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Getting the best out of several technologies
Developing an Integrated Platform
Jean-Marc Ferran Consultant & Owner Mobile +45 60 16 04 56 Email: [email protected] Qualiance ApS Guldbergsgade 25, st th 2200 Copenhagen N www.qualiance.dk Bart Van Win & Sebastien Roland Developers Tel +32 2 774 11 00 Fax +32 2 774 11 99 Mobile +32 476 54 59 17 [email protected] [email protected]
Contract Research Organisation Business & Decision Life Sciences Sint-Lambertusstraat 141 Rue Saint-Lambert 1200 Brussels www.businessdecision-lifesciences.com
Technical Platform - high level flow DATA COLLECTION
AREA
STUDY SPECIFICATION
DATA MANAGEMENT AREA
DATA STANDARDS
LIBRARY
COMPARISON
STUDY SDTM DATA &
METADATA
VALIDATION
ISSUE REPORTS
DM
ISSUE REPORTS
STUDY METADATA
SPECIFICATION
DBA
EDC
CRO
STUDY METADATA
REPOSITORY
DEFINE.XML
DH10: “Time Travel for Librarians: Versioning
Complex Library Metadata for Past, Present or Future
Retrieval”
SD04: “An Integrated Platform for Standards Management and Study
Conduct”
SD05: “Data Validation, Getting Full Control over your Data Standards Compliance
and Data Flow”
CD14: “Is your Library a Success: Manage and Measure Conformance Across Partners and
Projects”
TS06: “Developing an Integrated Platform,
Getting the Best out of Several Technologies”
CC06: “Dynamic SASProgramming with
XMLTemplates”
Implementation
• Architecture and solution overview
• Main processes – Data standards library overview – Study metadata build process – Study validation process
• Integration features
– Single user access model implementation – Reporting capability and project-level access – Audit trailing – Library and Study Metadata validation flow
Architecture and solution overview
SDD
LIBRARY MANAGEMENT
STUDY SPECIFCATION andMETADATA REPOSITORY
STUDY VALIDATION and ISSUE TRACKING
USER INFORMATION
AUDIT LOG
SDD OBJECT METADATA
DATA STANDARD LIBRARY
STUDY METADATA REPOSITORY
ISSUE TRACKING
AUDIT TRAIL
SDD DATABASE
ORACLE DATABASE
USER INTERFACE SDD SAS DRUG
DEVELOPMENT 4.2
SAS PROGRAMS
STUDY DATA
FILES
SAS DATASETSDEFINE.XML
DOCUMENTS OUTPUTS
USER INTERFACEEXTENDED APPLICATIONS
CREATEJOB
RUN JOB DOWNLOAD MOVE
OBJECTS
READ OBJECT
ATTRIBUTESUPLOAD SEND
NOTIFICATIONSLOG IN
CREATE FOLDER
STRUCTURE & PERMISSIONS
SDD API
CREATE MAKE OBSOLETE COPY QUERY VALIDATEEDIT ACCESS
WORKSPACE REPORT
JAVASERVICE LAYER
APPLICATION LAYER
Data Standards Library
DATA STANDARDS LIBRARY
DATA COLLECTION MODULES
SDTM 1.3 SDTM IG 3.1.3
THERAPEUTIC AREA METADATA
• The Data Standards Library contains : – Data Collection Modules:
• using CDASH metadata • with clustered SDTM metadata • annotated for CDASH • annotated for SDTM
– Metadata Definitions : • SDTM Standards • Therapeutic Area Standards
Data Collection Modules - CDASH DATA COLLECTION MODULES LIBRARY
DM 1
VS 2
EG 1
...
DM 2
VS 1
• CRF template using CDASH annotations
Data Collection Modules - SDTM DATA COLLECTION MODULES LIBRARY
DM 1
VS 2
EG 1
...
