000200.v11.pht000998.v6.phv00078437.v6_. dbGap Name: **AGE**, Desc: **Age at screening**, Table: **f2_rel1**. - * _phs000200.v11.pht000999.v6.phv00078507.v6_. dbGap Name: **F30DAYS**, Desc: **F30 Days since randomization/enrollment**, Table: **f30_rel2**. - * _phs000200.v11.pht000999.v6.phv00078560.v6_. dbGap Name: **ANGINA**, Desc: **Angina ever**, Table: **f30_rel2**. + * _phs000200.v11.pht000998.v6.phv00078436.v6_ + * dbGap name: **F2DAYS** + * dbGap desc: **F2 Days since randomization** + * dbGap table: **f2_rel1** + * No permissible values listed in PIC-SURE data dictionary + * _phs000200.v11.pht000998.v6.phv00078437.v6_ + * dbGap name: **AGE** + * dbGap desc: **Age at screening** + * dbGap table: **f2_rel1** + * No permissible values listed in PIC-SURE data dictionary + * _phs000200.v11.pht000999.v6.phv00078507.v6_ + * dbGap name: **F30DAYS** + * dbGap desc: **F30 Days since randomization/enrollment** + * dbGap table: **f30_rel2** + * No permissible values listed in PIC-SURE data dictionary + * _phs000200.v11.pht000999.v6.phv00078560.v6_ + * dbGap name: **ANGINA** + * dbGap desc: **Angina ever** + * dbGap table: **f30_rel2** + * PIC-SURE permissible values: No, Yes * **Function:** ```r harmonize <- function(phen_list){ @@ -256,10 +308,26 @@ * ### atherosclerosis_events_prior/cabg_prior_1 -- **ARIC Atherosclerosis Risk in Communities (ARIC) Cohort**: * 4 component_study_variables - * _phs000280.v5.pht004063.v2.phv00204712.v1_. dbGap Name: **V1AGE01**, Desc: **Age at visit 1 [Cohort. Visit 1]**, Table: **DERIVE13**. - * _phs000280.v5.pht004143.v2.phv00208845.v1_. dbGap Name: **PHEA06**, Desc: **[Invasive procedures]. Have you ever had surgery on your heart, or on the arteries of your neck or legs, excluding surgery for vericose veins? Q6 [Physical Examination Form. PHEA. Visit 1]**, Table: **PHEA**. - * _phs000280.v5.pht004143.v2.phv00208846.v1_. dbGap Name: **PHEA07A**, Desc: **[Invasive procedures]. Have you ever had surgery on your heart, or on the arteries of your neck or legs, excluding surgery for vericose veins? Coronary bypass. Q7a [Physical Examination Form. PHEA. Visit 1]**, Table: **PHEA**. - * _phs000280.v5.pht004143.v2.phv00208853.v1_. dbGap Name: **PHEA08**, Desc: **[Invasive procedures]. Have you ever had a balloon angioplasty on the arteries of your heart or legs? Q8 [Physical Examination Form. PHEA. Visit 1]**, Table: **PHEA**. + * _phs000280.v5.pht004063.v2.phv00204712.v1_ + * dbGap name: **V1AGE01** + * dbGap desc: **Age at visit 1 [Cohort. Visit 1]** + * dbGap table: **DERIVE13** + * varId _phv00204712_ not found in PIC-SURE data dictionary + * _phs000280.v5.pht004143.v2.phv00208845.v1_ + * dbGap name: **PHEA06** + * dbGap desc: **[Invasive procedures]. Have you ever had surgery on your heart, or on the arteries of your neck or legs, excluding surgery for vericose veins? Q6 [Physical Examination Form. PHEA. Visit 1]** + * dbGap table: **PHEA** + * varId _phv00208845_ not found in PIC-SURE data dictionary + * _phs000280.v5.pht004143.v2.phv00208846.v1_ + * dbGap name: **PHEA07A** + * dbGap desc: **[Invasive procedures]. Have you ever had surgery on your heart, or on the arteries of your neck or legs, excluding surgery for vericose veins? Coronary bypass. Q7a [Physical Examination Form. PHEA. Visit 1]** + * dbGap table: **PHEA** + * varId _phv00208846_ not found in PIC-SURE data dictionary + * _phs000280.v5.pht004143.v2.phv00208853.v1_ + * dbGap name: **PHEA08** + * dbGap desc: **[Invasive procedures]. Have you ever had a balloon angioplasty on the arteries of your heart or legs? Q8 [Physical Examination Form. PHEA. Visit 1]** + * dbGap table: **PHEA** + * varId _phv00208853_ not found in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -302,8 +370,16 @@ * ### atherosclerosis_events_prior/cabg_prior_1 -- **CHS Cardiovascular Health Study (CHS) Cohort: an NHLBI-funded observational study of risk factors for cardiovascular disease in adults 65 years or older**: * 2 component_study_variables - * _phs000287.v6.pht001452.v1.phv00100487.v1_. dbGap Name: **AGEBL**, Desc: **CALCULATED AGE AT BASELINE**, Table: **BASEBOTH**. - * _phs000287.v6.pht001464.v1.phv00100785.v1_. dbGap Name: **BPSSURBL**, Desc: **CORONARY BYPASS SURGERY AT BL**, Table: **EVENT_SUMMARY**. + * _phs000287.v6.pht001452.v1.phv00100487.v1_ + * dbGap name: **AGEBL** + * dbGap desc: **CALCULATED AGE AT BASELINE** + * dbGap table: **BASEBOTH** + * No permissible values listed in PIC-SURE data dictionary + * _phs000287.v6.pht001464.v1.phv00100785.v1_ + * dbGap name: **BPSSURBL** + * dbGap desc: **CORONARY BYPASS SURGERY AT BL** + * dbGap table: **EVENT_SUMMARY** + * PIC-SURE permissible values: NO, YES * **Function:** ```r harmonize <- function(phen_list){ @@ -321,8 +397,12 @@ * ### atherosclerosis_events_prior/cabg_prior_1 -- **COPDGene **: * 2 component_study_variables - * _phs000179.v5.pht002239.v4.phv00159631.v4_. No dbGap metadata available. - * _phs000179.v5.pht002239.v4.phv00159836.v4_. No dbGap metadata available. + * _phs000179.v5.pht002239.v4.phv00159631.v4_ + * No dbGap metadata available + * PIC-SURE permissible values: No, Yes + * _phs000179.v5.pht002239.v4.phv00159836.v4_ + * No dbGap metadata available + * No permissible values listed in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -337,11 +417,31 @@ * ### atherosclerosis_events_prior/cabg_prior_1 -- **FHS Framingham Cohort**: * 5 component_study_variables - * _phs000007.v30.pht000389.v10.phv00054697.v8_. dbGap Name: **procdate**, Desc: **Date of cardiovascular procedure**, Table: **vr_cvdproc_2020_a_1313s**. - * _phs000007.v30.pht000389.v10.phv00163410.v7_. dbGap Name: **vessel**, Desc: **Coronary Artery Bypass Graft (CABG) - Number of vessels bypassed - PROCNUM = 141**, Table: **vr_cvdproc_2020_a_1313s**. - * _phs000007.v30.pht003099.v5.phv00177930.v5_. dbGap Name: **age1**, Desc: **Age at Exam 1**, Table: **vr_dates_2019_a_1175s**. - * _phs000007.v30.pht003316.v7.phv00190817.v7_. dbGap Name: **cvd**, Desc: **Cardiovascular Disease (CVD) status**, Table: **vr_survcvd_2019_a_1334s**. - * _phs000007.v30.pht003316.v7.phv00190823.v7_. dbGap Name: **cvddate**, Desc: **Date of Cardiovascular Disease (CVD) status**, Table: **vr_survcvd_2019_a_1334s**. + * _phs000007.v30.pht000389.v10.phv00054697.v8_ + * dbGap name: **procdate** + * dbGap desc: **Date of cardiovascular procedure** + * dbGap table: **vr_cvdproc_2020_a_1313s** + * No permissible values listed in PIC-SURE data dictionary + * _phs000007.v30.pht000389.v10.phv00163410.v7_ + * dbGap name: **vessel** + * dbGap desc: **Coronary Artery Bypass Graft (CABG) - Number of vessels bypassed - PROCNUM = 141** + * dbGap table: **vr_cvdproc_2020_a_1313s** + * PIC-SURE permissible values: CABG Procedure not done, Five (5) vessels bypassed, Four (4) vessels bypassed, One (1) vessel bypassed, Seven (7) vessels bypassed, Six (6) vessels bypassed, Three (3) vessels bypassed, Two (2) vessels bypassed + * _phs000007.v30.pht003099.v5.phv00177930.v5_ + * dbGap name: **age1** + * dbGap desc: **Age at Exam 1** + * dbGap table: **vr_dates_2019_a_1175s** + * No permissible values listed in PIC-SURE data dictionary + * _phs000007.v30.pht003316.v7.phv00190817.v7_ + * dbGap name: **cvd** + * dbGap desc: **Cardiovascular Disease (CVD) status** + * dbGap table: **vr_survcvd_2019_a_1334s** + * PIC-SURE permissible values: No, Yes + * _phs000007.v30.pht003316.v7.phv00190823.v7_ + * dbGap name: **cvddate** + * dbGap desc: **Date of Cardiovascular Disease (CVD) status** + * dbGap table: **vr_survcvd_2019_a_1334s** + * No permissible values listed in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -417,12 +517,34 @@ * ### atherosclerosis_events_prior/cabg_prior_1 -- **JHS Jackson Heart Study (JHS) Cohort**: * 6 component_study_variables - * _phs000286.v5.pht001949.v1.phv00126009.v1_. No dbGap metadata available. - * _phs000286.v5.pht001963.v1.phv00127727.v1_. dbGap Name: **MHXA51**, Desc: **Q51. F. Invasive procedures. Ever had surgery on heart, arteries of neck or legs? [Visit 1] [Medical History Form, MHX]**, Table: **mhxa**. - * _phs000286.v5.pht001963.v1.phv00127728.v1_. dbGap Name: **MHXA52A**, Desc: **Q52a. F. Invasive procedures. Did you have a coronary bypass? [Visit 1] [Medical History Form, MHX]**, Table: **mhxa**. - * _phs000286.v5.pht001963.v1.phv00127731.v1_. dbGap Name: **MHXA52C**, Desc: **Q52c. F. Invasive procedures. Have you had carotid endarterectomy? [Visit 1] [Medical History Form, MHX]**, Table: **mhxa**. - * _phs000286.v5.pht001963.v1.phv00127733.v1_. dbGap Name: **MHXA52E1**, Desc: **Q52e1. F. Invasive procedures. Had other revascularization or bypass? [Visit 1] [Medical History Form, MHX]**, Table: **mhxa**. - * _phs000286.v5.pht001963.v1.phv00127740.v1_. dbGap Name: **MHXA55A**, Desc: **Q55a. F. Invasive procedures. Ever had heart catheterization? [Visit 1] [Medical History Form, MHX]**, Table: **mhxa**. + * _phs000286.v5.pht001949.v1.phv00126009.v1_ + * No dbGap metadata available + * varId _phv00126009_ not found in PIC-SURE data dictionary + * _phs000286.v5.pht001963.v1.phv00127727.v1_ + * dbGap name: **MHXA51** + * dbGap desc: **Q51. F. Invasive procedures. Ever had surgery on heart, arteries of neck or legs? [Visit 1] [Medical History Form, MHX]** + * dbGap table: **mhxa** + * varId _phv00127727_ not found in PIC-SURE data dictionary + * _phs000286.v5.pht001963.v1.phv00127728.v1_ + * dbGap name: **MHXA52A** + * dbGap desc: **Q52a. F. Invasive procedures. Did you have a coronary bypass? [Visit 1] [Medical History Form, MHX]** + * dbGap table: **mhxa** + * varId _phv00127728_ not found in PIC-SURE data dictionary + * _phs000286.v5.pht001963.v1.phv00127731.v1_ + * dbGap name: **MHXA52C** + * dbGap desc: **Q52c. F. Invasive procedures. Have you had carotid endarterectomy? [Visit 1] [Medical History Form, MHX]** + * dbGap table: **mhxa** + * varId _phv00127731_ not found in PIC-SURE data dictionary + * _phs000286.v5.pht001963.v1.phv00127733.v1_ + * dbGap name: **MHXA52E1** + * dbGap desc: **Q52e1. F. Invasive procedures. Had other revascularization or bypass? [Visit 1] [Medical History Form, MHX]** + * dbGap table: **mhxa** + * varId _phv00127733_ not found in PIC-SURE data dictionary + * _phs000286.v5.pht001963.v1.phv00127740.v1_ + * dbGap name: **MHXA55A** + * dbGap desc: **Q55a. F. Invasive procedures. Ever had heart catheterization? [Visit 1] [Medical History Form, MHX]** + * dbGap table: **mhxa** + * varId _phv00127740_ not found in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -463,7 +585,11 @@ * ### atherosclerosis_events_prior/cabg_prior_1 -- **MESA Multi-Ethnic Study of Atherosclerosis (MESA) Cohort**: * 1 component_study_variables - * _phs000209.v13.pht001116.v10.phv00084442.v3_. dbGap Name: **age1c**, Desc: **AGE**, Table: **MESA_Exam1Main**. + * _phs000209.v13.pht001116.v10.phv00084442.v3_ + * dbGap name: **age1c** + * dbGap desc: **AGE** + * dbGap table: **MESA_Exam1Main** + * No permissible values listed in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -476,10 +602,26 @@ * ### atherosclerosis_events_prior/cabg_prior_1 -- **WHI Women's Health Initiative**: * 4 component_study_variables - * _phs000200.v11.pht000998.v6.phv00078436.v6_. dbGap Name: **F2DAYS**, Desc: **F2 Days since randomization**, Table: **f2_rel1**. - * _phs000200.v11.pht000998.v6.phv00078437.v6_. dbGap Name: **AGE**, Desc: **Age at screening**, Table: **f2_rel1**. - * _phs000200.v11.pht000999.v6.phv00078507.v6_. dbGap Name: **F30DAYS**, Desc: **F30 Days since randomization/enrollment**, Table: **f30_rel2**. - * _phs000200.v11.pht000999.v6.phv00078535.v6_. dbGap Name: **CABG**, Desc: **Coronary bypass surgery ever**, Table: **f30_rel2**. + * _phs000200.v11.pht000998.v6.phv00078436.v6_ + * dbGap name: **F2DAYS** + * dbGap desc: **F2 Days since randomization** + * dbGap table: **f2_rel1** + * No permissible values listed in PIC-SURE data dictionary + * _phs000200.v11.pht000998.v6.phv00078437.v6_ + * dbGap name: **AGE** + * dbGap desc: **Age at screening** + * dbGap table: **f2_rel1** + * No permissible values listed in PIC-SURE data dictionary + * _phs000200.v11.pht000999.v6.phv00078507.v6_ + * dbGap name: **F30DAYS** + * dbGap desc: **F30 Days since randomization/enrollment** + * dbGap table: **f30_rel2** + * No permissible values listed in PIC-SURE data dictionary + * _phs000200.v11.pht000999.v6.phv00078535.v6_ + * dbGap name: **CABG** + * dbGap desc: **Coronary bypass surgery ever** + * dbGap table: **f30_rel2** + * PIC-SURE permissible values: No, Yes * **Function:** ```r harmonize <- function(phen_list){ @@ -532,10 +674,26 @@ * ### atherosclerosis_events_prior/coronary_angioplasty_prior_1 -- **ARIC Atherosclerosis Risk in Communities (ARIC) Cohort**: * 4 component_study_variables - * _phs000280.v5.pht004063.v2.phv00204712.v1_. dbGap Name: **V1AGE01**, Desc: **Age at visit 1 [Cohort. Visit 1]**, Table: **DERIVE13**. - * _phs000280.v5.pht004143.v2.phv00208845.v1_. dbGap Name: **PHEA06**, Desc: **[Invasive procedures]. Have you ever had surgery on your heart, or on the arteries of your neck or legs, excluding surgery for vericose veins? Q6 [Physical Examination Form. PHEA. Visit 1]**, Table: **PHEA**. - * _phs000280.v5.pht004143.v2.phv00208853.v1_. dbGap Name: **PHEA08**, Desc: **[Invasive procedures]. Have you ever had a balloon angioplasty on the arteries of your heart or legs? Q8 [Physical Examination Form. PHEA. Visit 1]**, Table: **PHEA**. - * _phs000280.v5.pht004143.v2.phv00208854.v1_. dbGap Name: **PHEA09A**, Desc: **[Invasive procedures]. [Probe for type of procedure]. Angioplasty of coronary artery(ies)? Q9a [Physical Examination Form. PHEA. Visit 1]**, Table: **PHEA**. + * _phs000280.v5.pht004063.v2.phv00204712.v1_ + * dbGap name: **V1AGE01** + * dbGap desc: **Age at visit 1 [Cohort. Visit 1]** + * dbGap table: **DERIVE13** + * varId _phv00204712_ not found in PIC-SURE data dictionary + * _phs000280.v5.pht004143.v2.phv00208845.v1_ + * dbGap name: **PHEA06** + * dbGap desc: **[Invasive procedures]. Have you ever had surgery on your heart, or on the arteries of your neck or legs, excluding surgery for vericose veins? Q6 [Physical Examination Form. PHEA. Visit 1]** + * dbGap table: **PHEA** + * varId _phv00208845_ not found in PIC-SURE data dictionary + * _phs000280.v5.pht004143.v2.phv00208853.v1_ + * dbGap name: **PHEA08** + * dbGap desc: **[Invasive procedures]. Have you ever had a balloon angioplasty on the arteries of your heart or legs? Q8 [Physical Examination Form. PHEA. Visit 1]** + * dbGap table: **PHEA** + * varId _phv00208853_ not found in PIC-SURE data dictionary + * _phs000280.v5.pht004143.v2.phv00208854.v1_ + * dbGap name: **PHEA09A** + * dbGap desc: **[Invasive procedures]. [Probe for type of procedure]. Angioplasty of coronary artery(ies)? Q9a [Physical Examination Form. PHEA. Visit 1]** + * dbGap table: **PHEA** + * varId _phv00208854_ not found in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -575,8 +733,16 @@ * ### atherosclerosis_events_prior/coronary_angioplasty_prior_1 -- **CHS Cardiovascular Health Study (CHS) Cohort: an NHLBI-funded observational study of risk factors for cardiovascular disease in adults 65 years or older**: * 2 component_study_variables - * _phs000287.v6.pht001452.v1.phv00100322.v1_. dbGap Name: **CORART**, Desc: **CORONARY ARTERY ANGIOPLASTY**, Table: **BASEBOTH**. - * _phs000287.v6.pht001452.v1.phv00100487.v1_. dbGap Name: **AGEBL**, Desc: **CALCULATED AGE AT BASELINE**, Table: **BASEBOTH**. + * _phs000287.v6.pht001452.v1.phv00100322.v1_ + * dbGap name: **CORART** + * dbGap desc: **CORONARY ARTERY ANGIOPLASTY** + * dbGap table: **BASEBOTH** + * PIC-SURE permissible values: No, Yes + * _phs000287.v6.pht001452.v1.phv00100487.v1_ + * dbGap name: **AGEBL** + * dbGap desc: **CALCULATED AGE AT BASELINE** + * dbGap table: **BASEBOTH** + * No permissible values listed in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -592,8 +758,12 @@ * ### atherosclerosis_events_prior/coronary_angioplasty_prior_1 -- **COPDGene **: * 2 component_study_variables - * _phs000179.v5.pht002239.v4.phv00159632.v4_. No dbGap metadata available. - * _phs000179.v5.pht002239.v4.phv00159836.v4_. No dbGap metadata available. + * _phs000179.v5.pht002239.v4.phv00159632.v4_ + * No dbGap metadata available + * PIC-SURE permissible values: No, Yes + * _phs000179.v5.pht002239.v4.phv00159836.v4_ + * No dbGap metadata available + * No permissible values listed in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -609,12 +779,34 @@ * ### atherosclerosis_events_prior/coronary_angioplasty_prior_1 -- **JHS Jackson Heart Study (JHS) Cohort**: * 6 component_study_variables - * _phs000286.v5.pht001949.v1.phv00126009.v1_. No dbGap metadata available. - * _phs000286.v5.pht001963.v1.phv00127727.v1_. dbGap Name: **MHXA51**, Desc: **Q51. F. Invasive procedures. Ever had surgery on heart, arteries of neck or legs? [Visit 1] [Medical History Form, MHX]**, Table: **mhxa**. - * _phs000286.v5.pht001963.v1.phv00127731.v1_. dbGap Name: **MHXA52C**, Desc: **Q52c. F. Invasive procedures. Have you had carotid endarterectomy? [Visit 1] [Medical History Form, MHX]**, Table: **mhxa**. - * _phs000286.v5.pht001963.v1.phv00127733.v1_. dbGap Name: **MHXA52E1**, Desc: **Q52e1. F. Invasive procedures. Had other revascularization or bypass? [Visit 1] [Medical History Form, MHX]**, Table: **mhxa**. - * _phs000286.v5.pht001963.v1.phv00127737.v1_. dbGap Name: **MHXA54A**, Desc: **Q54a. F. Invasive procedures. Ever had angioplasty of coronary arteries? [Visit 1] [Medical History Form, MHX]**, Table: **mhxa**. - * _phs000286.v5.pht001963.v1.phv00127740.v1_. dbGap Name: **MHXA55A**, Desc: **Q55a. F. Invasive procedures. Ever had heart catheterization? [Visit 1] [Medical History Form, MHX]**, Table: **mhxa**. + * _phs000286.v5.pht001949.v1.phv00126009.v1_ + * No dbGap metadata available + * varId _phv00126009_ not found in PIC-SURE data dictionary + * _phs000286.v5.pht001963.v1.phv00127727.v1_ + * dbGap name: **MHXA51** + * dbGap desc: **Q51. F. Invasive procedures. Ever had surgery on heart, arteries of neck or legs? [Visit 1] [Medical History Form, MHX]** + * dbGap table: **mhxa** + * varId _phv00127727_ not found in PIC-SURE data dictionary + * _phs000286.v5.pht001963.v1.phv00127731.v1_ + * dbGap name: **MHXA52C** + * dbGap desc: **Q52c. F. Invasive procedures. Have you had carotid endarterectomy? [Visit 1] [Medical History Form, MHX]** + * dbGap table: **mhxa** + * varId _phv00127731_ not found in PIC-SURE data dictionary + * _phs000286.v5.pht001963.v1.phv00127733.v1_ + * dbGap name: **MHXA52E1** + * dbGap desc: **Q52e1. F. Invasive procedures. Had other revascularization or bypass? [Visit 1] [Medical History Form, MHX]** + * dbGap table: **mhxa** + * varId _phv00127733_ not found in PIC-SURE data dictionary + * _phs000286.v5.pht001963.v1.phv00127737.v1_ + * dbGap name: **MHXA54A** + * dbGap desc: **Q54a. F. Invasive procedures. Ever had angioplasty of coronary arteries? [Visit 1] [Medical History Form, MHX]** + * dbGap table: **mhxa** + * varId _phv00127737_ not found in PIC-SURE data dictionary + * _phs000286.v5.pht001963.v1.phv00127740.v1_ + * dbGap name: **MHXA55A** + * dbGap desc: **Q55a. F. Invasive procedures. Ever had heart catheterization? [Visit 1] [Medical History Form, MHX]** + * dbGap table: **mhxa** + * varId _phv00127740_ not found in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -651,7 +843,11 @@ * ### atherosclerosis_events_prior/coronary_angioplasty_prior_1 -- **MESA Multi-Ethnic Study of Atherosclerosis (MESA) Cohort**: * 1 component_study_variables - * _phs000209.v13.pht001116.v10.phv00084442.v3_. dbGap Name: **age1c**, Desc: **AGE**, Table: **MESA_Exam1Main**. + * _phs000209.v13.pht001116.v10.phv00084442.v3_ + * dbGap name: **age1c** + * dbGap desc: **AGE** + * dbGap table: **MESA_Exam1Main** + * No permissible values listed in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -664,10 +860,26 @@ * ### atherosclerosis_events_prior/coronary_angioplasty_prior_1 -- **WHI Women's Health Initiative**: * 4 component_study_variables - * _phs000200.v11.pht000998.v6.phv00078436.v6_. dbGap Name: **F2DAYS**, Desc: **F2 Days since randomization**, Table: **f2_rel1**. - * _phs000200.v11.pht000998.v6.phv00078437.v6_. dbGap Name: **AGE**, Desc: **Age at screening**, Table: **f2_rel1**. - * _phs000200.v11.pht000999.v6.phv00078507.v6_. dbGap Name: **F30DAYS**, Desc: **F30 Days since randomization/enrollment**, Table: **f30_rel2**. - * _phs000200.v11.pht000999.v6.phv00078536.v6_. dbGap Name: **PTCA**, Desc: **Angioplasty of coronary arteries ever**, Table: **f30_rel2**. + * _phs000200.v11.pht000998.v6.phv00078436.v6_ + * dbGap name: **F2DAYS** + * dbGap desc: **F2 Days since randomization** + * dbGap table: **f2_rel1** + * No permissible values listed in PIC-SURE data dictionary + * _phs000200.v11.pht000998.v6.phv00078437.v6_ + * dbGap name: **AGE** + * dbGap desc: **Age at screening** + * dbGap table: **f2_rel1** + * No permissible values listed in PIC-SURE data dictionary + * _phs000200.v11.pht000999.v6.phv00078507.v6_ + * dbGap name: **F30DAYS** + * dbGap desc: **F30 Days since randomization/enrollment** + * dbGap table: **f30_rel2** + * No permissible values listed in PIC-SURE data dictionary + * _phs000200.v11.pht000999.v6.phv00078536.v6_ + * dbGap name: **PTCA** + * dbGap desc: **Angioplasty of coronary arteries ever** + * dbGap table: **f30_rel2** + * PIC-SURE permissible values: No, Yes * **Function:** ```r harmonize <- function(phen_list){ @@ -748,8 +960,16 @@ * ### atherosclerosis_events_prior/mi_prior_1 -- **ARIC Atherosclerosis Risk in Communities (ARIC) Cohort**: * 2 component_study_variables - * _phs000280.v5.pht004063.v2.phv00204705.v1_. dbGap Name: **PREVMI05**, Desc: **Prevalent MI from ECG or medical history [Cohort. Visit 1]**, Table: **DERIVE13**. - * _phs000280.v5.pht004063.v2.phv00204712.v1_. dbGap Name: **V1AGE01**, Desc: **Age at visit 1 [Cohort. Visit 1]**, Table: **DERIVE13**. + * _phs000280.v5.pht004063.v2.phv00204705.v1_ + * dbGap name: **PREVMI05** + * dbGap desc: **Prevalent MI from ECG or medical history [Cohort. Visit 1]** + * dbGap table: **DERIVE13** + * varId _phv00204705_ not found in PIC-SURE data dictionary + * _phs000280.v5.pht004063.v2.phv00204712.v1_ + * dbGap name: **V1AGE01** + * dbGap desc: **Age at visit 1 [Cohort. Visit 1]** + * dbGap table: **DERIVE13** + * varId _phv00204712_ not found in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -777,8 +997,16 @@ * ### atherosclerosis_events_prior/mi_prior_1 -- **CHS Cardiovascular Health Study (CHS) Cohort: an NHLBI-funded observational study of risk factors for cardiovascular disease in adults 65 years or older**: * 2 component_study_variables - * _phs000287.v6.pht001452.v1.phv00100487.v1_. dbGap Name: **AGEBL**, Desc: **CALCULATED AGE AT BASELINE**, Table: **BASEBOTH**. - * _phs000287.v6.pht001452.v1.phv00100508.v1_. dbGap Name: **MIBLMOD**, Desc: **MI MODIFIED BL STAT**, Table: **BASEBOTH**. + * _phs000287.v6.pht001452.v1.phv00100487.v1_ + * dbGap name: **AGEBL** + * dbGap desc: **CALCULATED AGE AT BASELINE** + * dbGap table: **BASEBOTH** + * No permissible values listed in PIC-SURE data dictionary + * _phs000287.v6.pht001452.v1.phv00100508.v1_ + * dbGap name: **MIBLMOD** + * dbGap desc: **MI MODIFIED BL STAT** + * dbGap table: **BASEBOTH** + * PIC-SURE permissible values: Incident, Prevalent * **Function:** ```r harmonize <- function(phen_list){ @@ -794,8 +1022,12 @@ * ### atherosclerosis_events_prior/mi_prior_1 -- **COPDGene **: * 2 component_study_variables - * _phs000179.v5.pht002239.v4.phv00159615.v4_. No dbGap metadata available. - * _phs000179.v5.pht002239.v4.phv00159836.v4_. No dbGap metadata available. + * _phs000179.v5.pht002239.v4.phv00159615.v4_ + * No dbGap metadata available + * PIC-SURE permissible values: No, Yes + * _phs000179.v5.pht002239.v4.phv00159836.v4_ + * No dbGap metadata available + * No permissible values listed in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -818,11 +1050,31 @@ * ### atherosclerosis_events_prior/mi_prior_1 -- **FHS Framingham Cohort**: * 5 component_study_variables - * _phs000007.v30.pht000309.v13.phv00036469.v12_. dbGap Name: **EVENT**, Desc: **Event Number**, Table: **vr_soe_2020_a_1340s**. - * _phs000007.v30.pht000309.v13.phv00036471.v12_. dbGap Name: **DATE**, Desc: **Date of Event**, Table: **vr_soe_2020_a_1340s**. - * _phs000007.v30.pht003099.v5.phv00177930.v5_. dbGap Name: **age1**, Desc: **Age at Exam 1**, Table: **vr_dates_2019_a_1175s**. - * _phs000007.v30.pht003316.v7.phv00190817.v7_. dbGap Name: **cvd**, Desc: **Cardiovascular Disease (CVD) status**, Table: **vr_survcvd_2019_a_1334s**. - * _phs000007.v30.pht003316.v7.phv00190823.v7_. dbGap Name: **cvddate**, Desc: **Date of Cardiovascular Disease (CVD) status**, Table: **vr_survcvd_2019_a_1334s**. + * _phs000007.v30.pht000309.v13.phv00036469.v12_ + * dbGap name: **EVENT** + * dbGap desc: **Event Number** + * dbGap table: **vr_soe_2020_a_1340s** + * PIC-SURE permissible values: ABI (Atherothrombotic Infarction of brain), AP, first episode only, Acute MI by autopsy, previously coded as 1 or 2, CHF, hospitalized, CHF, not hospitalized, diagnosed on basis of on exam or MD notes, CHF, questionable CHF at exam 1, CI, definite by both history and ECG, CVA, definite CVA, type unknown, Cerebral embolism, Death, CHD sudden, within 1 hour, Death, CHD, 1-23 hours, non sudden, Death, CHD, 24-47 hours, non sudden, Death, CHD, 48 hours or more, non sudden, Death, CVA, Death, Cancer, Death, cause unknown, Death, other CVD, Death, other causes, Definite CVA at exam 1, but questionable type, IC, first episode only, IC, questionable IC at exam 1, Intracerebral hemorrhage, MI recognized, with diagnostic ECG, MI recognized, without diagnostic ECG, with autopsy evidence, new event (see also code 9), MI recognized, without diagnostic ECG, with enzymes and history, MI unrecognized, not silent, MI unrecognized, silent, Other CVA, Questionable CVA at exam 1, Questionable MI at exam 1, Subarachnoid hemorrhage, TIA (Transient Ischemic Attack) only the 1st TIA is coded, TIA with positive imaging + * _phs000007.v30.pht000309.v13.phv00036471.v12_ + * dbGap name: **DATE** + * dbGap desc: **Date of Event** + * dbGap table: **vr_soe_2020_a_1340s** + * No permissible values listed in PIC-SURE data dictionary + * _phs000007.v30.pht003099.v5.phv00177930.v5_ + * dbGap name: **age1** + * dbGap desc: **Age at Exam 1** + * dbGap table: **vr_dates_2019_a_1175s** + * No permissible values listed in PIC-SURE data dictionary + * _phs000007.v30.pht003316.v7.phv00190817.v7_ + * dbGap name: **cvd** + * dbGap desc: **Cardiovascular Disease (CVD) status** + * dbGap table: **vr_survcvd_2019_a_1334s** + * PIC-SURE permissible values: No, Yes + * _phs000007.v30.pht003316.v7.phv00190823.v7_ + * dbGap name: **cvddate** + * dbGap desc: **Date of Cardiovascular Disease (CVD) status** + * dbGap table: **vr_survcvd_2019_a_1334s** + * No permissible values listed in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -909,8 +1161,12 @@ * ### atherosclerosis_events_prior/mi_prior_1 -- **JHS Jackson Heart Study (JHS) Cohort**: * 2 component_study_variables - * _phs000286.v5.pht001949.v1.phv00126009.v1_. No dbGap metadata available. - * _phs000286.v5.pht001949.v1.phv00126088.v1_. No dbGap metadata available. + * _phs000286.v5.pht001949.v1.phv00126009.v1_ + * No dbGap metadata available + * varId _phv00126009_ not found in PIC-SURE data dictionary + * _phs000286.v5.pht001949.v1.phv00126088.v1_ + * No dbGap metadata available + * varId _phv00126088_ not found in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -936,7 +1192,11 @@ * ### atherosclerosis_events_prior/mi_prior_1 -- **MESA Multi-Ethnic Study of Atherosclerosis (MESA) Cohort**: * 1 component_study_variables - * _phs000209.v13.pht001116.v10.phv00084442.v3_. dbGap Name: **age1c**, Desc: **AGE**, Table: **MESA_Exam1Main**. + * _phs000209.v13.pht001116.v10.phv00084442.v3_ + * dbGap name: **age1c** + * dbGap desc: **AGE** + * dbGap table: **MESA_Exam1Main** + * No permissible values listed in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -949,9 +1209,21 @@ * ### atherosclerosis_events_prior/mi_prior_1 -- **WHI Women's Health Initiative**: * 3 component_study_variables - * _phs000200.v11.pht000998.v6.phv00078436.v6_. dbGap Name: **F2DAYS**, Desc: **F2 Days since randomization**, Table: **f2_rel1**. - * _phs000200.v11.pht000998.v6.phv00078437.v6_. dbGap Name: **AGE**, Desc: **Age at screening**, Table: **f2_rel1**. - * _phs000200.v11.pht000998.v6.phv00078482.v6_. dbGap Name: **MI**, Desc: **MI ever**, Table: **f2_rel1**. + * _phs000200.v11.pht000998.v6.phv00078436.v6_ + * dbGap name: **F2DAYS** + * dbGap desc: **F2 Days since randomization** + * dbGap table: **f2_rel1** + * No permissible values listed in PIC-SURE data dictionary + * _phs000200.v11.pht000998.v6.phv00078437.v6_ + * dbGap name: **AGE** + * dbGap desc: **Age at screening** + * dbGap table: **f2_rel1** + * No permissible values listed in PIC-SURE data dictionary + * _phs000200.v11.pht000998.v6.phv00078482.v6_ + * dbGap name: **MI** + * dbGap desc: **MI ever** + * dbGap table: **f2_rel1** + * PIC-SURE permissible values: No, Yes * **Function:** ```r harmonize <- function(phen_list){ @@ -1012,8 +1284,16 @@ * ### atherosclerosis_events_prior/pad_prior_1 -- **ARIC Atherosclerosis Risk in Communities (ARIC) Cohort**: * 2 component_study_variables - * _phs000280.v5.pht004063.v2.phv00204712.v1_. dbGap Name: **V1AGE01**, Desc: **Age at visit 1 [Cohort. Visit 1]**, Table: **DERIVE13**. - * _phs000280.v5.pht004063.v2.phv00204795.v1_. dbGap Name: **PAD02**, Desc: **Peripheral artery disease visit 1, definition 2 - same for both genders [Cohort. Visit 1]**, Table: **DERIVE13**. + * _phs000280.v5.pht004063.v2.phv00204712.v1_ + * dbGap name: **V1AGE01** + * dbGap desc: **Age at visit 1 [Cohort. Visit 1]** + * dbGap table: **DERIVE13** + * varId _phv00204712_ not found in PIC-SURE data dictionary + * _phs000280.v5.pht004063.v2.phv00204795.v1_ + * dbGap name: **PAD02** + * dbGap desc: **Peripheral artery disease visit 1, definition 2 - same for both genders [Cohort. Visit 1]** + * dbGap table: **DERIVE13** + * varId _phv00204795_ not found in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -1037,10 +1317,26 @@ * ### atherosclerosis_events_prior/pad_prior_1 -- **CHS Cardiovascular Health Study (CHS) Cohort: an NHLBI-funded observational study of risk factors for cardiovascular disease in adults 65 years or older**: * 4 component_study_variables - * _phs000287.v6.pht001452.v1.phv00100330.v1_. dbGap Name: **ABTLEG**, Desc: **LEG ARTERY BYPASS**, Table: **BASEBOTH**. - * _phs000287.v6.pht001452.v1.phv00100333.v1_. dbGap Name: **EXTART**, Desc: **LOW EXTREM ANGIOPLASTY**, Table: **BASEBOTH**. - * _phs000287.v6.pht001452.v1.phv00100487.v1_. dbGap Name: **AGEBL**, Desc: **CALCULATED AGE AT BASELINE**, Table: **BASEBOTH**. - * _phs000287.v6.pht001452.v1.phv00100507.v1_. dbGap Name: **CLBLMOD**, Desc: **CLD MODIFIED BL STAT**, Table: **BASEBOTH**. + * _phs000287.v6.pht001452.v1.phv00100330.v1_ + * dbGap name: **ABTLEG** + * dbGap desc: **LEG ARTERY BYPASS** + * dbGap table: **BASEBOTH** + * PIC-SURE permissible values: No, Yes + * _phs000287.v6.pht001452.v1.phv00100333.v1_ + * dbGap name: **EXTART** + * dbGap desc: **LOW EXTREM ANGIOPLASTY** + * dbGap table: **BASEBOTH** + * PIC-SURE permissible values: No, Yes + * _phs000287.v6.pht001452.v1.phv00100487.v1_ + * dbGap name: **AGEBL** + * dbGap desc: **CALCULATED AGE AT BASELINE** + * dbGap table: **BASEBOTH** + * No permissible values listed in PIC-SURE data dictionary + * _phs000287.v6.pht001452.v1.phv00100507.v1_ + * dbGap name: **CLBLMOD** + * dbGap desc: **CLD MODIFIED BL STAT** + * dbGap table: **BASEBOTH** + * PIC-SURE permissible values: Incident, Prevalent * **Function:** ```r harmonize <- function(phen_list){ @@ -1064,8 +1360,12 @@ * ### atherosclerosis_events_prior/pad_prior_1 -- **COPDGene **: * 2 component_study_variables - * _phs000179.v5.pht002239.v4.phv00159618.v4_. No dbGap metadata available. - * _phs000179.v5.pht002239.v4.phv00159836.v4_. No dbGap metadata available. + * _phs000179.v5.pht002239.v4.phv00159618.v4_ + * No dbGap metadata available + * PIC-SURE permissible values: No, Yes + * _phs000179.v5.pht002239.v4.phv00159836.v4_ + * No dbGap metadata available + * No permissible values listed in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -1088,11 +1388,31 @@ * ### atherosclerosis_events_prior/pad_prior_1 -- **FHS Framingham Cohort**: * 5 component_study_variables - * _phs000007.v30.pht000309.v13.phv00036469.v12_. dbGap Name: **EVENT**, Desc: **Event Number**, Table: **vr_soe_2020_a_1340s**. - * _phs000007.v30.pht000309.v13.phv00036471.v12_. dbGap Name: **DATE**, Desc: **Date of Event**, Table: **vr_soe_2020_a_1340s**. - * _phs000007.v30.pht003099.v5.phv00177930.v5_. dbGap Name: **age1**, Desc: **Age at Exam 1**, Table: **vr_dates_2019_a_1175s**. - * _phs000007.v30.pht003316.v7.phv00190817.v7_. dbGap Name: **cvd**, Desc: **Cardiovascular Disease (CVD) status**, Table: **vr_survcvd_2019_a_1334s**. - * _phs000007.v30.pht003316.v7.phv00190823.v7_. dbGap Name: **cvddate**, Desc: **Date of Cardiovascular Disease (CVD) status**, Table: **vr_survcvd_2019_a_1334s**. + * _phs000007.v30.pht000309.v13.phv00036469.v12_ + * dbGap name: **EVENT** + * dbGap desc: **Event Number** + * dbGap table: **vr_soe_2020_a_1340s** + * PIC-SURE permissible values: ABI (Atherothrombotic Infarction of brain), AP, first episode only, Acute MI by autopsy, previously coded as 1 or 2, CHF, hospitalized, CHF, not hospitalized, diagnosed on basis of on exam or MD notes, CHF, questionable CHF at exam 1, CI, definite by both history and ECG, CVA, definite CVA, type unknown, Cerebral embolism, Death, CHD sudden, within 1 hour, Death, CHD, 1-23 hours, non sudden, Death, CHD, 24-47 hours, non sudden, Death, CHD, 48 hours or more, non sudden, Death, CVA, Death, Cancer, Death, cause unknown, Death, other CVD, Death, other causes, Definite CVA at exam 1, but questionable type, IC, first episode only, IC, questionable IC at exam 1, Intracerebral hemorrhage, MI recognized, with diagnostic ECG, MI recognized, without diagnostic ECG, with autopsy evidence, new event (see also code 9), MI recognized, without diagnostic ECG, with enzymes and history, MI unrecognized, not silent, MI unrecognized, silent, Other CVA, Questionable CVA at exam 1, Questionable MI at exam 1, Subarachnoid hemorrhage, TIA (Transient Ischemic Attack) only the 1st TIA is coded, TIA with positive imaging + * _phs000007.v30.pht000309.v13.phv00036471.v12_ + * dbGap name: **DATE** + * dbGap desc: **Date of Event** + * dbGap table: **vr_soe_2020_a_1340s** + * No permissible values listed in PIC-SURE data dictionary + * _phs000007.v30.pht003099.v5.phv00177930.v5_ + * dbGap name: **age1** + * dbGap desc: **Age at Exam 1** + * dbGap table: **vr_dates_2019_a_1175s** + * No permissible values listed in PIC-SURE data dictionary + * _phs000007.v30.pht003316.v7.phv00190817.v7_ + * dbGap name: **cvd** + * dbGap desc: **Cardiovascular Disease (CVD) status** + * dbGap table: **vr_survcvd_2019_a_1334s** + * PIC-SURE permissible values: No, Yes + * _phs000007.v30.pht003316.v7.phv00190823.v7_ + * dbGap name: **cvddate** + * dbGap desc: **Date of Cardiovascular Disease (CVD) status** + * dbGap table: **vr_survcvd_2019_a_1334s** + * No permissible values listed in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -1180,13 +1500,39 @@ * ### atherosclerosis_events_prior/pad_prior_1 -- **JHS Jackson Heart Study (JHS) Cohort**: * 7 component_study_variables - * _phs000286.v5.pht001921.v1.phv00124562.v1_. dbGap Name: **ABBA7**, Desc: **7. B. Measures. First brachial Doppler blood pressure (mm Hg) [Visit 1] [Ankle-Brachial Blood Pressure]**, Table: **abba**. - * _phs000286.v5.pht001921.v1.phv00124563.v1_. dbGap Name: **ABBA8**, Desc: **8. B. Measures. First right posterior tibia blood pressure (mm Hg) [Visit 1] [Ankle-Brachial Blood Pressure]**, Table: **abba**. - * _phs000286.v5.pht001921.v1.phv00124564.v1_. dbGap Name: **ABBA9**, Desc: **9. B. Measures. First left posterior tibia blood pressure (mm Hg) [Visit 1] [Ankle-Brachial Blood Pressure]**, Table: **abba**. - * _phs000286.v5.pht001921.v1.phv00124565.v1_. dbGap Name: **ABBA10**, Desc: **10. B. Measures. Second left posterior tibia [Visit 1] [Ankle-Brachial Blood Pressure]**, Table: **abba**. - * _phs000286.v5.pht001921.v1.phv00124566.v1_. dbGap Name: **ABBA11**, Desc: **11. B. Measures. Second right posterior tibia blood pressure (mm Hg) [Visit 1] [Ankle-Brachial Blood Pressure]**, Table: **abba**. - * _phs000286.v5.pht001921.v1.phv00124567.v1_. dbGap Name: **ABBA12**, Desc: **12. B. Measures. Second brachial blood pressure (mm Hg) [Visit 1] [Ankle-Brachial Blood Pressure]**, Table: **abba**. - * _phs000286.v5.pht001949.v1.phv00126009.v1_. No dbGap metadata available. + * _phs000286.v5.pht001921.v1.phv00124562.v1_ + * dbGap name: **ABBA7** + * dbGap desc: **7. B. Measures. First brachial Doppler blood pressure (mm Hg) [Visit 1] [Ankle-Brachial Blood Pressure]** + * dbGap table: **abba** + * varId _phv00124562_ not found in PIC-SURE data dictionary + * _phs000286.v5.pht001921.v1.phv00124563.v1_ + * dbGap name: **ABBA8** + * dbGap desc: **8. B. Measures. First right posterior tibia blood pressure (mm Hg) [Visit 1] [Ankle-Brachial Blood Pressure]** + * dbGap table: **abba** + * varId _phv00124563_ not found in PIC-SURE data dictionary + * _phs000286.v5.pht001921.v1.phv00124564.v1_ + * dbGap name: **ABBA9** + * dbGap desc: **9. B. Measures. First left posterior tibia blood pressure (mm Hg) [Visit 1] [Ankle-Brachial Blood Pressure]** + * dbGap table: **abba** + * varId _phv00124564_ not found in PIC-SURE data dictionary + * _phs000286.v5.pht001921.v1.phv00124565.v1_ + * dbGap name: **ABBA10** + * dbGap desc: **10. B. Measures. Second left posterior tibia [Visit 1] [Ankle-Brachial Blood Pressure]** + * dbGap table: **abba** + * varId _phv00124565_ not found in PIC-SURE data dictionary + * _phs000286.v5.pht001921.v1.phv00124566.v1_ + * dbGap name: **ABBA11** + * dbGap desc: **11. B. Measures. Second right posterior tibia blood pressure (mm Hg) [Visit 1] [Ankle-Brachial Blood Pressure]** + * dbGap table: **abba** + * varId _phv00124566_ not found in PIC-SURE data dictionary + * _phs000286.v5.pht001921.v1.phv00124567.v1_ + * dbGap name: **ABBA12** + * dbGap desc: **12. B. Measures. Second brachial blood pressure (mm Hg) [Visit 1] [Ankle-Brachial Blood Pressure]** + * dbGap table: **abba** + * varId _phv00124567_ not found in PIC-SURE data dictionary + * _phs000286.v5.pht001949.v1.phv00126009.v1_ + * No dbGap metadata available + * varId _phv00126009_ not found in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -1235,7 +1581,11 @@ * ### atherosclerosis_events_prior/pad_prior_1 -- **MESA Multi-Ethnic Study of Atherosclerosis (MESA) Cohort**: * 1 component_study_variables - * _phs000209.v13.pht001116.v10.phv00084442.v3_. dbGap Name: **age1c**, Desc: **AGE**, Table: **MESA_Exam1Main**. + * _phs000209.v13.pht001116.v10.phv00084442.v3_ + * dbGap name: **age1c** + * dbGap desc: **AGE** + * dbGap table: **MESA_Exam1Main** + * No permissible values listed in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -1248,10 +1598,26 @@ * ### atherosclerosis_events_prior/pad_prior_1 -- **WHI Women's Health Initiative**: * 4 component_study_variables - * _phs000200.v11.pht000998.v6.phv00078436.v6_. dbGap Name: **F2DAYS**, Desc: **F2 Days since randomization**, Table: **f2_rel1**. - * _phs000200.v11.pht000998.v6.phv00078437.v6_. dbGap Name: **AGE**, Desc: **Age at screening**, Table: **f2_rel1**. - * _phs000200.v11.pht000999.v6.phv00078507.v6_. dbGap Name: **F30DAYS**, Desc: **F30 Days since randomization/enrollment**, Table: **f30_rel2**. - * _phs000200.v11.pht000999.v6.phv00078562.v6_. dbGap Name: **PAD**, Desc: **Peripheral arterial disease ever**, Table: **f30_rel2**. + * _phs000200.v11.pht000998.v6.phv00078436.v6_ + * dbGap name: **F2DAYS** + * dbGap desc: **F2 Days since randomization** + * dbGap table: **f2_rel1** + * No permissible values listed in PIC-SURE data dictionary + * _phs000200.v11.pht000998.v6.phv00078437.v6_ + * dbGap name: **AGE** + * dbGap desc: **Age at screening** + * dbGap table: **f2_rel1** + * No permissible values listed in PIC-SURE data dictionary + * _phs000200.v11.pht000999.v6.phv00078507.v6_ + * dbGap name: **F30DAYS** + * dbGap desc: **F30 Days since randomization/enrollment** + * dbGap table: **f30_rel2** + * No permissible values listed in PIC-SURE data dictionary + * _phs000200.v11.pht000999.v6.phv00078562.v6_ + * dbGap name: **PAD** + * dbGap desc: **Peripheral arterial disease ever** + * dbGap table: **f30_rel2** + * PIC-SURE permissible values: No, Yes * **Function:** ```r harmonize <- function(phen_list){ diff --git a/resources/human-readable-harmonized-variable-documentation/generated-doc-pages/baseline_common_covariates.md b/resources/human-readable-harmonized-variable-documentation/generated-doc-pages/baseline_common_covariates.md index 2cef89c..c956ac1 100644 --- a/resources/human-readable-harmonized-variable-documentation/generated-doc-pages/baseline_common_covariates.md +++ b/resources/human-readable-harmonized-variable-documentation/generated-doc-pages/baseline_common_covariates.md @@ -144,10 +144,26 @@ * ### baseline_common_covariates/current_smoker_baseline_1 -- **ARIC Atherosclerosis Risk in Communities (ARIC) Cohort**: * 4 component_study_variables - * _phs000280.v5.pht004063.v2.phv00204712.v1_. dbGap Name: **V1AGE01**, Desc: **Age at visit 1 [Cohort. Visit 1]**, Table: **DERIVE13**. - * _phs000280.v5.pht004111.v2.phv00207368.v1_. dbGap Name: **HOM28**, Desc: **Have you ever smoked cigarettes? Q28 [Home Interview. HOM. Visit 1]**, Table: **HOM**. - * _phs000280.v5.pht004111.v2.phv00207370.v1_. dbGap Name: **HOM30**, Desc: **Do you now smoke cigarettes? Q30 [Home Interview. HOM. Visit 1]**, Table: **HOM**. - * _phs000280.v5.pht004111.v2.phv00207372.v1_. dbGap Name: **HOM32**, Desc: **Number of cigarettes smoked per day. Q32 [Home Interview. HOM. Visit 1]**, Table: **HOM**. + * _phs000280.v5.pht004063.v2.phv00204712.v1_ + * dbGap name: **V1AGE01** + * dbGap desc: **Age at visit 1 [Cohort. Visit 1]** + * dbGap table: **DERIVE13** + * varId _phv00204712_ not found in PIC-SURE data dictionary + * _phs000280.v5.pht004111.v2.phv00207368.v1_ + * dbGap name: **HOM28** + * dbGap desc: **Have you ever smoked cigarettes? Q28 [Home Interview. HOM. Visit 1]** + * dbGap table: **HOM** + * varId _phv00207368_ not found in PIC-SURE data dictionary + * _phs000280.v5.pht004111.v2.phv00207370.v1_ + * dbGap name: **HOM30** + * dbGap desc: **Do you now smoke cigarettes? Q30 [Home Interview. HOM. Visit 1]** + * dbGap table: **HOM** + * varId _phv00207370_ not found in PIC-SURE data dictionary + * _phs000280.v5.pht004111.v2.phv00207372.v1_ + * dbGap name: **HOM32** + * dbGap desc: **Number of cigarettes smoked per day. Q32 [Home Interview. HOM. Visit 1]** + * dbGap table: **HOM** + * varId _phv00207372_ not found in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -178,9 +194,21 @@ * ### baseline_common_covariates/current_smoker_baseline_1 -- **CARDIA CARDIA Cohort**: * 3 component_study_variables - * _phs000285.v3.pht001559.v2.phv00112439.v2_. dbGap Name: **A01AGE2**, Desc: **AGE VERIFY**, Table: **A4F01**. - * _phs000285.v3.pht001572.v2.phv00113168.v2_. dbGap Name: **A09SMKNW**, Desc: **STILL SMOKES CIGARETTES REGULARLY? Q 2.01**, Table: **A4F09TOB**. - * _phs000285.v3.pht001573.v2.phv00113213.v2_. dbGap Name: **A10CIGS**, Desc: **SUBJECT HAS SMOKED CIGARETTES. Q 2**, Table: **A4F10**. + * _phs000285.v3.pht001559.v2.phv00112439.v2_ + * dbGap name: **A01AGE2** + * dbGap desc: **AGE VERIFY** + * dbGap table: **A4F01** + * varId _phv00112439_ not found in PIC-SURE data dictionary + * _phs000285.v3.pht001572.v2.phv00113168.v2_ + * dbGap name: **A09SMKNW** + * dbGap desc: **STILL SMOKES CIGARETTES REGULARLY? Q 2.01** + * dbGap table: **A4F09TOB** + * varId _phv00113168_ not found in PIC-SURE data dictionary + * _phs000285.v3.pht001573.v2.phv00113213.v2_ + * dbGap name: **A10CIGS** + * dbGap desc: **SUBJECT HAS SMOKED CIGARETTES. Q 2** + * dbGap table: **A4F10** + * varId _phv00113213_ not found in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -209,11 +237,31 @@ * ### baseline_common_covariates/current_smoker_baseline_1 -- **CHS Cardiovascular Health Study (CHS) Cohort: an NHLBI-funded observational study of risk factors for cardiovascular disease in adults 65 years or older**: * 5 component_study_variables - * _phs000287.v6.pht001450.v1.phv00098844.v1_. dbGap Name: **SMOKE101**, Desc: **SMOKED IN LIFETIME**, Table: **BASE1**. - * _phs000287.v6.pht001450.v1.phv00098845.v1_. dbGap Name: **SMOKE201**, Desc: **SMOKED CIGARETTES LAST 30 DAYS**, Table: **BASE1**. - * _phs000287.v6.pht001452.v1.phv00100487.v1_. dbGap Name: **AGEBL**, Desc: **CALCULATED AGE AT BASELINE**, Table: **BASEBOTH**. - * _phs000287.v6.pht001490.v1.phv00105143.v1_. dbGap Name: **SMOKE101**, Desc: **SMOKED IN LIFETIME**, Table: **YR5NEW**. - * _phs000287.v6.pht001490.v1.phv00105144.v1_. dbGap Name: **SMOKE201**, Desc: **SMOKED CIGARETTES LAST 30 DAYS**, Table: **YR5NEW**. + * _phs000287.v6.pht001450.v1.phv00098844.v1_ + * dbGap name: **SMOKE101** + * dbGap desc: **SMOKED IN LIFETIME** + * dbGap table: **BASE1** + * PIC-SURE permissible values: NO, YES + * _phs000287.v6.pht001450.v1.phv00098845.v1_ + * dbGap name: **SMOKE201** + * dbGap desc: **SMOKED CIGARETTES LAST 30 DAYS** + * dbGap table: **BASE1** + * PIC-SURE permissible values: NO, YES + * _phs000287.v6.pht001452.v1.phv00100487.v1_ + * dbGap name: **AGEBL** + * dbGap desc: **CALCULATED AGE AT BASELINE** + * dbGap table: **BASEBOTH** + * No permissible values listed in PIC-SURE data dictionary + * _phs000287.v6.pht001490.v1.phv00105143.v1_ + * dbGap name: **SMOKE101** + * dbGap desc: **SMOKED IN LIFETIME** + * dbGap table: **YR5NEW** + * PIC-SURE permissible values: NO, YES + * _phs000287.v6.pht001490.v1.phv00105144.v1_ + * dbGap name: **SMOKE201** + * dbGap desc: **SMOKED CIGARETTES LAST 30 DAYS** + * dbGap table: **YR5NEW** + * PIC-SURE permissible values: NO, YES * **Function:** ```r harmonize <- function(phen_list){ @@ -242,15 +290,33 @@ * ### baseline_common_covariates/current_smoker_baseline_1 -- **COPDGene **: * 9 component_study_variables - * _phs000179.v5.pht002239.v4.phv00159636.v4_. No dbGap metadata available. - * _phs000179.v5.pht002239.v4.phv00159637.v4_. No dbGap metadata available. - * _phs000179.v5.pht002239.v4.phv00159640.v4_. No dbGap metadata available. - * _phs000179.v5.pht002239.v4.phv00159749.v4_. No dbGap metadata available. - * _phs000179.v5.pht002239.v4.phv00159750.v4_. No dbGap metadata available. - * _phs000179.v5.pht002239.v4.phv00159754.v4_. No dbGap metadata available. - * _phs000179.v5.pht002239.v4.phv00159755.v4_. No dbGap metadata available. - * _phs000179.v5.pht002239.v4.phv00159756.v4_. No dbGap metadata available. - * _phs000179.v5.pht002239.v4.phv00159836.v4_. No dbGap metadata available. + * _phs000179.v5.pht002239.v4.phv00159636.v4_ + * No dbGap metadata available + * PIC-SURE permissible values: After 60 min, Between 31-60 min, Between 6-30 min, With 5 min + * _phs000179.v5.pht002239.v4.phv00159637.v4_ + * No dbGap metadata available + * PIC-SURE permissible values: No, Yes + * _phs000179.v5.pht002239.v4.phv00159640.v4_ + * No dbGap metadata available + * PIC-SURE permissible values: No, Yes + * _phs000179.v5.pht002239.v4.phv00159749.v4_ + * No dbGap metadata available + * PIC-SURE permissible values: No, Yes + * _phs000179.v5.pht002239.v4.phv00159750.v4_ + * No dbGap metadata available + * No permissible values listed in PIC-SURE data dictionary + * _phs000179.v5.pht002239.v4.phv00159754.v4_ + * No dbGap metadata available + * No permissible values listed in PIC-SURE data dictionary + * _phs000179.v5.pht002239.v4.phv00159755.v4_ + * No dbGap metadata available + * No permissible values listed in PIC-SURE data dictionary + * _phs000179.v5.pht002239.v4.phv00159756.v4_ + * No dbGap metadata available + * No permissible values listed in PIC-SURE data dictionary + * _phs000179.v5.pht002239.v4.phv00159836.v4_ + * No dbGap metadata available + * No permissible values listed in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -280,11 +346,31 @@ * ### baseline_common_covariates/current_smoker_baseline_1 -- **HCHS_SOL Hispanic Community Health Study /Study of Latinos (HCHS/SOL)**: * 5 component_study_variables - * _phs000810.v1.pht004715.v1.phv00226251.v1_. dbGap Name: **AGE**, Desc: **Age**, Table: **HCHS_SOL_Cohort_Subject_Phenotypes**. - * _phs000810.v1.pht004715.v1.phv00258106.v1_. dbGap Name: **TBEA1**, Desc: **Smoke at least 100 cigs in lifetime (TBEA1)**, Table: **HCHS_SOL_Cohort_Subject_Phenotypes**. - * _phs000810.v1.pht004715.v1.phv00258107.v1_. dbGap Name: **TBEA3**, Desc: **Present Smoking Status (TBEA3)**, Table: **HCHS_SOL_Cohort_Subject_Phenotypes**. - * _phs000810.v1.pht004715.v1.phv00258108.v1_. dbGap Name: **TBEA4**, Desc: **Daily: Cigs per Day - Present (TBEA4)**, Table: **HCHS_SOL_Cohort_Subject_Phenotypes**. - * _phs000810.v1.pht004715.v1.phv00258110.v1_. dbGap Name: **TBEA5A**, Desc: **Some: Past 30 days - quit smoking 6 months or longer (TBEA5A)**, Table: **HCHS_SOL_Cohort_Subject_Phenotypes**. + * _phs000810.v1.pht004715.v1.phv00226251.v1_ + * dbGap name: **AGE** + * dbGap desc: **Age** + * dbGap table: **HCHS_SOL_Cohort_Subject_Phenotypes** + * No permissible values listed in PIC-SURE data dictionary + * _phs000810.v1.pht004715.v1.phv00258106.v1_ + * dbGap name: **TBEA1** + * dbGap desc: **Smoke at least 100 cigs in lifetime (TBEA1)** + * dbGap table: **HCHS_SOL_Cohort_Subject_Phenotypes** + * PIC-SURE permissible values: No, Yes + * _phs000810.v1.pht004715.v1.phv00258107.v1_ + * dbGap name: **TBEA3** + * dbGap desc: **Present Smoking Status (TBEA3)** + * dbGap table: **HCHS_SOL_Cohort_Subject_Phenotypes** + * PIC-SURE permissible values: Daily, Not at all, Some days + * _phs000810.v1.pht004715.v1.phv00258108.v1_ + * dbGap name: **TBEA4** + * dbGap desc: **Daily: Cigs per Day - Present (TBEA4)** + * dbGap table: **HCHS_SOL_Cohort_Subject_Phenotypes** + * No permissible values listed in PIC-SURE data dictionary + * _phs000810.v1.pht004715.v1.phv00258110.v1_ + * dbGap name: **TBEA5A** + * dbGap desc: **Some: Past 30 days - quit smoking 6 months or longer (TBEA5A)** + * dbGap table: **HCHS_SOL_Cohort_Subject_Phenotypes** + * No permissible values listed in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -315,9 +401,19 @@ * ### baseline_common_covariates/current_smoker_baseline_1 -- **JHS Jackson Heart Study (JHS) Cohort**: * 3 component_study_variables - * _phs000286.v5.pht001949.v1.phv00126009.v1_. No dbGap metadata available. - * _phs000286.v5.pht001977.v1.phv00128496.v1_. dbGap Name: **TOBA1**, Desc: **Q1. Smoked at least 400 cigarettes in your lifetime [Visit 1] [Health Practices: Tobacco Use, TOB]**, Table: **toba**. - * _phs000286.v5.pht001977.v1.phv00128498.v1_. dbGap Name: **TOBA3**, Desc: **Q3. Do you now smoke cigarettes [Visit 1] [Health Practices: Tobacco Use, TOB]**, Table: **toba**. + * _phs000286.v5.pht001949.v1.phv00126009.v1_ + * No dbGap metadata available + * varId _phv00126009_ not found in PIC-SURE data dictionary + * _phs000286.v5.pht001977.v1.phv00128496.v1_ + * dbGap name: **TOBA1** + * dbGap desc: **Q1. Smoked at least 400 cigarettes in your lifetime [Visit 1] [Health Practices: Tobacco Use, TOB]** + * dbGap table: **toba** + * varId _phv00128496_ not found in PIC-SURE data dictionary + * _phs000286.v5.pht001977.v1.phv00128498.v1_ + * dbGap name: **TOBA3** + * dbGap desc: **Q3. Do you now smoke cigarettes [Visit 1] [Health Practices: Tobacco Use, TOB]** + * dbGap table: **toba** + * varId _phv00128498_ not found in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -339,15 +435,51 @@ * ### baseline_common_covariates/current_smoker_baseline_1 -- **MESA Multi-Ethnic Study of Atherosclerosis (MESA) Cohort**: * 9 component_study_variables - * _phs000209.v13.pht001111.v4.phv00082639.v2_. dbGap Name: **age1c**, Desc: **AGE**, Table: **MESA_AirNRExamMain**. - * _phs000209.v13.pht001111.v4.phv00083243.v1_. dbGap Name: **evsmk1**, Desc: **SMOKED AT LEAST 100 CIGARETTES IN LIFETIME**, Table: **MESA_AirNRExamMain**. - * _phs000209.v13.pht001111.v4.phv00083245.v1_. dbGap Name: **cursmk1**, Desc: **CIGARETTES: SMOKED IN LAST 30 DAYS**, Table: **MESA_AirNRExamMain**. - * _phs000209.v13.pht001116.v10.phv00084442.v3_. dbGap Name: **age1c**, Desc: **AGE**, Table: **MESA_Exam1Main**. - * _phs000209.v13.pht001116.v10.phv00085570.v2_. dbGap Name: **evsmk1**, Desc: **SMOKED AT LEAST 100 CIGARETTES IN LIFETIME**, Table: **MESA_Exam1Main**. - * _phs000209.v13.pht001116.v10.phv00085572.v2_. dbGap Name: **cursmk1**, Desc: **CIGARETTES: SMOKED IN LAST 30 DAYS**, Table: **MESA_Exam1Main**. - * _phs000209.v13.pht001121.v3.phv00087071.v1_. dbGap Name: **agefc**, Desc: **AGE**, Table: **MESA_FamilyExamMain**. - * _phs000209.v13.pht001121.v3.phv00087252.v1_. dbGap Name: **evsmkf**, Desc: **SMOKED 100+ CIGARETTES IN LIFETIME**, Table: **MESA_FamilyExamMain**. - * _phs000209.v13.pht001121.v3.phv00087254.v1_. dbGap Name: **cursmkf**, Desc: **SMOKED