yamaa / Benchmark

SDTM.DM

One Collected Answer per Subject

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: derive SEX and AGE for one record per subject, each from the one record that holds the subject's answer.

Input: long-form Operational Data Model (ODM) data with one row per collected item, carrying the visit (StudyEventOID), the form, the item (ItemOID), and the stored value (Value).

Variables:

  • SEX is the sex answered at screening. A subject who is asked again at a later visit keeps the screening answer.
  • AGE is the age collected for the subject; a subject with no age record keeps a missing age.

Note: an answer is read only when exactly one record holds it, so two records of one question at one visit stop the run even when they agree. Items the record does not read, such as a weight, play no part.

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
STUDYIDUSUBJIDSEXAGE
STUDY01F34
STUDY01M—
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 IdentifierCharCollectedCopy value from ODM.StudyOID.SDTM1
USUBJIDUnique Subject IdentifierCharCollectedCopy value from ODM.SubjectKey.SDTM2
SEXSexCharCollectedRead collected ODM item IT.DM.SEX in event SCREENING; no identified record yields blank.SDTM3
AGEAgeNumCollectedRead collected ODM item IT.DM.AGE; no identified record yields blank.SDTM4
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