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Tutorial: define.xml. Monika Kawohl Statistical Programming Accovion GmbH. Overview. Requirements Regulatory Technical define.xml Sections/Elements Process Flow at Accovion. Regulatory Requirements. eCTD‘s Study Data Specifications V1.5.1. ADaM. SDTM.

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monika kawohl statistical programming accovion gmbh

Tutorial:define.xml

Monika Kawohl

Statistical Programming

Accovion GmbH

overview
Overview
  • Requirements
    • Regulatory
    • Technical
  • define.xml Sections/Elements
  • Process Flow at Accovion
regulatory requirements
Regulatory Requirements
  • eCTD‘s Study Data Specifications V1.5.1

ADaM

SDTM

  • “Dataset documentation includes data definitions and annotated case report forms.”
    • SDTM: define.xml
    • ADaM: define.pdf / define.xml ?
why define xml
Why define.xml
  • Metadata = data about data
  • Human-readable description to familiarize with data
    • What is included?
    • Where does the data come from?
    • Derivation rules, if applicable
  • Machine-readable metadata to facilitate ...
    • SDTM data consistency check
    • Upload into JANUS data warehouse
  • Preferred => mandatory format: define.xml
  • Benefit of define.xml not restricted to submissions
xml basics
XML Basics
  • Schema (extension: .XSD)
    • Declaration of elements and their attributes
    • Prerequisite for machine-readability
  • XML File (extension: .XML)
    • Data and metadata in machine-readable format
    • Usage of elements and attributes as defined in schema
  • Style Sheet (extension: .XSL)
    • Definition of layout in browser tool for Human-Readability
    • Usage of elements and attributes as defined in schema
slide8

style sheet

reference

Advantages of XML – Basic Technology

<?xml version="1.0" encoding="ISO-8859-1"?>

<?xml-stylesheet type="text/xsl" href="define1-0-0.xsl"?>

<ODM

...

<ItemGroupDef OID="DM"

Name="DM"

Repeating="No"

IsReferenceData="No"

Purpose="Tabulation"

def:Label="Demographics"

def:Structure="One record per subject"

def:DomainKeys="STUDYID, USUBJID"

def:Class="Special Purpose"

def:ArchiveLocationID="Location.DM">

...

define xml sections elements
define.xml Sections/Elements
  • Data Metadata (TOC)
  • Variable Metadata
  • Variable Value Level Metadata
  • (Computational Algorithms)
  • Controlled Terminology/Code Lists
  • Annotated CRF
  • Optional: Supplemental Data Definition Document
  • Navigation via Bookmarks and Hyperlinks
variable metadata
Variable Metadata

Change for Origin in SDTM IG 3.1.2: Sponsor Defined, Assigned, eDT, Protocol

variable metadata xml code
Variable Metadata – XML Code

<ItemGroupDef OID="LB"

...

<ItemRef ItemOID="LB.LBTESTCD"

OrderNumber="5" Mandatory="Yes" Role="Topic"/>

...

<ItemRef ItemOID="LB.LBBLFL"

OrderNumber="22" Mandatory="No" Role="Record Qualifier"/>

</ItemGroupDef>

...

<ItemDef OID="LB.LBTESTCD" Name="LBTESTCD" DataType="text"

Length="8" Origin="CRF Pages 5, 10, 15, 20" Comment=""

def:Label="LAB Test or Examination Short Name">

<def:ValueListRef ValueListOID="ValueList.LB.LBTESTCD"/> </ItemDef>

...

<ItemDef OID="LB.LBBLFL" Name="LBBLFL" DataType="text"

Length="1" Origin="Derived"def:Label="Baseline Flag"

def:ComputationMethodOID="COMPMETHOD.LBBLFL">

<CodeListRef CodeListOID="YF"/>

</ItemDef>

computational algorithms
Computational Algorithms
  • Complex Derivations
  • Derivations Used More than Once
controlled terminology code lists
Controlled Terminology/Code Lists
  • External dictionary references incl. versions
    • e.g., MEDDRA, WHODRUG
slide16

Annotated CRF (blankcrf.pdf)

  • See Draft CDISC Metadata Submission Guidelines
  • Annotate unique pages, reference from repeat pages
  • Annotate variables, variables values (cf. value level metadata)
  • Mark items that are not submitted
sdtm process flow at accovion

Specifications

AnnotatedCRF

define.xml (SDTM)

Mapping

programs

SDTM

Communication

SDTM Process Flow at Accovion

= dataset templates

= source for define.xml

red: e-submission deliverables

adam process flow at accovion

ADaM Specifications

Datasets

creation

programs

- Analysis datasets

define.xml (ADaM)

ADaM

- Analysis results

Results

creation

programs

SAP

SDTM

Analysis

results

(TLGs)

source for define.xml

Communication

ADaM Process Flow at Accovion

= dataset templates

red: (potential) e-submission deliverables

references
References
  • CDISC Website(http://www.cdisc.org/)
    • CRT-DDS (define.xml) standard V1.0(http://www.cdisc.org/models/def/v1.0/index.html)
    • Metadata Submission Guidelines, Appendix to SDTM IG V3.1.1(http://www.cdisc.org/content1210)
    • CDISC SDTM/ADaM Pilot (sample submission package)(http://www.cdisc.org/content1037)
  • eCTD‘s Study Data Specifications V1.5.1(http://www.fda.gov/downloads/Drugs/DevelopmentApprovalProcess/FormsSubmissionRequirements/ElectronicSubmissions/UCM199759.pdf)
thank you questions
Thank you!Questions?

Contact Information:Monika Kawohl Senior Statistical ProgrammerAccovion GmbH Softwarecenter 3 35037 Marburg Germany Phone: +49-6421-94849-20 Fax: +49-6421-94849-61Email: monika.kawohl@accovion.com