Tabulate nonclinical body weights with SENDIG 3.1.1

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Summary

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README.md

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

Goal: build one body-weight finding per weighing of an animal, carrying BWSEQ, BWTESTCD, BWTEST, the result as collected and standardized, and BWDTC, and submit it as the SAS transport file bw.xpt beside its data-definition document.

Input: the weighings the test facility's in-life data-collection system records, one row per animal per weighing, with the weighing occasion (routine or terminal), date, weight and unit.

Variables:

BWSEQ numbers each animal's weighings from 1 in date order, whatever order the facility exported them in.
BWTESTCD is BW for a routine weighing and TERMBW for the terminal weighing taken before necropsy; BWTEST is Body Weight or Terminal Body Weight.
BWORRES and BWORRESU are the weight and unit as collected.
BWSTRESN is the collected weight as a number, and BWSTRESC that number as text, so a collected 281.0 is standardized to 281.
BWSTRESU is the collected unit; no weight is converted.
BWDTC is the date the animal was weighed.

Note: the study declares the nonclinical implementation guide SENDIG 3.1.1, and the data-definition document records it. The test facility collects every result, so the document names no collecting party or annotated case report form for it; a nonclinical study identifies its test facility in its trial summary instead.

YAML specification

1 spec file

spec.yaml

Edit199 lines

1yamaa: '1.0'2type: spec3model: SEND4domain: BW5keys:6- STUDYID7- USUBJID8- BWSEQ9input:10  WEIGHING:11    path: input/body_weights.csv12    types:13      WEIGHDT: date1415output:16  path: bw.csv17  columns:18  - DOMAIN19  - STUDYID20  - USUBJID21  - BWSEQ22  - BWTESTCD23  - BWTEST24  - BWORRES25  - BWORRESU26  - BWSTRESC27  - BWSTRESN28  - BWSTRESU29  - BWDTC30  order_by:31  - STUDYID32  - USUBJID33  - BWSEQ3435columns:36- name: DOMAIN37  type: str38  label: Domain Abbreviation39  derivation: '''BW'''40  submission:41    core: Req42    role: Identifier43    length: 244    origins:45    - type: Assigned46      source: Sponsor4748- name: STUDYID49  type: str50  label: Study Identifier51  derivation: WEIGHING.STUDYID52  submission:53    core: Req54    role: Identifier55    length: 2056    origins:57    - type: Protocol58      source: Sponsor5960- name: USUBJID61  type: str62  label: Unique Subject Identifier63  derivation: WEIGHING.USUBJID64  submission:65    core: Req66    role: Identifier67    length: 4068    origins:69    - type: Assigned70      source: Sponsor7172- name: BWSEQ73  type: int74  label: Sequence Number75  derivation:76    row_number:77      window:78        group_by: [STUDYID, USUBJID]79        order_by: [WEIGHING.WEIGHDT]80  submission:81    core: Req82    role: Identifier83    length: 884    origins:85    - type: Derived86      source: Sponsor87    method: Number each animal's weighings in date order.8889- name: BWTESTCD90  type: str91  label: Test Short Name92  derivation:93    mapping:94      source: WEIGHING.OCCASION95      dict:96        ROUTINE: BW97        TERMINAL: TERMBW98  submission:99    core: Req100    role: Topic101    length: 8102    origins:103    - type: Assigned104      source: Sponsor105106- name: BWTEST107  type: str108  label: Test Name109  derivation:110    mapping:111      source: BWTESTCD112      dict:113        BW: Body Weight114        TERMBW: Terminal Body Weight115  submission:116    core: Req117    role: Synonym Qualifier118    length: 40119    origins:120    - type: Assigned121      source: Sponsor122123- name: BWORRES124  type: str125  label: Result or Findings as Collected126  derivation: WEIGHING.WEIGHT127  submission:128    core: Exp129    role: Result Qualifier130    length: 20131    origins:132    - type: Collected133134- name: BWORRESU135  type: str136  label: Unit of the Original Result137  derivation: WEIGHING.UNIT138  submission:139    core: Exp140    role: Variable Qualifier141    length: 10142    origins:143    - type: Collected144145- name: BWSTRESN146  type: float147  label: Standardized Result in Numeric Format148  derivation: BWORRES149  submission:150    core: Exp151    role: Result Qualifier152    length: 8153    significant_digits: 1154    origins:155    - type: Derived156      source: Sponsor157    method: The collected result read as a number.158159- name: BWSTRESC160  type: str161  label: Standardized Result in Character Format162  derivation: BWSTRESN163  submission:164    core: Exp165    role: Result Qualifier166    length: 20167    origins:168    - type: Derived169      source: Sponsor170    method: The standardized numeric result written as text.171172- name: BWSTRESU173  type: str174  label: Unit of the Standardized Result175  derivation: BWORRESU176  submission:177    core: Exp178    role: Variable Qualifier179    length: 10180    origins:181    - type: Derived182      source: Sponsor183    method: The collected unit, since no result is converted.184185- name: BWDTC186  type: date187  label: Date/Time Animal Weighed188  derivation: WEIGHING.WEIGHDT189  submission:190    core: Exp191    role: Timing192    origins:193    - type: Collected194195submission:196  label: Body Weight197  class: FINDINGS198  structure: One record per test per observation time per subject199  repeating: true

