Describe Central and Site Laboratory Results Apart

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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 describes the results the site tests apart from all the others.

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.
LBORRES is the result as reported, in the reporting laboratory's units.

Note: the site tests the pregnancy (HCG) and urine pH (PH) samples and records them on page 14 of the case report form; the central laboratory reports every other test. The document describes LBORRES once for the tests other than those two, as transmitted by the central laboratory, and once for the two, as collected by the investigator. The two descriptions select no common row.

YAML specification

1 spec file

spec.yaml

Edit116 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: 560      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: 2472      origins:73        - type: Protocol74          source: Sponsor7576  # The site tests the pregnancy and urine pH samples itself and records the77  # results on page 14 of the case report form; the central laboratory tests78  # everything else.79  - name: LBORRES80    type: str81    label: Result or Finding in Original Units82    derivation: LAB.LBORRES83    submission:84      core: Exp85      role: Result Qualifier86      length: 887      origins:88        - type: Collected89          source: Vendor90        - type: Collected91          source: Investigator92          documents:93            - document: acrf94              pages: {type: PhysicalRef, refs: "14"}95      value_level:96        - id: CENTRAL97          where: {LBTESTCD: {comparator: NOTIN, values: [HCG, PH]}}98          label: Central Laboratory Result99          origins:100            - type: Collected101              source: Vendor102        - id: SITE103          where: {LBTESTCD: [HCG, PH]}104          label: Site Laboratory Result105          origins:106            - type: Collected107              source: Investigator108              documents:109                - document: acrf110                  pages: {type: PhysicalRef, refs: "14"}111112submission:113  label: Laboratory Test Results114  class: FINDINGS115  structure: One record per lab test per subject116  repeating: true

Inputs

Under review1 source file

input/lab.csv

Edit4 rows

input/lab.csv
STUDYID	LBTESTCD	LBTEST	LBORRES
LAB02	ALT	Alanine Aminotransferase	24
LAB02	CREAT	Creatinine	0.9
LAB02	HCG	Choriogonadotropin Beta	NEGATIVE
LAB02	PH	pH	6.0

Expected output

Under review4 expected rows

expected/define.xml

EditDefine-XML

Define-XML 2.1.11: LAB02

Example study testing most samples at a central laboratory; LAB-02; 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	5	Protocol; Sponsor
LBTEST	Lab Test or Examination Name	text	Synonym Qualifier	24	Protocol; Sponsor
LBORRES	Result or Finding in Original Units	text	Result Qualifier	8	Collected; Vendor Collected; Investigator; Annotated Case Report Form (acrf.pdf); pages 14

LB.LBORRES value-level metadata
Where Condition	Variable	Label / Description	Type	Role	Length or Display Format	Controlled Terms or ISO Format	Origin / Source / Method / Comment
LBTESTCD not in HCG, PH	LBORRES	Central Laboratory Result	text	Result Qualifier	8		Collected; Vendor
LBTESTCD in HCG, PH	LBORRES	Site Laboratory Result	text	Result Qualifier	8		Collected; Investigator; Annotated Case Report Form (acrf.pdf); pages 14

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="LAB02.sdtm.Define-XML_2.1" CreationDateTime="2026-09-11T00:00:00" SourceSystem="yamaa" SourceSystemVersion="1.0" def:Context="Other">
  <Study OID="STDY.LAB02">
    <GlobalVariables>
      <StudyName>LAB02</StudyName>
      <StudyDescription>Example study testing most samples at a central laboratory</StudyDescription>
      <ProtocolName>LAB-02</ProtocolName>
    </GlobalVariables>
    <MetaDataVersion OID="MDV.LAB02.sdtm" Name="LAB02 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>
      <def:ValueListDef OID="VL.LB.LBORRES">
        <ItemRef ItemOID="IT.LB.LBORRES.CENTRAL" OrderNumber="1" Mandatory="No" Role="Result Qualifier">
          <def:WhereClauseRef WhereClauseOID="WC.LB.LBORRES.CENTRAL"/>
        </ItemRef>
        <ItemRef ItemOID="IT.LB.LBORRES.SITE" OrderNumber="2" Mandatory="No" Role="Result Qualifier">
          <def:WhereClauseRef WhereClauseOID="WC.LB.LBORRES.SITE"/>
        </ItemRef>
      </def:ValueListDef>
      <def:WhereClauseDef OID="WC.LB.LBORRES.CENTRAL">
        <RangeCheck Comparator="NOTIN" SoftHard="Soft" def:ItemOID="IT.LB.LBTESTCD">
          <CheckValue>HCG</CheckValue>
          <CheckValue>PH</CheckValue>
        </RangeCheck>
      </def:WhereClauseDef>
      <def:WhereClauseDef OID="WC.LB.LBORRES.SITE">
        <RangeCheck Comparator="IN" SoftHard="Soft" def:ItemOID="IT.LB.LBTESTCD">
          <CheckValue>HCG</CheckValue>
          <CheckValue>PH</CheckValue>
        </RangeCheck>
      </def:WhereClauseDef>
      <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="5" 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="24" 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="8" 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="14" Type="PhysicalRef"/>
          </def:DocumentRef>
        </def:Origin>
        <def:ValueListRef ValueListOID="VL.LB.LBORRES"/>
      </ItemDef>
      <ItemDef OID="IT.LB.LBORRES.CENTRAL" Name="LBORRES" DataType="text" Length="8" SASFieldName="LBORRES">
        <Description>
          <TranslatedText xml:lang="en">Central Laboratory Result</TranslatedText>
        </Description>
        <def:Origin Type="Collected" Source="Vendor"/>
      </ItemDef>
      <ItemDef OID="IT.LB.LBORRES.SITE" Name="LBORRES" DataType="text" Length="8" SASFieldName="LBORRES">
        <Description>
          <TranslatedText xml:lang="en">Site Laboratory Result</TranslatedText>
        </Description>
        <def:Origin Type="Collected" Source="Investigator">
          <def:DocumentRef leafID="LF.acrf">
            <def:PDFPageRef PageRefs="14" 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

Edit4 rows

expected/lb.csv
DOMAIN	STUDYID	LBTESTCD	LBTEST	LBORRES
LB	LAB02	ALT	Alanine Aminotransferase	24
LB	LAB02	CREAT	Creatinine	0.9
LB	LAB02	HCG	Choriogonadotropin Beta	NEGATIVE
LB	LAB02	PH	pH	6.0

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	5	Protocol	Req	Copy value from LAB.LBTESTCD.	SDTM	4
LBTEST	Lab Test or Examination Name	Char	24	Protocol	Req	Copy value from LAB.LBTEST.	SDTM	5
LBORRES	Result or Finding in Original Units	Char	8	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: LAB02

LB

expected/lb.csv

Your review

Mapping spec

yamaa code

R

Python