yamaa / Benchmark

SDTM.DI

Bind Each Dataset to the Implementation Guide It Names

input files
2
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: submit demographics and device identifiers with one data-definition document that cites both implementation guides they follow, each dataset pointing at its own.

Input: two spec files and the project that lists them:

  • spec_dm.yaml builds demographics (DM) from the study's subjects and names no guide;
  • spec_di.yaml builds device identifiers (DI) from the identifying attributes of each study device, one row per attribute as its manufacturer supplies them, and names the medical device supplement to the tabulation guide;
  • project.yaml cites the general tabulation guide first and the medical device supplement second.

Variables:

  • SPDEVID is the sponsor's identifier for one device.
  • DIPARMCD and DIPARM name the identifying attribute: MODEL for the model number and SERIAL for the serial number.
  • DIVAL is that attribute's value as the manufacturer printed it on the device.

Note: the data-definition document cites every guide the project lists, in the project's order. Each dataset's definition points at the guide its spec names, or at the first guide when it names none, so demographics follows the general guide and the device identifiers follow the supplement.

Inputs

Under review2 source files

input/devices.csv

Edit4 rows
STUDYIDSPDEVIDDIPARMCDDIPARMDIVAL
DEV01GS-001MODELModel NumberGS200
DEV01GS-001SERIALSerial NumberSN10458
DEV01GS-002MODELModel NumberGS200
DEV01GS-002SERIALSerial NumberSN10461

input/subjects.csv

Edit2 rows
STUDYIDUSUBJID
DEV01
DEV01

Expected output

Under review6 expected rows

expected/define.xml

EditDefine-XML

Define-XML 2.1.11: DEV01

Example study of an implanted glucose sensor; DEV-01; SDTMIG 3.4; SDTMIG-MD 1.1

Datasets
DatasetDescriptionClassStructurePurposeKeysDocumentationLocation
DMDemographicsSPECIAL PURPOSEOne record per subjectTabulationSTUDYID, USUBJIDdm.csv
DIDevice IdentifiersSTUDY REFERENCEOne record per device identifier per deviceTabulationSTUDYID, SPDEVID, DIPARMCDdi.csv

DM

DM variables
VariableLabel / DescriptionTypeRoleLength or Display FormatControlled Terms or ISO FormatOrigin / Source / Method / Comment
DOMAINDomain AbbreviationtextIdentifier2Assigned; Sponsor
STUDYIDStudy IdentifiertextIdentifier5Protocol; Sponsor
USUBJIDUnique Subject IdentifiertextIdentifier9Assigned; Sponsor

