sdtm.terminology is an R data package providing CDISC SDTM terminology (release 2023-12-15).
CDISC SDTM Controlled Terminology refers to a standardized set of terms developed by the Clinical Data Interchange Standards Consortium (CDISC) specifically for use with the Standard Data Tabulation Model (SDTM). Controlled terminology provides a consistent vocabulary for coding various types of data that are collected during clinical trials. This standardization is crucial for ensuring that data from different studies, sponsors, and sites can be understood, compared, and analyzed in a consistent manner.
In addition to supplying SDTM terminology data, this package includes several utility functions designed to facilitate the conversion between codes and terms, as well as to verify the association of terms with specific code lists.
Installation
# install.packages("devtools")
devtools::install_github("patterninstitute/sdtm.terminology")Quick usage example
Convert terms to codes and codes to terms, and determine if a term is included in a terminology code list:
# Convert a code list term to respective C-code and back again
cl_term_to_code("UNIT")
#> [1] "C71620"
cl_code_to_term("C71620")
#> [1] "UNIT"
# Are "%" and "%/s" terms from the UNIT code list?
is_term(c("%", "%/s"), cl_term_to_code("UNIT"))
#> [1] TRUE TRUE
# Find "%" and "%/s" codes within C71620 code list.
term_to_code(c("%", "%/s"), "C71620")
#> [1] "C25613" "C163560"
# It seems "%" is also a term in the VSRESU code list but not "%/s".
is_term(c("%", "%/s"), cl_term_to_code("VSRESU"))
#> [1] TRUE FALSE
# Or, equivalently, query using codes instead...
is_code(c("C25613", "C163560"), cl_term_to_code("VSRESU"))
#> [1] TRUE FALSE
# Find which code lists contain the terms "DNA" or "RNA"
match_code_list_from_term(c("DNA", "RNA"))
#> # A tibble: 6 × 4
#> code term cl_code cl_name
#> <chr> <chr> <chr> <chr>
#> 1 C184459 DNA C101832 Findings About Test Code
#> 2 C449 DNA C111114 Genetic Sample Type
#> 3 C135409 DNA C65047 Laboratory Test Code
#> 4 C184459 DNA C163027 Type 1 Diabetes Findings About Test Code
#> 5 C812 RNA C111114 Genetic Sample Type
#> 6 C132301 RNA C65047 Laboratory Test CodeData
sdtm.terminology bundles three data sets:
-
sdtm_terminology: This is the same data set as provided upstream by CDISC, except for variable renaming and conversion of “Yes”/“No” values toTRUE/FALSEvalues in theis_extensiblecolumn. -
sdtm_code_lists: A subset ofsdtm_terminologycontaining only code lists. -
sdtm_code_terms: A subset ofsdtm_terminologycontaining terms other than code lists.
sdtm_terminology
# SDTM controlled terminology version
sdtm_ct_version()
#> $quarter
#> [1] "Q4 2023"
#>
#> $release
#> [1] "2023-12-15"
# SDTM terminology main data set
sdtm_terminology
#> # A tibble: 40,816 × 8
#> code term cl_code is_extensible cl_name synonym definition nci_term
#> <chr> <chr> <chr> <lgl> <chr> <chr> <chr> <chr>
#> 1 C141657 TENMW1TC <NA> FALSE 10-Met… 10-Met… 10-Meter … CDISC F…
#> 2 C174106 TENMW101 C141657 NA 10-Met… TENMW1… 10-Meter … 10-Mete…
#> 3 C141700 TENMW102 C141657 NA 10-Met… TENMW1… 10-Meter … 10-Mete…
#> 4 C147592 TENMW103 C141657 NA 10-Met… TENMW1… 10-Meter … 10-Mete…
#> 5 C141701 TENMW104 C141657 NA 10-Met… TENMW1… 10-Meter … 10-Mete…
#> 6 C141656 TENMW1TN <NA> FALSE 10-Met… 10-Met… 10-Meter … CDISC F…
#> 7 C141701 TENMW1-Tes… C141656 NA 10-Met… TENMW1… 10-Meter … 10-Mete…
#> 8 C141700 TENMW1-Tim… C141656 NA 10-Met… TENMW1… 10-Meter … 10-Mete…
#> 9 C174106 TENMW1-Was… C141656 NA 10-Met… TENMW1… 10-Meter … 10-Mete…
#> 10 C147592 TENMW1-Wea… C141656 NA 10-Met… TENMW1… 10-Meter … 10-Mete…
#> # ℹ 40,806 more rows
sdtm_code_lists
# SDTM code lists
sdtm_code_lists
#> # A tibble: 1,081 × 7
#> code term is_extensible cl_name synonym definition nci_term
#> <chr> <chr> <lgl> <chr> <chr> <chr> <chr>
#> 1 C141657 TENMW1TC FALSE 10-Meter Wal… 10-Met… 10-Meter … CDISC F…
#> 2 C141656 TENMW1TN FALSE 10-Meter Wal… 10-Met… 10-Meter … CDISC F…
#> 3 C141663 A4STR1TC FALSE 4-Stair Asce… 4-Stai… 4-Stair A… CDISC F…
#> 4 C141662 A4STR1TN FALSE 4-Stair Asce… 4-Stai… 4-Stair A… CDISC F…
#> 5 C141661 D4STR1TC FALSE 4-Stair Desc… 4-Stai… 4-Stair D… CDISC F…
#> 6 C141660 D4STR1TN FALSE 4-Stair Desc… 4-Stai… 4-Stair D… CDISC F…
#> 7 C115388 SIXMW1TC FALSE 6 Minute Wal… 6 Minu… 6 Minute … CDISC F…
#> 8 C115387 SIXMW1TN FALSE 6 Minute Wal… 6 Minu… 6 Minute … CDISC F…
#> 9 C182464 AIMS0101T07OR FALSE Abnormal Inv… Abnorm… Abnormal … CDISC C…
#> 10 C182465 AIMS0108T09OR FALSE Abnormal Inv… Abnorm… Abnormal … CDISC C…
#> # ℹ 1,071 more rows
sdtm_code_terms
# SDTM terms (other than code lists)
sdtm_code_terms
#> # A tibble: 39,735 × 6
#> cl_code code term synonym definition nci_term
#> <chr> <chr> <chr> <chr> <chr> <chr>
#> 1 C141657 C174106 TENMW101 TENMW1… 10-Meter … 10-Mete…
#> 2 C141657 C141700 TENMW102 TENMW1… 10-Meter … 10-Mete…
#> 3 C141657 C147592 TENMW103 TENMW1… 10-Meter … 10-Mete…
#> 4 C141657 C141701 TENMW104 TENMW1… 10-Meter … 10-Mete…
#> 5 C141656 C141701 TENMW1-Test Grade TENMW1… 10-Meter … 10-Mete…
#> 6 C141656 C141700 TENMW1-Time to Walk/Run 10 Meters TENMW1… 10-Meter … 10-Mete…
#> 7 C141656 C174106 TENMW1-Was Walk/Run Performed TENMW1… 10-Meter … 10-Mete…
#> 8 C141656 C147592 TENMW1-Wear Orthoses TENMW1… 10-Meter … 10-Mete…
#> 9 C141663 C174103 A4STR101 A4STR1… 4-Stair A… 4-Stair…
#> 10 C141663 C141706 A4STR102 A4STR1… 4-Stair A… 4-Stair…
#> # ℹ 39,725 more rows