Title: CDISC SDTM Controlled Terminology
Version: 2025-3-25
Description: Clinical Data Interchange Standards Consortium (CDISC) Standard Data Tabulation Model (SDTM) controlled terminology, 2025-03-25. Source: https://evs.nci.nih.gov/ftp1/CDISC/SDTM/.
License: Apache License (≥ 2)
Encoding: UTF-8
RoxygenNote: 7.3.2
Depends: R (≥ 4.1.0)
Imports: dplyr, tibble
URL: https://github.com/patterninstitute/sdtm.terminology, https://www.pattern.institute/sdtm.terminology/
BugReports: https://github.com/patterninstitute/sdtm.terminology/issues
Config/Needs/website: patterninstitute/chic
NeedsCompilation: no
Packaged: 2025-04-04 13:21:25 UTC; rmagno
Author: Ramiro Magno ORCID iD [aut, cre], Pattern Institute [cph, fnd]
Maintainer: Ramiro Magno <rmagno@pattern.institute>
Repository: CRAN
Date/Publication: 2025-04-07 16:30:01 UTC

sdtm.terminology: CDISC SDTM Controlled Terminology

Description

Clinical Data Interchange Standards Consortium (CDISC) Standard Data Tabulation Model (SDTM) controlled terminology, 2025-03-25. Source: https://evs.nci.nih.gov/ftp1/CDISC/SDTM/.

Author(s)

Maintainer: Ramiro Magno rmagno@pattern.institute (ORCID)

Other contributors:

See Also

Useful links:

SDTM codelist code to respective term

Description

clst_code_to_term() maps SDTM terminology codelists' C-codes to respective terms. For mapping codes other than those representing codelists, use code_to_term() instead.

Usage

clst_code_to_term(code)

Arguments

code

A C-code with a leading character C followed by a sequence of digits used for uniquely identifying each SDTM terminology codelist.

Value

A character vector of SDTM terms for codelists. The number of elements returned matches the number of elements in code, i.e. there is a one-to-one correspondence between input and output. Invalid codes in code are mapped to NA.

See Also

See clst_term_to_code() for the inverse operation.

Examples

clst_code_to_term(code = "C66731")

# `code` is vectorized.
clst_code_to_term(code = c("C66731", "C66733"))

# Invalid codes (e.g. `"C007"`) map to `NA`.
clst_code_to_term(code = c("C66731", "C66733", "C007"))

SDTM code list term to respective code

Description

clst_term_to_code() maps SDTM terminology codelists' terms to respective C-codes. For mapping terms other than those representing codelists, use term_to_code() instead.

Usage

clst_term_to_code(term)

Arguments

term

A SDTM controlled terminology term referring to a codelist.

Value

A character vector of SDTM codes for codelists. The number of elements returned matches the number of elements in term, i.e. there is a one-to-one correspondence between input and output. Invalid codes in term are mapped to NA.

See Also

See clst_code_to_term() for the inverse operation.

Examples

clst_term_to_code(term = "SEX")

# `term` is vectorized.
clst_term_to_code(term = c("SEX", "SIZE"))

# Invalid codes (e.g. `"YODA"`) map to `NA`.
clst_term_to_code(term = c("SEX", "SIZE", "YODA"))

SDTM code to term

Description

code_to_term() maps SDTM terminology C-codes to respective terms. For mapping codes representing codelists, use clst_code_to_term() instead.

Usage

code_to_term(code, clst_code)

Arguments

code

A C-code with a leading character C followed by a sequence of digits used for uniquely identifying each concept in NCI Thesaurus (NCIt), including all CDISC concepts.

clst_code

Parent codelist code.

Value

A character vector of SDTM controlled terminology terms. The number of elements returned matches the number of elements in code, i.e. there is a one-to-one correspondence between input and output. Invalid codes in code are mapped to NA.

See Also

See term_to_code() for the inverse operation.

Examples

code_to_term(code = "C174106", clst_code = "C141657")

# Both `code` and `clst_code` are vectorized. `clst_code` will be recycled
# to match `code` number of elements.
code_to_term(code = c("C174106", "C141700"), clst_code = "C141657")

# You may mix codelists as long as `code` and `clst_code` have the same
# number of elements; they will be matched element-wise.
code_to_term(
  code = c("C174106", "C141700", "C141701"),
  clst_code = c("C141657", "C141657", "C141656")
)

# Invalid codes (e.g. `"C00000"`) map to `NA`.
code_to_term(code = c("C174106", "C141700", "C00000"), clst_code = "C141657")

Retrieve CDISC SDTM Controlled Terminology

Description

Returns a tibble of CDISC SDTM controlled terminology, optionally filtered to include only term-level entries, only code list definitions, or both.

Usage

ct(subset = c("term", "list", "all"))

Arguments

subset

One of "term", "list", or "all" to specify which part of the terminology to return.

