optimizing data extracts from oracle clinical sas views

© 2009 Confidential and proprietary property of RadPharm, all rights reserved.

OCUG Annual Conference – October 2009

Optimizing Data Extracts from OC SAS

Views

Prashant Rajopadhye, PMPRadPharm, Inc.

OncologyTrials

To Date

Outline

• About RadPharm, Inc.• Problem Overview

– BDL File Formats– Old Extraction Method

• Solution– Implementation Details– Process Flow

• Key Success Factor• Contact

© 2009 Confidential and proprietary property of RadPharm, all rights reserved.

• 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

About RadPharm, Inc.

© 2009 Confidential and proprietary property of RadPharm, all rights reserved.

• 15 years experience in– oncology– cardiovascular– musculoskeletal– diagnostic contrast imaging agents– Medical device studies

About RadPharm, Inc. (cont.)

© 2009 Confidential and proprietary property of RadPharm, all rights reserved.

• 300 Clinical Trials• Across 60 countries

About RadPharm, Inc. (cont.)

© 2009 Confidential and proprietary property of RadPharm, all rights reserved.

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.

BDL A File Format

P A T I E N T _ I D | V I S I T | S U B E V E N T | V I S I T _ D A T E | D C I | D C M | D C M _ S U B S E T | Q U E S T I O N _ G R O U P |

Q U E S T I O N | Q U E S T I O N _ O C C U R R E N C E _ S E Q U E N C E _ N U M B E R | R E P E A T _ S E Q U E N C E _ N U M B E R | V A L U E | C O M M E N T

BDL B File Format

I N V E S T I G A T O R | S I T E | P A T I E N T _ I D | V I S I T | S U B E V E N T

| V I S I T _ D A T E | D C I | D C M | D C M _ S U B S E T | Q U E S T I O N _ G R O U P | Q U E S T I O N | Q U E S T I O N _ O C C U R R E N C E _ S E Q U E N C E _ N U M B E R | R E P E A T _ S E Q U E N C E _ N U M B E R | V A L U E |

C O M M E N T

Preview File Format

P A T I E N T _ I D | V I S I T | S U B E V E N T | V I S I T _ D A TE | D C I | D C M | D C M _ S U B S E T | Q U E S T I O N _ G R O U P | Q U E S T I O N _ O C C U R R E N C E _ S E Q U E N C E _ N U M B E R | R E P E A T _ S E Q U E N C E _ N U M B E R |

R E A D E R _ I D | R E A D _ T Y P E _ S P | S I T E | 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 _ D T | N E W _ N Y | S A M P L E _ N Y | G R A D E _ C D | P E R F O R M E D _ N Y | CR I T E R I A _ M E T _ N Y | C O M M E N T S _ 1 | C O M M E N T S _ 2 |C O M M E N T S _ 3 | C O M M E N T S _ 4 | C O M M E N T S _ 5 | L E S I O N _ I D |

S T U DY | I N V S I T E | P T | V I S I T | S U B E V E | C P E V E N T | Q U A L I F Y V

© 2009 Confidential and proprietary property of RadPharm, all rights reserved.

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.

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

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;

