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Optimizing Data Extracts from Oracle Clinical SAS Views
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Optimizing Data Extracts from Oracle Clinical SAS Views

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This presentation delivered at OCUG Annual Conference 2009 at New Orleans is on a new way developed to optimize SAS dataset extracts in Batch Data Load (BDL) format from Oracle Clinical SAS views.

This presentation delivered at OCUG Annual Conference 2009 at New Orleans is on a new way developed to optimize SAS dataset extracts in Batch Data Load (BDL) format from Oracle Clinical SAS views.

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  • 1. OCUG Annual Conference – October 2009 Optimizing Data Extracts from OC SAS Oncology Views Trials To Date Prashant Rajopadhye, PMP RadPharm, Inc. © 2009 Confidential and proprietary property of RadPharm, all rights reserved.
  • 2. Outline • About RadPharm, Inc. • Problem Overview – BDL File Formats – Old Extraction Method • Solution – Implementation Details – Process Flow • Key Success Factor • Contact
  • 3. About RadPharm, Inc. • Leading full service imaging core lab • Managing all facets of the imaging segment of global clinical trials, Phases I-IV. – Computed Tomography (CT) – Magnetic Resonance Imaging (MRI) – Positron Emission Tomography (PET) and PET/CT – Single Photon Emission Computed Tomography (SPECT) – Ultrasound – X-ray © 2009 Confidential and proprietary property of RadPharm, all rights reserved.
  • 4. About RadPharm, Inc. (cont.) • 15 years experience in – oncology – cardiovascular – musculoskeletal – diagnostic contrast imaging agents – Medical device studies © 2009 Confidential and proprietary property of RadPharm, all rights reserved.
  • 5. About RadPharm, Inc. (cont.) • 300 Clinical Trials • Across 60 countries © 2009 Confidential and proprietary property of RadPharm, all rights reserved.
  • 6. Problem • Phase 3 Study data extraction – 15 Files • 5 BDL Files of ‘A’ type • 5 BDL Files of ‘B’ type • 5 ASCII Preview Files for the Clinical Data Coordinator – Total Extraction Time about 12 hours – One dataset alone took over 9 hours – Would cause database performance issues – Needed to stop PSUB during extraction © 2009 Confidential and proprietary property of RadPharm, all rights reserved.
  • 7. BDL A File Format PATIENT_ID | VISIT | SUBEVENT | VISIT_DATE | DCI | DCM | DCM_ SUBSET | QUESTION_GROUP | QUESTION | QUESTION_OCCURREN CE_SEQUENCE_NUMBER | REPEAT _SEQUENCE_NUMBER | VALUE | COMMENT © 2009 Confidential and proprietary property of RadPharm, all rights reserved.
  • 8. BDL B File Format INVESTIGATOR | SITE | PATIENT_ID | VISIT | SUBEVENT | VISIT_DATE | DCI | DCM |DCM_ SUBSET | QUESTION_GROUP | QU ESTION | QUESTION_OCCURRENC E_SEQUENCE_NUMBER | REPEAT_ SEQUENCE_NUMBER | VALUE| COMMENT
  • 9. Preview File Format PATIENT_ID | VISIT | SUBEVENT | VISIT_ D A TE | D C I | D C M | D C M _ S U B S E T | Q U ESTION_GROUP | QUESTION_OCCURREN CE_SEQUENCE_NUMBER | REPEAT_SEQU ENCE_NUMBER| READER_ID | READ_TYPE_SP | SITE | R E S P O N S E _ N Y | E XA M _ S P | A S S E S S M E N T_DT | NEW_NY | SAMPLE_NY | GRADE_ C D | P E R F O R M E D _ N Y | CR I T E R I A _ M E T _ NY | COMMENTS_1 | COMMENTS_2 | COMMENTS_3 | COMMENTS_4 | COMMEN TS_5 | LESION_ID| S T U DY | I N V S I T E | P T | V I S I T | SUBEVE | CPEVENT | QUALIFYV
  • 10. Old way to extract FRACSP dataset • Run the BDL A file, BDL B file and Preview file SQL extraction scripts directly against the OC SAS views one at a time • Resulting datasets spooled to files © 2009 Confidential and proprietary property of RadPharm, all rights reserved.