DM 2
VS 1
Metadata Definitions
DATA STANDARDS LIBRARY
DATA COLLECTION MODULES
SDTM 1.3 SDTM IG 3.1.3
THERAPEUTIC AREA METADATA
• 5 levels of metadata • SDTM IG 3.1.3 and TA metadata
stored in the same physical tables
METADATA DEFINITIONS
DOMAIN METADATA
VARIABLE METADATA
VALUE LEVEL METADATA
COMPUTATIONAL ALGORITHMS
CONTROLLED TERMINOLOGY
Study Metadata Build Process (Overview) DATA STANDARDS LIBRARY
DATA COLLECTION MODULES LIBRARY
STUDYTEMPORARY BUILD
REPOSITORY
SDTM 1.3SDTM IG 3.1.3
THERAPEUTIC AREA METADATA
STUDY METADATA
STUDY SPECIFICATION MODULE
STUDY PARAMETERSVISIT SCHEDULE
TRIAL DESIGN DATA
BUILD
STUDYMETADATA
REPOSITORYSTUDY METADATA
STUDY PARAMETERSVISIT SCHEDULE
TRIAL DESIGN DATA
STUDY METADATA COMPARISON WITH
PREVIOUS BUILDDEFINE.XML
V2
VS003
EX001
EG005
V1
DM001
VS002
IE005
EG004
VALIDATE API API
SAS ENVIRONMENT
SAS PROGRAMS
STUDY DATA
FILES
SAS DATASETSDEFINE.XML
DOCUMENTS OUTPUTS
STUDYMETADATA
REPOSITORYSTUDY METADATA
EXCEPTION TABLES
COMPARE
CREATE AND RUN CHECKS
JOB OF CHECKS
COMPARE AGAINST STUDY
METADATA
EXCEPTIONREPORTS
DATA STANDARDS LIBRARY
GLOBAL AND THERAPEUTIC
METADATA
Study Validation Process (Overview)
API
Study validation SAS/SDD job of checks
SAS ENVIRONMENT
SAS PROGRAMS
STUDY DATA
FILES
SAS DATASETSDEFINE.XML
DOCUMENTS OUTPUTS
CREATE AND RUN CHECKS
JOB OF CHECKS
EXCEPTIONREPORTS
SAS ENVIRONMENT
SAS PROGRAMS
STUDY DATA
FILES
SAS DATASETSDEFINE.XML
DOCUMENTS OUTPUTS
STUDYMETADATA
REPOSITORYSTUDY METADATA
EXCEPTION TABLES
COMPARE
CREATE AND RUN CHECKS
JOB OF CHECKS
COMPARE AGAINST STUDY
METADATA
EXCEPTIONREPORTS
DATA STANDARDS LIBRARY
GLOBAL AND THERAPEUTIC
METADATA
API
Integration features
SDD
LIBRARY MANAGEMENT
STUDY SPECIFCATION andMETADATA REPOSITORY
STUDY VALIDATION and ISSUE TRACKING
USER INFORMATION
AUDIT LOG
SDD OBJECT METADATA
DATA STANDARD LIBRARY
STUDY METADATA REPOSITORY
ISSUE TRACKING
AUDIT TRAIL
SDD DATABASE
ORACLE DATABASE
USER INTERFACE SDD SAS DRUG
DEVELOPMENT 4.2
SAS PROGRAMS
STUDY DATA
FILES
SAS DATASETSDEFINE.XML
DOCUMENTS OUTPUTS
USER INTERFACEEXTENDED APPLICATIONS
CREATEJOB
RUN JOB DOWNLOAD MOVE
OBJECTS
READ OBJECT
ATTRIBUTESUPLOAD SEND
NOTIFICATIONSLOG IN
CREATE FOLDER
STRUCTURE & PERMISSIONS
SDD API
CREATE MAKE OBSOLETE COPY QUERY VALIDATEEDIT ACCESS
WORKSPACE REPORT
JAVASERVICE LAYER
APPLICATION LAYER
Integration features (1) User access and security model
Accesses to modules, functionalities, projects and studies according to SDD roles, groups and accesses
1 access model and log-in
SDD USER INFORMATION
AUDIT LOG
SDD OBJECT METADATA
SDD DATABASE
USER INTERFACE SDD SAS DRUG
DEVELOPMENT 4.2
SAS PROGRAMS
STUDY DATA
FILES
SAS DATASETSDEFINE.XML
DOCUMENTS OUTPUTS
CREATEJOB
RUN JOB DOWNLOAD MOVE
OBJECTS
READ OBJECT
ATTRIBUTESUPLOAD SEND
NOTIFICATIONSLOG IN
CREATE FOLDER
STRUCTURE & PERMISSIONS
SDD APISERVICE LAYER
APPLICATION LAYER
1a - Log in to SDDRecover user roles, groups
and accesses
1b - Open simultaneouslySDD session in new tab
2 – Return log in sucess/failure and user’s
roles, groups and accesses
• Roles
• Projects accesses
• Studies accesses
API
Integration features (2) Reporting capability and access to Oracle
Data Standards Library Comparison Study metadata comparison across study versions
Implementation Guides Study metadata comparison across projects
Completion Guides Define.xml
Trial summary-based search reports Export of trial design datasets
Metrics reports Study metadata-based search reports
DATA STANDARD LIBRARY
STUDY METADATA REPOSITORY
ISSUE TRACKING
AUDIT TRAIL
ORACLE DATABASE
SAS PROGRAMS
STUDY DATA
FILES
SAS DATASETSDEFINE.XML
DOCUMENTS OUTPUTS
SAS ENVIRONMENT
Integration features (2) Project/study-level access to Oracle tables
