XML in a SAS World Mike Molter d-Wise Technologies

Agenda What is XML? Examples of industry XML standards (schemas) SAS tools for working with XML

What is XML? eXtensible Markup Language 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

Eastern Atlantic Detroit Western Pacific Calgary Eastern Metropolitan New Jersey XML document is made of elements (nhl, team, conference) Elements are marked with a start tag and an end tag (, ) Elements may be nested within other elements (location is nested within team) Elements may contain attributes (team element contains the name attribute) An element's value is the text outside of a nested element between the element's start and end tags (Pacific is a value of the division element) Each XML document must contain a root element (nhl)

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 keywords no processor

XML Schema (or standard) XML Schema (informal) - A specific set of elements and attributes, along with a set of rules that govern their use, for the purpose of transferring data between systems and developing applications for processing such data. An XML schema can be a combination of new elements along with other XML schemas (extensible) XML schema file - A well-formed XML file used for enforcing the rules of an XML schema, or validating an XML document.

XML Schema Examples NHL (Ok, I made this one up) XSL (eXtensible Stylesheet Language,.xsl) Transforms XML into something else XML schema files (.xsd) Validates an XML document XML Spreadsheet 2003 (.xml) Read and displayed by Excel ODM, Define, SDS Clinical Trials data, metadata

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 SDS-XML Submission data in ODM structure

XML in Pharma Collected Data Data Transformations Data Submission Metadata Submission ODM.XMLSAS SDS.XML Define.XML

Clinical Data ODM ItemGroup (dataset-level) Metadata

Clinical Data ItemGroup (dataset-level) Metadata Item (variable-level) Metadata ODM

Item (variable-level) Metadata Codelist Metadata (allowable values) ODM

Define-XML

Teams.sas7bdat Exporting XML

libname xmlout xml 'C:\teams_generic.xml' ; data xmlout.xteams ; set teams ; run; Exporting XML with the LIBNAME statement

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

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

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 ;

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 ;

References A SAS Programmer's Guide to Generating Define.xml, 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 ;

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

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 ;

Importing XML libname xmlout xml 'C:\teams_generic.xml' ; data xmlout.xteams ; set teams ; run; Export data sasteams ; set xmlout.xteams ; run; Import

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

Importing XML with an XML map An XML map 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;

Importing XML with an XML map /nhl/team character string 20 /nhl/team/conference character string 20  Name of data set to be created  Observation boundary  Variable Definition

XML Mapper

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, XSL stylesheets) Learning curve

Clinical Standards Toolkit (CST) …or PROC XSL

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

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)