Value

A tibble containing the requested subset of CDISC controlled terminology:

clst_code

C-code of the code list that the term belongs to. Identifies the parent code list concept (e.g., C66742 for Yes/No/Unknown).

is_clst

Logical indicator: TRUE if the row represents a code list definition; FALSE if it represents a term within a code list.

code

C-code of the concept (either a term or a code list). Each term and list has a unique NCI Thesaurus concept code (e.g., C49487 for "Yes").

term

Submission value or label for the term (e.g., "Y", "TENMW1-Was Walk/Run Performed"). For code list rows, this may be the list name.

ext

Extensibility of the code list (TRUE, FALSE, or NA). NA for term-level rows.

name

Name of the code list or term category (e.g., "Yes/No/Unknown Response" or "10-Meter Walk/Run Functional Test Test Code").

syn

Synonyms or alternative names for the term, often used in CRF annotations or mappings.

def

Definition or description of the term or code list, taken from the NCI Thesaurus.

nci

Preferred label from the NCI Thesaurus; usually a short human-readable label for the concept.

Version

Controlled terminology data comes from the release dated 2025-03-25.

Source

https://evs.nci.nih.gov/ftp1/CDISC/SDTM/SDTM%20Terminology.txt

Examples

# Return only the terms
ct("term")

# Return only the code lists
ct("list")

# Return the full terminology (code lists and individual terms)
ct("all")

CDISC SDTM Controlled Terminology Release Date

Description

SDTM terminology release date.

Usage

ct_release()

Value

A Date object.

Examples

ct_release()

Is a code or term in a code list?

Description

is_code() and is_term() evaluate whether query codes or terms are part of the SDTM controlled terminology within the context of a code list.

Usage

is_term(term, clst_code)

is_code(code, clst_code)

Arguments

term

A character vector of terms (e.g. "TENMW102").

clst_code

A character vector of codes referring to SDTM terminology codelists (e.g. "C141657").

code

A character vector of C-codes (e.g. "C174106").

Value

A logical vector, where TRUE indicates that term is a controlled terminology term within the clst_code provided, and FALSE, otherwise.

Examples

is_term(term = "TENMW101", clst_code = "C141657")

# Note that the clst_code term itself (`"TENMW1TC"`) is not part of its own
# code list (`"C141657"`).
is_term(term = "TENMW1TC", clst_code = "C141657")

# `is_term()` is vectorized over `term` and `clst_code`
is_term(term = c("TENMW101", "TENMW104"), clst_code = "C141657")

is_code(code = "C174106", clst_code = "C141657")

# Note that the code list code itself (`"C141657"`) is not part of its own
# code list (`"C141657"`).
is_code(code = "C141657", clst_code = "C141657")

# `is_code()` is vectorized over `code` and `clst_code`
is_code(code = c("C174106", "C141701"), clst_code = "C141657")

Match code lists

Description

match_code_list_from_term() takes terms as queries to look for associated code lists.

match_code_list_from_code() does the same starting from C-codes.

Note that both mappings are potentially one to many as the same code or term may associate with more than one code list.

Usage

match_code_list_from_term(term)

match_code_list_from_code(code)

Arguments

term

A character vector of SDTM terminology terms.

code

A character vector of SDTM terminology C-codes.

Value

A tibble with at least as many rows as there are elements in term, but potentially more because of one-to-many mappings. The returned tibble comprises three columns:

code

An SDTM terminology code (e.g. "C141701").

term

An SDTM terminology term (e.g. "TENMW104").

clst_code

The code of the associated code list.

Examples

# Find code lists where "DNA" and "RNA" are used.
match_code_list_from_term(c("DNA", "RNA"))

# Find code lists where "Yes"/"No" terms are controlled vocabulary.
match_code_list_from_term(c("Yes", "No"))

# C163560 is found in code list C71620.
match_code_list_from_code("C163560")

# C25613 however is mapped to many code lists.
match_code_list_from_code("C25613")

# Unmappable codes or terms map to `NA`.
match_code_list_from_code("Yoda")
match_code_list_from_term("R2D2")

# Codes for code lists are for all intents and purposes not mappable to
# parent code lists.
match_code_list_from_code(code = "C141657")

Get package name

Description

pkg_name() returns package name.

Usage

pkg_name()

Value

Package name as character.

Get package version

Description

pkg_name() returns package version

Usage

pkg_version()

Value

Package version as an object of class package_version.

SDTM term to code

Description

term_to_code() maps SDTM terminology terms to respective C-codes. For mapping terms referring to codelists, use clst_term_to_code() instead.

Usage

term_to_code(term, clst_code)

Arguments

term

A SDTM controlled terminology term (as expected in submissions).

clst_code

Parent codelist code.

Value

A character vector of SDTM controlled terminology C-codes. The number of elements returned matches the number of elements in term, i.e. there is a one-to-one correspondence between input and output. Invalid codes in term are mapped to NA.

See Also

See code_to_term() for the inverse operation.

Examples

term_to_code(term = "TENMW101", clst_code = "C141657")

# Both `term` and `clst_code` are vectorized. `clst_code` will be recycled
# to match `term` number of elements.
term_to_code(term = c("TENMW101", "TENMW102"), clst_code = "C141657")

# You may mix codelists as long as `term` and `clst_code` have the same
# number of elements; they will be matched element-wise.
term_to_code(
  term = c("TENMW101", "TENMW102", "TENMW1-Test Grade"),
  clst_code = c("C141657", "C141657", "C141656")
)

# Invalid terms (e.g. `"Gambelas"`) map to `NA`.
term_to_code(term = c("TENMW101", "TENMW102", "Gambelas"), clst_code = "C141657")

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