yamaa / Benchmark

SDTM.LB

Lab Results with Their Own Sample Dates

input files
1
subjects
2
expected rows
6
Review ask

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Summary

Lifecycle: draftEditUnder reviewWhat this benchmark means
README.md

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

Goal: derive one laboratory record per collected result, dated by the sample the result came from.

Input: long-form Operational Data Model (ODM) data as an EDC vendor exports it, one row per collected item. The vendor writes every field name in capitals and adds a site and a user field. Each lab sample is one repeat of the lab item group: a collection date and its results.

Variables:

  • LBSEQ numbers each subject's results by collection date, then test.
  • VISIT is the visit the sample was collected at.
  • LBTESTCD is the test of the result item, ALT or AST.
  • LBORRES is the result as collected; an empty result stays missing.
  • LBDTC is the collection date of the result's own sample, never of another sample at the same visit; a sample with no date keeps a missing date.

Note: field names match whatever their case, and the vendor's own fields take no part. A date recorded twice for one sample stops the run.

Inputs

Under review1 source file

input/odm.csv

Edit10 rows
STUDYOIDMETADATAVERSIONOIDSUBJECTKEYSTUDYEVENTOIDSTUDYEVENTREPEATKEYFORMOIDFORMREPEATKEYITEMGROUPOIDITEMGROUPREPEATKEYITEMOIDVALUESITEIDENTEREDBY
STUDY01MDV.1101SCREENING1FO.DM1IG.DM1IT.DM.SEXFSITE01jdoe
STUDY01MDV.1101SCREENING1FO.LB1IG.LB1IT.LB.LBDTC2025-01-05SITE01jdoe
STUDY01MDV.1101SCREENING1FO.LB1IG.LB1IT.LB.ALT32SITE01jdoe
STUDY01MDV.1101SCREENING1FO.LB1IG.LB1IT.LB.AST28SITE01jdoe
STUDY01MDV.1101WEEK21FO.LB1IG.LB1IT.LB.LBDTC2025-01-19SITE01jdoe
STUDY01MDV.1101WEEK21FO.LB1IG.LB1IT.LB.ALT41SITE01jdoe
STUDY01MDV.1101WEEK21FO.LB1IG.LB2IT.LB.LBDTC2025-01-20SITE01asmith
STUDY01MDV.1101WEEK21FO.LB1IG.LB2IT.LB.ALT39SITE01asmith
STUDY01MDV.1102SCREENING1FO.LB1IG.LB1IT.LB.ALT25SITE02bkim
STUDY01MDV.1102SCREENING1FO.LB1IG.LB1IT.LB.AST—SITE02bkim

Expected output

Under review6 expected rows

expected/lb.csv

Edit6 rows
STUDYIDUSUBJIDLBSEQVISITLBTESTCDLBORRESLBDTC
STUDY011SCREENINGALT322025-01-05
STUDY012SCREENINGAST282025-01-05
STUDY013WEEK2ALT412025-01-19
STUDY014WEEK2ALT392025-01-20
STUDY011SCREENINGALT25—
STUDY012SCREENINGAST——
Shaded columns are derived— = missing value

Human review and assessment

Your review

2 questions and your comments · View benchmark 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
VISITVisit NameCharCollectedCopy value from ODM.StudyEventOID.SDTM3
LBTESTCDLab Test or Examination Short NameCharDerivedSet per constructed row; see the Row construction sheet.SDTM4
LBORRESResult or Finding in Original UnitsCharDerivedSet per constructed row; see the Row construction sheet.SDTM5
LBDTCDate/Time of Specimen CollectionCharISO 8601CollectedRead collected ODM item IT.LB.LBDTC; no identified record yields blank.SDTM6
LBSEQSequence NumberNumDerivedRow number within each group of STUDYID, USUBJID, ordered by LBDTC then LBTESTCD.SDTM7
TemplateInclude whenLBTESTCDLBORRES
resultLBTESTCD IS NOT NULLRecode ODM.ItemOID: "IT.LB.ALT" → "ALT", "IT.LB.AST" → "AST"; missing or unlisted values stay missingCopy ODM.Value
VersionDateAuthorDescriptionReviewerSign-off
1.72026-10-20yamaa docs buildRead 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
1.62026-10-17yamaa docs buildDescribe collected date parts written as ISO 8601 date text and times of day counted in seconds since midnight
1.52026-10-17yamaa docs buildName 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
1.42026-10-15yamaa docs buildState datetime precision codes through the hour and minute, and complete only the time parts a collected datetime lacks
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

Public calls generated from benchmark.yaml; results must match the expected output

R

Edit3 lines
library(yamaa)yamaa_spec("spec.yaml")$run()$output

Python

Edit3 lines
import yamaayamaa.spec("spec.yaml").run().output