Inputs

Under review1 source file

input/body_weights.csv

Edit6 rows

input/body_weights.csv
STUDYID	OCCASION	WEIGHDT	WEIGHT	UNIT
TOX01	ROUTINE	2026-03-02	245.3	g
TOX01	ROUTINE	2026-03-02	182.6	g
TOX01	ROUTINE	2026-03-09	281.0	g
TOX01	TERMINAL	2026-03-30	341.8	g
TOX01	TERMINAL	2026-03-30	226.4	g
TOX01	ROUTINE	2026-03-09	198.2	g

Expected output

Under review6 expected rows

expected/bw.csv

Edit6 rows

expected/bw.csv
DOMAIN	STUDYID	BWSEQ	BWTESTCD	BWTEST	BWORRES	BWORRESU	BWSTRESC	BWSTRESN	BWSTRESU	BWDTC
BW	TOX01	1	BW	Body Weight	245.3	g	245.3	245.3	g	2026-03-02
BW	TOX01	2	BW	Body Weight	281.0	g	281	281	g	2026-03-09
BW	TOX01	3	TERMBW	Terminal Body Weight	341.8	g	341.8	341.8	g	2026-03-30
BW	TOX01	1	BW	Body Weight	182.6	g	182.6	182.6	g	2026-03-02
BW	TOX01	2	BW	Body Weight	198.2	g	198.2	198.2	g	2026-03-09
BW	TOX01	3	TERMBW	Terminal Body Weight	226.4	g	226.4	226.4	g	2026-03-30

expected/define.xml

EditDefine-XML

Define-XML 2.1.11: TOX01

Four-week oral toxicity study in rats; TOX01; SENDIG 3.1.1

Datasets
Dataset	Description	Class	Structure	Purpose	Keys	Documentation	Location
BW	Body Weight	FINDINGS	One record per test per observation time per subject	Tabulation	STUDYID, USUBJID, BWSEQ		bw.xpt

BW

BW 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	5		Protocol; Sponsor
USUBJID	Unique Subject Identifier	text	Identifier	10		Assigned; Sponsor
BWSEQ	Sequence Number	integer	Identifier	8		Derived; Sponsor Number each animal's weighings in date order.
BWTESTCD	Test Short Name	text	Topic	6		Assigned; Sponsor
BWTEST	Test Name	text	Synonym Qualifier	20		Assigned; Sponsor
BWORRES	Result or Findings as Collected	text	Result Qualifier	5		Collected
BWORRESU	Unit of the Original Result	text	Variable Qualifier	1		Collected
BWSTRESC	Standardized Result in Character Format	text	Result Qualifier	5		Derived; Sponsor The standardized numeric result written as text.
BWSTRESN	Standardized Result in Numeric Format	float	Result Qualifier	8		Derived; Sponsor The collected result read as a number.
BWSTRESU	Unit of the Standardized Result	text	Variable Qualifier	1		Derived; Sponsor The collected unit, since no result is converted.
BWDTC	Date/Time Animal Weighed	date	Timing		ISO 8601	Collected

