yamaa / Benchmark

SDTM.LB

Form-Scoped Items

input files
1
subjects
1
expected rows
5
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: reviewedEditUnder reviewWhat this benchmark means
README.md

Goal: derive LBTESTCD, LBTEST, LBCAT, LBORRES, and LBDTC for one record per reported laboratory result, reading each item only within the form that collected it.

Input: long-form Operational Data Model (ODM) data with one row per item, carrying the collection form (FormOID), the item (ItemOID), and the stored value (Value). Result rows use item IT.LB.RESULT; date rows use item IT.LB.LBDTC, the same identifier on every form.

Variables:

  • LBTESTCD is the short test code for the collection form.
  • LBTEST is the test name for the collection form.
  • LBCAT is the test category for the collection form.
  • LBORRES is the reported result, the value on the result row of that form.
  • LBDTC is the collection date from the same form, the value on that form's date row. A form with no date row keeps its result with a missing date.

Note: form identity is part of the collection setting: a date row from one form never supplies the date for a result on another form at the same subject and visit. Within each study and subject, records are numbered in a fixed form order: chemistry, hematology, thyroid, urinalysis, then coagulation.

Inputs

Under review1 source file

input/odm.csv

Edit9 rows
StudyOIDMetaDataVersionOIDSubjectKeyStudyEventOIDStudyEventRepeatKeyFormOIDFormRepeatKeyItemGroupOIDItemGroupRepeatKeyItemOIDValue
PILOT7MDV.1P7-001C1D11FO.LB_CHEM1IG.LB1IT.LB.LBDTC2025-01-02
PILOT7MDV.1P7-001C1D11FO.LB_CHEM1IG.LB1IT.LB.RESULT32
PILOT7MDV.1P7-001C1D11FO.LB_HEM1IG.LB1IT.LB.LBDTC2025-01-03
PILOT7MDV.1P7-001C1D11FO.LB_HEM1IG.LB1IT.LB.RESULT11.4
PILOT7MDV.1P7-001C1D11FO.LB_THY1IG.LB1IT.LB.LBDTC2025-01-04
PILOT7MDV.1P7-001C1D11FO.LB_THY1IG.LB1IT.LB.RESULT2.1
PILOT7MDV.1P7-001C1D11FO.LB_UA1IG.LB1IT.LB.LBDTC2025-01-05
PILOT7MDV.1P7-001C1D11FO.LB_UA1IG.LB1IT.LB.RESULTNEGATIVE
PILOT7MDV.1P7-001C1D11FO.LB_EXTRA1IG.LB1IT.LB.RESULT7.8

Expected output

Under review5 expected rows

expected/lb.csv

Edit5 rows
DOMAINSTUDYIDUSUBJIDLBSEQLBTESTCDLBTESTLBCATLBORRESLBDTC
LBPILOT71ALTAlanine AminotransferaseCHEMISTRY322025-01-02
LBPILOT72HGBHemoglobinHEMATOLOGY11.42025-01-03
LBPILOT73TSHThyrotropinTHYROID2.12025-01-04
LBPILOT74URPROTUrine ProteinURINALYSISNEGATIVE2025-01-05
LBPILOT75FIBFibrinogenCOAGULATION7.8—
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
DOMAINDomain AbbreviationCharAssignedSet constant value "LB".SDTM1
STUDYIDStudy IdentifierCharCollectedCopy value from ODM.StudyOID.SDTM2
USUBJIDUnique Subject IdentifierCharCollectedCopy value from ODM.SubjectKey.SDTM3
LBTESTCDLab Test or Examination Short NameCharCollectedRecode ODM.FormOID: "FO.LB_CHEM" → "ALT", "FO.LB_HEM" → "HGB", "FO.LB_THY" → "TSH", "FO.LB_UA" → "URPROT", "FO.LB_EXTRA" → "FIB"; missing or unlisted values are errors.SDTM4
LBTESTLab Test or Examination NameCharCollectedRecode ODM.FormOID: "FO.LB_CHEM" → "Alanine Aminotransferase", "FO.LB_HEM" → "Hemoglobin", "FO.LB_THY" → "Thyrotropin", "FO.LB_UA" → "Urine Protein", "FO.LB_EXTRA" → "Fibrinogen"; missing or unlisted values are errors.SDTM5
LBCATCategory for Lab TestCharCollectedRecode ODM.FormOID: "FO.LB_CHEM" → "CHEMISTRY", "FO.LB_HEM" → "HEMATOLOGY", "FO.LB_THY" → "THYROID", "FO.LB_UA" → "URINALYSIS", "FO.LB_EXTRA" → "COAGULATION"; missing or unlisted values are errors.SDTM6
LBORRESResult or Finding in Original UnitsCharDerivedSet per constructed row; see the Row construction sheet.SDTM7
LBDTCDate/Time of Specimen CollectionCharISO 8601DerivedSet per constructed row; see the Row construction sheet.SDTM8
LBSEQSequence NumberNumDerivedRow number within each group of STUDYID, USUBJID, ordered by FORMORD.SDTM9
TemplateInclude whenLBORRESLBDTC
reported-resultLBORRES IS NOT NULLAggregate ONLY(ODM.Value) over records matching on the shared output keys, where ODM.ItemOID = 'IT.LB.RESULT'Aggregate ONLY(ODM.Value) over records matching on the shared output keys, where ODM.ItemOID = 'IT.LB.LBDTC'
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)lb <- yamaa_domain("spec.yaml")$outputlb

run.py

Edit4 lines
import yamaalb = yamaa.yamaa_domain("spec.yaml").outputlb