Using SAS ETL Studio to Create a CDISC-Compliant Clinical Data Warehouse Barry Cohen
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1 Octagon - 1 Using SAS ETL Studio to Create a CDISC-Compliant Clinical Data Warehouse Barry Cohen PhilaSUG Spring Meeting June 15, 2005
2 Octagon - 2 Background Octagon Research Solutions (1) E-publication of NDA documents (2) CDISC/SDTM expertise! Clinical Data Strategies dept: Migrate data to SDTM Clinical Data Warehouse & strategic uses Earlier w/o ETL Studio, now with it Building and refining processes Topical, hence present some thoughts
3 Octagon - 3 Overview CDISC/SDTM background Migration scenarios Migration process Two approaches to migration Why use ETL Studio?
4 Octagon - 4 CDISC / SDTM
5 Octagon - 5 CDISC SDTM (1) CDISC Clinical Data Interchange Standards Consortium SDTM Study Data Tabulation Model (the std) FDA issued guidance for SDTM use FDA desires SDTM data. Future: require SDTM FDA developing tools to process SDTM data, and build warehouse on this standard
6 Octagon - 6 CDISC SDTM (2) No tutorial about SDTM today Today: Process of migrating data to SDTM, and use of ETL Studio in the process SDTM info and training resources available through CDISC Published info on web site CDISC-sponsored training by certified orgs Octagon Research is certified
7 Octagon - 7 Migration Scenarios
8 Octagon - 8 Migration Scenarios (1) From what and where, to what (SDTM) and when Many scenarios, based on: Data mgmt history Data to be used for reporting & analysis Multiple in-house structures No in-house standard all dif. strucs In-house standard new mix std and dif. strucs Work done by CROs using own standards Many-to-one migration
9 Octagon - 9 Migration Scenarios (2) Multiple in-house structures Migrate to SDTM early: SDTM for reporting and analysis, per study SDTM to integrate data for ISS/ISE SDTM for submission Migrate to SDTM late: Various struc for reporting & analysis, per study Ad hoc integrate various struc for ISS/ISE (or SDTM for ISS/ISE) SDTM for submission
10 Octagon - 10 Migration Scenarios (3) Single in-house structure Stable standard used in-house CROs deliver in standard One-to-one migration May have some multiple-to-one cases, too
11 Octagon - 11 Migration Scenarios (4) Migrate to SDTM early: OperDB for collect/clean/manage SDTM for rpting and analysis, per CSR SDTM to integrate data for ISS/ISE rpting and analysis SDTM for submission Migrate to SDTM late: OperDB for collect/clean/manage OperDB for rpting and analysis, per CSR OperDB to integrate data for ISS/ISE rpting and analysis SDTM for submission
12 Octagon - 12 Migration Scenarios (5) Three-Levels Scenario Legacy data in various structures Building in-house std now (prospective use) Migrate legacy data to in-house std For current subm. (CSR, ISS) For future Clinical Data Warehouse Analysis and reporting from in-house std Migrate from in-house std to SDTM for subm. Many-to-one-to-one migration
13 Octagon - 13 Migration Process
14 Octagon - 14 Migration Process (1) Process: From source to target Source Clinical data in DB (Oracle, SAS) Multiple tables/datasets one per domain Data sets today Target Same Individual files, or integrated in warehouse
15 Octagon - 15 Migration Process (2) Top-level steps Build and maintain metadata for the target (std) Build metadata for each source Map source to target - specs Develop programs as per specs Execute programs Integrate std data in warehouse
16 Octagon - 16 Migration Process (3) Build and maintain metadata for the target (std) Tables and structure Items and attributes (name, label, type, length) Item controlled content (terminology) Items display format Study CRFs annotated to SDTM
17 Octagon - 17 Migration Process (4) Build metadata for each source Same pieces as for target (except controlled terms) Study CRFs annotated to source
18 Octagon - 18 Migration Process (5) Map source to target - specs what goes to what and how (rules) not pgms Transformations: One-to-one, no other transform To single table, single item, w transform To single table, multiple items To multiple tables, multiple items
19 Octagon - 19 Migration Process (6) Develop programs as per specs Programming task Programs may be written, else auto generated by ETL tool Execute Programs/Job Test and Production Error check / resolve Manage production jobs (logs, audits)
20 Octagon - 20 Migration Process (7) Integrate std data in warehouse Another (final) step in the migration process. The Load step. Immediate: For ISS/ISE reporting, if reporting from SDTM data ( Submission-level ) Long-term: Multiple studies, subm s, and compounds stored together for analysis and reporting ( Company-level )