Access to study metadata can be restricted by projects at row level access using virtual private databases
• Virtual Private Database Policies attached to each study metadata table
• Dynamic where clausing automatically applied according to Oracle user id
• Ex: Where project_nb=project 1
Project 1
Project 2
Project 3
SDD
USER INTERFACE SDD SAS DRUG
DEVELOPMENT 4.2
SAS PROGRAMS
STUDY DATA
FILES
SAS DATASETSDEFINE.XML
DOCUMENTS OUTPUTS
Virtual Private
Database Policies
User_project_1 -> where project_nb = ’project 1’
User_project_2 -> where project_nb = ’project 2’
User_project_3 -> where project_nb = ’project 3’
Ref: http://docs.oracle.com/cd/B28359_01/network.111/b28531/vpd.htm
Integration features (2) Use of encoded passwords in SAS
• Oracle password is encrypted in SAS using proc pwencode
• Programs creating the libnames are stored in designated area with restriced access
Ref: Keep your database passwords out of the clear: Quick and easy tips to protect yourself, Steven, PNWSUG 2007
Integration features (3) Audit trail
Audit trails in same structure is easily integrated for reporting
USER INFORMATION
AUDIT LOG
SDD OBJECT METADATA
STUDY METADATA REPOSITORY
ISSUE TRACKING
AUDIT TRAIL
SDD DATABASE
ORACLE DATABASE
Extracted on a regular
basis from SDD
database
DATA STANDARD LIBRARY
Read from SDD
SDD
USER INTERFACE SDD SAS DRUG
DEVELOPMENT 4.2
SAS PROGRAMS
STUDY DATA
FILES
SAS DATASETSDEFINE.XML
DOCUMENTS OUTPUTS
Integration features (3) Audit trail structure
• 2 tables – Main table
• 1 row per action – Log-in, log-out – Edit/Create/Validate metadata – Make obsolete – Etc.
– Detailed table • Linked to main table per action id • 1 set of rows per action • 1 row for every change
– listing old and new values
Integration features (4) Library/Study Metadata validation flow (1)
SDD
USER INTERFACE SDD SAS DRUG
DEVELOPMENT 4.2
SAS PROGRAMS
STUDY DATA
FILES
SAS DATASETSDEFINE.XML
DOCUMENTS OUTPUTS
USER INTERFACE BDLS APPLICATIONS
CREATEJOB
RUN JOB DOWNLOAD MOVE
OBJECTS
READ OBJECT
ATTRIBUTESUPLOAD SEND
NOTIFICATIONSLOG IN
CREATE FOLDER
STRUCTURE & PERMISSIONS
SDD APISERVICE LAYER
1- User select metadata to validate
2 – Job of consistency checks programs is created accordingly and run in SDD
3a – Consistency report is created
DATA STANDARD LIBRARY
STUDY METADATA REPOSITORY
ISSUE TRACKING
AUDIT TRAIL
ORACLE DATABASE
3b – Oracle table is updated
4 – Feedback is returned to UI
SQL > Grant update(validation_flag)
SQL> Grant select, insert, update(issue_status)
Integration features (4) Library/Study Metadata validation flow (2)
• Integrity checks – Java based – Ensure database integrity – Updates require new minor release under
Computer Validation procedures
• Metadata consistency and study checks – SAS based – Stored in SAS environment – Ensure compliance with CDISC rules – Controled via look-up tables – Can be updated/enhanced following Use-of-the-
System procedures
Conclusion (1) • No redundance in information
– User information, privileges and project/study accesses located and managed in one place
– No duplication of metadata, continous access to metadata repository in Oracle
• Java, SAS, Oracle provide each great benefits – Java technologies:
• User friendly web interfaces • Services for integration
– SAS: • Analytical power • Well-known by users • Code can be updated outside new release
– Oracle: • Row-level access and locking • Further security features • Use of virtual private database policies
Conclusion (2)
• Next steps
– Improving feedback on SAS jobs status within web-applications UI
– Optimize use of virtual private database policy concepts
