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END TO END SDTM AUTOMATION A METADATA CENTRIC APPROACH
Roman RadelickiTeam Manager Data Programming
PhUSE US Connect 2019, February 25th
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2© CDISC 2015
OVERVIEW
n Introduction
n MDR – metadata repository
n MDR driven tools§ Annotation Tool § SDTM Mapping Tool § Metadata Center§ YADLi
n Conclusion
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3© CDISC 2015
OVERVIEW
n Introduction
n MDR – metadata repository
n MDR driven tools§ Annotation Tool § SDTM Mapping Tool § Metadata Center§ YADLi
n Conclusion
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4© CDISC 2015
INTRODUCTION
n What is the key to creating clinical databases that are compliant with CDISC SDTM standards?§ Metadata driven approach§ Seamless integration of processes and people
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5© CDISC 2015
OVERVIEW
n Introduction
n MDR – metadata repository
n MDR driven tools§ Annotation Tool § SDTM Mapping Tool § Metadata Center§ YADLi
n Conclusion
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6© CDISC 2015
MDR – METADATA REPOSITORY
n Master source of metadata containing multiple metadata libraries.
SGS IG v5.0 CLIENT X IG v1.0
CLIENT Y IG v1.0
CLIENT Z IG v3.2
CLIENT Y IG v2.0
CLIENT Z IG v3.3
MDR
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7© CDISC 2015
MDR – METADATA REPOSITORY
n Structure based on the Define-XML model
n Contains all available domains, variables, valuelists, codelists, comments and computational methods
Domains
Variables
Value lists
Code lists
Comments
Methods
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8© CDISC 2015
MDR – METADATA REPOSITORY
n 3 types of MDR libraries
• Maintained by SGS • Dictated by the client• Maintained together
with the client
• Maintained by the Client
• Implemented by SGS
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9© CDISC 2015
MDR – METADATA REPOSITORY
Client A – Trial A
SGS IG v5.0
CLIENT X IG v1.0
CLIENT Y IG v1.0
CLIENT Z IG v3.2
CLIENT Y IG v2.0
CLIENT Z IG v3.3
MDR
SGS IG v5.0Client B – Trial B
SGS IG v5.0
Client Y – Trial Y
CLIENT Y IG v2.0
Trials
Client B – Trial C
SGS IG v5.0
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10© CDISC 2015
OVERVIEW
n Introduction
n MDR – metadata repository
n MDR driven tools§ Annotation Tool § SDTM Mapping Tool § Metadata Center§ YADLi
n Conclusion
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11© CDISC 2015
MDR DRIVEN TOOLS
Client A – Trial A
SGS IG v5.0
CLIENT X IG v1.0
CLIENT Y IG v1.0
CLIENT Z IG v3.2
CLIENT Y IG v2.0
CLIENT Z IG v3.3
MDR
SGS IG v5.0Client B – Trial B
SGS IG v5.0
Client Y – Trial Y
CLIENT Y IG v2.0
Trials
Annotation Tool
MDR Driven Tools
Mapping Tool
Metadata Center
YADLi Define.xml
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12© CDISC 2015
OVERVIEW
n Introduction
n MDR – metadata repository
n MDR driven tools§ Annotation Tool § SDTM Mapping Tool § Metadata Center§ YADLi
n Conclusion
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13© CDISC 2015
ANNOTATION TOOL
n How we used to annotate a CRF
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14© CDISC 2015
ANNOTATION TOOL
n Font: Courier vs Arial
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15© CDISC 2015
ANNOTATION TOOL
n Size: 11 vs 18
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16© CDISC 2015
ANNOTATION TOOL
n Color
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17© CDISC 2015
ANNOTATION TOOL
n Domain missing
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18© CDISC 2015
ANNOTATION TOOL
n Annotation properties
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19© CDISC 2015
ANNOTATION TOOL
n Domain colors
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20© CDISC 2015
ANNOTATION TOOL
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21© CDISC 2015
ANNOTATION TOOL
n Driven by the MDR
n Guide the user in generating annotations
n Provide automatic layout consistency
n Provide automatic adherence to client specifications
n The more the tool is used, the smarter it gets
Annotation Tool
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22© CDISC 2015
ANNOTATION TOOL
n Annotation type§ Annotation templates§ Guide the user § Configurable per MDR
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23© CDISC 2015
ANNOTATION TOOL
n Annotation type demo§ Weight of a subject § TESTCD
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24© CDISC 2015
ANNOTATION TOOL
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25© CDISC 2015
ANNOTATION TOOL
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26© CDISC 2015
ANNOTATION TOOL
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27© CDISC 2015
ANNOTATION TOOL
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28© CDISC 2015
ANNOTATION TOOL
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29© CDISC 2015
ANNOTATION TOOL
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30© CDISC 2015
ANNOTATION TOOL
n Tracking review process§ Statuses§ Multiple users at the same time
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31© CDISC 2015
ANNOTATION TOOL
n Advantages§ More accurate and better quality aCRF§ Annotations stored/available in database
