yamaa / Benchmark

SDTM.ZE

Submit sponsor-defined examination records

input files
1
subjects
4
expected rows
2
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: carry examination sequence (ZESEQ) and name (ZETERM) in a sponsor-defined domain (DOMAIN is ZE), with submission metadata and a transport file.

Input: project.yaml composes spec.yaml into a Define-XML 2.1 submission with a transport. The specification marks the examination domain as sponsor-defined and maps input/examinations.csv into examination records.

Variables:

  • ZESEQ identifies the examination record within the subject.
  • ZETERM carries the examination name as recorded.

Note: the examination dataset is explicitly marked sponsor-defined. Its Define-XML 2.1 metadata records that status rather than claiming an implementation-guide definition, and links its SAS transport file. The collected examination name cites page 1 of the annotated case report form.

Inputs

Under review1 source file

input/examinations.csv

Edit2 rows
USUBJIDSEQTERM
1Slit lamp
1Fundoscopy

Expected output

Under review2 expected rows

expected/define.xml

EditDefine-XML

Define-XML 2.1.11: Custom examination study

Sponsor-defined examination records; NS01; SDTMIG 3.4

Datasets
DatasetDescriptionClassStructurePurposeKeysDocumentationLocation
ZEEye ExaminationsFINDINGSOne record per examination per subjectTabulationSTUDYID, USUBJID, ZESEQze.xpt

ZE

ZE variables
VariableLabel / DescriptionTypeRoleLength or Display FormatControlled Terms or ISO FormatOrigin / Source / Method / Comment
DOMAINDomain AbbreviationtextIdentifier2Assigned; Sponsor
STUDYIDStudy IdentifiertextIdentifier4Protocol; Sponsor
USUBJIDUnique Subject IdentifiertextIdentifier7Assigned; Sponsor
ZESEQSequence NumberintegerIdentifier8Assigned; Sponsor
ZETERMExamination NametextTopic10Collected; Investigator; Annotated Case Report Form (acrf.pdf); pages 1
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="NS01.sdtm.Define-XML_2.1" CreationDateTime="2026-09-11T00:00:00" SourceSystem="yamaa" SourceSystemVersion="1.0" def:Context="Submission">
  <Study OID="STDY.NS01">
    <GlobalVariables>
      <StudyName>Custom examination study</StudyName>
      <StudyDescription>Sponsor-defined examination records</StudyDescription>
      <ProtocolName>NS01</ProtocolName>
    </GlobalVariables>
    <MetaDataVersion OID="MDV.NS01.sdtm" Name="Custom examination study 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.ZE" Name="ZE" Domain="ZE" Purpose="Tabulation" SASDatasetName="ZE" Repeating="Yes" IsReferenceData="No" def:Structure="One record per examination per subject" def:ArchiveLocationID="LF.ZE" def:IsNonStandard="Yes">
        <Description>
          <TranslatedText xml:lang="en">Eye Examinations</TranslatedText>
        </Description>
        <ItemRef ItemOID="IT.ZE.DOMAIN" OrderNumber="1" Mandatory="Yes" Role="Identifier"/>
        <ItemRef ItemOID="IT.ZE.STUDYID" OrderNumber="2" Mandatory="Yes" KeySequence="1" Role="Identifier"/>
        <ItemRef ItemOID="IT.ZE.USUBJID" OrderNumber="3" Mandatory="Yes" KeySequence="2" Role="Identifier"/>
        <ItemRef ItemOID="IT.ZE.ZESEQ" OrderNumber="4" Mandatory="Yes" KeySequence="3" Role="Identifier"/>
        <ItemRef ItemOID="IT.ZE.ZETERM" OrderNumber="5" Mandatory="Yes" Role="Topic"/>
        <def:Class Name="FINDINGS"/>
        <def:leaf ID="LF.ZE" xlink:href="ze.xpt">
          <def:title>ze.xpt</def:title>
        </def:leaf>
      </ItemGroupDef>
      <ItemDef OID="IT.ZE.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.ZE.STUDYID" Name="STUDYID" DataType="text" Length="4" SASFieldName="STUDYID">
        <Description>
          <TranslatedText xml:lang="en">Study Identifier</TranslatedText>
        </Description>
        <def:Origin Type="Protocol" Source="Sponsor"/>
      </ItemDef>
      <ItemDef OID="IT.ZE.USUBJID" Name="USUBJID" DataType="text" Length="7" SASFieldName="USUBJID">
        <Description>
          <TranslatedText xml:lang="en">Unique Subject Identifier</TranslatedText>
        </Description>
        <def:Origin Type="Assigned" Source="Sponsor"/>
      </ItemDef>
      <ItemDef OID="IT.ZE.ZESEQ" Name="ZESEQ" DataType="integer" Length="8" SASFieldName="ZESEQ">
        <Description>
          <TranslatedText xml:lang="en">Sequence Number</TranslatedText>
        </Description>
        <def:Origin Type="Assigned" Source="Sponsor"/>
      </ItemDef>
      <ItemDef OID="IT.ZE.ZETERM" Name="ZETERM" DataType="text" Length="10" SASFieldName="ZETERM">
        <Description>
          <TranslatedText xml:lang="en">Examination Name</TranslatedText>
        </Description>
        <def:Origin Type="Collected" Source="Investigator">
          <def:DocumentRef leafID="LF.acrf">
            <def:PDFPageRef PageRefs="1" 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/ze.csv

Edit2 rows
DOMAINSTUDYIDUSUBJIDZESEQZETERM
ZENS011Slit lamp
ZENS011Fundoscopy
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
DOMAINDomain AbbreviationChar2AssignedReqSet constant value "ZE".SDTM1
STUDYIDStudy IdentifierChar4ProtocolReqSet constant value "NS01".SDTM2
USUBJIDUnique Subject IdentifierChar7AssignedReqCopy value from EYE_RAW.USUBJID.SDTM3
ZESEQSequence NumberNum8AssignedReqCopy value from EYE_RAW.SEQ.SDTM4
ZETERMExamination NameChar10CollectedReqCopy value from EYE_RAW.TERM.SDTM5
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_project("project.yaml")$spec("ZE")$run()$output

Python

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