cross check between define.xml and blankcrf.pdf
DESCRIPTION
Cross Check between Define.xml and blankcrf.pdf. Galderma, LLT Jeff Xia, Sangeetha Mahalingam. SDTM Submission Package. FDA has specific rules in organizing study files in a NDA submission. SDTM Define package. SDTM define package is stored in the subfolder of Tabulations define.xml - PowerPoint PPT PresentationTRANSCRIPT
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Cross Check between Define.xml and blankcrf.pdf
Galderma, LLTJeff Xia, Sangeetha Mahalingam
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SDTM Submission Package
• FDA has specific rules in organizing study files in a NDA submission
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SDTM Define package
• SDTM define package is stored in the subfolder of Tabulations– define.xml– blankcrf.pdf– SAS xpt files– Supporting documents, e.g., style sheet
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Importance of Define.xml
• 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.
• An insufficiently documented define file is a common deficiency that reviewers have noted, including the Origin of the variable
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Origin field in Define.xml
• Indicator of the origin of the variable.– CRF Page #– Derived– eDT– Assigned– Protocol
• Hyperlink is provided to display the specific CRF Pages by using the stylesheet
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Validity of Origin field
• The CRF Page number is valid• If the reviewer clicks the hyperlink of a CRF
Page, then there should be a annotation in corresponding CRF Page
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Validity of Origin field (Cont.)
• All the CRF Page with the same annotation should be listed in the Origin field for that variable in the define.xml
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Too much to check manually
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A programming way to check
• Step 1: Read define.xml into SAS dataset• Setp 2: Read annotation of blankcrf.pdf into
SAS dataset• Origin compare checks between the datasets
created in Step 1 and Step 2 and the discrepancies are outputted in a listing
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XML Mapper
• Download SAS XML mapper– http://support.sas.com/demosdownloads/setupca
t.jsp?cat=Base+SAS+Software
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How to customize a xml mapper
• Wendi L Wright, 2010, How to Create an XML Map with the XML Mapper
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Syntax for reading xml into SAS dataset
• filename define “---\define.xml"; **** Define file location;• filename sxlemap “---\DefineXML.map"; ****
define XML mapper file location;• libname define XML XMLMAP=sxlemap
access=readonly;
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Read Comments in PDF to SAS Dataset
• Export Annotation in blankcrf to Data file (XFDF, a xml version of form data in PDF)
• Version: Adobe Acrobat Pro
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Read Comments in PDF to SAS Dataset (cont.)
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Read Comments in PDF to SAS Dataset (cont.)
• Develop a customized xml mapper for XFDF• Read XFDF into SAS Dataset
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SAS Dataset of CRF Annotation
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Sample Findings of Cross Check
CDISC - Compare define origin with CRF annotation
XML Page CRF Page CRF Annotation Message
6 6STUDYIDVariable : STUDYID annotated in CRF, but in Define.xml, origin is not mentioned as CRF Page
6 6EDUOTHVariable : EDUOTH annotated in CRF, but in Define.xml, origin is not mentioned as CRF Page
7 7MHPRESPVariable : MHPRESP annotated in CRF, but in Define.xml, origin is not mentioned as CRF Page
7 7MHOCCURVariable : MHOCCUR annotated in CRF, but in Define.xml, origin is not mentioned as CRF Page
10 10 PESTATVariable : PESTAT annotated in CRF, but in Define.xml, origin is not mentioned as CRF Page
12 12 EGCLSPVariable : EGCLSP annotated in CRF, but in Define.xml, origin is not mentioned as CRF Page
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Standard Expression of Annotation
• Consistent across studies in the same NDA submission,
• Easier for programming in the cross check– RACEOTH in SUPPDM– SUPPDM.QVAL where QNAM = RACEOTH– VSORRES where VSTESTCD = HEIGHT– Domain: VS– VS: Vital Signs
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More checks
• Check the QNAM, --TESTCD, --TEST among define.xml, SAS xpt files and annotation of blankcrf
• Check the contents in the TOC section of define.xml– Class– Structure– Key– Location – Significant digits in VLM– Comments for common variables, e.g. STUDYID
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Reference
• Joel Campbell, Ryan Wilkins, Importing and Parsing Comments From a PDF Document With Help From Perl Regular Expressions, PgarmaSUG 2011
• Prafulla Girase, Robert Agostinelli, Automating Validation of Define.xml using SAS, PharmaSUG 2013
• FDA, CDER Common Data Standards Issues Document, Version 1.1, Dec 2011
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Thanks
• The SAS Implementation of the cross check in this presentation was done by Sangeetha Mahalingam.