OCUG Annual Conference – October 2009



                                                             Optimizing Data
    ...
Outline
• About RadPharm, Inc.
• Problem Overview
  – BDL File Formats
  – Old Extraction Method
• Solution
  – Implementa...
About RadPharm, Inc.

     • Leading full service imaging core lab
     • Managing all facets of the imaging segment of
  ...
About RadPharm, Inc.                                             (cont.)




     • 15 years experience in
               ...
About RadPharm, Inc.                                             (cont.)




     • 300 Clinical Trials
     • Across 60 c...
Problem

     • Phase 3 Study data extraction
               – 15 Files
                         • 5 BDL Files of ‘A’ type...
BDL A File Format
     PATIENT_ID | VISIT | SUBEVENT |
      VISIT_DATE | DCI | DCM | DCM_
      SUBSET | QUESTION_GROUP |...
BDL B File Format

INVESTIGATOR | SITE |
PATIENT_ID | VISIT | SUBEVENT
  | VISIT_DATE | DCI | DCM |DCM_
  SUBSET | QUESTIO...
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_GRO...
Old way to extract FRACSP dataset

     • Run the BDL A file, BDL B file and Preview
       file SQL extraction scripts di...
Solution
     • SELECT data from OC SAS views
     • INSERT into a set a three indexed tables
               – SRE_EXTRACT...
New way: Package PKG_SRE_FRACSP

CREATE OR REPLACE PACKAGE PKG_SRE_FRACSP as

PROCEDURE fracsp_fill (
                  p_...
TABLE
                     SRE_EXTRACT_TPHD
ID       Column Name         N u ll?   Data Type
     1   STUDY               ...
TABLE
                 SRE_EXTRACT_COMMENTS
ID       Column Name       N u ll?   Data Type
     1   STUDY             N   ...
TABLE
          SRE_EXTRACT_DATA_WORK
ID   Column Name                   N u ll?   Data Type
 1   DTP_INVESTIGATOR        ...
TABLE
     SRE_EXTRACT_DATA_WORK (Cont.)
14   DTP_READ_TYPE_SP    Y   VARCHAR2 (50 Byte)
15   DTP_SITE            Y   VARC...
TABLE
     SRE_EXTRACT_DATA_WORK (Cont.)
28   CREATED_DATE     Y   DATE

29   STUDY            N   VARCHAR2 (10 Byte)

30 ...
TABLE
             SRE_BDL_QUESTION_MAP

ID       Column Name     N u ll?   Data Type
     1   STUDY           N         V...
SRE_BDL_QUESTION_MAP Data
STUDY         DATASET   QUESTION_NAME
Protocol###   FRACSP    COMMENT1
Protocol###   FRACSP    C...
TABLE
                    SRE_A_B_FILE_MAP
ID       Column Name        N u ll?   Data Type
     1   REC_TYPE           N  ...
Execution

• exec pkg_sre_fracsp.fracsp_fill
  (‘PROTOCOL###', 'STABLE');


• exec pkg_sre_fracsp.fracsp_write_file
  (‘PR...
Process Flow
                             OC SAS Views

                 VERTFRAC,   Timepoint Header View   Reader Commen...
Key Success Factor

     • FRACSP Dataset BDL A file, BDL B file,
       Preview file
               – Old Method: 9 hours...
Contact


Prashant Rajopadhye, PMP
Oracle Database Administrator
RadPharm, Inc.
Phone: +1 609 936 2600 x 2526
E-mail: rajo...
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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.

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Optimizing Data Extracts from Oracle Clinical SAS Views

  1. 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. 2. Outline • About RadPharm, Inc. • Problem Overview – BDL File Formats – Old Extraction Method • Solution – Implementation Details – Process Flow • Key Success Factor • Contact
  3. 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. 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. 5. About RadPharm, Inc. (cont.) • 300 Clinical Trials • Across 60 countries © 2009 Confidential and proprietary property of RadPharm, all rights reserved.
  6. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 21. Execution • exec pkg_sre_fracsp.fracsp_fill (‘PROTOCOL###', 'STABLE'); • exec pkg_sre_fracsp.fracsp_write_file (‘PROTOCOL###', 'STABLE');
  22. 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. 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. 24. Contact Prashant Rajopadhye, PMP Oracle Database Administrator RadPharm, Inc. Phone: +1 609 936 2600 x 2526 E-mail: rajopadhye@radpharm.com

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