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lovrot/variable_naming_convention.tsv

Last active November 9, 2015 12:43
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A variable naming convention for breast cancer study data
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variable_naming_convention.tsv
variableName labelDescription type RClass controlledTermsOrFormat reference comment
studyid Study Identifier Char character SDTM 2.2.4
siteid Study Site Identifier Char character
usubjid Unique Subject Identifier Char character SDTM 2.2.4
subjid Subject Identifier for the Study Char character
brthdtc Date of Birth - Character Char character ISO 8601 SDSIG 4.1.4.1
brthdtm Date of Birth Num Date R's Date class SDSIG 4.1.4.3
age Age at Reference Date Num integer SDSIG 5.1.1
ageu Age Units Char character decades, years, months, days SDSIG 5.1.1
agerfdt Reference Date for Age Char character ISO 8601, vaiable name, or free text (e.g. 'Diagnosis') 'rf' from CDISC naming fragments; 'dt' see SDSIG 4.1.4.2
sex Sex Char factor M, F, U SDSIG 5.1.1
diagdtc Date of Diagnosis - Character Char character ISO 8601 SDSIG 4.1.4.1 'dtc' from CDISC naming fragments
diagdtm Date of Diagnosis Num Date R's Date class SDSIG 4.1.4.3
surgdtc Date of Surgery - Character Char character ISO 8601 SDSIG 4.1.4.1 'dtc' from CDISC naming fragments
surgdtm Date of Surgery Num Date R's Date class SDSIG 4.1.4.3
tumsize Tumour Size Num numeric
tumsizeu Tumour Size Units Char character cm, mm 'u' from CDISC naming fragments
lnstat Lymph Node Status Char factor LN-, LN+ 'stat' from CDISC naming fragments
histgrn Histological Grade, Elston-Ellis Score, Numeric Total Grade Num integer 1, 2, 3 'gr' and 'n' from CDISC naming fragments
histgr Histological Grade, Elston-Ellis Score, Total Grade Char factor G1, G2, G3 'gr' from CDISC naming fragments
erstat Oestrogen Receptor Status Char factor ER-, ER+ 'stat' from CDISC naming fragments
erval Oestrogen Receptor Value Num numeric 'val' from CDISC naming fragments
ervalu Oestrogen Receptor Value Units Char character 'val' and 'u' from CDISC naming fragments
prstat Progesterone Receptor Status Char factor PR-, PR+ 'stat' from CDISC naming fragments
prval Progesterone Receptor Value Num numeric 'val' from CDISC naming fragments
prvalu Progesterone Value Units Char character 'val' and 'u' from CDISC naming fragments
her2stat HER2/neu Status Char factor HER2-, HER2+ 'stat' from CDISC naming fragments
her2val HER2/neu Value Num numeric 'val' from CDISC naming fragments
her2mth HER2/neu Method Char character 'mth' from CDISC naming fragments
subtype Molecular Intrinsic Subtype Char factor Luminal A, Luminal B, HER2-enriched, Claudin-low, Basal-like, Normal Breast-like, No subtype Terms inspired by PMID 21147047, Fig 1
subtypecd Molecular Intrinsic Subtype Code Char factor LA, LB, H2, CL, BL, NBL, none Terms inspired by PMID 21147047, Fig 1
visitnum Visit Number Num integer SDSIG 7.8; SDSIG 4.1.4.5
visit Visit Name Char character SDSIG 7.8; SDSIG 4.1.4.5
visitdy Planned Study Day of Visit Num integer SDSIG 7.8; SDSIG 4.1.4.5
tptnum Planned Time Point Number Num integer
tpt Planned Time Point Name Char character
armcd Planned Arm Code Char character SDSIG 5.1.1
arm Description of Planned Arm Char factor SDSIG 5.1.1
trtcd Treatment Code Char character See SDSIG 5.1.1
trt Treatment Name Char factor inspired by cmtrt and extrt in CDISC SDTM
trtgrp Treatment Group Char character See SDSIG 5.1.1
sustdtc Start Date of Substance Use - Character Char character ISO 8601 SDSIG 6.1.3; SDSIG 4.1.4.3
sustdtm Start Date of Substance Use Num Date R's Date class
bioploc Location of Biopsy Char character 'loc' from CDISC naming fragments