21 Octagon - 21 Two Approaches Build process/programs w/o ETL tool Build process/programs w ETL tool (ETL-Studio)
22 Octagon - 22 Without ETL Tool
23 Octagon - 23 Without ETL Tool (1) Build and maintain metadata for SDTM (target) In Excel SS s or SAS data sets or other CDISC provides SDTM metadata in Excel SS Annotate study CRFs to SDTM Build metadata for each source In Excel SS s or SAS data sets or other Annotate study CRFs to source
24 Octagon - 24 Without ETL Tool (2) Map source to target - specs Source-centric SS s - one row per source item SrcDataSet.Varname to SdtmDataSet.Varname, plus how rules Done by clinical/sdtm-aware person Resources: Annotated CRFs (to source, to target) Metadata SS s SDTM Implementation Guide
25 Octagon - 25 Without ETL Tool (3) Develop programs as per specs SAS programmer, using map specs SS Levels of sophistication Fully ad hoc Table-driven, auto-generated program, for oneto-one process, using: Map specs SS; Source & target metadata (Excel, SAS) Macros for common transformations referenced in map specs SS
26 Octagon - 26 Without ETL Tool (4) Levels of sophistication Table-driven full job, not just for indv ( one-toone ) processes: e.g., transpose, sort, validate, load Notes: Plus ad hoc code for remainder of program(s) May be building robust application
27 Octagon - 27 Without ETL Tool (5) Execute programs/job Controlled by programmer, unless robust application developed Integrate std data in warehouse Last program in the process Submission-level, company-level
28 Octagon - 28 With ETL Studio
29 Octagon - 29 With ETL Studio (1) Build and maintain metadata for SDTM (target) Stored in the target metadata library CDISC provides SDTM metadata in Excel SS SAS provides a load process Annotate study CRFs to SDTM Build metadata for each source Stored in the source metadata library Build by loading the source SAS dataset Annotate study CRFs to source
30 Octagon - 30 With ETL Studio (2) Map source to target - specs Same process as w/o ETL Studio Map specs Excel SS s Done by clinical/sdtm-aware person Resources: Annotated CRFs (to source, to target) Metadata SS s SDTM Implementation Guide
31 Octagon - 31 With ETL Studio (3) Develop programs as per specs Work shared by ETL developer and SAS pgmr ETL Developer Job comprised of processes Process Design wizard for full job Process Properties wndw to define ea. process Process ~ SAS data step(s) Code for job is auto-generated Uses map specs SS (CRFs as needed)
32 Octagon - 32 With ETL Studio (4) Process might have: Map, Transform, Sort, Transpose, Join, Validate Auto-generated code, or user-written code SAS programmer: Develop code and load to ETL-S, to be engaged by ETL developer Ad hoc: one-time transformations Macros: repeating transformations
33 Octagon - 33 ETL Studio Screen Shots
34 Octagon - 34 With ETL Studio (6) Execute programs/process Run by ETL developer Using ETL Studio job scheduler Define method of error reporting (rpt, table, msg) Integrate std data in warehouse Last ad hoc program in the process Submission-level, company-level
35 Octagon - 35 Why Use ETL Studio?
36 Octagon - 36 Why use ETL-Studio? (1) Central metadata uses SAS Metadata Server SDTM metadata Other metadata (eg, libraries, servers) Available for all processes in larger workflow Available for all SAS products in larger workflow Enterprise Guide Web Report Studio Valuable for Clinical Data Warehouse analysis and reporting
37 Octagon - 37 Why use ETL-Studio? (2) Programmer Perspective Code generation, minimize code written Metadata management Documentation of indv processes and full job Flexible Staffing (Clinical/SDTM-aware staff does map specs SS) ETL Developer builds and executes jobs SAS programmer generates utility programs Other code by ETL-S; Not managing jobs
38 Octagon - 38 Why use ETL-Studio? (3) Change Management For collaborative work Valuable: Large projects! Multiple developers! Update the same resources Project Management Organized, structured, managed env. for data, programs, and processes
39 Octagon - 39 Why use ETL-Studio? (4) Impact Analysis Easy to assess change Valuable: Migrations can be large projects Deploy Jobs to SAS Drug Development Ability to do this now Improvement planned
40 Octagon - 40 Why use ETL-Studio? (5) SDTM Metadata loader Upon request Easy Re-use of Work Process and job metadata Leverage workflow for: New sources New SDTM domains Startpoint for in-house standard
41 Octagon - 41 Questions
42 Octagon - 42 Contact Information Barry Cohen (bcohen@octagonresearch.com) x East Swedesford Road, Suite 200 Wayne, PA 19087
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