Standardize morphology results with SDTMIG 3.3

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Summary

EditUnder reviewWhat this benchmark means

README.md

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

Goal: Preserve the collected cell type result and report its standardized form in the morphology domain.

Input: Cell type findings and collection dates from a morphology form.

Variables:

MOSEQ identifies a finding within a subject.
MOTESTCD and MOTEST identify the cell type assessment.
MOORRES retains the collected result.
MOSTRESC reports NORMAL or ABNORMAL.
MODTC retains the collection date.

Note: project.yaml declares SDTMIG 3.3. The data-definition document records that guide and points to the SAS Transport version 5 dataset.

YAML specification

1 spec file

spec.yaml

Edit157 lines

1yamaa: '1.0'2type: spec3model: SDTM4domain: MO5keys:6- STUDYID7- USUBJID8- MOSEQ9input:10  MORPH:11    path: input/morphology.csv12    types:13      SEQ: int14      DATE: date1516output:17  path: mo.csv18  columns:19  - DOMAIN20  - STUDYID21  - USUBJID22  - MOSEQ23  - MOTESTCD24  - MOTEST25  - MOORRES26  - MOSTRESC27  - MODTC2829columns:30- name: DOMAIN31  type: str32  label: Domain Abbreviation33  derivation: '''MO'''34  submission:35    core: Req36    role: Identifier37    length: 8038    origins:39    - type: Assigned40      source: Sponsor4142- name: STUDYID43  type: str44  label: Study Identifier45  derivation: MORPH.STUDYID46  submission:47    core: Req48    role: Identifier49    length: 8050    origins:51    - type: Protocol52      source: Sponsor5354- name: USUBJID55  type: str56  label: Unique Subject Identifier57  derivation: MORPH.USUBJID58  submission:59    core: Req60    role: Identifier61    length: 8062    origins:63    - type: Assigned64      source: Sponsor6566- name: MOSEQ67  type: int68  label: Sequence Number69  derivation: MORPH.SEQ70  submission:71    core: Req72    role: Identifier73    length: 874    origins:75    - type: Assigned76      source: Sponsor7778- name: MOTESTCD79  type: str80  label: Morphology Test Short Name81  derivation: '''CELLTYPE'''82  submission:83    core: Req84    role: Topic85    length: 8086    origins:87    - type: Assigned88      source: Sponsor8990- name: MOTEST91  type: str92  label: Morphology Test Name93  derivation: '''Cell Type'''94  submission:95    core: Req96    role: Synonym Qualifier97    length: 8098    origins:99    - type: Assigned100      source: Sponsor101102- name: MOORRES103  type: str104  label: Result or Finding in Original Units105  derivation: MORPH.RESULT106  submission:107    core: Exp108    role: Result Qualifier109    length: 80110    origins:111    - type: Collected112      source: Investigator113      documents:114      - document: acrf115        pages:116          type: PhysicalRef117          refs: '1'118119- name: MOSTRESC120  type: str121  label: Character Result/Finding in Std Format122  derivation:123    mapping:124      source: MORPH.RESULT125      dict:126        normal: NORMAL127        abnormal: ABNORMAL128  submission:129    core: Exp130    role: Result Qualifier131    length: 80132    origins:133    - type: Derived134      source: Sponsor135    method: Standardize the collected cell type result.136137- name: MODTC138  type: date139  label: Date/Time of Collection140  derivation: MORPH.DATE141  submission:142    core: Exp143    role: Timing144    origins:145    - type: Collected146      source: Investigator147      documents:148      - document: acrf149        pages:150          type: PhysicalRef151          refs: '1'152153submission:154  label: Morphology155  class: FINDINGS156  structure: One record per subject per test157  repeating: true

Inputs

Under review1 source file

input/morphology.csv

Edit2 rows

input/morphology.csv
STUDYID	USUBJID	SEQ	RESULT	DATE
CATH		1	normal	2025-01-08
CATH		1	abnormal	2025-01-09

