© 2008 Octagon Research Solutions, Inc. All Rights Reserved.1© 2008 Octagon Research Solutions, Inc. All Rights Reserved.

PhUSE 2010Berlin

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Accessing the metadata from the define.xml using XSLT transformations

Lex Jansen

Octagon Research Solutions, Inc.Leading the Electronic Transformation

of Clinical R&D

© 2008 Octagon Research Solutions, Inc. All Rights Reserved.2

Contents

• Introduction• define.xml: Regulatory landscape• Data Definition Tables (pdf / xml)• What is the define.xml• Displaying the define.xml• XSLT

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Introduction

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• This presentation is NOT about CREATING a

define.xml file

• It is about how the information (metadata) in a

define.xml file can be USED

• Before we can USE the metadata from the

define.xml file, we need to be able to ACCESS that

metadata

• This presentation has a focus on XML technologies

(XSLT) to access that metadata

Introduction

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Define.xml:

Regulatory landscape

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Regulatory Landscape (FDA)

• July 2004 – FDA adds Study Data Specifications v1.0 to draft eCTD Guidance. This specification references the CDISC SDTM for data tabulation datasets

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Regulatory Landscape (FDA)

• March 2005 – Study Data Specifications v1.1:Updates Specifications for Data Set Documentation

- data definitions- annotated case report forms (CRFs)

• “The specification for the data definitions for datasets provided using the CDISC SDTM is included in the Case Report Tabulation Data Definition Specification (define.xml) developed by the CDISC define.xml Team”

• … Include a reference to the style sheet as defined in the specification and place the corresponding style sheet in the same folder as the define.xml file …

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Regulatory Landscape (FDA)

November 2009 - Study Data Specifications v1.5:• "For datasets not prepared using the CDISC SDTM

specifications, consult Appendix 2 for information concerning the preparation of a define.pdf data definition file."

• Appendix 2 specifies a define.pdf specification similar to the 1999 guidance

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Data Definition Tables in PDF

Data Definition Tables - PDF

• Study Data Specifications:

"For datasets not prepared using the CDISC SDTM

specifications, consult Appendix 2 for information concerning

the preparation of a define.pdf data definition file"

Data Definition Tables - PDF

• "Sponsors should also provide a link to the appropriate

annotated case report form file (blankcrf.pdf)"

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Data Definition Tables in XML

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Data Definition Tables - XML

• As of January 1, 2008: follow the eCTD guidance and document submitted data by including data definition tables (define.xml) and annotated case report forms (blankcrf.pdf)

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Data Definition Tables - XML

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Displaying the define.xml

… with a stylesheet

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define.xml

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define.xml

• Case Report Tabulation Data Specification (CRT-DDS, or define.xml): Production version: 1.0.0

• Extension of the CDISC Operational Data Model (ODM), an XML specification to facilitate the archival and interchange of the metadata and data for clinical research

• Maintained by CDISC’s XML Technologies Team (formerly known as the ODM team)

• New define.xml version 2 in development with additional metadata support for SDTM and ADaM(results metadata)

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define.xml

XML schema definitions (XSD) describe the structure of the define.xml

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define.xml

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define.xml – Specifications

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define.xml

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Displaying the define.xml

Define.xml

• define.xml contains metadata and is machine readable

• define.xml becomes human readable with a stylesheet

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Displaying the define.xml

define.xml becomes human readable with an XSL stylesheet

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Displaying the define.xml

… and looks even fancier with a different stylesheet

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Displaying the define.xml

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Displaying the define.xml

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Displaying the define.xml

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XSLT

XSLT

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• eXtensible Stylesheet Language Transformations (XSLT) is a language that lets you convert XML documents into other XML documents, into HTML documents, or into any other text based document (like a SAS program), or even a PDF file

• XSLT is a language "for transforming the structure and content of an XML document"

XSLT

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• XSL transformations are like Rubik's cube!

•XML

•HTML

•PDF

•TEXT

XSL

• The mandatory "hello world" XML

XSL

• The mandatory "hello Berlin" XML

XSL

• XSL stylesheet

XSL

• Example: XML + XSL = HTML

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Other examples of using the define.xml metadata

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Examples

• Use dataset and variable information (type, length, label) to create zero-observation datasets that can serve as data conversion targets

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DATASET TEMPLATES from the define.xml

Examples

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Examples

• Use codelist information (codes/decodes) to create a PROC FORMAT

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PROC FORMAT from the define.xml

Examples

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Examples

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Running XSLT with SAS

Experimental

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Using Xalan

Using Xalan

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• In case you get serious about XSLT …

• Get a good XML editor

– Oxygen (http://www.oxygenxml.com/)

– XMLSpy (http://www.altova.com) has some

issues in validating define.xml

– Check out the define.xml white paper on

http://www.cdisc.org/define-xml

Last words

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