CIGARETTES IN THE LAST 30 DAYS**, Table: **MESA_FamilyExamMain**. + * _phs000209.v13.pht001111.v4.phv00082639.v2_ + * dbGap name: **age1c** + * dbGap desc: **AGE** + * dbGap table: **MESA_AirNRExamMain** + * No permissible values listed in PIC-SURE data dictionary + * _phs000209.v13.pht001111.v4.phv00083243.v1_ + * dbGap name: **evsmk1** + * dbGap desc: **SMOKED AT LEAST 100 CIGARETTES IN LIFETIME** + * dbGap table: **MESA_AirNRExamMain** + * PIC-SURE permissible values: NO, YES + * _phs000209.v13.pht001111.v4.phv00083245.v1_ + * dbGap name: **cursmk1** + * dbGap desc: **CIGARETTES: SMOKED IN LAST 30 DAYS** + * dbGap table: **MESA_AirNRExamMain** + * PIC-SURE permissible values: NO, YES + * _phs000209.v13.pht001116.v10.phv00084442.v3_ + * dbGap name: **age1c** + * dbGap desc: **AGE** + * dbGap table: **MESA_Exam1Main** + * No permissible values listed in PIC-SURE data dictionary + * _phs000209.v13.pht001116.v10.phv00085570.v2_ + * dbGap name: **evsmk1** + * dbGap desc: **SMOKED AT LEAST 100 CIGARETTES IN LIFETIME** + * dbGap table: **MESA_Exam1Main** + * PIC-SURE permissible values: NO, YES + * _phs000209.v13.pht001116.v10.phv00085572.v2_ + * dbGap name: **cursmk1** + * dbGap desc: **CIGARETTES: SMOKED IN LAST 30 DAYS** + * dbGap table: **MESA_Exam1Main** + * PIC-SURE permissible values: NO, YES + * _phs000209.v13.pht001121.v3.phv00087071.v1_ + * dbGap name: **agefc** + * dbGap desc: **AGE** + * dbGap table: **MESA_FamilyExamMain** + * No permissible values listed in PIC-SURE data dictionary + * _phs000209.v13.pht001121.v3.phv00087252.v1_ + * dbGap name: **evsmkf** + * dbGap desc: **SMOKED 100+ CIGARETTES IN LIFETIME** + * dbGap table: **MESA_FamilyExamMain** + * PIC-SURE permissible values: NO, YES + * _phs000209.v13.pht001121.v3.phv00087254.v1_ + * dbGap name: **cursmkf** + * dbGap desc: **SMOKED CIGARETTES IN THE LAST 30 DAYS** + * dbGap table: **MESA_FamilyExamMain** + * PIC-SURE permissible values: NO, YES * **Function:** ```r harmonize <- function(phen_list){ @@ -376,11 +508,31 @@ * ### baseline_common_covariates/current_smoker_baseline_1 -- **WHI Women's Health Initiative**: * 5 component_study_variables - * _phs000200.v11.pht000998.v6.phv00078436.v6_. dbGap Name: **F2DAYS**, Desc: **F2 Days since randomization**, Table: **f2_rel1**. - * _phs000200.v11.pht000998.v6.phv00078437.v6_. dbGap Name: **AGE**, Desc: **Age at screening**, Table: **f2_rel1**. - * _phs000200.v11.pht001003.v6.phv00078773.v6_. dbGap Name: **F34DAYS**, Desc: **F34 Days since randomization/enrollment**, Table: **f34_rel2**. - * _phs000200.v11.pht001003.v6.phv00078774.v6_. dbGap Name: **SMOKEVR**, Desc: **Smoked at least 100 cigarettes ever**, Table: **f34_rel2**. - * _phs000200.v11.pht001003.v6.phv00078776.v6_. dbGap Name: **SMOKNOW**, Desc: **Smoke cigarettes now**, Table: **f34_rel2**. + * _phs000200.v11.pht000998.v6.phv00078436.v6_ + * dbGap name: **F2DAYS** + * dbGap desc: **F2 Days since randomization** + * dbGap table: **f2_rel1** + * No permissible values listed in PIC-SURE data dictionary + * _phs000200.v11.pht000998.v6.phv00078437.v6_ + * dbGap name: **AGE** + * dbGap desc: **Age at screening** + * dbGap table: **f2_rel1** + * No permissible values listed in PIC-SURE data dictionary + * _phs000200.v11.pht001003.v6.phv00078773.v6_ + * dbGap name: **F34DAYS** + * dbGap desc: **F34 Days since randomization/enrollment** + * dbGap table: **f34_rel2** + * No permissible values listed in PIC-SURE data dictionary + * _phs000200.v11.pht001003.v6.phv00078774.v6_ + * dbGap name: **SMOKEVR** + * dbGap desc: **Smoked at least 100 cigarettes ever** + * dbGap table: **f34_rel2** + * PIC-SURE permissible values: No, Yes + * _phs000200.v11.pht001003.v6.phv00078776.v6_ + * dbGap name: **SMOKNOW** + * dbGap desc: **Smoke cigarettes now** + * dbGap table: **f34_rel2** + * PIC-SURE permissible values: No, Yes * **Function:** ```r harmonize <- function(phen_list){ @@ -477,12 +629,36 @@ * ### baseline_common_covariates/ever_smoker_baseline_1 -- **ARIC Atherosclerosis Risk in Communities (ARIC) Cohort**: * 6 component_study_variables - * _phs000280.v5.pht004063.v2.phv00204712.v1_. dbGap Name: **V1AGE01**, Desc: **Age at visit 1 [Cohort. Visit 1]**, Table: **DERIVE13**. - * _phs000280.v5.pht004111.v2.phv00207368.v1_. dbGap Name: **HOM28**, Desc: **Have you ever smoked cigarettes? Q28 [Home Interview. HOM. Visit 1]**, Table: **HOM**. - * _phs000280.v5.pht004111.v2.phv00207369.v1_. dbGap Name: **HOM29**, Desc: **How old were you when you first started regular cigarette smoking? Q29 [Home Interview. HOM. Visit 1]**, Table: **HOM**. - * _phs000280.v5.pht004111.v2.phv00207370.v1_. dbGap Name: **HOM30**, Desc: **Do you now smoke cigarettes? Q30 [Home Interview. HOM. Visit 1]**, Table: **HOM**. - * _phs000280.v5.pht004111.v2.phv00207375.v1_. dbGap Name: **HOM35**, Desc: **On the average of the entire time you smoked, how many cigarettes did you usually smoke per day? Q35 [Home Interview. HOM. Visit 1]**, Table: **HOM**. - * _phs000280.v5.pht004111.v2.phv00207376.v1_. dbGap Name: **HOM36**, Desc: **(Do/did) you inhale the cigarette smoke? Q36 [Home Interview. HOM. Visit 1]**, Table: **HOM**. + * _phs000280.v5.pht004063.v2.phv00204712.v1_ + * dbGap name: **V1AGE01** + * dbGap desc: **Age at visit 1 [Cohort. Visit 1]** + * dbGap table: **DERIVE13** + * varId _phv00204712_ not found in PIC-SURE data dictionary + * _phs000280.v5.pht004111.v2.phv00207368.v1_ + * dbGap name: **HOM28** + * dbGap desc: **Have you ever smoked cigarettes? Q28 [Home Interview. HOM. Visit 1]** + * dbGap table: **HOM** + * varId _phv00207368_ not found in PIC-SURE data dictionary + * _phs000280.v5.pht004111.v2.phv00207369.v1_ + * dbGap name: **HOM29** + * dbGap desc: **How old were you when you first started regular cigarette smoking? Q29 [Home Interview. HOM. Visit 1]** + * dbGap table: **HOM** + * varId _phv00207369_ not found in PIC-SURE data dictionary + * _phs000280.v5.pht004111.v2.phv00207370.v1_ + * dbGap name: **HOM30** + * dbGap desc: **Do you now smoke cigarettes? Q30 [Home Interview. HOM. Visit 1]** + * dbGap table: **HOM** + * varId _phv00207370_ not found in PIC-SURE data dictionary + * _phs000280.v5.pht004111.v2.phv00207375.v1_ + * dbGap name: **HOM35** + * dbGap desc: **On the average of the entire time you smoked, how many cigarettes did you usually smoke per day? Q35 [Home Interview. HOM. Visit 1]** + * dbGap table: **HOM** + * varId _phv00207375_ not found in PIC-SURE data dictionary + * _phs000280.v5.pht004111.v2.phv00207376.v1_ + * dbGap name: **HOM36** + * dbGap desc: **(Do/did) you inhale the cigarette smoke? Q36 [Home Interview. HOM. Visit 1]** + * dbGap table: **HOM** + * varId _phv00207376_ not found in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -513,8 +689,16 @@ * ### baseline_common_covariates/ever_smoker_baseline_1 -- **CARDIA CARDIA Cohort**: * 2 component_study_variables - * _phs000285.v3.pht001559.v2.phv00112439.v2_. dbGap Name: **A01AGE2**, Desc: **AGE VERIFY**, Table: **A4F01**. - * _phs000285.v3.pht001573.v2.phv00113213.v2_. dbGap Name: **A10CIGS**, Desc: **SUBJECT HAS SMOKED CIGARETTES. Q 2**, Table: **A4F10**. + * _phs000285.v3.pht001559.v2.phv00112439.v2_ + * dbGap name: **A01AGE2** + * dbGap desc: **AGE VERIFY** + * dbGap table: **A4F01** + * varId _phv00112439_ not found in PIC-SURE data dictionary + * _phs000285.v3.pht001573.v2.phv00113213.v2_ + * dbGap name: **A10CIGS** + * dbGap desc: **SUBJECT HAS SMOKED CIGARETTES. Q 2** + * dbGap table: **A4F10** + * varId _phv00113213_ not found in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -540,15 +724,51 @@ * ### baseline_common_covariates/ever_smoker_baseline_1 -- **CHS Cardiovascular Health Study (CHS) Cohort: an NHLBI-funded observational study of risk factors for cardiovascular disease in adults 65 years or older**: * 9 component_study_variables - * _phs000287.v6.pht001450.v1.phv00098844.v1_. dbGap Name: **SMOKE101**, Desc: **SMOKED IN LIFETIME**, Table: **BASE1**. - * _phs000287.v6.pht001450.v1.phv00098845.v1_. dbGap Name: **SMOKE201**, Desc: **SMOKED CIGARETTES LAST 30 DAYS**, Table: **BASE1**. - * _phs000287.v6.pht001450.v1.phv00099157.v1_. dbGap Name: **SMKAGE08**, Desc: **HOW OLD WHEN YOU STARTED TO SMOKE**, Table: **BASE1**. - * _phs000287.v6.pht001450.v1.phv00099159.v1_. dbGap Name: **AMOUNT08**, Desc: **HOW MANY DID YOU SMOKE PER DAY ON AVER (99=UNKNOWN)**, Table: **BASE1**. - * _phs000287.v6.pht001452.v1.phv00100487.v1_. dbGap Name: **AGEBL**, Desc: **CALCULATED AGE AT BASELINE**, Table: **BASEBOTH**. - * _phs000287.v6.pht001490.v1.phv00105143.v1_. dbGap Name: **SMOKE101**, Desc: **SMOKED IN LIFETIME**, Table: **YR5NEW**. - * _phs000287.v6.pht001490.v1.phv00105144.v1_. dbGap Name: **SMOKE201**, Desc: **SMOKED CIGARETTES LAST 30 DAYS**, Table: **YR5NEW**. - * _phs000287.v6.pht001490.v1.phv00106198.v1_. dbGap Name: **SMKAGE58**, Desc: **HOW OLD WHEN YOU STARTED TO SMOKE**, Table: **YR5NEW**. - * _phs000287.v6.pht001490.v1.phv00106200.v1_. dbGap Name: **AMOUNT58**, Desc: **HOW MANY DID YOU SMOKE PER DAY ON AVER.**, Table: **YR5NEW**. + * _phs000287.v6.pht001450.v1.phv00098844.v1_ + * dbGap name: **SMOKE101** + * dbGap desc: **SMOKED IN LIFETIME** + * dbGap table: **BASE1** + * PIC-SURE permissible values: NO, YES + * _phs000287.v6.pht001450.v1.phv00098845.v1_ + * dbGap name: **SMOKE201** + * dbGap desc: **SMOKED CIGARETTES LAST 30 DAYS** + * dbGap table: **BASE1** + * PIC-SURE permissible values: NO, YES + * _phs000287.v6.pht001450.v1.phv00099157.v1_ + * dbGap name: **SMKAGE08** + * dbGap desc: **HOW OLD WHEN YOU STARTED TO SMOKE** + * dbGap table: **BASE1** + * No permissible values listed in PIC-SURE data dictionary + * _phs000287.v6.pht001450.v1.phv00099159.v1_ + * dbGap name: **AMOUNT08** + * dbGap desc: **HOW MANY DID YOU SMOKE PER DAY ON AVER (99=UNKNOWN)** + * dbGap table: **BASE1** + * No permissible values listed in PIC-SURE data dictionary + * _phs000287.v6.pht001452.v1.phv00100487.v1_ + * dbGap name: **AGEBL** + * dbGap desc: **CALCULATED AGE AT BASELINE** + * dbGap table: **BASEBOTH** + * No permissible values listed in PIC-SURE data dictionary + * _phs000287.v6.pht001490.v1.phv00105143.v1_ + * dbGap name: **SMOKE101** + * dbGap desc: **SMOKED IN LIFETIME** + * dbGap table: **YR5NEW** + * PIC-SURE permissible values: NO, YES + * _phs000287.v6.pht001490.v1.phv00105144.v1_ + * dbGap name: **SMOKE201** + * dbGap desc: **SMOKED CIGARETTES LAST 30 DAYS** + * dbGap table: **YR5NEW** + * PIC-SURE permissible values: NO, YES + * _phs000287.v6.pht001490.v1.phv00106198.v1_ + * dbGap name: **SMKAGE58** + * dbGap desc: **HOW OLD WHEN YOU STARTED TO SMOKE** + * dbGap table: **YR5NEW** + * No permissible values listed in PIC-SURE data dictionary + * _phs000287.v6.pht001490.v1.phv00106200.v1_ + * dbGap name: **AMOUNT58** + * dbGap desc: **HOW MANY DID YOU SMOKE PER DAY ON AVER.** + * dbGap table: **YR5NEW** + * No permissible values listed in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -593,22 +813,54 @@ * ### baseline_common_covariates/ever_smoker_baseline_1 -- **COPDGene **: * 16 component_study_variables - * _phs000179.v5.pht002239.v4.phv00159636.v4_. No dbGap metadata available. - * _phs000179.v5.pht002239.v4.phv00159637.v4_. No dbGap metadata available. - * _phs000179.v5.pht002239.v4.phv00159638.v4_. No dbGap metadata available. - * _phs000179.v5.pht002239.v4.phv00159639.v4_. No dbGap metadata available. - * _phs000179.v5.pht002239.v4.phv00159640.v4_. No dbGap metadata available. - * _phs000179.v5.pht002239.v4.phv00159641.v4_. No dbGap metadata available. - * _phs000179.v5.pht002239.v4.phv00159747.v4_. No dbGap metadata available. - * _phs000179.v5.pht002239.v4.phv00159748.v4_. No dbGap metadata available. - * _phs000179.v5.pht002239.v4.phv00159749.v4_. No dbGap metadata available. - * _phs000179.v5.pht002239.v4.phv00159750.v4_. No dbGap metadata available. - * _phs000179.v5.pht002239.v4.phv00159752.v4_. No dbGap metadata available. - * _phs000179.v5.pht002239.v4.phv00159754.v4_. No dbGap metadata available. - * _phs000179.v5.pht002239.v4.phv00159755.v4_. No dbGap metadata available. - * _phs000179.v5.pht002239.v4.phv00159756.v4_. No dbGap metadata available. - * _phs000179.v5.pht002239.v4.phv00159836.v4_. No dbGap metadata available. - * _phs000179.v5.pht002239.v4.phv00169388.v3_. No dbGap metadata available. + * _phs000179.v5.pht002239.v4.phv00159636.v4_ + * No dbGap metadata available + * PIC-SURE permissible values: After 60 min, Between 31-60 min, Between 6-30 min, With 5 min + * _phs000179.v5.pht002239.v4.phv00159637.v4_ + * No dbGap metadata available + * PIC-SURE permissible values: No, Yes + * _phs000179.v5.pht002239.v4.phv00159638.v4_ + * No dbGap metadata available + * PIC-SURE permissible values: Any other cigarette of the day, First cigarette of the day + * _phs000179.v5.pht002239.v4.phv00159639.v4_ + * No dbGap metadata available + * PIC-SURE permissible values: No, Yes + * _phs000179.v5.pht002239.v4.phv00159640.v4_ + * No dbGap metadata available + * PIC-SURE permissible values: No, Yes + * _phs000179.v5.pht002239.v4.phv00159641.v4_ + * No dbGap metadata available + * PIC-SURE permissible values: No, Yes + * _phs000179.v5.pht002239.v4.phv00159747.v4_ + * No dbGap metadata available + * PIC-SURE permissible values: No, Yes + * _phs000179.v5.pht002239.v4.phv00159748.v4_ + * No dbGap metadata available + * No permissible values listed in PIC-SURE data dictionary + * _phs000179.v5.pht002239.v4.phv00159749.v4_ + * No dbGap metadata available + * PIC-SURE permissible values: No, Yes + * _phs000179.v5.pht002239.v4.phv00159750.v4_ + * No dbGap metadata available + * No permissible values listed in PIC-SURE data dictionary + * _phs000179.v5.pht002239.v4.phv00159752.v4_ + * No dbGap metadata available + * No permissible values listed in PIC-SURE data dictionary + * _phs000179.v5.pht002239.v4.phv00159754.v4_ + * No dbGap metadata available + * No permissible values listed in PIC-SURE data dictionary + * _phs000179.v5.pht002239.v4.phv00159755.v4_ + * No dbGap metadata available + * No permissible values listed in PIC-SURE data dictionary + * _phs000179.v5.pht002239.v4.phv00159756.v4_ + * No dbGap metadata available + * No permissible values listed in PIC-SURE data dictionary + * _phs000179.v5.pht002239.v4.phv00159836.v4_ + * No dbGap metadata available + * No permissible values listed in PIC-SURE data dictionary + * _phs000179.v5.pht002239.v4.phv00169388.v3_ + * No dbGap metadata available + * No permissible values listed in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -633,11 +885,31 @@ * ### baseline_common_covariates/ever_smoker_baseline_1 -- **HCHS_SOL Hispanic Community Health Study /Study of Latinos (HCHS/SOL)**: * 5 component_study_variables - * _phs000810.v1.pht004715.v1.phv00226251.v1_. dbGap Name: **AGE**, Desc: **Age**, Table: **HCHS_SOL_Cohort_Subject_Phenotypes**. - * _phs000810.v1.pht004715.v1.phv00258106.v1_. dbGap Name: **TBEA1**, Desc: **Smoke at least 100 cigs in lifetime (TBEA1)**, Table: **HCHS_SOL_Cohort_Subject_Phenotypes**. - * _phs000810.v1.pht004715.v1.phv00258107.v1_. dbGap Name: **TBEA3**, Desc: **Present Smoking Status (TBEA3)**, Table: **HCHS_SOL_Cohort_Subject_Phenotypes**. - * _phs000810.v1.pht004715.v1.phv00258108.v1_. dbGap Name: **TBEA4**, Desc: **Daily: Cigs per Day - Present (TBEA4)**, Table: **HCHS_SOL_Cohort_Subject_Phenotypes**. - * _phs000810.v1.pht004715.v1.phv00258110.v1_. dbGap Name: **TBEA5A**, Desc: **Some: Past 30 days - quit smoking 6 months or longer (TBEA5A)**, Table: **HCHS_SOL_Cohort_Subject_Phenotypes**. + * _phs000810.v1.pht004715.v1.phv00226251.v1_ + * dbGap name: **AGE** + * dbGap desc: **Age** + * dbGap table: **HCHS_SOL_Cohort_Subject_Phenotypes** + * No permissible values listed in PIC-SURE data dictionary + * _phs000810.v1.pht004715.v1.phv00258106.v1_ + * dbGap name: **TBEA1** + * dbGap desc: **Smoke at least 100 cigs in lifetime (TBEA1)** + * dbGap table: **HCHS_SOL_Cohort_Subject_Phenotypes** + * PIC-SURE permissible values: No, Yes + * _phs000810.v1.pht004715.v1.phv00258107.v1_ + * dbGap name: **TBEA3** + * dbGap desc: **Present Smoking Status (TBEA3)** + * dbGap table: **HCHS_SOL_Cohort_Subject_Phenotypes** + * PIC-SURE permissible values: Daily, Not at all, Some days + * _phs000810.v1.pht004715.v1.phv00258108.v1_ + * dbGap name: **TBEA4** + * dbGap desc: **Daily: Cigs per Day - Present (TBEA4)** + * dbGap table: **HCHS_SOL_Cohort_Subject_Phenotypes** + * No permissible values listed in PIC-SURE data dictionary + * _phs000810.v1.pht004715.v1.phv00258110.v1_ + * dbGap name: **TBEA5A** + * dbGap desc: **Some: Past 30 days - quit smoking 6 months or longer (TBEA5A)** + * dbGap table: **HCHS_SOL_Cohort_Subject_Phenotypes** + * No permissible values listed in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -670,13 +942,39 @@ * ### baseline_common_covariates/ever_smoker_baseline_1 -- **JHS Jackson Heart Study (JHS) Cohort**: * 7 component_study_variables - * _phs000286.v5.pht001949.v1.phv00126009.v1_. No dbGap metadata available. - * _phs000286.v5.pht001977.v1.phv00128496.v1_. dbGap Name: **TOBA1**, Desc: **Q1. Smoked at least 400 cigarettes in your lifetime [Visit 1] [Health Practices: Tobacco Use, TOB]**, Table: **toba**. - * _phs000286.v5.pht001977.v1.phv00128498.v1_. dbGap Name: **TOBA3**, Desc: **Q3. Do you now smoke cigarettes [Visit 1] [Health Practices: Tobacco Use, TOB]**, Table: **toba**. - * _phs000286.v5.pht001977.v1.phv00128502.v1_. dbGap Name: **TOBA6**, Desc: **Q6. Do you smoke more frequently during the first few hours after awakening than during the rest of the day? [Visit 1] [Health Practices: Tobacco Use, TOB]**, Table: **toba**. - * _phs000286.v5.pht001977.v1.phv00128503.v1_. dbGap Name: **TOBA7**, Desc: **Q7. How soon after you wake up do you smoke your first cigarette? [Visit 1] [Health Practices: Tobacco Use, TOB]**, Table: **toba**. - * _phs000286.v5.pht001977.v1.phv00128506.v1_. dbGap Name: **TOBA10**, Desc: **Q10. Do you smoke if you are so ill that you are in bed most of the day? [Visit 1] [Health Practices: Tobacco Use, TOB]**, Table: **toba**. - * _phs000286.v5.pht001977.v1.phv00128507.v1_. dbGap Name: **TOBA11**, Desc: **Q11. On the average for the entire time you have smoked, how many cigarettes did you smoke usually per day? [Visit 1] [Health Practices: Tobacco Use, TOB]**, Table: **toba**. + * _phs000286.v5.pht001949.v1.phv00126009.v1_ + * No dbGap metadata available + * varId _phv00126009_ not found in PIC-SURE data dictionary + * _phs000286.v5.pht001977.v1.phv00128496.v1_ + * dbGap name: **TOBA1** + * dbGap desc: **Q1. Smoked at least 400 cigarettes in your lifetime [Visit 1] [Health Practices: Tobacco Use, TOB]** + * dbGap table: **toba** + * varId _phv00128496_ not found in PIC-SURE data dictionary + * _phs000286.v5.pht001977.v1.phv00128498.v1_ + * dbGap name: **TOBA3** + * dbGap desc: **Q3. Do you now smoke cigarettes [Visit 1] [Health Practices: Tobacco Use, TOB]** + * dbGap table: **toba** + * varId _phv00128498_ not found in PIC-SURE data dictionary + * _phs000286.v5.pht001977.v1.phv00128502.v1_ + * dbGap name: **TOBA6** + * dbGap desc: **Q6. Do you smoke more frequently during the first few hours after awakening than during the rest of the day? [Visit 1] [Health Practices: Tobacco Use, TOB]** + * dbGap table: **toba** + * varId _phv00128502_ not found in PIC-SURE data dictionary + * _phs000286.v5.pht001977.v1.phv00128503.v1_ + * dbGap name: **TOBA7** + * dbGap desc: **Q7. How soon after you wake up do you smoke your first cigarette? [Visit 1] [Health Practices: Tobacco Use, TOB]** + * dbGap table: **toba** + * varId _phv00128503_ not found in PIC-SURE data dictionary + * _phs000286.v5.pht001977.v1.phv00128506.v1_ + * dbGap name: **TOBA10** + * dbGap desc: **Q10. Do you smoke if you are so ill that you are in bed most of the day? [Visit 1] [Health Practices: Tobacco Use, TOB]** + * dbGap table: **toba** + * varId _phv00128506_ not found in PIC-SURE data dictionary + * _phs000286.v5.pht001977.v1.phv00128507.v1_ + * dbGap name: **TOBA11** + * dbGap desc: **Q11. On the average for the entire time you have smoked, how many cigarettes did you smoke usually per day? [Visit 1] [Health Practices: Tobacco Use, TOB]** + * dbGap table: **toba** + * varId _phv00128507_ not found in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -711,18 +1009,66 @@ * ### baseline_common_covariates/ever_smoker_baseline_1 -- **MESA Multi-Ethnic Study of Atherosclerosis (MESA) Cohort**: * 12 component_study_variables - * _phs000209.v13.pht001111.v4.phv00082639.v2_. dbGap Name: **age1c**, Desc: **AGE**, Table: **MESA_AirNRExamMain**. - * _phs000209.v13.pht001111.v4.phv00083243.v1_. dbGap Name: **evsmk1**, Desc: **SMOKED AT LEAST 100 CIGARETTES IN LIFETIME**, Table: **MESA_AirNRExamMain**. - * _phs000209.v13.pht001111.v4.phv00083245.v1_. dbGap Name: **cursmk1**, Desc: **CIGARETTES: SMOKED IN LAST 30 DAYS**, Table: **MESA_AirNRExamMain**. - * _phs000209.v13.pht001111.v4.phv00083247.v1_. dbGap Name: **cigsday1**, Desc: **CIGARETTES: AVERAGE # SMOKED PER DAY**, Table: **MESA_AirNRExamMain**. - * _phs000209.v13.pht001116.v10.phv00084442.v3_. dbGap Name: **age1c**, Desc: **AGE**, Table: **MESA_Exam1Main**. - * _phs000209.v13.pht001116.v10.phv00085570.v2_. dbGap Name: **evsmk1**, Desc: **SMOKED AT LEAST 100 CIGARETTES IN LIFETIME**, Table: **MESA_Exam1Main**. - * _phs000209.v13.pht001116.v10.phv00085572.v2_. dbGap Name: **cursmk1**, Desc: **CIGARETTES: SMOKED IN LAST 30 DAYS**, Table: **MESA_Exam1Main**. - * _phs000209.v13.pht001116.v10.phv00085574.v2_. dbGap Name: **cigsday1**, Desc: **CIGARETTES: AVERAGE # SMOKED PER DAY**, Table: **MESA_Exam1Main**. - * _phs000209.v13.pht001121.v3.phv00087071.v1_. dbGap Name: **agefc**, Desc: **AGE**, Table: **MESA_FamilyExamMain**. - * _phs000209.v13.pht001121.v3.phv00087252.v1_. dbGap Name: **evsmkf**, Desc: **SMOKED 100+ CIGARETTES IN LIFETIME**, Table: **MESA_FamilyExamMain**. - * _phs000209.v13.pht001121.v3.phv00087254.v1_. dbGap Name: **cursmkf**, Desc: **SMOKED CIGARETTES IN THE LAST 30 DAYS**, Table: **MESA_FamilyExamMain**. - * _phs000209.v13.pht001121.v3.phv00087256.v1_. dbGap Name: **cigsdayf**, Desc: **AVERAGE NUMBER OF CIGARETTES SMOKED PER DAY**, Table: **MESA_FamilyExamMain**. + * _phs000209.v13.pht001111.v4.phv00082639.v2_ + * dbGap name: **age1c** + * dbGap desc: **AGE** + * dbGap table: **MESA_AirNRExamMain** + * No permissible values listed in PIC-SURE data dictionary + * _phs000209.v13.pht001111.v4.phv00083243.v1_ + * dbGap name: **evsmk1** + * dbGap desc: **SMOKED AT LEAST 100 CIGARETTES IN LIFETIME** + * dbGap table: **MESA_AirNRExamMain** + * PIC-SURE permissible values: NO, YES + * _phs000209.v13.pht001111.v4.phv00083245.v1_ + * dbGap name: **cursmk1** + * dbGap desc: **CIGARETTES: SMOKED IN LAST 30 DAYS** + * dbGap table: **MESA_AirNRExamMain** + * PIC-SURE permissible values: NO, YES + * _phs000209.v13.pht001111.v4.phv00083247.v1_ + * dbGap name: **cigsday1** + * dbGap desc: **CIGARETTES: AVERAGE # SMOKED PER DAY** + * dbGap table: **MESA_AirNRExamMain** + * PIC-SURE permissible values: 0, 1, 10, 15, 18, 2, 20, 25, 28, 3, 30, 35, 4, 40, 45, 5, 50, 6, 60, 7, 8 + * _phs000209.v13.pht001116.v10.phv00084442.v3_ + * dbGap name: **age1c** + * dbGap desc: **AGE** + * dbGap table: **MESA_Exam1Main** + * No permissible values listed in PIC-SURE data dictionary + * _phs000209.v13.pht001116.v10.phv00085570.v2_ + * dbGap name: **evsmk1** + * dbGap desc: **SMOKED AT LEAST 100 CIGARETTES IN LIFETIME** + * dbGap table: **MESA_Exam1Main** + * PIC-SURE permissible values: NO, YES + * _phs000209.v13.pht001116.v10.phv00085572.v2_ + * dbGap name: **cursmk1** + * dbGap desc: **CIGARETTES: SMOKED IN LAST 30 DAYS** + * dbGap table: **MESA_Exam1Main** + * PIC-SURE permissible values: NO, YES + * _phs000209.v13.pht001116.v10.phv00085574.v2_ + * dbGap name: **cigsday1** + * dbGap desc: **CIGARETTES: AVERAGE # SMOKED PER DAY** + * dbGap table: **MESA_Exam1Main** + * PIC-SURE permissible values: 0, 1, 10, 100, 11, 12, 120, 13, 14, 15, 16, 17, 18, 19, 2, 20, 21, 22, 220, 23, 24, 25, 26, 28, 3, 30, 32, 35, 36, 4, 40, 400, 44, 444, 45, 5, 50, 55, 6, 60, 7, 70, 72, 75, 8, 80, 9, 90 + * _phs000209.v13.pht001121.v3.phv00087071.v1_ + * dbGap name: **agefc** + * dbGap desc: **AGE** + * dbGap table: **MESA_FamilyExamMain** + * No permissible values listed in PIC-SURE data dictionary + * _phs000209.v13.pht001121.v3.phv00087252.v1_ + * dbGap name: **evsmkf** + * dbGap desc: **SMOKED 100+ CIGARETTES IN LIFETIME** + * dbGap table: **MESA_FamilyExamMain** + * PIC-SURE permissible values: NO, YES + * _phs000209.v13.pht001121.v3.phv00087254.v1_ + * dbGap name: **cursmkf** + * dbGap desc: **SMOKED CIGARETTES IN THE LAST 30 DAYS** + * dbGap table: **MESA_FamilyExamMain** + * PIC-SURE permissible values: NO, YES + * _phs000209.v13.pht001121.v3.phv00087256.v1_ + * dbGap name: **cigsdayf** + * dbGap desc: **AVERAGE NUMBER OF CIGARETTES SMOKED PER DAY** + * dbGap table: **MESA_FamilyExamMain** + * PIC-SURE permissible values: 0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 2, 20, 21, 22, 24, 25, 28, 3, 30, 4, 40, 45, 5, 50, 6, 60, 7, 8, 80, 9 * **Function:** ```r harmonize <- function(phen_list){ @@ -758,10 +1104,26 @@ * ### baseline_common_covariates/ever_smoker_baseline_1 -- **WHI Women's Health Initiative**: * 4 component_study_variables - * _phs000200.v11.pht000998.v6.phv00078436.v6_. dbGap Name: **F2DAYS**, Desc: **F2 Days since randomization**, Table: **f2_rel1**. - * _phs000200.v11.pht000998.v6.phv00078437.v6_. dbGap Name: **AGE**, Desc: **Age at screening**, Table: **f2_rel1**. - * _phs000200.v11.pht001003.v6.phv00078773.v6_. dbGap Name: **F34DAYS**, Desc: **F34 Days since randomization/enrollment**, Table: **f34_rel2**. - * _phs000200.v11.pht001003.v6.phv00078774.v6_. dbGap Name: **SMOKEVR**, Desc: **Smoked at least 100 cigarettes ever**, Table: **f34_rel2**. + * _phs000200.v11.pht000998.v6.phv00078436.v6_ + * dbGap name: **F2DAYS** + * dbGap desc: **F2 Days since randomization** + * dbGap table: **f2_rel1** + * No permissible values listed in PIC-SURE data dictionary + * _phs000200.v11.pht000998.v6.phv00078437.v6_ + * dbGap name: **AGE** + * dbGap desc: **Age at screening** + * dbGap table: **f2_rel1** + * No permissible values listed in PIC-SURE data dictionary + * _phs000200.v11.pht001003.v6.phv00078773.v6_ + * dbGap name: **F34DAYS** + * dbGap desc: **F34 Days since randomization/enrollment** + * dbGap table: **f34_rel2** + * No permissible values listed in PIC-SURE data dictionary + * _phs000200.v11.pht001003.v6.phv00078774.v6_ + * dbGap name: **SMOKEVR** + * dbGap desc: **Smoked at least 100 cigarettes ever** + * dbGap table: **f34_rel2** + * PIC-SURE permissible values: No, Yes * **Function:** ```r harmonize <- function(phen_list){ @@ -859,8 +1221,16 @@ * ### baseline_common_covariates/height_baseline_1 -- **ARIC Atherosclerosis Risk in Communities (ARIC) Cohort**: * 2 component_study_variables - * _phs000280.v5.pht004032.v2.phv00203151.v1_. dbGap Name: **ANTA01**, Desc: **[Height and weight]. Standing height (to the nearest cm). Q1 [Anthropometry Form, ANTA. Visit 1]**, Table: **ANTA**. - * _phs000280.v5.pht004063.v2.phv00204712.v1_. dbGap Name: **V1AGE01**, Desc: **Age at visit 1 [Cohort. Visit 1]**, Table: **DERIVE13**. + * _phs000280.v5.pht004032.v2.phv00203151.v1_ + * dbGap name: **ANTA01** + * dbGap desc: **[Height and weight]. Standing height (to the nearest cm). Q1 [Anthropometry Form, ANTA. Visit 1]** + * dbGap table: **ANTA** + * varId _phv00203151_ not found in PIC-SURE data dictionary + * _phs000280.v5.pht004063.v2.phv00204712.v1_ + * dbGap name: **V1AGE01** + * dbGap desc: **Age at visit 1 [Cohort. Visit 1]** + * dbGap table: **DERIVE13** + * varId _phv00204712_ not found in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -883,8 +1253,16 @@ * ### baseline_common_covariates/height_baseline_1 -- **CARDIA CARDIA Cohort**: * 2 component_study_variables - * _phs000285.v3.pht001559.v2.phv00112439.v2_. dbGap Name: **A01AGE2**, Desc: **AGE VERIFY**, Table: **A4F01**. - * _phs000285.v3.pht001583.v2.phv00113634.v2_. dbGap Name: **A20HGT**, Desc: **PT'S HGT, CM. Q 1**, Table: **A4F20**. + * _phs000285.v3.pht001559.v2.phv00112439.v2_ + * dbGap name: **A01AGE2** + * dbGap desc: **AGE VERIFY** + * dbGap table: **A4F01** + * varId _phv00112439_ not found in PIC-SURE data dictionary + * _phs000285.v3.pht001583.v2.phv00113634.v2_ + * dbGap name: **A20HGT** + * dbGap desc: **PT'S HGT, CM. Q 1** + * dbGap table: **A4F20** + * varId _phv00113634_ not found in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -902,8 +1280,16 @@ * ### baseline_common_covariates/height_baseline_1 -- **CHS Cardiovascular Health Study (CHS) Cohort: an NHLBI-funded observational study of risk factors for cardiovascular disease in adults 65 years or older**: * 2 component_study_variables - * _phs000287.v6.pht001452.v1.phv00100382.v1_. dbGap Name: **STHT13**, Desc: **STANDING HEIGHT - CM**, Table: **BASEBOTH**. - * _phs000287.v6.pht001452.v1.phv00100487.v1_. dbGap Name: **AGEBL**, Desc: **CALCULATED AGE AT BASELINE**, Table: **BASEBOTH**. + * _phs000287.v6.pht001452.v1.phv00100382.v1_ + * dbGap name: **STHT13** + * dbGap desc: **STANDING HEIGHT - CM** + * dbGap table: **BASEBOTH** + * No permissible values listed in PIC-SURE data dictionary + * _phs000287.v6.pht001452.v1.phv00100487.v1_ + * dbGap name: **AGEBL** + * dbGap desc: **CALCULATED AGE AT BASELINE** + * dbGap table: **BASEBOTH** + * No permissible values listed in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -923,8 +1309,12 @@ * ### baseline_common_covariates/height_baseline_1 -- **COPDGene **: * 2 component_study_variables - * _phs000179.v5.pht002239.v4.phv00159592.v4_. No dbGap metadata available. - * _phs000179.v5.pht002239.v4.phv00159836.v4_. No dbGap metadata available. + * _phs000179.v5.pht002239.v4.phv00159592.v4_ + * No dbGap metadata available + * No permissible values listed in PIC-SURE data dictionary + * _phs000179.v5.pht002239.v4.phv00159836.v4_ + * No dbGap metadata available + * No permissible values listed in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -943,8 +1333,16 @@ * ### baseline_common_covariates/height_baseline_1 -- **HCHS_SOL Hispanic Community Health Study /Study of Latinos (HCHS/SOL)**: * 2 component_study_variables - * _phs000810.v1.pht004715.v1.phv00226251.v1_. dbGap Name: **AGE**, Desc: **Age**, Table: **HCHS_SOL_Cohort_Subject_Phenotypes**. - * _phs000810.v1.pht004715.v1.phv00226281.v1_. dbGap Name: **HEIGHT**, Desc: **Height (corrected)**, Table: **HCHS_SOL_Cohort_Subject_Phenotypes**. + * _phs000810.v1.pht004715.v1.phv00226251.v1_ + * dbGap name: **AGE** + * dbGap desc: **Age** + * dbGap table: **HCHS_SOL_Cohort_Subject_Phenotypes** + * No permissible values listed in PIC-SURE data dictionary + * _phs000810.v1.pht004715.v1.phv00226281.v1_ + * dbGap name: **HEIGHT** + * dbGap desc: **Height (corrected)** + * dbGap table: **HCHS_SOL_Cohort_Subject_Phenotypes** + * No permissible values listed in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -962,8 +1360,14 @@ * ### baseline_common_covariates/height_baseline_1 -- **JHS Jackson Heart Study (JHS) Cohort**: * 2 component_study_variables - * _phs000286.v5.pht001940.v1.phv00125860.v1_. dbGap Name: **antv1**, Desc: **A. Height and weight. 1: Standing height to nearest cm [Visit 1]**, Table: **antv**. - * _phs000286.v5.pht001949.v1.phv00126009.v1_. No dbGap metadata available. + * _phs000286.v5.pht001940.v1.phv00125860.v1_ + * dbGap name: **antv1** + * dbGap desc: **A. Height and weight. 1: Standing height to nearest cm [Visit 1]** + * dbGap table: **antv** + * varId _phv00125860_ not found in PIC-SURE data dictionary + * _phs000286.v5.pht001949.v1.phv00126009.v1_ + * No dbGap metadata available + * varId _phv00126009_ not found in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -986,12 +1390,36 @@ * ### baseline_common_covariates/height_baseline_1 -- **MESA Multi-Ethnic Study of Atherosclerosis (MESA) Cohort**: * 6 component_study_variables - * _phs000209.v13.pht001111.v4.phv00082639.v2_. dbGap Name: **age1c**, Desc: **AGE**, Table: **MESA_AirNRExamMain**. - * _phs000209.v13.pht001111.v4.phv00082683.v1_. dbGap Name: **htcm1**, Desc: **HEIGHT (cm)**, Table: **MESA_AirNRExamMain**. - * _phs000209.v13.pht001116.v10.phv00084442.v3_. dbGap Name: **age1c**, Desc: **AGE**, Table: **MESA_Exam1Main**. - * _phs000209.v13.pht001116.v10.phv00084482.v2_. dbGap Name: **htcm1**, Desc: **HEIGHT (cm)**, Table: **MESA_Exam1Main**. - * _phs000209.v13.pht001121.v3.phv00087071.v1_. dbGap Name: **agefc**, Desc: **AGE**, Table: **MESA_FamilyExamMain**. - * _phs000209.v13.pht001121.v3.phv00087078.v1_. dbGap Name: **htcmf**, Desc: **HEIGHT (cm)**, Table: **MESA_FamilyExamMain**. + * _phs000209.v13.pht001111.v4.phv00082639.v2_ + * dbGap name: **age1c** + * dbGap desc: **AGE** + * dbGap table: **MESA_AirNRExamMain** + * No permissible values listed in PIC-SURE data dictionary + * _phs000209.v13.pht001111.v4.phv00082683.v1_ + * dbGap name: **htcm1** + * dbGap desc: **HEIGHT (cm)** + * dbGap table: **MESA_AirNRExamMain** + * No permissible values listed in PIC-SURE data dictionary + * _phs000209.v13.pht001116.v10.phv00084442.v3_ + * dbGap name: **age1c** + * dbGap desc: **AGE** + * dbGap table: **MESA_Exam1Main** + * No permissible values listed in PIC-SURE data dictionary + * _phs000209.v13.pht001116.v10.phv00084482.v2_ + * dbGap name: **htcm1** + * dbGap desc: **HEIGHT (cm)** + * dbGap table: **MESA_Exam1Main** + * No permissible values listed in PIC-SURE data dictionary + * _phs000209.v13.pht001121.v3.phv00087071.v1_ + * dbGap name: **agefc** + * dbGap desc: **AGE** + * dbGap table: **MESA_FamilyExamMain** + * No permissible values listed in PIC-SURE data dictionary + * _phs000209.v13.pht001121.v3.phv00087078.v1_ + * dbGap name: **htcmf** + * dbGap desc: **HEIGHT (cm)** + * dbGap table: **MESA_FamilyExamMain** + * No permissible values listed in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -1017,11 +1445,31 @@ * ### baseline_common_covariates/height_baseline_1 -- **WHI Women's Health Initiative**: * 5 component_study_variables - * _phs000200.v11.pht000998.v6.phv00078436.v6_. dbGap Name: **F2DAYS**, Desc: **F2 Days since randomization**, Table: **f2_rel1**. - * _phs000200.v11.pht000998.v6.phv00078437.v6_. dbGap Name: **AGE**, Desc: **Age at screening**, Table: **f2_rel1**. - * _phs000200.v11.pht001019.v6.phv00079851.v6_. dbGap Name: **F80VY**, Desc: **Visit year**, Table: **f80_rel1**. - * _phs000200.v11.pht001019.v6.phv00079852.v6_. dbGap Name: **F80DAYS**, Desc: **F80 Days since randomization/enrollment**, Table: **f80_rel1**. - * _phs000200.v11.pht001019.v6.phv00079858.v6_. dbGap Name: **HEIGHTX**, Desc: **F80 Height cm**, Table: **f80_rel1**. + * _phs000200.v11.pht000998.v6.phv00078436.v6_ + * dbGap name: **F2DAYS** + * dbGap desc: **F2 Days since randomization** + * dbGap table: **f2_rel1** + * No permissible values listed in PIC-SURE data dictionary + * _phs000200.v11.pht000998.v6.phv00078437.v6_ + * dbGap name: **AGE** + * dbGap desc: **Age at screening** + * dbGap table: **f2_rel1** + * No permissible values listed in PIC-SURE data dictionary + * _phs000200.v11.pht001019.v6.phv00079851.v6_ + * dbGap name: **F80VY** + * dbGap desc: **Visit year** + * dbGap table: **f80_rel1** + * No permissible values listed in PIC-SURE data dictionary + * _phs000200.v11.pht001019.v6.phv00079852.v6_ + * dbGap name: **F80DAYS** + * dbGap desc: **F80 Days since randomization/enrollment** + * dbGap table: **f80_rel1** + * No permissible values listed in PIC-SURE data dictionary + * _phs000200.v11.pht001019.v6.phv00079858.v6_ + * dbGap name: **HEIGHTX** + * dbGap desc: **F80 Height cm** + * dbGap table: **f80_rel1** + * No permissible values listed in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -1132,8 +1580,16 @@ * ### baseline_common_covariates/weight_baseline_1 -- **ARIC Atherosclerosis Risk in Communities (ARIC) Cohort**: * 2 component_study_variables - * _phs000280.v5.pht004032.v2.phv00203154.v1_. dbGap Name: **ANTA04**, Desc: **[Height and weight]. Weight (to the nearest lb). Q4 [Anthropometry Form, ANTA. Visit 1]**, Table: **ANTA**. - * _phs000280.v5.pht004063.v2.phv00204712.v1_. dbGap Name: **V1AGE01**, Desc: **Age at visit 1 [Cohort. Visit 1]**, Table: **DERIVE13**. + * _phs000280.v5.pht004032.v2.phv00203154.v1_ + * dbGap name: **ANTA04** + * dbGap desc: **[Height and weight]. Weight (to the nearest lb). Q4 [Anthropometry Form, ANTA. Visit 1]** + * dbGap table: **ANTA** + * varId _phv00203154_ not found in PIC-SURE data dictionary + * _phs000280.v5.pht004063.v2.phv00204712.v1_ + * dbGap name: **V1AGE01** + * dbGap desc: **Age at visit 1 [Cohort. Visit 1]** + * dbGap table: **DERIVE13** + * varId _phv00204712_ not found in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -1158,8 +1614,16 @@ * ### baseline_common_covariates/weight_baseline_1 -- **CARDIA CARDIA Cohort**: * 2 component_study_variables - * _phs000285.v3.pht001559.v2.phv00112439.v2_. dbGap Name: **A01AGE2**, Desc: **AGE VERIFY**, Table: **A4F01**. - * _phs000285.v3.pht001583.v2.phv00113635.v2_. dbGap Name: **A20WGT**, Desc: **PT'S WGT, LBS. Q 2**, Table: **A4F20**. + * _phs000285.v3.pht001559.v2.phv00112439.v2_ + * dbGap name: **A01AGE2** + * dbGap desc: **AGE VERIFY** + * dbGap table: **A4F01** + * varId _phv00112439_ not found in PIC-SURE data dictionary + * _phs000285.v3.pht001583.v2.phv00113635.v2_ + * dbGap name: **A20WGT** + * dbGap desc: **PT'S WGT, LBS. Q 2** + * dbGap table: **A4F20** + * varId _phv00113635_ not found in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -1176,8 +1640,16 @@ * ### baseline_common_covariates/weight_baseline_1 -- **CHS Cardiovascular Health Study (CHS) Cohort: an NHLBI-funded observational study of risk factors for cardiovascular disease in adults 65 years or older**: * 2 component_study_variables - * _phs000287.v6.pht001452.v1.phv00100383.v1_. dbGap Name: **WEIGHT13**, Desc: **WEIGHT - LBS**, Table: **BASEBOTH**. - * _phs000287.v6.pht001452.v1.phv00100487.v1_. dbGap Name: **AGEBL**, Desc: **CALCULATED AGE AT BASELINE**, Table: **BASEBOTH**. + * _phs000287.v6.pht001452.v1.phv00100383.v1_ + * dbGap name: **WEIGHT13** + * dbGap desc: **WEIGHT - LBS** + * dbGap table: **BASEBOTH** + * No permissible values listed in PIC-SURE data dictionary + * _phs000287.v6.pht001452.v1.phv00100487.v1_ + * dbGap name: **AGEBL** + * dbGap desc: **CALCULATED AGE AT BASELINE** + * dbGap table: **BASEBOTH** + * No permissible values listed in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -1196,8 +1668,12 @@ * ### baseline_common_covariates/weight_baseline_1 -- **COPDGene **: * 2 component_study_variables - * _phs000179.v5.pht002239.v4.phv00159591.v4_. No dbGap metadata available. - * _phs000179.v5.pht002239.v4.phv00159836.v4_. No dbGap metadata available. + * _phs000179.v5.pht002239.v4.phv00159591.v4_ + * No dbGap metadata available + * No permissible values listed in PIC-SURE data dictionary + * _phs000179.v5.pht002239.v4.phv00159836.v4_ + * No dbGap metadata available + * No permissible values listed in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -1217,8 +1693,16 @@ * ### baseline_common_covariates/weight_baseline_1 -- **HCHS_SOL Hispanic Community Health Study /Study of Latinos (HCHS/SOL)**: * 2 component_study_variables - * _phs000810.v1.pht004715.v1.phv00226251.v1_. dbGap Name: **AGE**, Desc: **Age**, Table: **HCHS_SOL_Cohort_Subject_Phenotypes**. - * _phs000810.v1.pht004715.v1.phv00253218.v1_. dbGap Name: **ANTA4**, Desc: **Weight (kg) (ANTA4)**, Table: **HCHS_SOL_Cohort_Subject_Phenotypes**. + * _phs000810.v1.pht004715.v1.phv00226251.v1_ + * dbGap name: **AGE** + * dbGap desc: **Age** + * dbGap table: **HCHS_SOL_Cohort_Subject_Phenotypes** + * No permissible values listed in PIC-SURE data dictionary + * _phs000810.v1.pht004715.v1.phv00253218.v1_ + * dbGap name: **ANTA4** + * dbGap desc: **Weight (kg) (ANTA4)** + * dbGap table: **HCHS_SOL_Cohort_Subject_Phenotypes** + * No permissible values listed in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -1236,8 +1720,14 @@ * ### baseline_common_covariates/weight_baseline_1 -- **JHS Jackson Heart Study (JHS) Cohort**: * 2 component_study_variables - * _phs000286.v5.pht001940.v1.phv00125861.v1_. dbGap Name: **antv2**, Desc: **A. Height and weight. 2: Weight to nearest kilogram [Visit 1]**, Table: **antv**. - * _phs000286.v5.pht001949.v1.phv00126009.v1_. No dbGap metadata available. + * _phs000286.v5.pht001940.v1.phv00125861.v1_ + * dbGap name: **antv2** + * dbGap desc: **A. Height and weight. 2: Weight to nearest kilogram [Visit 1]** + * dbGap table: **antv** + * varId _phv00125861_ not found in PIC-SURE data dictionary + * _phs000286.v5.pht001949.v1.phv00126009.v1_ + * No dbGap metadata available + * varId _phv00126009_ not found in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -1260,12 +1750,36 @@ * ### baseline_common_covariates/weight_baseline_1 -- **MESA Multi-Ethnic Study of Atherosclerosis (MESA) Cohort**: * 6 component_study_variables - * _phs000209.v13.pht001111.v4.phv00082639.v2_. dbGap Name: **age1c**, Desc: **AGE**, Table: **MESA_AirNRExamMain**. - * _phs000209.v13.pht001111.v4.phv00082685.v1_. dbGap Name: **wtlb1**, Desc: **WEIGHT (lbs)**, Table: **MESA_AirNRExamMain**. - * _phs000209.v13.pht001116.v10.phv00084442.v3_. dbGap Name: **age1c**, Desc: **AGE**, Table: **MESA_Exam1Main**. - * _phs000209.v13.pht001116.v10.phv00084484.v2_. dbGap Name: **wtlb1**, Desc: **WEIGHT (lbs)**, Table: **MESA_Exam1Main**. - * _phs000209.v13.pht001121.v3.phv00087071.v1_. dbGap Name: **agefc**, Desc: **AGE**, Table: **MESA_FamilyExamMain**. - * _phs000209.v13.pht001121.v3.phv00087079.v1_. dbGap Name: **wtlbf**, Desc: **WEIGHT (lbs)**, Table: **MESA_FamilyExamMain**. + * _phs000209.v13.pht001111.v4.phv00082639.v2_ + * dbGap name: **age1c** + * dbGap desc: **AGE** + * dbGap table: **MESA_AirNRExamMain** + * No permissible values listed in PIC-SURE data dictionary + * _phs000209.v13.pht001111.v4.phv00082685.v1_ + * dbGap name: **wtlb1** + * dbGap desc: **WEIGHT (lbs)** + * dbGap table: **MESA_AirNRExamMain** + * No permissible values listed in PIC-SURE data dictionary + * _phs000209.v13.pht001116.v10.phv00084442.v3_ + * dbGap name: **age1c** + * dbGap desc: **AGE** + * dbGap table: **MESA_Exam1Main** + * No permissible values listed in PIC-SURE data dictionary + * _phs000209.v13.pht001116.v10.phv00084484.v2_ + * dbGap name: **wtlb1** + * dbGap desc: **WEIGHT (lbs)** + * dbGap table: **MESA_Exam1Main** + * No permissible values listed in PIC-SURE data dictionary + * _phs000209.v13.pht001121.v3.phv00087071.v1_ + * dbGap name: **agefc** + * dbGap desc: **AGE** + * dbGap table: **MESA_FamilyExamMain** + * No permissible values listed in PIC-SURE data dictionary + * _phs000209.v13.pht001121.v3.phv00087079.v1_ + * dbGap name: **wtlbf** + * dbGap desc: **WEIGHT (lbs)** + * dbGap table: **MESA_FamilyExamMain** + * No permissible values listed in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -1290,11 +1804,31 @@ * ### baseline_common_covariates/weight_baseline_1 -- **WHI Women's Health Initiative**: * 5 component_study_variables - * _phs000200.v11.pht000998.v6.phv00078436.v6_. dbGap Name: **F2DAYS**, Desc: **F2 Days since randomization**, Table: **f2_rel1**. - * _phs000200.v11.pht000998.v6.phv00078437.v6_. dbGap Name: **AGE**, Desc: **Age at screening**, Table: **f2_rel1**. - * _phs000200.v11.pht001019.v6.phv00079851.v6_. dbGap Name: **F80VY**, Desc: **Visit year**, Table: **f80_rel1**. - * _phs000200.v11.pht001019.v6.phv00079852.v6_. dbGap Name: **F80DAYS**, Desc: **F80 Days since randomization/enrollment**, Table: **f80_rel1**. - * _phs000200.v11.pht001019.v6.phv00079859.v6_. dbGap Name: **WEIGHTX**, Desc: **F80 Weight kg**, Table: **f80_rel1**. + * _phs000200.v11.pht000998.v6.phv00078436.v6_ + * dbGap name: **F2DAYS** + * dbGap desc: **F2 Days since randomization** + * dbGap table: **f2_rel1** + * No permissible values listed in PIC-SURE data dictionary + * _phs000200.v11.pht000998.v6.phv00078437.v6_ + * dbGap name: **AGE** + * dbGap desc: **Age at screening** + * dbGap table: **f2_rel1** + * No permissible values listed in PIC-SURE data dictionary + * _phs000200.v11.pht001019.v6.phv00079851.v6_ + * dbGap name: **F80VY** + * dbGap desc: **Visit year** + * dbGap table: **f80_rel1** + * No permissible values listed in PIC-SURE data dictionary + * _phs000200.v11.pht001019.v6.phv00079852.v6_ + * dbGap name: **F80DAYS** + * dbGap desc: **F80 Days since randomization/enrollment** + * dbGap table: **f80_rel1** + * No permissible values listed in PIC-SURE data dictionary + * _phs000200.v11.pht001019.v6.phv00079859.v6_ + * dbGap name: **WEIGHTX** + * dbGap desc: **F80 Weight kg** + * dbGap table: **f80_rel1** + * No permissible values listed in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ diff --git a/resources/human-readable-harmonized-variable-documentation/generated-doc-pages/blood_cell_count.md b/resources/human-readable-harmonized-variable-documentation/generated-doc-pages/blood_cell_count.md index f0f911a..661d1a0 100644 --- a/resources/human-readable-harmonized-variable-documentation/generated-doc-pages/blood_cell_count.md +++ b/resources/human-readable-harmonized-variable-documentation/generated-doc-pages/blood_cell_count.md @@ -67,12 +67,34 @@ * ### blood_cell_count/basophil_ncnc_bld_1 -- **ARIC Atherosclerosis Risk in Communities (ARIC) Cohort**: * 6 component_study_variables - * _phs000280.v4.pht004062.v2.phv00204623.v1_. No dbGap metadata available. - * _phs000280.v4.pht004063.v2.phv00204712.v1_. dbGap Name: **V1AGE01**, Desc: **Age at visit 1 [Cohort. Visit 1]**, Table: **DERIVE13**. - * _phs000280.v4.pht004107.v2.phv00207257.v1_. dbGap Name: **HMTA03**, Desc: **White blood count x1000/mm3 (MAV). Q3 [Hematology Form. HMTA. Visit 1]**, Table: **HMTA**. - * _phs000280.v4.pht004107.v2.phv00207264.v1_. dbGap Name: **HMTA10**, Desc: **Basophils % Q10 [Hematology Form. HMTA. Visit 1]**, Table: **HMTA**. - * _phs000280.v4.pht004108.v2.phv00207272.v1_. dbGap Name: **HMTB03**, Desc: **White blood count x1000/mm3 (MAV). Q3 [Hematology Form. HMTB. Visit 2]**, Table: **HMTB**. - * _phs000280.v4.pht004108.v2.phv00207279.v1_. dbGap Name: **HMTB10**, Desc: **Basophils %. Q10 [Hematology Form. HMTB. Visit 2]**, Table: **HMTB**. + * _phs000280.v4.pht004062.v2.phv00204623.v1_ + * No dbGap metadata available + * varId _phv00204623_ not found in PIC-SURE data dictionary + * _phs000280.v4.pht004063.v2.phv00204712.v1_ + * dbGap name: **V1AGE01** + * dbGap desc: **Age at visit 1 [Cohort. Visit 1]** + * dbGap table: **DERIVE13** + * varId _phv00204712_ not found in PIC-SURE data dictionary + * _phs000280.v4.pht004107.v2.phv00207257.v1_ + * dbGap name: **HMTA03** + * dbGap desc: **White blood count x1000/mm3 (MAV). Q3 [Hematology Form. HMTA. Visit 1]** + * dbGap table: **HMTA** + * varId _phv00207257_ not found in PIC-SURE data dictionary + * _phs000280.v4.pht004107.v2.phv00207264.v1_ + * dbGap name: **HMTA10** + * dbGap desc: **Basophils % Q10 [Hematology Form. HMTA. Visit 1]** + * dbGap table: **HMTA** + * varId _phv00207264_ not found in PIC-SURE data dictionary + * _phs000280.v4.pht004108.v2.phv00207272.v1_ + * dbGap name: **HMTB03** + * dbGap desc: **White blood count x1000/mm3 (MAV). Q3 [Hematology Form. HMTB. Visit 2]** + * dbGap table: **HMTB** + * varId _phv00207272_ not found in PIC-SURE data dictionary + * _phs000280.v4.pht004108.v2.phv00207279.v1_ + * dbGap name: **HMTB10** + * dbGap desc: **Basophils %. Q10 [Hematology Form. HMTB. Visit 2]** + * dbGap table: **HMTB** + * varId _phv00207279_ not found in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -141,9 +163,21 @@ * ### blood_cell_count/basophil_ncnc_bld_1 -- **CARDIA CARDIA Cohort**: * 3 component_study_variables - * _phs000285.v3.pht001559.v2.phv00112439.v2_. dbGap Name: **A01AGE2**, Desc: **AGE VERIFY**, Table: **A4F01**. - * _phs000285.v3.pht001563.v2.phv00112686.v2_. dbGap Name: **A05WBC**, Desc: **WHITE CELL COUNT (X 1000)**, Table: **A4F05**. - * _phs000285.v3.pht001563.v2.phv00112696.v2_. dbGap Name: **A05BASO**, Desc: **BASOPHILS (%)**, Table: **A4F05**. + * _phs000285.v3.pht001559.v2.phv00112439.v2_ + * dbGap name: **A01AGE2** + * dbGap desc: **AGE VERIFY** + * dbGap table: **A4F01** + * varId _phv00112439_ not found in PIC-SURE data dictionary + * _phs000285.v3.pht001563.v2.phv00112686.v2_ + * dbGap name: **A05WBC** + * dbGap desc: **WHITE CELL COUNT (X 1000)** + * dbGap table: **A4F05** + * varId _phv00112686_ not found in PIC-SURE data dictionary + * _phs000285.v3.pht001563.v2.phv00112696.v2_ + * dbGap name: **A05BASO** + * dbGap desc: **BASOPHILS (%)** + * dbGap table: **A4F05** + * varId _phv00112696_ not found in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -171,9 +205,21 @@ * ### blood_cell_count/basophil_ncnc_bld_1 -- **HCHS_SOL Hispanic Community Health Study /Study of Latinos (HCHS/SOL)**: * 3 component_study_variables - * _phs000810.v1.pht004715.v1.phv00226251.v1_. dbGap Name: **AGE**, Desc: **Age**, Table: **HCHS_SOL_Cohort_Subject_Phenotypes**. - * _phs000810.v1.pht004715.v1.phv00226283.v1_. dbGap Name: **LABA1**, Desc: **White Blood Count (x10e9) (LABA1)**, Table: **HCHS_SOL_Cohort_Subject_Phenotypes**. - * _phs000810.v1.pht004715.v1.phv00226288.v1_. dbGap Name: **LABA14**, Desc: **% Basophils (LABA14)**, Table: **HCHS_SOL_Cohort_Subject_Phenotypes**. + * _phs000810.v1.pht004715.v1.phv00226251.v1_ + * dbGap name: **AGE** + * dbGap desc: **Age** + * dbGap table: **HCHS_SOL_Cohort_Subject_Phenotypes** + * No permissible values listed in PIC-SURE data dictionary + * _phs000810.v1.pht004715.v1.phv00226283.v1_ + * dbGap name: **LABA1** + * dbGap desc: **White Blood Count (x10e9) (LABA1)** + * dbGap table: **HCHS_SOL_Cohort_Subject_Phenotypes** + * No permissible values listed in PIC-SURE data dictionary + * _phs000810.v1.pht004715.v1.phv00226288.v1_ + * dbGap name: **LABA14** + * dbGap desc: **% Basophils (LABA14)** + * dbGap table: **HCHS_SOL_Cohort_Subject_Phenotypes** + * No permissible values listed in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -194,9 +240,19 @@ * ### blood_cell_count/basophil_ncnc_bld_1 -- **JHS Jackson Heart Study (JHS) Cohort**: * 3 component_study_variables - * _phs000286.v5.pht001949.v1.phv00126009.v1_. No dbGap metadata available. - * _phs000286.v5.pht001959.v1.phv00127620.v1_. dbGap Name: **BASO**, Desc: **Baso: diff measure % [Visit 1]**, Table: **loca**. - * _phs000286.v5.pht001959.v1.phv00127631.v1_. dbGap Name: **WBC**, Desc: **White blood cells TH/CMM [Visit 1]**, Table: **loca**. + * _phs000286.v5.pht001949.v1.phv00126009.v1_ + * No dbGap metadata available + * varId _phv00126009_ not found in PIC-SURE data dictionary + * _phs000286.v5.pht001959.v1.phv00127620.v1_ + * dbGap name: **BASO** + * dbGap desc: **Baso: diff measure % [Visit 1]** + * dbGap table: **loca** + * varId _phv00127620_ not found in PIC-SURE data dictionary + * _phs000286.v5.pht001959.v1.phv00127631.v1_ + * dbGap name: **WBC** + * dbGap desc: **White blood cells TH/CMM [Visit 1]** + * dbGap table: **loca** + * varId _phv00127631_ not found in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list) { @@ -231,8 +287,16 @@ * ### blood_cell_count/basophil_ncnc_bld_1 -- **MESA Multi-Ethnic Study of Atherosclerosis (MESA) Cohort**: * 2 component_study_variables - * _phs000209.v13.pht003091.v3.phv00176011.v1_. dbGap Name: **age5c**, Desc: **AGE AT EXAM 5**, Table: **MESA_Exam5Main**. - * _phs000209.v13.pht004319.v1.phv00219002.v1_. dbGap Name: **basosa5**, Desc: **BASOPHIL (ABSOLUTE) (x10E3/uL)**, Table: **MESA_AncilMesaEpigenomicCBC**. + * _phs000209.v13.pht003091.v3.phv00176011.v1_ + * dbGap name: **age5c** + * dbGap desc: **AGE AT EXAM 5** + * dbGap table: **MESA_Exam5Main** + * PIC-SURE permissible values: 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94 + * _phs000209.v13.pht004319.v1.phv00219002.v1_ + * dbGap name: **basosa5** + * dbGap desc: **BASOPHIL (ABSOLUTE) (x10E3/uL)** + * dbGap table: **MESA_AncilMesaEpigenomicCBC** + * PIC-SURE permissible values: .1, .2, 0 * **Function:** ```r harmonize <- function(phen_list){ @@ -305,12 +369,34 @@ * ### blood_cell_count/eosinophil_ncnc_bld_1 -- **ARIC Atherosclerosis Risk in Communities (ARIC) Cohort**: * 6 component_study_variables - * _phs000280.v4.pht004062.v2.phv00204623.v1_. No dbGap metadata available. - * _phs000280.v4.pht004063.v2.phv00204712.v1_. dbGap Name: **V1AGE01**, Desc: **Age at visit 1 [Cohort. Visit 1]**, Table: **DERIVE13**. - * _phs000280.v4.pht004107.v2.phv00207257.v1_. dbGap Name: **HMTA03**, Desc: **White blood count x1000/mm3 (MAV). Q3 [Hematology Form. HMTA. Visit 1]**, Table: **HMTA**. - * _phs000280.v4.pht004107.v2.phv00207263.v1_. dbGap Name: **HMTA09**, Desc: **Eosinophils % Q9 [Hematology Form. HMTA. Visit 1]**, Table: **HMTA**. - * _phs000280.v4.pht004108.v2.phv00207272.v1_. dbGap Name: **HMTB03**, Desc: **White blood count x1000/mm3 (MAV). Q3 [Hematology Form. HMTB. Visit 2]**, Table: **HMTB**. - * _phs000280.v4.pht004108.v2.phv00207278.v1_. dbGap Name: **HMTB09**, Desc: **Eosinophils %. Q9 [Hematology Form. HMTB. Visit 2]**, Table: **HMTB**. + * _phs000280.v4.pht004062.v2.phv00204623.v1_ + * No dbGap metadata available + * varId _phv00204623_ not found in PIC-SURE data dictionary + * _phs000280.v4.pht004063.v2.phv00204712.v1_ + * dbGap name: **V1AGE01** + * dbGap desc: **Age at visit 1 [Cohort. Visit 1]** + * dbGap table: **DERIVE13** + * varId _phv00204712_ not found in PIC-SURE data dictionary + * _phs000280.v4.pht004107.v2.phv00207257.v1_ + * dbGap name: **HMTA03** + * dbGap desc: **White blood count x1000/mm3 (MAV). Q3 [Hematology Form. HMTA. Visit 1]** + * dbGap table: **HMTA** + * varId _phv00207257_ not found in PIC-SURE data dictionary + * _phs000280.v4.pht004107.v2.phv00207263.v1_ + * dbGap name: **HMTA09** + * dbGap desc: **Eosinophils % Q9 [Hematology Form. HMTA. Visit 1]** + * dbGap table: **HMTA** + * varId _phv00207263_ not found in PIC-SURE data dictionary + * _phs000280.v4.pht004108.v2.phv00207272.v1_ + * dbGap name: **HMTB03** + * dbGap desc: **White blood count x1000/mm3 (MAV). Q3 [Hematology Form. HMTB. Visit 2]** + * dbGap table: **HMTB** + * varId _phv00207272_ not found in PIC-SURE data dictionary + * _phs000280.v4.pht004108.v2.phv00207278.v1_ + * dbGap name: **HMTB09** + * dbGap desc: **Eosinophils %. Q9 [Hematology Form. HMTB. Visit 2]** + * dbGap table: **HMTB** + * varId _phv00207278_ not found in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -379,9 +465,21 @@ * ### blood_cell_count/eosinophil_ncnc_bld_1 -- **CARDIA CARDIA Cohort**: * 3 component_study_variables - * _phs000285.v3.pht001559.v2.phv00112439.v2_. dbGap Name: **A01AGE2**, Desc: **AGE VERIFY**, Table: **A4F01**. - * _phs000285.v3.pht001563.v2.phv00112686.v2_. dbGap Name: **A05WBC**, Desc: **WHITE CELL COUNT (X 1000)**, Table: **A4F05**. - * _phs000285.v3.pht001563.v2.phv00112693.v2_. dbGap Name: **A05EOSIN**, Desc: **EOSINPHILS (%)**, Table: **A4F05**. + * _phs000285.v3.pht001559.v2.phv00112439.v2_ + * dbGap name: **A01AGE2** + * dbGap desc: **AGE VERIFY** + * dbGap table: **A4F01** + * varId _phv00112439_ not found in PIC-SURE data dictionary + * _phs000285.v3.pht001563.v2.phv00112686.v2_ + * dbGap name: **A05WBC** + * dbGap desc: **WHITE CELL COUNT (X 1000)** + * dbGap table: **A4F05** + * varId _phv00112686_ not found in PIC-SURE data dictionary + * _phs000285.v3.pht001563.v2.phv00112693.v2_ + * dbGap name: **A05EOSIN** + * dbGap desc: **EOSINPHILS (%)** + * dbGap table: **A4F05** + * varId _phv00112693_ not found in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -409,9 +507,21 @@ * ### blood_cell_count/eosinophil_ncnc_bld_1 -- **HCHS_SOL Hispanic Community Health Study /Study of Latinos (HCHS/SOL)**: * 3 component_study_variables - * _phs000810.v1.pht004715.v1.phv00226251.v1_. dbGap Name: **AGE**, Desc: **Age**, Table: **HCHS_SOL_Cohort_Subject_Phenotypes**. - * _phs000810.v1.pht004715.v1.phv00226283.v1_. dbGap Name: **LABA1**, Desc: **White Blood Count (x10e9) (LABA1)**, Table: **HCHS_SOL_Cohort_Subject_Phenotypes**. - * _phs000810.v1.pht004715.v1.phv00226287.v1_. dbGap Name: **LABA13**, Desc: **% Eosiniphils (LABA13)**, Table: **HCHS_SOL_Cohort_Subject_Phenotypes**. + * _phs000810.v1.pht004715.v1.phv00226251.v1_ + * dbGap name: **AGE** + * dbGap desc: **Age** + * dbGap table: **HCHS_SOL_Cohort_Subject_Phenotypes** + * No permissible values listed in PIC-SURE data dictionary + * _phs000810.v1.pht004715.v1.phv00226283.v1_ + * dbGap name: **LABA1** + * dbGap desc: **White Blood Count (x10e9) (LABA1)** + * dbGap table: **HCHS_SOL_Cohort_Subject_Phenotypes** + * No permissible values listed in PIC-SURE data dictionary + * _phs000810.v1.pht004715.v1.phv00226287.v1_ + * dbGap name: **LABA13** + * dbGap desc: **% Eosiniphils (LABA13)** + * dbGap table: **HCHS_SOL_Cohort_Subject_Phenotypes** + * No permissible values listed in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -432,9 +542,19 @@ * ### blood_cell_count/eosinophil_ncnc_bld_1 -- **JHS Jackson Heart Study (JHS) Cohort**: * 3 component_study_variables - * _phs000286.v5.pht001949.v1.phv00126009.v1_. No dbGap metadata available. - * _phs000286.v5.pht001959.v1.phv00127621.v1_. dbGap Name: **EOSIN**, Desc: **Eosin: diff measure % [Visit 1]**, Table: **loca**. - * _phs000286.v5.pht001959.v1.phv00127631.v1_. dbGap Name: **WBC**, Desc: **White blood cells TH/CMM [Visit 1]**, Table: **loca**. + * _phs000286.v5.pht001949.v1.phv00126009.v1_ + * No dbGap metadata available + * varId _phv00126009_ not found in PIC-SURE data dictionary + * _phs000286.v5.pht001959.v1.phv00127621.v1_ + * dbGap name: **EOSIN** + * dbGap desc: **Eosin: diff measure % [Visit 1]** + * dbGap table: **loca** + * varId _phv00127621_ not found in PIC-SURE data dictionary + * _phs000286.v5.pht001959.v1.phv00127631.v1_ + * dbGap name: **WBC** + * dbGap desc: **White blood cells TH/CMM [Visit 1]** + * dbGap table: **loca** + * varId _phv00127631_ not found in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list) { @@ -469,8 +589,16 @@ * ### blood_cell_count/eosinophil_ncnc_bld_1 -- **MESA Multi-Ethnic Study of Atherosclerosis (MESA) Cohort**: * 2 component_study_variables - * _phs000209.v13.pht003091.v3.phv00176011.v1_. dbGap Name: **age5c**, Desc: **AGE AT EXAM 5**, Table: **MESA_Exam5Main**. - * _phs000209.v13.pht004319.v1.phv00219001.v1_. dbGap Name: **eosa5**, Desc: **EOSINOPHILS (ABSOLUTE) (x10E3/uL)**, Table: **MESA_AncilMesaEpigenomicCBC**. + * _phs000209.v13.pht003091.v3.phv00176011.v1_ + * dbGap name: **age5c** + * dbGap desc: **AGE AT EXAM 5** + * dbGap table: **MESA_Exam5Main** + * PIC-SURE permissible values: 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94 + * _phs000209.v13.pht004319.v1.phv00219001.v1_ + * dbGap name: **eosa5** + * dbGap desc: **EOSINOPHILS (ABSOLUTE) (x10E3/uL)** + * dbGap table: **MESA_AncilMesaEpigenomicCBC** + * PIC-SURE permissible values: .1, .2, .3, .4, .5, .6, .7, .8, .9, 0, 1, 1.2, 1.3, 1.4, 1.6, 1.7 * **Function:** ```r harmonize <- function(phen_list){ @@ -534,16 +662,50 @@ * ### blood_cell_count/hematocrit_vfr_bld_1 -- **ARIC Atherosclerosis Risk in Communities (ARIC) Cohort**: * 10 component_study_variables - * _phs000280.v4.pht004062.v2.phv00204623.v1_. No dbGap metadata available. - * _phs000280.v4.pht004063.v2.phv00204712.v1_. dbGap Name: **V1AGE01**, Desc: **Age at visit 1 [Cohort. Visit 1]**, Table: **DERIVE13**. - * _phs000280.v4.pht004064.v2.phv00204871.v1_. dbGap Name: **V3AGE31**, Desc: **Age at visit 3 [Cohort. Visit 3]**, Table: **DERIVE37**. - * _phs000280.v4.pht004065.v2.phv00204975.v1_. No dbGap metadata available. - * _phs000280.v4.pht004107.v2.phv00207255.v1_. dbGap Name: **HMTA01**, Desc: **Hematocrit % (MAV). Q1 [Hematology Form. HMTA. Visit 1]**, Table: **HMTA**. - * _phs000280.v4.pht004108.v2.phv00207270.v1_. dbGap Name: **HMTB01**, Desc: **Hematocrit % (MAV). Q1 [Hematology Form. HMTB. Visit 2]**, Table: **HMTB**. - * _phs000280.v4.pht004109.v2.phv00207289.v1_. dbGap Name: **HMTC5**, Desc: **Hematocrit. Q5 [Hematology Lab. HMTCV301. Visit 3]**, Table: **HMTCV301**. - * _phs000280.v4.pht004110.v2.phv00207301.v1_. dbGap Name: **HMTC5**, Desc: **Hematocrit. Q5 [Hematology Lab. HMTCV401. Visit 4]**, Table: **HMTCV401**. - * _phs000280.v4.pht006422.v1.phv00294957.v1_. dbGap Name: **CBC6**, Desc: **Hematocrit, Hct [Complete Blood Count, CBC, Visit 5]**, Table: **CBC**. - * _phs000280.v4.pht006431.v1.phv00295623.v1_. No dbGap metadata available. + * _phs000280.v4.pht004062.v2.phv00204623.v1_ + * No dbGap metadata available + * varId _phv00204623_ not found in PIC-SURE data dictionary + * _phs000280.v4.pht004063.v2.phv00204712.v1_ + * dbGap name: **V1AGE01** + * dbGap desc: **Age at visit 1 [Cohort. Visit 1]** + * dbGap table: **DERIVE13** + * varId _phv00204712_ not found in PIC-SURE data dictionary + * _phs000280.v4.pht004064.v2.phv00204871.v1_ + * dbGap name: **V3AGE31** + * dbGap desc: **Age at visit 3 [Cohort. Visit 3]** + * dbGap table: **DERIVE37** + * varId _phv00204871_ not found in PIC-SURE data dictionary + * _phs000280.v4.pht004065.v2.phv00204975.v1_ + * No dbGap metadata available + * varId _phv00204975_ not found in PIC-SURE data dictionary + * _phs000280.v4.pht004107.v2.phv00207255.v1_ + * dbGap name: **HMTA01** + * dbGap desc: **Hematocrit % (MAV). Q1 [Hematology Form. HMTA. Visit 1]** + * dbGap table: **HMTA** + * varId _phv00207255_ not found in PIC-SURE data dictionary + * _phs000280.v4.pht004108.v2.phv00207270.v1_ + * dbGap name: **HMTB01** + * dbGap desc: **Hematocrit % (MAV). Q1 [Hematology Form. HMTB. Visit 2]** + * dbGap table: **HMTB** + * varId _phv00207270_ not found in PIC-SURE data dictionary + * _phs000280.v4.pht004109.v2.phv00207289.v1_ + * dbGap name: **HMTC5** + * dbGap desc: **Hematocrit. Q5 [Hematology Lab. HMTCV301. Visit 3]** + * dbGap table: **HMTCV301** + * varId _phv00207289_ not found in PIC-SURE data dictionary + * _phs000280.v4.pht004110.v2.phv00207301.v1_ + * dbGap name: **HMTC5** + * dbGap desc: **Hematocrit. Q5 [Hematology Lab. HMTCV401. Visit 4]** + * dbGap table: **HMTCV401** + * varId _phv00207301_ not found in PIC-SURE data dictionary + * _phs000280.v4.pht006422.v1.phv00294957.v1_ + * dbGap name: **CBC6** + * dbGap desc: **Hematocrit, Hct [Complete Blood Count, CBC, Visit 5]** + * dbGap table: **CBC** + * varId _phv00294957_ not found in PIC-SURE data dictionary + * _phs000280.v4.pht006431.v1.phv00295623.v1_ + * No dbGap metadata available + * varId _phv00295623_ not found in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -617,8 +779,16 @@ * ### blood_cell_count/hematocrit_vfr_bld_1 -- **CARDIA CARDIA Cohort**: * 2 component_study_variables - * _phs000285.v3.pht001559.v2.phv00112439.v2_. dbGap Name: **A01AGE2**, Desc: **AGE VERIFY**, Table: **A4F01**. - * _phs000285.v3.pht001563.v2.phv00112689.v2_. dbGap Name: **A05HCT**, Desc: **HEMATOCRIT (%)**, Table: **A4F05**. + * _phs000285.v3.pht001559.v2.phv00112439.v2_ + * dbGap name: **A01AGE2** + * dbGap desc: **AGE VERIFY** + * dbGap table: **A4F01** + * varId _phv00112439_ not found in PIC-SURE data dictionary + * _phs000285.v3.pht001563.v2.phv00112689.v2_ + * dbGap name: **A05HCT** + * dbGap desc: **HEMATOCRIT (%)** + * dbGap table: **A4F05** + * varId _phv00112689_ not found in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -644,8 +814,16 @@ * ### blood_cell_count/hematocrit_vfr_bld_1 -- **CHS Cardiovascular Health Study (CHS) Cohort: an NHLBI-funded observational study of risk factors for cardiovascular disease in adults 65 years or older**: * 2 component_study_variables - * _phs000287.v6.pht001452.v1.phv00100413.v1_. dbGap Name: **HEMATO23**, Desc: **HEMATOCRIT (%)**, Table: **BASEBOTH**. - * _phs000287.v6.pht001452.v1.phv00100487.v1_. dbGap Name: **AGEBL**, Desc: **CALCULATED AGE AT BASELINE**, Table: **BASEBOTH**. + * _phs000287.v6.pht001452.v1.phv00100413.v1_ + * dbGap name: **HEMATO23** + * dbGap desc: **HEMATOCRIT (%)** + * dbGap table: **BASEBOTH** + * No permissible values listed in PIC-SURE data dictionary + * _phs000287.v6.pht001452.v1.phv00100487.v1_ + * dbGap name: **AGEBL** + * dbGap desc: **CALCULATED AGE AT BASELINE** + * dbGap table: **BASEBOTH** + * No permissible values listed in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -665,8 +843,16 @@ * ### blood_cell_count/hematocrit_vfr_bld_1 -- **HCHS_SOL Hispanic Community Health Study /Study of Latinos (HCHS/SOL)**: * 2 component_study_variables - * _phs000810.v1.pht004715.v1.phv00226251.v1_. dbGap Name: **AGE**, Desc: **Age**, Table: **HCHS_SOL_Cohort_Subject_Phenotypes**. - * _phs000810.v1.pht004715.v1.phv00226303.v1_. dbGap Name: **LABA4**, Desc: **% Hematocrit (LABA4)**, Table: **HCHS_SOL_Cohort_Subject_Phenotypes**. + * _phs000810.v1.pht004715.v1.phv00226251.v1_ + * dbGap name: **AGE** + * dbGap desc: **Age** + * dbGap table: **HCHS_SOL_Cohort_Subject_Phenotypes** + * No permissible values listed in PIC-SURE data dictionary + * _phs000810.v1.pht004715.v1.phv00226303.v1_ + * dbGap name: **LABA4** + * dbGap desc: **% Hematocrit (LABA4)** + * dbGap table: **HCHS_SOL_Cohort_Subject_Phenotypes** + * No permissible values listed in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -686,8 +872,14 @@ * ### blood_cell_count/hematocrit_vfr_bld_1 -- **JHS Jackson Heart Study (JHS) Cohort**: * 2 component_study_variables - * _phs000286.v5.pht001949.v1.phv00126009.v1_. No dbGap metadata available. - * _phs000286.v5.pht001959.v1.phv00127614.v1_. dbGap Name: **HEMATOCRIT**, Desc: **Hematocrit % [Visit 1]**, Table: **loca**. + * _phs000286.v5.pht001949.v1.phv00126009.v1_ + * No dbGap metadata available + * varId _phv00126009_ not found in PIC-SURE data dictionary + * _phs000286.v5.pht001959.v1.phv00127614.v1_ + * dbGap name: **HEMATOCRIT** + * dbGap desc: **Hematocrit % [Visit 1]** + * dbGap table: **loca** + * varId _phv00127614_ not found in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list) { @@ -717,8 +909,16 @@ * ### blood_cell_count/hematocrit_vfr_bld_1 -- **MESA Multi-Ethnic Study of Atherosclerosis (MESA) Cohort**: * 2 component_study_variables - * _phs000209.v13.pht003091.v3.phv00176011.v1_. dbGap Name: **age5c**, Desc: **AGE AT EXAM 5**, Table: **MESA_Exam5Main**. - * _phs000209.v13.pht004319.v1.phv00218992.v1_. dbGap Name: **hct5**, Desc: **HEMATOCRIT (%)**, Table: **MESA_AncilMesaEpigenomicCBC**. + * _phs000209.v13.pht003091.v3.phv00176011.v1_ + * dbGap name: **age5c** + * dbGap desc: **AGE AT EXAM 5** + * dbGap table: **MESA_Exam5Main** + * PIC-SURE permissible values: 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94 + * _phs000209.v13.pht004319.v1.phv00218992.v1_ + * dbGap name: **hct5** + * dbGap desc: **HEMATOCRIT (%)** + * dbGap table: **MESA_AncilMesaEpigenomicCBC** + * No permissible values listed in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -743,11 +943,31 @@ * ### blood_cell_count/hematocrit_vfr_bld_1 -- **WHI Women's Health Initiative**: * 5 component_study_variables - * _phs000200.v11.pht000986.v6.phv00077362.v6_. dbGap Name: **CBCVY**, Desc: **CBC Visit year**, Table: **cbc_rel1**. - * _phs000200.v11.pht000986.v6.phv00077363.v6_. dbGap Name: **CBCDAYS**, Desc: **CBC Days since randomization/enrollment**, Table: **cbc_rel1**. - * _phs000200.v11.pht000986.v6.phv00077365.v6_. dbGap Name: **HEMATOCR**, Desc: **Hematocrit (%)**, Table: **cbc_rel1**. - * _phs000200.v11.pht000998.v6.phv00078436.v6_. dbGap Name: **F2DAYS**, Desc: **F2 Days since randomization**, Table: **f2_rel1**. - * _phs000200.v11.pht000998.v6.phv00078437.v6_. dbGap Name: **AGE**, Desc: **Age at screening**, Table: **f2_rel1**. + * _phs000200.v11.pht000986.v6.phv00077362.v6_ + * dbGap name: **CBCVY** + * dbGap desc: **CBC Visit year** + * dbGap table: **cbc_rel1** + * No permissible values listed in PIC-SURE data dictionary + * _phs000200.v11.pht000986.v6.phv00077363.v6_ + * dbGap name: **CBCDAYS** + * dbGap desc: **CBC Days since randomization/enrollment** + * dbGap table: **cbc_rel1** + * No permissible values listed in PIC-SURE data dictionary + * _phs000200.v11.pht000986.v6.phv00077365.v6_ + * dbGap name: **HEMATOCR** + * dbGap desc: **Hematocrit (%)** + * dbGap table: **cbc_rel1** + * No permissible values listed in PIC-SURE data dictionary + * _phs000200.v11.pht000998.v6.phv00078436.v6_ + * dbGap name: **F2DAYS** + * dbGap desc: **F2 Days since randomization** + * dbGap table: **f2_rel1** + * No permissible values listed in PIC-SURE data dictionary + * _phs000200.v11.pht000998.v6.phv00078437.v6_ + * dbGap name: **AGE** + * dbGap desc: **Age at screening** + * dbGap table: **f2_rel1** + * No permissible values listed in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -817,16 +1037,50 @@ * ### blood_cell_count/hemoglobin_mcnc_bld_1 -- **ARIC Atherosclerosis Risk in Communities (ARIC) Cohort**: * 10 component_study_variables - * _phs000280.v4.pht004062.v2.phv00204623.v1_. No dbGap metadata available. - * _phs000280.v4.pht004063.v2.phv00204712.v1_. dbGap Name: **V1AGE01**, Desc: **Age at visit 1 [Cohort. Visit 1]**, Table: **DERIVE13**. - * _phs000280.v4.pht004064.v2.phv00204871.v1_. dbGap Name: **V3AGE31**, Desc: **Age at visit 3 [Cohort. Visit 3]**, Table: **DERIVE37**. - * _phs000280.v4.pht004065.v2.phv00204975.v1_. No dbGap metadata available. - * _phs000280.v4.pht004107.v2.phv00207256.v1_. dbGap Name: **HMTA02**, Desc: **Hemoglobin g/dL (MAV). Q2 [Hematology Form. HMTA. Visit 1]**, Table: **HMTA**. - * _phs000280.v4.pht004108.v2.phv00207271.v1_. dbGap Name: **HMTB02**, Desc: **Hemoglobin g/dL (MAV). Q2 [Hematology Form. HMTB. Visit 2]**, Table: **HMTB**. - * _phs000280.v4.pht004109.v2.phv00207288.v1_. dbGap Name: **HMTC4**, Desc: **Hemoglobin. Q4 [Hematology Lab. HMTCV301. Visit 3]**, Table: **HMTCV301**. - * _phs000280.v4.pht004110.v2.phv00207300.v1_. dbGap Name: **HMTC4**, Desc: **Hemoglobin. Q4 [Hematology Lab. HMTCV401. Visit 4]**, Table: **HMTCV401**. - * _phs000280.v4.pht006422.v1.phv00294956.v1_. dbGap Name: **CBC5**, Desc: **Hemoglobin, Hgb [Complete Blood Count, CBC, Visit 5]**, Table: **CBC**. - * _phs000280.v4.pht006431.v1.phv00295623.v1_. No dbGap metadata available. + * _phs000280.v4.pht004062.v2.phv00204623.v1_ + * No dbGap metadata available + * varId _phv00204623_ not found in PIC-SURE data dictionary + * _phs000280.v4.pht004063.v2.phv00204712.v1_ + * dbGap name: **V1AGE01** + * dbGap desc: **Age at visit 1 [Cohort. Visit 1]** + * dbGap table: **DERIVE13** + * varId _phv00204712_ not found in PIC-SURE data dictionary + * _phs000280.v4.pht004064.v2.phv00204871.v1_ + * dbGap name: **V3AGE31** + * dbGap desc: **Age at visit 3 [Cohort. Visit 3]** + * dbGap table: **DERIVE37** + * varId _phv00204871_ not found in PIC-SURE data dictionary + * _phs000280.v4.pht004065.v2.phv00204975.v1_ + * No dbGap metadata available + * varId _phv00204975_ not found in PIC-SURE data dictionary + * _phs000280.v4.pht004107.v2.phv00207256.v1_ + * dbGap name: **HMTA02** + * dbGap desc: **Hemoglobin g/dL (MAV). Q2 [Hematology Form. HMTA. Visit 1]** + * dbGap table: **HMTA** + * varId _phv00207256_ not found in PIC-SURE data dictionary + * _phs000280.v4.pht004108.v2.phv00207271.v1_ + * dbGap name: **HMTB02** + * dbGap desc: **Hemoglobin g/dL (MAV). Q2 [Hematology Form. HMTB. Visit 2]** + * dbGap table: **HMTB** + * varId _phv00207271_ not found in PIC-SURE data dictionary + * _phs000280.v4.pht004109.v2.phv00207288.v1_ + * dbGap name: **HMTC4** + * dbGap desc: **Hemoglobin. Q4 [Hematology Lab. HMTCV301. Visit 3]** + * dbGap table: **HMTCV301** + * varId _phv00207288_ not found in PIC-SURE data dictionary + * _phs000280.v4.pht004110.v2.phv00207300.v1_ + * dbGap name: **HMTC4** + * dbGap desc: **Hemoglobin. Q4 [Hematology Lab. HMTCV401. Visit 4]** + * dbGap table: **HMTCV401** + * varId _phv00207300_ not found in PIC-SURE data dictionary + * _phs000280.v4.pht006422.v1.phv00294956.v1_ + * dbGap name: **CBC5** + * dbGap desc: **Hemoglobin, Hgb [Complete Blood Count, CBC, Visit 5]** + * dbGap table: **CBC** + * varId _phv00294956_ not found in PIC-SURE data dictionary + * _phs000280.v4.pht006431.v1.phv00295623.v1_ + * No dbGap metadata available + * varId _phv00295623_ not found in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -900,8 +1154,16 @@ * ### blood_cell_count/hemoglobin_mcnc_bld_1 -- **CARDIA CARDIA Cohort**: * 2 component_study_variables - * _phs000285.v3.pht001559.v2.phv00112439.v2_. dbGap Name: **A01AGE2**, Desc: **AGE VERIFY**, Table: **A4F01**. - * _phs000285.v3.pht001563.v2.phv00112688.v2_. dbGap Name: **A05HGB**, Desc: **HEMOGLOBIN (G/DL)**, Table: **A4F05**. + * _phs000285.v3.pht001559.v2.phv00112439.v2_ + * dbGap name: **A01AGE2** + * dbGap desc: **AGE VERIFY** + * dbGap table: **A4F01** + * varId _phv00112439_ not found in PIC-SURE data dictionary + * _phs000285.v3.pht001563.v2.phv00112688.v2_ + * dbGap name: **A05HGB** + * dbGap desc: **HEMOGLOBIN (G/DL)** + * dbGap table: **A4F05** + * varId _phv00112688_ not found in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -927,8 +1189,16 @@ * ### blood_cell_count/hemoglobin_mcnc_bld_1 -- **CHS Cardiovascular Health Study (CHS) Cohort: an NHLBI-funded observational study of risk factors for cardiovascular disease in adults 65 years or older**: * 2 component_study_variables - * _phs000287.v6.pht001452.v1.phv00100412.v1_. dbGap Name: **HEMOGL23**, Desc: **HEMOGLOBIN (g/dl)**, Table: **BASEBOTH**. - * _phs000287.v6.pht001452.v1.phv00100487.v1_. dbGap Name: **AGEBL**, Desc: **CALCULATED AGE AT BASELINE**, Table: **BASEBOTH**. + * _phs000287.v6.pht001452.v1.phv00100412.v1_ + * dbGap name: **HEMOGL23** + * dbGap desc: **HEMOGLOBIN (g/dl)** + * dbGap table: **BASEBOTH** + * No permissible values listed in PIC-SURE data dictionary + * _phs000287.v6.pht001452.v1.phv00100487.v1_ + * dbGap name: **AGEBL** + * dbGap desc: **CALCULATED AGE AT BASELINE** + * dbGap table: **BASEBOTH** + * No permissible values listed in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -946,8 +1216,16 @@ * ### blood_cell_count/hemoglobin_mcnc_bld_1 -- **HCHS_SOL Hispanic Community Health Study /Study of Latinos (HCHS/SOL)**: * 2 component_study_variables - * _phs000810.v1.pht004715.v1.phv00226251.v1_. dbGap Name: **AGE**, Desc: **Age**, Table: **HCHS_SOL_Cohort_Subject_Phenotypes**. - * _phs000810.v1.pht004715.v1.phv00226302.v1_. dbGap Name: **LABA3**, Desc: **Hemoglobin (g/dL) (LABA3)**, Table: **HCHS_SOL_Cohort_Subject_Phenotypes**. + * _phs000810.v1.pht004715.v1.phv00226251.v1_ + * dbGap name: **AGE** + * dbGap desc: **Age** + * dbGap table: **HCHS_SOL_Cohort_Subject_Phenotypes** + * No permissible values listed in PIC-SURE data dictionary + * _phs000810.v1.pht004715.v1.phv00226302.v1_ + * dbGap name: **LABA3** + * dbGap desc: **Hemoglobin (g/dL) (LABA3)** + * dbGap table: **HCHS_SOL_Cohort_Subject_Phenotypes** + * No permissible values listed in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -967,8 +1245,14 @@ * ### blood_cell_count/hemoglobin_mcnc_bld_1 -- **JHS Jackson Heart Study (JHS) Cohort**: * 2 component_study_variables - * _phs000286.v5.pht001949.v1.phv00126009.v1_. No dbGap metadata available. - * _phs000286.v5.pht001959.v1.phv00127615.v1_. dbGap Name: **HEMOGLOBIN**, Desc: **Hemoglobin G/DL [Visit 1]**, Table: **loca**. + * _phs000286.v5.pht001949.v1.phv00126009.v1_ + * No dbGap metadata available + * varId _phv00126009_ not found in PIC-SURE data dictionary + * _phs000286.v5.pht001959.v1.phv00127615.v1_ + * dbGap name: **HEMOGLOBIN** + * dbGap desc: **Hemoglobin G/DL [Visit 1]** + * dbGap table: **loca** + * varId _phv00127615_ not found in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list) { @@ -998,8 +1282,16 @@ * ### blood_cell_count/hemoglobin_mcnc_bld_1 -- **MESA Multi-Ethnic Study of Atherosclerosis (MESA) Cohort**: * 2 component_study_variables - * _phs000209.v13.pht003091.v3.phv00176011.v1_. dbGap Name: **age5c**, Desc: **AGE AT EXAM 5**, Table: **MESA_Exam5Main**. - * _phs000209.v13.pht004319.v1.phv00218993.v1_. dbGap Name: **hgb5**, Desc: **HEMOGLOBIN (g/dL)**, Table: **MESA_AncilMesaEpigenomicCBC**. + * _phs000209.v13.pht003091.v3.phv00176011.v1_ + * dbGap name: **age5c** + * dbGap desc: **AGE AT EXAM 5** + * dbGap table: **MESA_Exam5Main** + * PIC-SURE permissible values: 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94 + * _phs000209.v13.pht004319.v1.phv00218993.v1_ + * dbGap name: **hgb5** + * dbGap desc: **HEMOGLOBIN (g/dL)** + * dbGap table: **MESA_AncilMesaEpigenomicCBC** + * No permissible values listed in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -1023,11 +1315,31 @@ * ### blood_cell_count/hemoglobin_mcnc_bld_1 -- **WHI Women's Health Initiative**: * 5 component_study_variables - * _phs000200.v11.pht000986.v6.phv00077362.v6_. dbGap Name: **CBCVY**, Desc: **CBC Visit year**, Table: **cbc_rel1**. - * _phs000200.v11.pht000986.v6.phv00077363.v6_. dbGap Name: **CBCDAYS**, Desc: **CBC Days since randomization/enrollment**, Table: **cbc_rel1**. - * _phs000200.v11.pht000986.v6.phv00077366.v6_. dbGap Name: **HEMOGLBN**, Desc: **Hemoglobin (gm/dl)**, Table: **cbc_rel1**. - * _phs000200.v11.pht000998.v6.phv00078436.v6_. dbGap Name: **F2DAYS**, Desc: **F2 Days since randomization**, Table: **f2_rel1**. - * _phs000200.v11.pht000998.v6.phv00078437.v6_. dbGap Name: **AGE**, Desc: **Age at screening**, Table: **f2_rel1**. + * _phs000200.v11.pht000986.v6.phv00077362.v6_ + * dbGap name: **CBCVY** + * dbGap desc: **CBC Visit year** + * dbGap table: **cbc_rel1** + * No permissible values listed in PIC-SURE data dictionary + * _phs000200.v11.pht000986.v6.phv00077363.v6_ + * dbGap name: **CBCDAYS** + * dbGap desc: **CBC Days since randomization/enrollment** + * dbGap table: **cbc_rel1** + * No permissible values listed in PIC-SURE data dictionary + * _phs000200.v11.pht000986.v6.phv00077366.v6_ + * dbGap name: **HEMOGLBN** + * dbGap desc: **Hemoglobin (gm/dl)** + * dbGap table: **cbc_rel1** + * No permissible values listed in PIC-SURE data dictionary + * _phs000200.v11.pht000998.v6.phv00078436.v6_ + * dbGap name: **F2DAYS** + * dbGap desc: **F2 Days since randomization** + * dbGap table: **f2_rel1** + * No permissible values listed in PIC-SURE data dictionary + * _phs000200.v11.pht000998.v6.phv00078437.v6_ + * dbGap name: **AGE** + * dbGap desc: **Age at screening** + * dbGap table: **f2_rel1** + * No permissible values listed in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -1109,15 +1421,47 @@ * ### blood_cell_count/lymphocyte_ncnc_bld_1 -- **ARIC Atherosclerosis Risk in Communities (ARIC) Cohort**: * 9 component_study_variables - * _phs000280.v4.pht004062.v2.phv00204623.v1_. No dbGap metadata available. - * _phs000280.v4.pht004063.v2.phv00204712.v1_. dbGap Name: **V1AGE01**, Desc: **Age at visit 1 [Cohort. Visit 1]**, Table: **DERIVE13**. - * _phs000280.v4.pht004107.v2.phv00207257.v1_. dbGap Name: **HMTA03**, Desc: **White blood count x1000/mm3 (MAV). Q3 [Hematology Form. HMTA. Visit 1]**, Table: **HMTA**. - * _phs000280.v4.pht004107.v2.phv00207261.v1_. dbGap Name: **HMTA07**, Desc: **Lymphocytes % Q7 [Hematology Form. HMTA. Visit 1]**, Table: **HMTA**. - * _phs000280.v4.pht004108.v2.phv00207272.v1_. dbGap Name: **HMTB03**, Desc: **White blood count x1000/mm3 (MAV). Q3 [Hematology Form. HMTB. Visit 2]**, Table: **HMTB**. - * _phs000280.v4.pht004108.v2.phv00207276.v1_. dbGap Name: **HMTB07**, Desc: **Lymphocytes %. Q7 [Hematology Form. HMTB. Visit 2]**, Table: **HMTB**. - * _phs000280.v4.pht006422.v1.phv00294954.v1_. dbGap Name: **CBC3**, Desc: **White blood cell count, Wbc [Complete Blood Count, CBC, Visit 5]**, Table: **CBC**. - * _phs000280.v4.pht006422.v1.phv00294964.v1_. dbGap Name: **CBC13**, Desc: **Lymphocyte percentage, Ly [Complete Blood Count, CBC, Visit 5]**, Table: **CBC**. - * _phs000280.v4.pht006431.v1.phv00295623.v1_. No dbGap metadata available. + * _phs000280.v4.pht004062.v2.phv00204623.v1_ + * No dbGap metadata available + * varId _phv00204623_ not found in PIC-SURE data dictionary + * _phs000280.v4.pht004063.v2.phv00204712.v1_ + * dbGap name: **V1AGE01** + * dbGap desc: **Age at visit 1 [Cohort. Visit 1]** + * dbGap table: **DERIVE13** + * varId _phv00204712_ not found in PIC-SURE data dictionary + * _phs000280.v4.pht004107.v2.phv00207257.v1_ + * dbGap name: **HMTA03** + * dbGap desc: **White blood count x1000/mm3 (MAV). Q3 [Hematology Form. HMTA. Visit 1]** + * dbGap table: **HMTA** + * varId _phv00207257_ not found in PIC-SURE data dictionary + * _phs000280.v4.pht004107.v2.phv00207261.v1_ + * dbGap name: **HMTA07** + * dbGap desc: **Lymphocytes % Q7 [Hematology Form. HMTA. Visit 1]** + * dbGap table: **HMTA** + * varId _phv00207261_ not found in PIC-SURE data dictionary + * _phs000280.v4.pht004108.v2.phv00207272.v1_ + * dbGap name: **HMTB03** + * dbGap desc: **White blood count x1000/mm3 (MAV). Q3 [Hematology Form. HMTB. Visit 2]** + * dbGap table: **HMTB** + * varId _phv00207272_ not found in PIC-SURE data dictionary + * _phs000280.v4.pht004108.v2.phv00207276.v1_ + * dbGap name: **HMTB07** + * dbGap desc: **Lymphocytes %. Q7 [Hematology Form. HMTB. Visit 2]** + * dbGap table: **HMTB** + * varId _phv00207276_ not found in PIC-SURE data dictionary + * _phs000280.v4.pht006422.v1.phv00294954.v1_ + * dbGap name: **CBC3** + * dbGap desc: **White blood cell count, Wbc [Complete Blood Count, CBC, Visit 5]** + * dbGap table: **CBC** + * varId _phv00294954_ not found in PIC-SURE data dictionary + * _phs000280.v4.pht006422.v1.phv00294964.v1_ + * dbGap name: **CBC13** + * dbGap desc: **Lymphocyte percentage, Ly [Complete Blood Count, CBC, Visit 5]** + * dbGap table: **CBC** + * varId _phv00294964_ not found in PIC-SURE data dictionary + * _phs000280.v4.pht006431.v1.phv00295623.v1_ + * No dbGap metadata available + * varId _phv00295623_ not found in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -1194,9 +1538,21 @@ * ### blood_cell_count/lymphocyte_ncnc_bld_1 -- **CARDIA CARDIA Cohort**: * 3 component_study_variables - * _phs000285.v3.pht001559.v2.phv00112439.v2_. dbGap Name: **A01AGE2**, Desc: **AGE VERIFY**, Table: **A4F01**. - * _phs000285.v3.pht001563.v2.phv00112686.v2_. dbGap Name: **A05WBC**, Desc: **WHITE CELL COUNT (X 1000)**, Table: **A4F05**. - * _phs000285.v3.pht001563.v2.phv00112691.v2_. dbGap Name: **A05LYMPH**, Desc: **LYMPHOCYTE COUNT**, Table: **A4F05**. + * _phs000285.v3.pht001559.v2.phv00112439.v2_ + * dbGap name: **A01AGE2** + * dbGap desc: **AGE VERIFY** + * dbGap table: **A4F01** + * varId _phv00112439_ not found in PIC-SURE data dictionary + * _phs000285.v3.pht001563.v2.phv00112686.v2_ + * dbGap name: **A05WBC** + * dbGap desc: **WHITE CELL COUNT (X 1000)** + * dbGap table: **A4F05** + * varId _phv00112686_ not found in PIC-SURE data dictionary + * _phs000285.v3.pht001563.v2.phv00112691.v2_ + * dbGap name: **A05LYMPH** + * dbGap desc: **LYMPHOCYTE COUNT** + * dbGap table: **A4F05** + * varId _phv00112691_ not found in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -1225,9 +1581,21 @@ * ### blood_cell_count/lymphocyte_ncnc_bld_1 -- **HCHS_SOL Hispanic Community Health Study /Study of Latinos (HCHS/SOL)**: * 3 component_study_variables - * _phs000810.v1.pht004715.v1.phv00226251.v1_. dbGap Name: **AGE**, Desc: **Age**, Table: **HCHS_SOL_Cohort_Subject_Phenotypes**. - * _phs000810.v1.pht004715.v1.phv00226283.v1_. dbGap Name: **LABA1**, Desc: **White Blood Count (x10e9) (LABA1)**, Table: **HCHS_SOL_Cohort_Subject_Phenotypes**. - * _phs000810.v1.pht004715.v1.phv00226285.v1_. dbGap Name: **LABA11**, Desc: **% Lymphocytes (LABA11)**, Table: **HCHS_SOL_Cohort_Subject_Phenotypes**. + * _phs000810.v1.pht004715.v1.phv00226251.v1_ + * dbGap name: **AGE** + * dbGap desc: **Age** + * dbGap table: **HCHS_SOL_Cohort_Subject_Phenotypes** + * No permissible values listed in PIC-SURE data dictionary + * _phs000810.v1.pht004715.v1.phv00226283.v1_ + * dbGap name: **LABA1** + * dbGap desc: **White Blood Count (x10e9) (LABA1)** + * dbGap table: **HCHS_SOL_Cohort_Subject_Phenotypes** + * No permissible values listed in PIC-SURE data dictionary + * _phs000810.v1.pht004715.v1.phv00226285.v1_ + * dbGap name: **LABA11** + * dbGap desc: **% Lymphocytes (LABA11)** + * dbGap table: **HCHS_SOL_Cohort_Subject_Phenotypes** + * No permissible values listed in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -1248,9 +1616,19 @@ * ### blood_cell_count/lymphocyte_ncnc_bld_1 -- **JHS Jackson Heart Study (JHS) Cohort**: * 3 component_study_variables - * _phs000286.v5.pht001949.v1.phv00126009.v1_. No dbGap metadata available. - * _phs000286.v5.pht001959.v1.phv00127622.v1_. dbGap Name: **LYMPHS**, Desc: **Lymphs: diff measure % [Visit 1]**, Table: **loca**. - * _phs000286.v5.pht001959.v1.phv00127631.v1_. dbGap Name: **WBC**, Desc: **White blood cells TH/CMM [Visit 1]**, Table: **loca**. + * _phs000286.v5.pht001949.v1.phv00126009.v1_ + * No dbGap metadata available + * varId _phv00126009_ not found in PIC-SURE data dictionary + * _phs000286.v5.pht001959.v1.phv00127622.v1_ + * dbGap name: **LYMPHS** + * dbGap desc: **Lymphs: diff measure % [Visit 1]** + * dbGap table: **loca** + * varId _phv00127622_ not found in PIC-SURE data dictionary + * _phs000286.v5.pht001959.v1.phv00127631.v1_ + * dbGap name: **WBC** + * dbGap desc: **White blood cells TH/CMM [Visit 1]** + * dbGap table: **loca** + * varId _phv00127631_ not found in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list) { @@ -1285,8 +1663,16 @@ * ### blood_cell_count/lymphocyte_ncnc_bld_1 -- **MESA Multi-Ethnic Study of Atherosclerosis (MESA) Cohort**: * 2 component_study_variables - * _phs000209.v13.pht003091.v3.phv00176011.v1_. dbGap Name: **age5c**, Desc: **AGE AT EXAM 5**, Table: **MESA_Exam5Main**. - * _phs000209.v13.pht004319.v1.phv00218998.v1_. dbGap Name: **lymphsa5**, Desc: **LYMPHOCYTES (ABSOLUTE) (x10E3/uL)**, Table: **MESA_AncilMesaEpigenomicCBC**. + * _phs000209.v13.pht003091.v3.phv00176011.v1_ + * dbGap name: **age5c** + * dbGap desc: **AGE AT EXAM 5** + * dbGap table: **MESA_Exam5Main** + * PIC-SURE permissible values: 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94 + * _phs000209.v13.pht004319.v1.phv00218998.v1_ + * dbGap name: **lymphsa5** + * dbGap desc: **LYMPHOCYTES (ABSOLUTE) (x10E3/uL)** + * dbGap table: **MESA_AncilMesaEpigenomicCBC** + * PIC-SURE permissible values: .2, .4, .5, .6, .7, .8, .9, 1, 1.1, 1.2, 1.3, 1.4, 1.5, 1.6, 1.7, 1.8, 1.9, 2, 2.1, 2.2, 2.3, 2.4, 2.5, 2.6, 2.7, 2.8, 2.9, 3, 3.1, 3.2, 3.3, 3.4, 3.5, 3.6, 3.7, 3.8, 3.9, 33.3, 37.6, 4, 4.6, 4.8, 5.8, 6.1, 8 * **Function:** ```r harmonize <- function(phen_list){ @@ -1354,12 +1740,32 @@ * ### blood_cell_count/mch_entmass_rbc_1 -- **ARIC Atherosclerosis Risk in Communities (ARIC) Cohort**: * 6 component_study_variables - * _phs000280.v4.pht004064.v2.phv00204871.v1_. dbGap Name: **V3AGE31**, Desc: **Age at visit 3 [Cohort. Visit 3]**, Table: **DERIVE37**. - * _phs000280.v4.pht004065.v2.phv00204975.v1_. No dbGap metadata available. - * _phs000280.v4.pht004109.v2.phv00207290.v1_. dbGap Name: **HMTC7**, Desc: **MCH. Q7 [Hematology Lab. HMTCV301. Visit 3]**, Table: **HMTCV301**. - * _phs000280.v4.pht004110.v2.phv00207302.v1_. dbGap Name: **HMTC7**, Desc: **MCH. Q7 [Hematology Lab. HMTCV401. Visit 4]**, Table: **HMTCV401**. - * _phs000280.v4.pht006422.v1.phv00294960.v1_. dbGap Name: **CBC9**, Desc: **Mean corpuscular hemoglobin, Mch [Complete Blood Count, CBC, Visit 5]**, Table: **CBC**. - * _phs000280.v4.pht006431.v1.phv00295623.v1_. No dbGap metadata available. + * _phs000280.v4.pht004064.v2.phv00204871.v1_ + * dbGap name: **V3AGE31** + * dbGap desc: **Age at visit 3 [Cohort. Visit 3]** + * dbGap table: **DERIVE37** + * varId _phv00204871_ not found in PIC-SURE data dictionary + * _phs000280.v4.pht004065.v2.phv00204975.v1_ + * No dbGap metadata available + * varId _phv00204975_ not found in PIC-SURE data dictionary + * _phs000280.v4.pht004109.v2.phv00207290.v1_ + * dbGap name: **HMTC7** + * dbGap desc: **MCH. Q7 [Hematology Lab. HMTCV301. Visit 3]** + * dbGap table: **HMTCV301** + * varId _phv00207290_ not found in PIC-SURE data dictionary + * _phs000280.v4.pht004110.v2.phv00207302.v1_ + * dbGap name: **HMTC7** + * dbGap desc: **MCH. Q7 [Hematology Lab. HMTCV401. Visit 4]** + * dbGap table: **HMTCV401** + * varId _phv00207302_ not found in PIC-SURE data dictionary + * _phs000280.v4.pht006422.v1.phv00294960.v1_ + * dbGap name: **CBC9** + * dbGap desc: **Mean corpuscular hemoglobin, Mch [Complete Blood Count, CBC, Visit 5]** + * dbGap table: **CBC** + * varId _phv00294960_ not found in PIC-SURE data dictionary + * _phs000280.v4.pht006431.v1.phv00295623.v1_ + * No dbGap metadata available + * varId _phv00295623_ not found in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -1423,9 +1829,21 @@ * ### blood_cell_count/mch_entmass_rbc_1 -- **CARDIA CARDIA Cohort**: * 3 component_study_variables - * _phs000285.v3.pht001559.v2.phv00112439.v2_. dbGap Name: **A01AGE2**, Desc: **AGE VERIFY**, Table: **A4F01**. - * _phs000285.v3.pht001563.v2.phv00112687.v2_. dbGap Name: **A05RBC**, Desc: **RED CELL COUNT (X 1,000,000)**, Table: **A4F05**. - * _phs000285.v3.pht001563.v2.phv00112688.v2_. dbGap Name: **A05HGB**, Desc: **HEMOGLOBIN (G/DL)**, Table: **A4F05**. + * _phs000285.v3.pht001559.v2.phv00112439.v2_ + * dbGap name: **A01AGE2** + * dbGap desc: **AGE VERIFY** + * dbGap table: **A4F01** + * varId _phv00112439_ not found in PIC-SURE data dictionary + * _phs000285.v3.pht001563.v2.phv00112687.v2_ + * dbGap name: **A05RBC** + * dbGap desc: **RED CELL COUNT (X 1,000,000)** + * dbGap table: **A4F05** + * varId _phv00112687_ not found in PIC-SURE data dictionary + * _phs000285.v3.pht001563.v2.phv00112688.v2_ + * dbGap name: **A05HGB** + * dbGap desc: **HEMOGLOBIN (G/DL)** + * dbGap table: **A4F05** + * varId _phv00112688_ not found in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -1453,8 +1871,16 @@ * ### blood_cell_count/mch_entmass_rbc_1 -- **HCHS_SOL Hispanic Community Health Study /Study of Latinos (HCHS/SOL)**: * 2 component_study_variables - * _phs000810.v1.pht004715.v1.phv00226251.v1_. dbGap Name: **AGE**, Desc: **Age**, Table: **HCHS_SOL_Cohort_Subject_Phenotypes**. - * _phs000810.v1.pht004715.v1.phv00226305.v1_. dbGap Name: **LABA6**, Desc: **Mean Corpuscular Hemoglobin (pg) (LABA6)**, Table: **HCHS_SOL_Cohort_Subject_Phenotypes**. + * _phs000810.v1.pht004715.v1.phv00226251.v1_ + * dbGap name: **AGE** + * dbGap desc: **Age** + * dbGap table: **HCHS_SOL_Cohort_Subject_Phenotypes** + * No permissible values listed in PIC-SURE data dictionary + * _phs000810.v1.pht004715.v1.phv00226305.v1_ + * dbGap name: **LABA6** + * dbGap desc: **Mean Corpuscular Hemoglobin (pg) (LABA6)** + * dbGap table: **HCHS_SOL_Cohort_Subject_Phenotypes** + * No permissible values listed in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -1475,8 +1901,14 @@ * ### blood_cell_count/mch_entmass_rbc_1 -- **JHS Jackson Heart Study (JHS) Cohort**: * 2 component_study_variables - * _phs000286.v5.pht001949.v1.phv00126009.v1_. No dbGap metadata available. - * _phs000286.v5.pht001959.v1.phv00127623.v1_. dbGap Name: **MCH**, Desc: **MCH PG [Visit 1]**, Table: **loca**. + * _phs000286.v5.pht001949.v1.phv00126009.v1_ + * No dbGap metadata available + * varId _phv00126009_ not found in PIC-SURE data dictionary + * _phs000286.v5.pht001959.v1.phv00127623.v1_ + * dbGap name: **MCH** + * dbGap desc: **MCH PG [Visit 1]** + * dbGap table: **loca** + * varId _phv00127623_ not found in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list) { @@ -1506,9 +1938,21 @@ * ### blood_cell_count/mch_entmass_rbc_1 -- **MESA Multi-Ethnic Study of Atherosclerosis (MESA) Cohort**: * 3 component_study_variables - * _phs000209.v13.pht003091.v3.phv00176011.v1_. dbGap Name: **age5c**, Desc: **AGE AT EXAM 5**, Table: **MESA_Exam5Main**. - * _phs000209.v13.pht004319.v1.phv00218990.v1_. dbGap Name: **rbc5**, Desc: **RED BLOOD CELL (RBC) (x10E6/uL)**, Table: **MESA_AncilMesaEpigenomicCBC**. - * _phs000209.v13.pht004319.v1.phv00218993.v1_. dbGap Name: **hgb5**, Desc: **HEMOGLOBIN (g/dL)**, Table: **MESA_AncilMesaEpigenomicCBC**. + * _phs000209.v13.pht003091.v3.phv00176011.v1_ + * dbGap name: **age5c** + * dbGap desc: **AGE AT EXAM 5** + * dbGap table: **MESA_Exam5Main** + * PIC-SURE permissible values: 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94 + * _phs000209.v13.pht004319.v1.phv00218990.v1_ + * dbGap name: **rbc5** + * dbGap desc: **RED BLOOD CELL (RBC) (x10E6/uL)** + * dbGap table: **MESA_AncilMesaEpigenomicCBC** + * PIC-SURE permissible values: 2.36, 2.39, 2.75, 2.99, 3.01, 3.06, 3.09, 3.1, 3.13, 3.16, 3.19, 3.21, 3.22, 3.23, 3.24, 3.25, 3.26, 3.27, 3.28, 3.29, 3.3, 3.31, 3.33, 3.34, 3.35, 3.37, 3.38, 3.4, 3.41, 3.42, 3.43, 3.44, 3.45, 3.47, 3.48, 3.49, 3.5, 3.51, 3.52, 3.53, 3.54, 3.55, 3.56, 3.57, 3.58, 3.59, 3.6, 3.61, 3.62, 3.63, 3.64, 3.65, 3.66, 3.67, 3.68, 3.69, 3.7, 3.71, 3.72, 3.73, 3.74, 3.75, 3.76, 3.77, 3.78, 3.79, 3.8, 3.81, 3.82, 3.83, 3.84, 3.85, 3.86, 3.87, 3.88, 3.89, 3.9, 3.91, 3.92, 3.93, 3.94, 3.95, 3.96, 3.97, 3.98, 3.99, 4, 4.01, 4.02, 4.03, 4.04, 4.05, 4.06, 4.07, 4.08, 4.09, 4.1, 4.11, 4.12, 4.13, 4.14, 4.15, 4.16, 4.17, 4.18, 4.19, 4.2, 4.21, 4.22, 4.23, 4.24, 4.25, 4.26, 4.27, 4.28, 4.29, 4.3, 4.31, 4.32, 4.33, 4.34, 4.35, 4.36, 4.37, 4.38, 4.39, 4.4, 4.41, 4.42, 4.43, 4.44, 4.45, 4.46, 4.47, 4.48, 4.49, 4.5, 4.51, 4.52, 4.53, 4.54, 4.55, 4.56, 4.57, 4.58, 4.59, 4.6, 4.61, 4.62, 4.63, 4.64, 4.65, 4.66, 4.67, 4.68, 4.69, 4.7, 4.71, 4.72, 4.73, 4.74, 4.75, 4.76, 4.77, 4.78, 4.79, 4.8, 4.81, 4.82, 4.83, 4.84, 4.85, 4.86, 4.87, 4.88, 4.89, 4.9, 4.91, 4.92, 4.93, 4.94, 4.95, 4.96, 4.97, 4.98, 4.99, 5, 5.01, 5.02, 5.03, 5.04, 5.05, 5.06, 5.07, 5.08, 5.09, 5.1, 5.11, 5.12, 5.13, 5.14, 5.15, 5.16, 5.17, 5.18, 5.19, 5.2, 5.21, 5.22, 5.23, 5.24, 5.25, 5.26, 5.27, 5.28, 5.29, 5.3, 5.31, 5.32, 5.33, 5.34, 5.35, 5.36, 5.37, 5.38, 5.39, 5.4, 5.41, 5.42, 5.43, 5.45, 5.46, 5.47, 5.48, 5.49, 5.5, 5.51, 5.53, 5.54, 5.55, 5.56, 5.57, 5.58, 5.59, 5.6, 5.61, 5.65, 5.66, 5.67, 5.7, 5.71, 5.72, 5.73, 5.74, 5.76, 5.78, 5.81, 5.82, 5.85, 5.89, 5.9, 5.95, 5.97, 6.05, 6.07, 6.09, 6.14, 6.17, 6.35, 6.41, 6.81 + * _phs000209.v13.pht004319.v1.phv00218993.v1_ + * dbGap name: **hgb5** + * dbGap desc: **HEMOGLOBIN (g/dL)** + * dbGap table: **MESA_AncilMesaEpigenomicCBC** + * No permissible values listed in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list) { @@ -1589,21 +2033,75 @@ * ### blood_cell_count/mchc_mcnc_rbc_1 -- **ARIC Atherosclerosis Risk in Communities (ARIC) Cohort**: * 15 component_study_variables - * _phs000280.v4.pht004062.v2.phv00204623.v1_. No dbGap metadata available. - * _phs000280.v4.pht004063.v2.phv00204712.v1_. dbGap Name: **V1AGE01**, Desc: **Age at visit 1 [Cohort. Visit 1]**, Table: **DERIVE13**. - * _phs000280.v4.pht004064.v2.phv00204871.v1_. dbGap Name: **V3AGE31**, Desc: **Age at visit 3 [Cohort. Visit 3]**, Table: **DERIVE37**. - * _phs000280.v4.pht004065.v2.phv00204975.v1_. No dbGap metadata available. - * _phs000280.v4.pht004107.v2.phv00207255.v1_. dbGap Name: **HMTA01**, Desc: **Hematocrit % (MAV). Q1 [Hematology Form. HMTA. Visit 1]**, Table: **HMTA**. - * _phs000280.v4.pht004107.v2.phv00207256.v1_. dbGap Name: **HMTA02**, Desc: **Hemoglobin g/dL (MAV). Q2 [Hematology Form. HMTA. Visit 1]**, Table: **HMTA**. - * _phs000280.v4.pht004108.v2.phv00207270.v1_. dbGap Name: **HMTB01**, Desc: **Hematocrit % (MAV). Q1 [Hematology Form. HMTB. Visit 2]**, Table: **HMTB**. - * _phs000280.v4.pht004108.v2.phv00207271.v1_. dbGap Name: **HMTB02**, Desc: **Hemoglobin g/dL (MAV). Q2 [Hematology Form. HMTB. Visit 2]**, Table: **HMTB**. - * _phs000280.v4.pht004109.v2.phv00207288.v1_. dbGap Name: **HMTC4**, Desc: **Hemoglobin. Q4 [Hematology Lab. HMTCV301. Visit 3]**, Table: **HMTCV301**. - * _phs000280.v4.pht004109.v2.phv00207289.v1_. dbGap Name: **HMTC5**, Desc: **Hematocrit. Q5 [Hematology Lab. HMTCV301. Visit 3]**, Table: **HMTCV301**. - * _phs000280.v4.pht004110.v2.phv00207300.v1_. dbGap Name: **HMTC4**, Desc: **Hemoglobin. Q4 [Hematology Lab. HMTCV401. Visit 4]**, Table: **HMTCV401**. - * _phs000280.v4.pht004110.v2.phv00207301.v1_. dbGap Name: **HMTC5**, Desc: **Hematocrit. Q5 [Hematology Lab. HMTCV401. Visit 4]**, Table: **HMTCV401**. - * _phs000280.v4.pht006422.v1.phv00294956.v1_. dbGap Name: **CBC5**, Desc: **Hemoglobin, Hgb [Complete Blood Count, CBC, Visit 5]**, Table: **CBC**. - * _phs000280.v4.pht006422.v1.phv00294957.v1_. dbGap Name: **CBC6**, Desc: **Hematocrit, Hct [Complete Blood Count, CBC, Visit 5]**, Table: **CBC**. - * _phs000280.v4.pht006431.v1.phv00295623.v1_. No dbGap metadata available. + * _phs000280.v4.pht004062.v2.phv00204623.v1_ + * No dbGap metadata available + * varId _phv00204623_ not found in PIC-SURE data dictionary + * _phs000280.v4.pht004063.v2.phv00204712.v1_ + * dbGap name: **V1AGE01** + * dbGap desc: **Age at visit 1 [Cohort. Visit 1]** + * dbGap table: **DERIVE13** + * varId _phv00204712_ not found in PIC-SURE data dictionary + * _phs000280.v4.pht004064.v2.phv00204871.v1_ + * dbGap name: **V3AGE31** + * dbGap desc: **Age at visit 3 [Cohort. Visit 3]** + * dbGap table: **DERIVE37** + * varId _phv00204871_ not found in PIC-SURE data dictionary + * _phs000280.v4.pht004065.v2.phv00204975.v1_ + * No dbGap metadata available + * varId _phv00204975_ not found in PIC-SURE data dictionary + * _phs000280.v4.pht004107.v2.phv00207255.v1_ + * dbGap name: **HMTA01** + * dbGap desc: **Hematocrit % (MAV). Q1 [Hematology Form. HMTA. Visit 1]** + * dbGap table: **HMTA** + * varId _phv00207255_ not found in PIC-SURE data dictionary + * _phs000280.v4.pht004107.v2.phv00207256.v1_ + * dbGap name: **HMTA02** + * dbGap desc: **Hemoglobin g/dL (MAV). Q2 [Hematology Form. HMTA. Visit 1]** + * dbGap table: **HMTA** + * varId _phv00207256_ not found in PIC-SURE data dictionary + * _phs000280.v4.pht004108.v2.phv00207270.v1_ + * dbGap name: **HMTB01** + * dbGap desc: **Hematocrit % (MAV). Q1 [Hematology Form. HMTB. Visit 2]** + * dbGap table: **HMTB** + * varId _phv00207270_ not found in PIC-SURE data dictionary + * _phs000280.v4.pht004108.v2.phv00207271.v1_ + * dbGap name: **HMTB02** + * dbGap desc: **Hemoglobin g/dL (MAV). Q2 [Hematology Form. HMTB. Visit 2]** + * dbGap table: **HMTB** + * varId _phv00207271_ not found in PIC-SURE data dictionary + * _phs000280.v4.pht004109.v2.phv00207288.v1_ + * dbGap name: **HMTC4** + * dbGap desc: **Hemoglobin. Q4 [Hematology Lab. HMTCV301. Visit 3]** + * dbGap table: **HMTCV301** + * varId _phv00207288_ not found in PIC-SURE data dictionary + * _phs000280.v4.pht004109.v2.phv00207289.v1_ + * dbGap name: **HMTC5** + * dbGap desc: **Hematocrit. Q5 [Hematology Lab. HMTCV301. Visit 3]** + * dbGap table: **HMTCV301** + * varId _phv00207289_ not found in PIC-SURE data dictionary + * _phs000280.v4.pht004110.v2.phv00207300.v1_ + * dbGap name: **HMTC4** + * dbGap desc: **Hemoglobin. Q4 [Hematology Lab. HMTCV401. Visit 4]** + * dbGap table: **HMTCV401** + * varId _phv00207300_ not found in PIC-SURE data dictionary + * _phs000280.v4.pht004110.v2.phv00207301.v1_ + * dbGap name: **HMTC5** + * dbGap desc: **Hematocrit. Q5 [Hematology Lab. HMTCV401. Visit 4]** + * dbGap table: **HMTCV401** + * varId _phv00207301_ not found in PIC-SURE data dictionary + * _phs000280.v4.pht006422.v1.phv00294956.v1_ + * dbGap name: **CBC5** + * dbGap desc: **Hemoglobin, Hgb [Complete Blood Count, CBC, Visit 5]** + * dbGap table: **CBC** + * varId _phv00294956_ not found in PIC-SURE data dictionary + * _phs000280.v4.pht006422.v1.phv00294957.v1_ + * dbGap name: **CBC6** + * dbGap desc: **Hematocrit, Hct [Complete Blood Count, CBC, Visit 5]** + * dbGap table: **CBC** + * varId _phv00294957_ not found in PIC-SURE data dictionary + * _phs000280.v4.pht006431.v1.phv00295623.v1_ + * No dbGap metadata available + * varId _phv00295623_ not found in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -1686,9 +2184,21 @@ * ### blood_cell_count/mchc_mcnc_rbc_1 -- **CARDIA CARDIA Cohort**: * 3 component_study_variables - * _phs000285.v3.pht001559.v2.phv00112439.v2_. dbGap Name: **A01AGE2**, Desc: **AGE VERIFY**, Table: **A4F01**. - * _phs000285.v3.pht001563.v2.phv00112688.v2_. dbGap Name: **A05HGB**, Desc: **HEMOGLOBIN (G/DL)**, Table: **A4F05**. - * _phs000285.v3.pht001563.v2.phv00112689.v2_. dbGap Name: **A05HCT**, Desc: **HEMATOCRIT (%)**, Table: **A4F05**. + * _phs000285.v3.pht001559.v2.phv00112439.v2_ + * dbGap name: **A01AGE2** + * dbGap desc: **AGE VERIFY** + * dbGap table: **A4F01** + * varId _phv00112439_ not found in PIC-SURE data dictionary + * _phs000285.v3.pht001563.v2.phv00112688.v2_ + * dbGap name: **A05HGB** + * dbGap desc: **HEMOGLOBIN (G/DL)** + * dbGap table: **A4F05** + * varId _phv00112688_ not found in PIC-SURE data dictionary + * _phs000285.v3.pht001563.v2.phv00112689.v2_ + * dbGap name: **A05HCT** + * dbGap desc: **HEMATOCRIT (%)** + * dbGap table: **A4F05** + * varId _phv00112689_ not found in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -1716,9 +2226,21 @@ * ### blood_cell_count/mchc_mcnc_rbc_1 -- **CHS Cardiovascular Health Study (CHS) Cohort: an NHLBI-funded observational study of risk factors for cardiovascular disease in adults 65 years or older**: * 3 component_study_variables - * _phs000287.v6.pht001452.v1.phv00100412.v1_. dbGap Name: **HEMOGL23**, Desc: **HEMOGLOBIN (g/dl)**, Table: **BASEBOTH**. - * _phs000287.v6.pht001452.v1.phv00100413.v1_. dbGap Name: **HEMATO23**, Desc: **HEMATOCRIT (%)**, Table: **BASEBOTH**. - * _phs000287.v6.pht001452.v1.phv00100487.v1_. dbGap Name: **AGEBL**, Desc: **CALCULATED AGE AT BASELINE**, Table: **BASEBOTH**. + * _phs000287.v6.pht001452.v1.phv00100412.v1_ + * dbGap name: **HEMOGL23** + * dbGap desc: **HEMOGLOBIN (g/dl)** + * dbGap table: **BASEBOTH** + * No permissible values listed in PIC-SURE data dictionary + * _phs000287.v6.pht001452.v1.phv00100413.v1_ + * dbGap name: **HEMATO23** + * dbGap desc: **HEMATOCRIT (%)** + * dbGap table: **BASEBOTH** + * No permissible values listed in PIC-SURE data dictionary + * _phs000287.v6.pht001452.v1.phv00100487.v1_ + * dbGap name: **AGEBL** + * dbGap desc: **CALCULATED AGE AT BASELINE** + * dbGap table: **BASEBOTH** + * No permissible values listed in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -1740,8 +2262,16 @@ * ### blood_cell_count/mchc_mcnc_rbc_1 -- **HCHS_SOL Hispanic Community Health Study /Study of Latinos (HCHS/SOL)**: * 2 component_study_variables - * _phs000810.v1.pht004715.v1.phv00226251.v1_. dbGap Name: **AGE**, Desc: **Age**, Table: **HCHS_SOL_Cohort_Subject_Phenotypes**. - * _phs000810.v1.pht004715.v1.phv00226306.v1_. dbGap Name: **LABA7**, Desc: **Mean Corpuscular Hemoglobin Concentration (g/dL)(LABA7)**, Table: **HCHS_SOL_Cohort_Subject_Phenotypes**. + * _phs000810.v1.pht004715.v1.phv00226251.v1_ + * dbGap name: **AGE** + * dbGap desc: **Age** + * dbGap table: **HCHS_SOL_Cohort_Subject_Phenotypes** + * No permissible values listed in PIC-SURE data dictionary + * _phs000810.v1.pht004715.v1.phv00226306.v1_ + * dbGap name: **LABA7** + * dbGap desc: **Mean Corpuscular Hemoglobin Concentration (g/dL)(LABA7)** + * dbGap table: **HCHS_SOL_Cohort_Subject_Phenotypes** + * No permissible values listed in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -1762,8 +2292,14 @@ * ### blood_cell_count/mchc_mcnc_rbc_1 -- **JHS Jackson Heart Study (JHS) Cohort**: * 2 component_study_variables - * _phs000286.v5.pht001949.v1.phv00126009.v1_. No dbGap metadata available. - * _phs000286.v5.pht001959.v1.phv00127624.v1_. dbGap Name: **MCHC**, Desc: **Mchc % [Visit 1]**, Table: **loca**. + * _phs000286.v5.pht001949.v1.phv00126009.v1_ + * No dbGap metadata available + * varId _phv00126009_ not found in PIC-SURE data dictionary + * _phs000286.v5.pht001959.v1.phv00127624.v1_ + * dbGap name: **MCHC** + * dbGap desc: **Mchc % [Visit 1]** + * dbGap table: **loca** + * varId _phv00127624_ not found in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list) { @@ -1793,9 +2329,21 @@ * ### blood_cell_count/mchc_mcnc_rbc_1 -- **MESA Multi-Ethnic Study of Atherosclerosis (MESA) Cohort**: * 3 component_study_variables - * _phs000209.v13.pht003091.v3.phv00176011.v1_. dbGap Name: **age5c**, Desc: **AGE AT EXAM 5**, Table: **MESA_Exam5Main**. - * _phs000209.v13.pht004319.v1.phv00218992.v1_. dbGap Name: **hct5**, Desc: **HEMATOCRIT (%)**, Table: **MESA_AncilMesaEpigenomicCBC**. - * _phs000209.v13.pht004319.v1.phv00218993.v1_. dbGap Name: **hgb5**, Desc: **HEMOGLOBIN (g/dL)**, Table: **MESA_AncilMesaEpigenomicCBC**. + * _phs000209.v13.pht003091.v3.phv00176011.v1_ + * dbGap name: **age5c** + * dbGap desc: **AGE AT EXAM 5** + * dbGap table: **MESA_Exam5Main** + * PIC-SURE permissible values: 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94 + * _phs000209.v13.pht004319.v1.phv00218992.v1_ + * dbGap name: **hct5** + * dbGap desc: **HEMATOCRIT (%)** + * dbGap table: **MESA_AncilMesaEpigenomicCBC** + * No permissible values listed in PIC-SURE data dictionary + * _phs000209.v13.pht004319.v1.phv00218993.v1_ + * dbGap name: **hgb5** + * dbGap desc: **HEMOGLOBIN (g/dL)** + * dbGap table: **MESA_AncilMesaEpigenomicCBC** + * No permissible values listed in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list) { @@ -1871,14 +2419,40 @@ * ### blood_cell_count/mcv_entvol_rbc_1 -- **ARIC Atherosclerosis Risk in Communities (ARIC) Cohort**: * 8 component_study_variables - * _phs000280.v4.pht004062.v2.phv00204623.v1_. No dbGap metadata available. - * _phs000280.v4.pht004064.v2.phv00204871.v1_. dbGap Name: **V3AGE31**, Desc: **Age at visit 3 [Cohort. Visit 3]**, Table: **DERIVE37**. - * _phs000280.v4.pht004065.v2.phv00204975.v1_. No dbGap metadata available. - * _phs000280.v4.pht004108.v2.phv00207282.v1_. dbGap Name: **HMTB13**, Desc: **Mean corpuscular volume (MCV) (to nearest whole unit). Q13 [Hematology Form. HMTB. Visit 2]**, Table: **HMTB**. - * _phs000280.v4.pht004109.v2.phv00207293.v1_. dbGap Name: **HMTC6**, Desc: **MCV. Q6 [Hematology Lab. HMTCV301. Visit 3]**, Table: **HMTCV301**. - * _phs000280.v4.pht004110.v2.phv00207305.v1_. dbGap Name: **HMTC6**, Desc: **MCV. Q6 [Hematology Lab. HMTCV401. Visit 4]**, Table: **HMTCV401**. - * _phs000280.v4.pht006422.v1.phv00294959.v1_. dbGap Name: **CBC8**, Desc: **Mean cell volume, Mcv [Complete Blood Count, CBC, Visit 5]**, Table: **CBC**. - * _phs000280.v4.pht006431.v1.phv00295623.v1_. No dbGap metadata available. + * _phs000280.v4.pht004062.v2.phv00204623.v1_ + * No dbGap metadata available + * varId _phv00204623_ not found in PIC-SURE data dictionary + * _phs000280.v4.pht004064.v2.phv00204871.v1_ + * dbGap name: **V3AGE31** + * dbGap desc: **Age at visit 3 [Cohort. Visit 3]** + * dbGap table: **DERIVE37** + * varId _phv00204871_ not found in PIC-SURE data dictionary + * _phs000280.v4.pht004065.v2.phv00204975.v1_ + * No dbGap