  • 11. Solution • SELECT data from OC SAS views • INSERT into a set a three indexed tables – SRE_EXTRACT_TPHD – SRE_EXTRACT_COMMENTS – SRE_EXTRACT_DATA_WORK • UPDATE table SRE_EXTRACT_DATA_WORK with time point header and reader comments data • WRITE files to OS using following mapping tables and final data – SRE_BDL_QUESTION_MAP – SRE_A_B_FILE_MAP – SRE_EXTRACT_DATA_WORK © 2009 Confidential and proprietary property of RadPharm, all rights reserved.
  • 12. New way: Package PKG_SRE_FRACSP CREATE OR REPLACE PACKAGE PKG_SRE_FRACSP as PROCEDURE fracsp_fill ( p_study_name varchar2 , p_view_type varchar2 DEFAULT 'STABLE', p_schema varchar2 DEFAULT 'RADPHARM', p_a_b_file_map_table varchar2 DEFAULT ‘SRE_A_B_FILE_MAP'); PROCEDURE fracsp_write_file( p_study_name varchar2 , p_view_type varchar2 DEFAULT 'STABLE', p_file_type varchar2 DEFAULT 'all', p_schema varchar2 DEFAULT 'RADPHARM', p_map_table varchar2 DEFAULT 'SRE_BDL_QUESTION_MAP'); END PKG_SRE_FRACSP;
  • 13. TABLE SRE_EXTRACT_TPHD ID Column Name N u ll? Data Type 1 STUDY N VARCHAR2 (10 Byte) 2 PT N VARCHAR2 (10 Byte) 3 INVSITE N VARCHAR2 (10 Byte) 4 CPEVENT N VARCHAR2 (20 Byte) 5 VISIT N NUMBER (5) 6 SUBEVE N NUMBER (2) 7 QUALIFYV N VARCHAR2 (70 Byte) 8 DTP_PATIENT_ID Y VARCHAR2 (200 Byte) 9 DTP_VISIT Y VARCHAR2 (100 Byte) 10 DTP_SUBEVENT Y VARCHAR2 (200 Byte) 11 DTP_VISIT_DATE Y VARCHAR2 (200 Byte) 12 DTP_READER_ID Y VARCHAR2 (200 Byte) 13 DTP_READ_TYPE_SP Y VARCHAR2 (200 Byte)
  • 14. TABLE SRE_EXTRACT_COMMENTS ID Column Name N u ll? Data Type 1 STUDY N VARCHAR2 (10 Byte) 2 INVSITE N VARCHAR2 (10 Byte) 3 PT N VARCHAR2 (10 Byte) 4 VISIT N NUMBER (5) 5 SUBEVE N NUMBER (2) 6 QUALIFYV N VARCHAR2 (70 Byte) 7 DTP_COMMENT1 Y VARCHAR2 (200 Byte) 8 DTP_COMMENT2 Y VARCHAR2 (200 Byte) 9 DTP_COMMENT3 Y VARCHAR2 (200 Byte) 10 DTP_COMMENT4 Y VARCHAR2 (200 Byte) 11 DTP_COMMENT5 Y VARCHAR2 (200 Byte)
  • 15. TABLE SRE_EXTRACT_DATA_WORK ID Column Name N u ll? Data Type 1 DTP_INVESTIGATOR Y VARCHAR2 (50 Byte) 2 DTP_RAD_SITE Y VARCHAR2 (50 Byte) 3 DTP_PATIENT_ID Y VARCHAR2 (50 Byte) 4 DTP_VISIT Y VARCHAR2 (50 Byte) 5 DTP_SUBEVENT Y NUMBER 6 DTP_VISIT_DATE Y VARCHAR2 (50 Byte) 7 DTP_DCI Y VARCHAR2 (50 Byte) 8 DTP_DCM Y VARCHAR2 (50 Byte) 9 DTP_DCM_SUBSET Y VARCHAR2 (50 Byte) 10 DTP_QUESTION_GROUP Y VARCHAR2 (50 Byte) 11 DTP_QUESTION_OCCURRENCE_SEQ Y NUMBER 12 DTP_REPEAT_SEQUENCE_NUMBER Y NUMBER 13 DTP_READER_ID Y VARCHAR2 (50 Byte)