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="TOX01.send.Define-XML_2.1" CreationDateTime="2026-09-11T00:00:00" SourceSystem="yamaa" SourceSystemVersion="1.0" def:Context="Submission">
  <Study OID="STDY.TOX01">
    <GlobalVariables>
      <StudyName>TOX01</StudyName>
      <StudyDescription>Four-week oral toxicity study in rats</StudyDescription>
      <ProtocolName>TOX01</ProtocolName>
    </GlobalVariables>
    <MetaDataVersion OID="MDV.TOX01.send" Name="TOX01 send metadata" def:DefineVersion="2.1.11">
      <def:Standards>
        <def:Standard OID="STD.SENDIG" Name="SENDIG" Type="IG" Version="3.1.1" Status="Final"/>
      </def:Standards>
      <ItemGroupDef OID="IG.BW" Name="BW" Domain="BW" Purpose="Tabulation" SASDatasetName="BW" Repeating="Yes" IsReferenceData="No" def:Structure="One record per test per observation time per subject" def:ArchiveLocationID="LF.BW" def:StandardOID="STD.SENDIG">
        <Description>
          <TranslatedText xml:lang="en">Body Weight</TranslatedText>
        </Description>
        <ItemRef ItemOID="IT.BW.DOMAIN" OrderNumber="1" Mandatory="Yes" Role="Identifier"/>
        <ItemRef ItemOID="IT.BW.STUDYID" OrderNumber="2" Mandatory="Yes" KeySequence="1" Role="Identifier"/>
        <ItemRef ItemOID="IT.BW.USUBJID" OrderNumber="3" Mandatory="Yes" KeySequence="2" Role="Identifier"/>
        <ItemRef ItemOID="IT.BW.BWSEQ" OrderNumber="4" Mandatory="Yes" KeySequence="3" Role="Identifier" MethodOID="MT.BW.BWSEQ"/>
        <ItemRef ItemOID="IT.BW.BWTESTCD" OrderNumber="5" Mandatory="Yes" Role="Topic"/>
        <ItemRef ItemOID="IT.BW.BWTEST" OrderNumber="6" Mandatory="Yes" Role="Synonym Qualifier"/>
        <ItemRef ItemOID="IT.BW.BWORRES" OrderNumber="7" Mandatory="No" Role="Result Qualifier"/>
        <ItemRef ItemOID="IT.BW.BWORRESU" OrderNumber="8" Mandatory="No" Role="Variable Qualifier"/>
        <ItemRef ItemOID="IT.BW.BWSTRESC" OrderNumber="9" Mandatory="No" Role="Result Qualifier" MethodOID="MT.BW.BWSTRESC"/>
        <ItemRef ItemOID="IT.BW.BWSTRESN" OrderNumber="10" Mandatory="No" Role="Result Qualifier" MethodOID="MT.BW.BWSTRESN"/>
        <ItemRef ItemOID="IT.BW.BWSTRESU" OrderNumber="11" Mandatory="No" Role="Variable Qualifier" MethodOID="MT.BW.BWSTRESU"/>
        <ItemRef ItemOID="IT.BW.BWDTC" OrderNumber="12" Mandatory="No" Role="Timing"/>
        <def:Class Name="FINDINGS"/>
        <def:leaf ID="LF.BW" xlink:href="bw.xpt">
          <def:title>bw.xpt</def:title>
        </def:leaf>
      </ItemGroupDef>
      <ItemDef OID="IT.BW.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.BW.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.BW.USUBJID" Name="USUBJID" DataType="text" Length="10" SASFieldName="USUBJID">
        <Description>
          <TranslatedText xml:lang="en">Unique Subject Identifier</TranslatedText>
        </Description>
        <def:Origin Type="Assigned" Source="Sponsor"/>
      </ItemDef>
      <ItemDef OID="IT.BW.BWSEQ" Name="BWSEQ" DataType="integer" Length="8" SASFieldName="BWSEQ">
        <Description>
          <TranslatedText xml:lang="en">Sequence Number</TranslatedText>
        </Description>
        <def:Origin Type="Derived" Source="Sponsor"/>
      </ItemDef>
      <ItemDef OID="IT.BW.BWTESTCD" Name="BWTESTCD" DataType="text" Length="6" SASFieldName="BWTESTCD">
        <Description>
          <TranslatedText xml:lang="en">Test Short Name</TranslatedText>
        </Description>
        <def:Origin Type="Assigned" Source="Sponsor"/>
      </ItemDef>
      <ItemDef OID="IT.BW.BWTEST" Name="BWTEST" DataType="text" Length="20" SASFieldName="BWTEST">
        <Description>
          <TranslatedText xml:lang="en">Test Name</TranslatedText>
        </Description>
        <def:Origin Type="Assigned" Source="Sponsor"/>
      </ItemDef>
      <ItemDef OID="IT.BW.BWORRES" Name="BWORRES" DataType="text" Length="5" SASFieldName="BWORRES">
        <Description>
          <TranslatedText xml:lang="en">Result or Findings as Collected</TranslatedText>
        </Description>
        <def:Origin Type="Collected"/>
      </ItemDef>
      <ItemDef OID="IT.BW.BWORRESU" Name="BWORRESU" DataType="text" Length="1" SASFieldName="BWORRESU">
        <Description>
          <TranslatedText xml:lang="en">Unit of the Original Result</TranslatedText>
        </Description>
        <def:Origin Type="Collected"/>
      </ItemDef>
      <ItemDef OID="IT.BW.BWSTRESC" Name="BWSTRESC" DataType="text" Length="5" SASFieldName="BWSTRESC">
        <Description>
          <TranslatedText xml:lang="en">Standardized Result in Character Format</TranslatedText>
        </Description>
        <def:Origin Type="Derived" Source="Sponsor"/>
      </ItemDef>
      <ItemDef OID="IT.BW.BWSTRESN" Name="BWSTRESN" DataType="float" Length="8" SignificantDigits="1" SASFieldName="BWSTRESN">
        <Description>
          <TranslatedText xml:lang="en">Standardized Result in Numeric Format</TranslatedText>
        </Description>
        <def:Origin Type="Derived" Source="Sponsor"/>
      </ItemDef>
      <ItemDef OID="IT.BW.BWSTRESU" Name="BWSTRESU" DataType="text" Length="1" SASFieldName="BWSTRESU">
        <Description>
          <TranslatedText xml:lang="en">Unit of the Standardized Result</TranslatedText>
        </Description>
        <def:Origin Type="Derived" Source="Sponsor"/>
      </ItemDef>
      <ItemDef OID="IT.BW.BWDTC" Name="BWDTC" DataType="date" SASFieldName="BWDTC">
        <Description>
          <TranslatedText xml:lang="en">Date/Time Animal Weighed</TranslatedText>
        </Description>
        <def:Origin Type="Collected"/>
      </ItemDef>
      <MethodDef OID="MT.BW.BWSEQ" Name="BW.BWSEQ" Type="Computation">
        <Description>
          <TranslatedText xml:lang="en">Number each animal's weighings in date order.</TranslatedText>
        </Description>
      </MethodDef>
      <MethodDef OID="MT.BW.BWSTRESC" Name="BW.BWSTRESC" Type="Computation">
        <Description>
          <TranslatedText xml:lang="en">The standardized numeric result written as text.</TranslatedText>
        </Description>
      </MethodDef>
      <MethodDef OID="MT.BW.BWSTRESN" Name="BW.BWSTRESN" Type="Computation">
        <Description>
          <TranslatedText xml:lang="en">The collected result read as a number.</TranslatedText>
        </Description>
      </MethodDef>
      <MethodDef OID="MT.BW.BWSTRESU" Name="BW.BWSTRESU" Type="Computation">
        <Description>
          <TranslatedText xml:lang="en">The collected unit, since no result is converted.</TranslatedText>
        </Description>
      </MethodDef>
    </MetaDataVersion>
  </Study>
</ODM>

