Creating Define-XML v2 with the SAS Clinical Standards Toolkit 1.6 Lex Jansen, SAS

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1 Creating Define-XML v2 with the SAS Clinical Standards Toolkit 1.6 Lex Jansen, SAS

2 Agenda Introduction to the SAS Clinical Standards Toolkit (CST) Define-XML History and Background What is Define-XML? Creating the Define-XML v2 with CST Questions

3 INTRODUCTION TO THE SAS CLINICAL STANDARDS TOOLKIT (CST)

4 SAS Clinical Standards Toolkit 1.6 INTRODUCTION Framework to primarily support Clinical Research activities (CDISC). Designed as an integral part of Clinical Data Integration (CDI) Available to all licensed SAS customers as open source SAS Macros and metadata at no additional charge. Designed to supersede PROC CDISC Framework: designed to customize and extend

5 SAS Clinical Standards Toolkit 1.6 INTRODUCTION A collection of metadata and "tools", providing an initial set of standards and functionality that is evolving and growing with updates and releases. Provides SAS representation of published standards as SAS data sets and catalogs Contents standards: SDTM, ADaM, SEND XML standards: Define-XML and ODM Controlled Terminology (CDISC/NCI)

6 SAS Clinical Standards Toolkit 1.6 INTRODUCTION Supported CDISC standards in Toolkit 1.6: SDTM 3.1.1, 3.1.2, and 3.2 ADaM 2.1 (ADSL, Basic Data Structure, ADAE and ADTTE) and Analysis Results Metadata templates; v1.1 of the ADaM validation checks) SEND 3.0 (initial implementation) CRT-DDS 1.0 (Define-XML - Create / Import / Validate) Define-XML 2.0 (Create / Import / Validate) ODM 1.3.0, Read / Write / Validate NCI CDISC Controlled Terminology (December 2013) (import/export of ODM XML through CT 1.0 standard)

7 SAS Clinical Standards Toolkit 1.6 INTRODUCTION SDTM CDISC NCI Controlled Terminology SDTM

8 SAS Clinical Standards Toolkit 1.6 INTRODUCTION

9 SAS Clinical Standards Toolkit 1.6 INTRODUCTION

10 SAS Clinical Standards Toolkit 1.6 INTRODUCTION

11 SAS Clinical Standards Toolkit 1.6 INTRODUCTION

12 SAS Clinical Standards Toolkit 1.6 INTRODUCTION Supported with SAS 9.3M2 and 9.4M1 on the following operating systems: Windows x64 Linux x64 Separately orderable component Available at no additional charge to currently licensed SAS customers. Contact your SAS Account Representative concerning availability

17 DEFINE-XML HISTORY AND BACKGROUND

Define-XML HISTORY AND BACKGROUND July 2004 - FDA adds Study Data Specifications v1.

18 Define-XML HISTORY AND BACKGROUND July FDA adds Study Data Specifications v1.0 to draft ectd Guidance. This specification references the CDISC SDTM for data tabulation datasets

19 Define-XML HISTORY AND BACKGROUND March Study Data Specifications v1.1 Update: Specifications for Data Set Documentation includes: - 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 For datasets not prepared using the CDISC SDTM specifications, consult Appendix 2 for information concerning the preparation of a define.pdf data definition file.

20 Define-XML HISTORY AND BACKGROUND June 2011 Study Data Specifications v1.6: The specification for the data definitions for datasets provided using the CDISC SDTM IG or SEND IG is included in the Case Report Tabulation Data Definition Specification... July 2012 Study Data Specifications v2.0: The specification for the data definitions for datasets provided using CDISC is included in the Case Report Tabulation Data Definition Specification...

21 Define-XML HISTORY AND BACKGROUND December 2011 CDER Common Data Standards Issues Document (Version 1.1): "A critical component of data submission is the define file. A properly functioning define.xml file is an important part of the submission of standardized electronic datasets and should not be considered optional." "In addition to the define.xml, a printable define.pdf should be provided if the define.xml cannot be printed properly." "Additionally, sponsors should make certain that every data variable s code list, origin, and derivation is clearly and easily accessible from the define file. An insufficiently documented define file is a common deficiency that reviewers have noted."

23 Define-XML HISTORY AND BACKGROUND February 2014 CDER/CBER Study Data Technical Conformance Guide: "If a define.xml version 2.0 or later version is submitted, then a define.pdf does not need to be included in the submission."