  • 16. TABLE SRE_EXTRACT_DATA_WORK (Cont.) 14 DTP_READ_TYPE_SP Y VARCHAR2 (50 Byte) 15 DTP_SITE Y VARCHAR2 (50 Byte) 16 DTP_RESPONSE_NY Y VARCHAR2 (50 Byte) 17 DTP_EXAM_SP Y VARCHAR2 (50 Byte) 18 DTP_ASSESSMENT_DT Y VARCHAR2 (50 Byte) 19 DTP_NEW_NY Y VARCHAR2 (50 Byte) 20 DTP_SAMPLE_NY Y VARCHAR2 (50 Byte) 21 DTP_GRADE_CD Y VARCHAR2 (50 Byte) 22 DTP_PERFORMED_NY Y VARCHAR2 (50 Byte) 23 DTP_COMMENT1 Y VARCHAR2 (250 Byte) 24 DTP_COMMENT2 Y VARCHAR2 (250 Byte) 25 DTP_COMMENT3 Y VARCHAR2 (250 Byte) 26 DTP_COMMENT4 Y VARCHAR2 (250 Byte) 27 DTP_COMMENT5 Y VARCHAR2 (250 Byte)
  • 17. TABLE SRE_EXTRACT_DATA_WORK (Cont.) 28 CREATED_DATE Y DATE 29 STUDY N VARCHAR2 (10 Byte) 30 PT N VARCHAR2 (10 Byte) 31 INVSITE N VARCHAR2 (10 Byte) 32 CPEVENT N VARCHAR2 (50 Byte) 33 VISIT N NUMBER (5) 34 SUBEVE N NUMBER (2) 35 QUALIFYV N VARCHAR2 (70 Byte) 36 REPEATSN Y NUMBER 37 LESION_ID Y VARCHAR2 (50 Byte)
  • 18. TABLE SRE_BDL_QUESTION_MAP ID Column Name N u ll? Data Type 1 STUDY N VARCHAR2 (10 Byte) 2 DATASET N VARCHAR2 (50 Byte) 3 QUESTION_NAME N VARCHAR2 (50 Byte)
  • 19. SRE_BDL_QUESTION_MAP Data STUDY DATASET QUESTION_NAME Protocol### FRACSP COMMENT1 Protocol### FRACSP COMMENT2 Protocol### FRACSP COMMENT3 Protocol### FRACSP COMMENT4 Protocol### FRACSP COMMENT5 Protocol### FRACSP READER_ID Protocol### FRACSP READ_TYPE_SP Protocol### FRACSP SITE Protocol### FRACSP RESPONSE_NY Protocol### FRACSP EXAM_SP Protocol### FRACSP ASSESSMENT_DT Protocol### FRACSP NEW_NY Protocol### FRACSP SAMPLE_NY Protocol### FRACSP GRADE_CD Protocol### FRACSP PERFORMED_NY Protocol### FRACSP CRITERIA_MET_NY
  • 20. TABLE SRE_A_B_FILE_MAP ID Column Name N u ll? Data Type 1 REC_TYPE N CHAR (1 Byte) 2 START_DATE Y VARCHAR2 (8 Byte) 3 TERMINATION_DATE Y VARCHAR2 (8 Byte) 4 DESTINATION_FILE N CHAR (1 Byte) 5 STUDY N VARCHAR2 (50 Byte) 6 INVSITE N VARCHAR2 (50 Byte) 7 PT N VARCHAR2 (50 Byte) 8 RAD_SITE N VARCHAR2 (50 Byte) 9 RAD_PATIENT N VARCHAR2 (50 Byte) 10 INVESTIGATOR N VARCHAR2 (50 Byte) 11 PROTOCOL N VARCHAR2 (200 Byte)
  • 21. Execution • exec pkg_sre_fracsp.fracsp_fill (‘PROTOCOL###', 'STABLE'); • exec pkg_sre_fracsp.fracsp_write_file (‘PROTOCOL###', 'STABLE');
  • 22. Process Flow OC SAS Views VERTFRAC, Timepoint Header View Reader Comments View OVETFRAC, VTF2FRAC VIEWS Procedure FRACSP_FILL T T T ER ER ER INS INS INS BDL A File BDL B File Preview File Procedure FRACSP_ WRITE_FILE
  • 23. Key Success Factor • FRACSP Dataset BDL A file, BDL B file, Preview file – Old Method: 9 hours – New Method: 1 hour 25 minutes • Full set of files – Old Method: 12 hours – New Method: 3 hours • Overall improvement – 400% © 2009 Confidential and proprietary property of RadPharm, all rights reserved.
  • 24. Contact Prashant Rajopadhye, PMP Oracle Database Administrator RadPharm, Inc. Phone: +1 609 936 2600 x 2526 E-mail: rajopadhye@radpharm.com