Pres1_Cross Check between Define

Report
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
– blankcrf.pdf
– SAS xpt files
– Supporting documents, e.g., style sheet
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
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
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
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
Too much to check manually
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
XML Mapper
• Download SAS XML mapper
– http://support.sas.com/demosdownloads/setupca
t.jsp?cat=Base+SAS+Software
How to customize a xml mapper
• Wendi L Wright, 2010, How to Create an XML
Map with the XML Mapper
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;
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
Read Comments in PDF to SAS Dataset
(cont.)
Read Comments in PDF to SAS Dataset
(cont.)
• Develop a customized xml mapper for XFDF
• Read XFDF into SAS Dataset
SAS Dataset of CRF Annotation
Sample Findings of Cross Check
CDISC - Compare define origin with CRF annotation
XML Page
CRF Page
CRF Annotation
6
6 STUDYID
6
6 EDUOTH
7
7 MHPRESP
7
7 MHOCCUR
10
10 PESTAT
12
12 EGCLSP
Message
Variable : STUDYID annotated in CRF, but in Define.xml, origin is not mentioned as
CRF Page
Variable : EDUOTH annotated in CRF, but in Define.xml, origin is not mentioned as
CRF Page
Variable : MHPRESP annotated in CRF, but in Define.xml, origin is not mentioned
as CRF Page
Variable : MHOCCUR annotated in CRF, but in Define.xml, origin is not mentioned
as CRF Page
Variable : PESTAT annotated in CRF, but in Define.xml, origin is not mentioned as
CRF Page
Variable : EGCLSP annotated in CRF, but in Define.xml, origin is not mentioned as
CRF Page
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
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
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
Thanks
• The SAS Implementation of the cross check in
this presentation was done by Sangeetha
Mahalingam.

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