24 Don't give this message with a define.xml file

25 WHAT IS DEFINE-XML?

26 Define-XML WHAT IS IT? Extension of the CDISC Operational Data Model (ODM), a vendor neutral, platform independent XML format to facilitate the archival and interchange of the metadata and data for clinical research Define-XML: metadata structures to describe data sets Maintained by CDISC s XML Technologies Team

27 Define-XML 2.0 WHAT S NEW Define-XML version 2.0 can be used to transmit metadata for the following CDISC standards: SDTM Implementation Guide Versions and higher ADaM Implementation Guide Versions 1.0 and higher SEND Implementation Guide Versions 3.0 and higher Not backward compatible with to allow for a clearer and less ambiguous model Production version since March 2013 (Minor stylesheet update April 2013) Accepted by the FDA since August 2013

28 Define-XML SPECIFICATIONS

29 Define-XML WHAT IS IT? Provides metadata about: Study Name, Description, Protocol name Domains Name, Label, Structure, Class, Purpose, Keys, Dataset Location,... Variables Name, Label, Data Type, Length, Display Format, Controlled Terms, Origin, Derivations, Comments... Controlled Terminology / Dictionaries Derivations (algorithms, computations, methods) Supporting Documents (acrf, Supplemental Data Definitions,..) (Parameter) Value Level Metadata Concepts as SuppQuals, Split domains...

30 Define-XML WHAT IS IT? Specification for describing data sets (metadata) Does not describe how this metadata should be displayed Display is not part of the standard

An example stylesheet is provided, however this can be altered

31 Define-XML DISPLAY The Define-XML standard does not dictate how a stylesheet should display a define.xml file. An example stylesheet is provided, however this can be altered to satisfy alternate visualization needs. The example stylesheet is only one file

32 Define-XML DISPLAY The example stylesheet conforms to web standards and follows accessibility guidelines It should behave much better than older stylesheets Uses JavaScript, but degrades gracefully when JavaScript is disabled Printing looks quite acceptable It might make sense to also submit the HTML rendition; since not every browser allows rendition of the stylesheet

33 Define-XML WHAT IS IT?

34 Define-XML WHAT IS IT? How does it look in a browser

35 CREATING THE DEFINE-XML V2 WITH CST

36 SAS CLINICAL STANDARDS TOOLKIT 1.6 TYPICAL PROGRAM FLOW Define global macro variables ("properties") %cst_setstandardproperties (_cststandard=cst-framework,_cstsubtype=initialize); Define inputs / outputs (libname refs, filename refs, SAS autocall macros,...) 1. Create SASReferences dataset 2. %cstutil_processsetup(); Run process specific macro: %define_sourcetodefine %define_write %cstutilxmlvalidate %define_read

37 ADAM / SDTM TO DEFINE.XML Table Metadata Column Metadata Value Level Metadata Codelist Metadata XML Study Metadata Document Metadata Validation Process SAS representation of Define-XML (31/46 SAS data sets)

38 SDTM TO DEFINE.XML

39 SAS CLINICAL STANDARDS TOOLKIT 1.6 SOURCE_STUDY

40 SAS CLINICAL STANDARDS TOOLKIT 1.6 SOURCE_TABLES

41 SAS CLINICAL STANDARDS TOOLKIT 1.6 SOURCE_COLUMNS

42 SAS CLINICAL STANDARDS TOOLKIT 1.6 SOURCE_CODELISTS

43 SAS CLINICAL STANDARDS TOOLKIT 1.6 SOURCE_VALUES

44 SAS CLINICAL STANDARDS TOOLKIT 1.6 SOURCE_DOCUMENTS

45 ADAM / SDTM TO DEFINE.XML Table Metadata Column Metadata Value Level Metadata Codelist Metadata XML Study Metadata Document Metadata Validation Process SAS representation of Define-XML (31/46 SAS data sets)

46 SAS CLINICAL STANDARDS TOOLKIT 1.6

47 SAS CLINICAL STANDARDS TOOLKIT 1.6

48 SAS CLINICAL STANDARDS TOOLKIT 1.6

49 SAS CLINICAL STANDARDS TOOLKIT 1.6 define.xml define2-0-0.xsl

50 SAS CLINICAL STANDARDS TOOLKIT 1.6

51 DEMO

52 Thank You! Questions?

Creating Define-XML v2 with the SAS Clinical Standards Toolkit

SAS Super Demo Creating Define-XML v2 with the SAS Clinical Standards Toolkit Lex Jansen, SAS SAS Clinical Standards Toolkit 1.7 INTRODUCTION Framework to primarily support Clinical Research activities