yamaa / Benchmark

SDTM.DM

Replace Collected Sex with a Reviewed Unknown Value

input files
1
subjects
2
expected rows
2
Review ask

As a clinical trial statistician or programmer, challenge anything in this benchmark: describe a problem in Comments, or propose a fix with the Edit button on any source file.

  1. Task: Would a real study need this derivation, specified this way? Does it follow CDISC SDTM: variable names, controlled terms, record structure? Flag any rule that is ambiguous or that a sponsor would handle differently.
  2. Inputs: Do they look like data collected in a real trial, and do they include the situations you would expect to meet in one?
  3. Expected output: Would independent QC programming reproduce every value from these inputs and rules?

The other tabs beside Comments are background for assessment, not under review.

Summary

Lifecycle: draftEditUnder reviewWhat this benchmark means
README.md

Goal: record SEX as unknown for each subject after review, even when the extract contains a collected answer.

Input: long-form Operational Data Model (ODM) data with one row per collected item, including a repeated sex answer at another visit.

Variables:

  • SEX is U for each subject. The reviewed value replaces the collected answer, including when that answer appears more than once.

Inputs

Under review1 source file

input/odm.csv

Edit5 rows
StudyOIDMetaDataVersionOIDSubjectKeyStudyEventOIDStudyEventRepeatKeyFormOIDFormRepeatKeyItemGroupOIDItemGroupRepeatKeyItemOIDValue
STUDY01MDV.1001SCREENING1FO.DM1IG.DM1IT.DM.SEXF
STUDY01MDV.1001SCREENING1FO.DM1IG.DM1IT.DM.AGE34
STUDY01MDV.1001SCREENING1FO.VS1IG.VS1IT.VS.WEIGHT61
STUDY01MDV.1001BASELINE1FO.DM1IG.DM1IT.DM.SEXF
STUDY01MDV.1002SCREENING1FO.DM1IG.DM1IT.DM.SEXM

Expected output

Under review2 expected rows

expected/dm.csv

Edit2 rows
STUDYIDUSUBJIDSEX
STUDY01U
STUDY01U
Shaded columns are derived— = missing value

Comments and assessment materials

Comments

Signed in with GitHub; saved in repository Discussions

Mapping spec

Generated from the benchmark YAML; do not edit by hand

Variable NameVariable LabelTypeLengthControlled Terms or FormatOriginCoreConversion DefinitionVariable TypeVariable OrderComments for Define
STUDYIDStudy IdentifierCharDerivedSet per constructed row; see the Row construction sheet.SDTM1
USUBJIDUnique Subject IdentifierCharDerivedSet per constructed row; see the Row construction sheet.SDTM2
SEXSexCharCollectedRead collected ODM item IT.DM.SEX; no identified record yields blank.SDTM3
TemplateInclude whenSTUDYIDUSUBJIDSEX
subjectsCopy ODM.StudyOIDCopy ODM.SubjectKeyConstant "U"
VersionDateAuthorDescriptionReviewerSign-off
1.32026-09-29yamaa docs buildShow study codelist names, external dictionaries, and ISO 8601 formats in variable rows; list the document's codelist values and metadata
1.22026-09-29yamaa docs buildClassify ADaM copies from a declared input as Predecessor and recodes as Derived, and SDTM recodes of locally derived columns as Derived
1.12026-09-29yamaa docs buildResolve lookups into the donor record they select, and give every derivation shape a plain-language rule instead of its raw YAML
1.0yamaa docs buildInitial generation from spec.yaml

yamaa code

Runs the yamaa specification; its result must match the expected output

run.R

Edit4 lines
library(yamaa)dm <- yamaa_domain("spec.yaml")$outputdm

run.py

Edit4 lines
import yamaadm = yamaa.yamaa_domain("spec.yaml").outputdm