DI

DI variables
VariableLabel / DescriptionTypeRoleLength or Display FormatControlled Terms or ISO FormatOrigin / Source / Method / Comment
DOMAINDomain AbbreviationtextIdentifier2Assigned; Sponsor
STUDYIDStudy IdentifiertextIdentifier5Protocol; Sponsor
SPDEVIDSponsor Device IdentifiertextIdentifier6Assigned; Sponsor
DIPARMCDDevice Identifier Element Short NametextTopic6Assigned; Sponsor
DIPARMDevice Identifier Element NametextSynonym Qualifier13Assigned; Sponsor
DIVALDevice Identifier Element ValuetextResult Qualifier7Collected; Vendor
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="DEV01.sdtm.Define-XML_2.1" CreationDateTime="2026-09-11T00:00:00" SourceSystem="yamaa" SourceSystemVersion="1.0" def:Context="Other">
  <Study OID="STDY.DEV01">
    <GlobalVariables>
      <StudyName>DEV01</StudyName>
      <StudyDescription>Example study of an implanted glucose sensor</StudyDescription>
      <ProtocolName>DEV-01</ProtocolName>
    </GlobalVariables>
    <MetaDataVersion OID="MDV.DEV01.sdtm" Name="DEV01 sdtm metadata" def:DefineVersion="2.1.11">
      <def:Standards>
        <def:Standard OID="STD.SDTMIG" Name="SDTMIG" Type="IG" Version="3.4" Status="Final"/>
        <def:Standard OID="STD.SDTMIG-MD" Name="SDTMIG-MD" Type="IG" Version="1.1" Status="Final"/>
      </def:Standards>
      <ItemGroupDef OID="IG.DM" Name="DM" Domain="DM" Purpose="Tabulation" SASDatasetName="DM" Repeating="No" IsReferenceData="No" def:Structure="One record per subject" def:ArchiveLocationID="LF.DM" def:StandardOID="STD.SDTMIG">
        <Description>
          <TranslatedText xml:lang="en">Demographics</TranslatedText>
        </Description>
        <ItemRef ItemOID="IT.DM.DOMAIN" OrderNumber="1" Mandatory="Yes" Role="Identifier"/>
        <ItemRef ItemOID="IT.DM.STUDYID" OrderNumber="2" Mandatory="Yes" KeySequence="1" Role="Identifier"/>
        <ItemRef ItemOID="IT.DM.USUBJID" OrderNumber="3" Mandatory="Yes" KeySequence="2" Role="Identifier"/>
        <def:Class Name="SPECIAL PURPOSE"/>
        <def:leaf ID="LF.DM" xlink:href="dm.csv">
          <def:title>dm.csv</def:title>
        </def:leaf>
      </ItemGroupDef>
      <ItemGroupDef OID="IG.DI" Name="DI" Domain="DI" Purpose="Tabulation" SASDatasetName="DI" Repeating="No" IsReferenceData="Yes" def:Structure="One record per device identifier per device" def:ArchiveLocationID="LF.DI" def:StandardOID="STD.SDTMIG-MD">
        <Description>
          <TranslatedText xml:lang="en">Device Identifiers</TranslatedText>
        </Description>
        <ItemRef ItemOID="IT.DI.DOMAIN" OrderNumber="1" Mandatory="Yes" Role="Identifier"/>
        <ItemRef ItemOID="IT.DI.STUDYID" OrderNumber="2" Mandatory="Yes" KeySequence="1" Role="Identifier"/>
        <ItemRef ItemOID="IT.DI.SPDEVID" OrderNumber="3" Mandatory="Yes" KeySequence="2" Role="Identifier"/>
        <ItemRef ItemOID="IT.DI.DIPARMCD" OrderNumber="4" Mandatory="Yes" KeySequence="3" Role="Topic"/>
        <ItemRef ItemOID="IT.DI.DIPARM" OrderNumber="5" Mandatory="Yes" Role="Synonym Qualifier"/>
        <ItemRef ItemOID="IT.DI.DIVAL" OrderNumber="6" Mandatory="Yes" Role="Result Qualifier"/>
        <def:Class Name="STUDY REFERENCE"/>
        <def:leaf ID="LF.DI" xlink:href="di.csv">
          <def:title>di.csv</def:title>
        </def:leaf>
      </ItemGroupDef>
      <ItemDef OID="IT.DM.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.DM.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.DM.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.DI.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.DI.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.DI.SPDEVID" Name="SPDEVID" DataType="text" Length="6" SASFieldName="SPDEVID">
        <Description>
          <TranslatedText xml:lang="en">Sponsor Device Identifier</TranslatedText>
        </Description>
        <def:Origin Type="Assigned" Source="Sponsor"/>
      </ItemDef>
      <ItemDef OID="IT.DI.DIPARMCD" Name="DIPARMCD" DataType="text" Length="6" SASFieldName="DIPARMCD">
        <Description>
          <TranslatedText xml:lang="en">Device Identifier Element Short Name</TranslatedText>
        </Description>
        <def:Origin Type="Assigned" Source="Sponsor"/>
      </ItemDef>
      <ItemDef OID="IT.DI.DIPARM" Name="DIPARM" DataType="text" Length="13" SASFieldName="DIPARM">
        <Description>
          <TranslatedText xml:lang="en">Device Identifier Element Name</TranslatedText>
        </Description>
        <def:Origin Type="Assigned" Source="Sponsor"/>
      </ItemDef>
      <ItemDef OID="IT.DI.DIVAL" Name="DIVAL" DataType="text" Length="7" SASFieldName="DIVAL">
        <Description>
          <TranslatedText xml:lang="en">Device Identifier Element Value</TranslatedText>
        </Description>
        <def:Origin Type="Collected" Source="Vendor"/>
      </ItemDef>
    </MetaDataVersion>
  </Study>
</ODM>

expected/di.csv

Edit4 rows
DOMAINSTUDYIDSPDEVIDDIPARMCDDIPARMDIVAL
DIDEV01GS-001MODELModel NumberGS200
DIDEV01GS-001SERIALSerial NumberSN10458
DIDEV01GS-002MODELModel NumberGS200
DIDEV01GS-002SERIALSerial NumberSN10461

expected/dm.csv

Edit2 rows
DOMAINSTUDYIDUSUBJID
DMDEV01
DMDEV01
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 "DI".SDTM1
STUDYIDStudy IdentifierChar5ProtocolReqCopy value from DEVICES.STUDYID.SDTM2
SPDEVIDSponsor Device IdentifierChar6AssignedReqCopy value from DEVICES.SPDEVID.SDTM3
DIPARMCDDevice Identifier Element Short NameChar6AssignedReqCopy value from DEVICES.DIPARMCD.SDTM4
DIPARMDevice Identifier Element NameChar13AssignedReqCopy value from DEVICES.DIPARM.SDTM5
DIVALDevice Identifier Element ValueChar7CollectedReqCopy value from DEVICES.DIVAL.SDTM6
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

Edit4 lines
library(yamaa)yamaa_project("project.yaml")$spec("DM")$run()$save()yamaa_project("project.yaml")$spec("DI")$run()$output

Python

Edit4 lines
import yamaayamaa.project("project.yaml").spec("DM").run().save()yamaa.project("project.yaml").spec("DI").run().output