Reject Two Releases of SDTM Terminology in One Data Definition

Review ask

As a clinical trial statistician or programmer, answer two short questions in Your review: the task and the inputs. Agreeing with both approves this benchmark; disagreeing with either needs a comment. Propose a fix with the Edit button on any source file, or add it to your comments.

We suggest spending no more than 5 minutes on a review. The other tabs beside Your review are background for assessment, not under review.

Summary

EditUnder reviewWhat this benchmark means

README.md

Public entries: Python and R. Passing coverage requires an installed inventory.

Goal: submit DM with its data-definition document, coding the age unit (AGEU) and sex (SEX) with SDTM controlled terminology.

Input: one row per subject carrying the age and the recorded sex code.

Variables:

AGE and SEX are as collected; SEX is one of the codes the sex terminology lists: F, M or U.
AGEU is YEARS for every subject, since age is collected in whole years.

Note: the data-definition document identifies the SDTM terminology it cites by that name alone, without its release, so one document cites one release of it. The sex codes are taken from the December 2023 release and the age unit from the March 2024 release, so the submission stops before any file is written.

How to fix

Choose the one release of SDTM terminology the study follows, check each list's codes against it, and declare that release once for both lists:

codelists:
- standard:
    name: CDISC/NCI
    publishing_set: SDTM
    version: '2024-03-29'
  codelists:
  - id: SEX
    name: Sex
    alias: C66731
    items:
    - {value: F, decode: Female, alias: C16576}
    - {value: M, decode: Male, alias: C20197}
    - {value: U, decode: Unknown, alias: C17998}
  - id: AGEU
    name: Age Unit
    alias: C66781
    items:
    - {value: YEARS, alias: C29848}

Lists may stay in separate sources when every source names the same release.

Expected failure

Editthe run is rejected; no artifact is accepted

expected/error.yaml

phase: validation
condition: duplicate_define_identifier
rule: DEFINE-10

expected/error.yaml

phase: validation
condition: duplicate_define_identifier
spec_paths:
  - codelists[1].standard.publishing_set
rule: DEFINE-10
context:
  detail: STD.CT_SDTM

YAML specification

1 spec file

spec.yaml

Edit113 lines

1yamaa: "1.0"2type: spec3model: SDTM4domain: DM5keys: [STUDYID, USUBJID]6input:7  DM_RAW: input/dm_raw.csv89output:10  path: dm.csv11  columns: [DOMAIN, STUDYID, USUBJID, SUBJID, AGE, AGEU, SEX]1213columns:14  - name: DOMAIN15    type: str16    label: Domain Abbreviation17    derivation: "'DM'"18    submission:19      core: Req20      role: Identifier21      length: 222      origins:23        - type: Assigned24          source: Sponsor2526  - name: STUDYID27    type: str28    label: Study Identifier29    derivation: DM_RAW.STUDYID30    submission:31      core: Req32      role: Identifier33      length: 2034      origins:35        - type: Protocol36          source: Sponsor3738  - name: USUBJID39    type: str40    label: Unique Subject Identifier41    derivation: DM_RAW.USUBJID42    submission:43      core: Req44      role: Identifier45      length: 3046      origins:47        - type: Assigned48          source: Sponsor4950  - name: SUBJID51    type: str52    label: Subject Identifier for the Study53    derivation: DM_RAW.SUBJID54    submission:55      core: Req56      role: Topic57      length: 1058      origins:59        - type: Collected60          source: Investigator61          documents:62            - document: acrf63              pages: {type: PhysicalRef, refs: "1"}6465  - name: AGE66    type: int67    label: Age68    derivation: DM_RAW.AGE69    submission:70      core: Exp71      role: Record Qualifier72      length: 373      origins:74        - type: Collected75          source: Investigator76          documents:77            - document: acrf78              pages: {type: PhysicalRef, refs: "1"}7980  - name: AGEU81    type: str82    label: Age Units83    derivation: "'YEARS'"84    submission:85      core: Exp86      role: Variable Qualifier87      length: 588      codelist: AGEU89      origins:90        - type: Assigned91          source: Sponsor9293  - name: SEX94    type: str95    label: Sex96    derivation: DM_RAW.SEX97    submission:98      core: Req99      role: Record Qualifier100      length: 1101      codelist: SEX102      origins:103        - type: Collected104          source: Investigator105          documents:106            - document: acrf107              pages: {type: PhysicalRef, refs: "1"}108109submission:110  label: Demographics111  class: SPECIAL PURPOSE112  structure: One record per subject113  repeating: false

