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1 www.d-Wise.com XML in a SAS World Mike Molter d-Wise Technologies

2 www.d-Wise.com Mike Teresa Lauren Ryan Sydney

3 www.d-Wise.com Background Author: Mike Molter Company: d-Wise Committees: CDISC XML Technologies, Phuse Working Group Best Practices Reason for presentation: Increasing prevalence of XML in our industry

4 www.d-Wise.com Agenda What is XML? Comparison to HTML Purpose and use Examples of XML standards (schemas) Tools for working with XML (SAS and non-SAS) XML in the pharmaceutical industry

5 www.d-Wise.com XML and HTML Made of elements Elements have names Elements are identified by a pair of tags (start tag and end tag)

6 www.d-Wise.com XML and HTML Some elements have one or more attributes Attributes are specified as name-value pairs

7 www.d-Wise.com XML and HTML Elements can have stuff between the start tag and end tag Nested elements

8 www.d-Wise.com XML and HTML Elements can have stuff between the start tag and end tag One or more nested elements Element content HTML web page content or XML data

9 www.d-Wise.com XML and HTML Each document contains a root element - an element that nests all other elements The rest of the document

10 www.d-Wise.com HTML Hypertext Markup Language Language of the web Provides instructions to web browsers for displaying content Pre-defined elements Team Conference Division Red Wings Eastern Atlantic

11 www.d-Wise.com What is XML? eXtensible Markup Language A data container - used for structure, storage, and transport of data (w3schools.com) Like any other computer language… textual gibberish set of rules (structural, syntax) vocabulary elements attributes tags schemas

12 www.d-Wise.com What is XML? Like any other computer language… textual gibberish set of rules (structural, syntax) vocabulary elements attributes tags schemas Unlike other computer languages… no pre-defined element (no keywords) no processor

13 www.d-Wise.com Mike Teresa Lauren Ryan Sydney

14 www.d-Wise.com Eastern Atlantic Detroit Western Pacific Calgary Eastern Metropolitan New Jersey What is XML?

15 www.d-Wise.com XML Schema XML Schema (or Language, or Vocabulary) - A specific set of elements and attributes, along with a set of rules that govern their use An XML schema can be a combination of new elements along with other XML schemas (extensible) A schema file lays out the rules of an XML language. An XML schema language is a computer language in which schema files are written. Examples: DTD, XSD An XML validator is a piece of software that uses the schema file to validate an XML file.

16 www.d-Wise.com XML Language Examples NHL (Ok, I made this one up) XSL (eXtensible Stylesheet Language,.xsl) Transforms XML into something else XML Schema Definition (.xsd) Validates an XML document XML Spreadsheet 2003 (.xml) Read and displayed by Excel ODM, Define, Dataset-XML, Analysis Results Metadata, OpenCDISC Clinical Trials data, metadata

17 www.d-Wise.com

18 Teams.sas7bdat Exporting XML

19 www.d-Wise.com filename xmlout4 'C:\teams_datastep.xml' ; data _null_ ; file xmlout4 ; set teams end=thatsit ; if _n_ eq 1 then put ' ' ; put ' ' ; put ' ' conference ' ' ; put ' ' division ' ' ; put ' ' location ' ' ; put ' ' ; if thatsit then put ' ' ; run; Exporting XML with a DATA step

20 www.d-Wise.com libname xmlout xml 'C:\teams_generic.xml' ; data xmlout.xteams ; set teams ; run; Exporting XML with the LIBNAME statement

21 www.d-Wise.com libname xmlout xml 'C:\teams_oracle.xml' xmltype=oracle ; data xmlout.xteams ; set teams ; run; Exporting XML with the LIBNAME statement

22 www.d-Wise.com Exporting XML with the LIBNAME statement or ODS using tagsets libname xmlout xml 'C:\teams_tagset_libname.xml' tagset= ; data xmlout.xteams ; set teams ; run; ods markup tagset= file='C:\teams_tagset_ods.xml'; proc print noobs data=teams ; run; ods markup close ;

23 www.d-Wise.com Exporting XML with ODS using SAS's ExcelXP tagset ods markup tagset=excelxp file='C:\teams_excel.xml'; proc print noobs data=teams ; run; ods markup close ;

24 www.d-Wise.com References Tips and Tricks for Creating Multi-Sheet Microsoft Excel Workbooks, Vince DelGobbo, SAS Global Forum 2009 ODS Markup: The SAS Reports You've Always Dreamed of, Eric Gebhart, SUGI 30 ExcelXP on Steroids: Adding Custom Options to the ExcelXP Tagset, Mike Molter, SAS Global Forum 2011

25 www.d-Wise.com References ExcelXP on Steroids: Adding Custom Options to the ExcelXP Tagset, SAS Global Forum 2011 ods markup tagset=myexcel file='define.xml' options (tab_color='45') ; proc print noobs data=dataset1; run; ods markup close ;

26 www.d-Wise.com Importing XML libname xmlout xml 'C:\teams_generic.xml' ; data xmlout.xteams ; set teams ; run; Export data sasteams ; set xmlout.xteams ; run; Import