Expected output

Under review2 expected rows

expected/define.xml

EditDefine-XML

Define-XML 2.1.11: CATH

Morphology; CATH-01; SDTMIG 3.3

Datasets
Dataset	Description	Class	Structure	Purpose	Keys	Documentation	Location
MO	Morphology	FINDINGS	One record per subject per test	Tabulation	STUDYID, USUBJID, MOSEQ		mo.xpt

MO

MO variables
Variable	Label / Description	Type	Role	Length or Display Format	Controlled Terms or ISO Format	Origin / Source / Method / Comment
DOMAIN	Domain Abbreviation	text	Identifier	2		Assigned; Sponsor
STUDYID	Study Identifier	text	Identifier	4		Protocol; Sponsor
USUBJID	Unique Subject Identifier	text	Identifier	7		Assigned; Sponsor
MOSEQ	Sequence Number	integer	Identifier	8		Assigned; Sponsor
MOTESTCD	Morphology Test Short Name	text	Topic	8		Assigned; Sponsor
MOTEST	Morphology Test Name	text	Synonym Qualifier	9		Assigned; Sponsor
MOORRES	Result or Finding in Original Units	text	Result Qualifier	8		Collected; Investigator; Annotated Case Report Form (acrf.pdf); pages 1
MOSTRESC	Character Result/Finding in Std Format	text	Result Qualifier	8		Derived; Sponsor Standardize the collected cell type result.
MODTC	Date/Time of Collection	date	Timing		ISO 8601	Collected; 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="CATH.sdtm.Define-XML_2.1" CreationDateTime="2026-09-11T00:00:00" SourceSystem="yamaa" SourceSystemVersion="1.0" def:Context="Submission">
  <Study OID="STDY.CATH">
    <GlobalVariables>
      <StudyName>CATH</StudyName>
      <StudyDescription>Morphology</StudyDescription>
      <ProtocolName>CATH-01</ProtocolName>
    </GlobalVariables>
    <MetaDataVersion OID="MDV.CATH.sdtm" Name="CATH sdtm metadata" def:DefineVersion="2.1.11">
      <def:Standards>
        <def:Standard OID="STD.SDTMIG" Name="SDTMIG" Type="IG" Version="3.3" Status="Final"/>
      </def:Standards>
      <def:AnnotatedCRF>
        <def:DocumentRef leafID="LF.acrf"/>
      </def:AnnotatedCRF>
      <ItemGroupDef OID="IG.MO" Name="MO" Domain="MO" Purpose="Tabulation" SASDatasetName="MO" Repeating="Yes" IsReferenceData="No" def:Structure="One record per subject per test" def:ArchiveLocationID="LF.MO" def:StandardOID="STD.SDTMIG">
        <Description>
          <TranslatedText xml:lang="en">Morphology</TranslatedText>
        </Description>
        <ItemRef ItemOID="IT.MO.DOMAIN" OrderNumber="1" Mandatory="Yes" Role="Identifier"/>
        <ItemRef ItemOID="IT.MO.STUDYID" OrderNumber="2" Mandatory="Yes" KeySequence="1" Role="Identifier"/>
        <ItemRef ItemOID="IT.MO.USUBJID" OrderNumber="3" Mandatory="Yes" KeySequence="2" Role="Identifier"/>
        <ItemRef ItemOID="IT.MO.MOSEQ" OrderNumber="4" Mandatory="Yes" KeySequence="3" Role="Identifier"/>
        <ItemRef ItemOID="IT.MO.MOTESTCD" OrderNumber="5" Mandatory="Yes" Role="Topic"/>
        <ItemRef ItemOID="IT.MO.MOTEST" OrderNumber="6" Mandatory="Yes" Role="Synonym Qualifier"/>
        <ItemRef ItemOID="IT.MO.MOORRES" OrderNumber="7" Mandatory="No" Role="Result Qualifier"/>
        <ItemRef ItemOID="IT.MO.MOSTRESC" OrderNumber="8" Mandatory="No" Role="Result Qualifier" MethodOID="MT.MO.MOSTRESC"/>
