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Importance of Define.xml in NDA Submissions: Cross-Check Methodology with SAS Datasets

This document outlines the critical role of the Define.xml file in FDA NDA submissions, emphasizing its significance in organizing study files and facilitating the review process. A streamlined cross-check methodology is described, detailing steps to read Define.xml and annotated blank CRFs into SAS datasets for comparison. Discrepancies identified through this process highlight the importance of properly documenting the Origin field, while providing insights into the automation of validation processes. The goal is to enhance consistency and accuracy in submitting standardized electronic datasets.

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Importance of Define.xml in NDA Submissions: Cross-Check Methodology with SAS Datasets

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  1. Cross Check between Define.xml and blankcrf.pdf Galderma, LLT Jeff Xia, Sangeetha Mahalingam

  2. SDTM Submission Package • FDA has specific rules in organizing study files in a NDA submission

  3. 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

  4. 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

  5. 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

  6. 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

  7. 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

  8. Too much to check manually

  9. 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

  10. XML Mapper • Download SAS XML mapper • http://support.sas.com/demosdownloads/setupcat.jsp?cat=Base+SAS+Software

  11. How to customize a xml mapper • Wendi L Wright, 2010, How to Create an XML Map with the XML Mapper

  12. 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;

  13. 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

  14. Read Comments in PDF to SAS Dataset (cont.)

  15. Read Comments in PDF to SAS Dataset (cont.) • Develop a customized xml mapper for XFDF • Read XFDF into SAS Dataset

  16. SAS Dataset of CRF Annotation

  17. Sample Findings of Cross Check

  18. 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

  19. 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

  20. Reference • Joel Campbell, Ryan Wilkins, Importing and Parsing Comments From a PDF Document With Help From Perl Regular Expressions, PgarmaSUG 2011 • PrafullaGirase, Robert Agostinelli, Automating Validation of Define.xml using SAS, PharmaSUG 2013 • FDA, CDER Common Data Standards Issues Document, Version 1.1, Dec 2011

  21. Thanks • The SAS Implementation of the cross check in this presentation was done by Sangeetha Mahalingam.

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