TABLESRE_EXTRACT_TPHD

VARCHAR2 (200 Byte)YDTP_READ_TYPE_SP13

VARCHAR2 (200 Byte)YDTP_READER_ID12

VARCHAR2 (200 Byte)YDTP_VISIT_DATE11

VARCHAR2 (200 Byte)YDTP_SUBEVENT10

VARCHAR2 (100 Byte)YDTP_VISIT9

VARCHAR2 (200 Byte)YDTP_PATIENT_ID8

VARCHAR2 (70 Byte)NQUALIFYV7

NUMBER (2)NSUBEVE6

NUMBER (5)NVISIT5

VARCHAR2 (20 Byte)NCPEVENT4

VARCHAR2 (10 Byte)NINVSITE3

VARCHAR2 (10 Byte)NPT2

VARCHAR2 (10 Byte)NSTUDY1

D a t a T y p eN u ll?C o l u m n N a m eI D

TABLESRE_EXTRACT_COMMENTS

VARCHAR2 (200 Byte)YDTP_COMMENT511

VARCHAR2 (200 Byte)YDTP_COMMENT410

VARCHAR2 (200 Byte)YDTP_COMMENT39

VARCHAR2 (200 Byte)YDTP_COMMENT28

VARCHAR2 (200 Byte)YDTP_COMMENT17

VARCHAR2 (70 Byte)NQUALIFYV6

NUMBER (2)NSUBEVE5

NUMBER (5)NVISIT4

VARCHAR2 (10 Byte)NPT3

VARCHAR2 (10 Byte)NINVSITE2

VARCHAR2 (10 Byte)NSTUDY1

D a t a T y p eN u ll?C o l u m n N a m eI D

TABLESRE_EXTRACT_DATA_WORK

VARCHAR2 (50 Byte)YDTP_READER_ID13

NUMBERYDTP_REPEAT_SEQUENCE_NUMBER12

NUMBERYDTP_QUESTION_OCCURRENCE_SEQ11

VARCHAR2 (50 Byte)YDTP_QUESTION_GROUP10

VARCHAR2 (50 Byte)YDTP_DCM_SUBSET9

VARCHAR2 (50 Byte)YDTP_DCM8

VARCHAR2 (50 Byte)YDTP_DCI7

VARCHAR2 (50 Byte)YDTP_VISIT_DATE6

NUMBERYDTP_SUBEVENT5

VARCHAR2 (50 Byte)YDTP_VISIT4

VARCHAR2 (50 Byte)YDTP_PATIENT_ID3

VARCHAR2 (50 Byte)YDTP_RAD_SITE2

VARCHAR2 (50 Byte)YDTP_INVESTIGATOR1

D a t a T y p eN u ll?C o l u m n N a m eI D

TABLESRE_EXTRACT_DATA_WORK (Cont.)

VARCHAR2 (250 Byte)YDTP_COMMENT527

VARCHAR2 (250 Byte)YDTP_COMMENT426

VARCHAR2 (250 Byte)YDTP_COMMENT325

VARCHAR2 (250 Byte)YDTP_COMMENT224

VARCHAR2 (250 Byte)YDTP_COMMENT123

VARCHAR2 (50 Byte)YDTP_PERFORMED_NY22

VARCHAR2 (50 Byte)YDTP_GRADE_CD21

VARCHAR2 (50 Byte)YDTP_SAMPLE_NY20

VARCHAR2 (50 Byte)YDTP_NEW_NY19

VARCHAR2 (50 Byte)YDTP_ASSESSMENT_DT18

VARCHAR2 (50 Byte)YDTP_EXAM_SP17

VARCHAR2 (50 Byte)YDTP_RESPONSE_NY16

VARCHAR2 (50 Byte)YDTP_SITE15

VARCHAR2 (50 Byte)YDTP_READ_TYPE_SP14

TABLESRE_EXTRACT_DATA_WORK (Cont.)

VARCHAR2 (50 Byte)YLESION_ID37

NUMBERYREPEATSN36

VARCHAR2 (70 Byte)NQUALIFYV35

NUMBER (2)NSUBEVE34

NUMBER (5)NVISIT33

VARCHAR2 (50 Byte)NCPEVENT32

VARCHAR2 (10 Byte)NINVSITE31

VARCHAR2 (10 Byte)NPT30

VARCHAR2 (10 Byte)NSTUDY29

DATEYCREATED_DATE28

TABLESRE_BDL_QUESTION_MAP

VARCHAR2 (50 Byte)NQUESTION_NAME3

VARCHAR2 (50 Byte)NDATASET2

VARCHAR2 (10 Byte)NSTUDY1

D a t a T y p eN u ll?C o l u m n N a m eI D

SRE_BDL_QUESTION_MAP Data

CRITERIA_MET_NYFRACSPProtocol###

PERFORMED_NYFRACSPProtocol###

GRADE_CDFRACSPProtocol###

SAMPLE_NYFRACSPProtocol###

NEW_NYFRACSPProtocol###

ASSESSMENT_DTFRACSPProtocol###

EXAM_SPFRACSPProtocol###

RESPONSE_NYFRACSPProtocol###

SITEFRACSPProtocol###

READ_TYPE_SPFRACSPProtocol###

READER_IDFRACSPProtocol###

COMMENT5FRACSPProtocol###

COMMENT4FRACSPProtocol###

COMMENT3FRACSPProtocol###

COMMENT2FRACSPProtocol###

COMMENT1FRACSPProtocol###

Q U E S T I O N _ N A M ED A T A S E TS T U D Y

TABLESRE_A_B_FILE_MAP

VARCHAR2 (200 Byte)NPROTOCOL11

VARCHAR2 (50 Byte)NINVESTIGATOR10

VARCHAR2 (50 Byte)NRAD_PATIENT9

VARCHAR2 (50 Byte)NRAD_SITE8

VARCHAR2 (50 Byte)NPT7

VARCHAR2 (50 Byte)NINVSITE6

VARCHAR2 (50 Byte)NSTUDY5

CHAR (1 Byte)NDESTINATION_FILE4

VARCHAR2 (8 Byte)YTERMINATION_DATE3

VARCHAR2 (8 Byte)YSTART_DATE2

CHAR (1 Byte)NREC_TYPE1

D a t a T y p eN u ll?C o l u m n N a m eI D

Execution

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

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

Process Flow

VERTFRAC, OVETFRAC, VTF2FRAC

VIEWS

Timepoint Header View Reader Comments View

OC SAS Views

INSE

RT

INSE

RT

INSE

RT

Procedure FRACSP_FILL

Procedure FRACSP_

WRITE_FILE

BDL A FileBDL B File

Preview File

© 2009 Confidential and proprietary property of RadPharm, all rights reserved.

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%

Contact

Prashant Rajopadhye, PMPOracle Database AdministratorRadPharm, Inc.Phone: +1 609 936 2600 x 2526E-mail: rajopadhye@radpharm.com