        <ItemRef ItemOID="IT.MO.MODTC" OrderNumber="9" Mandatory="No" Role="Timing"/>
        <def:Class Name="FINDINGS"/>
        <def:leaf ID="LF.MO" xlink:href="mo.xpt">
          <def:title>mo.xpt</def:title>
        </def:leaf>
      </ItemGroupDef>
      <ItemDef OID="IT.MO.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.MO.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.MO.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.MO.MOSEQ" Name="MOSEQ" DataType="integer" Length="8" SASFieldName="MOSEQ">
        <Description>
          <TranslatedText xml:lang="en">Sequence Number</TranslatedText>
        </Description>
        <def:Origin Type="Assigned" Source="Sponsor"/>
      </ItemDef>
      <ItemDef OID="IT.MO.MOTESTCD" Name="MOTESTCD" DataType="text" Length="8" SASFieldName="MOTESTCD">
        <Description>
          <TranslatedText xml:lang="en">Morphology Test Short Name</TranslatedText>
        </Description>
        <def:Origin Type="Assigned" Source="Sponsor"/>
      </ItemDef>
      <ItemDef OID="IT.MO.MOTEST" Name="MOTEST" DataType="text" Length="9" SASFieldName="MOTEST">
        <Description>
          <TranslatedText xml:lang="en">Morphology Test Name</TranslatedText>
        </Description>
        <def:Origin Type="Assigned" Source="Sponsor"/>
      </ItemDef>
      <ItemDef OID="IT.MO.MOORRES" Name="MOORRES" DataType="text" Length="8" SASFieldName="MOORRES">
        <Description>
          <TranslatedText xml:lang="en">Result or Finding in Original Units</TranslatedText>
        </Description>
        <def:Origin Type="Collected" Source="Investigator">
          <def:DocumentRef leafID="LF.acrf">
            <def:PDFPageRef PageRefs="1" Type="PhysicalRef"/>
          </def:DocumentRef>
        </def:Origin>
      </ItemDef>
      <ItemDef OID="IT.MO.MOSTRESC" Name="MOSTRESC" DataType="text" Length="8" SASFieldName="MOSTRESC">
        <Description>
          <TranslatedText xml:lang="en">Character Result/Finding in Std Format</TranslatedText>
        </Description>
        <def:Origin Type="Derived" Source="Sponsor"/>
      </ItemDef>
      <ItemDef OID="IT.MO.MODTC" Name="MODTC" DataType="date" SASFieldName="MODTC">
        <Description>
          <TranslatedText xml:lang="en">Date/Time of Collection</TranslatedText>
        </Description>
        <def:Origin Type="Collected" Source="Investigator">
          <def:DocumentRef leafID="LF.acrf">
            <def:PDFPageRef PageRefs="1" Type="PhysicalRef"/>
          </def:DocumentRef>
        </def:Origin>
      </ItemDef>
      <MethodDef OID="MT.MO.MOSTRESC" Name="MO.MOSTRESC" Type="Computation">
        <Description>
          <TranslatedText xml:lang="en">Standardize the collected cell type result.</TranslatedText>
        </Description>
      </MethodDef>
      <def:leaf ID="LF.acrf" xlink:href="acrf.pdf">
        <def:title>Annotated Case Report Form</def:title>
      </def:leaf>
    </MetaDataVersion>
  </Study>
</ODM>

expected/mo.csv

Edit2 rows

expected/mo.csv
DOMAIN	STUDYID	USUBJID	MOSEQ	MOTESTCD	MOTEST	MOORRES	MOSTRESC	MODTC
MO	CATH		1	CELLTYPE	Cell Type	normal	NORMAL	2025-01-08
MO	CATH		1	CELLTYPE	Cell Type	abnormal	ABNORMAL	2025-01-09