metadata available + * varId _phv00204975_ not found in PIC-SURE data dictionary + * _phs000280.v4.pht004108.v2.phv00207282.v1_ + * dbGap name: **HMTB13** + * dbGap desc: **Mean corpuscular volume (MCV) (to nearest whole unit). Q13 [Hematology Form. HMTB. Visit 2]** + * dbGap table: **HMTB** + * varId _phv00207282_ not found in PIC-SURE data dictionary + * _phs000280.v4.pht004109.v2.phv00207293.v1_ + * dbGap name: **HMTC6** + * dbGap desc: **MCV. Q6 [Hematology Lab. HMTCV301. Visit 3]** + * dbGap table: **HMTCV301** + * varId _phv00207293_ not found in PIC-SURE data dictionary + * _phs000280.v4.pht004110.v2.phv00207305.v1_ + * dbGap name: **HMTC6** + * dbGap desc: **MCV. Q6 [Hematology Lab. HMTCV401. Visit 4]** + * dbGap table: **HMTCV401** + * varId _phv00207305_ not found in PIC-SURE data dictionary + * _phs000280.v4.pht006422.v1.phv00294959.v1_ + * dbGap name: **CBC8** + * dbGap desc: **Mean cell volume, Mcv [Complete Blood Count, CBC, Visit 5]** + * dbGap table: **CBC** + * varId _phv00294959_ not found in PIC-SURE data dictionary + * _phs000280.v4.pht006431.v1.phv00295623.v1_ + * No dbGap metadata available + * varId _phv00295623_ not found in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -1947,9 +2521,21 @@ * ### blood_cell_count/mcv_entvol_rbc_1 -- **CARDIA CARDIA Cohort**: * 3 component_study_variables - * _phs000285.v3.pht001559.v2.phv00112439.v2_. dbGap Name: **A01AGE2**, Desc: **AGE VERIFY**, Table: **A4F01**. - * _phs000285.v3.pht001563.v2.phv00112687.v2_. dbGap Name: **A05RBC**, Desc: **RED CELL COUNT (X 1,000,000)**, Table: **A4F05**. - * _phs000285.v3.pht001563.v2.phv00112689.v2_. dbGap Name: **A05HCT**, Desc: **HEMATOCRIT (%)**, Table: **A4F05**. + * _phs000285.v3.pht001559.v2.phv00112439.v2_ + * dbGap name: **A01AGE2** + * dbGap desc: **AGE VERIFY** + * dbGap table: **A4F01** + * varId _phv00112439_ not found in PIC-SURE data dictionary + * _phs000285.v3.pht001563.v2.phv00112687.v2_ + * dbGap name: **A05RBC** + * dbGap desc: **RED CELL COUNT (X 1,000,000)** + * dbGap table: **A4F05** + * varId _phv00112687_ not found in PIC-SURE data dictionary + * _phs000285.v3.pht001563.v2.phv00112689.v2_ + * dbGap name: **A05HCT** + * dbGap desc: **HEMATOCRIT (%)** + * dbGap table: **A4F05** + * varId _phv00112689_ not found in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -1977,8 +2563,16 @@ * ### blood_cell_count/mcv_entvol_rbc_1 -- **HCHS_SOL Hispanic Community Health Study /Study of Latinos (HCHS/SOL)**: * 2 component_study_variables - * _phs000810.v1.pht004715.v1.phv00226251.v1_. dbGap Name: **AGE**, Desc: **Age**, Table: **HCHS_SOL_Cohort_Subject_Phenotypes**. - * _phs000810.v1.pht004715.v1.phv00226304.v1_. dbGap Name: **LABA5**, Desc: **Mean Corpuscular Volume (fl) (LABA5)**, Table: **HCHS_SOL_Cohort_Subject_Phenotypes**. + * _phs000810.v1.pht004715.v1.phv00226251.v1_ + * dbGap name: **AGE** + * dbGap desc: **Age** + * dbGap table: **HCHS_SOL_Cohort_Subject_Phenotypes** + * No permissible values listed in PIC-SURE data dictionary + * _phs000810.v1.pht004715.v1.phv00226304.v1_ + * dbGap name: **LABA5** + * dbGap desc: **Mean Corpuscular Volume (fl) (LABA5)** + * dbGap table: **HCHS_SOL_Cohort_Subject_Phenotypes** + * No permissible values listed in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -1999,8 +2593,14 @@ * ### blood_cell_count/mcv_entvol_rbc_1 -- **JHS Jackson Heart Study (JHS) Cohort**: * 2 component_study_variables - * _phs000286.v5.pht001949.v1.phv00126009.v1_. No dbGap metadata available. - * _phs000286.v5.pht001959.v1.phv00127625.v1_. dbGap Name: **MCV**, Desc: **Mcv FL [Visit 1]**, Table: **loca**. + * _phs000286.v5.pht001949.v1.phv00126009.v1_ + * No dbGap metadata available + * varId _phv00126009_ not found in PIC-SURE data dictionary + * _phs000286.v5.pht001959.v1.phv00127625.v1_ + * dbGap name: **MCV** + * dbGap desc: **Mcv FL [Visit 1]** + * dbGap table: **loca** + * varId _phv00127625_ not found in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list) { @@ -2030,9 +2630,21 @@ * ### blood_cell_count/mcv_entvol_rbc_1 -- **MESA Multi-Ethnic Study of Atherosclerosis (MESA) Cohort**: * 3 component_study_variables - * _phs000209.v13.pht003091.v3.phv00176011.v1_. dbGap Name: **age5c**, Desc: **AGE AT EXAM 5**, Table: **MESA_Exam5Main**. - * _phs000209.v13.pht004319.v1.phv00218990.v1_. dbGap Name: **rbc5**, Desc: **RED BLOOD CELL (RBC) (x10E6/uL)**, Table: **MESA_AncilMesaEpigenomicCBC**. - * _phs000209.v13.pht004319.v1.phv00218992.v1_. dbGap Name: **hct5**, Desc: **HEMATOCRIT (%)**, Table: **MESA_AncilMesaEpigenomicCBC**. + * _phs000209.v13.pht003091.v3.phv00176011.v1_ + * dbGap name: **age5c** + * dbGap desc: **AGE AT EXAM 5** + * dbGap table: **MESA_Exam5Main** + * PIC-SURE permissible values: 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94 + * _phs000209.v13.pht004319.v1.phv00218990.v1_ + * dbGap name: **rbc5** + * dbGap desc: **RED BLOOD CELL (RBC) (x10E6/uL)** + * dbGap table: **MESA_AncilMesaEpigenomicCBC** + * PIC-SURE permissible values: 2.36, 2.39, 2.75, 2.99, 3.01, 3.06, 3.09, 3.1, 3.13, 3.16, 3.19, 3.21, 3.22, 3.23, 3.24, 3.25, 3.26, 3.27, 3.28, 3.29, 3.3, 3.31, 3.33, 3.34, 3.35, 3.37, 3.38, 3.4, 3.41, 3.42, 3.43, 3.44, 3.45, 3.47, 3.48, 3.49, 3.5, 3.51, 3.52, 3.53, 3.54, 3.55, 3.56, 3.57, 3.58, 3.59, 3.6, 3.61, 3.62, 3.63, 3.64, 3.65, 3.66, 3.67, 3.68, 3.69, 3.7, 3.71, 3.72, 3.73, 3.74, 3.75, 3.76, 3.77, 3.78, 3.79, 3.8, 3.81, 3.82, 3.83, 3.84, 3.85, 3.86, 3.87, 3.88, 3.89, 3.9, 3.91, 3.92, 3.93, 3.94, 3.95, 3.96, 3.97, 3.98, 3.99, 4, 4.01, 4.02, 4.03, 4.04, 4.05, 4.06, 4.07, 4.08, 4.09, 4.1, 4.11, 4.12, 4.13, 4.14, 4.15, 4.16, 4.17, 4.18, 4.19, 4.2, 4.21, 4.22, 4.23, 4.24, 4.25, 4.26, 4.27, 4.28, 4.29, 4.3, 4.31, 4.32, 4.33, 4.34, 4.35, 4.36, 4.37, 4.38, 4.39, 4.4, 4.41, 4.42, 4.43, 4.44, 4.45, 4.46, 4.47, 4.48, 4.49, 4.5, 4.51, 4.52, 4.53, 4.54, 4.55, 4.56, 4.57, 4.58, 4.59, 4.6, 4.61, 4.62, 4.63, 4.64, 4.65, 4.66, 4.67, 4.68, 4.69, 4.7, 4.71, 4.72, 4.73, 4.74, 4.75, 4.76, 4.77, 4.78, 4.79, 4.8, 4.81, 4.82, 4.83, 4.84, 4.85, 4.86, 4.87, 4.88, 4.89, 4.9, 4.91, 4.92, 4.93, 4.94, 4.95, 4.96, 4.97, 4.98, 4.99, 5, 5.01, 5.02, 5.03, 5.04, 5.05, 5.06, 5.07, 5.08, 5.09, 5.1, 5.11, 5.12, 5.13, 5.14, 5.15, 5.16, 5.17, 5.18, 5.19, 5.2, 5.21, 5.22, 5.23, 5.24, 5.25, 5.26, 5.27, 5.28, 5.29, 5.3, 5.31, 5.32, 5.33, 5.34, 5.35, 5.36, 5.37, 5.38, 5.39, 5.4, 5.41, 5.42, 5.43, 5.45, 5.46, 5.47, 5.48, 5.49, 5.5, 5.51, 5.53, 5.54, 5.55, 5.56, 5.57, 5.58, 5.59, 5.6, 5.61, 5.65, 5.66, 5.67, 5.7, 5.71, 5.72, 5.73, 5.74, 5.76, 5.78, 5.81, 5.82, 5.85, 5.89, 5.9, 5.95, 5.97, 6.05, 6.07, 6.09, 6.14, 6.17, 6.35, 6.41, 6.81 + * _phs000209.v13.pht004319.v1.phv00218992.v1_ + * dbGap name: **hct5** + * dbGap desc: **HEMATOCRIT (%)** + * dbGap table: **MESA_AncilMesaEpigenomicCBC** + * No permissible values listed in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list) { @@ -2113,15 +2725,47 @@ * ### blood_cell_count/monocyte_ncnc_bld_1 -- **ARIC Atherosclerosis Risk in Communities (ARIC) Cohort**: * 9 component_study_variables - * _phs000280.v4.pht004062.v2.phv00204623.v1_. No dbGap metadata available. - * _phs000280.v4.pht004063.v2.phv00204712.v1_. dbGap Name: **V1AGE01**, Desc: **Age at visit 1 [Cohort. Visit 1]**, Table: **DERIVE13**. - * _phs000280.v4.pht004107.v2.phv00207257.v1_. dbGap Name: **HMTA03**, Desc: **White blood count x1000/mm3 (MAV). Q3 [Hematology Form. HMTA. Visit 1]**, Table: **HMTA**. - * _phs000280.v4.pht004107.v2.phv00207262.v1_. dbGap Name: **HMTA08**, Desc: **Monocytes % Q8 [Hematology Form. HMTA. Visit 1]**, Table: **HMTA**. - * _phs000280.v4.pht004108.v2.phv00207272.v1_. dbGap Name: **HMTB03**, Desc: **White blood count x1000/mm3 (MAV). Q3 [Hematology Form. HMTB. Visit 2]**, Table: **HMTB**. - * _phs000280.v4.pht004108.v2.phv00207277.v1_. dbGap Name: **HMTB08**, Desc: **Monocytes %. Q8 [Hematology Form. HMTB. Visit 2]**, Table: **HMTB**. - * _phs000280.v4.pht006422.v1.phv00294954.v1_. dbGap Name: **CBC3**, Desc: **White blood cell count, Wbc [Complete Blood Count, CBC, Visit 5]**, Table: **CBC**. - * _phs000280.v4.pht006422.v1.phv00294965.v1_. dbGap Name: **CBC14**, Desc: **Monocyte percentage, Mo [Complete Blood Count, CBC, Visit 5]**, Table: **CBC**. - * _phs000280.v4.pht006431.v1.phv00295623.v1_. No dbGap metadata available. + * _phs000280.v4.pht004062.v2.phv00204623.v1_ + * No dbGap metadata available + * varId _phv00204623_ not found in PIC-SURE data dictionary + * _phs000280.v4.pht004063.v2.phv00204712.v1_ + * dbGap name: **V1AGE01** + * dbGap desc: **Age at visit 1 [Cohort. Visit 1]** + * dbGap table: **DERIVE13** + * varId _phv00204712_ not found in PIC-SURE data dictionary + * _phs000280.v4.pht004107.v2.phv00207257.v1_ + * dbGap name: **HMTA03** + * dbGap desc: **White blood count x1000/mm3 (MAV). Q3 [Hematology Form. HMTA. Visit 1]** + * dbGap table: **HMTA** + * varId _phv00207257_ not found in PIC-SURE data dictionary + * _phs000280.v4.pht004107.v2.phv00207262.v1_ + * dbGap name: **HMTA08** + * dbGap desc: **Monocytes % Q8 [Hematology Form. HMTA. Visit 1]** + * dbGap table: **HMTA** + * varId _phv00207262_ not found in PIC-SURE data dictionary + * _phs000280.v4.pht004108.v2.phv00207272.v1_ + * dbGap name: **HMTB03** + * dbGap desc: **White blood count x1000/mm3 (MAV). Q3 [Hematology Form. HMTB. Visit 2]** + * dbGap table: **HMTB** + * varId _phv00207272_ not found in PIC-SURE data dictionary + * _phs000280.v4.pht004108.v2.phv00207277.v1_ + * dbGap name: **HMTB08** + * dbGap desc: **Monocytes %. Q8 [Hematology Form. HMTB. Visit 2]** + * dbGap table: **HMTB** + * varId _phv00207277_ not found in PIC-SURE data dictionary + * _phs000280.v4.pht006422.v1.phv00294954.v1_ + * dbGap name: **CBC3** + * dbGap desc: **White blood cell count, Wbc [Complete Blood Count, CBC, Visit 5]** + * dbGap table: **CBC** + * varId _phv00294954_ not found in PIC-SURE data dictionary + * _phs000280.v4.pht006422.v1.phv00294965.v1_ + * dbGap name: **CBC14** + * dbGap desc: **Monocyte percentage, Mo [Complete Blood Count, CBC, Visit 5]** + * dbGap table: **CBC** + * varId _phv00294965_ not found in PIC-SURE data dictionary + * _phs000280.v4.pht006431.v1.phv00295623.v1_ + * No dbGap metadata available + * varId _phv00295623_ not found in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -2198,9 +2842,21 @@ * ### blood_cell_count/monocyte_ncnc_bld_1 -- **CARDIA CARDIA Cohort**: * 3 component_study_variables - * _phs000285.v3.pht001559.v2.phv00112439.v2_. dbGap Name: **A01AGE2**, Desc: **AGE VERIFY**, Table: **A4F01**. - * _phs000285.v3.pht001563.v2.phv00112686.v2_. dbGap Name: **A05WBC**, Desc: **WHITE CELL COUNT (X 1000)**, Table: **A4F05**. - * _phs000285.v3.pht001563.v2.phv00112692.v2_. dbGap Name: **A05MONO**, Desc: **MONOCYTES (%)**, Table: **A4F05**. + * _phs000285.v3.pht001559.v2.phv00112439.v2_ + * dbGap name: **A01AGE2** + * dbGap desc: **AGE VERIFY** + * dbGap table: **A4F01** + * varId _phv00112439_ not found in PIC-SURE data dictionary + * _phs000285.v3.pht001563.v2.phv00112686.v2_ + * dbGap name: **A05WBC** + * dbGap desc: **WHITE CELL COUNT (X 1000)** + * dbGap table: **A4F05** + * varId _phv00112686_ not found in PIC-SURE data dictionary + * _phs000285.v3.pht001563.v2.phv00112692.v2_ + * dbGap name: **A05MONO** + * dbGap desc: **MONOCYTES (%)** + * dbGap table: **A4F05** + * varId _phv00112692_ not found in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -2228,9 +2884,21 @@ * ### blood_cell_count/monocyte_ncnc_bld_1 -- **HCHS_SOL Hispanic Community Health Study /Study of Latinos (HCHS/SOL)**: * 3 component_study_variables - * _phs000810.v1.pht004715.v1.phv00226251.v1_. dbGap Name: **AGE**, Desc: **Age**, Table: **HCHS_SOL_Cohort_Subject_Phenotypes**. - * _phs000810.v1.pht004715.v1.phv00226283.v1_. dbGap Name: **LABA1**, Desc: **White Blood Count (x10e9) (LABA1)**, Table: **HCHS_SOL_Cohort_Subject_Phenotypes**. - * _phs000810.v1.pht004715.v1.phv00226286.v1_. dbGap Name: **LABA12**, Desc: **% Monocytes (LABA12)**, Table: **HCHS_SOL_Cohort_Subject_Phenotypes**. + * _phs000810.v1.pht004715.v1.phv00226251.v1_ + * dbGap name: **AGE** + * dbGap desc: **Age** + * dbGap table: **HCHS_SOL_Cohort_Subject_Phenotypes** + * No permissible values listed in PIC-SURE data dictionary + * _phs000810.v1.pht004715.v1.phv00226283.v1_ + * dbGap name: **LABA1** + * dbGap desc: **White Blood Count (x10e9) (LABA1)** + * dbGap table: **HCHS_SOL_Cohort_Subject_Phenotypes** + * No permissible values listed in PIC-SURE data dictionary + * _phs000810.v1.pht004715.v1.phv00226286.v1_ + * dbGap name: **LABA12** + * dbGap desc: **% Monocytes (LABA12)** + * dbGap table: **HCHS_SOL_Cohort_Subject_Phenotypes** + * No permissible values listed in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -2251,9 +2919,19 @@ * ### blood_cell_count/monocyte_ncnc_bld_1 -- **JHS Jackson Heart Study (JHS) Cohort**: * 3 component_study_variables - * _phs000286.v5.pht001949.v1.phv00126009.v1_. No dbGap metadata available. - * _phs000286.v5.pht001959.v1.phv00127626.v1_. dbGap Name: **MONOS**, Desc: **Monos: diff % [Visit 1]**, Table: **loca**. - * _phs000286.v5.pht001959.v1.phv00127631.v1_. dbGap Name: **WBC**, Desc: **White blood cells TH/CMM [Visit 1]**, Table: **loca**. + * _phs000286.v5.pht001949.v1.phv00126009.v1_ + * No dbGap metadata available + * varId _phv00126009_ not found in PIC-SURE data dictionary + * _phs000286.v5.pht001959.v1.phv00127626.v1_ + * dbGap name: **MONOS** + * dbGap desc: **Monos: diff % [Visit 1]** + * dbGap table: **loca** + * varId _phv00127626_ not found in PIC-SURE data dictionary + * _phs000286.v5.pht001959.v1.phv00127631.v1_ + * dbGap name: **WBC** + * dbGap desc: **White blood cells TH/CMM [Visit 1]** + * dbGap table: **loca** + * varId _phv00127631_ not found in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list) { @@ -2288,8 +2966,16 @@ * ### blood_cell_count/monocyte_ncnc_bld_1 -- **MESA Multi-Ethnic Study of Atherosclerosis (MESA) Cohort**: * 2 component_study_variables - * _phs000209.v13.pht003091.v3.phv00176011.v1_. dbGap Name: **age5c**, Desc: **AGE AT EXAM 5**, Table: **MESA_Exam5Main**. - * _phs000209.v13.pht004319.v1.phv00219000.v1_. dbGap Name: **monosa5**, Desc: **MONOCYTES(ABSOLUTE) (x10E3/uL)**, Table: **MESA_AncilMesaEpigenomicCBC**. + * _phs000209.v13.pht003091.v3.phv00176011.v1_ + * dbGap name: **age5c** + * dbGap desc: **AGE AT EXAM 5** + * dbGap table: **MESA_Exam5Main** + * PIC-SURE permissible values: 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94 + * _phs000209.v13.pht004319.v1.phv00219000.v1_ + * dbGap name: **monosa5** + * dbGap desc: **MONOCYTES(ABSOLUTE) (x10E3/uL)** + * dbGap table: **MESA_AncilMesaEpigenomicCBC** + * PIC-SURE permissible values: .1, .2, .3, .4, .5, .6, .7, .8, .9, 0, 1, 1.1, 1.2, 1.3, 1.4, 2.6 * **Function:** ```r harmonize <- function(phen_list){ @@ -2367,14 +3053,44 @@ * ### blood_cell_count/neutrophil_ncnc_bld_1 -- **ARIC Atherosclerosis Risk in Communities (ARIC) Cohort**: * 8 component_study_variables - * _phs000280.v4.pht004062.v2.phv00204623.v1_. No dbGap metadata available. - * _phs000280.v4.pht004063.v2.phv00204712.v1_. dbGap Name: **V1AGE01**, Desc: **Age at visit 1 [Cohort. Visit 1]**, Table: **DERIVE13**. - * _phs000280.v4.pht004107.v2.phv00207257.v1_. dbGap Name: **HMTA03**, Desc: **White blood count x1000/mm3 (MAV). Q3 [Hematology Form. HMTA. Visit 1]**, Table: **HMTA**. - * _phs000280.v4.pht004107.v2.phv00207259.v1_. dbGap Name: **HMTA05**, Desc: **Neutrophils % Q5 [Hematology Form. HMTA. Visit 1]**, Table: **HMTA**. - * _phs000280.v4.pht004107.v2.phv00207260.v1_. dbGap Name: **HMTA06**, Desc: **Neutrophil Bands % Q6 [Hematology Form. HMTA. Visit 1]**, Table: **HMTA**. - * _phs000280.v4.pht004108.v2.phv00207272.v1_. dbGap Name: **HMTB03**, Desc: **White blood count x1000/mm3 (MAV). Q3 [Hematology Form. HMTB. Visit 2]**, Table: **HMTB**. - * _phs000280.v4.pht004108.v2.phv00207274.v1_. dbGap Name: **HMTB05**, Desc: **Neutrophils % Q5. Q5 [Hematology Form. HMTB. Visit 2]**, Table: **HMTB**. - * _phs000280.v4.pht004108.v2.phv00207275.v1_. dbGap Name: **HMTB06**, Desc: **Neutrophil Bands %.Q6 [Hematology Form. HMTB. Visit 2]**, Table: **HMTB**. + * _phs000280.v4.pht004062.v2.phv00204623.v1_ + * No dbGap metadata available + * varId _phv00204623_ not found in PIC-SURE data dictionary + * _phs000280.v4.pht004063.v2.phv00204712.v1_ + * dbGap name: **V1AGE01** + * dbGap desc: **Age at visit 1 [Cohort. Visit 1]** + * dbGap table: **DERIVE13** + * varId _phv00204712_ not found in PIC-SURE data dictionary + * _phs000280.v4.pht004107.v2.phv00207257.v1_ + * dbGap name: **HMTA03** + * dbGap desc: **White blood count x1000/mm3 (MAV). Q3 [Hematology Form. HMTA. Visit 1]** + * dbGap table: **HMTA** + * varId _phv00207257_ not found in PIC-SURE data dictionary + * _phs000280.v4.pht004107.v2.phv00207259.v1_ + * dbGap name: **HMTA05** + * dbGap desc: **Neutrophils % Q5 [Hematology Form. HMTA. Visit 1]** + * dbGap table: **HMTA** + * varId _phv00207259_ not found in PIC-SURE data dictionary + * _phs000280.v4.pht004107.v2.phv00207260.v1_ + * dbGap name: **HMTA06** + * dbGap desc: **Neutrophil Bands % Q6 [Hematology Form. HMTA. Visit 1]** + * dbGap table: **HMTA** + * varId _phv00207260_ not found in PIC-SURE data dictionary + * _phs000280.v4.pht004108.v2.phv00207272.v1_ + * dbGap name: **HMTB03** + * dbGap desc: **White blood count x1000/mm3 (MAV). Q3 [Hematology Form. HMTB. Visit 2]** + * dbGap table: **HMTB** + * varId _phv00207272_ not found in PIC-SURE data dictionary + * _phs000280.v4.pht004108.v2.phv00207274.v1_ + * dbGap name: **HMTB05** + * dbGap desc: **Neutrophils % Q5. Q5 [Hematology Form. HMTB. Visit 2]** + * dbGap table: **HMTB** + * varId _phv00207274_ not found in PIC-SURE data dictionary + * _phs000280.v4.pht004108.v2.phv00207275.v1_ + * dbGap name: **HMTB06** + * dbGap desc: **Neutrophil Bands %.Q6 [Hematology Form. HMTB. Visit 2]** + * dbGap table: **HMTB** + * varId _phv00207275_ not found in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -2449,12 +3165,36 @@ * ### blood_cell_count/neutrophil_ncnc_bld_1 -- **CARDIA CARDIA Cohort**: * 6 component_study_variables - * _phs000285.v3.pht001559.v2.phv00112439.v2_. dbGap Name: **A01AGE2**, Desc: **AGE VERIFY**, Table: **A4F01**. - * _phs000285.v3.pht001563.v2.phv00112686.v2_. dbGap Name: **A05WBC**, Desc: **WHITE CELL COUNT (X 1000)**, Table: **A4F05**. - * _phs000285.v3.pht001563.v2.phv00112694.v2_. dbGap Name: **A05NEUTR**, Desc: **NEUTROPHILS (%)**, Table: **A4F05**. - * _phs000285.v3.pht001563.v2.phv00112695.v2_. dbGap Name: **A05GRAN**, Desc: **GRANULOCYTES (%)**, Table: **A4F05**. - * _phs000285.v3.pht001563.v2.phv00112697.v2_. dbGap Name: **A05BANDS**, Desc: **BANDS (%)**, Table: **A4F05**. - * _phs000285.v3.pht001563.v2.phv00112698.v2_. dbGap Name: **A05SEGS**, Desc: **SEGS (%)**, Table: **A4F05**. + * _phs000285.v3.pht001559.v2.phv00112439.v2_ + * dbGap name: **A01AGE2** + * dbGap desc: **AGE VERIFY** + * dbGap table: **A4F01** + * varId _phv00112439_ not found in PIC-SURE data dictionary + * _phs000285.v3.pht001563.v2.phv00112686.v2_ + * dbGap name: **A05WBC** + * dbGap desc: **WHITE CELL COUNT (X 1000)** + * dbGap table: **A4F05** + * varId _phv00112686_ not found in PIC-SURE data dictionary + * _phs000285.v3.pht001563.v2.phv00112694.v2_ + * dbGap name: **A05NEUTR** + * dbGap desc: **NEUTROPHILS (%)** + * dbGap table: **A4F05** + * varId _phv00112694_ not found in PIC-SURE data dictionary + * _phs000285.v3.pht001563.v2.phv00112695.v2_ + * dbGap name: **A05GRAN** + * dbGap desc: **GRANULOCYTES (%)** + * dbGap table: **A4F05** + * varId _phv00112695_ not found in PIC-SURE data dictionary + * _phs000285.v3.pht001563.v2.phv00112697.v2_ + * dbGap name: **A05BANDS** + * dbGap desc: **BANDS (%)** + * dbGap table: **A4F05** + * varId _phv00112697_ not found in PIC-SURE data dictionary + * _phs000285.v3.pht001563.v2.phv00112698.v2_ + * dbGap name: **A05SEGS** + * dbGap desc: **SEGS (%)** + * dbGap table: **A4F05** + * varId _phv00112698_ not found in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -2496,9 +3236,21 @@ * ### blood_cell_count/neutrophil_ncnc_bld_1 -- **HCHS_SOL Hispanic Community Health Study /Study of Latinos (HCHS/SOL)**: * 3 component_study_variables - * _phs000810.v1.pht004715.v1.phv00226251.v1_. dbGap Name: **AGE**, Desc: **Age**, Table: **HCHS_SOL_Cohort_Subject_Phenotypes**. - * _phs000810.v1.pht004715.v1.phv00226283.v1_. dbGap Name: **LABA1**, Desc: **White Blood Count (x10e9) (LABA1)**, Table: **HCHS_SOL_Cohort_Subject_Phenotypes**. - * _phs000810.v1.pht004715.v1.phv00226284.v1_. dbGap Name: **LABA10**, Desc: **% Neutrophils (LABA10)**, Table: **HCHS_SOL_Cohort_Subject_Phenotypes**. + * _phs000810.v1.pht004715.v1.phv00226251.v1_ + * dbGap name: **AGE** + * dbGap desc: **Age** + * dbGap table: **HCHS_SOL_Cohort_Subject_Phenotypes** + * No permissible values listed in PIC-SURE data dictionary + * _phs000810.v1.pht004715.v1.phv00226283.v1_ + * dbGap name: **LABA1** + * dbGap desc: **White Blood Count (x10e9) (LABA1)** + * dbGap table: **HCHS_SOL_Cohort_Subject_Phenotypes** + * No permissible values listed in PIC-SURE data dictionary + * _phs000810.v1.pht004715.v1.phv00226284.v1_ + * dbGap name: **LABA10** + * dbGap desc: **% Neutrophils (LABA10)** + * dbGap table: **HCHS_SOL_Cohort_Subject_Phenotypes** + * No permissible values listed in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -2519,10 +3271,24 @@ * ### blood_cell_count/neutrophil_ncnc_bld_1 -- **JHS Jackson Heart Study (JHS) Cohort**: * 4 component_study_variables - * _phs000286.v5.pht001949.v1.phv00126009.v1_. No dbGap metadata available. - * _phs000286.v5.pht001959.v1.phv00127630.v1_. dbGap Name: **SEGS**, Desc: **Segs: diff measure % [Visit 1]**, Table: **loca**. - * _phs000286.v5.pht001959.v1.phv00127631.v1_. dbGap Name: **WBC**, Desc: **White blood cells TH/CMM [Visit 1]**, Table: **loca**. - * _phs000286.v5.pht001959.v1.phv00127632.v1_. dbGap Name: **BANDS**, Desc: **Bands: diff measure % [Visit 1]**, Table: **loca**. + * _phs000286.v5.pht001949.v1.phv00126009.v1_ + * No dbGap metadata available + * varId _phv00126009_ not found in PIC-SURE data dictionary + * _phs000286.v5.pht001959.v1.phv00127630.v1_ + * dbGap name: **SEGS** + * dbGap desc: **Segs: diff measure % [Visit 1]** + * dbGap table: **loca** + * varId _phv00127630_ not found in PIC-SURE data dictionary + * _phs000286.v5.pht001959.v1.phv00127631.v1_ + * dbGap name: **WBC** + * dbGap desc: **White blood cells TH/CMM [Visit 1]** + * dbGap table: **loca** + * varId _phv00127631_ not found in PIC-SURE data dictionary + * _phs000286.v5.pht001959.v1.phv00127632.v1_ + * dbGap name: **BANDS** + * dbGap desc: **Bands: diff measure % [Visit 1]** + * dbGap table: **loca** + * varId _phv00127632_ not found in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list) { @@ -2563,8 +3329,16 @@ * ### blood_cell_count/neutrophil_ncnc_bld_1 -- **MESA Multi-Ethnic Study of Atherosclerosis (MESA) Cohort**: * 2 component_study_variables - * _phs000209.v13.pht003091.v3.phv00176011.v1_. dbGap Name: **age5c**, Desc: **AGE AT EXAM 5**, Table: **MESA_Exam5Main**. - * _phs000209.v13.pht004319.v1.phv00218999.v1_. dbGap Name: **polysa5**, Desc: **NEUTROPHILS (ABSOLUTE) (x10E3/uL)**, Table: **MESA_AncilMesaEpigenomicCBC**. + * _phs000209.v13.pht003091.v3.phv00176011.v1_ + * dbGap name: **age5c** + * dbGap desc: **AGE AT EXAM 5** + * dbGap table: **MESA_Exam5Main** + * PIC-SURE permissible values: 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94 + * _phs000209.v13.pht004319.v1.phv00218999.v1_ + * dbGap name: **polysa5** + * dbGap desc: **NEUTROPHILS (ABSOLUTE) (x10E3/uL)** + * dbGap table: **MESA_AncilMesaEpigenomicCBC** + * PIC-SURE permissible values: .1, .6, .7, .9, 1, 1.1, 1.2, 1.3, 1.4, 1.5, 1.6, 1.7, 1.8, 1.9, 11.1, 11.5, 12.7, 2, 2.1, 2.2, 2.3, 2.4, 2.5, 2.6, 2.7, 2.8, 2.9, 3, 3.1, 3.2, 3.3, 3.4, 3.5, 3.6, 3.7, 3.8, 3.9, 4, 4.1, 4.2, 4.3, 4.4, 4.5, 4.6, 4.7, 4.8, 4.9, 5, 5.1, 5.2, 5.3, 5.4, 5.5, 5.6, 5.7, 5.8, 5.9, 6, 6.1, 6.2, 6.3, 6.4, 6.5, 6.6, 6.7, 6.8, 6.9, 7, 7.1, 7.2, 7.3, 7.4, 7.5, 7.6, 7.7, 7.8, 7.9, 8, 8.1, 8.2, 8.3, 8.4, 8.6, 8.8, 8.9, 9, 9.3 * **Function:** ```r harmonize <- function(phen_list){ @@ -2624,16 +3398,50 @@ * ### blood_cell_count/platelet_ncnc_bld_1 -- **ARIC Atherosclerosis Risk in Communities (ARIC) Cohort**: * 10 component_study_variables - * _phs000280.v4.pht004062.v2.phv00204623.v1_. No dbGap metadata available. - * _phs000280.v4.pht004063.v2.phv00204712.v1_. dbGap Name: **V1AGE01**, Desc: **Age at visit 1 [Cohort. Visit 1]**, Table: **DERIVE13**. - * _phs000280.v4.pht004064.v2.phv00204871.v1_. dbGap Name: **V3AGE31**, Desc: **Age at visit 3 [Cohort. Visit 3]**, Table: **DERIVE37**. - * _phs000280.v4.pht004065.v2.phv00204975.v1_. No dbGap metadata available. - * _phs000280.v4.pht004107.v2.phv00207258.v1_. dbGap Name: **HMTA04**, Desc: **Platelet count x1000/mm3 (MAV). Q4 [Hematology Form. HMTA. Visit 1]**, Table: **HMTA**. - * _phs000280.v4.pht004108.v2.phv00207273.v1_. dbGap Name: **HMTB04**, Desc: **Platelet count x1000/mm3 (MAV). Q4 [Hematology Form. HMTB. Visit 2]**, Table: **HMTB**. - * _phs000280.v4.pht004109.v2.phv00207294.v1_. dbGap Name: **HMTC10**, Desc: **Platelet count Q10 [Hematology Lab. HMTCV301. Visit 3]**, Table: **HMTCV301**. - * _phs000280.v4.pht004110.v2.phv00207306.v1_. dbGap Name: **HMTC10**, Desc: **Platelet count. Q10 [Hematology Lab. HMTCV401. Visit 4]**, Table: **HMTCV401**. - * _phs000280.v4.pht006422.v1.phv00294958.v1_. dbGap Name: **CBC7**, Desc: **Platelet count, Plt [Complete Blood Count, CBC, Visit 5]**, Table: **CBC**. - * _phs000280.v4.pht006431.v1.phv00295623.v1_. No dbGap metadata available. + * _phs000280.v4.pht004062.v2.phv00204623.v1_ + * No dbGap metadata available + * varId _phv00204623_ not found in PIC-SURE data dictionary + * _phs000280.v4.pht004063.v2.phv00204712.v1_ + * dbGap name: **V1AGE01** + * dbGap desc: **Age at visit 1 [Cohort. Visit 1]** + * dbGap table: **DERIVE13** + * varId _phv00204712_ not found in PIC-SURE data dictionary + * _phs000280.v4.pht004064.v2.phv00204871.v1_ + * dbGap name: **V3AGE31** + * dbGap desc: **Age at visit 3 [Cohort. Visit 3]** + * dbGap table: **DERIVE37** + * varId _phv00204871_ not found in PIC-SURE data dictionary + * _phs000280.v4.pht004065.v2.phv00204975.v1_ + * No dbGap metadata available + * varId _phv00204975_ not found in PIC-SURE data dictionary + * _phs000280.v4.pht004107.v2.phv00207258.v1_ + * dbGap name: **HMTA04** + * dbGap desc: **Platelet count x1000/mm3 (MAV). Q4 [Hematology Form. HMTA. Visit 1]** + * dbGap table: **HMTA** + * varId _phv00207258_ not found in PIC-SURE data dictionary + * _phs000280.v4.pht004108.v2.phv00207273.v1_ + * dbGap name: **HMTB04** + * dbGap desc: **Platelet count x1000/mm3 (MAV). Q4 [Hematology Form. HMTB. Visit 2]** + * dbGap table: **HMTB** + * varId _phv00207273_ not found in PIC-SURE data dictionary + * _phs000280.v4.pht004109.v2.phv00207294.v1_ + * dbGap name: **HMTC10** + * dbGap desc: **Platelet count Q10 [Hematology Lab. HMTCV301. Visit 3]** + * dbGap table: **HMTCV301** + * varId _phv00207294_ not found in PIC-SURE data dictionary + * _phs000280.v4.pht004110.v2.phv00207306.v1_ + * dbGap name: **HMTC10** + * dbGap desc: **Platelet count. Q10 [Hematology Lab. HMTCV401. Visit 4]** + * dbGap table: **HMTCV401** + * varId _phv00207306_ not found in PIC-SURE data dictionary + * _phs000280.v4.pht006422.v1.phv00294958.v1_ + * dbGap name: **CBC7** + * dbGap desc: **Platelet count, Plt [Complete Blood Count, CBC, Visit 5]** + * dbGap table: **CBC** + * varId _phv00294958_ not found in PIC-SURE data dictionary + * _phs000280.v4.pht006431.v1.phv00295623.v1_ + * No dbGap metadata available + * varId _phv00295623_ not found in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -2707,8 +3515,16 @@ * ### blood_cell_count/platelet_ncnc_bld_1 -- **CARDIA CARDIA Cohort**: * 2 component_study_variables - * _phs000285.v3.pht001559.v2.phv00112439.v2_. dbGap Name: **A01AGE2**, Desc: **AGE VERIFY**, Table: **A4F01**. - * _phs000285.v3.pht001563.v2.phv00112690.v2_. dbGap Name: **A05PLATL**, Desc: **PLATELET COUNT**, Table: **A4F05**. + * _phs000285.v3.pht001559.v2.phv00112439.v2_ + * dbGap name: **A01AGE2** + * dbGap desc: **AGE VERIFY** + * dbGap table: **A4F01** + * varId _phv00112439_ not found in PIC-SURE data dictionary + * _phs000285.v3.pht001563.v2.phv00112690.v2_ + * dbGap name: **A05PLATL** + * dbGap desc: **PLATELET COUNT** + * dbGap table: **A4F05** + * varId _phv00112690_ not found in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -2735,8 +3551,16 @@ * ### blood_cell_count/platelet_ncnc_bld_1 -- **CHS Cardiovascular Health Study (CHS) Cohort: an NHLBI-funded observational study of risk factors for cardiovascular disease in adults 65 years or older**: * 2 component_study_variables - * _phs000287.v6.pht001452.v1.phv00100414.v1_. dbGap Name: **PLATE23**, Desc: **PLATELET COUNT (/cc.mm)**, Table: **BASEBOTH**. - * _phs000287.v6.pht001452.v1.phv00100487.v1_. dbGap Name: **AGEBL**, Desc: **CALCULATED AGE AT BASELINE**, Table: **BASEBOTH**. + * _phs000287.v6.pht001452.v1.phv00100414.v1_ + * dbGap name: **PLATE23** + * dbGap desc: **PLATELET COUNT (/cc.mm)** + * dbGap table: **BASEBOTH** + * No permissible values listed in PIC-SURE data dictionary + * _phs000287.v6.pht001452.v1.phv00100487.v1_ + * dbGap name: **AGEBL** + * dbGap desc: **CALCULATED AGE AT BASELINE** + * dbGap table: **BASEBOTH** + * No permissible values listed in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -2755,8 +3579,16 @@ * ### blood_cell_count/platelet_ncnc_bld_1 -- **HCHS_SOL Hispanic Community Health Study /Study of Latinos (HCHS/SOL)**: * 2 component_study_variables - * _phs000810.v1.pht004715.v1.phv00226251.v1_. dbGap Name: **AGE**, Desc: **Age**, Table: **HCHS_SOL_Cohort_Subject_Phenotypes**. - * _phs000810.v1.pht004715.v1.phv00226310.v1_. dbGap Name: **LABA9**, Desc: **Platelet Count (x10e9) (LABA9)**, Table: **HCHS_SOL_Cohort_Subject_Phenotypes**. + * _phs000810.v1.pht004715.v1.phv00226251.v1_ + * dbGap name: **AGE** + * dbGap desc: **Age** + * dbGap table: **HCHS_SOL_Cohort_Subject_Phenotypes** + * No permissible values listed in PIC-SURE data dictionary + * _phs000810.v1.pht004715.v1.phv00226310.v1_ + * dbGap name: **LABA9** + * dbGap desc: **Platelet Count (x10e9) (LABA9)** + * dbGap table: **HCHS_SOL_Cohort_Subject_Phenotypes** + * No permissible values listed in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -2777,8 +3609,14 @@ * ### blood_cell_count/platelet_ncnc_bld_1 -- **JHS Jackson Heart Study (JHS) Cohort**: * 2 component_study_variables - * _phs000286.v5.pht001949.v1.phv00126009.v1_. No dbGap metadata available. - * _phs000286.v5.pht001959.v1.phv00127616.v1_. dbGap Name: **PLATELET**, Desc: **Platelet TH/CMM [Visit 1]**, Table: **loca**. + * _phs000286.v5.pht001949.v1.phv00126009.v1_ + * No dbGap metadata available + * varId _phv00126009_ not found in PIC-SURE data dictionary + * _phs000286.v5.pht001959.v1.phv00127616.v1_ + * dbGap name: **PLATELET** + * dbGap desc: **Platelet TH/CMM [Visit 1]** + * dbGap table: **loca** + * varId _phv00127616_ not found in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list) { @@ -2808,8 +3646,16 @@ * ### blood_cell_count/platelet_ncnc_bld_1 -- **MESA Multi-Ethnic Study of Atherosclerosis (MESA) Cohort**: * 2 component_study_variables - * _phs000209.v13.pht003091.v3.phv00176011.v1_. dbGap Name: **age5c**, Desc: **AGE AT EXAM 5**, Table: **MESA_Exam5Main**. - * _phs000209.v13.pht004319.v1.phv00218991.v1_. dbGap Name: **plt5**, Desc: **PLATELETS (x10E3/uL)**, Table: **MESA_AncilMesaEpigenomicCBC**. + * _phs000209.v13.pht003091.v3.phv00176011.v1_ + * dbGap name: **age5c** + * dbGap desc: **AGE AT EXAM 5** + * dbGap table: **MESA_Exam5Main** + * PIC-SURE permissible values: 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94 + * _phs000209.v13.pht004319.v1.phv00218991.v1_ + * dbGap name: **plt5** + * dbGap desc: **PLATELETS (x10E3/uL)** + * dbGap table: **MESA_AncilMesaEpigenomicCBC** + * No permissible values listed in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -2835,11 +3681,31 @@ * ### blood_cell_count/platelet_ncnc_bld_1 -- **WHI Women's Health Initiative**: * 5 component_study_variables - * _phs000200.v11.pht000986.v6.phv00077362.v6_. dbGap Name: **CBCVY**, Desc: **CBC Visit year**, Table: **cbc_rel1**. - * _phs000200.v11.pht000986.v6.phv00077363.v6_. dbGap Name: **CBCDAYS**, Desc: **CBC Days since randomization/enrollment**, Table: **cbc_rel1**. - * _phs000200.v11.pht000986.v6.phv00077367.v6_. dbGap Name: **PLATELET**, Desc: **Platelet count (Kcell/microliter)**, Table: **cbc_rel1**. - * _phs000200.v11.pht000998.v6.phv00078436.v6_. dbGap Name: **F2DAYS**, Desc: **F2 Days since randomization**, Table: **f2_rel1**. - * _phs000200.v11.pht000998.v6.phv00078437.v6_. dbGap Name: **AGE**, Desc: **Age at screening**, Table: **f2_rel1**. + * _phs000200.v11.pht000986.v6.phv00077362.v6_ + * dbGap name: **CBCVY** + * dbGap desc: **CBC Visit year** + * dbGap table: **cbc_rel1** + * No permissible values listed in PIC-SURE data dictionary + * _phs000200.v11.pht000986.v6.phv00077363.v6_ + * dbGap name: **CBCDAYS** + * dbGap desc: **CBC Days since randomization/enrollment** + * dbGap table: **cbc_rel1** + * No permissible values listed in PIC-SURE data dictionary + * _phs000200.v11.pht000986.v6.phv00077367.v6_ + * dbGap name: **PLATELET** + * dbGap desc: **Platelet count (Kcell/microliter)** + * dbGap table: **cbc_rel1** + * No permissible values listed in PIC-SURE data dictionary + * _phs000200.v11.pht000998.v6.phv00078436.v6_ + * dbGap name: **F2DAYS** + * dbGap desc: **F2 Days since randomization** + * dbGap table: **f2_rel1** + * No permissible values listed in PIC-SURE data dictionary + * _phs000200.v11.pht000998.v6.phv00078437.v6_ + * dbGap name: **AGE** + * dbGap desc: **Age at screening** + * dbGap table: **f2_rel1** + * No permissible values listed in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -2890,8 +3756,14 @@ * ### blood_cell_count/pmv_entvol_bld_1 -- **ARIC Atherosclerosis Risk in Communities (ARIC) Cohort**: * 2 component_study_variables - * _phs000280.v4.pht006422.v1.phv00294963.v1_. dbGap Name: **CBC12**, Desc: **Mean platelet volume, Mpv [Complete Blood Count, CBC, Visit 5]**, Table: **CBC**. - * _phs000280.v4.pht006431.v1.phv00295623.v1_. No dbGap metadata available. + * _phs000280.v4.pht006422.v1.phv00294963.v1_ + * dbGap name: **CBC12** + * dbGap desc: **Mean platelet volume, Mpv [Complete Blood Count, CBC, Visit 5]** + * dbGap table: **CBC** + * varId _phv00294963_ not found in PIC-SURE data dictionary + * _phs000280.v4.pht006431.v1.phv00295623.v1_ + * No dbGap metadata available + * varId _phv00295623_ not found in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -2920,8 +3792,14 @@ * ### blood_cell_count/pmv_entvol_bld_1 -- **JHS Jackson Heart Study (JHS) Cohort**: * 2 component_study_variables - * _phs000286.v5.pht001949.v1.phv00126009.v1_. No dbGap metadata available. - * _phs000286.v5.pht001959.v1.phv00127627.v1_. dbGap Name: **MPV**, Desc: **Mpv FL [Visit 1]**, Table: **loca**. + * _phs000286.v5.pht001949.v1.phv00126009.v1_ + * No dbGap metadata available + * varId _phv00126009_ not found in PIC-SURE data dictionary + * _phs000286.v5.pht001959.v1.phv00127627.v1_ + * dbGap name: **MPV** + * dbGap desc: **Mpv FL [Visit 1]** + * dbGap table: **loca** + * varId _phv00127627_ not found in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list) { @@ -2983,12 +3861,32 @@ * ### blood_cell_count/rbc_ncnc_bld_1 -- **ARIC Atherosclerosis Risk in Communities (ARIC) Cohort**: * 6 component_study_variables - * _phs000280.v4.pht004064.v2.phv00204871.v1_. dbGap Name: **V3AGE31**, Desc: **Age at visit 3 [Cohort. Visit 3]**, Table: **DERIVE37**. - * _phs000280.v4.pht004065.v2.phv00204975.v1_. No dbGap metadata available. - * _phs000280.v4.pht004109.v2.phv00207287.v1_. dbGap Name: **HMTC3**, Desc: **Red blood count. Q3 [Hematology Lab. HMTCV301. Visit 3]**, Table: **HMTCV301**. - * _phs000280.v4.pht004110.v2.phv00207299.v1_. dbGap Name: **HMTC3**, Desc: **Red blood count. Q3 [Hematology Lab. HMTCV401. Visit 4]**, Table: **HMTCV401**. - * _phs000280.v4.pht006422.v1.phv00294955.v1_. dbGap Name: **CBC4**, Desc: **Red blood cell count, Rbc [Complete Blood Count, CBC, Visit 5]**, Table: **CBC**. - * _phs000280.v4.pht006431.v1.phv00295623.v1_. No dbGap metadata available. + * _phs000280.v4.pht004064.v2.phv00204871.v1_ + * dbGap name: **V3AGE31** + * dbGap desc: **Age at visit 3 [Cohort. Visit 3]** + * dbGap table: **DERIVE37** + * varId _phv00204871_ not found in PIC-SURE data dictionary + * _phs000280.v4.pht004065.v2.phv00204975.v1_ + * No dbGap metadata available + * varId _phv00204975_ not found in PIC-SURE data dictionary + * _phs000280.v4.pht004109.v2.phv00207287.v1_ + * dbGap name: **HMTC3** + * dbGap desc: **Red blood count. Q3 [Hematology Lab. HMTCV301. Visit 3]** + * dbGap table: **HMTCV301** + * varId _phv00207287_ not found in PIC-SURE data dictionary + * _phs000280.v4.pht004110.v2.phv00207299.v1_ + * dbGap name: **HMTC3** + * dbGap desc: **Red blood count. Q3 [Hematology Lab. HMTCV401. Visit 4]** + * dbGap table: **HMTCV401** + * varId _phv00207299_ not found in PIC-SURE data dictionary + * _phs000280.v4.pht006422.v1.phv00294955.v1_ + * dbGap name: **CBC4** + * dbGap desc: **Red blood cell count, Rbc [Complete Blood Count, CBC, Visit 5]** + * dbGap table: **CBC** + * varId _phv00294955_ not found in PIC-SURE data dictionary + * _phs000280.v4.pht006431.v1.phv00295623.v1_ + * No dbGap metadata available + * varId _phv00295623_ not found in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -3052,8 +3950,16 @@ * ### blood_cell_count/rbc_ncnc_bld_1 -- **CARDIA CARDIA Cohort**: * 2 component_study_variables - * _phs000285.v3.pht001559.v2.phv00112439.v2_. dbGap Name: **A01AGE2**, Desc: **AGE VERIFY**, Table: **A4F01**. - * _phs000285.v3.pht001563.v2.phv00112687.v2_. dbGap Name: **A05RBC**, Desc: **RED CELL COUNT (X 1,000,000)**, Table: **A4F05**. + * _phs000285.v3.pht001559.v2.phv00112439.v2_ + * dbGap name: **A01AGE2** + * dbGap desc: **AGE VERIFY** + * dbGap table: **A4F01** + * varId _phv00112439_ not found in PIC-SURE data dictionary + * _phs000285.v3.pht001563.v2.phv00112687.v2_ + * dbGap name: **A05RBC** + * dbGap desc: **RED CELL COUNT (X 1,000,000)** + * dbGap table: **A4F05** + * varId _phv00112687_ not found in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -3079,8 +3985,16 @@ * ### blood_cell_count/rbc_ncnc_bld_1 -- **HCHS_SOL Hispanic Community Health Study /Study of Latinos (HCHS/SOL)**: * 2 component_study_variables - * _phs000810.v1.pht004715.v1.phv00226251.v1_. dbGap Name: **AGE**, Desc: **Age**, Table: **HCHS_SOL_Cohort_Subject_Phenotypes**. - * _phs000810.v1.pht004715.v1.phv00226294.v1_. dbGap Name: **LABA2**, Desc: **Red Blood Count (x10e12) (LABA2)**, Table: **HCHS_SOL_Cohort_Subject_Phenotypes**. + * _phs000810.v1.pht004715.v1.phv00226251.v1_ + * dbGap name: **AGE** + * dbGap desc: **Age** + * dbGap table: **HCHS_SOL_Cohort_Subject_Phenotypes** + * No permissible values listed in PIC-SURE data dictionary + * _phs000810.v1.pht004715.v1.phv00226294.v1_ + * dbGap name: **LABA2** + * dbGap desc: **Red Blood Count (x10e12) (LABA2)** + * dbGap table: **HCHS_SOL_Cohort_Subject_Phenotypes** + * No permissible values listed in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -3101,8 +4015,14 @@ * ### blood_cell_count/rbc_ncnc_bld_1 -- **JHS Jackson Heart Study (JHS) Cohort**: * 2 component_study_variables - * _phs000286.v5.pht001949.v1.phv00126009.v1_. No dbGap metadata available. - * _phs000286.v5.pht001959.v1.phv00127629.v1_. dbGap Name: **RED_CELL_COUNT**, Desc: **Red cell count M/CMM [Visit 1]**, Table: **loca**. + * _phs000286.v5.pht001949.v1.phv00126009.v1_ + * No dbGap metadata available + * varId _phv00126009_ not found in PIC-SURE data dictionary + * _phs000286.v5.pht001959.v1.phv00127629.v1_ + * dbGap name: **RED_CELL_COUNT** + * dbGap desc: **Red cell count M/CMM [Visit 1]** + * dbGap table: **loca** + * varId _phv00127629_ not found in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list) { @@ -3132,8 +4052,16 @@ * ### blood_cell_count/rbc_ncnc_bld_1 -- **MESA Multi-Ethnic Study of Atherosclerosis (MESA) Cohort**: * 2 component_study_variables - * _phs000209.v13.pht003091.v3.phv00176011.v1_. dbGap Name: **age5c**, Desc: **AGE AT EXAM 5**, Table: **MESA_Exam5Main**. - * _phs000209.v13.pht004319.v1.phv00218990.v1_. dbGap Name: **rbc5**, Desc: **RED BLOOD CELL (RBC) (x10E6/uL)**, Table: **MESA_AncilMesaEpigenomicCBC**. + * _phs000209.v13.pht003091.v3.phv00176011.v1_ + * dbGap name: **age5c** + * dbGap desc: **AGE AT EXAM 5** + * dbGap table: **MESA_Exam5Main** + * PIC-SURE permissible values: 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94 + * _phs000209.v13.pht004319.v1.phv00218990.v1_ + * dbGap name: **rbc5** + * dbGap desc: **RED BLOOD CELL (RBC) (x10E6/uL)** + * dbGap table: **MESA_AncilMesaEpigenomicCBC** + * PIC-SURE permissible values: 2.36, 2.39, 2.75, 2.99, 3.01, 3.06, 3.09, 3.1, 3.13, 3.16, 3.19, 3.21, 3.22, 3.23, 3.24, 3.25, 3.26, 3.27, 3.28, 3.29, 3.3, 3.31, 3.33, 3.34, 3.35, 3.37, 3.38, 3.4, 3.41, 3.42, 3.43, 3.44, 3.45, 3.47, 3.48, 3.49, 3.5, 3.51, 3.52, 3.53, 3.54, 3.55, 3.56, 3.57, 3.58, 3.59, 3.6, 3.61, 3.62, 3.63, 3.64, 3.65, 3.66, 3.67, 3.68, 3.69, 3.7, 3.71, 3.72, 3.73, 3.74, 3.75, 3.76, 3.77, 3.78, 3.79, 3.8, 3.81, 3.82, 3.83, 3.84, 3.85, 3.86, 3.87, 3.88, 3.89, 3.9, 3.91, 3.92, 3.93, 3.94, 3.95, 3.96, 3.97, 3.98, 3.99, 4, 4.01, 4.02, 4.03, 4.04, 4.05, 4.06, 4.07, 4.08, 4.09, 4.1, 4.11, 4.12, 4.13, 4.14, 4.15, 4.16, 4.17, 4.18, 4.19, 4.2, 4.21, 4.22, 4.23, 4.24, 4.25, 4.26, 4.27, 4.28, 4.29, 4.3, 4.31, 4.32, 4.33, 4.34, 4.35, 4.36, 4.37, 4.38, 4.39, 4.4, 4.41, 4.42, 4.43, 4.44, 4.45, 4.46, 4.47, 4.48, 4.49, 4.5, 4.51, 4.52, 4.53, 4.54, 4.55, 4.56, 4.57, 4.58, 4.59, 4.6, 4.61, 4.62, 4.63, 4.64, 4.65, 4.66, 4.67, 4.68, 4.69, 4.7, 4.71, 4.72, 4.73, 4.74, 4.75, 4.76, 4.77, 4.78, 4.79, 4.8, 4.81, 4.82, 4.83, 4.84, 4.85, 4.86, 4.87, 4.88, 4.89, 4.9, 4.91, 4.92, 4.93, 4.94, 4.95, 4.96, 4.97, 4.98, 4.99, 5, 5.01, 5.02, 5.03, 5.04, 5.05, 5.06, 5.07, 5.08, 5.09, 5.1, 5.11, 5.12, 5.13, 5.14, 5.15, 5.16, 5.17, 5.18, 5.19, 5.2, 5.21, 5.22, 5.23, 5.24, 5.25, 5.26, 5.27, 5.28, 5.29, 5.3, 5.31, 5.32, 5.33, 5.34, 5.35, 5.36, 5.37, 5.38, 5.39, 5.4, 5.41, 5.42, 5.43, 5.45, 5.46, 5.47, 5.48, 5.49, 5.5, 5.51, 5.53, 5.54, 5.55, 5.56, 5.57, 5.58, 5.59, 5.6, 5.61, 5.65, 5.66, 5.67, 5.7, 5.71, 5.72, 5.73, 5.74, 5.76, 5.78, 5.81, 5.82, 5.85, 5.89, 5.9, 5.95, 5.97, 6.05, 6.07, 6.09, 6.14, 6.17, 6.35, 6.41, 6.81 * **Function:** ```r harmonize <- function(phen_list){ @@ -3181,12 +4109,32 @@ * ### blood_cell_count/rdw_ratio_rbc_1 -- **ARIC Atherosclerosis Risk in Communities (ARIC) Cohort**: * 6 component_study_variables - * _phs000280.v4.pht004064.v2.phv00204871.v1_. dbGap Name: **V3AGE31**, Desc: **Age at visit 3 [Cohort. Visit 3]**, Table: **DERIVE37**. - * _phs000280.v4.pht004065.v2.phv00204975.v1_. No dbGap metadata available. - * _phs000280.v4.pht004109.v2.phv00207292.v1_. dbGap Name: **HMTC9**, Desc: **RBC distribution width. Q9 [Hematology Lab. HMTCV301. Visit 3]**, Table: **HMTCV301**. - * _phs000280.v4.pht004110.v2.phv00207304.v1_. dbGap Name: **HMTC9**, Desc: **RBC distribution width. Q9 [Hematology Lab. HMTCV401. Visit 4]**, Table: **HMTCV401**. - * _phs000280.v4.pht006422.v1.phv00294962.v1_. dbGap Name: **CBC11**, Desc: **Red cell distribution width, Rdw [Complete Blood Count, CBC, Visit 5]**, Table: **CBC**. - * _phs000280.v4.pht006431.v1.phv00295623.v1_. No dbGap metadata available. + * _phs000280.v4.pht004064.v2.phv00204871.v1_ + * dbGap name: **V3AGE31** + * dbGap desc: **Age at visit 3 [Cohort. Visit 3]** + * dbGap table: **DERIVE37** + * varId _phv00204871_ not found in PIC-SURE data dictionary + * _phs000280.v4.pht004065.v2.phv00204975.v1_ + * No dbGap metadata available + * varId _phv00204975_ not found in PIC-SURE data dictionary + * _phs000280.v4.pht004109.v2.phv00207292.v1_ + * dbGap name: **HMTC9** + * dbGap desc: **RBC distribution width. Q9 [Hematology Lab. HMTCV301. Visit 3]** + * dbGap table: **HMTCV301** + * varId _phv00207292_ not found in PIC-SURE data dictionary + * _phs000280.v4.pht004110.v2.phv00207304.v1_ + * dbGap name: **HMTC9** + * dbGap desc: **RBC distribution width. Q9 [Hematology Lab. HMTCV401. Visit 4]** + * dbGap table: **HMTCV401** + * varId _phv00207304_ not found in PIC-SURE data dictionary + * _phs000280.v4.pht006422.v1.phv00294962.v1_ + * dbGap name: **CBC11** + * dbGap desc: **Red cell distribution width, Rdw [Complete Blood Count, CBC, Visit 5]** + * dbGap table: **CBC** + * varId _phv00294962_ not found in PIC-SURE data dictionary + * _phs000280.v4.pht006431.v1.phv00295623.v1_ + * No dbGap metadata available + * varId _phv00295623_ not found in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -3250,8 +4198,16 @@ * ### blood_cell_count/rdw_ratio_rbc_1 -- **HCHS_SOL Hispanic Community Health Study /Study of Latinos (HCHS/SOL)**: * 2 component_study_variables - * _phs000810.v1.pht004715.v1.phv00226251.v1_. dbGap Name: **AGE**, Desc: **Age**, Table: **HCHS_SOL_Cohort_Subject_Phenotypes**. - * _phs000810.v1.pht004715.v1.phv00226308.v1_. dbGap Name: **LABA8**, Desc: **% Red Cell Distribution Width (LABA8)**, Table: **HCHS_SOL_Cohort_Subject_Phenotypes**. + * _phs000810.v1.pht004715.v1.phv00226251.v1_ + * dbGap name: **AGE** + * dbGap desc: **Age** + * dbGap table: **HCHS_SOL_Cohort_Subject_Phenotypes** + * No permissible values listed in PIC-SURE data dictionary + * _phs000810.v1.pht004715.v1.phv00226308.v1_ + * dbGap name: **LABA8** + * dbGap desc: **% Red Cell Distribution Width (LABA8)** + * dbGap table: **HCHS_SOL_Cohort_Subject_Phenotypes** + * No permissible values listed in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -3272,8 +4228,14 @@ * ### blood_cell_count/rdw_ratio_rbc_1 -- **JHS Jackson Heart Study (JHS) Cohort**: * 2 component_study_variables - * _phs000286.v5.pht001949.v1.phv00126009.v1_. No dbGap metadata available. - * _phs000286.v5.pht001959.v1.phv00127628.v1_. dbGap Name: **RDW**, Desc: **RDW [Visit 1]**, Table: **loca**. + * _phs000286.v5.pht001949.v1.phv00126009.v1_ + * No dbGap metadata available + * varId _phv00126009_ not found in PIC-SURE data dictionary + * _phs000286.v5.pht001959.v1.phv00127628.v1_ + * dbGap name: **RDW** + * dbGap desc: **RDW [Visit 1]** + * dbGap table: **loca** + * varId _phv00127628_ not found in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list) { @@ -3343,16 +4305,50 @@ * ### blood_cell_count/wbc_ncnc_bld_1 -- **ARIC Atherosclerosis Risk in Communities (ARIC) Cohort**: * 10 component_study_variables - * _phs000280.v4.pht004062.v2.phv00204623.v1_. No dbGap metadata available. - * _phs000280.v4.pht004063.v2.phv00204712.v1_. dbGap Name: **V1AGE01**, Desc: **Age at visit 1 [Cohort. Visit 1]**, Table: **DERIVE13**. - * _phs000280.v4.pht004064.v2.phv00204871.v1_. dbGap Name: **V3AGE31**, Desc: **Age at visit 3 [Cohort. Visit 3]**, Table: **DERIVE37**. - * _phs000280.v4.pht004065.v2.phv00204975.v1_. No dbGap metadata available. - * _phs000280.v4.pht004107.v2.phv00207257.v1_. dbGap Name: **HMTA03**, Desc: **White blood count x1000/mm3 (MAV). Q3 [Hematology Form. HMTA. Visit 1]**, Table: **HMTA**. - * _phs000280.v4.pht004108.v2.phv00207272.v1_. dbGap Name: **HMTB03**, Desc: **White blood count x1000/mm3 (MAV). Q3 [Hematology Form. HMTB. Visit 2]**, Table: **HMTB**. - * _phs000280.v4.pht004109.v2.phv00207286.v1_. dbGap Name: **HMTC2**, Desc: **White blood count. Q2 [Hematology Lab. HMTCV301. Visit 3]**, Table: **HMTCV301**. - * _phs000280.v4.pht004110.v2.phv00207298.v1_. dbGap Name: **HMTC2**, Desc: **White blood count. Q2 [Hematology Lab. HMTCV401. Visit 4]**, Table: **HMTCV401**. - * _phs000280.v4.pht006422.v1.phv00294954.v1_. dbGap Name: **CBC3**, Desc: **White blood cell count, Wbc [Complete Blood Count, CBC, Visit 5]**, Table: **CBC**. - * _phs000280.v4.pht006431.v1.phv00295623.v1_. No dbGap metadata available. + * _phs000280.v4.pht004062.v2.phv00204623.v1_ + * No dbGap metadata available + * varId _phv00204623_ not found in PIC-SURE data dictionary + * _phs000280.v4.pht004063.v2.phv00204712.v1_ + * dbGap name: **V1AGE01** + * dbGap desc: **Age at visit 1 [Cohort. Visit 1]** + * dbGap table: **DERIVE13** + * varId _phv00204712_ not found in PIC-SURE data dictionary + * _phs000280.v4.pht004064.v2.phv00204871.v1_ + * dbGap name: **V3AGE31** + * dbGap desc: **Age at visit 3 [Cohort. Visit 3]** + * dbGap table: **DERIVE37** + * varId _phv00204871_ not found in PIC-SURE data dictionary + * _phs000280.v4.pht004065.v2.phv00204975.v1_ + * No dbGap metadata available + * varId _phv00204975_ not found in PIC-SURE data dictionary + * _phs000280.v4.pht004107.v2.phv00207257.v1_ + * dbGap name: **HMTA03** + * dbGap desc: **White blood count x1000/mm3 (MAV). Q3 [Hematology Form. HMTA. Visit 1]** + * dbGap table: **HMTA** + * varId _phv00207257_ not found in PIC-SURE data dictionary + * _phs000280.v4.pht004108.v2.phv00207272.v1_ + * dbGap name: **HMTB03** + * dbGap desc: **White blood count x1000/mm3 (MAV). Q3 [Hematology Form. HMTB. Visit 2]** + * dbGap table: **HMTB** + * varId _phv00207272_ not found in PIC-SURE data dictionary + * _phs000280.v4.pht004109.v2.phv00207286.v1_ + * dbGap name: **HMTC2** + * dbGap desc: **White blood count. Q2 [Hematology Lab. HMTCV301. Visit 3]** + * dbGap table: **HMTCV301** + * varId _phv00207286_ not found in PIC-SURE data dictionary + * _phs000280.v4.pht004110.v2.phv00207298.v1_ + * dbGap name: **HMTC2** + * dbGap desc: **White blood count. Q2 [Hematology Lab. HMTCV401. Visit 4]** + * dbGap table: **HMTCV401** + * varId _phv00207298_ not found in PIC-SURE data dictionary + * _phs000280.v4.pht006422.v1.phv00294954.v1_ + * dbGap name: **CBC3** + * dbGap desc: **White blood cell count, Wbc [Complete Blood Count, CBC, Visit 5]** + * dbGap table: **CBC** + * varId _phv00294954_ not found in PIC-SURE data dictionary + * _phs000280.v4.pht006431.v1.phv00295623.v1_ + * No dbGap metadata available + * varId _phv00295623_ not found in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -3426,8 +4422,16 @@ * ### blood_cell_count/wbc_ncnc_bld_1 -- **CARDIA CARDIA Cohort**: * 2 component_study_variables - * _phs000285.v3.pht001559.v2.phv00112439.v2_. dbGap Name: **A01AGE2**, Desc: **AGE VERIFY**, Table: **A4F01**. - * _phs000285.v3.pht001563.v2.phv00112686.v2_. dbGap Name: **A05WBC**, Desc: **WHITE CELL COUNT (X 1000)**, Table: **A4F05**. + * _phs000285.v3.pht001559.v2.phv00112439.v2_ + * dbGap name: **A01AGE2** + * dbGap desc: **AGE VERIFY** + * dbGap table: **A4F01** + * varId _phv00112439_ not found in PIC-SURE data dictionary + * _phs000285.v3.pht001563.v2.phv00112686.v2_ + * dbGap name: **A05WBC** + * dbGap desc: **WHITE CELL COUNT (X 1000)** + * dbGap table: **A4F05** + * varId _phv00112686_ not found in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -3453,8 +4457,16 @@ * ### blood_cell_count/wbc_ncnc_bld_1 -- **CHS Cardiovascular Health Study (CHS) Cohort: an NHLBI-funded observational study of risk factors for cardiovascular disease in adults 65 years or older**: * 2 component_study_variables - * _phs000287.v6.pht001452.v1.phv00100411.v1_. dbGap Name: **WBLD23**, Desc: **WHITE BLOOD COUNT (x1, 000/cubic mm)**, Table: **BASEBOTH**. - * _phs000287.v6.pht001452.v1.phv00100487.v1_. dbGap Name: **AGEBL**, Desc: **CALCULATED AGE AT BASELINE**, Table: **BASEBOTH**. + * _phs000287.v6.pht001452.v1.phv00100411.v1_ + * dbGap name: **WBLD23** + * dbGap desc: **WHITE BLOOD COUNT (x1, 000/cubic mm)** + * dbGap table: **BASEBOTH** + * No permissible values listed in PIC-SURE data dictionary + * _phs000287.v6.pht001452.v1.phv00100487.v1_ + * dbGap name: **AGEBL** + * dbGap desc: **CALCULATED AGE AT BASELINE** + * dbGap table: **BASEBOTH** + * No permissible values listed in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -3473,8 +4485,16 @@ * ### blood_cell_count/wbc_ncnc_bld_1 -- **HCHS_SOL Hispanic Community Health Study /Study of Latinos (HCHS/SOL)**: * 2 component_study_variables - * _phs000810.v1.pht004715.v1.phv00226251.v1_. dbGap Name: **AGE**, Desc: **Age**, Table: **HCHS_SOL_Cohort_Subject_Phenotypes**. - * _phs000810.v1.pht004715.v1.phv00226283.v1_. dbGap Name: **LABA1**, Desc: **White Blood Count (x10e9) (LABA1)**, Table: **HCHS_SOL_Cohort_Subject_Phenotypes**. + * _phs000810.v1.pht004715.v1.phv00226251.v1_ + * dbGap name: **AGE** + * dbGap desc: **Age** + * dbGap table: **HCHS_SOL_Cohort_Subject_Phenotypes** + * No permissible values listed in PIC-SURE data dictionary + * _phs000810.v1.pht004715.v1.phv00226283.v1_ + * dbGap name: **LABA1** + * dbGap desc: **White Blood Count (x10e9) (LABA1)** + * dbGap table: **HCHS_SOL_Cohort_Subject_Phenotypes** + * No permissible values listed in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -3495,8 +4515,14 @@ * ### blood_cell_count/wbc_ncnc_bld_1 -- **JHS Jackson Heart Study (JHS) Cohort**: * 2 component_study_variables - * _phs000286.v5.pht001949.v1.phv00126009.v1_. No dbGap metadata available. - * _phs000286.v5.pht001959.v1.phv00127631.v1_. dbGap Name: **WBC**, Desc: **White blood cells TH/CMM [Visit 1]**, Table: **loca**. + * _phs000286.v5.pht001949.v1.phv00126009.v1_ + * No dbGap metadata available + * varId _phv00126009_ not found in PIC-SURE data dictionary + * _phs000286.v5.pht001959.v1.phv00127631.v1_ + * dbGap name: **WBC** + * dbGap desc: **White blood cells TH/CMM [Visit 1]** + * dbGap table: **loca** + * varId _phv00127631_ not found in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list) { @@ -3526,8 +4552,16 @@ * ### blood_cell_count/wbc_ncnc_bld_1 -- **MESA Multi-Ethnic Study of Atherosclerosis (MESA) Cohort**: * 2 component_study_variables - * _phs000209.v13.pht003091.v3.phv00176011.v1_. dbGap Name: **age5c**, Desc: **AGE AT EXAM 5**, Table: **MESA_Exam5Main**. - * _phs000209.v13.pht004319.v1.phv00218997.v1_. dbGap Name: **wbc5**, Desc: **WHITE BLOOD CELL COUNT (x10E3/uL)**, Table: **MESA_AncilMesaEpigenomicCBC**. + * _phs000209.v13.pht003091.v3.phv00176011.v1_ + * dbGap name: **age5c** + * dbGap desc: **AGE AT EXAM 5** + * dbGap table: **MESA_Exam5Main** + * PIC-SURE permissible values: 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94 + * _phs000209.v13.pht004319.v1.phv00218997.v1_ + * dbGap name: **wbc5** + * dbGap desc: **WHITE BLOOD CELL COUNT (x10E3/uL)** + * dbGap table: **MESA_AncilMesaEpigenomicCBC** + * No permissible values listed in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -3552,11 +4586,31 @@ * ### blood_cell_count/wbc_ncnc_bld_1 -- **WHI Women's Health Initiative**: * 5 component_study_variables - * _phs000200.v11.pht000986.v6.phv00077362.v6_. dbGap Name: **CBCVY**, Desc: **CBC Visit year**, Table: **cbc_rel1**. - * _phs000200.v11.pht000986.v6.phv00077363.v6_. dbGap Name: **CBCDAYS**, Desc: **CBC Days since randomization/enrollment**, Table: **cbc_rel1**. - * _phs000200.v11.pht000986.v6.phv00077368.v6_. dbGap Name: **WBC**, Desc: **White blood cell (Kcell/microliter)**, Table: **cbc_rel1**. - * _phs000200.v11.pht000998.v6.phv00078436.v6_. dbGap Name: **F2DAYS**, Desc: **F2 Days since randomization**, Table: **f2_rel1**. - * _phs000200.v11.pht000998.v6.phv00078437.v6_. dbGap Name: **AGE**, Desc: **Age at screening**, Table: **f2_rel1**. + * _phs000200.v11.pht000986.v6.phv00077362.v6_ + * dbGap name: **CBCVY** + * dbGap desc: **CBC Visit year** + * dbGap table: **cbc_rel1** + * No permissible values listed in PIC-SURE data dictionary + * _phs000200.v11.pht000986.v6.phv00077363.v6_ + * dbGap name: **CBCDAYS** + * dbGap desc: **CBC Days since randomization/enrollment** + * dbGap table: **cbc_rel1** + * No permissible values listed in PIC-SURE data dictionary + * _phs000200.v11.pht000986.v6.phv00077368.v6_ + * dbGap name: **WBC** + * dbGap desc: **White blood cell (Kcell/microliter)** + * dbGap table: **cbc_rel1** + * No permissible values listed in PIC-SURE data dictionary + * _phs000200.v11.pht000998.v6.phv00078436.v6_ + * dbGap name: **F2DAYS** + * dbGap desc: **F2 Days since randomization** + * dbGap table: **f2_rel1** + * No permissible values listed in PIC-SURE data dictionary + * _phs000200.v11.pht000998.v6.phv00078437.v6_ + * dbGap name: **AGE** + * dbGap desc: **Age at screening** + * dbGap table: **f2_rel1** + * No permissible values listed in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ diff --git a/resources/human-readable-harmonized-variable-documentation/generated-doc-pages/blood_pressure.md b/resources/human-readable-harmonized-variable-documentation/generated-doc-pages/blood_pressure.md index 283713e..0b9f85a 100644 --- a/resources/human-readable-harmonized-variable-documentation/generated-doc-pages/blood_pressure.md +++ b/resources/human-readable-harmonized-variable-documentation/generated-doc-pages/blood_pressure.md @@ -40,8 +40,16 @@ * ### blood_pressure/antihypertensive_meds_1 -- **ARIC Atherosclerosis Risk in Communities (ARIC) Cohort**: * 2 component_study_variables - * _phs000280.v4.pht004063.v2.phv00204712.v1_. dbGap Name: **V1AGE01**, Desc: **Age at visit 1 [Cohort. Visit 1]**, Table: **DERIVE13**. - * _phs000280.v4.pht004063.v2.phv00204754.v1_. dbGap Name: **HYPTMD01**, Desc: **Blood pressure lowering medications in the past 2 weeks [Cohort. Visit 1]**, Table: **DERIVE13**. + * _phs000280.v4.pht004063.v2.phv00204712.v1_ + * dbGap name: **V1AGE01** + * dbGap desc: **Age at visit 1 [Cohort. Visit 1]** + * dbGap table: **DERIVE13** + * varId _phv00204712_ not found in PIC-SURE data dictionary + * _phs000280.v4.pht004063.v2.phv00204754.v1_ + * dbGap name: **HYPTMD01** + * dbGap desc: **Blood pressure lowering medications in the past 2 weeks [Cohort. Visit 1]** + * dbGap table: **DERIVE13** + * varId _phv00204754_ not found in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -67,10 +75,26 @@ * ### blood_pressure/antihypertensive_meds_1 -- **CARDIA CARDIA Cohort**: * 4 component_study_variables - * _phs000285.v3.pht001569.v2.phv00113012.v2_. dbGap Name: **A08BPMED**, Desc: **EVER TAKEN MEDS FOR HIGH BLOOD PRESSURE**, Table: **A4F08**. - * _phs000285.v3.pht001571.v2.phv00113154.v2_. dbGap Name: **A09MDTYP**, Desc: **MEDIC'N FOLL'UP PAGE NAME (MED TYPE)**, Table: **A4F09MED**. - * _phs000285.v3.pht001571.v2.phv00113155.v2_. dbGap Name: **A09MDNOW**, Desc: **TAKING MED NOW?