automated sdtm creation and discrepancy detection jobs: the numbers tell the tale
DESCRIPTION
The FDA is advising use of data standards as early as possible in the study lifecycle. As a result, Data Management centers are using the Study Data Tabulation Model (SDTM) to drive operations from First Patient In till Database Lock. Many tools on the market allow for the creation of SDTM datasets via intuitive user interfaces. However, targeted tools are needed to manage nightly jobs taking care of data source downloads (eCRF, ePRO, Lab, etc), data uploads in a staging database, converting to SDTM and running edit checks before the Clinical Data Manager arrives in the morning.TRANSCRIPT
AUTOMATED SDTM CREATION AND DISCREPANCY DETECTIONAND DISCREPANCY DETECTION JOBS:THE NUMBERS TELL THE TALE
Joris De Bondt
PhUSE Conference 2014
12-15 Oct 2014
OUTLINE
Setting the scene
OUTLINE
g• SGS’ Conversion Center
• SDTM data sources
• Timing for CDMS data refresh
SGS’ Conversion Center
• Glossary
• Technologies usedTechnologies used
• What is it?
• Code snippets• Code snippets
• Performance tuning
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SETTING THE SCENE: SGS’ CONVERSION CENTER
A central tool to manage the end-to-end flow of refreshing the
SGS CONVERSION CENTER
REQUEST g gData Management study databases
• REQUEST: sends an automatic data request via:
DOWN LOAD
INSTALL REQUEST: sends an automatic data request via:
Web browser, on a variety of vendor specific platforms
SAS Connect
INSTALL
CONVERT
SAS Connect
to obtain a new extract of the data
(unless scheduled transfer is available)
META DATA
REPORTS( )
• DOWNLOAD: downloads new data extract from:
PAGES 2 LOCK
A2O
Web browser, on a variety of vendor specific platforms
SAS ConnectSAS
CLIN
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sFTP serverCLIN
TRIAL
SETTING THE SCENE: SGS’ CONVERSION CENTER
• INSTALL: loads new data extract (Oracle dmp, CSV, SAS,
SGS CONVERSION CENTER
REQUEST ( pexcel, etc.) into the Data Management database
• CONVERT: converts all current study data into SDTM format
DOWN LOAD
INSTALL
• METADATA: generates new metadata files for the SDTM data
• REPORTS: generates reports for external distribution
INSTALL
CONVERT
REPORTS: generates reports for external distribution
• PAGES2LOCK: generates overview of eCRF pages that meet locking criteria
META DATA
REPORTS g
• A2O: refreshes output of checks and listings
• SAS: creates SAS datasets from the SDTM data
PAGES 2 LOCK
A2O • SAS: creates SAS datasets from the SDTM data
• CLINTRIAL: starts the synchronisation of the SDTM database to Clintrial
SAS
CLIN
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ClintrialCLIN TRIAL
SETTING THE SCENE: SDTM DATA SOURCESSDTM DATA SOURCES
Site specificsystems
eCRF Paper CRF eSource ePRO Lab, imaging, etc.
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SETTING THE SCENE: TIMING FOR CDMS DATA REFRESH
Refreshing
TIMING FOR CDMS DATA REFRESH
REQUEST g• the SDTM database
• the output of checks and listings
DOWN LOAD
INSTALL p g
impacts the work of Data Management (DM), so
INSTALL
CONVERT
impacts the work of Data Management (DM), so• the best time is overnight, when DM staff is not at work
• but also DM Programmers are not around
META DATA
REPORTSg
meaning that the entire end-to-end flow should run unattended
PAGES 2 LOCK
A2O g
SAS
CLIN
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CLIN TRIAL
SGS’ CONVERSION CENTERGLOSSARY
Windows Powershell
GLOSSARY
• Microsoft's task automation and configuration management framework
• Consists of a command-line shell and associated scripting language built on .NET FrameworkFramework
• Administrative tasks are generally performed by cmdlets (pronounced command-lets), which are specialized .NET classes implementing a particular operation
• Sets of cmdlets may be combined into scripts, executables (which are standaloneSets of cmdlets may be combined into scripts, executables (which are standalone applications).
jQuery• cross-platform JavaScript library designed to simplify the client-side scripting of
HTML
• free, open source software, licensed under the MIT License
• jQuery's syntax is designed to make it easier to navigate a document, select DOM elements, create animations, handle events, and develop Ajax applications.
VMWare
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• provides cloud and virtualization software and services
SGS’ CONVERSION CENTERTECHNOLOGIES USED
VMWare, Powershell
TECHNOLOGIES USED
REQUEST
VMWare, Powershell
VMWare Powershell Oracle PL/SQL
DOWN LOAD
INSTALL VMWare, Powershell, Oracle PL/SQL
VMWare, Powershell, Oracle PL/SQLjQuery
INSTALL
CONVERT
VMWare, Powershell, Oracle PL/SQL
VMWare, Powershell, Oracle PL/SQL, Crystal Reports
jQuery,PHP
META DATA
REPORTS
VMWare, Powershell, Oracle PL/SQL
VMWare, Powershell, Oracle PL/SQL
PAGES 2 LOCK
A2O , ,
VMWare, Powershell, Oracle PL/SQL, SAS
VMW P h ll O l PL/SQL
SAS
CLIN
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VMWare, Powershell, Oracle PL/SQLCLIN TRIAL
SGS’ CONVERSION CENTERWHAT IS IT?WHAT IS IT?