Shaded columns are derived— = missing value

Human review and assessment

Variable Name	Variable Label	Type	Length	Controlled Terms or Format	Origin	Core	Conversion Definition	Variable Type	Variable Order
DOMAIN	Domain Abbreviation	Char	80		Assigned	Req	Set constant value "MO".	SDTM	1
STUDYID	Study Identifier	Char	80		Protocol	Req	Copy value from MORPH.STUDYID.	SDTM	2
USUBJID	Unique Subject Identifier	Char	80		Assigned	Req	Copy value from MORPH.USUBJID.	SDTM	3
MOSEQ	Sequence Number	Num	8		Assigned	Req	Copy value from MORPH.SEQ.	SDTM	4
MOTESTCD	Morphology Test Short Name	Char	80		Assigned	Req	Set constant value "CELLTYPE".	SDTM	5
MOTEST	Morphology Test Name	Char	80		Assigned	Req	Set constant value "Cell Type".	SDTM	6
MOORRES	Result or Finding in Original Units	Char	80		Collected	Exp	Copy value from MORPH.RESULT.	SDTM	7
MOSTRESC	Character Result/Finding in Std Format	Char	80		Derived	Exp	Standardize the collected cell type result.	SDTM	8
MODTC	Date/Time of Collection	Char		ISO 8601	Collected	Exp	Copy value from MORPH.DATE.	SDTM	9

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

prompts/sdtm-mo-sdtmig33/full.md

Edit14 lines

Following CDISC SDTM standards, use the provided MORPHOLOGY dataset to create an MO dataset with one record per cell type finding per subject.

The output dataset should contain the following columns in this order: DOMAIN, STUDYID, USUBJID, MOSEQ, MOTESTCD, MOTEST, MOORRES, MOSTRESC, MODTC

Use SDTMIG 3.3. DOMAIN is "MO". MOSEQ is the finding identifier supplied by SEQ within each subject. MOTESTCD is "CELLTYPE" and MOTEST is "Cell Type". MOORRES is the collected RESULT, and MODTC is the collection DATE. MOSTRESC is "NORMAL" for a RESULT of "normal" and "ABNORMAL" for a RESULT of "abnormal".

Read the source datasets from /app/input and save the completed dataset as /app/output/mo.csv.

prompts/sdtm-mo-sdtmig33/conventions.md

Edit11 lines

Following CDISC SDTM standards, use the provided MORPHOLOGY dataset to create an MO dataset with one record per cell type finding per subject.

The output dataset should contain the following columns in this order: DOMAIN, STUDYID, USUBJID, MOSEQ, MOTESTCD, MOTEST, MOORRES, MOSTRESC, MODTC

Use SDTMIG 3.3. DOMAIN is "MO". MOTESTCD is "CELLTYPE" and MOTEST is "Cell Type".

Read the source datasets from /app/input and save the completed dataset as /app/output/mo.csv.

prompts/sdtm-mo-sdtmig33/brief.md

Edit8 lines

Following CDISC SDTM standards, use the provided MORPHOLOGY dataset to create an MO dataset with one record per cell type finding per subject.

The output dataset should contain the following columns in this order: DOMAIN, STUDYID, USUBJID, MOSEQ, MOTESTCD, MOTEST, MOORRES, MOSTRESC, MODTC

Read the source datasets from /app/input and save the completed dataset as /app/output/mo.csv.

