Creating Define-XML v2 with the SAS Clinical Standards Toolkit
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1 SAS Super Demo Creating Define-XML v2 with the SAS Clinical Standards Toolkit Lex Jansen, SAS
2 SAS Clinical Standards Toolkit 1.7 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
3 SAS Clinical Standards Toolkit 1.7 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, Datset-XML and ODM Controlled Terminology (CDISC/NCI)
4 SAS Clinical Standards Toolkit 1.7 INTRODUCTION Supported CDISC standards in Toolkit 1.7: SDTM 3.1.2, and 3.2 ADaM 2.1 (ADSL, Basic Data Structure, ADAE and ADTTE) CDASH 1.1 Domain definitions SEND 3.0 (initial implementation) CRT-DDS 1.0 (Define-XML - Create / Import / Validate) Define-XML 2.0 (Create / Import / Validate) Dataset-XML 1.0 (Create / Import / Validate) ODM 1.3.0, Read / Write / Validate NCI CDISC Controlled Terminology (June 2014) (import/export of ODM XML through CT 1.0 standard)
5 SAS Clinical Standards Toolkit 1.7 EXAMPLE: SDTM SDTM CDISC NCI Controlled Terminology SDTM
6 SAS Clinical Standards Toolkit 1.7 SDTM DATASET METADATA
7 SAS Clinical Standards Toolkit 1.7 SDTM VARIABLE METADATA
8 SAS Clinical Standards Toolkit 1.7 SDTM CLASS METADATA
9 SAS Clinical Standards Toolkit 1.7 CONTROLLED TERMINOLOGY
10 SAS Clinical Standards Toolkit 1.7 INTRODUCTION Supported with SAS 9.4M 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
11 CREATING THE DEFINE-XML V2 WITH CST
12 SAS Clinical Standards Toolkit 1.7 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
13 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)
14 ADaM / SDTM to define.xml
15 ADaM / SDTM to define.xml define_createsrcmetafromsaslib - derives source metadata files from a data library that contains SAS study domain data sets. define_createsrcmetafromdefine - derives source metadata files from a data library that contains the SAS representation of a Define- XML V2.0 define.xml file for a study cstutilmigratecrtdds2define - migrates source metadata data sets from CRT-DDS v1.0 to Define-XML v2.0 cstutilgetncimetadata - create the source_codelists dataset from a list of format catalogs that define the study formats and a SAS data set that contains CDISC/NCI codelist metadata
16 SAS Clinical Standards Toolkit 1.7 SOURCE_STUDY
17 SAS Clinical Standards Toolkit 1.7 SOURCE_TABLES
18 SAS Clinical Standards Toolkit 1.7 SOURCE_COLUMNS
19 SAS CLINICAL STANDARDS TOOLKIT 1.7 SOURCE_CODELISTS
20 SAS CLINICAL STANDARDS TOOLKIT 1.7 SOURCE_VALUES
21 SAS CLINICAL STANDARDS TOOLKIT 1.7 SOURCE_DOCUMENTS
22 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)
23 SAS CLINICAL STANDARDS TOOLKIT 1.7
24 SAS CLINICAL STANDARDS TOOLKIT 1.7
25 SAS CLINICAL STANDARDS TOOLKIT 1.7 define.xml define2-0-0.xsl
26 SAS CLINICAL STANDARDS TOOLKIT 1.7
27 DEMO
28 Thank You! Questions?
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