• Use in other processes: SDTM mapping, define.xml
§ Maintenace of MDR• Request for new values in valuelist/codelist (MDR)
§ Future proof: Plug & play MDR
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32© CDISC 2015
ANNOTATION TOOL
n Challenges§ Screen vs exported PDF file
n Opportunities§ Further automatisation: auto copy annotations from the
library or previously annotated CRF’s
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33© CDISC 2015
OVERVIEW
n Introduction
n MDR – metadata repository
n MDR driven tools§ Annotation Tool § SDTM Mapping Tool § Metadata Center§ YADLi
n Conclusion
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34© CDISC 2015
SDTM MAPPING TOOL
n Transform EDC source data to SDTM
n Guide the programmer in performing the mapping
n High flexibility
n High quality CDISC SDTM datasets
Mapping Tool
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35© CDISC 2015
SDTM MAPPING TOOL
n Transform EDC source data to SDTM
n Guide the programmer in performing the mapping
n High flexibility
n High quality CDISC SDTM datasets
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36© CDISC 2015
SDTM MAPPING TOOL
n To learn more about our pre-conversionPieter Blomme: paper DH03
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37© CDISC 2015
SDTM MAPPING TOOL
n
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38© CDISC 2015
SDTM MAPPING TOOL
n All input fields, radio buttons and checkboxespresented like a pivot table
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39© CDISC 2015
OVERVIEW
n Introduction
n MDR – metadata repository
n MDR driven tools§ Annotation Tool § SDTM Mapping Tool § Metadata Center§ YADLi
n Conclusion
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40© CDISC 2015
METADATA CENTER
n Automate setup of trial specific metadata
n Start: copy the complete MDR libraryprogrammer will make the metadata trial specific
Metadata Center
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41© CDISC 2015
METADATA CENTER
n Automate setup of trial specific metadata
n Start: copy the complete MDR libraryprogrammer will make the metadata trial specific
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42© CDISC 2015
METADATA CENTER
n Automate setup of trial specific metadata
n Start: copy the complete MDR libraryprogrammer will make the metadata trial specific
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43© CDISC 2015
METADATA CENTER
n Automation § Use the information collected via other in-house
developed applications§ Annotation tool
• SGSSTATE flag • ORIGIN• CRF pages
§ SDTM mapping tool• Calculate the maximum length of the variables in the
SDTM datasets
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44© CDISC 2015
METADATA CENTER
n Metadata checks§ Addition to Pinnacle21 validation§ Validate metadata integrity and compliance with the
specific MDR library
n Audit trail§ Record every manipulation of metadata on trial level
• What was manipulated + Old value• Person perfomed the manipulation• When it was manipulated
§ Produce reports• All manipulations performed from a specific date• Retrieve metadata as it was on a specific date
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45© CDISC 2015
METADATA CENTER
n Opportunities§ Past: creation of metadata late in the process of
creating SDTM datasets
§ Now: move the creation of the metadata to the front of the process
• Pave the path for future tasks
• Discuss and agree upon metadata with the client upfront
• In line with define.xml purpose
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46© CDISC 2015
OVERVIEW
n Introduction
n MDR – metadata repository
n MDR driven tools§ Annotation Tool § SDTM Mapping Tool § Metadata Center§ YADLi
n Conclusion
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47© CDISC 2015
YADLI
n YADLi = Yet Another Data Loader improved§ Load any kind of source data§ Perform data manipulations
YADLi
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48© CDISC 2015
YADLI
n DTA – Data Transfer Agreementagree on format and structure
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49© CDISC 2015
YADLI
n YADLi loads the file into the database
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50© CDISC 2015
YADLI
n Programmer maps the data to SDTM
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51© CDISC 2015
YADLI
n YADLi produces output that can be used in SDTM datasets
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52© CDISC 2015
YADLI
n Best features§ Handles any type of format§ Logging and traceability
n Challenge§ Load any kind of format and structure
n Opportunity§ Further integration into the SDTM mapping tool
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53© CDISC 2015
OVERVIEW
n Introduction
n MDR – metadata repository
n MDR driven tools§ Annotation Tool § SDTM Mapping Tool § Metadata Center§ YADLi
n Conclusion
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54© CDISC 2015
CONCLUSION
n MDR to automate SDTM workflows paid off
n Road hasn’t been easy
n Work in progress
Thank you for your attention!
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55© CDISC 2015
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