© 2008 octagon research solutions, inc. all rights reserved. 1 phuse 2010 berlin * accessing the...
TRANSCRIPT
© 2008 Octagon Research Solutions, Inc. All Rights Reserved.1© 2008 Octagon Research Solutions, Inc. All Rights Reserved.
PhUSE 2010Berlin
*
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
© 2008 Octagon Research Solutions, Inc. All Rights Reserved.3
Introduction
© 2008 Octagon Research Solutions, Inc. All Rights Reserved.4
• 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
© 2008 Octagon Research Solutions, Inc. All Rights Reserved.5
Define.xml:
Regulatory landscape
© 2008 Octagon Research Solutions, Inc. All Rights Reserved.6
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
© 2008 Octagon Research Solutions, Inc. All Rights Reserved.7
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 …
© 2008 Octagon Research Solutions, Inc. All Rights Reserved.8
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
© 2008 Octagon Research Solutions, Inc. All Rights Reserved.9
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)"
© 2008 Octagon Research Solutions, Inc. All Rights Reserved.12
Data Definition Tables in XML
© 2008 Octagon Research Solutions, Inc. All Rights Reserved.13
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)
© 2008 Octagon Research Solutions, Inc. All Rights Reserved.14
Data Definition Tables - XML
© 2008 Octagon Research Solutions, Inc. All Rights Reserved.15
Displaying the define.xml
… with a stylesheet
© 2008 Octagon Research Solutions, Inc. All Rights Reserved.16
define.xml
© 2008 Octagon Research Solutions, Inc. All Rights Reserved.17
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)
© 2008 Octagon Research Solutions, Inc. All Rights Reserved.18
define.xml
XML schema definitions (XSD) describe the structure of the define.xml
© 2008 Octagon Research Solutions, Inc. All Rights Reserved.19
define.xml
© 2008 Octagon Research Solutions, Inc. All Rights Reserved.20
define.xml – Specifications
© 2008 Octagon Research Solutions, Inc. All Rights Reserved.21
define.xml
© 2008 Octagon Research Solutions, Inc. All Rights Reserved.22
Displaying the define.xml
Define.xml
• define.xml contains metadata and is machine readable
• define.xml becomes human readable with a stylesheet
© 2008 Octagon Research Solutions, Inc. All Rights Reserved.24
Displaying the define.xml
define.xml becomes human readable with an XSL stylesheet
© 2008 Octagon Research Solutions, Inc. All Rights Reserved.25
Displaying the define.xml
… and looks even fancier with a different stylesheet
© 2008 Octagon Research Solutions, Inc. All Rights Reserved.27
Displaying the define.xml
© 2008 Octagon Research Solutions, Inc. All Rights Reserved.28
Displaying the define.xml
© 2008 Octagon Research Solutions, Inc. All Rights Reserved.29
Displaying the define.xml
© 2008 Octagon Research Solutions, Inc. All Rights Reserved.30
XSLT
XSLT
© 2008 Octagon Research Solutions, Inc. All Rights Reserved.31
• 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
© 2008 Octagon Research Solutions, Inc. All Rights Reserved.32
• XSL transformations are like Rubik's cube!
•XML
•HTML
•TEXT
XSL
• The mandatory "hello world" XML
XSL
• The mandatory "hello Berlin" XML
XSL
• XSL stylesheet
XSL
• Example: XML + XSL = HTML
© 2008 Octagon Research Solutions, Inc. All Rights Reserved.37
Other examples of using the define.xml metadata
© 2009 Octagon Research Solutions, Inc. All Rights Reserved.38
Examples
• Use dataset and variable information (type, length, label) to create zero-observation datasets that can serve as data conversion targets
© 2008 Octagon Research Solutions, Inc. All Rights Reserved.39
DATASET TEMPLATES from the define.xml
Examples
© 2009 Octagon Research Solutions, Inc. All Rights Reserved.40
Examples
• Use codelist information (codes/decodes) to create a PROC FORMAT
© 2008 Octagon Research Solutions, Inc. All Rights Reserved.41
PROC FORMAT from the define.xml
Examples
© 2008 Octagon Research Solutions, Inc. All Rights Reserved.42
Examples
© 2008 Octagon Research Solutions, Inc. All Rights Reserved.43
© 2008 Octagon Research Solutions, Inc. All Rights Reserved.44
© 2008 Octagon Research Solutions, Inc. All Rights Reserved.45
Running XSLT with SAS
Experimental
© 2008 Octagon Research Solutions, Inc. All Rights Reserved.46
Using Xalan
Using Xalan
© 2008 Octagon Research Solutions, Inc. All Rights Reserved.49
• 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
© 2008 Octagon Research Solutions, Inc. All Rights Reserved.50
Find this paper and more than 11,000 other SAS papers at http://www.lexjansen.com