biopdtc Date of Biopsy - Character Char character ISO 8601 SDSIG 4.1.4.1 'dtc' from CDISC naming fragments
biopdtm Date of Biopsy Num Date R's Date class SDSIG 4.1.4.3
assaynum Assay Number Num integer 'num' from CDISC naming fragments
assayid Assay Identifier Char character 'id' from CDISC naming fragments
reldtc Date of Relapse or Censoring - Character Char character ISO 8601 SDSIG 4.1.4.1 'dtc' from CDISC naming fragments
reldtm Date of Relapse or Censoring Num Date R's Date class SDSIG 4.1.4.3
survreltm Elapsed Time until Relapse or Censoring Num numeric
survreltmu Units of Elapsed Time until Relapse or Censoring Char character decades, years, months, days
survrelrfdt Reference Date for Elapsed Time until Relapse or Censoring Char character ISO 8601, vaiable name, or free text (e.g. 'Diagnosis') 'rf' from CDISC naming fragments; 'dt' see SDSIG 4.1.4.2
relstat Breast Cancer Relapse Status Indicator Num integer 0, 1 'stat' from CDISC naming fragments; status indicator values, 0 and 1, as in the function Surv in the R package survival
dmdtc Date of Distant Metastasis - Character Char character ISO 8601 SDSIG 4.1.4.1 'dtc' from CDISC naming fragments
dmdtm Date of Distant Metastasis Num Date R's Date class SDSIG 4.1.4.3
survdmtm Elapsed Time until Distant Metastasis or Cencoring Num numeric
survdmtmu Units of Elapsed Time until Distant Metastasis or Cencoring Char character decades, years, months, days
survdmrfdt Reference Date for Elapsed Time until Distant Metastasis or Censoring Char character ISO 8601, vaiable name, or free text (e.g. 'Diagnosis') 'ref' from CDISC naming fragments; 'dt' see SDSIG 4.1.4.2
dmstat Distant Metastasis Status Indicator Num integer 0, 1 'stat' from CDISC naming fragments; status indicator values, 0 and 1, as in the function Surv in the R package survival
progdtc Date of Progression - Character Char character ISO 8601 SDSIG 4.1.4.1 'dtc' from CDISC naming fragments
progdtm Date of Progression Num Date R's Date class SDSIG 4.1.4.3
survprogtm Elapsed Time until Progression or Cencoring Num numeric
survprogtmu Units of Elapsed Time until Progression or Cencoring Char character decades, years, months, days
survprogrfdt Reference Date for Elapsed Time until Progression or Censoring Char character ISO 8601, vaiable name, or free text (e.g. 'Diagnosis') 'ref' from CDISC naming fragments; 'dt' see SDSIG 4.1.4.2
progstat Progression Status Indicator Num integer 0, 1 'stat' from CDISC naming fragments; status indicator values, 0 and 1, as in the function Surv in the R package survival
dthdtc Date of Death or Censoring - Character Char character ISO 8601 SDSIG 4.1.4.1 'dth' and 'dtc' from CDISC naming fragments
dthdtm Date of Death or Censoring Num Date R's Date class SDSIG 4.1.4.3 'dth' from CDISC naming fragments
survdthtm Elapsed Time until Death or Censoring Num numeric 'dth' and 'dtc' from CDISC naming fragments
survdthtmu Units of Elapsed Time until Death or Censoring Char character decades, years, months, days 'dth' and 'dtc' from CDISC naming fragments
survdthrfdt Reference Date for Elapsed Time until Death or Censoring Char character ISO 8601, vaiable name, or free text (e.g. 'Diagnosis') 'dth', 'rf' from CDISC naming fragments; 'dt' see SDSIG 4.1.4.2
dthcd Death Code Char character
dthstat Death from Any Reason Num integer 0, 1 'dth', 'stat' from CDISC naming fragments; status indicator values, 0 and 1, as in the function Surv in the R package survival
dthbcstat Death due to Breast Cancer Num integer 0, 1 'dth', 'stat' from CDISC naming fragments; status indicator values, 0 and 1, as in the function Surv in the R package survival
com Comment Char character 'com' from CDISC naming fragments
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