**, Table: **A4F09MED**. - * _phs000285.v3.pht001645.v2.phv00115119.v2_. dbGap Name: **EXAMAGE**, Desc: **AGE AT EXAM 1 (VERIFIED AT EXAM 2)**, Table: **B2REF**. + * _phs000285.v3.pht001569.v2.phv00113012.v2_ + * dbGap name: **A08BPMED** + * dbGap desc: **EVER TAKEN MEDS FOR HIGH BLOOD PRESSURE** + * dbGap table: **A4F08** + * varId _phv00113012_ not found in PIC-SURE data dictionary + * _phs000285.v3.pht001571.v2.phv00113154.v2_ + * dbGap name: **A09MDTYP** + * dbGap desc: **MEDIC'N FOLL'UP PAGE NAME (MED TYPE)** + * dbGap table: **A4F09MED** + * varId _phv00113154_ not found in PIC-SURE data dictionary + * _phs000285.v3.pht001571.v2.phv00113155.v2_ + * dbGap name: **A09MDNOW** + * dbGap desc: **TAKING MED NOW?** + * dbGap table: **A4F09MED** + * varId _phv00113155_ not found in PIC-SURE data dictionary + * _phs000285.v3.pht001645.v2.phv00115119.v2_ + * dbGap name: **EXAMAGE** + * dbGap desc: **AGE AT EXAM 1 (VERIFIED AT EXAM 2)** + * dbGap table: **B2REF** + * varId _phv00115119_ not found in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -138,8 +162,16 @@ * ### blood_pressure/antihypertensive_meds_1 -- **CHS Cardiovascular Health Study (CHS) Cohort: an NHLBI-funded observational study of risk factors for cardiovascular disease in adults 65 years or older**: * 2 component_study_variables - * _phs000287.v6.pht001452.v1.phv00100487.v1_. dbGap Name: **AGEBL**, Desc: **CALCULATED AGE AT BASELINE**, Table: **BASEBOTH**. - * _phs000287.v6.pht001452.v1.phv00100595.v1_. dbGap Name: **HTNMED06**, Desc: **Any hypertension medication**, Table: **BASEBOTH**. + * _phs000287.v6.pht001452.v1.phv00100487.v1_ + * dbGap name: **AGEBL** + * dbGap desc: **CALCULATED AGE AT BASELINE** + * dbGap table: **BASEBOTH** + * No permissible values listed in PIC-SURE data dictionary + * _phs000287.v6.pht001452.v1.phv00100595.v1_ + * dbGap name: **HTNMED06** + * dbGap desc: **Any hypertension medication** + * dbGap table: **BASEBOTH** + * PIC-SURE permissible values: No, Yes * **Function:** ```r harmonize <- function(phen_list){ @@ -159,8 +191,16 @@ * ### blood_pressure/antihypertensive_meds_1 -- **HCHS_SOL Hispanic Community Health Study /Study of Latinos (HCHS/SOL)**: * 2 component_study_variables - * _phs000810.v1.pht004715.v1.phv00226251.v1_. dbGap Name: **AGE**, Desc: **Age**, Table: **HCHS_SOL_Cohort_Subject_Phenotypes**. - * _phs000810.v1.pht004715.v1.phv00226324.v1_. dbGap Name: **MED_ANTIHYPERT**, Desc: **Antihypertensives**, Table: **HCHS_SOL_Cohort_Subject_Phenotypes**. + * _phs000810.v1.pht004715.v1.phv00226251.v1_ + * dbGap name: **AGE** + * dbGap desc: **Age** + * dbGap table: **HCHS_SOL_Cohort_Subject_Phenotypes** + * No permissible values listed in PIC-SURE data dictionary + * _phs000810.v1.pht004715.v1.phv00226324.v1_ + * dbGap name: **MED_ANTIHYPERT** + * dbGap desc: **Antihypertensives** + * dbGap table: **HCHS_SOL_Cohort_Subject_Phenotypes** + * PIC-SURE permissible values: No, Yes * **Function:** ```r harmonize <- function(phen_list){ @@ -179,8 +219,12 @@ * ### blood_pressure/antihypertensive_meds_1 -- **JHS Jackson Heart Study (JHS) Cohort**: * 2 component_study_variables - * _phs000286.v5.pht001949.v1.phv00126009.v1_. No dbGap metadata available. - * _phs000286.v5.pht001949.v1.phv00126038.v1_. No dbGap metadata available. + * _phs000286.v5.pht001949.v1.phv00126009.v1_ + * No dbGap metadata available + * varId _phv00126009_ not found in PIC-SURE data dictionary + * _phs000286.v5.pht001949.v1.phv00126038.v1_ + * No dbGap metadata available + * varId _phv00126038_ not found in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -203,12 +247,36 @@ * ### blood_pressure/antihypertensive_meds_1 -- **MESA Multi-Ethnic Study of Atherosclerosis (MESA) Cohort**: * 6 component_study_variables - * _phs000209.v13.pht001111.v4.phv00082639.v2_. dbGap Name: **age1c**, Desc: **AGE**, Table: **MESA_AirNRExamMain**. - * _phs000209.v13.pht001111.v4.phv00083163.v1_. dbGap Name: **htnmed1c**, Desc: **HYPERTENSION MEDICATION**, Table: **MESA_AirNRExamMain**. - * _phs000209.v13.pht001116.v10.phv00084442.v3_. dbGap Name: **age1c**, Desc: **AGE**, Table: **MESA_Exam1Main**. - * _phs000209.v13.pht001116.v10.phv00085324.v2_. dbGap Name: **htnmed1c**, Desc: **HYPERTENSION MEDICATION**, Table: **MESA_Exam1Main**. - * _phs000209.v13.pht001121.v3.phv00087071.v1_. dbGap Name: **agefc**, Desc: **AGE**, Table: **MESA_FamilyExamMain**. - * _phs000209.v13.pht001121.v3.phv00087093.v1_. dbGap Name: **htnmedfc**, Desc: **ANY HYPERTENSION MEDICATION**, Table: **MESA_FamilyExamMain**. + * _phs000209.v13.pht001111.v4.phv00082639.v2_ + * dbGap name: **age1c** + * dbGap desc: **AGE** + * dbGap table: **MESA_AirNRExamMain** + * No permissible values listed in PIC-SURE data dictionary + * _phs000209.v13.pht001111.v4.phv00083163.v1_ + * dbGap name: **htnmed1c** + * dbGap desc: **HYPERTENSION MEDICATION** + * dbGap table: **MESA_AirNRExamMain** + * PIC-SURE permissible values: NO, YES + * _phs000209.v13.pht001116.v10.phv00084442.v3_ + * dbGap name: **age1c** + * dbGap desc: **AGE** + * dbGap table: **MESA_Exam1Main** + * No permissible values listed in PIC-SURE data dictionary + * _phs000209.v13.pht001116.v10.phv00085324.v2_ + * dbGap name: **htnmed1c** + * dbGap desc: **HYPERTENSION MEDICATION** + * dbGap table: **MESA_Exam1Main** + * PIC-SURE permissible values: NO, YES + * _phs000209.v13.pht001121.v3.phv00087071.v1_ + * dbGap name: **agefc** + * dbGap desc: **AGE** + * dbGap table: **MESA_FamilyExamMain** + * No permissible values listed in PIC-SURE data dictionary + * _phs000209.v13.pht001121.v3.phv00087093.v1_ + * dbGap name: **htnmedfc** + * dbGap desc: **ANY HYPERTENSION MEDICATION** + * dbGap table: **MESA_FamilyExamMain** + * PIC-SURE permissible values: NO, YES * **Function:** ```r harmonize <- function(phen_list){ @@ -236,14 +304,46 @@ * ### blood_pressure/antihypertensive_meds_1 -- **WHI Women's Health Initiative**: * 8 component_study_variables - * _phs000200.v11.pht000998.v6.phv00078436.v6_. dbGap Name: **F2DAYS**, Desc: **F2 Days since randomization**, Table: **f2_rel1**. - * _phs000200.v11.pht000998.v6.phv00078437.v6_. dbGap Name: **AGE**, Desc: **Age at screening**, Table: **f2_rel1**. - * _phs000200.v11.pht001019.v6.phv00079850.v6_. dbGap Name: **F80VTYP**, Desc: **Visit Type**, Table: **f80_rel1**. - * _phs000200.v11.pht001019.v6.phv00079852.v6_. dbGap Name: **F80DAYS**, Desc: **F80 Days since randomization/enrollment**, Table: **f80_rel1**. - * _phs000200.v11.pht002754.v4.phv00169603.v4_. dbGap Name: **F44VTYP**, Desc: **Visit Type**, Table: **f44_rel1**. - * _phs000200.v11.pht002754.v4.phv00169605.v4_. dbGap Name: **F44DAYS**, Desc: **F44 Days since randomization/enrollment**, Table: **f44_rel1**. - * _phs000200.v11.pht002754.v4.phv00169608.v4_. dbGap Name: **ADULTDY**, Desc: **F44 Adult duration of medication use (days)**, Table: **f44_rel1**. - * _phs000200.v11.pht002754.v4.phv00169611.v4_. dbGap Name: **TCCODE**, Desc: **F44 Medication Therapeutic Class Code**, Table: **f44_rel1**. + * _phs000200.v11.pht000998.v6.phv00078436.v6_ + * dbGap name: **F2DAYS** + * dbGap desc: **F2 Days since randomization** + * dbGap table: **f2_rel1** + * No permissible values listed in PIC-SURE data dictionary + * _phs000200.v11.pht000998.v6.phv00078437.v6_ + * dbGap name: **AGE** + * dbGap desc: **Age at screening** + * dbGap table: **f2_rel1** + * No permissible values listed in PIC-SURE data dictionary + * _phs000200.v11.pht001019.v6.phv00079850.v6_ + * dbGap name: **F80VTYP** + * dbGap desc: **Visit Type** + * dbGap table: **f80_rel1** + * PIC-SURE permissible values: Annual visit, Screening + * _phs000200.v11.pht001019.v6.phv00079852.v6_ + * dbGap name: **F80DAYS** + * dbGap desc: **F80 Days since randomization/enrollment** + * dbGap table: **f80_rel1** + * No permissible values listed in PIC-SURE data dictionary + * _phs000200.v11.pht002754.v4.phv00169603.v4_ + * dbGap name: **F44VTYP** + * dbGap desc: **Visit Type** + * dbGap table: **f44_rel1** + * PIC-SURE permissible values: Annual visit, Screening + * _phs000200.v11.pht002754.v4.phv00169605.v4_ + * dbGap name: **F44DAYS** + * dbGap desc: **F44 Days since randomization/enrollment** + * dbGap table: **f44_rel1** + * No permissible values listed in PIC-SURE data dictionary + * _phs000200.v11.pht002754.v4.phv00169608.v4_ + * dbGap name: **ADULTDY** + * dbGap desc: **F44 Adult duration of medication use (days)** + * dbGap table: **f44_rel1** + * No permissible values listed in PIC-SURE data dictionary + * _phs000200.v11.pht002754.v4.phv00169611.v4_ + * dbGap name: **TCCODE** + * dbGap desc: **F44 Medication Therapeutic Class Code** + * dbGap table: **f44_rel1** + * No permissible values listed in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -414,13 +514,41 @@ * ### blood_pressure/bp_diastolic_1 -- **ARIC Atherosclerosis Risk in Communities (ARIC) Cohort**: * 7 component_study_variables - * _phs000280.v4.pht004063.v2.phv00204712.v1_. dbGap Name: **V1AGE01**, Desc: **Age at visit 1 [Cohort. Visit 1]**, Table: **DERIVE13**. - * _phs000280.v4.pht004192.v2.phv00210284.v1_. dbGap Name: **SBPA15**, Desc: **[Second blood pressure measurement]. 2nd systolic. Q15 [Siting Blood Pressure. SBPA. Visit 1]**, Table: **SBPA02**. - * _phs000280.v4.pht004192.v2.phv00210285.v1_. dbGap Name: **SBPA16**, Desc: **[Second blood pressure measurement]. 2nd diastolic. Q16 [Siting Blood Pressure. SBPA. Visit 1]**, Table: **SBPA02**. - * _phs000280.v4.pht004192.v2.phv00210286.v1_. dbGap Name: **SBPA17**, Desc: **[Second blood pressure measurement]. 2nd zero reading. Q17 [Siting Blood Pressure. SBPA. Visit 1]**, Table: **SBPA02**. - * _phs000280.v4.pht004192.v2.phv00210287.v1_. dbGap Name: **SBPA18**, Desc: **[Third blood pressure measurement]. 3rd systolic. Q18 [Siting Blood Pressure. SBPA. Visit 1]**, Table: **SBPA02**. - * _phs000280.v4.pht004192.v2.phv00210288.v1_. dbGap Name: **SBPA19**, Desc: **[Third blood pressure measurement]. 3rd diastolic. Q19 [Siting Blood Pressure. SBPA. Visit 1]**, Table: **SBPA02**. - * _phs000280.v4.pht004192.v2.phv00210289.v1_. dbGap Name: **SBPA20**, Desc: **[Third blood pressure measurement]. 3rd zero reading. Q20 [Siting Blood Pressure. SBPA. Visit 1]**, Table: **SBPA02**. + * _phs000280.v4.pht004063.v2.phv00204712.v1_ + * dbGap name: **V1AGE01** + * dbGap desc: **Age at visit 1 [Cohort. Visit 1]** + * dbGap table: **DERIVE13** + * varId _phv00204712_ not found in PIC-SURE data dictionary + * _phs000280.v4.pht004192.v2.phv00210284.v1_ + * dbGap name: **SBPA15** + * dbGap desc: **[Second blood pressure measurement]. 2nd systolic. Q15 [Siting Blood Pressure. SBPA. Visit 1]** + * dbGap table: **SBPA02** + * varId _phv00210284_ not found in PIC-SURE data dictionary + * _phs000280.v4.pht004192.v2.phv00210285.v1_ + * dbGap name: **SBPA16** + * dbGap desc: **[Second blood pressure measurement]. 2nd diastolic. Q16 [Siting Blood Pressure. SBPA. Visit 1]** + * dbGap table: **SBPA02** + * varId _phv00210285_ not found in PIC-SURE data dictionary + * _phs000280.v4.pht004192.v2.phv00210286.v1_ + * dbGap name: **SBPA17** + * dbGap desc: **[Second blood pressure measurement]. 2nd zero reading. Q17 [Siting Blood Pressure. SBPA. Visit 1]** + * dbGap table: **SBPA02** + * varId _phv00210286_ not found in PIC-SURE data dictionary + * _phs000280.v4.pht004192.v2.phv00210287.v1_ + * dbGap name: **SBPA18** + * dbGap desc: **[Third blood pressure measurement]. 3rd systolic. Q18 [Siting Blood Pressure. SBPA. Visit 1]** + * dbGap table: **SBPA02** + * varId _phv00210287_ not found in PIC-SURE data dictionary + * _phs000280.v4.pht004192.v2.phv00210288.v1_ + * dbGap name: **SBPA19** + * dbGap desc: **[Third blood pressure measurement]. 3rd diastolic. Q19 [Siting Blood Pressure. SBPA. Visit 1]** + * dbGap table: **SBPA02** + * varId _phv00210288_ not found in PIC-SURE data dictionary + * _phs000280.v4.pht004192.v2.phv00210289.v1_ + * dbGap name: **SBPA20** + * dbGap desc: **[Third blood pressure measurement]. 3rd zero reading. Q20 [Siting Blood Pressure. SBPA. Visit 1]** + * dbGap table: **SBPA02** + * varId _phv00210289_ not found in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -487,15 +615,51 @@ * ### blood_pressure/bp_diastolic_1 -- **CARDIA CARDIA Cohort**: * 9 component_study_variables - * _phs000285.v3.pht001560.v2.phv00112481.v2_. dbGap Name: **A02R2S**, Desc: **SECOND READING SBP**, Table: **A4F02**. - * _phs000285.v3.pht001560.v2.phv00112482.v2_. dbGap Name: **A02R2D**, Desc: **SECOND READING DBP**, Table: **A4F02**. - * _phs000285.v3.pht001560.v2.phv00112483.v2_. dbGap Name: **A02RZ2S**, Desc: **RZ2 SBP**, Table: **A4F02**. - * _phs000285.v3.pht001560.v2.phv00112484.v2_. dbGap Name: **A02RZ2D**, Desc: **RZ2 DBP**, Table: **A4F02**. - * _phs000285.v3.pht001560.v2.phv00112487.v2_. dbGap Name: **A02R3S**, Desc: **THIRD READING SBP**, Table: **A4F02**. - * _phs000285.v3.pht001560.v2.phv00112488.v2_. dbGap Name: **A02R3D**, Desc: **THIRD READING DBP**, Table: **A4F02**. - * _phs000285.v3.pht001560.v2.phv00112489.v2_. dbGap Name: **A02RZ3S**, Desc: **RZ3 SBP**, Table: **A4F02**. - * _phs000285.v3.pht001560.v2.phv00112490.v2_. dbGap Name: **A02RZ3D**, Desc: **RZ3 DBP**, Table: **A4F02**. - * _phs000285.v3.pht001645.v2.phv00115119.v2_. dbGap Name: **EXAMAGE**, Desc: **AGE AT EXAM 1 (VERIFIED AT EXAM 2)**, Table: **B2REF**. + * _phs000285.v3.pht001560.v2.phv00112481.v2_ + * dbGap name: **A02R2S** + * dbGap desc: **SECOND READING SBP** + * dbGap table: **A4F02** + * varId _phv00112481_ not found in PIC-SURE data dictionary + * _phs000285.v3.pht001560.v2.phv00112482.v2_ + * dbGap name: **A02R2D** + * dbGap desc: **SECOND READING DBP** + * dbGap table: **A4F02** + * varId _phv00112482_ not found in PIC-SURE data dictionary + * _phs000285.v3.pht001560.v2.phv00112483.v2_ + * dbGap name: **A02RZ2S** + * dbGap desc: **RZ2 SBP** + * dbGap table: **A4F02** + * varId _phv00112483_ not found in PIC-SURE data dictionary + * _phs000285.v3.pht001560.v2.phv00112484.v2_ + * dbGap name: **A02RZ2D** + * dbGap desc: **RZ2 DBP** + * dbGap table: **A4F02** + * varId _phv00112484_ not found in PIC-SURE data dictionary + * _phs000285.v3.pht001560.v2.phv00112487.v2_ + * dbGap name: **A02R3S** + * dbGap desc: **THIRD READING SBP** + * dbGap table: **A4F02** + * varId _phv00112487_ not found in PIC-SURE data dictionary + * _phs000285.v3.pht001560.v2.phv00112488.v2_ + * dbGap name: **A02R3D** + * dbGap desc: **THIRD READING DBP** + * dbGap table: **A4F02** + * varId _phv00112488_ not found in PIC-SURE data dictionary + * _phs000285.v3.pht001560.v2.phv00112489.v2_ + * dbGap name: **A02RZ3S** + * dbGap desc: **RZ3 SBP** + * dbGap table: **A4F02** + * varId _phv00112489_ not found in PIC-SURE data dictionary + * _phs000285.v3.pht001560.v2.phv00112490.v2_ + * dbGap name: **A02RZ3D** + * dbGap desc: **RZ3 DBP** + * dbGap table: **A4F02** + * varId _phv00112490_ not found in PIC-SURE data dictionary + * _phs000285.v3.pht001645.v2.phv00115119.v2_ + * dbGap name: **EXAMAGE** + * dbGap desc: **AGE AT EXAM 1 (VERIFIED AT EXAM 2)** + * dbGap table: **B2REF** + * varId _phv00115119_ not found in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -546,9 +710,21 @@ * ### blood_pressure/bp_diastolic_1 -- **CHS Cardiovascular Health Study (CHS) Cohort: an NHLBI-funded observational study of risk factors for cardiovascular disease in adults 65 years or older**: * 3 component_study_variables - * _phs000287.v6.pht001452.v1.phv00100435.v1_. dbGap Name: **AVZMSYS**, Desc: **AVE ZERO MUD SYSTOL (mm Hg)**, Table: **BASEBOTH**. - * _phs000287.v6.pht001452.v1.phv00100436.v1_. dbGap Name: **AVZMDIA**, Desc: **AVE ZERO MUD DIASTOL-adj (mm Hg)**, Table: **BASEBOTH**. - * _phs000287.v6.pht001452.v1.phv00100487.v1_. dbGap Name: **AGEBL**, Desc: **CALCULATED AGE AT BASELINE**, Table: **BASEBOTH**. + * _phs000287.v6.pht001452.v1.phv00100435.v1_ + * dbGap name: **AVZMSYS** + * dbGap desc: **AVE ZERO MUD SYSTOL (mm Hg)** + * dbGap table: **BASEBOTH** + * No permissible values listed in PIC-SURE data dictionary + * _phs000287.v6.pht001452.v1.phv00100436.v1_ + * dbGap name: **AVZMDIA** + * dbGap desc: **AVE ZERO MUD DIASTOL-adj (mm Hg)** + * dbGap table: **BASEBOTH** + * No permissible values listed in PIC-SURE data dictionary + * _phs000287.v6.pht001452.v1.phv00100487.v1_ + * dbGap name: **AGEBL** + * dbGap desc: **CALCULATED AGE AT BASELINE** + * dbGap table: **BASEBOTH** + * No permissible values listed in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -577,9 +753,15 @@ * ### blood_pressure/bp_diastolic_1 -- **COPDGene **: * 3 component_study_variables - * _phs000179.v5.pht002239.v4.phv00159583.v4_. No dbGap metadata available. - * _phs000179.v5.pht002239.v4.phv00159590.v4_. No dbGap metadata available. - * _phs000179.v5.pht002239.v4.phv00159836.v4_. No dbGap metadata available. + * _phs000179.v5.pht002239.v4.phv00159583.v4_ + * No dbGap metadata available + * No permissible values listed in PIC-SURE data dictionary + * _phs000179.v5.pht002239.v4.phv00159590.v4_ + * No dbGap metadata available + * No permissible values listed in PIC-SURE data dictionary + * _phs000179.v5.pht002239.v4.phv00159836.v4_ + * No dbGap metadata available + * No permissible values listed in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -610,9 +792,21 @@ * ### blood_pressure/bp_diastolic_1 -- **HCHS_SOL Hispanic Community Health Study /Study of Latinos (HCHS/SOL)**: * 3 component_study_variables - * _phs000810.v1.pht004715.v1.phv00226251.v1_. dbGap Name: **AGE**, Desc: **Age**, Table: **HCHS_SOL_Cohort_Subject_Phenotypes**. - * _phs000810.v1.pht004715.v1.phv00226390.v1_. dbGap Name: **SBPA5**, Desc: **Average Systolic (SBPA5)**, Table: **HCHS_SOL_Cohort_Subject_Phenotypes**. - * _phs000810.v1.pht004715.v1.phv00226391.v1_. dbGap Name: **SBPA6**, Desc: **Average Diastolic (SBPA6)**, Table: **HCHS_SOL_Cohort_Subject_Phenotypes**. + * _phs000810.v1.pht004715.v1.phv00226251.v1_ + * dbGap name: **AGE** + * dbGap desc: **Age** + * dbGap table: **HCHS_SOL_Cohort_Subject_Phenotypes** + * No permissible values listed in PIC-SURE data dictionary + * _phs000810.v1.pht004715.v1.phv00226390.v1_ + * dbGap name: **SBPA5** + * dbGap desc: **Average Systolic (SBPA5)** + * dbGap table: **HCHS_SOL_Cohort_Subject_Phenotypes** + * No permissible values listed in PIC-SURE data dictionary + * _phs000810.v1.pht004715.v1.phv00226391.v1_ + * dbGap name: **SBPA6** + * dbGap desc: **Average Diastolic (SBPA6)** + * dbGap table: **HCHS_SOL_Cohort_Subject_Phenotypes** + * No permissible values listed in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -632,13 +826,39 @@ * ### blood_pressure/bp_diastolic_1 -- **JHS Jackson Heart Study (JHS) Cohort**: * 7 component_study_variables - * _phs000286.v5.pht001949.v1.phv00126009.v1_. No dbGap metadata available. - * _phs000286.v5.pht001974.v1.phv00128370.v1_. dbGap Name: **SBPA13**, Desc: **Q13. D. First blood pressure measurement. Systolic (first BP) [Visit 1] [Sitting Blood Pressure Form, SBP]**, Table: **sbpa**. - * _phs000286.v5.pht001974.v1.phv00128371.v1_. dbGap Name: **SBPA14**, Desc: **Q14. D. First blood pressure measurement. Diastolic (first BP) [Visit 1] [Sitting Blood Pressure Form, SBP]**, Table: **sbpa**. - * _phs000286.v5.pht001974.v1.phv00128372.v1_. dbGap Name: **SBPA15**, Desc: **Q15. D. First blood pressure measurement. Zero reading (first BP) [Visit 1] [Sitting Blood Pressure Form, SBP]**, Table: **sbpa**. - * _phs000286.v5.pht001974.v1.phv00128373.v1_. dbGap Name: **SBPA16**, Desc: **Q16. E. Second blood pressure measurement. Systolic (second BP) [Visit 1] [Sitting Blood Pressure Form, SBP]**, Table: **sbpa**. - * _phs000286.v5.pht001974.v1.phv00128374.v1_. dbGap Name: **SBPA17**, Desc: **Q17. E. Second blood pressure measurement. Diastolic (second BP) [Visit 1] [Sitting Blood Pressure Form, SBP]**, Table: **sbpa**. - * _phs000286.v5.pht001974.v1.phv00128375.v1_. dbGap Name: **SBPA18**, Desc: **Q18. E. Second blood pressure measurement. Zero Reading (second BP) [Visit 1] [Sitting Blood Pressure Form, SBP]**, Table: **sbpa**. + * _phs000286.v5.pht001949.v1.phv00126009.v1_ + * No dbGap metadata available + * varId _phv00126009_ not found in PIC-SURE data dictionary + * _phs000286.v5.pht001974.v1.phv00128370.v1_ + * dbGap name: **SBPA13** + * dbGap desc: **Q13. D. First blood pressure measurement. Systolic (first BP) [Visit 1] [Sitting Blood Pressure Form, SBP]** + * dbGap table: **sbpa** + * varId _phv00128370_ not found in PIC-SURE data dictionary + * _phs000286.v5.pht001974.v1.phv00128371.v1_ + * dbGap name: **SBPA14** + * dbGap desc: **Q14. D. First blood pressure measurement. Diastolic (first BP) [Visit 1] [Sitting Blood Pressure Form, SBP]** + * dbGap table: **sbpa** + * varId _phv00128371_ not found in PIC-SURE data dictionary + * _phs000286.v5.pht001974.v1.phv00128372.v1_ + * dbGap name: **SBPA15** + * dbGap desc: **Q15. D. First blood pressure measurement. Zero reading (first BP) [Visit 1] [Sitting Blood Pressure Form, SBP]** + * dbGap table: **sbpa** + * varId _phv00128372_ not found in PIC-SURE data dictionary + * _phs000286.v5.pht001974.v1.phv00128373.v1_ + * dbGap name: **SBPA16** + * dbGap desc: **Q16. E. Second blood pressure measurement. Systolic (second BP) [Visit 1] [Sitting Blood Pressure Form, SBP]** + * dbGap table: **sbpa** + * varId _phv00128373_ not found in PIC-SURE data dictionary + * _phs000286.v5.pht001974.v1.phv00128374.v1_ + * dbGap name: **SBPA17** + * dbGap desc: **Q17. E. Second blood pressure measurement. Diastolic (second BP) [Visit 1] [Sitting Blood Pressure Form, SBP]** + * dbGap table: **sbpa** + * varId _phv00128374_ not found in PIC-SURE data dictionary + * _phs000286.v5.pht001974.v1.phv00128375.v1_ + * dbGap name: **SBPA18** + * dbGap desc: **Q18. E. Second blood pressure measurement. Zero Reading (second BP) [Visit 1] [Sitting Blood Pressure Form, SBP]** + * dbGap table: **sbpa** + * varId _phv00128375_ not found in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -687,21 +907,81 @@ * ### blood_pressure/bp_diastolic_1 -- **MESA Multi-Ethnic Study of Atherosclerosis (MESA) Cohort**: * 15 component_study_variables - * _phs000209.v13.pht001111.v4.phv00082639.v2_. dbGap Name: **age1c**, Desc: **AGE**, Table: **MESA_AirNRExamMain**. - * _phs000209.v13.pht001111.v4.phv00083403.v1_. dbGap Name: **s2bp1**, Desc: **SEATED BP: SYSTOLIC 2ND READING (mmHg)**, Table: **MESA_AirNRExamMain**. - * _phs000209.v13.pht001111.v4.phv00083404.v1_. dbGap Name: **d2bp1**, Desc: **SEATED BP: DIASTOLIC 2ND READING (mmHg)**, Table: **MESA_AirNRExamMain**. - * _phs000209.v13.pht001111.v4.phv00083406.v1_. dbGap Name: **s3bp1**, Desc: **SEATED BP: SYSTOLIC 3RD READING (mmHg)**, Table: **MESA_AirNRExamMain**. - * _phs000209.v13.pht001111.v4.phv00083407.v1_. dbGap Name: **d3bp1**, Desc: **SEATED BP: DIASTOLIC 3RD READING (mmHg)**, Table: **MESA_AirNRExamMain**. - * _phs000209.v13.pht001116.v10.phv00084442.v3_. dbGap Name: **age1c**, Desc: **AGE**, Table: **MESA_Exam1Main**. - * _phs000209.v13.pht001116.v10.phv00085735.v2_. dbGap Name: **s2bp1**, Desc: **SEATED BP: SYSTOLIC 2ND READING (mmHg)**, Table: **MESA_Exam1Main**. - * _phs000209.v13.pht001116.v10.phv00085736.v2_. dbGap Name: **d2bp1**, Desc: **SEATED BP: DIASTOLIC 2ND READING (mmHg)**, Table: **MESA_Exam1Main**. - * _phs000209.v13.pht001116.v10.phv00085737.v2_. dbGap Name: **s3bp1**, Desc: **SEATED BP: SYSTOLIC 3RD READING (mmHg)**, Table: **MESA_Exam1Main**. - * _phs000209.v13.pht001116.v10.phv00085738.v2_. dbGap Name: **d3bp1**, Desc: **SEATED BP: DIASTOLIC 3RD READING (mmHg)**, Table: **MESA_Exam1Main**. - * _phs000209.v13.pht001121.v3.phv00087071.v1_. dbGap Name: **agefc**, Desc: **AGE**, Table: **MESA_FamilyExamMain**. - * _phs000209.v13.pht001121.v3.phv00087509.v1_. dbGap Name: **s2bpf**, Desc: **2ND READING: SEATED SYSTOLIC BP (mmHg)**, Table: **MESA_FamilyExamMain**. - * _phs000209.v13.pht001121.v3.phv00087510.v1_. dbGap Name: **d2bpf**, Desc: **2ND READING: SEATED DIASTOLIC BP (mmHg)**, Table: **MESA_FamilyExamMain**. - * _phs000209.v13.pht001121.v3.phv00087512.v1_. dbGap Name: **s3bpf**, Desc: **3RD READING: SEATED SYSTOLIC BP (mmHg)**, Table: **MESA_FamilyExamMain**. - * _phs000209.v13.pht001121.v3.phv00087513.v1_. dbGap Name: **d3bpf**, Desc: **3RD READING: SEATED DIASTOLIC BP (mmHg)**, Table: **MESA_FamilyExamMain**. + * _phs000209.v13.pht001111.v4.phv00082639.v2_ + * dbGap name: **age1c** + * dbGap desc: **AGE** + * dbGap table: **MESA_AirNRExamMain** + * No permissible values listed in PIC-SURE data dictionary + * _phs000209.v13.pht001111.v4.phv00083403.v1_ + * dbGap name: **s2bp1** + * dbGap desc: **SEATED BP: SYSTOLIC 2ND READING (mmHg)** + * dbGap table: **MESA_AirNRExamMain** + * No permissible values listed in PIC-SURE data dictionary + * _phs000209.v13.pht001111.v4.phv00083404.v1_ + * dbGap name: **d2bp1** + * dbGap desc: **SEATED BP: DIASTOLIC 2ND READING (mmHg)** + * dbGap table: **MESA_AirNRExamMain** + * No permissible values listed in PIC-SURE data dictionary + * _phs000209.v13.pht001111.v4.phv00083406.v1_ + * dbGap name: **s3bp1** + * dbGap desc: **SEATED BP: SYSTOLIC 3RD READING (mmHg)** + * dbGap table: **MESA_AirNRExamMain** + * No permissible values listed in PIC-SURE data dictionary + * _phs000209.v13.pht001111.v4.phv00083407.v1_ + * dbGap name: **d3bp1** + * dbGap desc: **SEATED BP: DIASTOLIC 3RD READING (mmHg)** + * dbGap table: **MESA_AirNRExamMain** + * No permissible values listed in PIC-SURE data dictionary + * _phs000209.v13.pht001116.v10.phv00084442.v3_ + * dbGap name: **age1c** + * dbGap desc: **AGE** + * dbGap table: **MESA_Exam1Main** + * No permissible values listed in PIC-SURE data dictionary + * _phs000209.v13.pht001116.v10.phv00085735.v2_ + * dbGap name: **s2bp1** + * dbGap desc: **SEATED BP: SYSTOLIC 2ND READING (mmHg)** + * dbGap table: **MESA_Exam1Main** + * No permissible values listed in PIC-SURE data dictionary + * _phs000209.v13.pht001116.v10.phv00085736.v2_ + * dbGap name: **d2bp1** + * dbGap desc: **SEATED BP: DIASTOLIC 2ND READING (mmHg)** + * dbGap table: **MESA_Exam1Main** + * No permissible values listed in PIC-SURE data dictionary + * _phs000209.v13.pht001116.v10.phv00085737.v2_ + * dbGap name: **s3bp1** + * dbGap desc: **SEATED BP: SYSTOLIC 3RD READING (mmHg)** + * dbGap table: **MESA_Exam1Main** + * No permissible values listed in PIC-SURE data dictionary + * _phs000209.v13.pht001116.v10.phv00085738.v2_ + * dbGap name: **d3bp1** + * dbGap desc: **SEATED BP: DIASTOLIC 3RD READING (mmHg)** + * dbGap table: **MESA_Exam1Main** + * No permissible values listed in PIC-SURE data dictionary + * _phs000209.v13.pht001121.v3.phv00087071.v1_ + * dbGap name: **agefc** + * dbGap desc: **AGE** + * dbGap table: **MESA_FamilyExamMain** + * No permissible values listed in PIC-SURE data dictionary + * _phs000209.v13.pht001121.v3.phv00087509.v1_ + * dbGap name: **s2bpf** + * dbGap desc: **2ND READING: SEATED SYSTOLIC BP (mmHg)** + * dbGap table: **MESA_FamilyExamMain** + * No permissible values listed in PIC-SURE data dictionary + * _phs000209.v13.pht001121.v3.phv00087510.v1_ + * dbGap name: **d2bpf** + * dbGap desc: **2ND READING: SEATED DIASTOLIC BP (mmHg)** + * dbGap table: **MESA_FamilyExamMain** + * No permissible values listed in PIC-SURE data dictionary + * _phs000209.v13.pht001121.v3.phv00087512.v1_ + * dbGap name: **s3bpf** + * dbGap desc: **3RD READING: SEATED SYSTOLIC BP (mmHg)** + * dbGap table: **MESA_FamilyExamMain** + * No permissible values listed in PIC-SURE data dictionary + * _phs000209.v13.pht001121.v3.phv00087513.v1_ + * dbGap name: **d3bpf** + * dbGap desc: **3RD READING: SEATED DIASTOLIC BP (mmHg)** + * dbGap table: **MESA_FamilyExamMain** + * No permissible values listed in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -753,14 +1033,46 @@ * ### blood_pressure/bp_diastolic_1 -- **WHI Women's Health Initiative**: * 8 component_study_variables - * _phs000200.v11.pht000998.v6.phv00078436.v6_. dbGap Name: **F2DAYS**, Desc: **F2 Days since randomization**, Table: **f2_rel1**. - * _phs000200.v11.pht000998.v6.phv00078437.v6_. dbGap Name: **AGE**, Desc: **Age at screening**, Table: **f2_rel1**. - * _phs000200.v11.pht001019.v6.phv00079850.v6_. dbGap Name: **F80VTYP**, Desc: **Visit Type**, Table: **f80_rel1**. - * _phs000200.v11.pht001019.v6.phv00079852.v6_. dbGap Name: **F80DAYS**, Desc: **F80 Days since randomization/enrollment**, Table: **f80_rel1**. - * _phs000200.v11.pht001019.v6.phv00079854.v6_. dbGap Name: **SYSTBP1**, Desc: **Systolic blood pressure (1st reading)**, Table: **f80_rel1**. - * _phs000200.v11.pht001019.v6.phv00079855.v6_. dbGap Name: **DIASBP1**, Desc: **Diastolic blood pressure (1st reading)**, Table: **f80_rel1**. - * _phs000200.v11.pht001019.v6.phv00079856.v6_. dbGap Name: **SYSTBP2**, Desc: **Systolic blood pressure (2nd reading)**, Table: **f80_rel1**. - * _phs000200.v11.pht001019.v6.phv00079857.v6_. dbGap Name: **DIASBP2**, Desc: **Diastolic blood pressure (2nd reading)**, Table: **f80_rel1**. + * _phs000200.v11.pht000998.v6.phv00078436.v6_ + * dbGap name: **F2DAYS** + * dbGap desc: **F2 Days since randomization** + * dbGap table: **f2_rel1** + * No permissible values listed in PIC-SURE data dictionary + * _phs000200.v11.pht000998.v6.phv00078437.v6_ + * dbGap name: **AGE** + * dbGap desc: **Age at screening** + * dbGap table: **f2_rel1** + * No permissible values listed in PIC-SURE data dictionary + * _phs000200.v11.pht001019.v6.phv00079850.v6_ + * dbGap name: **F80VTYP** + * dbGap desc: **Visit Type** + * dbGap table: **f80_rel1** + * PIC-SURE permissible values: Annual visit, Screening + * _phs000200.v11.pht001019.v6.phv00079852.v6_ + * dbGap name: **F80DAYS** + * dbGap desc: **F80 Days since randomization/enrollment** + * dbGap table: **f80_rel1** + * No permissible values listed in PIC-SURE data dictionary + * _phs000200.v11.pht001019.v6.phv00079854.v6_ + * dbGap name: **SYSTBP1** + * dbGap desc: **Systolic blood pressure (1st reading)** + * dbGap table: **f80_rel1** + * No permissible values listed in PIC-SURE data dictionary + * _phs000200.v11.pht001019.v6.phv00079855.v6_ + * dbGap name: **DIASBP1** + * dbGap desc: **Diastolic blood pressure (1st reading)** + * dbGap table: **f80_rel1** + * No permissible values listed in PIC-SURE data dictionary + * _phs000200.v11.pht001019.v6.phv00079856.v6_ + * dbGap name: **SYSTBP2** + * dbGap desc: **Systolic blood pressure (2nd reading)** + * dbGap table: **f80_rel1** + * No permissible values listed in PIC-SURE data dictionary + * _phs000200.v11.pht001019.v6.phv00079857.v6_ + * dbGap name: **DIASBP2** + * dbGap desc: **Diastolic blood pressure (2nd reading)** + * dbGap table: **f80_rel1** + * No permissible values listed in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -858,13 +1170,41 @@ * ### blood_pressure/bp_systolic_1 -- **ARIC Atherosclerosis Risk in Communities (ARIC) Cohort**: * 7 component_study_variables - * _phs000280.v4.pht004063.v2.phv00204712.v1_. dbGap Name: **V1AGE01**, Desc: **Age at visit 1 [Cohort. Visit 1]**, Table: **DERIVE13**. - * _phs000280.v4.pht004192.v2.phv00210284.v1_. dbGap Name: **SBPA15**, Desc: **[Second blood pressure measurement]. 2nd systolic. Q15 [Siting Blood Pressure. SBPA. Visit 1]**, Table: **SBPA02**. - * _phs000280.v4.pht004192.v2.phv00210285.v1_. dbGap Name: **SBPA16**, Desc: **[Second blood pressure measurement]. 2nd diastolic. Q16 [Siting Blood Pressure. SBPA. Visit 1]**, Table: **SBPA02**. - * _phs000280.v4.pht004192.v2.phv00210286.v1_. dbGap Name: **SBPA17**, Desc: **[Second blood pressure measurement]. 2nd zero reading. Q17 [Siting Blood Pressure. SBPA. Visit 1]**, Table: **SBPA02**. - * _phs000280.v4.pht004192.v2.phv00210287.v1_. dbGap Name: **SBPA18**, Desc: **[Third blood pressure measurement]. 3rd systolic. Q18 [Siting Blood Pressure. SBPA. Visit 1]**, Table: **SBPA02**. - * _phs000280.v4.pht004192.v2.phv00210288.v1_. dbGap Name: **SBPA19**, Desc: **[Third blood pressure measurement]. 3rd diastolic. Q19 [Siting Blood Pressure. SBPA. Visit 1]**, Table: **SBPA02**. - * _phs000280.v4.pht004192.v2.phv00210289.v1_. dbGap Name: **SBPA20**, Desc: **[Third blood pressure measurement]. 3rd zero reading. Q20 [Siting Blood Pressure. SBPA. Visit 1]**, Table: **SBPA02**. + * _phs000280.v4.pht004063.v2.phv00204712.v1_ + * dbGap name: **V1AGE01** + * dbGap desc: **Age at visit 1 [Cohort. Visit 1]** + * dbGap table: **DERIVE13** + * varId _phv00204712_ not found in PIC-SURE data dictionary + * _phs000280.v4.pht004192.v2.phv00210284.v1_ + * dbGap name: **SBPA15** + * dbGap desc: **[Second blood pressure measurement]. 2nd systolic. Q15 [Siting Blood Pressure. SBPA. Visit 1]** + * dbGap table: **SBPA02** + * varId _phv00210284_ not found in PIC-SURE data dictionary + * _phs000280.v4.pht004192.v2.phv00210285.v1_ + * dbGap name: **SBPA16** + * dbGap desc: **[Second blood pressure measurement]. 2nd diastolic. Q16 [Siting Blood Pressure. SBPA. Visit 1]** + * dbGap table: **SBPA02** + * varId _phv00210285_ not found in PIC-SURE data dictionary + * _phs000280.v4.pht004192.v2.phv00210286.v1_ + * dbGap name: **SBPA17** + * dbGap desc: **[Second blood pressure measurement]. 2nd zero reading. Q17 [Siting Blood Pressure. SBPA. Visit 1]** + * dbGap table: **SBPA02** + * varId _phv00210286_ not found in PIC-SURE data dictionary + * _phs000280.v4.pht004192.v2.phv00210287.v1_ + * dbGap name: **SBPA18** + * dbGap desc: **[Third blood pressure measurement]. 3rd systolic. Q18 [Siting Blood Pressure. SBPA. Visit 1]** + * dbGap table: **SBPA02** + * varId _phv00210287_ not found in PIC-SURE data dictionary + * _phs000280.v4.pht004192.v2.phv00210288.v1_ + * dbGap name: **SBPA19** + * dbGap desc: **[Third blood pressure measurement]. 3rd diastolic. Q19 [Siting Blood Pressure. SBPA. Visit 1]** + * dbGap table: **SBPA02** + * varId _phv00210288_ not found in PIC-SURE data dictionary + * _phs000280.v4.pht004192.v2.phv00210289.v1_ + * dbGap name: **SBPA20** + * dbGap desc: **[Third blood pressure measurement]. 3rd zero reading. Q20 [Siting Blood Pressure. SBPA. Visit 1]** + * dbGap table: **SBPA02** + * varId _phv00210289_ not found in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -931,15 +1271,51 @@ * ### blood_pressure/bp_systolic_1 -- **CARDIA CARDIA Cohort**: * 9 component_study_variables - * _phs000285.v3.pht001560.v2.phv00112481.v2_. dbGap Name: **A02R2S**, Desc: **SECOND READING SBP**, Table: **A4F02**. - * _phs000285.v3.pht001560.v2.phv00112482.v2_. dbGap Name: **A02R2D**, Desc: **SECOND READING DBP**, Table: **A4F02**. - * _phs000285.v3.pht001560.v2.phv00112483.v2_. dbGap Name: **A02RZ2S**, Desc: **RZ2 SBP**, Table: **A4F02**. - * _phs000285.v3.pht001560.v2.phv00112484.v2_. dbGap Name: **A02RZ2D**, Desc: **RZ2 DBP**, Table: **A4F02**. - * _phs000285.v3.pht001560.v2.phv00112487.v2_. dbGap Name: **A02R3S**, Desc: **THIRD READING SBP**, Table: **A4F02**. - * _phs000285.v3.pht001560.v2.phv00112488.v2_. dbGap Name: **A02R3D**, Desc: **THIRD READING DBP**, Table: **A4F02**. - * _phs000285.v3.pht001560.v2.phv00112489.v2_. dbGap Name: **A02RZ3S**, Desc: **RZ3 SBP**, Table: **A4F02**. - * _phs000285.v3.pht001560.v2.phv00112490.v2_. dbGap Name: **A02RZ3D**, Desc: **RZ3 DBP**, Table: **A4F02**. - * _phs000285.v3.pht001645.v2.phv00115119.v2_. dbGap Name: **EXAMAGE**, Desc: **AGE AT EXAM 1 (VERIFIED AT EXAM 2)**, Table: **B2REF**. + * _phs000285.v3.pht001560.v2.phv00112481.v2_ + * dbGap name: **A02R2S** + * dbGap desc: **SECOND READING SBP** + * dbGap table: **A4F02** + * varId _phv00112481_ not found in PIC-SURE data dictionary + * _phs000285.v3.pht001560.v2.phv00112482.v2_ + * dbGap name: **A02R2D** + * dbGap desc: **SECOND READING DBP** + * dbGap table: **A4F02** + * varId _phv00112482_ not found in PIC-SURE data dictionary + * _phs000285.v3.pht001560.v2.phv00112483.v2_ + * dbGap name: **A02RZ2S** + * dbGap desc: **RZ2 SBP** + * dbGap table: **A4F02** + * varId _phv00112483_ not found in PIC-SURE data dictionary + * _phs000285.v3.pht001560.v2.phv00112484.v2_ + * dbGap name: **A02RZ2D** + * dbGap desc: **RZ2 DBP** + * dbGap table: **A4F02** + * varId _phv00112484_ not found in PIC-SURE data dictionary + * _phs000285.v3.pht001560.v2.phv00112487.v2_ + * dbGap name: **A02R3S** + * dbGap desc: **THIRD READING SBP** + * dbGap table: **A4F02** + * varId _phv00112487_ not found in PIC-SURE data dictionary + * _phs000285.v3.pht001560.v2.phv00112488.v2_ + * dbGap name: **A02R3D** + * dbGap desc: **THIRD READING DBP** + * dbGap table: **A4F02** + * varId _phv00112488_ not found in PIC-SURE data dictionary + * _phs000285.v3.pht001560.v2.phv00112489.v2_ + * dbGap name: **A02RZ3S** + * dbGap desc: **RZ3 SBP** + * dbGap table: **A4F02** + * varId _phv00112489_ not found in PIC-SURE data dictionary + * _phs000285.v3.pht001560.v2.phv00112490.v2_ + * dbGap name: **A02RZ3D** + * dbGap desc: **RZ3 DBP** + * dbGap table: **A4F02** + * varId _phv00112490_ not found in PIC-SURE data dictionary + * _phs000285.v3.pht001645.v2.phv00115119.v2_ + * dbGap name: **EXAMAGE** + * dbGap desc: **AGE AT EXAM 1 (VERIFIED AT EXAM 2)** + * dbGap table: **B2REF** + * varId _phv00115119_ not found in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -990,9 +1366,21 @@ * ### blood_pressure/bp_systolic_1 -- **CHS Cardiovascular Health Study (CHS) Cohort: an NHLBI-funded observational study of risk factors for cardiovascular disease in adults 65 years or older**: * 3 component_study_variables - * _phs000287.v6.pht001452.v1.phv00100435.v1_. dbGap Name: **AVZMSYS**, Desc: **AVE ZERO MUD SYSTOL (mm Hg)**, Table: **BASEBOTH**. - * _phs000287.v6.pht001452.v1.phv00100436.v1_. dbGap Name: **AVZMDIA**, Desc: **AVE ZERO MUD DIASTOL-adj (mm Hg)**, Table: **BASEBOTH**. - * _phs000287.v6.pht001452.v1.phv00100487.v1_. dbGap Name: **AGEBL**, Desc: **CALCULATED AGE AT BASELINE**, Table: **BASEBOTH**. + * _phs000287.v6.pht001452.v1.phv00100435.v1_ + * dbGap name: **AVZMSYS** + * dbGap desc: **AVE ZERO MUD SYSTOL (mm Hg)** + * dbGap table: **BASEBOTH** + * No permissible values listed in PIC-SURE data dictionary + * _phs000287.v6.pht001452.v1.phv00100436.v1_ + * dbGap name: **AVZMDIA** + * dbGap desc: **AVE ZERO MUD DIASTOL-adj (mm Hg)** + * dbGap table: **BASEBOTH** + * No permissible values listed in PIC-SURE data dictionary + * _phs000287.v6.pht001452.v1.phv00100487.v1_ + * dbGap name: **AGEBL** + * dbGap desc: **CALCULATED AGE AT BASELINE** + * dbGap table: **BASEBOTH** + * No permissible values listed in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -1021,9 +1409,15 @@ * ### blood_pressure/bp_systolic_1 -- **COPDGene **: * 3 component_study_variables - * _phs000179.v5.pht002239.v4.phv00159583.v4_. No dbGap metadata available. - * _phs000179.v5.pht002239.v4.phv00159590.v4_. No dbGap metadata available. - * _phs000179.v5.pht002239.v4.phv00159836.v4_. No dbGap metadata available. + * _phs000179.v5.pht002239.v4.phv00159583.v4_ + * No dbGap metadata available + * No permissible values listed in PIC-SURE data dictionary + * _phs000179.v5.pht002239.v4.phv00159590.v4_ + * No dbGap metadata available + * No permissible values listed in PIC-SURE data dictionary + * _phs000179.v5.pht002239.v4.phv00159836.v4_ + * No dbGap metadata available + * No permissible values listed in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -1054,9 +1448,21 @@ * ### blood_pressure/bp_systolic_1 -- **HCHS_SOL Hispanic Community Health Study /Study of Latinos (HCHS/SOL)**: * 3 component_study_variables - * _phs000810.v1.pht004715.v1.phv00226251.v1_. dbGap Name: **AGE**, Desc: **Age**, Table: **HCHS_SOL_Cohort_Subject_Phenotypes**. - * _phs000810.v1.pht004715.v1.phv00226390.v1_. dbGap Name: **SBPA5**, Desc: **Average Systolic (SBPA5)**, Table: **HCHS_SOL_Cohort_Subject_Phenotypes**. - * _phs000810.v1.pht004715.v1.phv00226391.v1_. dbGap Name: **SBPA6**, Desc: **Average Diastolic (SBPA6)**, Table: **HCHS_SOL_Cohort_Subject_Phenotypes**. + * _phs000810.v1.pht004715.v1.phv00226251.v1_ + * dbGap name: **AGE** + * dbGap desc: **Age** + * dbGap table: **HCHS_SOL_Cohort_Subject_Phenotypes** + * No permissible values listed in PIC-SURE data dictionary + * _phs000810.v1.pht004715.v1.phv00226390.v1_ + * dbGap name: **SBPA5** + * dbGap desc: **Average Systolic (SBPA5)** + * dbGap table: **HCHS_SOL_Cohort_Subject_Phenotypes** + * No permissible values listed in PIC-SURE data dictionary + * _phs000810.v1.pht004715.v1.phv00226391.v1_ + * dbGap name: **SBPA6** + * dbGap desc: **Average Diastolic (SBPA6)** + * dbGap table: **HCHS_SOL_Cohort_Subject_Phenotypes** + * No permissible values listed in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -1076,13 +1482,39 @@ * ### blood_pressure/bp_systolic_1 -- **JHS Jackson Heart Study (JHS) Cohort**: * 7 component_study_variables - * _phs000286.v5.pht001949.v1.phv00126009.v1_. No dbGap metadata available. - * _phs000286.v5.pht001974.v1.phv00128370.v1_. dbGap Name: **SBPA13**, Desc: **Q13. D. First blood pressure measurement. Systolic (first BP) [Visit 1] [Sitting Blood Pressure Form, SBP]**, Table: **sbpa**. - * _phs000286.v5.pht001974.v1.phv00128371.v1_. dbGap Name: **SBPA14**, Desc: **Q14. D. First blood pressure measurement. Diastolic (first BP) [Visit 1] [Sitting Blood Pressure Form, SBP]**, Table: **sbpa**. - * _phs000286.v5.pht001974.v1.phv00128372.v1_. dbGap Name: **SBPA15**, Desc: **Q15. D. First blood pressure measurement. Zero reading (first BP) [Visit 1] [Sitting Blood Pressure Form, SBP]**, Table: **sbpa**. - * _phs000286.v5.pht001974.v1.phv00128373.v1_. dbGap Name: **SBPA16**, Desc: **Q16. E. Second blood pressure measurement. Systolic (second BP) [Visit 1] [Sitting Blood Pressure Form, SBP]**, Table: **sbpa**. - * _phs000286.v5.pht001974.v1.phv00128374.v1_. dbGap Name: **SBPA17**, Desc: **Q17. E. Second blood pressure measurement. Diastolic (second BP) [Visit 1] [Sitting Blood Pressure Form, SBP]**, Table: **sbpa**. - * _phs000286.v5.pht001974.v1.phv00128375.v1_. dbGap Name: **SBPA18**, Desc: **Q18. E. Second blood pressure measurement. Zero Reading (second BP) [Visit 1] [Sitting Blood Pressure Form, SBP]**, Table: **sbpa**. + * _phs000286.v5.pht001949.v1.phv00126009.v1_ + * No dbGap metadata available + * varId _phv00126009_ not found in PIC-SURE data dictionary + * _phs000286.v5.pht001974.v1.phv00128370.v1_ + * dbGap name: **SBPA13** + * dbGap desc: **Q13. D. First blood pressure measurement. Systolic (first BP) [Visit 1] [Sitting Blood Pressure Form, SBP]** + * dbGap table: **sbpa** + * varId _phv00128370_ not found in PIC-SURE data dictionary + * _phs000286.v5.pht001974.v1.phv00128371.v1_ + * dbGap name: **SBPA14** + * dbGap desc: **Q14. D. First blood pressure measurement. Diastolic (first BP) [Visit 1] [Sitting Blood Pressure Form, SBP]** + * dbGap table: **sbpa** + * varId _phv00128371_ not found in PIC-SURE data dictionary + * _phs000286.v5.pht001974.v1.phv00128372.v1_ + * dbGap name: **SBPA15** + * dbGap desc: **Q15. D. First blood pressure measurement. Zero reading (first BP) [Visit 1] [Sitting Blood Pressure Form, SBP]** + * dbGap table: **sbpa** + * varId _phv00128372_ not found in PIC-SURE data dictionary + * _phs000286.v5.pht001974.v1.phv00128373.v1_ + * dbGap name: **SBPA16** + * dbGap desc: **Q16. E. Second blood pressure measurement. Systolic (second BP) [Visit 1] [Sitting Blood Pressure Form, SBP]** + * dbGap table: **sbpa** + * varId _phv00128373_ not found in PIC-SURE data dictionary + * _phs000286.v5.pht001974.v1.phv00128374.v1_ + * dbGap name: **SBPA17** + * dbGap desc: **Q17. E. Second blood pressure measurement. Diastolic (second BP) [Visit 1] [Sitting Blood Pressure Form, SBP]** + * dbGap table: **sbpa** + * varId _phv00128374_ not found in PIC-SURE data dictionary + * _phs000286.v5.pht001974.v1.phv00128375.v1_ + * dbGap name: **SBPA18** + * dbGap desc: **Q18. E. Second blood pressure measurement. Zero Reading (second BP) [Visit 1] [Sitting Blood Pressure Form, SBP]** + * dbGap table: **sbpa** + * varId _phv00128375_ not found in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -1131,21 +1563,81 @@ * ### blood_pressure/bp_systolic_1 -- **MESA Multi-Ethnic Study of Atherosclerosis (MESA) Cohort**: * 15 component_study_variables - * _phs000209.v13.pht001111.v4.phv00082639.v2_. dbGap Name: **age1c**, Desc: **AGE**, Table: **MESA_AirNRExamMain**. - * _phs000209.v13.pht001111.v4.phv00083403.v1_. dbGap Name: **s2bp1**, Desc: **SEATED BP: SYSTOLIC 2ND READING (mmHg)**, Table: **MESA_AirNRExamMain**. - * _phs000209.v13.pht001111.v4.phv00083404.v1_. dbGap Name: **d2bp1**, Desc: **SEATED BP: DIASTOLIC 2ND READING (mmHg)**, Table: **MESA_AirNRExamMain**. - * _phs000209.v13.pht001111.v4.phv00083406.v1_. dbGap Name: **s3bp1**, Desc: **SEATED BP: SYSTOLIC 3RD READING (mmHg)**, Table: **MESA_AirNRExamMain**. - * _phs000209.v13.pht001111.v4.phv00083407.v1_. dbGap Name: **d3bp1**, Desc: **SEATED BP: DIASTOLIC 3RD READING (mmHg)**, Table: **MESA_AirNRExamMain**. - * _phs000209.v13.pht001116.v10.phv00084442.v3_. dbGap Name: **age1c**, Desc: **AGE**, Table: **MESA_Exam1Main**. - * _phs000209.v13.pht001116.v10.phv00085735.v2_. dbGap Name: **s2bp1**, Desc: **SEATED BP: SYSTOLIC 2ND READING (mmHg)**, Table: **MESA_Exam1Main**. - * _phs000209.v13.pht001116.v10.phv00085736.v2_. dbGap Name: **d2bp1**, Desc: **SEATED BP: DIASTOLIC 2ND READING (mmHg)**, Table: **MESA_Exam1Main**. - * _phs000209.v13.pht001116.v10.phv00085737.v2_. dbGap Name: **s3bp1**, Desc: **SEATED BP: SYSTOLIC 3RD READING (mmHg)**, Table: **MESA_Exam1Main**. - * _phs000209.v13.pht001116.v10.phv00085738.v2_. dbGap Name: **d3bp1**, Desc: **SEATED BP: DIASTOLIC 3RD READING (mmHg)**, Table: **MESA_Exam1Main**. - * _phs000209.v13.pht001121.v3.phv00087071.v1_. dbGap Name: **agefc**, Desc: **AGE**, Table: **MESA_FamilyExamMain**. - * _phs000209.v13.pht001121.v3.phv00087509.v1_. dbGap Name: **s2bpf**, Desc: **2ND READING: SEATED SYSTOLIC BP (mmHg)**, Table: **MESA_FamilyExamMain**. - * _phs000209.v13.pht001121.v3.phv00087510.v1_. dbGap Name: **d2bpf**, Desc: **2ND READING: SEATED DIASTOLIC BP (mmHg)**, Table: **MESA_FamilyExamMain**. - * _phs000209.v13.pht001121.v3.phv00087512.v1_. dbGap Name: **s3bpf**, Desc: **3RD READING: SEATED SYSTOLIC BP (mmHg)**, Table: **MESA_FamilyExamMain**. - * _phs000209.v13.pht001121.v3.phv00087513.v1_. dbGap Name: **d3bpf**, Desc: **3RD READING: SEATED DIASTOLIC BP (mmHg)**, Table: **MESA_FamilyExamMain**. + * _phs000209.v13.pht001111.v4.phv00082639.v2_ + * dbGap name: **age1c** + * dbGap desc: **AGE** + * dbGap table: **MESA_AirNRExamMain** + * No permissible values listed in PIC-SURE data dictionary + * _phs000209.v13.pht001111.v4.phv00083403.v1_ + * dbGap name: **s2bp1** + * dbGap desc: **SEATED BP: SYSTOLIC 2ND READING (mmHg)** + * dbGap table: **MESA_AirNRExamMain** + * No permissible values listed in PIC-SURE data dictionary + * _phs000209.v13.pht001111.v4.phv00083404.v1_ + * dbGap name: **d2bp1** + * dbGap desc: **SEATED BP: DIASTOLIC 2ND READING (mmHg)** + * dbGap table: **MESA_AirNRExamMain** + * No permissible values listed in PIC-SURE data dictionary + * _phs000209.v13.pht001111.v4.phv00083406.v1_ + * dbGap name: **s3bp1** + * dbGap desc: **SEATED BP: SYSTOLIC 3RD READING (mmHg)** + * dbGap table: **MESA_AirNRExamMain** + * No permissible values listed in PIC-SURE data dictionary + * _phs000209.v13.pht001111.v4.phv00083407.v1_ + * dbGap name: **d3bp1** + * dbGap desc: **SEATED BP: DIASTOLIC 3RD READING (mmHg)** + * dbGap table: **MESA_AirNRExamMain** + * No permissible values listed in PIC-SURE data dictionary + * _phs000209.v13.pht001116.v10.phv00084442.v3_ + * dbGap name: **age1c** + * dbGap desc: **AGE** + * dbGap table: **MESA_Exam1Main** + * No permissible values listed in PIC-SURE data dictionary + * _phs000209.v13.pht001116.v10.phv00085735.v2_ + * dbGap name: **s2bp1** + * dbGap desc: **SEATED BP: SYSTOLIC 2ND READING (mmHg)** + * dbGap table: **MESA_Exam1Main** + * No permissible values listed in PIC-SURE data dictionary + * _phs000209.v13.pht001116.v10.phv00085736.v2_ + * dbGap name: **d2bp1** + * dbGap desc: **SEATED BP: DIASTOLIC 2ND READING (mmHg)** + * dbGap table: **MESA_Exam1Main** + * No permissible values listed in PIC-SURE data dictionary + * _phs000209.v13.pht001116.v10.phv00085737.v2_ + * dbGap name: **s3bp1** + * dbGap desc: **SEATED BP: SYSTOLIC 3RD READING (mmHg)** + * dbGap table: **MESA_Exam1Main** + * No permissible values listed in PIC-SURE data dictionary + * _phs000209.v13.pht001116.v10.phv00085738.v2_ + * dbGap name: **d3bp1** + * dbGap desc: **SEATED BP: DIASTOLIC 3RD READING (mmHg)** + * dbGap table: **MESA_Exam1Main** + * No permissible values listed in PIC-SURE data dictionary + * _phs000209.v13.pht001121.v3.phv00087071.v1_ + * dbGap name: **agefc** + * dbGap desc: **AGE** + * dbGap table: **MESA_FamilyExamMain** + * No permissible values listed in PIC-SURE data dictionary + * _phs000209.v13.pht001121.v3.phv00087509.v1_ + * dbGap name: **s2bpf** + * dbGap desc: **2ND READING: SEATED SYSTOLIC BP (mmHg)** + * dbGap table: **MESA_FamilyExamMain** + * No permissible values listed in PIC-SURE data dictionary + * _phs000209.v13.pht001121.v3.phv00087510.v1_ + * dbGap name: **d2bpf** + * dbGap desc: **2ND READING: SEATED DIASTOLIC BP (mmHg)** + * dbGap table: **MESA_FamilyExamMain** + * No permissible values listed in PIC-SURE data dictionary + * _phs000209.v13.pht001121.v3.phv00087512.v1_ + * dbGap name: **s3bpf** + * dbGap desc: **3RD READING: SEATED SYSTOLIC BP (mmHg)** + * dbGap table: **MESA_FamilyExamMain** + * No permissible values listed in PIC-SURE data dictionary + * _phs000209.v13.pht001121.v3.phv00087513.v1_ + * dbGap name: **d3bpf** + * dbGap desc: **3RD READING: SEATED DIASTOLIC BP (mmHg)** + * dbGap table: **MESA_FamilyExamMain** + * No permissible values listed in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -1197,14 +1689,46 @@ * ### blood_pressure/bp_systolic_1 -- **WHI Women's Health Initiative**: * 8 component_study_variables - * _phs000200.v11.pht000998.v6.phv00078436.v6_. dbGap Name: **F2DAYS**, Desc: **F2 Days since randomization**, Table: **f2_rel1**. - * _phs000200.v11.pht000998.v6.phv00078437.v6_. dbGap Name: **AGE**, Desc: **Age at screening**, Table: **f2_rel1**. - * _phs000200.v11.pht001019.v6.phv00079850.v6_. dbGap Name: **F80VTYP**, Desc: **Visit Type**, Table: **f80_rel1**. - * _phs000200.v11.pht001019.v6.phv00079852.v6_. dbGap Name: **F80DAYS**, Desc: **F80 Days since randomization/enrollment**, Table: **f80_rel1**. - * _phs000200.v11.pht001019.v6.phv00079854.v6_. dbGap Name: **SYSTBP1**, Desc: **Systolic blood pressure (1st reading)**, Table: **f80_rel1**. - * _phs000200.v11.pht001019.v6.phv00079855.v6_. dbGap Name: **DIASBP1**, Desc: **Diastolic blood pressure (1st reading)**, Table: **f80_rel1**. - * _phs000200.v11.pht001019.v6.phv00079856.v6_. dbGap Name: **SYSTBP2**, Desc: **Systolic blood pressure (2nd reading)**, Table: **f80_rel1**. - * _phs000200.v11.pht001019.v6.phv00079857.v6_. dbGap Name: **DIASBP2**, Desc: **Diastolic blood pressure (2nd reading)**, Table: **f80_rel1**. + * _phs000200.v11.pht000998.v6.phv00078436.v6_ + * dbGap name: **F2DAYS** + * dbGap desc: **F2 Days since randomization** + * dbGap table: **f2_rel1** + * No permissible values listed in PIC-SURE data dictionary + * _phs000200.v11.pht000998.v6.phv00078437.v6_ + * dbGap name: **AGE** + * dbGap desc: **Age at screening** + * dbGap table: **f2_rel1** + * No permissible values listed in PIC-SURE data dictionary + * _phs000200.v11.pht001019.v6.phv00079850.v6_ + * dbGap name: **F80VTYP** + * dbGap desc: **Visit Type** + * dbGap table: **f80_rel1** + * PIC-SURE permissible values: Annual visit, Screening + * _phs000200.v11.pht001019.v6.phv00079852.v6_ + * dbGap name: **F80DAYS** + * dbGap desc: **F80 Days since randomization/enrollment** + * dbGap table: **f80_rel1** + * No permissible values listed in PIC-SURE data dictionary + * _phs000200.v11.pht001019.v6.phv00079854.v6_ + * dbGap name: **SYSTBP1** + * dbGap desc: **Systolic blood pressure (1st reading)** + * dbGap table: **f80_rel1** + * No permissible values listed in PIC-SURE data dictionary + * _phs000200.v11.pht001019.v6.phv00079855.v6_ + * dbGap name: **DIASBP1** + * dbGap desc: **Diastolic blood pressure (1st reading)** + * dbGap table: **f80_rel1** + * No permissible values listed in PIC-SURE data dictionary + * _phs000200.v11.pht001019.v6.phv00079856.v6_ + * dbGap name: **SYSTBP2** + * dbGap desc: **Systolic blood pressure (2nd reading)** + * dbGap table: **f80_rel1** + * No permissible values listed in PIC-SURE data dictionary + * _phs000200.v11.pht001019.v6.phv00079857.v6_ + * dbGap name: **DIASBP2** + * dbGap desc: **Diastolic blood pressure (2nd reading)** + * dbGap table: **f80_rel1** + * No permissible values listed in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ diff --git a/resources/human-readable-harmonized-variable-documentation/generated-doc-pages/demographic.md b/resources/human-readable-harmonized-variable-documentation/generated-doc-pages/demographic.md index bba3aad..4a4ed69 100644 --- a/resources/human-readable-harmonized-variable-documentation/generated-doc-pages/demographic.md +++ b/resources/human-readable-harmonized-variable-documentation/generated-doc-pages/demographic.md @@ -42,7 +42,11 @@ * ### demographic/annotated_sex_1 -- **ARIC Atherosclerosis Risk in Communities (ARIC) Cohort**: * 1 component_study_variables - * _phs000280.v5.pht004063.v2.phv00204711.v1_. dbGap Name: **GENDER**, Desc: **Sex (uncorrected from FTRA22) [Cohort. Visit 1]**, Table: **DERIVE13**. + * _phs000280.v5.pht004063.v2.phv00204711.v1_ + * dbGap name: **GENDER** + * dbGap desc: **Sex (uncorrected from FTRA22) [Cohort. Visit 1]** + * dbGap table: **DERIVE13** + * varId _phv00204711_ not found in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -68,7 +72,11 @@ * ### demographic/annotated_sex_1 -- **CARDIA CARDIA Cohort**: * 1 component_study_variables - * _phs000285.v3.pht001645.v2.phv00115114.v2_. dbGap Name: **SEX**, Desc: **SEX (VERIFIED AT EXAM 2)**, Table: **B2REF**. + * _phs000285.v3.pht001645.v2.phv00115114.v2_ + * dbGap name: **SEX** + * dbGap desc: **SEX (VERIFIED AT EXAM 2)** + * dbGap table: **B2REF** + * varId _phv00115114_ not found in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -90,7 +98,11 @@ * ### demographic/annotated_sex_1 -- **CHS Cardiovascular Health Study (CHS) Cohort: an NHLBI-funded observational study of risk factors for cardiovascular disease in adults 65 years or older**: * 1 component_study_variables - * _phs000287.v6.pht001452.v1.phv00100302.v1_. dbGap Name: **GEND01**, Desc: **GENDER**, Table: **BASEBOTH**. + * _phs000287.v6.pht001452.v1.phv00100302.v1_ + * dbGap name: **GEND01** + * dbGap desc: **GENDER** + * dbGap table: **BASEBOTH** + * PIC-SURE permissible values: Female, Male * **Function:** ```r harmonize <- function(phen_list){ @@ -115,7 +127,9 @@ * ### demographic/annotated_sex_1 -- **COPDGene **: * 1 component_study_variables - * _phs000179.v5.pht002239.v4.phv00159571.v4_. No dbGap metadata available. + * _phs000179.v5.pht002239.v4.phv00159571.v4_ + * No dbGap metadata available + * PIC-SURE permissible values: Female, Male * **Function:** ```r harmonize <- function(phen_list){ @@ -137,7 +151,11 @@ * ### demographic/annotated_sex_1 -- **FHS Framingham Cohort**: * 1 component_study_variables - * _phs000007.v30.pht003099.v5.phv00177929.v5_. dbGap Name: **sex**, Desc: **Participant gender**, Table: **vr_dates_2019_a_1175s**. + * _phs000007.v30.pht003099.v5.phv00177929.v5_ + * dbGap name: **sex** + * dbGap desc: **Participant gender** + * dbGap table: **vr_dates_2019_a_1175s** + * PIC-SURE permissible values: Female, Male * **Function:** ```r harmonize <- function(phen_list){ @@ -163,7 +181,11 @@ * ### demographic/annotated_sex_1 -- **HCHS_SOL Hispanic Community Health Study /Study of Latinos (HCHS/SOL)**: * 1 component_study_variables - * _phs000810.v1.pht004715.v1.phv00226279.v1_. dbGap Name: **GENDER**, Desc: **Gender (F=Female, M=Male)**, Table: **HCHS_SOL_Cohort_Subject_Phenotypes**. + * _phs000810.v1.pht004715.v1.phv00226279.v1_ + * dbGap name: **GENDER** + * dbGap desc: **Gender (F=Female, M=Male)** + * dbGap table: **HCHS_SOL_Cohort_Subject_Phenotypes** + * PIC-SURE permissible values: Female, Male * **Function:** ```r harmonize <- function(phen_list){ @@ -183,7 +205,9 @@ * ### demographic/annotated_sex_1 -- **JHS Jackson Heart Study (JHS) Cohort**: * 1 component_study_variables - * _phs000286.v5.pht001949.v1.phv00126012.v1_. No dbGap metadata available. + * _phs000286.v5.pht001949.v1.phv00126012.v1_ + * No dbGap metadata available + * varId _phv00126012_ not found in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -207,7 +231,11 @@ * ### demographic/annotated_sex_1 -- **WHI Women's Health Initiative**: * 1 component_study_variables - * _phs000200.v11.pht000982.v8.phv00077315.v8_. dbGap Name: **CONSENT**, Desc: **WHI dbGaP Consent Group**, Table: **WHI_Subject**. + * _phs000200.v11.pht000982.v8.phv00077315.v8_ + * dbGap name: **CONSENT** + * dbGap desc: **WHI dbGaP Consent Group** + * dbGap table: **WHI_Subject** + * PIC-SURE permissible values: Health/Medical/Biomedical (IRB) (HMB-IRB), Health/Medical/Biomedical (IRB, NPU) (HMB-IRB-NPU) * **Function:** ```r harmonize <- function(phen_list){ @@ -261,7 +289,11 @@ * ### demographic/geographic_site_1 -- **ARIC Atherosclerosis Risk in Communities (ARIC) Cohort**: * 1 component_study_variables - * _phs000280.v5.pht004063.v2.phv00204813.v1_. dbGap Name: **CENTERID**, Desc: **Recoded Center ID [Cohort. Visit 1]**, Table: **DERIVE13**. + * _phs000280.v5.pht004063.v2.phv00204813.v1_ + * dbGap name: **CENTERID** + * dbGap desc: **Recoded Center ID [Cohort. Visit 1]** + * dbGap table: **DERIVE13** + * varId _phv00204813_ not found in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -295,7 +327,11 @@ * ### demographic/geographic_site_1 -- **CARDIA CARDIA Cohort**: * 1 component_study_variables - * _phs000285.v3.pht001700.v2.phv00116398.v2_. dbGap Name: **CENTER_CARE**, Desc: **CENTER FOR CARE PROJECT**, Table: **CENTER**. + * _phs000285.v3.pht001700.v2.phv00116398.v2_ + * dbGap name: **CENTER_CARE** + * dbGap desc: **CENTER FOR CARE PROJECT** + * dbGap table: **CENTER** + * varId _phv00116398_ not found in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -327,7 +363,11 @@ * ### demographic/geographic_site_1 -- **CHS Cardiovascular Health Study (CHS) Cohort: an NHLBI-funded observational study of risk factors for cardiovascular disease in adults 65 years or older**: * 1 component_study_variables - * _phs000287.v6.pht001452.v1.phv00100291.v1_. dbGap Name: **CLINIC**, Desc: **CHS CLINIC**, Table: **BASEBOTH**. + * _phs000287.v6.pht001452.v1.phv00100291.v1_ + * dbGap name: **CLINIC** + * dbGap desc: **CHS CLINIC** + * dbGap table: **BASEBOTH** + * No permissible values listed in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -366,7 +406,9 @@ * ### demographic/geographic_site_1 -- **COPDGene **: * 1 component_study_variables - * _phs000179.v5.pht002239.v4.phv00159569.v4_. No dbGap metadata available. + * _phs000179.v5.pht002239.v4.phv00159569.v4_ + * No dbGap metadata available + * PIC-SURE permissible values: C01, C02, C03, C04, C05, C06, C07, C08, C09, C10, C11, C12, C13, C14, C15, C16, C17, C18, C19, C20, C21 * **Function:** ```r harmonize <- function(phen_list){ @@ -393,7 +435,11 @@ * ### demographic/geographic_site_1 -- **HCHS_SOL Hispanic Community Health Study /Study of Latinos (HCHS/SOL)**: * 1 component_study_variables - * _phs000810.v1.pht004715.v1.phv00226256.v1_. dbGap Name: **CENTER**, Desc: **Center**, Table: **HCHS_SOL_Cohort_Subject_Phenotypes**. + * _phs000810.v1.pht004715.v1.phv00226256.v1_ + * dbGap name: **CENTER** + * dbGap desc: **Center** + * dbGap table: **HCHS_SOL_Cohort_Subject_Phenotypes** + * PIC-SURE permissible values: Bronx, Chicago, Miami, San Diego * **Function:** ```r harmonize <- function(phen_list){ @@ -430,7 +476,9 @@ * ### demographic/geographic_site_1 -- **JHS Jackson Heart Study (JHS) Cohort**: * 1 component_study_variables - * _phs000286.v5.pht001949.v1.phv00126005.v1_. No dbGap metadata available. + * _phs000286.v5.pht001949.v1.phv00126005.v1_ + * No dbGap metadata available + * varId _phv00126005_ not found in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -460,7 +508,11 @@ * ### demographic/geographic_site_1 -- **WHI Women's Health Initiative**: * 1 component_study_variables - * _phs000200.v11.pht001031.v6.phv00080435.v6_. dbGap Name: **REGION**, Desc: **U. S. Region**, Table: **rand_rel2**. + * _phs000200.v11.pht001031.v6.phv00080435.v6_ + * dbGap name: **REGION** + * dbGap desc: **U. S. Region** + * dbGap table: **rand_rel2** + * PIC-SURE permissible values: Midwest, Northeast, South, West * **Function:** ```r harmonize <- function(phen_list){ @@ -554,7 +606,9 @@ * ### demographic/hispanic_or_latino_1 -- **COPDGene **: * 1 component_study_variables - * _phs000179.v5.pht002239.v4.phv00159573.v4_. No dbGap metadata available. + * _phs000179.v5.pht002239.v4.phv00159573.v4_ + * No dbGap metadata available + * PIC-SURE permissible values: Not Hispanic or Latino * **Function:** ```r harmonize <- function(phen_list){ @@ -577,7 +631,11 @@ * ### demographic/hispanic_or_latino_1 -- **HCHS_SOL Hispanic Community Health Study /Study of Latinos (HCHS/SOL)**: * 1 component_study_variables - * _phs000810.v1.pht004713.v1.phv00226241.v1_. dbGap Name: **CONSENT**, Desc: **Consent group**, Table: **HCHS_SOL_Cohort_Subject**. + * _phs000810.v1.pht004713.v1.phv00226241.v1_ + * dbGap name: **CONSENT** + * dbGap desc: **Consent group** + * dbGap table: **HCHS_SOL_Cohort_Subject** + * PIC-SURE permissible values: Health/Medical/Biomedical (HMB), Health/Medical/Biomedical (NPU) (HMB-NPU) * **Function:** ```r harmonize <- function(phen_list){ @@ -602,7 +660,11 @@ * ### demographic/hispanic_or_latino_1 -- **WHI Women's Health Initiative**: * 1 component_study_variables - * _phs000200.v11.pht000998.v6.phv00078450.v6_. dbGap Name: **RACE**, Desc: **Racial or ethnic group**, Table: **f2_rel1**. + * _phs000200.v11.pht000998.v6.phv00078450.v6_ + * dbGap name: **RACE** + * dbGap desc: **Racial or ethnic group** + * dbGap table: **f2_rel1** + * PIC-SURE permissible values: American Indian or Alaskan Native, Asian or Pacific Islander, Black or African-American, Hispanic/Latino, Other, White (not of Hispanic origin) * **Function:** ```r harmonize <- function(phen_list){ @@ -648,7 +710,11 @@ * ### demographic/hispanic_subgroup_1 -- **HCHS_SOL Hispanic Community Health Study /Study of Latinos (HCHS/SOL)**: * 1 component_study_variables - * _phs000810.v1.pht004715.v1.phv00226254.v1_. dbGap Name: **BKGRD1_C7**, Desc: **7-level re-classification of Hispanic/Latino Background**, Table: **HCHS_SOL_Cohort_Subject_Phenotypes**. + * _phs000810.v1.pht004715.v1.phv00226254.v1_ + * dbGap name: **BKGRD1_C7** + * dbGap desc: **7-level re-classification of Hispanic/Latino Background** + * dbGap table: **HCHS_SOL_Cohort_Subject_Phenotypes** + * PIC-SURE permissible values: Central American, Cuban, Dominican, Mexican, More than one heritage/Other, Puerto-Rican, South American * **Function:** ```r harmonize <- function(phen_list){ @@ -677,8 +743,16 @@ * ### demographic/hispanic_subgroup_1 -- **WHI Women's Health Initiative**: * 2 component_study_variables - * _phs000200.v11.pht000998.v6.phv00078450.v6_. dbGap Name: **RACE**, Desc: **Racial or ethnic group**, Table: **f2_rel1**. - * _phs000200.v11.pht001009.v6.phv00079316.v6_. dbGap Name: **SPANISH**, Desc: **Are you Spanish/Hispanic/Latino**, Table: **f41_rel1**. + * _phs000200.v11.pht000998.v6.phv00078450.v6_ + * dbGap name: **RACE** + * dbGap desc: **Racial or ethnic group** + * dbGap table: **f2_rel1** + * PIC-SURE permissible values: American Indian or Alaskan Native, Asian or Pacific Islander, Black or African-American, Hispanic/Latino, Other, White (not of Hispanic origin) + * _phs000200.v11.pht001009.v6.phv00079316.v6_ + * dbGap name: **SPANISH** + * dbGap desc: **Are you Spanish/Hispanic/Latino** + * dbGap table: **f41_rel1** + * PIC-SURE permissible values: No, Yes, Cuban, Yes, Mexican, Mexican American, Chicano, Yes, Puerto Rican, Yes, other Spanish/Hispanic/Latina * **Function:** ```r harmonize <- function(phen_list){ @@ -791,9 +865,17 @@ * ### demographic/race_us_1 -- **ARIC Atherosclerosis Risk in Communities (ARIC) Cohort**: * 3 component_study_variables - * _phs000280.v5.pht004062.v2.phv00204633.v1_. No dbGap metadata available. - * _phs000280.v5.pht004063.v2.phv00204710.v1_. dbGap Name: **RACEGRP**, Desc: **Race (from FTRA23) [Cohort. Visit 1]**, Table: **DERIVE13**. - * _phs000280.v5.pht004065.v2.phv00204962.v1_. No dbGap metadata available. + * _phs000280.v5.pht004062.v2.phv00204633.v1_ + * No dbGap metadata available + * varId _phv00204633_ not found in PIC-SURE data dictionary + * _phs000280.v5.pht004063.v2.phv00204710.v1_ + * dbGap name: **RACEGRP** + * dbGap desc: **Race (from FTRA23) [Cohort. Visit 1]** + * dbGap table: **DERIVE13** + * varId _phv00204710_ not found in PIC-SURE data dictionary + * _phs000280.v5.pht004065.v2.phv00204962.v1_ + * No dbGap metadata available + * varId _phv00204962_ not found in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -846,7 +928,11 @@ * ### demographic/race_us_1 -- **CARDIA CARDIA Cohort**: * 1 component_study_variables - * _phs000285.v3.pht001645.v2.phv00115113.v2_. dbGap Name: **RACE**, Desc: **RACE (VERIFIED AT EXAM 2)**, Table: **B2REF**. + * _phs000285.v3.pht001645.v2.phv00115113.v2_ + * dbGap name: **RACE** + * dbGap desc: **RACE (VERIFIED AT EXAM 2)** + * dbGap table: **B2REF** + * varId _phv00115113_ not found in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -883,7 +969,9 @@ * ### demographic/race_us_1 -- **COPDGene **: * 1 component_study_variables - * _phs000179.v5.pht002239.v4.phv00159572.v4_. No dbGap metadata available. + * _phs000179.v5.pht002239.v4.phv00159572.v4_ + * No dbGap metadata available + * PIC-SURE permissible values: African American, Caucasian * **Function:** ```r harmonize <- function(phen_list){ @@ -909,7 +997,11 @@ * ### demographic/race_us_1 -- **HCHS_SOL Hispanic Community Health Study /Study of Latinos (HCHS/SOL)**: * 1 component_study_variables - * _phs000810.v1.pht004713.v1.phv00226241.v1_. dbGap Name: **CONSENT**, Desc: **Consent group**, Table: **HCHS_SOL_Cohort_Subject**. + * _phs000810.v1.pht004713.v1.phv00226241.v1_ + * dbGap name: **CONSENT** + * dbGap desc: **Consent group** + * dbGap table: **HCHS_SOL_Cohort_Subject** + * PIC-SURE permissible values: Health/Medical/Biomedical (HMB), Health/Medical/Biomedical (NPU) (HMB-NPU) * **Function:** ```r harmonize <- function(phen_list){ @@ -934,7 +1026,11 @@ * ### demographic/race_us_1 -- **JHS Jackson Heart Study (JHS) Cohort**: * 1 component_study_variables - * _phs000286.v5.pht001920.v4.phv00124546.v3_. dbGap Name: **CONSENT**, Desc: **Consent group as determined by DAC**, Table: **JHS_Subject**. + * _phs000286.v5.pht001920.v4.phv00124546.v3_ + * dbGap name: **CONSENT** + * dbGap desc: **Consent group as determined by DAC** + * dbGap table: **JHS_Subject** + * varId _phv00124546_ not found in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -958,22 +1054,86 @@ * ### demographic/race_us_1 -- **WHI Women's Health Initiative**: * 16 component_study_variables - * _phs000200.v11.pht000998.v6.phv00078450.v6_. dbGap Name: **RACE**, Desc: **Racial or ethnic group**, Table: **f2_rel1**. - * _phs000200.v11.pht001009.v6.phv00079317.v6_. dbGap Name: **WHITE**, Desc: **White**, Table: **f41_rel1**. - * _phs000200.v11.pht001009.v6.phv00079318.v6_. dbGap Name: **BLACK**, Desc: **Black, African-American, or Negro**, Table: **f41_rel1**. - * _phs000200.v11.pht001009.v6.phv00079319.v6_. dbGap Name: **AMERINDIAN**, Desc: **American Indian or Alaskan Native**, Table: **f41_rel1**. - * _phs000200.v11.pht001009.v6.phv00079320.v6_. dbGap Name: **ASIAINDIAN**, Desc: **Asian Indian**, Table: **f41_rel1**. - * _phs000200.v11.pht001009.v6.phv00079321.v6_. dbGap Name: **CHINESE**, Desc: **Chinese**, Table: **f41_rel1**. - * _phs000200.v11.pht001009.v6.phv00079322.v6_. dbGap Name: **FILIPINO**, Desc: **Filipino**, Table: **f41_rel1**. - * _phs000200.v11.pht001009.v6.phv00079323.v6_. dbGap Name: **JAPANESE**, Desc: **Japanese**, Table: **f41_rel1**. - * _phs000200.v11.pht001009.v6.phv00079324.v6_. dbGap Name: **KOREAN**, Desc: **Korean**, Table: **f41_rel1**. - * _phs000200.v11.pht001009.v6.phv00079325.v6_. dbGap Name: **VIETNAMESE**, Desc: **Vietnamese**, Table: **f41_rel1**. - * _phs000200.v11.pht001009.v6.phv00079326.v6_. dbGap Name: **OTHERASIAN**, Desc: **Other Asian**, Table: **f41_rel1**. - * _phs000200.v11.pht001009.v6.phv00079327.v6_. dbGap Name: **HAWAIIAN**, Desc: **Native Hawaiian**, Table: **f41_rel1**. - * _phs000200.v11.pht001009.v6.phv00079328.v6_. dbGap Name: **GUAMANIAN**, Desc: **Guamanian or Chamorro**, Table: **f41_rel1**. - * _phs000200.v11.pht001009.v6.phv00079329.v6_. dbGap Name: **SAMOAN**, Desc: **Samoan**, Table: **f41_rel1**. - * _phs000200.v11.pht001009.v6.phv00079330.v6_. dbGap Name: **OTHRPACISL**, Desc: **Other Pacific Islander**, Table: **f41_rel1**. - * _phs000200.v11.pht001009.v6.phv00079331.v6_. dbGap Name: **OTHERRACE**, Desc: **Some other race**, Table: **f41_rel1**. + * _phs000200.v11.pht000998.v6.phv00078450.v6_ + * dbGap name: **RACE** + * dbGap desc: **Racial or ethnic group** + * dbGap table: **f2_rel1** + * PIC-SURE permissible values: American Indian or Alaskan Native, Asian or Pacific Islander, Black or African-American, Hispanic/Latino, Other, White (not of Hispanic origin) + * _phs000200.v11.pht001009.v6.phv00079317.v6_ + * dbGap name: **WHITE** + * dbGap desc: **White** + * dbGap table: **f41_rel1** + * PIC-SURE permissible values: No, Yes + * _phs000200.v11.pht001009.v6.phv00079318.v6_ + * dbGap name: **BLACK** + * dbGap desc: **Black, African-American, or Negro** + * dbGap table: **f41_rel1** + * PIC-SURE permissible values: No, Yes + * _phs000200.v11.pht001009.v6.phv00079319.v6_ + * dbGap name: **AMERINDIAN** + * dbGap desc: **American Indian or Alaskan Native** + * dbGap table: **f41_rel1** + * PIC-SURE permissible values: No, Yes + * _phs000200.v11.pht001009.v6.phv00079320.v6_ + * dbGap name: **ASIAINDIAN** + * dbGap desc: **Asian Indian** + * dbGap table: **f41_rel1** + * PIC-SURE permissible values: No, Yes + * _phs000200.v11.pht001009.v6.phv00079321.v6_ + * dbGap name: **CHINESE** + * dbGap desc: **Chinese** + * dbGap table: **f41_rel1** + * PIC-SURE permissible values: No, Yes + * _phs000200.v11.pht001009.v6.phv00079322.v6_ + * dbGap name: **FILIPINO** + * dbGap desc: **Filipino** + * dbGap table: **f41_rel1** + * PIC-SURE permissible values: No, Yes + * _phs000200.v11.pht001009.v6.phv00079323.v6_ + * dbGap name: **JAPANESE** + * dbGap desc: **Japanese** + * dbGap table: **f41_rel1** + * PIC-SURE permissible values: No, Yes + * _phs000200.v11.pht001009.v6.phv00079324.v6_ + * dbGap name: **KOREAN** + * dbGap desc: **Korean** + * dbGap table: **f41_rel1** + * PIC-SURE permissible values: No, Yes + * _phs000200.v11.pht001009.v6.phv00079325.v6_ + * dbGap name: **VIETNAMESE** + * dbGap desc: **Vietnamese** + * dbGap table: **f41_rel1** + * PIC-SURE permissible values: No, Yes + * _phs000200.v11.pht001009.v6.phv00079326.v6_ + * dbGap name: **OTHERASIAN** + * dbGap desc: **Other Asian** + * dbGap table: **f41_rel1** + * PIC-SURE permissible values: No, Yes + * _phs000200.v11.pht001009.v6.phv00079327.v6_ + * dbGap name: **HAWAIIAN** + * dbGap desc: **Native Hawaiian** + * dbGap table: **f41_rel1** + * PIC-SURE permissible values: No, Yes + * _phs000200.v11.pht001009.v6.phv00079328.v6_ + * dbGap name: **GUAMANIAN** + * dbGap desc: **Guamanian or Chamorro** + * dbGap table: **f41_rel1** + * PIC-SURE permissible values: No, Yes + * _phs000200.v11.pht001009.v6.phv00079329.v6_ + * dbGap name: **SAMOAN** + * dbGap desc: **Samoan** + * dbGap table: **f41_rel1** + * PIC-SURE permissible values: No, Yes + * _phs000200.v11.pht001009.v6.phv00079330.v6_ + * dbGap name: **OTHRPACISL** + * dbGap desc: **Other Pacific Islander** + * dbGap table: **f41_rel1** + * PIC-SURE permissible values: No, Yes + * _phs000200.v11.pht001009.v6.phv00079331.v6_ + * dbGap name: **OTHERRACE** + * dbGap desc: **Some other race** + * dbGap table: **f41_rel1** + * PIC-SURE permissible values: No, Yes * **Function:** ```r harmonize <- function(phen_list){ @@ -1134,7 +1294,11 @@ * ### demographic/subcohort_1 -- **ARIC Atherosclerosis Risk in Communities (ARIC) Cohort**: * 1 component_study_variables - * _phs000280.v5.pht001440.v5.phv00098580.v4_. dbGap Name: **CONSENT**, Desc: **Restriction on Use/Storage of DNA and Other**, Table: **ARIC_Subject**. + * _phs000280.v5.pht001440.v5.phv00098580.v4_ + * dbGap name: **CONSENT** + * dbGap desc: **Restriction on Use/Storage of DNA and Other** + * dbGap table: **ARIC_Subject** + * varId _phv00098580_ not found in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -1149,7 +1313,11 @@ * ### demographic/subcohort_1 -- **CARDIA CARDIA Cohort**: * 1 component_study_variables - * _phs000285.v3.pht001554.v3.phv00112395.v2_. dbGap Name: **Consent**, Desc: **Consent group**, Table: **CARDIA_Cohort_Subject**. + * _phs000285.v3.pht001554.v3.phv00112395.v2_ + * dbGap name: **Consent** + * dbGap desc: **Consent group** + * dbGap table: **CARDIA_Cohort_Subject** + * varId _phv00112395_ not found in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -1164,7 +1332,11 @@ * ### demographic/subcohort_1 -- **CHS Cardiovascular Health Study (CHS) Cohort: an NHLBI-funded observational study of risk factors for cardiovascular disease in adults 65 years or older**: * 1 component_study_variables - * _phs000287.v6.pht001452.v1.phv00100290.v1_. dbGap Name: **PERSTAT**, Desc: **COHORT**, Table: **BASEBOTH**. + * _phs000287.v6.pht001452.v1.phv00100290.v1_ + * dbGap name: **PERSTAT** + * dbGap desc: **COHORT** + * dbGap table: **BASEBOTH** + * PIC-SURE permissible values: NEW COHORT, OLD COHORT * **Function:** ```r harmonize <- function(phen_list){ @@ -1184,7 +1356,9 @@ * ### demographic/subcohort_1 -- **COPDGene **: * 1 component_study_variables - * _phs000179.v5.pht002237.v3.phv00159560.v3_. No dbGap metadata available. + * _phs000179.v5.pht002237.v3.phv00159560.v3_ + * No dbGap metadata available + * PIC-SURE permissible values: Disease-Specific (COPD and Smoking) (DS-CS), Health/Medical/Biomedical (HMB) * **Function:** ```r harmonize <- function(phen_list){ @@ -1199,7 +1373,11 @@ * ### demographic/subcohort_1 -- **FHS Framingham Cohort**: * 1 component_study_variables - * _phs000007.v30.pht003099.v5.phv00177928.v5_. dbGap Name: **idtype**, Desc: **Framingham Heart Study cohort identifier**, Table: **vr_dates_2019_a_1175s**. + * _phs000007.v30.pht003099.v5.phv00177928.v5_ + * dbGap name: **idtype** + * dbGap desc: **Framingham Heart Study cohort identifier** + * dbGap table: **vr_dates_2019_a_1175s** + * PIC-SURE permissible values: Generation 3 Cohort, New Offspring Spouse Cohort, Offspring Cohort, Omni 1 Cohort, Omni 2 Cohort, Original Cohort * **Function:** ```r harmonize <- function(phen_list){ @@ -1222,7 +1400,11 @@ * ### demographic/subcohort_1 -- **HCHS_SOL Hispanic Community Health Study /Study of Latinos (HCHS/SOL)**: * 1 component_study_variables - * _phs000810.v1.pht004713.v1.phv00226241.v1_. dbGap Name: **CONSENT**, Desc: **Consent group**, Table: **HCHS_SOL_Cohort_Subject**. + * _phs000810.v1.pht004713.v1.phv00226241.v1_ + * dbGap name: **CONSENT** + * dbGap desc: **Consent group** + * dbGap table: **HCHS_SOL_Cohort_Subject** + * PIC-SURE permissible values: Health/Medical/Biomedical (HMB), Health/Medical/Biomedical (NPU) (HMB-NPU) * **Function:** ```r harmonize <- function(phen_list){ @@ -1237,7 +1419,11 @@ * ### demographic/subcohort_1 -- **JHS Jackson Heart Study (JHS) Cohort**: * 1 component_study_variables - * _phs000286.v5.pht001920.v4.phv00124546.v3_. dbGap Name: **CONSENT**, Desc: **Consent group as determined by DAC**, Table: **JHS_Subject**. + * _phs000286.v5.pht001920.v4.phv00124546.v3_ + * dbGap name: **CONSENT** + * dbGap desc: **Consent group as determined by DAC** + * dbGap table: **JHS_Subject** + * varId _phv00124546_ not found in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -1252,8 +1438,16 @@ * ### demographic/subcohort_1 -- **WHI Women's Health Initiative**: * 2 component_study_variables - * _phs000200.v11.pht001031.v6.phv00080424.v6_. dbGap Name: **CTFLAG**, Desc: **CT Participant**, Table: **rand_rel2**. - * _phs000200.v11.pht001031.v6.phv00080425.v6_. dbGap Name: **OSFLAG**, Desc: **OS Participant**, Table: **rand_rel2**. + * _phs000200.v11.pht001031.v6.phv00080424.v6_ + * dbGap name: **CTFLAG** + * dbGap desc: **CT Participant** + * dbGap table: **rand_rel2** + * PIC-SURE permissible values: No, Yes + * _phs000200.v11.pht001031.v6.phv00080425.v6_ + * dbGap name: **OSFLAG** + * dbGap desc: **OS Participant** + * dbGap table: **rand_rel2** + * PIC-SURE permissible values: No, Yes * **Function:** ```r harmonize <- function(phen_list){ diff --git a/resources/human-readable-harmonized-variable-documentation/generated-doc-pages/inflammation.md b/resources/human-readable-harmonized-variable-documentation/generated-doc-pages/inflammation.md index 58acc81..497f476 100644 --- a/resources/human-readable-harmonized-variable-documentation/generated-doc-pages/inflammation.md +++ b/resources/human-readable-harmonized-variable-documentation/generated-doc-pages/inflammation.md @@ -74,8 +74,14 @@ * ### inflammation/cd40_1 -- **FHS Framingham Cohort**: * 2 component_study_variables - * _phs000007.v29.pht000079.v6.phv00021687.v5_. No dbGap metadata available. - * _phs000007.v29.pht003099.v4.phv00177942.v4_. dbGap Name: **age7**, Desc: **Age at Exam 7**, Table: **vr_dates_2019_a_1175s**. + * _phs000007.v29.pht000079.v6.phv00021687.v5_ + * No dbGap metadata available + * No permissible values listed in PIC-SURE data dictionary + * _phs000007.v29.pht003099.v4.phv00177942.v4_ + * dbGap name: **age7** + * dbGap desc: **Age at Exam 7** + * dbGap table: **vr_dates_2019_a_1175s** + * No permissible values listed in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -99,8 +105,16 @@ * ### inflammation/cd40_1 -- **MESA Multi-Ethnic Study of Atherosclerosis (MESA) Cohort**: * 2 component_study_variables - * _phs000209.v13.pht001116.v10.phv00084442.v3_. dbGap Name: **age1c**, Desc: **AGE**, Table: **MESA_Exam1Main**. - * _phs000209.v13.pht001116.v10.phv00085021.v2_. dbGap Name: **cd40l1**, Desc: **CD40 LIGAND (pg/mL)**, Table: **MESA_Exam1Main**. + * _phs000209.v13.pht001116.v10.phv00084442.v3_ + * dbGap name: **age1c** + * dbGap desc: **AGE** + * dbGap table: **MESA_Exam1Main** + * No permissible values listed in PIC-SURE data dictionary + * _phs000209.v13.pht001116.v10.phv00085021.v2_ + * dbGap name: **cd40l1** + * dbGap desc: **CD40 LIGAND (pg/mL)** + * dbGap table: **MESA_Exam1Main** + * PIC-SURE permissible values: .25, .27, .293, .49, .521, .598, .607, .628, .638, .675, .685, .688, .697, .716, .728, .732, .734, .748, .788, .791, .793, .803, .81, .811, .825, .827, .838, .872, .878, .936, .95, .993, .994, .995, .998, 1.012, 1.017, 1.018, 1.021, 1.033, 1.071, 1.079, 1.081, 1.084, 1.1, 1.102, 1.11, 1.117, 1.118, 1.128, 1.153, 1.157, 1.158, 1.166, 1.168, 1.17, 1.172, 1.187, 1.188, 1.217, 1.22, 1.238, 1.245, 1.249, 1.257, 1.262, 1.264, 1.267, 1.274, 1.282, 1.283, 1.289, 1.292, 1.31, 1.312, 1.319, 1.322, 1.334, 1.336, 1.34, 1.346, 1.361, 1.373, 1.376, 1.382, 1.386, 1.387, 1.389, 1.395, 1.398, 1.408, 1.409, 1.42, 1.421, 1.429, 1.433, 1.437, 1.446, 1.448, 1.452, 1.461, 1.464, 1.469, 1.472, 1.473, 1.478, 1.484, 1.486, 1.492, 1.512, 1.514, 1.515, 1.529, 1.533, 1.545, 1.546, 1.553, 1.556, 1.564, 1.572, 1.574, 1.582, 1.585, 1.594, 1.596, 1.602, 1.606, 1.607, 1.616, 1.617, 1.618, 1.619, 1.621, 1.626, 1.635, 1.649, 1.661, 1.665, 1.675, 1.676, 1.677, 1.685, 1.686, 1.698, 1.701, 1.712, 1.717, 1.726, 1.728, 1.733, 1.736, 1.75, 1.753, 1.76, 1.761, 1.764, 1.765, 1.772, 1.78, 1.783, 1.785, 1.79, 1.805, 1.807, 1.808, 1.81, 1.813, 1.819, 1.828, 1.833, 1.834, 1.837, 1.844, 1.847, 1.852, 1.871, 1.872, 1.875, 1.88, 1.898, 1.899, 1.937, 1.938, 1.946, 1.96, 1.962, 1.969, 1.974, 1.983, 1.994, 10.043, 10.249, 10.466, 10.594, 10.782, 10.844, 10.85, 10.889, 11.298, 11.443, 11.657, 11.73, 11.831, 12.087, 13.927, 14.146, 16.995, 17.764, 18.977, 2.004, 2.009, 2.011, 2.016, 2.025, 2.031, 2.037, 2.04, 2.041, 2.049, 2.05, 2.053, 2.068, 2.069, 2.08, 2.081, 2.082, 2.087, 2.096, 2.101, 2.102, 2.104, 2.107, 2.108, 2.112, 2.115, 2.126, 2.134, 2.136, 2.141, 2.152, 2.158, 2.16, 2.17, 2.171, 2.176, 2.182, 2.183, 2.187, 2.197, 2.201, 2.209, 2.212, 2.213, 2.219, 2.222, 2.223, 2.227, 2.239, 2.24, 2.27, 2.274, 2.28, 2.281, 2.293, 2.297, 2.298, 2.3, 2.302, 2.304, 2.312, 2.32, 2.327, 2.329, 2.346, 2.355, 2.361, 2.375, 2.379, 2.382, 2.383, 2.396, 2.401, 2.408, 2.411, 2.415, 2.417, 2.437, 2.438, 2.45, 2.459, 2.467, 2.472, 2.483, 2.484, 2.487, 2.49, 2.497, 2.504, 2.506, 2.516, 2.528, 2.531, 2.534, 2.535, 2.536, 2.539, 2.54, 2.542, 2.551, 2.554, 2.563, 2.571, 2.577, 2.585, 2.598, 2.6, 2.611, 2.613, 2.614, 2.616, 2.625, 2.626, 2.627, 2.634, 2.635, 2.643, 2.655, 2.666, 2.668, 2.67, 2.679, 2.683, 2.69, 2.694, 2.698, 2.701, 2.703, 2.718, 2.724, 2.747, 2.752, 2.755, 2.756, 2.758, 2.763, 2.766, 2.77, 2.776, 2.782, 2.785, 2.788, 2.79, 2.795, 2.804, 2.819, 2.82, 2.831, 2.847, 2.854, 2.857, 2.861, 2.869, 2.877, 2.884, 2.903, 2.909, 2.918, 2.92, 2.949, 2.951, 2.956, 2.957, 2.958, 2.964, 2.97, 2.975, 2.981, 2.999, 24.6, 3.007, 3.01, 3.012, 3.021, 3.022, 3.029, 3.031, 3.035, 3.04, 3.044, 3.046, 3.053, 3.059, 3.078, 3.079, 3.08, 3.082, 3.088, 3.093, 3.096, 3.108, 3.116, 3.118, 3.132, 3.138, 3.141, 3.148, 3.149, 3.153, 3.154, 3.157, 3.165, 3.166, 3.169, 3.17, 3.175, 3.185, 3.198, 3.199, 3.2, 3.209, 3.217, 3.223, 3.236, 3.237, 3.252, 3.261, 3.262, 3.263, 3.275, 3.278, 3.279, 3.282, 3.296, 3.298, 3.301, 3.303, 3.308, 3.309, 3.312, 3.316, 3.32, 3.326, 3.327, 3.336, 3.344, 3.351, 3.364, 3.377, 3.382, 3.406, 3.408, 3.413, 3.428, 3.431, 3.439, 3.453, 3.461, 3.465, 3.479, 3.488, 3.493, 3.5, 3.502, 3.52, 3.522, 3.531, 3.551, 3.554, 3.57, 3.576, 3.579, 3.607, 3.613, 3.615, 3.618, 3.619, 3.621, 3.625, 3.642, 3.646, 3.657, 3.661, 3.668, 3.675, 3.677, 3.678, 3.695, 3.708, 3.709, 3.711, 3.721, 3.722, 3.728, 3.733, 3.741, 3.743, 3.744, 3.745, 3.749, 3.758, 3.762, 3.764, 3.776, 3.777, 3.779, 3.791, 3.803, 3.808, 3.816, 3.82, 3.822, 3.828, 3.833, 3.84, 3.846, 3.861, 3.866, 3.885, 3.891, 3.894, 3.895, 3.898, 3.908, 3.926, 3.931, 3.946, 3.959, 3.96, 3.97, 3.974, 3.982, 3.987, 4.012, 4.018, 4.026, 4.04, 4.042, 4.048, 4.053, 4.056, 4.064, 4.07, 4.075, 4.077, 4.078, 4.087, 4.088, 4.09, 4.092, 4.094, 4.1, 4.104, 4.109, 4.111, 4.122, 4.124, 4.129, 4.14, 4.141, 4.142, 4.172, 4.174, 4.196, 4.209, 4.224, 4.227, 4.231, 4.233, 4.247, 4.251, 4.255, 4.261, 4.264, 4.265, 4.268, 4.272, 4.284, 4.287, 4.3, 4.302, 4.335, 4.342, 4.374, 4.382, 4.39, 4.398, 4.401, 4.407, 4.422, 4.425, 4.428, 4.434, 4.438, 4.458, 4.46, 4.464, 4.466, 4.467, 4.484, 4.494, 4.499, 4.51, 4.516, 4.519, 4.521, 4.524, 4.53, 4.534, 4.541, 4.542, 4.556, 4.576, 4.58, 4.581, 4.595, 4.603, 4.607, 4.609, 4.628, 4.645, 4.685, 4.695, 4.71, 4.711, 4.75, 4.755, 4.756, 4.777, 4.781, 4.798, 4.801, 4.808, 4.834, 4.846, 4.878, 4.882, 4.885, 4.887, 4.89, 4.891, 4.895, 4.897, 4.922, 4.923, 4.926, 4.94, 4.944, 4.956, 4.96, 4.969, 4.985, 5.013, 5.015, 5.022, 5.033, 5.041, 5.051, 5.056, 5.083, 5.087, 5.098, 5.102, 5.109, 5.11, 5.114, 5.124, 5.127, 5.14, 5.144, 5.15, 5.153, 5.177, 5.186, 5.187, 5.193, 5.201, 5.21, 5.244, 5.263, 5.264, 5.276, 5.29, 5.298, 5.301, 5.324, 5.335, 5.36, 5.362, 5.38, 5.386, 5.387, 5.437, 5.438, 5.462, 5.467, 5.507, 5.518, 5.54, 5.55, 5.558, 5.564, 5.58, 5.612, 5.615, 5.617, 5.643, 5.645, 5.646, 5.648, 5.655, 5.665, 5.676, 5.697, 5.726, 5.729, 5.742, 5.759, 5.783, 5.796, 5.805, 5.82, 5.822, 5.824, 5.825, 5.859, 5.865, 5.867, 5.875, 5.896, 5.9, 5.917, 5.936, 5.953, 5.955, 5.96, 5.975, 5.981, 5.995, 5.996, 6.014, 6.03, 6.031, 6.042, 6.047, 6.05, 6.062, 6.065, 6.081, 6.091, 6.092, 6.096, 6.116, 6.117, 6.134, 6.135, 6.142, 6.187, 6.191, 6.199, 6.247, 6.261, 6.275, 6.293, 6.296, 6.302, 6.314, 6.32, 6.355, 6.363, 6.365, 6.38, 6.399, 6.408, 6.423, 6.479, 6.482, 6.502, 6.51, 6.527, 6.564, 6.591, 6.601, 6.636, 6.64, 6.642, 6.643, 6.661, 6.687, 6.688, 6.709, 6.717, 6.765, 6.775, 6.784, 6.798, 6.8, 6.853, 6.871, 6.875, 6.915, 6.92, 6.924, 6.931, 6.945, 6.947, 6.948, 6.95, 6.968, 6.978, 6.983, 6.987, 7.006, 7.007, 7.016, 7.022, 7.048, 7.053, 7.075, 7.107, 7.17, 7.174, 7.211, 7.254, 7.266, 7.268, 7.288, 7.289, 7.351, 7.384, 7.395, 7.403, 7.408, 7.512, 7.514, 7.518, 7.54, 7.544, 7.556, 7.557, 7.594, 7.653, 7.697, 7.709, 7.804, 7.832, 7.862, 7.921, 7.959, 8.013, 8.021, 8.022, 8.04, 8.077, 8.091, 8.113, 8.114, 8.173, 8.186, 8.199, 8.204, 8.24, 8.249, 8.259, 8.289, 8.301, 8.319, 8.321, 8.366, 8.374, 8.403, 8.406, 8.456, 8.512, 8.584, 8.59, 8.593, 8.618, 8.629, 8.639, 8.67, 8.697, 8.709, 8.713, 8.731, 8.766, 8.774, 8.776, 8.819, 8.961, 8.971, 9.139, 9.208, 9.304, 9.481, 9.63, 9.823, 9.854, 9.908, 9.916, 9.945 * **Function:** ```r harmonize <- function(phen_list){ @@ -220,8 +234,14 @@ * ### inflammation/crp_1 -- **ARIC Atherosclerosis Risk in Communities (ARIC) Cohort**: * 2 component_study_variables - * _phs000280.v4.pht006431.v1.phv00295623.v1_. No dbGap metadata available. - * _phs000280.v4.pht006444.v1.phv00296696.v1_. dbGap Name: **LIP33**, Desc: **High sensitive C reactive protein [Central Lab Data]**, Table: **LIP**. + * _phs000280.v4.pht006431.v1.phv00295623.v1_ + * No dbGap metadata available + * varId _phv00295623_ not found in PIC-SURE data dictionary + * _phs000280.v4.pht006444.v1.phv00296696.v1_ + * dbGap name: **LIP33** + * dbGap desc: **High sensitive C reactive protein [Central Lab Data]** + * dbGap table: **LIP** + * varId _phv00296696_ not found in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -252,8 +272,16 @@ * ### inflammation/crp_1 -- **CARDIA CARDIA Cohort**: * 2 component_study_variables - * _phs000285.v3.pht001851.v2.phv00120748.v2_. dbGap Name: **EX6_AGE**, Desc: **CALCULATED AGE AT EXAM 6**, Table: **F1REF**. - * _phs000285.v3.pht001853.v2.phv00120759.v2_. dbGap Name: **FL6CRPBN**, Desc: **RERUN CRP (uG/ml - BNII METHOD)**, Table: **F2CRP**. + * _phs000285.v3.pht001851.v2.phv00120748.v2_ + * dbGap name: **EX6_AGE** + * dbGap desc: **CALCULATED AGE AT EXAM 6** + * dbGap table: **F1REF** + * varId _phv00120748_ not found in PIC-SURE data dictionary + * _phs000285.v3.pht001853.v2.phv00120759.v2_ + * dbGap name: **FL6CRPBN** + * dbGap desc: **RERUN CRP (uG/ml - BNII METHOD)** + * dbGap table: **F2CRP** + * varId _phv00120759_ not found in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -281,8 +309,16 @@ * ### inflammation/crp_1 -- **CHS Cardiovascular Health Study (CHS) Cohort: an NHLBI-funded observational study of risk factors for cardiovascular disease in adults 65 years or older**: * 2 component_study_variables - * _phs000287.v6.pht001452.v1.phv00100487.v1_. dbGap Name: **AGEBL**, Desc: **CALCULATED AGE AT BASELINE**, Table: **BASEBOTH**. - * _phs000287.v6.pht001452.v1.phv00100499.v1_. dbGap Name: **CRPBLADJ**, Desc: **C-reactive protein, adjusted original va**, Table: **BASEBOTH**. + * _phs000287.v6.pht001452.v1.phv00100487.v1_ + * dbGap name: **AGEBL** + * dbGap desc: **CALCULATED AGE AT BASELINE** + * dbGap table: **BASEBOTH** + * No permissible values listed in PIC-SURE data dictionary + * _phs000287.v6.pht001452.v1.phv00100499.v1_ + * dbGap name: **CRPBLADJ** + * dbGap desc: **C-reactive protein, adjusted original va** + * dbGap table: **BASEBOTH** + * No permissible values listed in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -307,8 +343,16 @@ * ### inflammation/crp_1 -- **HCHS_SOL Hispanic Community Health Study /Study of Latinos (HCHS/SOL)**: * 2 component_study_variables - * _phs000810.v1.pht004715.v1.phv00226251.v1_. dbGap Name: **AGE**, Desc: **Age**, Table: **HCHS_SOL_Cohort_Subject_Phenotypes**. - * _phs000810.v1.pht004715.v1.phv00258066.v1_. dbGap Name: **LABA91**, Desc: **High-sensitivity C-Reactive Protein (mg/L) (LABA91)**, Table: **HCHS_SOL_Cohort_Subject_Phenotypes**. + * _phs000810.v1.pht004715.v1.phv00226251.v1_ + * dbGap name: **AGE** + * dbGap desc: **Age** + * dbGap table: **HCHS_SOL_Cohort_Subject_Phenotypes** + * No permissible values listed in PIC-SURE data dictionary + * _phs000810.v1.pht004715.v1.phv00258066.v1_ + * dbGap name: **LABA91** + * dbGap desc: **High-sensitivity C-Reactive Protein (mg/L) (LABA91)** + * dbGap table: **HCHS_SOL_Cohort_Subject_Phenotypes** + * No permissible values listed in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -333,9 +377,19 @@ * ### inflammation/crp_1 -- **JHS Jackson Heart Study (JHS) Cohort**: * 3 component_study_variables - * _phs000286.v5.pht001945.v1.phv00125940.v1_. dbGap Name: **Hscrp_cresult**, Desc: **Character results for Hscrp [Visit 1]**, Table: **cena**. - * _phs000286.v5.pht001945.v1.phv00125941.v1_. dbGap Name: **HSCRP**, Desc: **Hscrp: high sensitivity C-reactive protein in mg/dL [Visit 1]**, Table: **cena**. - * _phs000286.v5.pht001949.v1.phv00126009.v1_. No dbGap metadata available. + * _phs000286.v5.pht001945.v1.phv00125940.v1_ + * dbGap name: **Hscrp_cresult** + * dbGap desc: **Character results for Hscrp [Visit 1]** + * dbGap table: **cena** + * varId _phv00125940_ not found in PIC-SURE data dictionary + * _phs000286.v5.pht001945.v1.phv00125941.v1_ + * dbGap name: **HSCRP** + * dbGap desc: **Hscrp: high sensitivity C-reactive protein in mg/dL [Visit 1]** + * dbGap table: **cena** + * varId _phv00125941_ not found in PIC-SURE data dictionary + * _phs000286.v5.pht001949.v1.phv00126009.v1_ + * No dbGap metadata available + * varId _phv00126009_ not found in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -419,11 +473,31 @@ * ### inflammation/eselectin_1 -- **MESA Multi-Ethnic Study of Atherosclerosis (MESA) Cohort**: * 5 component_study_variables - * _phs000209.v13.pht001111.v4.phv00082639.v2_. dbGap Name: **age1c**, Desc: **AGE**, Table: **MESA_AirNRExamMain**. - * _phs000209.v13.pht001111.v4.phv00082969.v1_. dbGap Name: **eselect1**, Desc: **E-SELECTIN (ng/mL)**, Table: **MESA_AirNRExamMain**. - * _phs000209.v13.pht001111.v4.phv00082970.v1_. dbGap Name: **eselect1m**, Desc: **E-SELECTIN MISSING VALUE**, Table: **MESA_AirNRExamMain**. - * _phs000209.v13.pht001116.v10.phv00084442.v3_. dbGap Name: **age1c**, Desc: **AGE**, Table: **MESA_Exam1Main**. - * _phs000209.v13.pht001116.v10.phv00085022.v2_. dbGap Name: **eselect1**, Desc: **E-SELECTIN (ng/mL)**, Table: **MESA_Exam1Main**. + * _phs000209.v13.pht001111.v4.phv00082639.v2_ + * dbGap name: **age1c** + * dbGap desc: **AGE** + * dbGap table: **MESA_AirNRExamMain** + * No permissible values listed in PIC-SURE data dictionary + * _phs000209.v13.pht001111.v4.phv00082969.v1_ + * dbGap name: **eselect1** + * dbGap desc: **E-SELECTIN (ng/mL)** + * dbGap table: **MESA_AirNRExamMain** + * No permissible values listed in PIC-SURE data dictionary + * _phs000209.v13.pht001111.v4.phv00082970.v1_ + * dbGap name: **eselect1m** + * dbGap desc: **E-SELECTIN MISSING VALUE** + * dbGap table: **MESA_AirNRExamMain** + * varId _phv00082970_ not found in PIC-SURE data dictionary + * _phs000209.v13.pht001116.v10.phv00084442.v3_ + * dbGap name: **age1c** + * dbGap desc: **AGE** + * dbGap table: **MESA_Exam1Main** + * No permissible values listed in PIC-SURE data dictionary + * _phs000209.v13.pht001116.v10.phv00085022.v2_ + * dbGap name: **eselect1** + * dbGap desc: **E-SELECTIN (ng/mL)** + * dbGap table: **MESA_Exam1Main** + * PIC-SURE permissible values: 10.11, 10.487, 10.975, 101.09, 101.32, 102.23, 102.62, 102.97, 104.8, 105.81, 105.97, 106.12, 106.51, 106.63, 107.5, 108.75, 109.51, 11.698, 110.53, 111.71, 113.2, 115.48, 115.89, 115.94, 116.13, 117.87, 118.03, 118.78, 119.31, 119.85, 12.167, 12.66, 12.784, 120.38, 120.55, 120.83, 120.92, 121.08, 121.24, 122.01, 124.01, 124.29, 126.45, 128.13, 13.146, 13.514, 13.929, 131.6, 139.36, 139.59, 14.103, 14.957, 143.01, 15.378, 15.379, 15.491, 15.652, 15.704, 15.863, 15.957, 156.2, 16.09, 16.301, 16.325, 16.468, 16.829, 16.897, 160.33, 160.63, 17.143, 17.168, 17.271, 17.337, 17.426, 17.561, 17.651, 17.671, 17.794, 17.972, 18.208, 18.763, 181.64, 184.73, 19.147, 19.258, 19.325, 19.692, 19.866, 19.869, 20.059, 20.239, 20.3, 20.416, 20.599, 20.71, 201.37, 21.125, 21.352, 21.59, 21.794, 21.812, 21.955, 22.234, 22.307, 22.445, 22.477, 22.6, 22.717, 22.803, 23.178, 23.189, 23.418, 23.499, 23.555, 23.578, 23.762, 23.958, 24.04, 24.054, 24.121, 24.237, 24.366, 24.38, 24.556, 24.573, 24.672, 24.988, 25.025, 25.177, 25.535, 25.613, 25.686, 25.727, 25.85, 25.986, 26.213, 26.359, 26.579, 26.621, 26.638, 26.648, 26.689, 26.704, 26.717, 26.98, 27.022, 27.204, 27.406, 27.476, 27.534, 27.911, 27.913, 27.955, 27.97, 28.146, 28.169, 28.387, 28.441, 28.539, 28.563, 28.608, 28.665, 28.674, 28.741, 28.749, 28.855, 28.904, 29.031, 29.206, 29.207, 29.321, 29.369, 29.499, 29.551, 29.592, 29.653, 29.727, 29.778, 29.888, 30.233, 30.248, 30.335, 30.347, 30.373, 30.434, 30.57, 30.585, 30.641, 30.725, 30.761, 30.791, 30.882, 30.905, 30.922, 30.945, 30.952, 30.996, 31.027, 31.185, 31.201, 31.277, 31.315, 31.331, 31.348, 31.379, 31.603, 31.742, 31.894, 31.927, 32.009, 32.306, 32.369, 32.385, 32.45, 32.503, 32.544, 32.56, 32.564, 32.645, 32.772, 32.831, 32.956, 33.132, 33.143, 33.199, 33.284, 33.305, 33.421, 33.43, 33.494, 33.585, 33.626, 33.762, 33.891, 33.942, 34.119, 34.125, 34.228, 34.263, 34.329, 34.351, 34.502, 34.529, 34.53, 34.566, 34.588, 34.605, 34.61, 34.662, 34.737, 34.759, 34.788, 34.872, 34.91, 34.938, 34.997, 35.278, 35.329, 35.377, 35.443, 35.529, 35.532, 35.688, 35.851, 35.909, 35.927, 35.993, 36.014, 36.31, 36.454, 36.468, 36.632, 36.696, 36.739, 36.769, 36.923, 36.936, 36.995, 37.156, 37.191, 37.212, 37.213, 37.486, 37.522, 37.638, 37.754, 37.8, 37.873, 37.905, 37.937, 38.05, 38.174, 38.271, 38.288, 38.37, 38.562, 38.566, 38.65, 38.785, 38.906, 38.909, 39.039, 39.186, 39.298, 39.454, 39.478, 39.61, 39.617, 39.641, 39.733, 39.839, 39.9, 39.917, 39.928, 39.994, 4.652, 4.789, 40.058, 40.168, 40.371, 40.428, 40.473, 40.609, 40.638, 40.651, 40.668, 40.736, 40.863, 40.901, 40.93, 41.055, 41.19, 41.216, 41.36, 41.363, 41.41, 41.445, 41.449, 41.519, 41.577, 41.637, 41.703, 41.715, 41.791, 41.866, 41.879, 41.908, 41.97, 41.999, 42.096, 42.126, 42.168, 42.217, 42.237, 42.303, 42.424, 42.444, 42.582, 42.7, 42.72, 42.745, 42.764, 42.815, 42.831, 42.856, 42.962, 42.98, 42.996, 43.014, 43.035, 43.079, 43.114, 43.132, 43.138, 43.317, 43.371, 43.41, 43.431, 43.494, 43.502, 43.545, 43.686, 43.693, 43.729, 43.782, 43.893, 43.945, 43.962, 43.965, 43.984, 44.02, 44.166, 44.169, 44.192, 44.389, 44.42, 44.621, 44.758, 44.771, 44.874, 44.953, 44.97, 44.976, 45.003, 45.012, 45.02, 45.042, 45.049, 45.078, 45.25, 45.3, 45.532, 45.731, 45.754, 45.76, 45.789, 45.808, 45.893, 45.895, 45.944, 45.962, 45.974, 46.205, 46.267, 46.305, 46.33, 46.359, 46.459, 46.643, 46.74, 46.79, 46.832, 47.008, 47.04, 47.053, 47.117, 47.118, 47.135, 47.27, 47.296, 47.312, 47.331, 47.342, 47.44, 47.49, 47.58, 47.692, 47.74, 47.827, 47.884, 48.016, 48.036, 48.04, 48.045, 48.116, 48.152, 48.223, 48.262, 48.303, 48.39, 48.424, 48.435, 48.437, 48.514, 48.626, 48.647, 48.652, 48.732, 48.773, 48.775, 48.819, 48.835, 48.861, 48.936, 49.053, 49.135, 49.374, 49.439, 49.548, 49.566, 49.701, 49.721, 49.76, 49.821, 49.9, 49.903, 49.957, 50.053, 50.064, 50.114, 50.125, 50.166, 50.195, 50.221, 50.239, 50.262, 50.318, 50.345, 50.368, 50.413, 50.533, 50.576, 50.591, 50.686, 50.722, 50.851, 50.898, 50.904, 50.988, 51.005, 51.114, 51.302, 51.369, 51.411, 51.496, 51.623, 51.627, 51.643, 51.657, 51.699, 51.726, 51.772, 51.809, 51.813, 51.818, 51.876, 51.968, 51.97, 52.094, 52.098, 52.13, 52.167, 52.29, 52.299, 52.325, 52.33, 52.391, 52.434, 52.453, 52.462, 52.511, 52.567, 52.681, 52.717, 52.768, 52.791, 52.864, 52.902, 52.918, 52.938, 53.014, 53.037, 53.097, 53.157, 53.238, 53.303, 53.375, 53.449, 53.466, 53.481, 53.492, 53.598, 53.621, 53.631, 53.643, 53.729, 53.756, 53.944, 54.031, 54.106, 54.151, 54.18, 54.372, 54.428, 54.498, 54.503, 54.558, 54.561, 54.581, 54.584, 54.591, 54.624, 54.644, 54.649, 54.745, 54.764, 54.802, 54.824, 54.875, 54.878, 54.89, 54.902, 54.918, 55.111, 55.203, 55.205, 55.26, 55.323, 55.374, 55.481, 55.55, 55.579, 55.591, 55.875, 55.889, 55.956, 55.964, 56.021, 56.043, 56.048, 56.077, 56.097, 56.179, 56.198, 56.256, 56.445, 56.462, 56.511, 56.636, 56.71, 56.866, 56.901, 56.909, 57.018, 57.019, 57.175, 57.275, 57.345, 57.483, 57.519, 57.576, 57.597, 57.887, 57.895, 57.898, 57.93, 57.945, 58.072, 58.098, 58.217, 58.353, 58.367, 58.374, 58.447, 58.526, 58.528, 58.543, 58.56, 58.892, 59.019, 59.054, 59.148, 59.185, 59.276, 59.316, 59.342, 59.536, 59.706, 59.714, 59.731, 59.851, 59.875, 59.895, 59.93, 60.021, 60.08, 60.172, 60.212, 60.236, 60.241, 60.307, 60.361, 60.414, 60.447, 60.516, 60.579, 60.587, 60.606, 60.655, 60.714, 60.764, 60.766, 60.769, 60.852, 60.878, 61.002, 61.115, 61.178, 61.269, 61.375, 61.453, 61.496, 61.598, 61.609, 61.617, 61.648, 61.779, 61.798, 61.867, 62.083, 62.085, 62.103, 62.142, 62.242, 62.283, 62.349, 62.487, 62.598, 63.05, 63.053, 63.169, 63.282, 63.464, 63.545, 63.551, 63.741, 63.847, 64.024, 64.172, 64.214, 64.32, 64.438, 64.503, 64.583, 64.608, 64.728, 64.818, 64.927, 64.937, 65.036, 65.041, 65.06, 65.063, 65.075, 65.101, 65.436, 65.475, 65.507, 65.508, 65.546, 65.796, 65.864, 66.082, 66.214, 66.221, 66.329, 66.33, 66.345, 66.384, 66.719, 66.766, 66.899, 67.115, 67.171, 67.199, 67.326, 67.344, 67.561, 67.721, 67.818, 67.858, 67.967, 67.978, 68.089, 68.181, 68.404, 68.415, 68.507, 68.72, 68.785, 68.799, 68.84, 68.891, 69.04, 69.279, 69.412, 69.551, 69.599, 69.629, 69.99, 70.007, 70.02, 70.077, 70.254, 70.36, 70.52, 70.526, 70.722, 71.037, 71.042, 71.139, 71.207, 71.258, 71.328, 71.446, 71.57, 71.971, 72.02, 72.067, 72.128, 72.371, 72.403, 72.446, 72.543, 72.606, 72.926, 72.976, 73.041, 73.103, 73.104, 73.211, 73.359, 73.371, 73.784, 73.827, 73.84, 74.187, 74.243, 74.353, 74.376, 74.46, 74.599, 74.604, 75.069, 75.45, 75.466, 75.55, 75.723, 75.782, 75.824, 75.967, 76.079, 76.207, 76.283, 76.519, 76.672, 76.673, 76.929, 76.93, 77.192, 77.267, 77.393, 77.408, 77.515, 77.559, 77.622, 77.707, 77.974, 78.046, 78.056, 78.381, 78.398, 78.692, 78.922, 78.979, 79.003, 79.085, 79.299, 79.767, 79.799, 79.809, 79.857, 79.926, 80.175, 80.522, 80.578, 80.701, 80.711, 80.796, 80.95, 81.141, 81.38, 81.598, 82.106, 82.259, 82.55, 82.675, 83.022, 83.569, 83.653, 83.863, 84.309, 84.367, 85.712, 85.89, 85.94, 85.972, 86.056, 86.472, 86.59, 86.693, 86.808, 86.859, 86.907, 86.965, 87.38, 87.441, 87.704, 87.72, 88.027, 88.089, 88.302, 88.421, 88.733, 89.166, 9.911, 90.421, 91.168, 91.498, 91.779, 92.108, 92.444, 92.602, 93.064, 93.123, 93.384, 93.451, 93.646, 94.965, 95.607, 95.748, 95.786, 95.869, 95.918, 96.666, 97.261, 97.281, 97.427, 97.561, 97.796, 97.846, 98.247, 98.527, 98.562, 98.73, 98.947, 99.608, 99.869 * **Function:** ```r harmonize <- function(phen_list){ @@ -522,8 +596,16 @@ * ### inflammation/icam1_1 -- **CARDIA CARDIA Cohort**: * 2 component_study_variables - * _phs000285.v3.pht001697.v2.phv00116390.v2_. dbGap Name: **EX3_AGE**, Desc: **CALCULATED AGE AT EXAM 3**, Table: **C1REF**. - * _phs000285.v3.pht001699.v2.phv00116396.v2_. dbGap Name: **sICAM1**, Desc: **SICAM1**, Table: **CARE_ICAM**. + * _phs000285.v3.pht001697.v2.phv00116390.v2_ + * dbGap name: **EX3_AGE** + * dbGap desc: **CALCULATED AGE AT EXAM 3** + * dbGap table: **C1REF** + * varId _phv00116390_ not found in PIC-SURE data dictionary + * _phs000285.v3.pht001699.v2.phv00116396.v2_ + * dbGap name: **sICAM1** + * dbGap desc: **SICAM1** + * dbGap table: **CARE_ICAM** + * varId _phv00116396_ not found in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list) { @@ -550,8 +632,16 @@ * ### inflammation/icam1_1 -- **CHS Cardiovascular Health Study (CHS) Cohort: an NHLBI-funded observational study of risk factors for cardiovascular disease in adults 65 years or older**: * 2 component_study_variables - * _phs000287.v6.pht001449.v1.phv00098764.v1_. dbGap Name: **ICAM1**, Desc: **BASELINE ICAM-1 -sample**, Table: **ADDITIONAL_BIOMARKERS**. - * _phs000287.v6.pht001452.v1.phv00100487.v1_. dbGap Name: **AGEBL**, Desc: **CALCULATED AGE AT BASELINE**, Table: **BASEBOTH**. + * _phs000287.v6.pht001449.v1.phv00098764.v1_ + * dbGap name: **ICAM1** + * dbGap desc: **BASELINE ICAM-1 -sample** + * dbGap table: **ADDITIONAL_BIOMARKERS** + * No permissible values listed in PIC-SURE data dictionary + * _phs000287.v6.pht001452.v1.phv00100487.v1_ + * dbGap name: **AGEBL** + * dbGap desc: **CALCULATED AGE AT BASELINE** + * dbGap table: **BASEBOTH** + * No permissible values listed in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -615,9 +705,21 @@ * ### inflammation/il10_1 -- **MESA Multi-Ethnic Study of Atherosclerosis (MESA) Cohort**: * 3 component_study_variables - * _phs000209.v13.pht001116.v10.phv00084442.v3_. dbGap Name: **age1c**, Desc: **AGE**, Table: **MESA_Exam1Main**. - * _phs000209.v13.pht002099.v2.phv00142666.v2_. dbGap Name: **il10a1**, Desc: **INTERLEUKIN-10**, Table: **MESA_AncilMesaIL10**. - * _phs000209.v13.pht002099.v2.phv00142667.v2_. dbGap Name: **il10a1m**, Desc: **MISSING INTERLEUKIN-10 VALUE: REASON**, Table: **MESA_AncilMesaIL10**. + * _phs000209.v13.pht001116.v10.phv00084442.v3_ + * dbGap name: **age1c** + * dbGap desc: **AGE** + * dbGap table: **MESA_Exam1Main** + * No permissible values listed in PIC-SURE data dictionary + * _phs000209.v13.pht002099.v2.phv00142666.v2_ + * dbGap name: **il10a1** + * dbGap desc: **INTERLEUKIN-10** + * dbGap table: **MESA_AncilMesaIL10** + * No permissible values listed in PIC-SURE data dictionary + * _phs000209.v13.pht002099.v2.phv00142667.v2_ + * dbGap name: **il10a1m** + * dbGap desc: **MISSING INTERLEUKIN-10 VALUE: REASON** + * dbGap table: **MESA_AncilMesaIL10** + * PIC-SURE permissible values: High > 10,000, Low < 0.13 * **Function:** ```r harmonize <- function(phen_list) { @@ -688,8 +790,14 @@ * ### inflammation/il18_1 -- **FHS Framingham Cohort**: * 2 component_study_variables - * _phs000007.v29.pht000671.v5.phv00066686.v4_. No dbGap metadata available. - * _phs000007.v29.pht003099.v4.phv00177942.v4_. dbGap Name: **age7**, Desc: **Age at Exam 7**, Table: **vr_dates_2019_a_1175s**. + * _phs000007.v29.pht000671.v5.phv00066686.v4_ + * No dbGap metadata available + * No permissible values listed in PIC-SURE data dictionary + * _phs000007.v29.pht003099.v4.phv00177942.v4_ + * dbGap name: **age7** + * dbGap desc: **Age at Exam 7** + * dbGap table: **vr_dates_2019_a_1175s** + * No permissible values listed in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -806,9 +914,21 @@ * ### inflammation/il6_1 -- **CARDIA CARDIA Cohort**: * 3 component_study_variables - * _phs000285.v3.pht001851.v2.phv00120748.v2_. dbGap Name: **EX6_AGE**, Desc: **CALCULATED AGE AT EXAM 6**, Table: **F1REF**. - * _phs000285.v3.pht001862.v2.phv00121064.v2_. dbGap Name: **FL6IL6**, Desc: **IL6 PG/ML**, Table: **F2IGFIL**. - * _phs000285.v3.pht001862.v2.phv00121065.v2_. dbGap Name: **FL6IL6CM**, Desc: **IL6 COMMENTS**, Table: **F2IGFIL**. + * _phs000285.v3.pht001851.v2.phv00120748.v2_ + * dbGap name: **EX6_AGE** + * dbGap desc: **CALCULATED AGE AT EXAM 6** + * dbGap table: **F1REF** + * varId _phv00120748_ not found in PIC-SURE data dictionary + * _phs000285.v3.pht001862.v2.phv00121064.v2_ + * dbGap name: **FL6IL6** + * dbGap desc: **IL6 PG/ML** + * dbGap table: **F2IGFIL** + * varId _phv00121064_ not found in PIC-SURE data dictionary + * _phs000285.v3.pht001862.v2.phv00121065.v2_ + * dbGap name: **FL6IL6CM** + * dbGap desc: **IL6 COMMENTS** + * dbGap table: **F2IGFIL** + * varId _phv00121065_ not found in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -842,8 +962,16 @@ * ### inflammation/il6_1 -- **CHS Cardiovascular Health Study (CHS) Cohort: an NHLBI-funded observational study of risk factors for cardiovascular disease in adults 65 years or older**: * 2 component_study_variables - * _phs000287.v6.pht001452.v1.phv00100487.v1_. dbGap Name: **AGEBL**, Desc: **CALCULATED AGE AT BASELINE**, Table: **BASEBOTH**. - * _phs000287.v6.pht001452.v1.phv00100500.v1_. dbGap Name: **IL6BL**, Desc: **IL-6 at baseline (pg/ml)**, Table: **BASEBOTH**. + * _phs000287.v6.pht001452.v1.phv00100487.v1_ + * dbGap name: **AGEBL** + * dbGap desc: **CALCULATED AGE AT BASELINE** + * dbGap table: **BASEBOTH** + * No permissible values listed in PIC-SURE data dictionary + * _phs000287.v6.pht001452.v1.phv00100500.v1_ + * dbGap name: **IL6BL** + * dbGap desc: **IL-6 at baseline (pg/ml)** + * dbGap table: **BASEBOTH** + * No permissible values listed in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -868,9 +996,21 @@ * ### inflammation/il6_1 -- **MESA Multi-Ethnic Study of Atherosclerosis (MESA) Cohort**: * 3 component_study_variables - * _phs000209.v13.pht001116.v10.phv00084442.v3_. dbGap Name: **age1c**, Desc: **AGE**, Table: **MESA_Exam1Main**. - * _phs000209.v13.pht001116.v10.phv00085009.v2_. dbGap Name: **il61**, Desc: **INTERLEUKIN-6 (IL-6) (pg/mL)**, Table: **MESA_Exam1Main**. - * _phs000209.v13.pht001116.v10.phv00085010.v2_. dbGap Name: **il61M**, Desc: **EXCEPTIONAL MISSING IL61**, Table: **MESA_Exam1Main**. + * _phs000209.v13.pht001116.v10.phv00084442.v3_ + * dbGap name: **age1c** + * dbGap desc: **AGE** + * dbGap table: **MESA_Exam1Main** + * No permissible values listed in PIC-SURE data dictionary + * _phs000209.v13.pht001116.v10.phv00085009.v2_ + * dbGap name: **il61** + * dbGap desc: **INTERLEUKIN-6 (IL-6) (pg/mL)** + * dbGap table: **MESA_Exam1Main** + * No permissible values listed in PIC-SURE data dictionary + * _phs000209.v13.pht001116.v10.phv00085010.v2_ + * dbGap name: **il61M** + * dbGap desc: **EXCEPTIONAL MISSING IL61** + * dbGap table: **MESA_Exam1Main** + * PIC-SURE permissible values: INVALID (UNREPORTABLE) RESULT, VALUE < 0.09 (BELOW MEASUREMENT LIMITS), VALUE > 13 * **Function:** ```r harmonize <- function(phen_list){ @@ -955,13 +1095,35 @@ * ### inflammation/isoprostane_8_epi_pgf2a_1 -- **FHS Framingham Cohort**: * 7 component_study_variables - * _phs000007.v29.pht000162.v6.phv00023800.v5_. No dbGap metadata available. - * _phs000007.v29.pht002852.v2.phv00171864.v2_. No dbGap metadata available. - * _phs000007.v29.pht002853.v4.phv00171873.v4_. No dbGap metadata available. - * _phs000007.v29.pht003099.v4.phv00177928.v4_. dbGap Name: **idtype**, Desc: **Framingham Heart Study cohort identifier**, Table: **vr_dates_2019_a_1175s**. - * _phs000007.v29.pht003099.v4.phv00177930.v4_. dbGap Name: **age1**, Desc: **Age at Exam 1**, Table: **vr_dates_2019_a_1175s**. - * _phs000007.v29.pht003099.v4.phv00177934.v4_. dbGap Name: **age3**, Desc: **Age at Exam 3**, Table: **vr_dates_2019_a_1175s**. - * _phs000007.v29.pht003099.v4.phv00177942.v4_. dbGap Name: **age7**, Desc: **Age at Exam 7**, Table: **vr_dates_2019_a_1175s**. + * _phs000007.v29.pht000162.v6.phv00023800.v5_ + * No dbGap metadata available + * No permissible values listed in PIC-SURE data dictionary + * _phs000007.v29.pht002852.v2.phv00171864.v2_ + * No dbGap metadata available + * No permissible values listed in PIC-SURE data dictionary + * _phs000007.v29.pht002853.v4.phv00171873.v4_ + * No dbGap metadata available + * No permissible values listed in PIC-SURE data dictionary + * _phs000007.v29.pht003099.v4.phv00177928.v4_ + * dbGap name: **idtype** + * dbGap desc: **Framingham Heart Study cohort identifier** + * dbGap table: **vr_dates_2019_a_1175s** + * PIC-SURE permissible values: Generation 3 Cohort, New Offspring Spouse Cohort, Offspring Cohort, Omni 1 Cohort, Omni 2 Cohort, Original Cohort + * _phs000007.v29.pht003099.v4.phv00177930.v4_ + * dbGap name: **age1** + * dbGap desc: **Age at Exam 1** + * dbGap table: **vr_dates_2019_a_1175s** + * No permissible values listed in PIC-SURE data dictionary + * _phs000007.v29.pht003099.v4.phv00177934.v4_ + * dbGap name: **age3** + * dbGap desc: **Age at Exam 3** + * dbGap table: **vr_dates_2019_a_1175s** + * No permissible values listed in PIC-SURE data dictionary + * _phs000007.v29.pht003099.v4.phv00177942.v4_ + * dbGap name: **age7** + * dbGap desc: **Age at Exam 7** + * dbGap table: **vr_dates_2019_a_1175s** + * No permissible values listed in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -1060,8 +1222,16 @@ * ### inflammation/lppla2_act_1 -- **CHS Cardiovascular Health Study (CHS) Cohort: an NHLBI-funded observational study of risk factors for cardiovascular disease in adults 65 years or older**: * 2 component_study_variables - * _phs000287.v6.pht001449.v1.phv00098770.v1_. dbGap Name: **LPPLA2AC**, Desc: **Baseline LP-PLA2 Activity (nmols/min/mL)**, Table: **ADDITIONAL_BIOMARKERS**. - * _phs000287.v6.pht001452.v1.phv00100487.v1_. dbGap Name: **AGEBL**, Desc: **CALCULATED AGE AT BASELINE**, Table: **BASEBOTH**. + * _phs000287.v6.pht001449.v1.phv00098770.v1_ + * dbGap name: **LPPLA2AC** + * dbGap desc: **Baseline LP-PLA2 Activity (nmols/min/mL)** + * dbGap table: **ADDITIONAL_BIOMARKERS** + * No permissible values listed in PIC-SURE data dictionary + * _phs000287.v6.pht001452.v1.phv00100487.v1_ + * dbGap name: **AGEBL** + * dbGap desc: **CALCULATED AGE AT BASELINE** + * dbGap table: **BASEBOTH** + * No permissible values listed in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -1086,13 +1256,35 @@ * ### inflammation/lppla2_act_1 -- **FHS Framingham Cohort**: * 7 component_study_variables - * _phs000007.v29.pht000164.v6.phv00023808.v5_. No dbGap metadata available. - * _phs000007.v29.pht000304.v5.phv00036408.v4_. No dbGap metadata available. - * _phs000007.v29.pht002892.v4.phv00172229.v4_. No dbGap metadata available. - * _phs000007.v29.pht003099.v4.phv00177928.v4_. dbGap Name: **idtype**, Desc: **Framingham Heart Study cohort identifier**, Table: **vr_dates_2019_a_1175s**. - * _phs000007.v29.pht003099.v4.phv00177930.v4_. dbGap Name: **age1**, Desc: **Age at Exam 1**, Table: **vr_dates_2019_a_1175s**. - * _phs000007.v29.pht003099.v4.phv00177934.v4_. dbGap Name: **age3**, Desc: **Age at Exam 3**, Table: **vr_dates_2019_a_1175s**. - * _phs000007.v29.pht003099.v4.phv00177942.v4_. dbGap Name: **age7**, Desc: **Age at Exam 7**, Table: **vr_dates_2019_a_1175s**. + * _phs000007.v29.pht000164.v6.phv00023808.v5_ + * No dbGap metadata available + * No permissible values listed in PIC-SURE data dictionary + * _phs000007.v29.pht000304.v5.phv00036408.v4_ + * No dbGap metadata available + * No permissible values listed in PIC-SURE data dictionary + * _phs000007.v29.pht002892.v4.phv00172229.v4_ + * No dbGap metadata available + * No permissible values listed in PIC-SURE data dictionary + * _phs000007.v29.pht003099.v4.phv00177928.v4_ + * dbGap name: **idtype** + * dbGap desc: **Framingham Heart Study cohort identifier** + * dbGap table: **vr_dates_2019_a_1175s** + * PIC-SURE permissible values: Generation 3 Cohort, New Offspring Spouse Cohort, Offspring Cohort, Omni 1 Cohort, Omni 2 Cohort, Original Cohort + * _phs000007.v29.pht003099.v4.phv00177930.v4_ + * dbGap name: **age1** + * dbGap desc: **Age at Exam 1** + * dbGap table: **vr_dates_2019_a_1175s** + * No permissible values listed in PIC-SURE data dictionary + * _phs000007.v29.pht003099.v4.phv00177934.v4_ + * dbGap name: **age3** + * dbGap desc: **Age at Exam 3** + * dbGap table: **vr_dates_2019_a_1175s** + * No permissible values listed in PIC-SURE data dictionary + * _phs000007.v29.pht003099.v4.phv00177942.v4_ + * dbGap name: **age7** + * dbGap desc: **Age at Exam 7** + * dbGap table: **vr_dates_2019_a_1175s** + * No permissible values listed in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -1134,8 +1326,16 @@ * ### inflammation/lppla2_act_1 -- **MESA Multi-Ethnic Study of Atherosclerosis (MESA) Cohort**: * 2 component_study_variables - * _phs000209.v13.pht001116.v10.phv00084442.v3_. dbGap Name: **age1c**, Desc: **AGE**, Table: **MESA_Exam1Main**. - * _phs000209.v13.pht002512.v1.phv00165052.v1_. dbGap Name: **cam1a**, Desc: **LIPOPROTEIN-ASSOCIATED PHOSPHOLIPASE A2: ACTIVITY**, Table: **MESA_AncilMesaLpPLA2**. + * _phs000209.v13.pht001116.v10.phv00084442.v3_ + * dbGap name: **age1c** + * dbGap desc: **AGE** + * dbGap table: **MESA_Exam1Main** + * No permissible values listed in PIC-SURE data dictionary + * _phs000209.v13.pht002512.v1.phv00165052.v1_ + * dbGap name: **cam1a** + * dbGap desc: **LIPOPROTEIN-ASSOCIATED PHOSPHOLIPASE A2: ACTIVITY** + * dbGap table: **MESA_AncilMesaLpPLA2** + * No permissible values listed in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -1219,8 +1419,16 @@ * ### inflammation/lppla2_mass_1 -- **CHS Cardiovascular Health Study (CHS) Cohort: an NHLBI-funded observational study of risk factors for cardiovascular disease in adults 65 years or older**: * 2 component_study_variables - * _phs000287.v6.pht001449.v1.phv00098769.v1_. dbGap Name: **LPPLA2**, Desc: **Baseline LP-PLA2 Mass (ng/ml)**, Table: **ADDITIONAL_BIOMARKERS**. - * _phs000287.v6.pht001452.v1.phv00100487.v1_. dbGap Name: **AGEBL**, Desc: **CALCULATED AGE AT BASELINE**, Table: **BASEBOTH**. + * _phs000287.v6.pht001449.v1.phv00098769.v1_ + * dbGap name: **LPPLA2** + * dbGap desc: **Baseline LP-PLA2 Mass (ng/ml)** + * dbGap table: **ADDITIONAL_BIOMARKERS** + * No permissible values listed in PIC-SURE data dictionary + * _phs000287.v6.pht001452.v1.phv00100487.v1_ + * dbGap name: **AGEBL** + * dbGap desc: **CALCULATED AGE AT BASELINE** + * dbGap table: **BASEBOTH** + * No permissible values listed in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -1245,13 +1453,35 @@ * ### inflammation/lppla2_mass_1 -- **FHS Framingham Cohort**: * 7 component_study_variables - * _phs000007.v29.pht000095.v6.phv00021963.v5_. No dbGap metadata available. - * _phs000007.v29.pht000305.v5.phv00036411.v4_. No dbGap metadata available. - * _phs000007.v29.pht002892.v4.phv00172227.v4_. No dbGap metadata available. - * _phs000007.v29.pht003099.v4.phv00177928.v4_. dbGap Name: **idtype**, Desc: **Framingham Heart Study cohort identifier**, Table: **vr_dates_2019_a_1175s**. - * _phs000007.v29.pht003099.v4.phv00177930.v4_. dbGap Name: **age1**, Desc: **Age at Exam 1**, Table: **vr_dates_2019_a_1175s**. - * _phs000007.v29.pht003099.v4.phv00177934.v4_. dbGap Name: **age3**, Desc: **Age at Exam 3**, Table: **vr_dates_2019_a_1175s**. - * _phs000007.v29.pht003099.v4.phv00177942.v4_. dbGap Name: **age7**, Desc: **Age at Exam 7**, Table: **vr_dates_2019_a_1175s**. + * _phs000007.v29.pht000095.v6.phv00021963.v5_ + * No dbGap metadata available + * No permissible values listed in PIC-SURE data dictionary + * _phs000007.v29.pht000305.v5.phv00036411.v4_ + * No dbGap metadata available + * No permissible values listed in PIC-SURE data dictionary + * _phs000007.v29.pht002892.v4.phv00172227.v4_ + * No dbGap metadata available + * No permissible values listed in PIC-SURE data dictionary + * _phs000007.v29.pht003099.v4.phv00177928.v4_ + * dbGap name: **idtype** + * dbGap desc: **Framingham Heart Study cohort identifier** + * dbGap table: **vr_dates_2019_a_1175s** + * PIC-SURE permissible values: Generation 3 Cohort, New Offspring Spouse Cohort, Offspring Cohort, Omni 1 Cohort, Omni 2 Cohort, Original Cohort + * _phs000007.v29.pht003099.v4.phv00177930.v4_ + * dbGap name: **age1** + * dbGap desc: **Age at Exam 1** + * dbGap table: **vr_dates_2019_a_1175s** + * No permissible values listed in PIC-SURE data dictionary + * _phs000007.v29.pht003099.v4.phv00177934.v4_ + * dbGap name: **age3** + * dbGap desc: **Age at Exam 3** + * dbGap table: **vr_dates_2019_a_1175s** + * No permissible values listed in PIC-SURE data dictionary + * _phs000007.v29.pht003099.v4.phv00177942.v4_ + * dbGap name: **age7** + * dbGap desc: **Age at Exam 7** + * dbGap table: **vr_dates_2019_a_1175s** + * No permissible values listed in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -1293,8 +1523,16 @@ * ### inflammation/lppla2_mass_1 -- **MESA Multi-Ethnic Study of Atherosclerosis (MESA) Cohort**: * 2 component_study_variables - * _phs000209.v13.pht001116.v10.phv00084442.v3_. dbGap Name: **age1c**, Desc: **AGE**, Table: **MESA_Exam1Main**. - * _phs000209.v13.pht002512.v1.phv00165050.v1_. dbGap Name: **plac1a**, Desc: **LIPOPROTEIN-ASSOCIATED PHOSPHOLIPASE A2: MASS**, Table: **MESA_AncilMesaLpPLA2**. + * _phs000209.v13.pht001116.v10.phv00084442.v3_ + * dbGap name: **age1c** + * dbGap desc: **AGE** + * dbGap table: **MESA_Exam1Main** + * No permissible values listed in PIC-SURE data dictionary + * _phs000209.v13.pht002512.v1.phv00165050.v1_ + * dbGap name: **plac1a** + * dbGap desc: **LIPOPROTEIN-ASSOCIATED PHOSPHOLIPASE A2: MASS** + * dbGap table: **MESA_AncilMesaLpPLA2** + * No permissible values listed in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -1394,8 +1632,16 @@ * ### inflammation/mmp9_1 -- **MESA Multi-Ethnic Study of Atherosclerosis (MESA) Cohort**: * 2 component_study_variables - * _phs000209.v13.pht001116.v10.phv00084442.v3_. dbGap Name: **age1c**, Desc: **AGE**, Table: **MESA_Exam1Main**. - * _phs000209.v13.pht001116.v10.phv00085027.v2_. dbGap Name: **mmp91**, Desc: **MATRIX METALLOPROTEINASE 9 (ng/mL)**, Table: **MESA_Exam1Main**. + * _phs000209.v13.pht001116.v10.phv00084442.v3_ + * dbGap name: **age1c** + * dbGap desc: **AGE** + * dbGap table: **MESA_Exam1Main** + * No permissible values listed in PIC-SURE data dictionary + * _phs000209.v13.pht001116.v10.phv00085027.v2_ + * dbGap name: **mmp91** + * dbGap desc: **MATRIX METALLOPROTEINASE 9 (ng/mL)** + * dbGap table: **MESA_Exam1Main** + * PIC-SURE permissible values: 100.5, 100.7, 101, 101.6, 102.2, 102.5, 102.7, 102.8, 103.9, 104.2, 105.1, 105.5, 106.1, 106.5, 106.6, 106.9, 108.3, 108.5, 108.7, 109, 109.4, 110.4, 110.9, 111.5, 111.9, 112.3, 114.2, 114.3, 114.7, 114.8, 115.4, 116, 116.2, 116.3, 116.7, 117.1, 117.5, 117.7, 118, 118.4, 118.8, 119.3, 119.4, 119.6, 120.5, 120.7, 121.5, 122.2, 122.4, 122.5, 122.8, 123.3, 123.5, 124.3, 124.4, 124.5, 124.8, 125, 125.8, 126.2, 126.6, 126.7, 126.8, 126.9, 127.1, 127.2, 127.3, 127.6, 127.7, 127.9, 128.1, 128.5, 128.7, 129.1, 129.4, 129.9, 130.1, 130.4, 131.1, 131.2, 131.4, 131.5, 132.6, 132.9, 133.3, 133.4, 133.9, 134.1, 134.9, 135.2, 135.6, 135.7, 135.9, 1351.6, 136.2, 136.6, 136.8, 137, 137.1, 138.4, 138.8, 139.5, 140.2, 140.4, 140.7, 140.9, 141, 141.1, 141.4, 141.8, 142, 142.1, 142.6, 143.3, 143.4, 143.5, 143.8, 145.1, 145.6, 145.7, 145.8, 146.8, 147.2, 147.7, 147.9, 148.4, 148.5, 148.9, 149.2, 149.6, 150, 150.1, 150.5, 150.9, 151.2, 151.4, 151.6, 151.8, 152.1, 152.4, 152.7, 152.8, 153, 153.1, 153.2, 153.3, 153.4, 153.7, 154, 154.3, 154.6, 155.3, 155.9, 156.1, 156.8, 157, 157.2, 157.6, 158.2, 158.3, 158.4, 158.8, 159.1, 159.2, 159.4, 159.5, 159.8, 160.6, 160.7, 160.8, 161, 161.5, 161.7, 161.8, 162.2, 162.8, 163.8, 163.9, 164.3, 164.5, 164.6, 164.8, 164.9, 165.4, 165.8, 165.9, 166.2, 166.9, 167.1, 167.3, 167.5, 167.7, 167.8, 168, 168.3, 169, 169.4, 169.8, 169.9, 170.3, 170.6, 171, 171.1, 171.5, 171.6, 172.1, 173.1, 173.2, 173.7, 174, 174.7, 175, 175.2, 175.8, 176.3, 176.4, 176.6, 176.7, 176.8, 177, 177.3, 177.6, 177.8, 178.1, 178.3, 178.6, 178.7, 179, 179.5, 179.8, 180.2, 180.8, 181.5, 181.6, 182.6, 182.7, 182.9, 183, 183.1, 183.3, 183.8, 183.9, 184.5, 184.6, 185.2, 185.8, 186, 186.2, 186.6, 187.4, 187.6, 187.7, 187.8, 188.1, 188.4, 188.5, 188.7, 189.2, 189.3, 189.8, 189.9, 190.3, 190.4, 190.5, 190.6, 191.2, 191.4, 191.7, 191.9, 192.1, 192.3, 192.4, 192.8, 193, 193.1, 193.3, 193.4, 193.5, 194.3, 194.5, 194.7, 194.8, 195, 195.5, 195.7, 195.8, 196.1, 196.4, 196.6, 197.1, 197.3, 197.6, 197.8, 197.9, 198, 198.7, 198.9, 199, 199.3, 199.5, 199.6, 201.3, 201.7, 202, 202.1, 202.2, 202.3, 203.4, 203.9, 204.2, 204.6, 204.9, 205.2, 205.5, 205.9, 206.2, 207.1, 207.2, 207.9, 208.4, 208.7, 209.1, 209.2, 209.9, 210.4, 210.5, 210.8, 211.2, 211.3, 211.8, 213.2, 213.5, 213.7, 213.9, 214.4, 214.6, 214.7, 214.9, 215, 215.1, 215.6, 215.8, 215.9, 216, 216.9, 217.2, 217.8, 217.9, 218.1, 218.2, 218.4, 219.5, 219.6, 220.2, 221, 221.1, 222.1, 222.2, 223.3, 223.6, 223.7, 223.8, 224, 225.3, 225.6, 226.1, 226.7, 227.5, 227.8, 227.9, 228, 228.8, 229.2, 229.5, 230.2, 230.7, 230.9, 231.1, 231.2, 231.3, 231.4, 231.7, 232.3, 232.6, 232.7, 233.2, 233.9, 234.1, 234.2, 234.8, 235, 235.4, 235.9, 236.7, 237.1, 238, 238.2, 238.3, 238.4, 238.7, 239.4, 239.6, 239.8, 240, 240.2, 240.3, 240.8, 241.3, 241.6, 242.5, 242.6, 242.8, 243.6, 243.7, 244, 244.7, 245.7, 246.6, 246.7, 247.3, 247.4, 247.7, 247.9, 248, 249, 249.4, 249.8, 249.9, 250.3, 250.4, 251.1, 251.7, 252.2, 252.3, 252.6, 252.8, 253.7, 253.8, 254, 254.5, 255.2, 255.5, 255.6, 256.4, 256.8, 257.4, 258.5, 259.4, 259.7, 260.1, 260.5, 260.8, 261.3, 261.7, 261.8, 262.1, 262.2, 262.9, 263.3, 263.9, 264.4, 265.1, 265.2, 265.4, 265.7, 265.8, 266.1, 266.2, 266.4, 266.6, 266.7, 266.9, 267, 267.6, 268.2, 268.3, 268.7, 268.9, 269.5, 269.7, 269.9, 270.3, 270.4, 271.3, 272.1, 272.2, 272.9, 273.3, 274.3, 274.8, 274.9, 275.9, 276.1, 277.2, 277.5, 278.6, 278.7, 278.9, 279.4, 279.5, 279.6, 280.4, 280.9, 281.9, 282.5, 282.7, 283, 283.2, 283.5, 285.1, 285.4, 286.2, 286.9, 287.8, 288.5, 289.5, 290, 290.2, 290.3, 291.1, 291.2, 291.5, 291.6, 291.9, 292, 292.3, 292.7, 293.1, 293.6, 293.8, 294.1, 295.8, 296.6, 298.7, 298.8, 299.3, 299.8, 300.1, 301, 301.2, 301.4, 301.8, 302.3, 302.9, 303.1, 303.4, 304, 304.5, 305.2, 305.4, 306.6, 308.1, 309.5, 310.9, 312.2, 312.4, 314.7, 315.3, 316.9, 317.9, 318, 318.1, 319.6, 320.1, 320.8, 321.4, 321.5, 322.5, 322.7, 323.1, 323.7, 324, 324.1, 325.5, 325.9, 326.3, 327.6, 328.7, 330.9, 332.2, 332.7, 333.4, 334.6, 334.7, 335.5, 336.1, 338.2, 338.3, 338.7, 339, 339.8, 34.2, 340.1, 340.3, 341.4, 341.5, 344.1, 344.7, 344.9, 345.9, 347.8, 349.3, 35.1, 350.3, 350.6, 351.9, 353.5, 353.7, 354.2, 355.2, 356.4, 356.7, 357, 357.9, 358.2, 358.7, 359.7, 360.9, 361.6, 361.8, 364.3, 367.1, 367.6, 368.1, 368.5, 369.9, 372, 374.7, 376, 376.1, 377.6, 377.9, 378.7, 38.6, 380.4, 381.3, 381.4, 381.7, 383.9, 384.5, 385.6, 386.2, 387.4, 388.6, 390.5, 394.6, 396.2, 396.8, 397.6, 399.4, 400, 400.7, 401, 402.9, 404.5, 408, 408.9, 409.9, 410.4, 410.6, 411.4, 411.7, 411.9, 412.2, 412.5, 414.2, 415.1, 416.9, 418, 418.9, 421.1, 421.9, 423.5, 424.3, 425.9, 426.5, 427.7, 428.4, 429.6, 43, 431.2, 433.5, 439, 440.4, 442.1, 442.4, 443.8, 444.1, 445.7, 45.9, 450, 450.4, 451.4, 453.9, 456.9, 457.4, 461.1, 461.2, 462.1, 462.4, 466.3, 467.7, 47, 471.8, 472.4, 473.3, 475.6, 476.2, 48.3, 482.7, 484.1, 487.6, 487.8, 490.6, 491.4, 492.9, 494.3, 498.4, 499, 50.4, 503, 505.5, 507.1, 507.9, 508.2, 510.2, 515.5, 516.9, 517.1, 517.9, 519.7, 52.4, 52.9, 53, 533.7, 536.1, 540.1, 542.7, 546.8, 552.1, 566.6, 567.8, 568.8, 571.9, 575.1, 584.1, 589.3, 595.1, 600.3, 604.6, 608.3, 61.6, 61.8, 612.9, 618.7, 62.7, 620.5, 621.3, 621.7, 630.1, 64.5, 64.7, 646.5, 65.5, 654.6, 66.4, 66.7, 66.9, 661.9, 663.9, 668.3, 67.1, 67.3, 67.8, 68, 68.5, 680.9, 695.3, 700.8, 707.1, 71, 712.4, 718, 74.1, 74.2, 74.5, 74.9, 75, 75.7, 76, 762.3, 77.6, 775.8, 78.3, 78.8, 78.9, 80.4, 80.9, 801.6, 81.2, 81.9, 82, 82.4, 83.5, 831.8, 836.9, 84.2, 85.2, 85.4, 85.8, 86.5, 87.6, 88.3, 88.4, 88.5, 88.7, 88.8, 89.3, 89.5, 890.3, 891.5, 91.1, 91.3, 91.4, 91.5, 92.4, 928.1, 93.1, 93.3, 93.4, 937.1, 94.4, 94.6, 94.8, 95, 95.6, 96.3, 96.8, 98.1, 98.8, 99.9 * **Function:** ```r harmonize <- function(phen_list){ @@ -1458,8 +1704,14 @@ * ### inflammation/mpo_1 -- **FHS Framingham Cohort**: * 2 component_study_variables - * _phs000007.v29.pht000167.v6.phv00023854.v5_. No dbGap metadata available. - * _phs000007.v29.pht003099.v4.phv00177942.v4_. dbGap Name: **age7**, Desc: **Age at Exam 7**, Table: **vr_dates_2019_a_1175s**. + * _phs000007.v29.pht000167.v6.phv00023854.v5_ + * No dbGap metadata available + * No permissible values listed in PIC-SURE data dictionary + * _phs000007.v29.pht003099.v4.phv00177942.v4_ + * dbGap name: **age7** + * dbGap desc: **Age at Exam 7** + * dbGap table: **vr_dates_2019_a_1175s** + * No permissible values listed in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -1638,8 +1890,14 @@ * ### inflammation/tnfa_1 -- **FHS Framingham Cohort**: * 2 component_study_variables - * _phs000007.v29.pht000111.v5.phv00022779.v4_. No dbGap metadata available. - * _phs000007.v29.pht003099.v4.phv00177942.v4_. dbGap Name: **age7**, Desc: **Age at Exam 7**, Table: **vr_dates_2019_a_1175s**. + * _phs000007.v29.pht000111.v5.phv00022779.v4_ + * No dbGap metadata available + * No permissible values listed in PIC-SURE data dictionary + * _phs000007.v29.pht003099.v4.phv00177942.v4_ + * dbGap name: **age7** + * dbGap desc: **Age at Exam 7** + * dbGap table: **vr_dates_2019_a_1175s** + * No permissible values listed in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -1663,11 +1921,31 @@ * ### inflammation/tnfa_1 -- **MESA Multi-Ethnic Study of Atherosclerosis (MESA) Cohort**: * 5 component_study_variables - * _phs000209.v13.pht001118.v8.phv00085773.v3_. dbGap Name: **age2c**, Desc: **AGE AT EXAM 2**, Table: **MESA_Exam2Main**. - * _phs000209.v13.pht001119.v8.phv00086259.v4_. dbGap Name: **age3c**, Desc: **AGE AT EXAM3**, Table: **MESA_Exam3Main**. - * _phs000209.v13.pht002198.v2.phv00160529.v1_. dbGap Name: **exam3**, Desc: **EXAM**, Table: **MESA_AncilMesaAbdBodyComposition**. - * _phs000209.v13.pht002198.v2.phv00160540.v1_. dbGap Name: **tnfa3**, Desc: **TNFa (pg/mL)**, Table: **MESA_AncilMesaAbdBodyComposition**. - * _phs000209.v13.pht002198.v2.phv00160541.v1_. dbGap Name: **tnfa3m**, Desc: **TNFa (MISSING VALUE REASON)**, Table: **MESA_AncilMesaAbdBodyComposition**. + * _phs000209.v13.pht001118.v8.phv00085773.v3_ + * dbGap name: **age2c** + * dbGap desc: **AGE AT EXAM 2** + * dbGap table: **MESA_Exam2Main** + * PIC-SURE permissible values: 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87 + * _phs000209.v13.pht001119.v8.phv00086259.v4_ + * dbGap name: **age3c** + * dbGap desc: **AGE AT EXAM3** + * dbGap table: **MESA_Exam3Main** + * PIC-SURE permissible values: 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88 + * _phs000209.v13.pht002198.v2.phv00160529.v1_ + * dbGap name: **exam3** + * dbGap desc: **EXAM** + * dbGap table: **MESA_AncilMesaAbdBodyComposition** + * PIC-SURE permissible values: Exam 2, Exam 3 + * _phs000209.v13.pht002198.v2.phv00160540.v1_ + * dbGap name: **tnfa3** + * dbGap desc: **TNFa (pg/mL)** + * dbGap table: **MESA_AncilMesaAbdBodyComposition** + * No permissible values listed in PIC-SURE data dictionary + * _phs000209.v13.pht002198.v2.phv00160541.v1_ + * dbGap name: **tnfa3m** + * dbGap desc: **TNFa (MISSING VALUE REASON)** + * dbGap table: **MESA_AncilMesaAbdBodyComposition** + * PIC-SURE permissible values: High > 12, Insufficient volume for testing, Low < 0.16, Unknown * **Function:** ```r harmonize <- function(phen_list){ @@ -1755,8 +2033,16 @@ * ### inflammation/tnfa_r1_1 -- **MESA Multi-Ethnic Study of Atherosclerosis (MESA) Cohort**: * 2 component_study_variables - * _phs000209.v13.pht001116.v10.phv00084442.v3_. dbGap Name: **age1c**, Desc: **AGE**, Table: **MESA_Exam1Main**. - * _phs000209.v13.pht001116.v10.phv00085029.v3_. dbGap Name: **tnfri1**, Desc: **TUMOR NECROSIS FACTOR-A SOLUBLE RECEPTORS (pg/ml)**, Table: **MESA_Exam1Main**. + * _phs000209.v13.pht001116.v10.phv00084442.v3_ + * dbGap name: **age1c** + * dbGap desc: **AGE** + * dbGap table: **MESA_Exam1Main** + * No permissible values listed in PIC-SURE data dictionary + * _phs000209.v13.pht001116.v10.phv00085029.v3_ + * dbGap name: **tnfri1** + * dbGap desc: **TUMOR NECROSIS FACTOR-A SOLUBLE RECEPTORS (pg/ml)** + * dbGap table: **MESA_Exam1Main** + * PIC-SURE permissible values: -555, -888, 1000, 1001, 1002, 1003, 1005, 1006, 1007, 1008, 1009, 1010, 1011, 1012, 1013, 1014, 1015, 1016, 1017, 1018, 1019, 1022, 1023, 1024, 1025, 1027, 1028, 1029, 1030, 1032, 1033, 1034, 1035, 1036, 1037, 1038, 1039, 1040, 1041, 1042, 1043, 1044, 1045, 1046, 1047, 1048, 1049, 1050, 1051, 1052, 1053, 1054, 1055, 1056, 1057, 1058, 1059, 1060, 1061, 1062, 1063, 1064, 1065, 1066, 1067, 1068, 1069, 1070, 1071, 1072, 1073, 1074, 1075, 1076, 1077, 1078, 1079, 1080, 1081, 1082, 1083, 1084, 1085, 1086, 1087, 1088, 1089, 1090, 1091, 1092, 1093, 1094, 1095, 1096, 1097, 1098, 1099, 1100, 1101, 1102, 1103, 1104, 1105, 1106, 1107, 1108, 1109, 1110, 1111, 1112, 1113, 1114, 1115, 1116, 1117, 1118, 1119, 1120, 1121, 1122, 1124, 1125, 1126, 1127, 1128, 1129, 1130, 1131, 1132, 1133, 1134, 1135, 1136, 1137, 1138, 1139, 1140, 1141, 1142, 1143, 1144, 1145, 1146, 1147, 1148, 1149, 1150, 1151, 1152, 1153, 1155, 1156, 1157, 1158, 1159, 1160, 1161, 1162, 1163, 1164, 1165, 1166, 1167, 1168, 1169, 1170, 1171, 1172, 1173, 1174, 1175, 1176, 1177, 1178, 1179, 1180, 1181, 1182, 1183, 1184, 1185, 1186, 1187, 1188, 1189, 1190, 1191, 1192, 1193, 1194, 1195, 1196, 1197, 1198, 1199, 1200, 1201, 1202, 1203, 1204, 1205, 1206, 1207, 1208, 1209, 1210, 1211, 1212, 1214, 1215, 1216, 1217, 1218, 1219, 1220, 1221, 1222, 1223, 1224, 1225, 1227, 1228, 1229, 1230, 1231, 1232, 1233, 1234, 1235, 1236, 1237, 1238, 1239, 1240, 1241, 1242, 1243, 1244, 1245, 1246, 1247, 1248, 1249, 1250, 1251, 1252, 1253, 1254, 1255, 1256, 1257, 1258, 1259, 1260, 1261, 1262, 1263, 1264, 1265, 1266, 1267, 1268, 1270, 1271, 1272, 1273, 1275, 1276, 1277, 1278, 1279, 1280, 1281, 1282, 1283, 1284, 1285, 1286, 1287, 1288, 1289, 1290, 1291, 1292, 1293, 1294, 1295, 1296, 1297, 1298, 1299, 1300, 1301, 1302, 1303, 1304, 1305, 1306, 1307, 1308, 1310, 1311, 1312, 1313, 1314, 1315, 1318, 1319, 1320, 1321, 1322, 1323, 1324, 1325, 1326, 1327, 1328, 1329, 1330, 1331, 1332, 1333, 1334, 1335, 1336, 1337, 1338, 1339, 1340, 1341, 1342, 1343, 1344, 1345, 1346, 1347, 1348, 1349, 1350, 1351, 1352, 1353, 1354, 1355, 1356, 1357, 1358, 1359, 1360, 1361, 1362, 1363, 1364, 1365, 1366, 1367, 1368, 1369, 1370, 1371, 1372, 1373, 1374, 1375, 1376, 1377, 1378, 1379, 1380, 1381, 1382, 1383, 1384, 1385, 1386, 1387, 1388, 1389, 1390, 1391, 1392, 1393, 1394, 1395, 1396, 1397, 1398, 1399, 1400, 1401, 1403, 1404, 1405, 1406, 1407, 1408, 1409, 1410, 1411, 1412, 1413, 1414, 1415, 1416, 1417, 1418, 1419, 1420, 1421, 1422, 1423, 1424, 1425, 1426, 1427, 1428, 1429, 1430, 1431, 1433, 1434, 1435, 1437, 1438, 1439, 1440, 1441, 1442, 1443, 1444, 1445, 1446, 1447, 1448, 1449, 1450, 1451, 1452, 1453, 1454, 1455, 1457, 1458, 1459, 1460, 1461, 1462, 1463, 1465, 1466, 1467, 1468, 1469, 1470, 1471, 1472, 1474, 1476, 1477, 1478, 1479, 1480, 1481, 1482, 1483, 1484, 1485, 1486, 1487, 1488, 1491, 1492, 1493, 1494, 1495, 1496, 1497, 1498, 1499, 1500, 1501, 1502, 1503, 1504, 1505, 1506, 1507, 1508, 1509, 1510, 1511, 1512, 1513, 1514, 1515, 1516, 1517, 1518, 1519, 1520, 1521, 1522, 1524, 1525, 1526, 1527, 1528, 1529, 1530, 1531, 1532, 1533, 1534, 1535, 1536, 1537, 1539, 1540, 1541, 1542, 1543, 1544, 1545, 1546, 1547, 1548, 1549, 1550, 1551, 1552, 1553, 1554, 1555, 1556, 1558, 1559, 1561, 1562, 1563, 1564, 1565, 1567, 1568, 1569, 1571, 1572, 1573, 1574, 1575, 1576, 1578, 1579, 1580, 1582, 1583, 1584, 1585, 1586, 1587, 1588, 1589, 1590, 1592, 1594, 1595, 1596, 1597, 1598, 1600, 1601, 1602, 1603, 1604, 1606, 1607, 1608, 1609, 1610, 1612, 1613, 1614, 1616, 1617, 1618, 1619, 1620, 1621, 1622, 1624, 1625, 1626, 1627, 1628, 1630, 1631, 1632, 1633, 1634, 1636, 1639, 1640, 1641, 1644, 1645, 1646, 1647, 1648, 1649, 1651, 1652, 1653, 1654, 1655, 1657, 1660, 1662, 1664, 1665, 1666, 1667, 1668, 1669, 1670, 1671, 1673, 1675, 1676, 1678, 1679, 1681, 1683, 1684, 1685, 1686, 1687, 1688, 1690, 1691, 1692, 1693, 1694, 1696, 1697, 1698, 1701, 1703, 1705, 1706, 1707, 1708, 1709, 1711, 1712, 1713, 1715, 1717, 1719, 1720, 1721, 1722, 1723, 1725, 1726, 1728, 1729, 1731, 1735, 1737, 1738, 1739, 1740, 1741, 1742, 1743, 1744, 1745, 1746, 1748, 1749, 1750, 1755, 1756, 1757, 1758, 1759, 1760, 1761, 1762, 1764, 1766, 1767, 1768, 1770, 1771, 1773, 1774, 1776, 1778, 1780, 1781, 1783, 1784, 1786, 1787, 1789, 1791, 1792, 1793, 1795, 1796, 1797, 1798, 1800, 1801, 1802, 1803, 1806, 1807, 1809, 1810, 1812, 1816, 1817, 1820, 1821, 1825, 1827, 1828, 1829, 1833, 1835, 1837, 1839, 1840, 1845, 1847, 1848, 1850, 1852, 1853, 1855, 1858, 1861, 1863, 1864, 1865, 1866, 1867, 1868, 1869, 1871, 1873, 1875, 1878, 1879, 1882, 1883, 1886, 1888, 1890, 1894, 1902, 1904, 1907, 1910, 1911, 1912, 1914, 1915, 1920, 1921, 1922, 1928, 1929, 1931, 1934, 1936, 1938, 1940, 1942, 1943, 1946, 1948, 1950, 1954, 1955, 1959, 1960, 1967, 1970, 1972, 1974, 1977, 1978, 1982, 1984, 1988, 1989, 1991, 1994, 1996, 1997, 2001, 2008, 2011, 2012, 2014, 2016, 2020, 2024, 2027, 2030, 2049, 2055, 2056, 2057, 2058, 2060, 2063, 2064, 2068, 2071, 2073, 2075, 2076, 2085, 2087, 2106, 2107, 2108, 2109, 2113, 2114, 2120, 2124, 2125, 2129, 2130, 2132, 2140, 2144, 2148, 2153, 2157, 2159, 2164, 2175, 2176, 2179, 2183, 2188, 2190, 2195, 2199, 2201, 2203, 2208, 2210, 2212, 2218, 2220, 2222, 2226, 2232, 2234, 2240, 2248, 2249, 2253, 2255, 2256, 2261, 2266, 2271, 2272, 2286, 2293, 2301, 2305, 2307, 2310, 2312, 2314, 2316, 2327, 2328, 2336, 2337, 2339, 2341, 2345, 2346, 2356, 2359, 2367, 2369, 2370, 2375, 2385, 2394, 2397, 2399, 2409, 2415, 2418, 2426, 2427, 2432, 2438, 2442, 2452, 2461, 2465, 2467, 2472, 2495, 2499, 2518, 2519, 2531, 2532, 2534, 2539, 2552, 2562, 2569, 2584, 2591, 2593, 2609, 2614, 2634, 2668, 2711, 2720, 2725, 2728, 2745, 2777, 2781, 2792, 2800, 2826, 2834, 2861, 2862, 2869, 2874, 2907, 2920, 2927, 2948, 2960, 2982, 2999, 3018, 3037, 3055, 3060, 3080, 3111, 3191, 3229, 3745, 3775, 3864, 4034, 4040, 4128, 4146, 4162, 4610, 4918, 5052, 5419, 5544, 603, 618, 622, 636, 653, 654, 663, 675, 696, 697, 699, 706, 736, 741, 742, 751, 753, 760, 764, 769, 771, 772, 773, 775, 779, 782, 783, 785, 788, 790, 791, 793, 794, 797, 798, 802, 804, 807, 810, 811, 813, 814, 815, 816, 817, 818, 819, 822, 823, 824, 827, 828, 830, 833, 834, 836, 837, 838, 839, 844, 845, 846, 847, 849, 851, 852, 853, 854, 858, 859, 860, 864, 865, 866, 867, 869, 870, 871, 872, 873, 875, 876, 877, 878, 879, 880, 881, 882, 885, 886, 887, 888, 889, 890, 892, 893, 894, 895, 898, 899, 901, 903, 904, 905, 906, 907, 909, 910, 911, 912, 913, 914, 915, 916, 917, 918, 919, 921, 925, 926, 927, 928, 929, 930, 931, 933, 934, 935, 936, 939, 940, 941, 942, 943, 944, 945, 946, 947, 948, 949, 950, 951, 953, 954, 955, 956, 957, 958, 959, 961, 963, 964, 966, 967, 969, 970, 971, 972, 973, 975, 976, 978, 979, 980, 981, 983, 984, 985, 986, 987, 988, 989, 990, 991, 992, 993, 994, 995, 996, 998, 999 * **Function:** ```r harmonize <- function(phen_list){ @@ -1831,13 +2117,35 @@ * ### inflammation/tnfr2_1 -- **FHS Framingham Cohort**: * 7 component_study_variables - * _phs000007.v29.pht000175.v6.phv00023913.v5_. No dbGap metadata available. - * _phs000007.v29.pht002898.v2.phv00172383.v2_. No dbGap metadata available. - * _phs000007.v29.pht002899.v4.phv00172391.v4_. No dbGap metadata available. - * _phs000007.v29.pht003099.v4.phv00177928.v4_. dbGap Name: **idtype**, Desc: **Framingham Heart Study cohort identifier**, Table: **vr_dates_2019_a_1175s**. - * _phs000007.v29.pht003099.v4.phv00177930.v4_. dbGap Name: **age1**, Desc: **Age at Exam 1**, Table: **vr_dates_2019_a_1175s**. - * _phs000007.v29.pht003099.v4.phv00177934.v4_. dbGap Name: **age3**, Desc: **Age at Exam 3**, Table: **vr_dates_2019_a_1175s**. - * _phs000007.v29.pht003099.v4.phv00177942.v4_. dbGap Name: **age7**, Desc: **Age at Exam 7**, Table: **vr_dates_2019_a_1175s**. + * _phs000007.v29.pht000175.v6.phv00023913.v5_ + * No dbGap metadata available + * No permissible values listed in PIC-SURE data dictionary + * _phs000007.v29.pht002898.v2.phv00172383.v2_ + * No dbGap metadata available + * No permissible values listed in PIC-SURE data dictionary + * _phs000007.v29.pht002899.v4.phv00172391.v4_ + * No dbGap metadata available + * No permissible values listed in PIC-SURE data dictionary + * _phs000007.v29.pht003099.v4.phv00177928.v4_ + * dbGap name: **idtype** + * dbGap desc: **Framingham Heart Study cohort identifier** + * dbGap table: **vr_dates_2019_a_1175s** + * PIC-SURE permissible values: Generation 3 Cohort, New Offspring Spouse Cohort, Offspring Cohort, Omni 1 Cohort, Omni 2 Cohort, Original Cohort + * _phs000007.v29.pht003099.v4.phv00177930.v4_ + * dbGap name: **age1** + * dbGap desc: **Age at Exam 1** + * dbGap table: **vr_dates_2019_a_1175s** + * No permissible values listed in PIC-SURE data dictionary + * _phs000007.v29.pht003099.v4.phv00177934.v4_ + * dbGap name: **age3** + * dbGap desc: **Age at Exam 3** + * dbGap table: **vr_dates_2019_a_1175s** + * No permissible values listed in PIC-SURE data dictionary + * _phs000007.v29.pht003099.v4.phv00177942.v4_ + * dbGap name: **age7** + * dbGap desc: **Age at Exam 7** + * dbGap table: **vr_dates_2019_a_1175s** + * No permissible values listed in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ diff --git a/resources/human-readable-harmonized-variable-documentation/generated-doc-pages/lipids.md b/resources/human-readable-harmonized-variable-documentation/generated-doc-pages/lipids.md index 0ea93d7..bad5fb1 100644 --- a/resources/human-readable-harmonized-variable-documentation/generated-doc-pages/lipids.md +++ b/resources/human-readable-harmonized-variable-documentation/generated-doc-pages/lipids.md @@ -50,8 +50,16 @@ * ### lipids/fasting_lipids_1 -- **ARIC Atherosclerosis Risk in Communities (ARIC) Cohort**: * 2 component_study_variables - * _phs000280.v4.pht004063.v2.phv00204712.v1_. dbGap Name: **V1AGE01**, Desc: **Age at visit 1 [Cohort. Visit 1]**, Table: **DERIVE13**. - * _phs000280.v4.pht004063.v2.phv00204732.v1_. dbGap Name: **FAST0802**, Desc: **Fasting time of 8 hours or more [Cohort. Visit 1]**, Table: **DERIVE13**. + * _phs000280.v4.pht004063.v2.phv00204712.v1_ + * dbGap name: **V1AGE01** + * dbGap desc: **Age at visit 1 [Cohort. Visit 1]** + * dbGap table: **DERIVE13** + * varId _phv00204712_ not found in PIC-SURE data dictionary + * _phs000280.v4.pht004063.v2.phv00204732.v1_ + * dbGap name: **FAST0802** + * dbGap desc: **Fasting time of 8 hours or more [Cohort. Visit 1]** + * dbGap table: **DERIVE13** + * varId _phv00204732_ not found in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -72,8 +80,16 @@ * ### lipids/fasting_lipids_1 -- **CARDIA CARDIA Cohort**: * 2 component_study_variables - * _phs000285.v3.pht001559.v2.phv00112439.v2_. dbGap Name: **A01AGE2**, Desc: **AGE VERIFY**, Table: **A4F01**. - * _phs000285.v3.pht001563.v2.phv00112661.v2_. dbGap Name: **A05FAST**, Desc: **12 HR FAST BEFORE BLOOD DRAWN**, Table: **A4F05**. + * _phs000285.v3.pht001559.v2.phv00112439.v2_ + * dbGap name: **A01AGE2** + * dbGap desc: **AGE VERIFY** + * dbGap table: **A4F01** + * varId _phv00112439_ not found in PIC-SURE data dictionary + * _phs000285.v3.pht001563.v2.phv00112661.v2_ + * dbGap name: **A05FAST** + * dbGap desc: **12 HR FAST BEFORE BLOOD DRAWN** + * dbGap table: **A4F05** + * varId _phv00112661_ not found in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -95,8 +111,16 @@ * ### lipids/fasting_lipids_1 -- **CHS Cardiovascular Health Study (CHS) Cohort: an NHLBI-funded observational study of risk factors for cardiovascular disease in adults 65 years or older**: * 2 component_study_variables - * _phs000287.v6.pht001451.v1.phv00099923.v1_. dbGap Name: **FAST30**, Desc: **HOURS SINCE LAST ATE OR DRANK**, Table: **BASE2**. - * _phs000287.v6.pht001452.v1.phv00100487.v1_. dbGap Name: **AGEBL**, Desc: **CALCULATED AGE AT BASELINE**, Table: **BASEBOTH**. + * _phs000287.v6.pht001451.v1.phv00099923.v1_ + * dbGap name: **FAST30** + * dbGap desc: **HOURS SINCE LAST ATE OR DRANK** + * dbGap table: **BASE2** + * No permissible values listed in PIC-SURE data dictionary + * _phs000287.v6.pht001452.v1.phv00100487.v1_ + * dbGap name: **AGEBL** + * dbGap desc: **CALCULATED AGE AT BASELINE** + * dbGap table: **BASEBOTH** + * No permissible values listed in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -119,8 +143,16 @@ * ### lipids/fasting_lipids_1 -- **HCHS_SOL Hispanic Community Health Study /Study of Latinos (HCHS/SOL)**: * 2 component_study_variables - * _phs000810.v1.pht004715.v1.phv00226251.v1_. dbGap Name: **AGE**, Desc: **Age**, Table: **HCHS_SOL_Cohort_Subject_Phenotypes**. - * _phs000810.v1.pht004715.v1.phv00253225.v1_. dbGap Name: **FASTTIME**, Desc: **Fasting time (hrs.)**, Table: **HCHS_SOL_Cohort_Subject_Phenotypes**. + * _phs000810.v1.pht004715.v1.phv00226251.v1_ + * dbGap name: **AGE** + * dbGap desc: **Age** + * dbGap table: **HCHS_SOL_Cohort_Subject_Phenotypes** + * No permissible values listed in PIC-SURE data dictionary + * _phs000810.v1.pht004715.v1.phv00253225.v1_ + * dbGap name: **FASTTIME** + * dbGap desc: **Fasting time (hrs.)** + * dbGap table: **HCHS_SOL_Cohort_Subject_Phenotypes** + * No permissible values listed in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -139,8 +171,12 @@ * ### lipids/fasting_lipids_1 -- **JHS Jackson Heart Study (JHS) Cohort**: * 2 component_study_variables - * _phs000286.v5.pht001949.v1.phv00126009.v1_. No dbGap metadata available. - * _phs000286.v5.pht001949.v1.phv00126044.v1_. No dbGap metadata available. + * _phs000286.v5.pht001949.v1.phv00126009.v1_ + * No dbGap metadata available + * varId _phv00126009_ not found in PIC-SURE data dictionary + * _phs000286.v5.pht001949.v1.phv00126044.v1_ + * No dbGap metadata available + * varId _phv00126044_ not found in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -165,12 +201,36 @@ * ### lipids/fasting_lipids_1 -- **MESA Multi-Ethnic Study of Atherosclerosis (MESA) Cohort**: * 6 component_study_variables - * _phs000209.v13.pht001111.v4.phv00082639.v2_. dbGap Name: **age1c**, Desc: **AGE**, Table: **MESA_AirNRExamMain**. - * _phs000209.v13.pht001111.v4.phv00083303.v1_. dbGap Name: **lastdrk1**, Desc: **HOW LONG AGO LAST DRINK OR EAT? (HRS)**, Table: **MESA_AirNRExamMain**. - * _phs000209.v13.pht001116.v10.phv00084442.v3_. dbGap Name: **age1c**, Desc: **AGE**, Table: **MESA_Exam1Main**. - * _phs000209.v13.pht001116.v10.phv00084980.v2_. dbGap Name: **lastdrk1**, Desc: **HOW LONG AGO LAST DRINK OR EAT? (HRS)**, Table: **MESA_Exam1Main**. - * _phs000209.v13.pht001121.v3.phv00087071.v1_. dbGap Name: **agefc**, Desc: **AGE**, Table: **MESA_FamilyExamMain**. - * _phs000209.v13.pht001121.v3.phv00087524.v1_. dbGap Name: **lastdrkf**, Desc: **HOW LONG AGO LAST DRINK OR EAT? (hrs)**, Table: **MESA_FamilyExamMain**. + * _phs000209.v13.pht001111.v4.phv00082639.v2_ + * dbGap name: **age1c** + * dbGap desc: **AGE** + * dbGap table: **MESA_AirNRExamMain** + * No permissible values listed in PIC-SURE data dictionary + * _phs000209.v13.pht001111.v4.phv00083303.v1_ + * dbGap name: **lastdrk1** + * dbGap desc: **HOW LONG AGO LAST DRINK OR EAT? (HRS)** + * dbGap table: **MESA_AirNRExamMain** + * No permissible values listed in PIC-SURE data dictionary + * _phs000209.v13.pht001116.v10.phv00084442.v3_ + * dbGap name: **age1c** + * dbGap desc: **AGE** + * dbGap table: **MESA_Exam1Main** + * No permissible values listed in PIC-SURE data dictionary + * _phs000209.v13.pht001116.v10.phv00084980.v2_ + * dbGap name: **lastdrk1** + * dbGap desc: **HOW LONG AGO LAST DRINK OR EAT? (HRS)** + * dbGap table: **MESA_Exam1Main** + * No permissible values listed in PIC-SURE data dictionary + * _phs000209.v13.pht001121.v3.phv00087071.v1_ + * dbGap name: **agefc** + * dbGap desc: **AGE** + * dbGap table: **MESA_FamilyExamMain** + * No permissible values listed in PIC-SURE data dictionary + * _phs000209.v13.pht001121.v3.phv00087524.v1_ + * dbGap name: **lastdrkf** + * dbGap desc: **HOW LONG AGO LAST DRINK OR EAT? (hrs)** + * dbGap table: **MESA_FamilyExamMain** + * No permissible values listed in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -240,8 +300,16 @@ * ### lipids/hdl_1 -- **ARIC Atherosclerosis Risk in Communities (ARIC) Cohort**: * 2 component_study_variables - * _phs000280.v4.pht004063.v2.phv00204712.v1_. dbGap Name: **V1AGE01**, Desc: **Age at visit 1 [Cohort. Visit 1]**, Table: **DERIVE13**. - * _phs000280.v4.pht004063.v2.phv00204761.v1_. dbGap Name: **HDL01**, Desc: **HDL cholesterol (recalibrated lipid) [Cohort. Visit 1]**, Table: **DERIVE13**. + * _phs000280.v4.pht004063.v2.phv00204712.v1_ + * dbGap name: **V1AGE01** + * dbGap desc: **Age at visit 1 [Cohort. Visit 1]** + * dbGap table: **DERIVE13** + * varId _phv00204712_ not found in PIC-SURE data dictionary + * _phs000280.v4.pht004063.v2.phv00204761.v1_ + * dbGap name: **HDL01** + * dbGap desc: **HDL cholesterol (recalibrated lipid) [Cohort. Visit 1]** + * dbGap table: **DERIVE13** + * varId _phv00204761_ not found in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -258,8 +326,16 @@ * ### lipids/hdl_1 -- **CARDIA CARDIA Cohort**: * 2 component_study_variables - * _phs000285.v3.pht001559.v2.phv00112439.v2_. dbGap Name: **A01AGE2**, Desc: **AGE VERIFY**, Table: **A4F01**. - * _phs000285.v3.pht001588.v2.phv00113702.v2_. dbGap Name: **AL1HDL**, Desc: **TOTAL HDL CHOLESTEROL (MG/DL)**, Table: **A4LIP**. + * _phs000285.v3.pht001559.v2.phv00112439.v2_ + * dbGap name: **A01AGE2** + * dbGap desc: **AGE VERIFY** + * dbGap table: **A4F01** + * varId _phv00112439_ not found in PIC-SURE data dictionary + * _phs000285.v3.pht001588.v2.phv00113702.v2_ + * dbGap name: **AL1HDL** + * dbGap desc: **TOTAL HDL CHOLESTEROL (MG/DL)** + * dbGap table: **A4LIP** + * varId _phv00113702_ not found in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -277,8 +353,16 @@ * ### lipids/hdl_1 -- **CHS Cardiovascular Health Study (CHS) Cohort: an NHLBI-funded observational study of risk factors for cardiovascular disease in adults 65 years or older**: * 2 component_study_variables - * _phs000287.v6.pht001452.v1.phv00100426.v1_. dbGap Name: **HDL44**, Desc: **HDL (mg/dl)**, Table: **BASEBOTH**. - * _phs000287.v6.pht001452.v1.phv00100487.v1_. dbGap Name: **AGEBL**, Desc: **CALCULATED AGE AT BASELINE**, Table: **BASEBOTH**. + * _phs000287.v6.pht001452.v1.phv00100426.v1_ + * dbGap name: **HDL44** + * dbGap desc: **HDL (mg/dl)** + * dbGap table: **BASEBOTH** + * No permissible values listed in PIC-SURE data dictionary + * _phs000287.v6.pht001452.v1.phv00100487.v1_ + * dbGap name: **AGEBL** + * dbGap desc: **CALCULATED AGE AT BASELINE** + * dbGap table: **BASEBOTH** + * No permissible values listed in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -295,8 +379,16 @@ * ### lipids/hdl_1 -- **HCHS_SOL Hispanic Community Health Study /Study of Latinos (HCHS/SOL)**: * 2 component_study_variables - * _phs000810.v1.pht004715.v1.phv00226251.v1_. dbGap Name: **AGE**, Desc: **Age**, Table: **HCHS_SOL_Cohort_Subject_Phenotypes**. - * _phs000810.v1.pht004715.v1.phv00253239.v1_. dbGap Name: **LABA68**, Desc: **HDL-cholesterol (mg/dL) (LABA68)**, Table: **HCHS_SOL_Cohort_Subject_Phenotypes**. + * _phs000810.v1.pht004715.v1.phv00226251.v1_ + * dbGap name: **AGE** + * dbGap desc: **Age** + * dbGap table: **HCHS_SOL_Cohort_Subject_Phenotypes** + * No permissible values listed in PIC-SURE data dictionary + * _phs000810.v1.pht004715.v1.phv00253239.v1_ + * dbGap name: **LABA68** + * dbGap desc: **HDL-cholesterol (mg/dL) (LABA68)** + * dbGap table: **HCHS_SOL_Cohort_Subject_Phenotypes** + * No permissible values listed in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -312,8 +404,14 @@ * ### lipids/hdl_1 -- **JHS Jackson Heart Study (JHS) Cohort**: * 2 component_study_variables - * _phs000286.v5.pht001945.v1.phv00125930.v1_. dbGap Name: **HDLC**, Desc: **Hdlc: HDL cholesterol - mg/dL [Visit 1]**, Table: **cena**. - * _phs000286.v5.pht001949.v1.phv00126009.v1_. No dbGap metadata available. + * _phs000286.v5.pht001945.v1.phv00125930.v1_ + * dbGap name: **HDLC** + * dbGap desc: **Hdlc: HDL cholesterol - mg/dL [Visit 1]** + * dbGap table: **cena** + * varId _phv00125930_ not found in PIC-SURE data dictionary + * _phs000286.v5.pht001949.v1.phv00126009.v1_ + * No dbGap metadata available + * varId _phv00126009_ not found in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -341,12 +439,36 @@ * ### lipids/hdl_1 -- **MESA Multi-Ethnic Study of Atherosclerosis (MESA) Cohort**: * 6 component_study_variables - * _phs000209.v13.pht001111.v4.phv00082639.v2_. dbGap Name: **age1c**, Desc: **AGE**, Table: **MESA_AirNRExamMain**. - * _phs000209.v13.pht001111.v4.phv00082952.v1_. dbGap Name: **hdl1**, Desc: **HDL CHOLESTEROL (mg/dl)**, Table: **MESA_AirNRExamMain**. - * _phs000209.v13.pht001116.v10.phv00084442.v3_. dbGap Name: **age1c**, Desc: **AGE**, Table: **MESA_Exam1Main**. - * _phs000209.v13.pht001116.v10.phv00084972.v2_. dbGap Name: **hdl1**, Desc: **HDL CHOLESTEROL (mg/dl)**, Table: **MESA_Exam1Main**. - * _phs000209.v13.pht001121.v3.phv00087071.v1_. dbGap Name: **agefc**, Desc: **AGE**, Table: **MESA_FamilyExamMain**. - * _phs000209.v13.pht001121.v3.phv00087099.v1_. dbGap Name: **hdlf**, Desc: **HDL CHOLESTEROL (mg/dl)**, Table: **MESA_FamilyExamMain**. + * _phs000209.v13.pht001111.v4.phv00082639.v2_ + * dbGap name: **age1c** + * dbGap desc: **AGE** + * dbGap table: **MESA_AirNRExamMain** + * No permissible values listed in PIC-SURE data dictionary + * _phs000209.v13.pht001111.v4.phv00082952.v1_ + * dbGap name: **hdl1** + * dbGap desc: **HDL CHOLESTEROL (mg/dl)** + * dbGap table: **MESA_AirNRExamMain** + * No permissible values listed in PIC-SURE data dictionary + * _phs000209.v13.pht001116.v10.phv00084442.v3_ + * dbGap name: **age1c** + * dbGap desc: **AGE** + * dbGap table: **MESA_Exam1Main** + * No permissible values listed in PIC-SURE data dictionary + * _phs000209.v13.pht001116.v10.phv00084972.v2_ + * dbGap name: **hdl1** + * dbGap desc: **HDL CHOLESTEROL (mg/dl)** + * dbGap table: **MESA_Exam1Main** + * No permissible values listed in PIC-SURE data dictionary + * _phs000209.v13.pht001121.v3.phv00087071.v1_ + * dbGap name: **agefc** + * dbGap desc: **AGE** + * dbGap table: **MESA_FamilyExamMain** + * No permissible values listed in PIC-SURE data dictionary + * _phs000209.v13.pht001121.v3.phv00087099.v1_ + * dbGap name: **hdlf** + * dbGap desc: **HDL CHOLESTEROL (mg/dl)** + * dbGap table: **MESA_FamilyExamMain** + * No permissible values listed in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -449,8 +571,16 @@ * ### lipids/lipid_lowering_medication_1 -- **ARIC Atherosclerosis Risk in Communities (ARIC) Cohort**: * 2 component_study_variables - * _phs000280.v4.pht004063.v2.phv00204712.v1_. dbGap Name: **V1AGE01**, Desc: **Age at visit 1 [Cohort. Visit 1]**, Table: **DERIVE13**. - * _phs000280.v4.pht004063.v2.phv00204802.v1_. dbGap Name: **CHOLMDCODE01**, Desc: **Cholesterol lowering medication in past 2 weeks: using 2004 Med. code, visit 1 [Cohort. Visit 1]**, Table: **DERIVE13**. + * _phs000280.v4.pht004063.v2.phv00204712.v1_ + * dbGap name: **V1AGE01** + * dbGap desc: **Age at visit 1 [Cohort. Visit 1]** + * dbGap table: **DERIVE13** + * varId _phv00204712_ not found in PIC-SURE data dictionary + * _phs000280.v4.pht004063.v2.phv00204802.v1_ + * dbGap name: **CHOLMDCODE01** + * dbGap desc: **Cholesterol lowering medication in past 2 weeks: using 2004 Med. code, visit 1 [Cohort. Visit 1]** + * dbGap table: **DERIVE13** + * varId _phv00204802_ not found in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -473,8 +603,16 @@ * ### lipids/lipid_lowering_medication_1 -- **CHS Cardiovascular Health Study (CHS) Cohort: an NHLBI-funded observational study of risk factors for cardiovascular disease in adults 65 years or older**: * 2 component_study_variables - * _phs000287.v6.pht001452.v1.phv00100487.v1_. dbGap Name: **AGEBL**, Desc: **CALCULATED AGE AT BASELINE**, Table: **BASEBOTH**. - * _phs000287.v6.pht001452.v1.phv00100594.v1_. dbGap Name: **LIPID06**, Desc: **Any lipid-lowering medication**, Table: **BASEBOTH**. + * _phs000287.v6.pht001452.v1.phv00100487.v1_ + * dbGap name: **AGEBL** + * dbGap desc: **CALCULATED AGE AT BASELINE** + * dbGap table: **BASEBOTH** + * No permissible values listed in PIC-SURE data dictionary + * _phs000287.v6.pht001452.v1.phv00100594.v1_ + * dbGap name: **LIPID06** + * dbGap desc: **Any lipid-lowering medication** + * dbGap table: **BASEBOTH** + * PIC-SURE permissible values: No, Yes * **Function:** ```r harmonize <- function(phen_list){ @@ -493,8 +631,16 @@ * ### lipids/lipid_lowering_medication_1 -- **HCHS_SOL Hispanic Community Health Study /Study of Latinos (HCHS/SOL)**: * 2 component_study_variables - * _phs000810.v1.pht004715.v1.phv00226251.v1_. dbGap Name: **AGE**, Desc: **Age**, Table: **HCHS_SOL_Cohort_Subject_Phenotypes**. - * _phs000810.v1.pht004715.v1.phv00226349.v1_. dbGap Name: **MED_LLD**, Desc: **Lipid lowering drugs/Antihyperlipidemics (LLD)**, Table: **HCHS_SOL_Cohort_Subject_Phenotypes**. + * _phs000810.v1.pht004715.v1.phv00226251.v1_ + * dbGap name: **AGE** + * dbGap desc: **Age** + * dbGap table: **HCHS_SOL_Cohort_Subject_Phenotypes** + * No permissible values listed in PIC-SURE data dictionary + * _phs000810.v1.pht004715.v1.phv00226349.v1_ + * dbGap name: **MED_LLD** + * dbGap desc: **Lipid lowering drugs/Antihyperlipidemics (LLD)** + * dbGap table: **HCHS_SOL_Cohort_Subject_Phenotypes** + * PIC-SURE permissible values: No, Yes * **Function:** ```r harmonize <- function(phen_list){ @@ -511,8 +657,12 @@ * ### lipids/lipid_lowering_medication_1 -- **JHS Jackson Heart Study (JHS) Cohort**: * 2 component_study_variables - * _phs000286.v5.pht001949.v1.phv00126009.v1_. No dbGap metadata available. - * _phs000286.v5.pht001949.v1.phv00126053.v1_. No dbGap metadata available. + * _phs000286.v5.pht001949.v1.phv00126009.v1_ + * No dbGap metadata available + * varId _phv00126009_ not found in PIC-SURE data dictionary + * _phs000286.v5.pht001949.v1.phv00126053.v1_ + * No dbGap metadata available + * varId _phv00126053_ not found in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -537,12 +687,36 @@ * ### lipids/lipid_lowering_medication_1 -- **MESA Multi-Ethnic Study of Atherosclerosis (MESA) Cohort**: * 6 component_study_variables - * _phs000209.v13.pht001111.v4.phv00082639.v2_. dbGap Name: **age1c**, Desc: **AGE**, Table: **MESA_AirNRExamMain**. - * _phs000209.v13.pht001111.v4.phv00083162.v1_. dbGap Name: **lipid1c**, Desc: **ANY LIPID-LOWERING MEDICATION**, Table: **MESA_AirNRExamMain**. - * _phs000209.v13.pht001116.v10.phv00084442.v3_. dbGap Name: **age1c**, Desc: **AGE**, Table: **MESA_Exam1Main**. - * _phs000209.v13.pht001116.v10.phv00085407.v2_. dbGap Name: **lipid1c**, Desc: **ANY LIPID-LOWERING MEDICATION**, Table: **MESA_Exam1Main**. - * _phs000209.v13.pht001121.v3.phv00087071.v1_. dbGap Name: **agefc**, Desc: **AGE**, Table: **MESA_FamilyExamMain**. - * _phs000209.v13.pht001121.v3.phv00087104.v1_. dbGap Name: **lipidfc**, Desc: **ANY LIPID-LOWERING MEDICATION**, Table: **MESA_FamilyExamMain**. + * _phs000209.v13.pht001111.v4.phv00082639.v2_ + * dbGap name: **age1c** + * dbGap desc: **AGE** + * dbGap table: **MESA_AirNRExamMain** + * No permissible values listed in PIC-SURE data dictionary + * _phs000209.v13.pht001111.v4.phv00083162.v1_ + * dbGap name: **lipid1c** + * dbGap desc: **ANY LIPID-LOWERING MEDICATION** + * dbGap table: **MESA_AirNRExamMain** + * PIC-SURE permissible values: NO, YES + * _phs000209.v13.pht001116.v10.phv00084442.v3_ + * dbGap name: **age1c** + * dbGap desc: **AGE** + * dbGap table: **MESA_Exam1Main** + * No permissible values listed in