Inputs

Under review1 source file

input/dm_raw.csv

Edit2 rows

input/dm_raw.csv
STUDYID	USUBJID	SUBJID	AGE	SEX
CATH		0001	34	F
CATH		0002	67	M

Unexpected Output

Under review2 rows presented to the failing check - not an accepted artifact

expected/dm.csv

Edit2 rows

expected/dm.csv
DOMAIN	STUDYID	USUBJID	SUBJID	AGE	AGEU	SEX
DM	CATH		0001	34	YEARS	F
DM	CATH		0002	67	YEARS	M

Shaded columns are derived— = missing value

Human review and assessment

Variable Name	Variable Label	Type	Length	Controlled Terms or Format	Origin	Core	Conversion Definition	Variable Type	Variable Order
DOMAIN	Domain Abbreviation	Char	2		Assigned	Req	Set constant value "DM".	SDTM	1
STUDYID	Study Identifier	Char	20		Protocol	Req	Copy value from DM_RAW.STUDYID.	SDTM	2
USUBJID	Unique Subject Identifier	Char	30		Assigned	Req	Copy value from DM_RAW.USUBJID.	SDTM	3
SUBJID	Subject Identifier for the Study	Char	10		Collected	Req	Copy value from DM_RAW.SUBJID.	SDTM	4
AGE	Age	Num	3		Collected	Exp	Copy value from DM_RAW.AGE.	SDTM	5
AGEU	Age Units	Char	5	Age Unit	Assigned	Exp	Set constant value "YEARS".	SDTM	6
SEX	Sex	Char	1	Sex	Collected	Req	Copy value from DM_RAW.SEX.	SDTM	7

Codelist ID	Name	Value	Decode	Codelist NCI alias	Value NCI alias	Extensible
SEX	Sex	F	Female	C66731	C16576	No
SEX	Sex	M	Male	C66731	C20197	No
SEX	Sex	U	Unknown	C66731	C17998	No
AGEU	Age Unit	YEARS		C66781	C29848	No

Version	Date	Author	Description
1.7	2026-10-20	yamaa docs build	Read a specification in the 1.0 surface as its 0.5 counterpart; state that missing values stay missing where a mapping declares no missing handler, and leave out a declared missing answer that restates a handler's default
1.6	2026-10-17	yamaa docs build	Describe collected date parts written as ISO 8601 date text and times of day counted in seconds since midnight
1.5	2026-10-17	yamaa docs build	Name collected precision in words instead of letter codes; state imputation fallbacks, minimum source precision, bounds ignored outside the collected period, and invalid text with no handler as an error; describe date and datetime shifts, imputation flag codes, and partial text giving no date part
1.4	2026-10-15	yamaa docs build	State datetime precision codes through the hour and minute, and complete only the time parts a collected datetime lacks
1.3	2026-09-29	yamaa docs build	Show study codelist names, external dictionaries, and ISO 8601 formats in variable rows; list the document's codelist values and metadata
1.2	2026-09-29	yamaa docs build	Classify ADaM copies from a declared input as Predecessor and recodes as Derived, and SDTM recodes of locally derived columns as Derived
1.1	2026-09-29	yamaa docs build	Resolve lookups into the donor record they select, and give every derivation shape a plain-language rule instead of its raw YAML
1.0		yamaa docs build	Initial generation from spec.yaml

How to fix

input/dm_raw.csv

expected/dm.csv

Your review

Mapping spec