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	2		Assigned	Req	Set constant value "BW".	SDTM	1
STUDYID	Study Identifier	Char	20		Protocol	Req	Copy value from WEIGHING.STUDYID.	SDTM	2
USUBJID	Unique Subject Identifier	Char	40		Assigned	Req	Copy value from WEIGHING.USUBJID.	SDTM	3
BWSEQ	Sequence Number	Num	8		Derived	Req	Number each animal's weighings in date order.	SDTM	4
BWTESTCD	Test Short Name	Char	8		Assigned	Req	Recode WEIGHING.OCCASION: "ROUTINE" → "BW", "TERMINAL" → "TERMBW"; missing values stay missing; unlisted values are errors.	SDTM	5
BWTEST	Test Name	Char	40		Assigned	Req	Recode BWTESTCD: "BW" → "Body Weight", "TERMBW" → "Terminal Body Weight"; missing values stay missing; unlisted values are errors.	SDTM	6
BWORRES	Result or Findings as Collected	Char	20		Collected	Exp	Copy value from WEIGHING.WEIGHT.	SDTM	7
BWORRESU	Unit of the Original Result	Char	10		Collected	Exp	Copy value from WEIGHING.UNIT.	SDTM	8
BWSTRESN	Standardized Result in Numeric Format	Num	8		Derived	Exp	The collected result read as a number.	SDTM	9
BWSTRESC	Standardized Result in Character Format	Char	20		Derived	Exp	The standardized numeric result written as text.	SDTM	10
BWSTRESU	Unit of the Standardized Result	Char	10		Derived	Exp	The collected unit, since no result is converted.	SDTM	11
BWDTC	Date/Time Animal Weighed	Char		ISO 8601	Collected	Exp	Copy value from WEIGHING.WEIGHDT.	SDTM	12

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")$spec("BW")$run()$output

Python

Edit3 lines

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

input/body_weights.csv

expected/bw.csv

expected/define.xml

Define-XML 2.1.11: TOX01

BW

Your review

Mapping spec

yamaa code

R

Python