PIC-SURE data dictionary + * _phs000209.v13.pht001116.v10.phv00085407.v2_ + * dbGap name: **lipid1c** + * dbGap desc: **ANY LIPID-LOWERING MEDICATION** + * dbGap table: **MESA_Exam1Main** + * PIC-SURE permissible values: NO, YES + * _phs000209.v13.pht001121.v3.phv00087071.v1_ + * dbGap name: **agefc** + * dbGap desc: **AGE** + * dbGap table: **MESA_FamilyExamMain** + * No permissible values listed in PIC-SURE data dictionary + * _phs000209.v13.pht001121.v3.phv00087104.v1_ + * dbGap name: **lipidfc** + * dbGap desc: **ANY LIPID-LOWERING MEDICATION** + * dbGap table: **MESA_FamilyExamMain** + * PIC-SURE permissible values: NO, YES * **Function:** ```r harmonize <- function(phen_list){ @@ -622,8 +796,16 @@ * ### lipids/total_cholesterol_1 -- **ARIC Atherosclerosis Risk in Communities (ARIC) Cohort**: * 2 component_study_variables - * _phs000280.v4.pht004063.v2.phv00204712.v1_. dbGap Name: **V1AGE01**, Desc: **Age at visit 1 [Cohort. Visit 1]**, Table: **DERIVE13**. - * _phs000280.v4.pht004063.v2.phv00204735.v1_. dbGap Name: **TCHSIU01**, Desc: **Total cholesterol in SI units [Cohort. Visit 1]**, Table: **DERIVE13**. + * _phs000280.v4.pht004063.v2.phv00204712.v1_ + * dbGap name: **V1AGE01** + * dbGap desc: **Age at visit 1 [Cohort. Visit 1]** + * dbGap table: **DERIVE13** + * varId _phv00204712_ not found in PIC-SURE data dictionary + * _phs000280.v4.pht004063.v2.phv00204735.v1_ + * dbGap name: **TCHSIU01** + * dbGap desc: **Total cholesterol in SI units [Cohort. Visit 1]** + * dbGap table: **DERIVE13** + * varId _phv00204735_ not found in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -649,8 +831,16 @@ * ### lipids/total_cholesterol_1 -- **CARDIA CARDIA Cohort**: * 2 component_study_variables - * _phs000285.v3.pht001559.v2.phv00112439.v2_. dbGap Name: **A01AGE2**, Desc: **AGE VERIFY**, Table: **A4F01**. - * _phs000285.v3.pht001588.v2.phv00113700.v2_. dbGap Name: **AL1CHOL**, Desc: **TOTAL CHOLESTEROL (MG/DL)**, Table: **A4LIP**. + * _phs000285.v3.pht001559.v2.phv00112439.v2_ + * dbGap name: **A01AGE2** + * dbGap desc: **AGE VERIFY** + * dbGap table: **A4F01** + * varId _phv00112439_ not found in PIC-SURE data dictionary + * _phs000285.v3.pht001588.v2.phv00113700.v2_ + * dbGap name: **AL1CHOL** + * dbGap desc: **TOTAL CHOLESTEROL (MG/DL)** + * dbGap table: **A4LIP** + * varId _phv00113700_ not found in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -669,8 +859,16 @@ * ### lipids/total_cholesterol_1 -- **CHS Cardiovascular Health Study (CHS) Cohort: an NHLBI-funded observational study of risk factors for cardiovascular disease in adults 65 years or older**: * 2 component_study_variables - * _phs000287.v6.pht001452.v1.phv00100487.v1_. dbGap Name: **AGEBL**, Desc: **CALCULATED AGE AT BASELINE**, Table: **BASEBOTH**. - * _phs000287.v6.pht001452.v1.phv00100491.v1_. dbGap Name: **CHOLADJ**, Desc: **Adjusted Cholesterol (mg/dl)**, Table: **BASEBOTH**. + * _phs000287.v6.pht001452.v1.phv00100487.v1_ + * dbGap name: **AGEBL** + * dbGap desc: **CALCULATED AGE AT BASELINE** + * dbGap table: **BASEBOTH** + * No permissible values listed in PIC-SURE data dictionary + * _phs000287.v6.pht001452.v1.phv00100491.v1_ + * dbGap name: **CHOLADJ** + * dbGap desc: **Adjusted Cholesterol (mg/dl)** + * dbGap table: **BASEBOTH** + * No permissible values listed in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -687,8 +885,16 @@ * ### lipids/total_cholesterol_1 -- **HCHS_SOL Hispanic Community Health Study /Study of Latinos (HCHS/SOL)**: * 2 component_study_variables - * _phs000810.v1.pht004715.v1.phv00226251.v1_. dbGap Name: **AGE**, Desc: **Age**, Table: **HCHS_SOL_Cohort_Subject_Phenotypes**. - * _phs000810.v1.pht004715.v1.phv00253238.v1_. dbGap Name: **LABA66**, Desc: **Total cholesterol (mg/dL) (LABA66)**, Table: **HCHS_SOL_Cohort_Subject_Phenotypes**. + * _phs000810.v1.pht004715.v1.phv00226251.v1_ + * dbGap name: **AGE** + * dbGap desc: **Age** + * dbGap table: **HCHS_SOL_Cohort_Subject_Phenotypes** + * No permissible values listed in PIC-SURE data dictionary + * _phs000810.v1.pht004715.v1.phv00253238.v1_ + * dbGap name: **LABA66** + * dbGap desc: **Total cholesterol (mg/dL) (LABA66)** + * dbGap table: **HCHS_SOL_Cohort_Subject_Phenotypes** + * No permissible values listed in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -705,8 +911,14 @@ * ### lipids/total_cholesterol_1 -- **JHS Jackson Heart Study (JHS) Cohort**: * 2 component_study_variables - * _phs000286.v5.pht001945.v1.phv00125927.v1_. dbGap Name: **CHR**, Desc: **Chr: total cholesterol - mg/dL [Visit 1]**, Table: **cena**. - * _phs000286.v5.pht001949.v1.phv00126009.v1_. No dbGap metadata available. + * _phs000286.v5.pht001945.v1.phv00125927.v1_ + * dbGap name: **CHR** + * dbGap desc: **Chr: total cholesterol - mg/dL [Visit 1]** + * dbGap table: **cena** + * varId _phv00125927_ not found in PIC-SURE data dictionary + * _phs000286.v5.pht001949.v1.phv00126009.v1_ + * No dbGap metadata available + * varId _phv00126009_ not found in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -734,12 +946,36 @@ * ### lipids/total_cholesterol_1 -- **MESA Multi-Ethnic Study of Atherosclerosis (MESA) Cohort**: * 6 component_study_variables - * _phs000209.v13.pht001111.v4.phv00082639.v2_. dbGap Name: **age1c**, Desc: **AGE**, Table: **MESA_AirNRExamMain**. - * _phs000209.v13.pht001111.v4.phv00082956.v1_. dbGap Name: **chol1**, Desc: **TOTAL CHOLESTEROL (mg/dl)**, Table: **MESA_AirNRExamMain**. - * _phs000209.v13.pht001116.v10.phv00084442.v3_. dbGap Name: **age1c**, Desc: **AGE**, Table: **MESA_Exam1Main**. - * _phs000209.v13.pht001116.v10.phv00084974.v2_. dbGap Name: **chol1**, Desc: **TOTAL CHOLESTEROL (mg/dl)**, Table: **MESA_Exam1Main**. - * _phs000209.v13.pht001121.v3.phv00087071.v1_. dbGap Name: **agefc**, Desc: **AGE**, Table: **MESA_FamilyExamMain**. - * _phs000209.v13.pht001121.v3.phv00087100.v1_. dbGap Name: **cholf**, Desc: **TOTAL CHOLESTEROL (mg/dl)**, Table: **MESA_FamilyExamMain**. + * _phs000209.v13.pht001111.v4.phv00082639.v2_ + * dbGap name: **age1c** + * dbGap desc: **AGE** + * dbGap table: **MESA_AirNRExamMain** + * No permissible values listed in PIC-SURE data dictionary + * _phs000209.v13.pht001111.v4.phv00082956.v1_ + * dbGap name: **chol1** + * dbGap desc: **TOTAL CHOLESTEROL (mg/dl)** + * dbGap table: **MESA_AirNRExamMain** + * No permissible values listed in PIC-SURE data dictionary + * _phs000209.v13.pht001116.v10.phv00084442.v3_ + * dbGap name: **age1c** + * dbGap desc: **AGE** + * dbGap table: **MESA_Exam1Main** + * No permissible values listed in PIC-SURE data dictionary + * _phs000209.v13.pht001116.v10.phv00084974.v2_ + * dbGap name: **chol1** + * dbGap desc: **TOTAL CHOLESTEROL (mg/dl)** + * dbGap table: **MESA_Exam1Main** + * No permissible values listed in PIC-SURE data dictionary + * _phs000209.v13.pht001121.v3.phv00087071.v1_ + * dbGap name: **agefc** + * dbGap desc: **AGE** + * dbGap table: **MESA_FamilyExamMain** + * No permissible values listed in PIC-SURE data dictionary + * _phs000209.v13.pht001121.v3.phv00087100.v1_ + * dbGap name: **cholf** + * dbGap desc: **TOTAL CHOLESTEROL (mg/dl)** + * dbGap table: **MESA_FamilyExamMain** + * No permissible values listed in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -807,8 +1043,16 @@ * ### lipids/triglycerides_1 -- **ARIC Atherosclerosis Risk in Communities (ARIC) Cohort**: * 2 component_study_variables - * _phs000280.v4.pht004063.v2.phv00204712.v1_. dbGap Name: **V1AGE01**, Desc: **Age at visit 1 [Cohort. Visit 1]**, Table: **DERIVE13**. - * _phs000280.v4.pht004063.v2.phv00204738.v1_. dbGap Name: **TRGSIU01**, Desc: **Total triglycerides In SI units [Cohort. Visit 1]**, Table: **DERIVE13**. + * _phs000280.v4.pht004063.v2.phv00204712.v1_ + * dbGap name: **V1AGE01** + * dbGap desc: **Age at visit 1 [Cohort. Visit 1]** + * dbGap table: **DERIVE13** + * varId _phv00204712_ not found in PIC-SURE data dictionary + * _phs000280.v4.pht004063.v2.phv00204738.v1_ + * dbGap name: **TRGSIU01** + * dbGap desc: **Total triglycerides In SI units [Cohort. Visit 1]** + * dbGap table: **DERIVE13** + * varId _phv00204738_ not found in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -836,8 +1080,16 @@ * ### lipids/triglycerides_1 -- **CARDIA CARDIA Cohort**: * 2 component_study_variables - * _phs000285.v3.pht001559.v2.phv00112439.v2_. dbGap Name: **A01AGE2**, Desc: **AGE VERIFY**, Table: **A4F01**. - * _phs000285.v3.pht001588.v2.phv00113701.v2_. dbGap Name: **AL1NTRIG**, Desc: **TRIGLYCERIDES (MG/DL)**, Table: **A4LIP**. + * _phs000285.v3.pht001559.v2.phv00112439.v2_ + * dbGap name: **A01AGE2** + * dbGap desc: **AGE VERIFY** + * dbGap table: **A4F01** + * varId _phv00112439_ not found in PIC-SURE data dictionary + * _phs000285.v3.pht001588.v2.phv00113701.v2_ + * dbGap name: **AL1NTRIG** + * dbGap desc: **TRIGLYCERIDES (MG/DL)** + * dbGap table: **A4LIP** + * varId _phv00113701_ not found in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -856,8 +1108,16 @@ * ### lipids/triglycerides_1 -- **CHS Cardiovascular Health Study (CHS) Cohort: an NHLBI-funded observational study of risk factors for cardiovascular disease in adults 65 years or older**: * 2 component_study_variables - * _phs000287.v6.pht001452.v1.phv00100425.v1_. dbGap Name: **TRIG44**, Desc: **TRIGLYCERIDE (mg/dl)**, Table: **BASEBOTH**. - * _phs000287.v6.pht001452.v1.phv00100487.v1_. dbGap Name: **AGEBL**, Desc: **CALCULATED AGE AT BASELINE**, Table: **BASEBOTH**. + * _phs000287.v6.pht001452.v1.phv00100425.v1_ + * dbGap name: **TRIG44** + * dbGap desc: **TRIGLYCERIDE (mg/dl)** + * dbGap table: **BASEBOTH** + * No permissible values listed in PIC-SURE data dictionary + * _phs000287.v6.pht001452.v1.phv00100487.v1_ + * dbGap name: **AGEBL** + * dbGap desc: **CALCULATED AGE AT BASELINE** + * dbGap table: **BASEBOTH** + * No permissible values listed in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -874,8 +1134,16 @@ * ### lipids/triglycerides_1 -- **HCHS_SOL Hispanic Community Health Study /Study of Latinos (HCHS/SOL)**: * 2 component_study_variables - * _phs000810.v1.pht004715.v1.phv00226251.v1_. dbGap Name: **AGE**, Desc: **Age**, Table: **HCHS_SOL_Cohort_Subject_Phenotypes**. - * _phs000810.v1.pht004715.v1.phv00253240.v1_. dbGap Name: **LABA67**, Desc: **Triglycerides (mg/dL) (LABA67)**, Table: **HCHS_SOL_Cohort_Subject_Phenotypes**. + * _phs000810.v1.pht004715.v1.phv00226251.v1_ + * dbGap name: **AGE** + * dbGap desc: **Age** + * dbGap table: **HCHS_SOL_Cohort_Subject_Phenotypes** + * No permissible values listed in PIC-SURE data dictionary + * _phs000810.v1.pht004715.v1.phv00253240.v1_ + * dbGap name: **LABA67** + * dbGap desc: **Triglycerides (mg/dL) (LABA67)** + * dbGap table: **HCHS_SOL_Cohort_Subject_Phenotypes** + * No permissible values listed in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -891,8 +1159,14 @@ * ### lipids/triglycerides_1 -- **JHS Jackson Heart Study (JHS) Cohort**: * 2 component_study_variables - * _phs000286.v5.pht001945.v1.phv00125933.v1_. dbGap Name: **TRR**, Desc: **Trr: triglyceride - mg/dL [Visit 1]**, Table: **cena**. - * _phs000286.v5.pht001949.v1.phv00126009.v1_. No dbGap metadata available. + * _phs000286.v5.pht001945.v1.phv00125933.v1_ + * dbGap name: **TRR** + * dbGap desc: **Trr: triglyceride - mg/dL [Visit 1]** + * dbGap table: **cena** + * varId _phv00125933_ not found in PIC-SURE data dictionary + * _phs000286.v5.pht001949.v1.phv00126009.v1_ + * No dbGap metadata available + * varId _phv00126009_ not found in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -920,12 +1194,36 @@ * ### lipids/triglycerides_1 -- **MESA Multi-Ethnic Study of Atherosclerosis (MESA) Cohort**: * 6 component_study_variables - * _phs000209.v13.pht001111.v4.phv00082639.v2_. dbGap Name: **age1c**, Desc: **AGE**, Table: **MESA_AirNRExamMain**. - * _phs000209.v13.pht001111.v4.phv00082950.v1_. dbGap Name: **trig1**, Desc: **TRIGLYCERIDES (mg/dl)**, Table: **MESA_AirNRExamMain**. - * _phs000209.v13.pht001116.v10.phv00084442.v3_. dbGap Name: **age1c**, Desc: **AGE**, Table: **MESA_Exam1Main**. - * _phs000209.v13.pht001116.v10.phv00084968.v2_. dbGap Name: **trig1**, Desc: **TRIGLYCERIDES (mg/dl)**, Table: **MESA_Exam1Main**. - * _phs000209.v13.pht001121.v3.phv00087071.v1_. dbGap Name: **agefc**, Desc: **AGE**, Table: **MESA_FamilyExamMain**. - * _phs000209.v13.pht001121.v3.phv00087101.v1_. dbGap Name: **trigf**, Desc: **TRIGLYCERIDES (mg/dl)**, Table: **MESA_FamilyExamMain**. + * _phs000209.v13.pht001111.v4.phv00082639.v2_ + * dbGap name: **age1c** + * dbGap desc: **AGE** + * dbGap table: **MESA_AirNRExamMain** + * No permissible values listed in PIC-SURE data dictionary + * _phs000209.v13.pht001111.v4.phv00082950.v1_ + * dbGap name: **trig1** + * dbGap desc: **TRIGLYCERIDES (mg/dl)** + * dbGap table: **MESA_AirNRExamMain** + * No permissible values listed in PIC-SURE data dictionary + * _phs000209.v13.pht001116.v10.phv00084442.v3_ + * dbGap name: **age1c** + * dbGap desc: **AGE** + * dbGap table: **MESA_Exam1Main** + * No permissible values listed in PIC-SURE data dictionary + * _phs000209.v13.pht001116.v10.phv00084968.v2_ + * dbGap name: **trig1** + * dbGap desc: **TRIGLYCERIDES (mg/dl)** + * dbGap table: **MESA_Exam1Main** + * No permissible values listed in PIC-SURE data dictionary + * _phs000209.v13.pht001121.v3.phv00087071.v1_ + * dbGap name: **agefc** + * dbGap desc: **AGE** + * dbGap table: **MESA_FamilyExamMain** + * No permissible values listed in PIC-SURE data dictionary + * _phs000209.v13.pht001121.v3.phv00087101.v1_ + * dbGap name: **trigf** + * dbGap desc: **TRIGLYCERIDES (mg/dl)** + * dbGap table: **MESA_FamilyExamMain** + * No permissible values listed in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ diff --git a/resources/human-readable-harmonized-variable-documentation/generated-doc-pages/sleep.md b/resources/human-readable-harmonized-variable-documentation/generated-doc-pages/sleep.md index 8c6991b..500b6d8 100644 --- a/resources/human-readable-harmonized-variable-documentation/generated-doc-pages/sleep.md +++ b/resources/human-readable-harmonized-variable-documentation/generated-doc-pages/sleep.md @@ -67,16 +67,38 @@ * ### sleep/sleep_duration_1 -- **ARIC Atherosclerosis Risk in Communities (ARIC) Cohort**: * 10 component_study_variables - * _phs000280.v5.pht004228.v2.phv00214261.v1_. No dbGap metadata available. - * _phs000280.v5.pht004228.v2.phv00214262.v1_. No dbGap metadata available. - * _phs000280.v5.pht004228.v2.phv00214263.v1_. No dbGap metadata available. - * _phs000280.v5.pht004228.v2.phv00214268.v1_. No dbGap metadata available. - * _phs000280.v5.pht004228.v2.phv00214269.v1_. No dbGap metadata available. - * _phs000280.v5.pht004228.v2.phv00214270.v1_. No dbGap metadata available. - * _phs000280.v5.pht004228.v2.phv00214274.v1_. No dbGap metadata available. - * _phs000280.v5.pht004228.v2.phv00215388.v1_. No dbGap metadata available. - * _phs000280.v5.pht006431.v1.phv00295623.v1_. No dbGap metadata available. - * _phs000280.v5.pht006479.v1.phv00298019.v1_. dbGap Name: **RSE21**, Desc: **F. Sleep. Q21. Hours of sleep in past month [Respiratory Symptoms Form. RSE. Visit 5]**, Table: **RSE**. + * _phs000280.v5.pht004228.v2.phv00214261.v1_ + * No dbGap metadata available + * varId _phv00214261_ not found in PIC-SURE data dictionary + * _phs000280.v5.pht004228.v2.phv00214262.v1_ + * No dbGap metadata available + * varId _phv00214262_ not found in PIC-SURE data dictionary + * _phs000280.v5.pht004228.v2.phv00214263.v1_ + * No dbGap metadata available + * varId _phv00214263_ not found in PIC-SURE data dictionary + * _phs000280.v5.pht004228.v2.phv00214268.v1_ + * No dbGap metadata available + * varId _phv00214268_ not found in PIC-SURE data dictionary + * _phs000280.v5.pht004228.v2.phv00214269.v1_ + * No dbGap metadata available + * varId _phv00214269_ not found in PIC-SURE data dictionary + * _phs000280.v5.pht004228.v2.phv00214270.v1_ + * No dbGap metadata available + * varId _phv00214270_ not found in PIC-SURE data dictionary + * _phs000280.v5.pht004228.v2.phv00214274.v1_ + * No dbGap metadata available + * varId _phv00214274_ not found in PIC-SURE data dictionary + * _phs000280.v5.pht004228.v2.phv00215388.v1_ + * No dbGap metadata available + * varId _phv00215388_ not found in PIC-SURE data dictionary + * _phs000280.v5.pht006431.v1.phv00295623.v1_ + * No dbGap metadata available + * varId _phv00295623_ not found in PIC-SURE data dictionary + * _phs000280.v5.pht006479.v1.phv00298019.v1_ + * dbGap name: **RSE21** + * dbGap desc: **F. Sleep. Q21. Hours of sleep in past month [Respiratory Symptoms Form. RSE. Visit 5]** + * dbGap table: **RSE** + * varId _phv00298019_ not found in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -138,8 +160,16 @@ * ### sleep/sleep_duration_1 -- **CARDIA CARDIA Cohort**: * 2 component_study_variables - * _phs000285.v3.pht001839.v2.phv00120534.v2_. dbGap Name: **F67SLPHR**, Desc: **PAST MONTH AVG SLEEPING HOURS. Q 7**, Table: **F1F67**. - * _phs000285.v3.pht001851.v2.phv00120748.v2_. dbGap Name: **EX6_AGE**, Desc: **CALCULATED AGE AT EXAM 6**, Table: **F1REF**. + * _phs000285.v3.pht001839.v2.phv00120534.v2_ + * dbGap name: **F67SLPHR** + * dbGap desc: **PAST MONTH AVG SLEEPING HOURS. Q 7** + * dbGap table: **F1F67** + * varId _phv00120534_ not found in PIC-SURE data dictionary + * _phs000285.v3.pht001851.v2.phv00120748.v2_ + * dbGap name: **EX6_AGE** + * dbGap desc: **CALCULATED AGE AT EXAM 6** + * dbGap table: **F1REF** + * varId _phv00120748_ not found in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -161,8 +191,16 @@ * ### sleep/sleep_duration_1 -- **CHS Cardiovascular Health Study (CHS) Cohort: an NHLBI-funded observational study of risk factors for cardiovascular disease in adults 65 years or older**: * 2 component_study_variables - * _phs000287.v6.pht001460.v1.phv00100694.v1_. dbGap Name: **AGE_S1**, Desc: **Age = StdyDtqa - DOB**, Table: **CHS_SHHS1_15K**. - * _phs000287.v6.pht001460.v1.phv00100712.v1_. dbGap Name: **HRSWD02**, Desc: **How many hours of sleep do you usually get at night (or your main sleep period) on weekdays or workdays?**, Table: **CHS_SHHS1_15K**. + * _phs000287.v6.pht001460.v1.phv00100694.v1_ + * dbGap name: **AGE_S1** + * dbGap desc: **Age = StdyDtqa - DOB** + * dbGap table: **CHS_SHHS1_15K** + * No permissible values listed in PIC-SURE data dictionary + * _phs000287.v6.pht001460.v1.phv00100712.v1_ + * dbGap name: **HRSWD02** + * dbGap desc: **How many hours of sleep do you usually get at night (or your main sleep period) on weekdays or workdays?** + * dbGap table: **CHS_SHHS1_15K** + * No permissible values listed in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -182,8 +220,16 @@ * ### sleep/sleep_duration_1 -- **HCHS_SOL Hispanic Community Health Study /Study of Latinos (HCHS/SOL)**: * 2 component_study_variables - * _phs000810.v1.pht004715.v1.phv00226251.v1_. dbGap Name: **AGE**, Desc: **Age**, Table: **HCHS_SOL_Cohort_Subject_Phenotypes**. - * _phs000810.v1.pht004715.v1.phv00258046.v1_. dbGap Name: **SLPDUR**, Desc: **Average sleep duration (hours)**, Table: **HCHS_SOL_Cohort_Subject_Phenotypes**. + * _phs000810.v1.pht004715.v1.phv00226251.v1_ + * dbGap name: **AGE** + * dbGap desc: **Age** + * dbGap table: **HCHS_SOL_Cohort_Subject_Phenotypes** + * No permissible values listed in PIC-SURE data dictionary + * _phs000810.v1.pht004715.v1.phv00258046.v1_ + * dbGap name: **SLPDUR** + * dbGap desc: **Average sleep duration (hours)** + * dbGap table: **HCHS_SOL_Cohort_Subject_Phenotypes** + * No permissible values listed in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -203,8 +249,14 @@ * ### sleep/sleep_duration_1 -- **JHS Jackson Heart Study (JHS) Cohort**: * 2 component_study_variables - * _phs000286.v5.pht001949.v1.phv00126009.v1_. No dbGap metadata available. - * _phs000286.v5.pht001963.v1.phv00127678.v1_. dbGap Name: **MHXA7**, Desc: **Q7. A. Sleep. During the past month, excluding naps, how many hours of actual sleep did you get at night (or day, if you work at night) on average (Hours)? [Visit 1] [Medical History Form, MHX]**, Table: **mhxa**. + * _phs000286.v5.pht001949.v1.phv00126009.v1_ + * No dbGap metadata available + * varId _phv00126009_ not found in PIC-SURE data dictionary + * _phs000286.v5.pht001963.v1.phv00127678.v1_ + * dbGap name: **MHXA7** + * dbGap desc: **Q7. A. Sleep. During the past month, excluding naps, how many hours of actual sleep did you get at night (or day, if you work at night) on average (Hours)? [Visit 1] [Medical History Form, MHX]** + * dbGap table: **mhxa** + * varId _phv00127678_ not found in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list){ @@ -221,8 +273,16 @@ * ### sleep/sleep_duration_1 -- **MESA Multi-Ethnic Study of Atherosclerosis (MESA) Cohort**: * 2 component_study_variables - * _phs000209.v13.pht001120.v10.phv00086727.v3_. dbGap Name: **age4c**, Desc: **AGE AT EXAM 4**, Table: **MESA_Exam4Main**. - * _phs000209.v13.pht001120.v10.phv00087048.v2_. dbGap Name: **slpwkhr4**, Desc: **NIGHT SLEEP HOURS ON WEEKDAY OR WORKDAY**, Table: **MESA_Exam4Main**. + * _phs000209.v13.pht001120.v10.phv00086727.v3_ + * dbGap name: **age4c** + * dbGap desc: **AGE AT EXAM 4** + * dbGap table: **MESA_Exam4Main** + * PIC-SURE permissible values: 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90 + * _phs000209.v13.pht001120.v10.phv00087048.v2_ + * dbGap name: **slpwkhr4** + * dbGap desc: **NIGHT SLEEP HOURS ON WEEKDAY OR WORKDAY** + * dbGap table: **MESA_Exam4Main** + * PIC-SURE permissible values: 0, 1, 10, 11, 12, 13, 14, 2, 24, 25, 3, 4, 5, 6, 7, 8, 9, 99 * **Function:** ```r harmonize <- function(phen_list){ @@ -242,11 +302,31 @@ * ### sleep/sleep_duration_1 -- **WHI Women's Health Initiative**: * 5 component_study_variables - * _phs000200.v11.pht000998.v6.phv00078436.v6_. dbGap Name: **F2DAYS**, Desc: **F2 Days since randomization**, Table: **f2_rel1**. - * _phs000200.v11.pht000998.v6.phv00078437.v6_. dbGap Name: **AGE**, Desc: **Age at screening**, Table: **f2_rel1**. - * _phs000200.v11.pht001005.v6.phv00078869.v6_. dbGap Name: **F37VY**, Desc: **Visit year**, Table: **f37_rel1**. - * _phs000200.v11.pht001005.v6.phv00078870.v6_. dbGap Name: **F37DAYS**, Desc: **F37 Days since randomization/enrollment**, Table: **f37_rel1**. - * _phs000200.v11.pht001005.v6.phv00079041.v6_. dbGap Name: **HRSSLP**, Desc: **How many hours of sleep**, Table: **f37_rel1**. + * _phs000200.v11.pht000998.v6.phv00078436.v6_ + * dbGap name: **F2DAYS** + * dbGap desc: **F2 Days since randomization** + * dbGap table: **f2_rel1** + * No permissible values listed in PIC-SURE data dictionary + * _phs000200.v11.pht000998.v6.phv00078437.v6_ + * dbGap name: **AGE** + * dbGap desc: **Age at screening** + * dbGap table: **f2_rel1** + * No permissible values listed in PIC-SURE data dictionary + * _phs000200.v11.pht001005.v6.phv00078869.v6_ + * dbGap name: **F37VY** + * dbGap desc: **Visit year** + * dbGap table: **f37_rel1** + * No permissible values listed in PIC-SURE data dictionary + * _phs000200.v11.pht001005.v6.phv00078870.v6_ + * dbGap name: **F37DAYS** + * dbGap desc: **F37 Days since randomization/enrollment** + * dbGap table: **f37_rel1** + * No permissible values listed in PIC-SURE data dictionary + * _phs000200.v11.pht001005.v6.phv00079041.v6_ + * dbGap name: **HRSSLP** + * dbGap desc: **How many hours of sleep** + * dbGap table: **f37_rel1** + * PIC-SURE permissible values: 10 or more hours, 5 or less hours, 6 hours, 7 hours, 8 hours, 9 hours * **Function:** ```r harmonize <- function(phen_list){ diff --git a/resources/human-readable-harmonized-variable-documentation/generated-doc-pages/vte.md b/resources/human-readable-harmonized-variable-documentation/generated-doc-pages/vte.md index 1a9c8ee..c17ed16 100644 --- a/resources/human-readable-harmonized-variable-documentation/generated-doc-pages/vte.md +++ b/resources/human-readable-harmonized-variable-documentation/generated-doc-pages/vte.md @@ -137,9 +137,17 @@ * ### vte/vte_case_status_1 -- **ARIC Atherosclerosis Risk in Communities (ARIC) Cohort**: * 3 component_study_variables - * _phs000280.v4.pht004063.v2.phv00204712.v1_. dbGap Name: **V1AGE01**, Desc: **Age at visit 1 [Cohort. Visit 1]**, Table: **DERIVE13**. - * _phs000280.v4.pht006485.v1.phv00298125.v1_. No dbGap metadata available. - * _phs000280.v4.pht006485.v1.phv00298126.v1_. No dbGap metadata available. + * _phs000280.v4.pht004063.v2.phv00204712.v1_ + * dbGap name: **V1AGE01** + * dbGap desc: **Age at visit 1 [Cohort. Visit 1]** + * dbGap table: **DERIVE13** + * varId _phv00204712_ not found in PIC-SURE data dictionary + * _phs000280.v4.pht006485.v1.phv00298125.v1_ + * No dbGap metadata available + * varId _phv00298125_ not found in PIC-SURE data dictionary + * _phs000280.v4.pht006485.v1.phv00298126.v1_ + * No dbGap metadata available + * varId _phv00298126_ not found in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list) { @@ -180,10 +188,26 @@ * ### vte/vte_case_status_1 -- **CHS Cardiovascular Health Study (CHS) Cohort: an NHLBI-funded observational study of risk factors for cardiovascular disease in adults 65 years or older**: * 4 component_study_variables - * _phs000287.v6.pht001452.v1.phv00100487.v1_. dbGap Name: **AGEBL**, Desc: **CALCULATED AGE AT BASELINE**, Table: **BASEBOTH**. - * _phs000287.v6.pht005981.v1.phv00273565.v1_. dbGap Name: **vt**, Desc: **Lite: VT case (through dec01)**, Table: **CHS_VTE_data**. - * _phs000287.v6.pht005981.v1.phv00273566.v1_. dbGap Name: **ttoevent**, Desc: **Days from baseline to VT or censoring (through dec01)**, Table: **CHS_VTE_data**. - * _phs000287.v6.pht005981.v1.phv00273567.v1_. dbGap Name: **vtpehx01**, Desc: **LITE : Self-report of DVT or PE at baseline**, Table: **CHS_VTE_data**. + * _phs000287.v6.pht001452.v1.phv00100487.v1_ + * dbGap name: **AGEBL** + * dbGap desc: **CALCULATED AGE AT BASELINE** + * dbGap table: **BASEBOTH** + * No permissible values listed in PIC-SURE data dictionary + * _phs000287.v6.pht005981.v1.phv00273565.v1_ + * dbGap name: **vt** + * dbGap desc: **Lite: VT case (through dec01)** + * dbGap table: **CHS_VTE_data** + * PIC-SURE permissible values: No, Yes + * _phs000287.v6.pht005981.v1.phv00273566.v1_ + * dbGap name: **ttoevent** + * dbGap desc: **Days from baseline to VT or censoring (through dec01)** + * dbGap table: **CHS_VTE_data** + * No permissible values listed in PIC-SURE data dictionary + * _phs000287.v6.pht005981.v1.phv00273567.v1_ + * dbGap name: **vtpehx01** + * dbGap desc: **LITE : Self-report of DVT or PE at baseline** + * dbGap table: **CHS_VTE_data** + * PIC-SURE permissible values: Missing, No, Yes * **Function:** ```r harmonize <- function(phen_list) { @@ -257,8 +281,14 @@ * ### vte/vte_followup_start_age_1 -- **ARIC Atherosclerosis Risk in Communities (ARIC) Cohort**: * 2 component_study_variables - * _phs000280.v4.pht004063.v2.phv00204712.v1_. dbGap Name: **V1AGE01**, Desc: **Age at visit 1 [Cohort. Visit 1]**, Table: **DERIVE13**. - * _phs000280.v4.pht006485.v1.phv00298125.v1_. No dbGap metadata available. + * _phs000280.v4.pht004063.v2.phv00204712.v1_ + * dbGap name: **V1AGE01** + * dbGap desc: **Age at visit 1 [Cohort. Visit 1]** + * dbGap table: **DERIVE13** + * varId _phv00204712_ not found in PIC-SURE data dictionary + * _phs000280.v4.pht006485.v1.phv00298125.v1_ + * No dbGap metadata available + * varId _phv00298125_ not found in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list) { @@ -288,7 +318,11 @@ * ### vte/vte_followup_start_age_1 -- **CHS Cardiovascular Health Study (CHS) Cohort: an NHLBI-funded observational study of risk factors for cardiovascular disease in adults 65 years or older**: * 1 component_study_variables - * _phs000287.v6.pht001452.v1.phv00100487.v1_. dbGap Name: **AGEBL**, Desc: **CALCULATED AGE AT BASELINE**, Table: **BASEBOTH**. + * _phs000287.v6.pht001452.v1.phv00100487.v1_ + * dbGap name: **AGEBL** + * dbGap desc: **CALCULATED AGE AT BASELINE** + * dbGap table: **BASEBOTH** + * No permissible values listed in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list) { @@ -373,8 +407,14 @@ * ### vte/vte_prior_history_1 -- **ARIC Atherosclerosis Risk in Communities (ARIC) Cohort**: * 2 component_study_variables - * _phs000280.v4.pht004063.v2.phv00204712.v1_. dbGap Name: **V1AGE01**, Desc: **Age at visit 1 [Cohort. Visit 1]**, Table: **DERIVE13**. - * _phs000280.v4.pht006485.v1.phv00298125.v1_. No dbGap metadata available. + * _phs000280.v4.pht004063.v2.phv00204712.v1_ + * dbGap name: **V1AGE01** + * dbGap desc: **Age at visit 1 [Cohort. Visit 1]** + * dbGap table: **DERIVE13** + * varId _phv00204712_ not found in PIC-SURE data dictionary + * _phs000280.v4.pht006485.v1.phv00298125.v1_ + * No dbGap metadata available + * varId _phv00298125_ not found in PIC-SURE data dictionary * **Function:** ```r harmonize <- function(phen_list) { @@ -407,8 +447,16 @@ * ### vte/vte_prior_history_1 -- **CHS Cardiovascular Health Study (CHS) Cohort: an NHLBI-funded observational study of risk factors for cardiovascular disease in adults 65 years or older**: * 2 component_study_variables - * _phs000287.v6.pht001452.v1.phv00100487.v1_. dbGap Name: **AGEBL**, Desc: **CALCULATED AGE AT BASELINE**, Table: **BASEBOTH**. - * _phs000287.v6.pht005981.v1.phv00273567.v1_. dbGap Name: **vtpehx01**, Desc: **LITE : Self-report of DVT or PE at baseline**, Table: **CHS_VTE_data**. + * _phs000287.v6.pht001452.v1.phv00100487.v1_ + * dbGap name: **AGEBL** + * dbGap desc: **CALCULATED AGE AT BASELINE** + * dbGap table: **BASEBOTH** + * No permissible values listed in PIC-SURE data dictionary + * _phs000287.v6.pht005981.v1.phv00273567.v1_ + * dbGap name: **vtpehx01** + * dbGap desc: **LITE : Self-report of DVT or PE at baseline** + * dbGap table: **CHS_VTE_data** + * PIC-SURE permissible values: Missing, No, Yes * **Function:** ```r harmonize <- function(phen_list) { diff --git a/resources/human-readable-harmonized-variable-documentation/harmonization_documentation_generator.py b/resources/human-readable-harmonized-variable-documentation/harmonization_documentation_generator.py index 261af74..2ff417a 100644 --- a/resources/human-readable-harmonized-variable-documentation/harmonization_documentation_generator.py +++ b/resources/human-readable-harmonized-variable-documentation/harmonization_documentation_generator.py @@ -3,6 +3,8 @@ from collections import defaultdict, Counter import re import pandas as pd +from .picsure_data_dict import picsure_dd_parse +from merged_TOPMed_harmonized_data_file.merge_files import extract_phv prioritized_studies = ['ARIC','CARDIA','CHS','COPDGene','FHS','HCHS_SOL','JHS','MESA','WHI'] @@ -21,7 +23,7 @@ def create_anchor(text): return text.lower().replace(' ', '-').replace('**', '').replace('(', '').replace(')', '').replace(',', '') -def generate_markdown(root_dir, output_dir, output_index): +def generate_markdown(root_dir, output_dir, output_index, picsure_dd): """Generate markdown documentation from JSON files""" root_path = Path(root_dir).resolve() sections = defaultdict(list) @@ -29,12 +31,15 @@ def generate_markdown(root_dir, output_dir, output_index): harmonization_units = 0 component_var_lists = {} study_vars = [] + component_study_vars = [] + study_vars_with_dbGap_metadata = [] + study_vars_with_picsure_metadata = [] harm_vars = [] # for printing out hyperlinks for google sheet: https://docs.google.com/spreadsheets/d/1G-AIk2m4UCDfh1OvFID3bewQXqxExeKNNmVxaswLT8E/edit?gid=979420329#gid=979420329&range=D:D var_links = {} # dbGap metadata is available for some phv vals - df = pd.read_csv('../merged-TOPMed-harmonized-data-file/merged_variables.csv') # Read the CSV file + df = pd.read_csv('./merged_TOPMed_harmonized_data_file/merged_variables.csv') # Read the CSV file df = df.drop('TOPMed Harmonized Variable', axis=1) df = df.drop_duplicates(keep='first') dbgap_metadata = df.set_index('TOPMed Component ID').to_dict('index') @@ -131,17 +136,31 @@ def generate_markdown(root_dir, output_dir, output_index): # section.append(f" * {len(unit['component_study_variables'])} component_study_variables: {vars_text}") section.append(f" * {len(unit['component_study_variables'])} component_study_variables") for var in file_study_vars: - vartext = f" * _{var}_" + component_study_vars.append(var) + section.append(f" * _{var}_") md = dbgap_metadata.get(var) - mdtext = [] if md: - mdtext.append(f"Name: **{md['dbGap Variable Name']}**") - mdtext.append(f"Desc: **{md['dbGap Variable Description']}**") - mdtext.append(f"Table: **{md['dbGap pht Name']}**") - vartext += f". dbGap {', '.join(mdtext)}." + section.append(f" * dbGap name: **{md['dbGap Variable Name']}**") + section.append(f" * dbGap desc: **{md['dbGap Variable Description']}**") + section.append(f" * dbGap table: **{md['dbGap pht Name']}**") + study_vars_with_dbGap_metadata.append(var) else: - vartext += f". No dbGap metadata available." - section.append(vartext) + section.append(f" * No dbGap metadata available") + + phv = extract_phv(var) + try: + picsure_rec = picsure_dd.loc[phv] + study_vars_with_picsure_metadata.append(var) + except KeyError: + section.append(f" * varId _{phv}_ not found in PIC-SURE data dictionary") + continue + + var_values = picsure_rec['values'] + if var_values: + section.append(f" * PIC-SURE permissible values: {', '.join(var_values)}") + else: + section.append(f" * No permissible values listed in PIC-SURE data dictionary") + component_var_lists[f"{directory}/{data['name']}/{unit['name']}"] = file_study_vars else: zeros.append("component_study_variables") @@ -201,12 +220,15 @@ def generate_markdown(root_dir, output_dir, output_index): with open(f"{output_dir}/{output_index}", 'w') as f: # Main TOC f.write("# TOPMed Variable Documentation\n") - f.write("### [List of component variables](#component_vars)\n") + # f.write("### [List of component variables](#component_vars)\n") f.write("## Contents\n") for directory in sorted(sections.keys()): f.write(f"* [{directory}]({directory.lower()}.md)\n") f.write("\n") + f.write(f"{len(study_vars_with_dbGap_metadata):,} of {len(component_study_vars):,} input study variables have dbGap metadata\n\n") + f.write(f"{len(study_vars_with_picsure_metadata):,} of {len(component_study_vars):,} input study variables have PIC-SURE metadata\n\n") + f.write('\n\n\n') list_lengths = Counter([len(l) for l in component_var_lists.values()]) keys = sorted(list_lengths.keys()) @@ -225,6 +247,7 @@ def generate_markdown(root_dir, output_dir, output_index): # f.write('\n'.join([f"{k}: {sc[k]}" for k in sc.keys()])) # f.write("\n") + # This stuff is for printing links to be used in google docs vars_in_gsheet_order = [ # for column D https://docs.google.com/spreadsheets/d/1G-AIk2m4UCDfh1OvFID3bewQXqxExeKNNmVxaswLT8E/edit?gid=979420329#gid=979420329 'angina_incident_1', 'cabg_incident_1', 'cad_followup_start_age_1', 'chd_death_definite_1', 'chd_death_probable_1', 'coronary_angioplasty_incident_1', 'mi_incident_1', 'pad_incident_1', 'angina_prior_1', @@ -274,17 +297,20 @@ def generate_markdown(root_dir, output_dir, output_index): print(f"""=CONCATENATE({', " | ", '.join(links)})""") else: print('=' + links[0]) + pass def main(): - input_dir = "../../../topmed-dcc-harmonized-phenotypes/harmonized-variable-documentation" + input_dir = "../../topmed-dcc-harmonized-phenotypes/harmonized-variable-documentation" output_index = "README.md" - output_dir = "generated-doc-pages" + output_dir = "./human-readable-harmonized-variable-documentation/generated-doc-pages" + picsure_dd, picsure_var_vals = picsure_dd_parse() + picsure_dd.set_index('varId', inplace=True) - generate_markdown(input_dir, output_dir, output_index) + generate_markdown(input_dir, output_dir, output_index, picsure_dd) print(f"Documentation generated in {output_dir}/{output_index}") if __name__ == "__main__": - main() \ No newline at end of file + main() diff --git a/resources/human-readable-harmonized-variable-documentation/picsure_data_dict.py b/resources/human-readable-harmonized-variable-documentation/picsure_data_dict.py new file mode 100644 index 0000000..43e2838 --- /dev/null +++ b/resources/human-readable-harmonized-variable-documentation/picsure_data_dict.py @@ -0,0 +1,134 @@ +import pandas as pd +from collections import defaultdict, Counter +import statistics + +PATH = './copies_of_external_source_files' + +def picsure_dd_parse(path=PATH): + cols_to_load = ['values', 'studyId', 'dtId', 'varId', 'is_categorical', 'is_continuous', + 'columnmeta_is_stigmatized', 'columnmeta_name', 'description', + 'columnmeta_min', 'HPDS_PATH', 'derived_group_id', + 'columnmeta_hpds_path', 'columnmeta_var_id', + 'columnmeta_var_group_description', 'derived_var_description', + 'derived_variable_level_data', 'data_hierarchy', + 'derived_group_description', 'columnmeta_max', 'columnmeta_description', + 'derived_study_id', 'hashed_var_id', 'columnmeta_data_type', + 'derived_var_id', 'columnmeta_study_id', 'is_stigmatized', + 'derived_var_name', 'derived_study_abv_name', + 'derived_study_description', 'columnmeta_var_group_id', + 'derived_group_name', 'columnmeta_HPDS_PATH', 'min', 'max'] + + dd = pd.read_csv( + f'{path}/picsure_data_dictionary.csv', + usecols=cols_to_load, + quoting=1, + low_memory=False + ) + + values = [eval(v) for v in list(dd['values'])] + + dd['values'] = values + return dd, values + +def analyze(path): + dd, values = picsure_dd_parse(path) + analyze_values(values) # Uncomment and run with your data + print() + pass + + print("DataFrame Info:") + print(dd.info()) + + print("\ndata_hierarchy unique values and counts:") + print(dd['data_hierarchy'].value_counts().head()) + + print(f"\nLoaded dataframe shape: {dd.shape}") + + # Optional: examine what's in rows where data_hierarchy is not null + non_null_hierarchy = dd[dd['data_hierarchy'].notna()] + if len(non_null_hierarchy) > 0: + print("\nSample row with non-null data_hierarchy:") + print(non_null_hierarchy.iloc[0][['columnmeta_name', 'data_hierarchy', 'description']]) + + dd.to_csv(f'{path}/data_dictionary_clean.csv', index=False) + + pass + + +def analyze_values(values): + # Check for duplicates within rows + print("\n=== Checking for duplicates within rows ===") + rows_with_dups = [] + for i, row in enumerate(values, 1): + if len(row) != len(set(row)): + rows_with_dups.append(i) + + if rows_with_dups: + print(f"Found {len(rows_with_dups)} rows with duplicate values") + print(f"First few affected rows: {rows_with_dups[:5]}") + else: + print("No rows contain duplicate values") + + # Analyze list lengths + print("\n=== List Length Distribution ===") + lengths = [len(row) for row in values] + print(f"Minimum length: {min(lengths)}") + print(f"Maximum length: {max(lengths)}") + print(f"Mean length: {statistics.mean(lengths):.2f}") + print(f"Median length: {statistics.median(lengths)}") + + # Group lengths into ranges for better visualization + length_ranges = [ + (0, 0), (1, 1), (2, 2), (3, 5), (6, 10), + (11, 100), (101, 1000), (1001, 10000), (10001, float('inf'))] + length_dist = defaultdict(int) + + for length in lengths: + for start, end in length_ranges: + if start <= length <= end: + length_dist[f"{start}-{end if end != float('inf') else '∞'}"] += 1 + break + + print("\nLength distribution:") + total_rows = len(values) + for range_str, count in length_dist.items(): + percentage = (count / total_rows) * 100 + print(f"{range_str}: {count} rows ({percentage:.1f}%)") + + # Analyze value frequencies across rows + print("\n=== Value Occurrence Distribution ===") + value_occurrences = defaultdict(set) + for i, row in enumerate(values): + for value in row: + value_occurrences[value].add(i) + + occurrence_counts = {value: len(rows) for value, rows in value_occurrences.items()} + + # Get most common values + most_common = Counter(occurrence_counts).most_common(25) + print("\nMost frequently occurring values:") + for value, count in most_common: + percentage = (count / total_rows) * 100 + print(f"{value}: appears in {count} rows ({percentage:.1f}%)") + + # Distribution of how many rows values appear in + occurrence_dist = defaultdict(int) + for count in occurrence_counts.values(): + occurrence_dist[count] += 1 + + print("\nDistribution of value occurrences:") + ranges = [(1, 1), (2, 5), (6, 10), (11, 50), (51, 100), (101, float('inf'))] + + for start, end in ranges: + count = sum(1 for c in occurrence_counts.values() if start <= c <= end) + percentage = (count / len(occurrence_counts)) * 100 + range_str = f"{start}-{end if end != float('inf') else '∞'}" + print(f"Values appearing in {range_str} rows: {count:,} ({percentage:.1f}%)") + + +def main(): + analyze(PATH) + + +if __name__ == "__main__": + main() diff --git a/resources/map-topmed-raw-to-harmonized/generate_mapping.py b/resources/map-topmed-raw-to-harmonized/generate_mapping.py index 6411056..b03733b 100644 --- a/resources/map-topmed-raw-to-harmonized/generate_mapping.py +++ b/resources/map-topmed-raw-to-harmonized/generate_mapping.py @@ -69,7 +69,7 @@ def write_csv(mappings, output_file): def main(): # Define input directory and output file - input_dir = "../../../topmed-dcc-harmonized-phenotypes/harmonized-variable-documentation" + input_dir = "./topmed-dcc-harmonized-phenotypes/harmonized-variable-documentation" output_file = "raw-to-harmonized-topmed-vars.csv" # Process JSON files and get mappings @@ -82,4 +82,4 @@ def main(): if __name__ == "__main__": - main() \ No newline at end of file + main() diff --git a/resources/merged-TOPMed-harmonized-data-file/merge-files.py b/resources/merged-TOPMed-harmonized-data-file/merge-files.py deleted file mode 100644 index 254ad59..0000000 --- a/resources/merged-TOPMed-harmonized-data-file/merge-files.py +++ /dev/null @@ -1,75 +0,0 @@ -import pandas as pd -import re - - -def extract_phv(text): - """Extract PHV number from a string using regex""" - match = re.search(r'phv\d+', text) - return match.group(0) if match else None - - -# Read the CSVs -dbgap_vars = pd.read_csv('../copies-of-external-source-files/dbgap_variables_priority_cohorts.csv') -raw_to_harm = pd.read_csv('../map-topmed-raw-to-harmonized/raw-to-harmonized-topmed-vars.csv') - -# Extract PHV numbers from the 'Variable accession' column -dbgap_vars['phv_number'] = dbgap_vars['Variable accession'].apply(extract_phv) - -# Extract PHV numbers from the 'raw' column -raw_to_harm['phv_number'] = raw_to_harm['raw'].apply(extract_phv) - -# Verify uniqueness of PHV numbers in both dataframes -if len(dbgap_vars['phv_number'].unique()) != len(dbgap_vars['phv_number']): - print("Warning: Duplicate PHV numbers found in ../copies-of-external-source-files/dbgap_variables_priority_cohorts.csv") - -# if len(raw_to_harm['phv_number'].unique()) != len(raw_to_harm['phv_number']): -# print("Warning: Duplicate PHV numbers found in ../map-topmed-raw-to-harmonized/raw-to-harmonized-topmed-vars.csv") - -# Merge dataframes on PHV number -merged_df = pd.merge( raw_to_harm, - dbgap_vars, - on='phv_number', - how='left') - -# Rename columns as needed (you can modify these names) -column_mapping = { - 'phv_number': 'Matched phv', - 'harmonized': 'TOPMed Harmonized Variable', - 'harmonized_unit': 'TOPMed Study', - 'raw': 'TOPMed Component ID', - 'Study': 'dbGap Study Name', - 'Variable name': 'dbGap Variable Name', - 'Variable description': 'dbGap Variable Description', - 'dbGaP Study Accession': 'dbGap phs', - 'Variable accession': 'dbGap phv', - 'Dataset accession': 'dbGap pht', - 'Dataset name': 'dbGap pht Name', -} -merged_df = merged_df.rename(columns=column_mapping) - -# Select and reorder columns as needed -columns_to_keep = [ - 'Matched phv', - 'TOPMed Study', - 'TOPMed Harmonized Variable', - 'dbGap Variable Description', - 'dbGap Variable Name', - 'TOPMed Component ID', - 'dbGap phs', - 'dbGap phv', - 'dbGap pht', - 'dbGap pht Name', - 'dbGap Study Name', - # 'cohort_name', - # 'study_name', - # 'variable_id', - # 'description', - # 'harmonized_variable', - # 'raw_variable', - # 'phv_number' -] - -final_df = merged_df[columns_to_keep] - -# Save to CSV -final_df.to_csv('merged_variables.csv', index=False) \ No newline at end of file diff --git a/resources/merged-TOPMed-harmonized-data-file/README.md b/resources/merged_TOPMed_harmonized_data_file/README.md similarity index 70% rename from resources/merged-TOPMed-harmonized-data-file/README.md rename to resources/merged_TOPMed_harmonized_data_file/README.md index ece0067..c37747b 100644 --- a/resources/merged-TOPMed-harmonized-data-file/README.md +++ b/resources/merged_TOPMed_harmonized_data_file/README.md @@ -1,7 +1,7 @@ ### Generating a TOPMed harmonized data file by merging -* [raw-to-harmonized-topmed-vars.csv](../map-topmed-raw-to-harmonized/raw-to-harmonized-topmed-vars.csv) and -* [dbgap_variables_priority_cohorts.csv](../copies-of-external-source-files/dbgap_variables_priority_cohorts.csv) +* [raw_to_harmonized_topmed_vars.csv](../map_topmed_raw_to_harmonized/raw-to-harmonized-topmed-vars.csv) and +* [dbgap_variables_priority_cohorts.csv](../copies_of_external_source_files/dbgap_variables_priority_cohorts.csv) using the PHS and PHV ID’s (Exclude the version numbers if needed). @@ -10,4 +10,4 @@ using the PHS and PHV ID’s (Exclude the version numbers if needed). Command for getting phv values common to both files: - comm -12 <(cat ../copies-of-external-source-files/dbgap_variables_priority_cohorts.csv | sed 's/^.*\(phv[0-1]*\)/\1/' | sed 's/\..*//' | sort -u) <(cat ../map-topmed-raw-to-harmonized/raw-to-harmonized-topmed-vars.csv | sed 's/^.*\(phv[0-1]*\)/\1/' | sed 's/\..*//' | sort -u) + comm -12 <(cat ../copies_of_external_source_files/dbgap_variables_priority_cohorts.csv | sed 's/^.*\(phv[0-1]*\)/\1/' | sed 's/\..*//' | sort -u) <(cat ../map-topmed-raw-to-harmonized/raw-to-harmonized-topmed-vars.csv | sed 's/^.*\(phv[0-1]*\)/\1/' | sed 's/\..*//' | sort -u) diff --git a/resources/merged_TOPMed_harmonized_data_file/__init__.py b/resources/merged_TOPMed_harmonized_data_file/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/resources/merged-TOPMed-harmonized-data-file/common-phv-values.txt b/resources/merged_TOPMed_harmonized_data_file/common-phv-values.txt similarity index 100% rename from resources/merged-TOPMed-harmonized-data-file/common-phv-values.txt rename to resources/merged_TOPMed_harmonized_data_file/common-phv-values.txt diff --git a/resources/merged_TOPMed_harmonized_data_file/merge_files.py b/resources/merged_TOPMed_harmonized_data_file/merge_files.py new file mode 100644 index 0000000..76e9455 --- /dev/null +++ b/resources/merged_TOPMed_harmonized_data_file/merge_files.py @@ -0,0 +1,97 @@ +import pandas as pd +import re +import os + + +def extract_phv(text): + """Extract PHV number from a string using regex""" + match = re.search(r'phv\d+', text) + return match.group(0) if match else None + + +def merge_files(): + # Read the CSVs + dbgap_vars = pd.read_csv('./copies_of_external_source_files/dbgap_variables_priority_cohorts.csv') + raw_to_harm = pd.read_csv('./map-topmed-raw-to-harmonized/raw-to-harmonized-topmed-vars.csv') + + # Extract PHV numbers from the 'Variable accession' column + dbgap_vars['phv_number'] = dbgap_vars['Variable accession'].apply(extract_phv) + + # Extract PHV numbers from the 'raw' column + raw_to_harm['phv_number'] = raw_to_harm['raw'].apply(extract_phv) + + # Verify uniqueness of PHV numbers in both dataframes + if len(dbgap_vars['phv_number'].unique()) != len(dbgap_vars['phv_number']): + print("Warning: Duplicate PHV numbers found in ./copies_of_external_source_files/dbgap_variables_priority_cohorts.csv") + + # if len(raw_to_harm['phv_number'].unique()) != len(raw_to_harm['phv_number']): + # print("Warning: Duplicate PHV numbers found in ./map-topmed-raw-to-harmonized/raw-to-harmonized-topmed-vars.csv") + + # Merge dataframes on PHV number + merged_df = pd.merge( raw_to_harm, + dbgap_vars, + on='phv_number', + how='inner') + + # Rename columns + column_mapping = { + 'phv_number': 'Matched phv', + 'harmonized': 'TOPMed Harmonized Variable', + 'harmonized_unit': 'TOPMed Study', + 'raw': 'TOPMed Component ID', + 'Study': 'dbGap Study Name', + 'Variable name': 'dbGap Variable Name', + 'Variable description': 'dbGap Variable Description', + 'dbGaP Study Accession': 'dbGap phs', + 'Variable accession': 'dbGap phv', + 'Dataset accession': 'dbGap pht', + 'Dataset name': 'dbGap pht Name', + } + merged_df_pretty = merged_df.rename(columns=column_mapping) + + # Select and reorder columns + columns_to_keep = [ + 'Matched phv', + 'TOPMed Study', + 'TOPMed Harmonized Variable', + 'dbGap Variable Description', + 'dbGap Variable Name', + 'TOPMed Component ID', + 'dbGap phs', + 'dbGap phv', + 'dbGap pht', + 'dbGap pht Name', + 'dbGap Study Name', + # 'cohort_name', + # 'study_name', + # 'variable_id', + # 'description', + # 'harmonized_variable', + # 'raw_variable', + # 'phv_number' + ] + + merged_df_pretty = merged_df_pretty[columns_to_keep] + + # Save to CSV + script_path = os.path.dirname(os.path.abspath(__file__)) + merged_df_pretty.to_csv(os.path.join(script_path, 'merged_variables.csv'), index=False) + + # anti-join, raw_to_harm but not in dbgap_vars + outer = raw_to_harm.merge(dbgap_vars, how='outer', indicator=True, on='phv_number') + outer = outer[[*raw_to_harm.columns, '_merge']] + raw_to_harm_only = outer[(outer._merge=='left_only')].drop('_merge', axis=1) + # raw_to_harm_only = raw_to_harm_only.rename(columns=column_mapping) + + output_path = os.path.join(script_path, 'raw_to_harm_only.csv') + + raw_to_harm_only.to_csv(output_path, index=False) + + pass + +def main(): + merge_files() + + +if __name__ == "__main__": + main() diff --git a/resources/merged-TOPMed-harmonized-data-file/merged_variables.csv b/resources/merged_TOPMed_harmonized_data_file/merged_variables.csv similarity index 100% rename from resources/merged-TOPMed-harmonized-data-file/merged_variables.csv rename to resources/merged_TOPMed_harmonized_data_file/merged_variables.csv diff --git a/resources/merged_TOPMed_harmonized_data_file/raw_to_harm_only.csv b/resources/merged_TOPMed_harmonized_data_file/raw_to_harm_only.csv new file mode 100644 index 0000000..abe036c --- /dev/null +++ b/resources/merged_TOPMed_harmonized_data_file/raw_to_harm_only.csv @@ -0,0 +1,177 @@ +harmonized,harmonized_unit,raw,phv_number +cd40_1,FHS,phs000007.v29.pht000079.v6.phv00021687.v5,phv00021687 +lppla2_mass_1,FHS,phs000007.v29.pht000095.v6.phv00021963.v5,phv00021963 +tnfa_1,FHS,phs000007.v29.pht000111.v5.phv00022779.v4,phv00022779 +isoprostane_8_epi_pgf2a_1,FHS,phs000007.v29.pht000162.v6.phv00023800.v5,phv00023800 +lppla2_act_1,FHS,phs000007.v29.pht000164.v6.phv00023808.v5,phv00023808 +mpo_1,FHS,phs000007.v29.pht000167.v6.phv00023854.v5,phv00023854 +tnfr2_1,FHS,phs000007.v29.pht000175.v6.phv00023913.v5,phv00023913 +lppla2_act_1,FHS,phs000007.v29.pht000304.v5.phv00036408.v4,phv00036408 +lppla2_mass_1,FHS,phs000007.v29.pht000305.v5.phv00036411.v4,phv00036411 +il18_1,FHS,phs000007.v29.pht000671.v5.phv00066686.v4,phv00066686 +geographic_site_1,JHS,phs000286.v5.pht001949.v1.phv00126005.v1,phv00126005 +coronary_angioplasty_prior_1,JHS,phs000286.v5.pht001949.v1.phv00126009.v1,phv00126009 +cabg_prior_1,JHS,phs000286.v5.pht001949.v1.phv00126009.v1,phv00126009 +pad_prior_1,JHS,phs000286.v5.pht001949.v1.phv00126009.v1,phv00126009 +mi_prior_1,JHS,phs000286.v5.pht001949.v1.phv00126009.v1,phv00126009 +height_baseline_1,JHS,phs000286.v5.pht001949.v1.phv00126009.v1,phv00126009 +current_smoker_baseline_1,JHS,phs000286.v5.pht001949.v1.phv00126009.v1,phv00126009 +weight_baseline_1,JHS,phs000286.v5.pht001949.v1.phv00126009.v1,phv00126009 +ever_smoker_baseline_1,JHS,phs000286.v5.pht001949.v1.phv00126009.v1,phv00126009 +sleep_duration_1,JHS,phs000286.v5.pht001949.v1.phv00126009.v1,phv00126009 +total_cholesterol_1,JHS,phs000286.v5.pht001949.v1.phv00126009.v1,phv00126009 +fasting_lipids_1,JHS,phs000286.v5.pht001949.v1.phv00126009.v1,phv00126009 +lipid_lowering_medication_1,JHS,phs000286.v5.pht001949.v1.phv00126009.v1,phv00126009 +triglycerides_1,JHS,phs000286.v5.pht001949.v1.phv00126009.v1,phv00126009 +hdl_1,JHS,phs000286.v5.pht001949.v1.phv00126009.v1,phv00126009 +cimt_2,JHS,phs000286.v5.pht001949.v1.phv00126009.v1,phv00126009 +carotid_plaque_1,JHS,phs000286.v5.pht001949.v1.phv00126009.v1,phv00126009 +cac_score_1,JHS,phs000286.v5.pht001949.v1.phv00126009.v1,phv00126009 +cimt_1,JHS,phs000286.v5.pht001949.v1.phv00126009.v1,phv00126009 +mcv_entvol_rbc_1,JHS,phs000286.v5.pht001949.v1.phv00126009.v1,phv00126009 +hematocrit_vfr_bld_1,JHS,phs000286.v5.pht001949.v1.phv00126009.v1,phv00126009 +basophil_ncnc_bld_1,JHS,phs000286.v5.pht001949.v1.phv00126009.v1,phv00126009 +monocyte_ncnc_bld_1,JHS,phs000286.v5.pht001949.v1.phv00126009.v1,phv00126009 +eosinophil_ncnc_bld_1,JHS,phs000286.v5.pht001949.v1.phv00126009.v1,phv00126009 +rbc_ncnc_bld_1,JHS,phs000286.v5.pht001949.v1.phv00126009.v1,phv00126009 +platelet_ncnc_bld_1,JHS,phs000286.v5.pht001949.v1.phv00126009.v1,phv00126009 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+vte_case_status_1,ARIC,phs000280.v4.pht006485.v1.phv00298126.v1,phv00298126 From 644a1a60bc6d12e7ab60886f7a41b08642b54f2d Mon Sep 17 00:00:00 2001 From: Sigfried Gold Date: Mon, 3 Feb 2025 15:48:47 -0500 Subject: [PATCH 4/4] Can't include picsure_data_dictionary.csv without git-lfs. Leaving out for now, but others won't be able to run the doc scripts unless they put a copy in copies_of_external_source_files.