27 www.d-Wise.com Eastern Atlantic Detroit Western Pacific Calgary Eastern Metropolitan New Jersey libname xmlin xml 'C:\teams_nhl.xml' ; data sasteam ; set xmlin.team ; run; NHL.XML SASTEAM.SAS7BDAT

28 www.d-Wise.com XML in Pharma Operational Data Model (ODM) Collected clinical trial data, metadata, administrative data, reference data, audit information Define-XML Metadata for submitted data in ODM structure Value-level metadata is in the define extension Dataset-XML Submission data in ODM structure

29 www.d-Wise.com XML in Pharma Analysis Results Metadata Metadata that describes the methods used for arriving at the results OpenCDISC Extension of Define-XML Describes validation checks applicable to each domain

30 www.d-Wise.com XML in Pharma Collected Data Data Transformations Data Submission Metadata Submission ODM.XMLSAS Dataset-XML Define.XML

31 www.d-Wise.com ODM Conventions item common element prefix represents a variable def common element suffix represents a definition ref common element suffix represents a reference to a def oid common attribute suffix object identifier represents a link to another part of the document

32 www.d-Wise.com Clinical Data ODM ItemGroup (dataset-level) Metadata

33 www.d-Wise.com Clinical Data ItemGroup (dataset-level) Metadata Item (variable-level) Metadata ODM

34 www.d-Wise.com Item (variable-level) Metadata Codelist Metadata (allowable values) ODM

35 www.d-Wise.com Define-XML

36 www.d-Wise.com Importing XML with an XML map XMLMap is an XML schema Provides instructions to the XML LIBNAME engine for reading XML Name and Label for the data set Which XML elements define observations How to define variables (attributes and values) Uses XPath syntax to navigate the XML document and identify its components filename mymap 'C:\mymap.map' ; libname xmlin xml 'C:\nhl.xml' xmlmap=mymap; data sasteams ; set xmlin.teams ; run;

37 www.d-Wise.com Importing XML with an XML map /nhl/team /nhl/team/@name character string 20 /nhl/team/conference character string 20  Name of data set to be created  Observation boundary  Variable Definition

38 www.d-Wise.com XML Mapper

39 www.d-Wise.com Extensible Stylesheet Language (XSL) XSLT - XSL Transformations - transforms XML into something else XSL is an XML schema An XSL processor reads through an XML document and generates text according to instructions in the stylesheet XSL processors: SAS (PROC XSL) Internet Explorer

40 www.d-Wise.com Extensible Stylesheet Language (XSL) SAS's PROC XSL creates an output file, given an input file and a stylesheet filename inxml 'C:\mysubmission\define.xml' ; filename outhtml 'C:\mysubmission\define.html' ; filename xslss 'C:\mysubmission\define.xsl' ; proc xsl in=inxml out=outhtml xsl=xslss ; run;

41 www.d-Wise.com Extensible Stylesheet Language (XSL) Internet Explorer renders XML as HTML Define.xml via text editor Define.xml via Internet Explorer Tabulation Datasets for Study CDISC01 (SDTM-IG 3.1.2) HTML generated by XSL

42 www.d-Wise.com Extensible Stylesheet Language (XSL) Tabulation Datasets for Study CDISC01 (SDTM-IG 3.1.2) Datasets for Study ( )

43 www.d-Wise.com Clinical Standards Toolkit (CST) A Base SAS framework for executing clinical data tasks such as verification of data compliance against standards and importing/exporting ODM and Define.xml. Contains all necessary files (SAS macros and driver programs, maps, property files, XSL stylesheets) Learning curve

44 www.d-Wise.com Clinical Standards Toolkit (CST) …or PROC XSL

45 www.d-Wise.com References Using the SAS Clinical Standards Toolkit 1.5 to Import CDISC ODM Files, Lex Jansen, Pharmasug 2013 Using the SAS Clinical Standards Toolkit for Define.xml Creation, Lex Jansen, Pharmasug 2011 Accessing the Metadata from the Define.xml Using XSLT Transformation, Lex Jansen, Phuse 2010

46 www.d-Wise.com References A SAS Programmer's Guide to Generating Define.xml, Mike Molter, SAS Global Forum 2009 ods markup tagset=mydefine file='define.xml' ; proc print noobs data=meta-dataset1; run; proc print noobs data=meta-dataset2; run; proc print noobs data=meta-dataset3; run; etc ods markup close ;

47 www.d-Wise.com Other Resources LinkedIn Groups CDISC XML Technologies CDISC Define-XML CDISC Dataset-XML CDISC-SDTM Experts wiki.cdisc.org http://www.cdisc.org

48 www.d-Wise.com In Summary… Options for Exporting XML XML LIBNAME engine (XMLTYPE=, TAGSET= options) ODS (SAS XML destinations or user-defined tagsets) DATA step XSL stylesheets CST (clinical) Options for Importing XML XML LIBNAME engine (XMLTYPE=, TAGSET= options) XML maps XSL stylesheets CST (clinical)

49 www.d-Wise.com In Summary… So what do I need to know???


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