R

Edit3 lines

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

Python

Edit3 lines

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

solutions/sdtm-mo-sdtmig33/result.R

Edit21 lines

1source_data <- read.csv("/app/input/morphology.csv", stringsAsFactors = FALSE,2                        colClasses = "character", check.names = FALSE)3required <- c("STUDYID", "USUBJID", "SEQ", "RESULT", "DATE")4stopifnot(all(required %in% names(source_data)))5standard_result <- rep(NA_character_, nrow(source_data))6standard_result[which(source_data$RESULT == "normal")] <- "NORMAL"7standard_result[which(source_data$RESULT == "abnormal")] <- "ABNORMAL"8mo <- data.frame(9  DOMAIN = rep("MO", nrow(source_data)),10  STUDYID = source_data$STUDYID,11  USUBJID = source_data$USUBJID,12  MOSEQ = as.integer(source_data$SEQ),13  MOTESTCD = rep("CELLTYPE", nrow(source_data)),14  MOTEST = rep("Cell Type", nrow(source_data)),15  MOORRES = source_data$RESULT,16  MOSTRESC = standard_result,17  MODTC = source_data$DATE,18  stringsAsFactors = FALSE19)20dir.create("/app/output", showWarnings = FALSE)21write.csv(mo, "/app/output/mo.csv", row.names = FALSE, na = "")

solutions/sdtm-mo-sdtmig33/result.py

Edit43 lines

1from pathlib import Path23import pandas as pd456INPUT_PATH = Path("/app/input/morphology.csv")7OUTPUT_PATH = Path("/app/output/mo.csv")8COLUMNS = [9    "DOMAIN",10    "STUDYID",11    "USUBJID",12    "MOSEQ",13    "MOTESTCD",14    "MOTEST",15    "MOORRES",16    "MOSTRESC",17    "MODTC",18]192021def main():22    source = pd.read_csv(INPUT_PATH, dtype=str, keep_default_na=False)23    standard_results = {"normal": "NORMAL", "abnormal": "ABNORMAL"}24    mo = pd.DataFrame(25        {26            "DOMAIN": "MO",27            "STUDYID": source["STUDYID"],28            "USUBJID": source["USUBJID"],29            "MOSEQ": source["SEQ"],30            "MOTESTCD": "CELLTYPE",31            "MOTEST": "Cell Type",32            "MOORRES": source["RESULT"],33            "MOSTRESC": source["RESULT"].map(standard_results),34            "MODTC": source["DATE"],35        },36        columns=COLUMNS,37    )38    OUTPUT_PATH.parent.mkdir(parents=True, exist_ok=True)39    mo.to_csv(OUTPUT_PATH, index=False)404142if __name__ == "__main__":43    main()

solutions/sdtm-mo-sdtmig33/result.sas

Edit20 lines

1proc import datafile='/app/input/morphology.csv' out=morphology dbms=csv replace;2  guessingrows=max;3run;45data mo;6  length DOMAIN $2 STUDYID $200 USUBJID $200 MOSEQ 8 MOTESTCD $8 MOTEST $40 MOORRES $200 MOSTRESC $8 MODTC $10;7  set morphology;8  DOMAIN = 'MO';9  MOSEQ = SEQ;10  MOTESTCD = 'CELLTYPE';11  MOTEST = 'Cell Type';12  MOORRES = RESULT;13  if RESULT = 'normal' then MOSTRESC = 'NORMAL';14  else if RESULT = 'abnormal' then MOSTRESC = 'ABNORMAL';15  MODTC = put(DATE, yymmdd10.);16  keep DOMAIN STUDYID USUBJID MOSEQ MOTESTCD MOTEST MOORRES MOSTRESC MODTC;17run;1819proc export data=mo outfile='/app/output/mo.csv' dbms=csv replace;20run;

input/morphology.csv

expected/define.xml

Define-XML 2.1.11: CATH

MO

expected/mo.csv

Your review

Mapping spec

Agent prompt

prompts/sdtm-mo-sdtmig33/full.md

prompts/sdtm-mo-sdtmig33/conventions.md

prompts/sdtm-mo-sdtmig33/brief.md

yamaa code

R

Python

Solution without yamaa

solutions/sdtm-mo-sdtmig33/result.R

solutions/sdtm-mo-sdtmig33/result.py

solutions/sdtm-mo-sdtmig33/result.sas