Describe a Result Reported by Two Laboratories

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Summary

EditUnder reviewWhat this benchmark means

README.md

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

Goal: submit the laboratory results (LBTESTCD, LBTEST, LBORRES) with a data-definition document that states both places a result can come from.

Input: spec.yaml reads the laboratory results, one row per test per subject, and project.yaml submits the dataset with the study's annotated case report form.

Variables:

LBTESTCD and LBTEST are the test's code and name: HGB, hemoglobin.
LBORRES is the result as reported, in the reporting laboratory's units.

Note: the central laboratory reports most results, but a site whose sample could not be shipped tests it in its own laboratory and records the result on page 12 of the case report form. No other variable tells the two apart, so the result's definition names both: transmitted by the central laboratory, and collected by the investigator on that page, in that order.

YAML specification

1 spec file

spec.yaml

Edit99 lines

1yamaa: "1.0"23type: spec45model: SDTM6domain: LB7keys: [STUDYID, USUBJID, LBTESTCD]8input:9  LAB: input/lab.csv1011output:12  path: lb.csv13  columns: [DOMAIN, STUDYID, USUBJID, LBTESTCD, LBTEST, LBORRES]1415columns:16  - name: DOMAIN17    type: str18    label: Domain Abbreviation19    derivation: "'LB'"20    submission:21      core: Req22      role: Identifier23      length: 224      origins:25        - type: Assigned26          source: Sponsor2728  - name: STUDYID29    type: str30    label: Study Identifier31    derivation: LAB.STUDYID32    submission:33      core: Req34      role: Identifier35      length: 536      origins:37        - type: Protocol38          source: Sponsor3940  - name: USUBJID41    type: str42    label: Unique Subject Identifier43    derivation: LAB.USUBJID44    submission:45      core: Req46      role: Identifier47      length: 948      origins:49        - type: Assigned50          source: Sponsor5152  - name: LBTESTCD53    type: str54    label: Lab Test or Examination Short Name55    derivation: LAB.LBTESTCD56    submission:57      core: Req58      role: Topic59      length: 360      origins:61        - type: Protocol62          source: Sponsor6364  - name: LBTEST65    type: str66    label: Lab Test or Examination Name67    derivation: LAB.LBTEST68    submission:69      core: Req70      role: Synonym Qualifier71      length: 1072      origins:73        - type: Protocol74          source: Sponsor7576  # The central laboratory reports most results; a site whose sample could not77  # be shipped records its own laboratory's result on the case report form.78  - name: LBORRES79    type: str80    label: Result or Finding in Original Units81    derivation: LAB.LBORRES82    submission:83      core: Exp84      role: Result Qualifier85      length: 486      origins:87        - type: Collected88          source: Vendor89        - type: Collected90          source: Investigator91          documents:92            - document: acrf93              pages: {type: PhysicalRef, refs: "12"}9495submission:96  label: Laboratory Test Results97  class: FINDINGS98  structure: One record per lab test per subject99  repeating: true

Inputs

Under review1 source file

input/lab.csv

Edit2 rows

input/lab.csv
STUDYID	USUBJID	LBTESTCD	LBTEST	LBORRES
LAB01		HGB	Hemoglobin	13.2
LAB01		HGB	Hemoglobin	12.8

Expected output

Under review2 expected rows

expected/define.xml

EditDefine-XML

Define-XML 2.1.11: LAB01

Example study testing samples at a central laboratory; LAB-01; SDTMIG 3.4

Datasets
Dataset	Description	Class	Structure	Purpose	Keys	Documentation	Location
LB	Laboratory Test Results	FINDINGS	One record per lab test per subject	Tabulation	STUDYID, USUBJID, LBTESTCD		lb.csv

LB

LB variables
Variable	Label / Description	Type	Role	Length or Display Format	Origin / Source / Method / Comment
DOMAIN	Domain Abbreviation	text	Identifier	2	Assigned; Sponsor
STUDYID	Study Identifier	text	Identifier	5	Protocol; Sponsor
USUBJID	Unique Subject Identifier	text	Identifier	9	Assigned; Sponsor
LBTESTCD	Lab Test or Examination Short Name	text	Topic	3	Protocol; Sponsor
LBTEST	Lab Test or Examination Name	text	Synonym Qualifier	10	Protocol; Sponsor
LBORRES	Result or Finding in Original Units	text	Result Qualifier	4	Collected; Vendor Collected; Investigator; Annotated Case Report Form (acrf.pdf); pages 12