All end-to-end study process information one-click-away in a single overview
Powershell
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Oracle
SGS’ CONVERSION CENTERWHAT IS IT?WHAT IS IT?
History information
Error information Error information
Powershell
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Oracle
SGS’ CONVERSION CENTERWHAT IS IT?WHAT IS IT?
Performance statistics, for detecting problems and possible improvements
Performance tuning
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Oracle
SGS’ CONVERSION CENTERPOWERSHELL CODE SNIPPETPOWERSHELL CODE SNIPPET
Automatic ‘On demand’ request of Rave SAS datasets
Via “InternetE plorer Application”• Via “InternetExplorer.Application” object
• Setting the URL
• Adding username and password
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Oracle
SGS’ CONVERSION CENTERJQUERY CODE SNIPPETJQUERY CODE SNIPPET
Customized SGS tooltip enablement to allow for a web 2.0 experienceweb 2.0 experience
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Oracle
SGS’ CONVERSION CENTERPERFORMANCE TUNINGPERFORMANCE TUNING
Processing time for small phase I trials large phase III trialsg p g p
From minutes to hours
When to start tuning efforts?
CONVERSIONstart date: 2014-08-26 05:07
When to start tuning efforts?
CONVERSIONt t d t 2014 08 25 00 58
CONVERSIONstart_date: 2014-08-26 03:48end_date: 2014-08-26 05:25d ti 01 36 08
_end_date: 2014-08-26 05:12duration: 00:05:15status: FINISHEDerror: start_date: 2014-08-25 00:58
end_date: 2014-08-25 04:29duration: 03:31:13status: FINISHED
duration: 01:36:08status: FINISHEDerror:
error:Phase I
Phase IIB status: FINISHEDerror:
Phase IIB
Phase III
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Oracle
SGS’ CONVERSION CENTERPERFORMANCE TUNINGPERFORMANCE TUNING
Based on overall cross-study comparisony p
REQUESTDOWNLOAD
INSTALL CONVERTMETADATA
REPORTS PAGES 2 LOCK A2O SAS
CLINTRIAL
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Oracle
SGS’ CONVERSION CENTERPERFORMANCE TUNINGPERFORMANCE TUNING
Based on overall timing evolution on study levelg y
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Oracle
SGS’ CONVERSION CENTERPERFORMANCE TUNINGPERFORMANCE TUNING
Based on task-timing evolution on study levelg y
“Expected Time of Arrival”
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Oracle
SGS’ CONVERSION CENTERPERFORMANCE TUNINGPERFORMANCE TUNING
Allowing for targeted performance tuning
DOWNLOADDOWNLOAD
g g p g
Data download
DOWNLOADstart_date: 2014-04-15 23:30end_date: 2014-04-15 23:56duration: 00:26:46t t FINISHED
DOWNLOADstart_date: 2014-04-06 23:30end_date: 2014-04-07 00:27duration: 00:57:45t t FINISHED status: FINISHED
error:status: FINISHEDerror:
CONVERSIONstart date: 2014 04 25 12:25
CONVERSIONstart date: 2014 04 07 01:40
SDTM conversion
start_date: 2014-04-25 12:25end_date: 2014-04-25 16:03duration: 03:37:27status: FINISHED
start_date: 2014-04-07 01:40end_date: 2014-04-07 06:08duration: 04:28:08status: FINISHED
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error:error: Oracle
TAKE HOME MESSAGESTAKE HOME MESSAGES
Data Management centers• face wide variety of
• source datasource data• data provider platforms
process small phase I to large phase III trialsreq ire minimal impact of data refresh for DM staff require minimal impact of data refresh for DM staff
IT solutions can be put in place to run a sequence of DM IT solutions can be put in place to run a sequence of DM actions unattended overnight allowing for DM Programmers to
T k t d• Track unexpected errors• Tune the process performance• Manage all trials with minimal oversight effort
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REQUESTDOWNLOAD
INSTALL CONVERTMETADATA
REPORTS PAGES 2 LOCK A2O SAS
CLINTRIAL
THANK YOU FOR YOUR ATTENTIONTHANK YOU FOR YOUR ATTENTION
Joris De BondtLife Science ServicesHead EDC and Data StandardsWHERE EXPERIENCE SGS Belgium NVGeneraal De Wittelaan 19A b52800 Mechelen – BelgiumPhone: +32 (0)15 29 93 40Mobile: +32 (0)473 746477Fax: +32 (0)15 27 32 50E il j i d b dt@
WHERE EXPERIENCEMEETS SPEED
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E-mail : [email protected]/CRO