Original source

<?xml version="1.0" encoding="UTF-8"?>
<ODM xmlns="http://www.cdisc.org/ns/odm/v1.3" xmlns:def="http://www.cdisc.org/ns/def/v2.1" xmlns:xlink="http://www.w3.org/1999/xlink" ODMVersion="1.3.2" FileType="Snapshot" FileOID="LAB01.sdtm.Define-XML_2.1" CreationDateTime="2026-09-11T00:00:00" SourceSystem="yamaa" SourceSystemVersion="1.0" def:Context="Other">
  <Study OID="STDY.LAB01">
    <GlobalVariables>
      <StudyName>LAB01</StudyName>
      <StudyDescription>Example study testing samples at a central laboratory</StudyDescription>
      <ProtocolName>LAB-01</ProtocolName>
    </GlobalVariables>
    <MetaDataVersion OID="MDV.LAB01.sdtm" Name="LAB01 sdtm metadata" def:DefineVersion="2.1.11">
      <def:Standards>
        <def:Standard OID="STD.SDTMIG" Name="SDTMIG" Type="IG" Version="3.4" Status="Final"/>
      </def:Standards>
      <def:AnnotatedCRF>
        <def:DocumentRef leafID="LF.acrf"/>
      </def:AnnotatedCRF>
      <ItemGroupDef OID="IG.LB" Name="LB" Domain="LB" Purpose="Tabulation" SASDatasetName="LB" Repeating="Yes" IsReferenceData="No" def:Structure="One record per lab test per subject" def:ArchiveLocationID="LF.LB" def:StandardOID="STD.SDTMIG">
        <Description>
          <TranslatedText xml:lang="en">Laboratory Test Results</TranslatedText>
        </Description>
        <ItemRef ItemOID="IT.LB.DOMAIN" OrderNumber="1" Mandatory="Yes" Role="Identifier"/>
        <ItemRef ItemOID="IT.LB.STUDYID" OrderNumber="2" Mandatory="Yes" KeySequence="1" Role="Identifier"/>
        <ItemRef ItemOID="IT.LB.USUBJID" OrderNumber="3" Mandatory="Yes" KeySequence="2" Role="Identifier"/>
        <ItemRef ItemOID="IT.LB.LBTESTCD" OrderNumber="4" Mandatory="Yes" KeySequence="3" Role="Topic"/>
        <ItemRef ItemOID="IT.LB.LBTEST" OrderNumber="5" Mandatory="Yes" Role="Synonym Qualifier"/>
        <ItemRef ItemOID="IT.LB.LBORRES" OrderNumber="6" Mandatory="No" Role="Result Qualifier"/>
        <def:Class Name="FINDINGS"/>
        <def:leaf ID="LF.LB" xlink:href="lb.csv">
          <def:title>lb.csv</def:title>
        </def:leaf>
      </ItemGroupDef>
      <ItemDef OID="IT.LB.DOMAIN" Name="DOMAIN" DataType="text" Length="2" SASFieldName="DOMAIN">
        <Description>
          <TranslatedText xml:lang="en">Domain Abbreviation</TranslatedText>
        </Description>
        <def:Origin Type="Assigned" Source="Sponsor"/>
      </ItemDef>
      <ItemDef OID="IT.LB.STUDYID" Name="STUDYID" DataType="text" Length="5" SASFieldName="STUDYID">
        <Description>
          <TranslatedText xml:lang="en">Study Identifier</TranslatedText>
        </Description>
        <def:Origin Type="Protocol" Source="Sponsor"/>
      </ItemDef>
      <ItemDef OID="IT.LB.USUBJID" Name="USUBJID" DataType="text" Length="9" SASFieldName="USUBJID">
        <Description>
          <TranslatedText xml:lang="en">Unique Subject Identifier</TranslatedText>
        </Description>
        <def:Origin Type="Assigned" Source="Sponsor"/>
      </ItemDef>
      <ItemDef OID="IT.LB.LBTESTCD" Name="LBTESTCD" DataType="text" Length="3" SASFieldName="LBTESTCD">
        <Description>
          <TranslatedText xml:lang="en">Lab Test or Examination Short Name</TranslatedText>
        </Description>
        <def:Origin Type="Protocol" Source="Sponsor"/>
      </ItemDef>
      <ItemDef OID="IT.LB.LBTEST" Name="LBTEST" DataType="text" Length="10" SASFieldName="LBTEST">
        <Description>
          <TranslatedText xml:lang="en">Lab Test or Examination Name</TranslatedText>
        </Description>
        <def:Origin Type="Protocol" Source="Sponsor"/>
      </ItemDef>
      <ItemDef OID="IT.LB.LBORRES" Name="LBORRES" DataType="text" Length="4" SASFieldName="LBORRES">
        <Description>
          <TranslatedText xml:lang="en">Result or Finding in Original Units</TranslatedText>
        </Description>
        <def:Origin Type="Collected" Source="Vendor"/>
        <def:Origin Type="Collected" Source="Investigator">
          <def:DocumentRef leafID="LF.acrf">
            <def:PDFPageRef PageRefs="12" Type="PhysicalRef"/>
          </def:DocumentRef>
        </def:Origin>
      </ItemDef>
      <def:leaf ID="LF.acrf" xlink:href="acrf.pdf">
        <def:title>Annotated Case Report Form</def:title>
      </def:leaf>
    </MetaDataVersion>
  </Study>
</ODM>

expected/lb.csv

Edit2 rows

expected/lb.csv
DOMAIN	STUDYID	USUBJID	LBTESTCD	LBTEST	LBORRES
LB	LAB01		HGB	Hemoglobin	13.2
LB	LAB01		HGB	Hemoglobin	12.8

Shaded columns are derived— = missing value

Human review and assessment

Variable Name	Variable Label	Type	Length	Origin	Core	Conversion Definition	Variable Type	Variable Order
DOMAIN	Domain Abbreviation	Char	2	Assigned	Req	Set constant value "LB".	SDTM	1
STUDYID	Study Identifier	Char	5	Protocol	Req	Copy value from LAB.STUDYID.	SDTM	2
USUBJID	Unique Subject Identifier	Char	9	Assigned	Req	Copy value from LAB.USUBJID.	SDTM	3
LBTESTCD	Lab Test or Examination Short Name	Char	3	Protocol	Req	Copy value from LAB.LBTESTCD.	SDTM	4
LBTEST	Lab Test or Examination Name	Char	10	Protocol	Req	Copy value from LAB.LBTEST.	SDTM	5
LBORRES	Result or Finding in Original Units	Char	4	Collected, Collected	Exp	Copy value from LAB.LBORRES.	SDTM	6

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

R

Edit3 lines

1library(yamaa)23yamaa_project("project.yaml")$spec("LB")$run()$output

Python

Edit3 lines

1import yamaa23yamaa.project("project.yaml").spec("LB").run().output

input/lab.csv

expected/define.xml

Define-XML 2.1.11: LAB01

LB

expected/lb.csv

Your review

Mapping spec

yamaa code

R

Python