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IBM Software Group ® The Use of OGSA-DAI with DB2 Content Manager in the eDiaMoND Project M Oevers, B Collins, A Knox, J Williams.

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Presentation on theme: "IBM Software Group ® The Use of OGSA-DAI with DB2 Content Manager in the eDiaMoND Project M Oevers, B Collins, A Knox, J Williams."— Presentation transcript:

1 IBM Software Group ® The Use of OGSA-DAI with DB2 Content Manager in the eDiaMoND Project M Oevers, B Collins, A Knox, J Williams

2 IBM Software Group Overview eDiaMoND the project Strategies for Virtualisation How DB2 and CM are used OGSA-DAI enablement of CM Lessons Learnt

3 IBM Software Group eDiamond – Project Announcement One of the pilot e-science projects is to develop a digital mammography archive, together with an intelligent medical decision support system for breast cancer diagnosis and treatment. An individual hospital will not have supercomputing facilities, but through the grid it could buy the time it needs. So the surgeon in the operating theatre will be able to pull up a high-resolution mammogram to identify exactly where the tumour can be found – Tony Blair (speech to the royal society – 23 may 2002)

4 IBM Software Group eDiaMoND Partners

5 IBM Software Group eDiaMoND – Project Deliverables Breast Screening Programmes eDiaMoND Phase 0 Prototype (end-2003) Phase 0 Prototype (end-2003) ? (Next Phase) ? (Next Phase) BluePrint Grid Infrastructure Grid-connected Workstation Database for Storage & Retrieval of Images & Metadata Computation for CADe, CADi and Statistical Analyses Required Hardware, Software & Network for given Service Levels Phase 1 Prototype (mid-2004) Phase 1 Prototype (mid-2004)

6 IBM Software Group eDiaMoND Functional Model

7 IBM Software Group Strategies for Virtualisation Use II & II4C Expose through OGSA-DAI Investigate DQP

8 IBM Software Group Virtualisation – things to remember Each Breast Care Unit (BCU) to operate independently from others Individual organisations coming together to for a Virtual Organisation Data loaded locally in each BCU Data is owned by the BCU Enable read access across all BCUs seamlessly Replication or Federation DB2 II & II4C Remember its got to be a Grid (eScience project) OGSA-DAI Distributed Query Processing (QDP) over OGSA-DAI

9 IBM Software Group How OGSA-DAI is used with DB2 and CM DB2 stores the non-image data in a structured form DICOM describes an ER model Patient – Study – Series – Image Flexible to allow for multiple modalities Allow flexibility of data modelling/access control/query rewrite CM is used to store and manage the (large 30MB) DICOM files Files contain both non-image data and image data Identified by DICOM SOP Instance UID Flat CM data model (Customer Requirement) Both exposed as OGSA-DAI services DICOM – Digital Imaging and Communications in Medicine

10 IBM Software Group Query Service Persistent OGSA-DAI Service Persistent Data Layer Grid Layer Client Layer Administration Client Screening Workflow Viewer Client Worklist Service Transient 1. Query 2. Worklist Create 3. Worklist Consume 4. Retrieve 1 23 DB2 Instance Patient ID DICOM ID Content Manager Instance DICOM ID URL – DICOM ID Retrieve Service Persistent OGSA-DAI Service Persistent 4

11 IBM Software Group Data Layer Grid Layer Grid Layer Client Layer CHU Grid Development – Phase 0 to Phase1 CM DB2 QUERY WORKLIST Admin RETRIEVE DB2 OGSA DAI Viewer CM OGSA DAI KCLUCLUED DB2 Fed. CM Fed. CM DB2 CM DB2 CM DB2 DB2 FED OGSA DAI CM FED OGSA DAI CM OGSA DAI DB2 OGSA DAI CM DB2 Data Loader Deploy

12 IBM Software Group CM Grid enablement – What it means Driver Class, e.g. Driver URI, e.g. jdbc:db2://localhost:50000/SAMP LE Connection DriverManager.getConnection() Metadata Table Schema for SQL XML schema for XML DB Mapping of Grid Certificates to DB user and password Datastore object, e.g Data store name, e.g. ICMNLSDB Connected Datastore Datastore.connect() Metadata ItemTyes and Attributes Could it be treated as an XML DB? Mapping of Grid Certificate to CM user and password It was possible to map CM concepts to corresponding JDBC concepts that are exposed in OGSA-DAI configuration files 2 XML files to edit and 2 Java classes to write OGSA-DAI conf/ext points Mapping to CM

13 IBM Software Group The Gory details

14 IBM Software Group Lessons Learnt OGSA-DAI is a flexible framework into which CM fits reasonably well Chaining of activities User defined activities Developer focus on writing activities Use of dynamic discovery to configure the system Useful during development/testing Register more in the registry Unifies the view of the system as far as data is concerned Experience of grid-enabling an existing product Have not explored how to expose CM metadata yet

15 IBM Software Group Thank You Manfred Oevers

16 IBM Software Group Data Load - High Level Design 1.DICOM file gets parsed 2.XML file created with Reference 3.XML file passed to load services 4.CM pulls DICOM file in 5.As simple as possible

17 IBM Software Group Data Load Detailed Design Plugin Architecture Decoupling Configuration of Plugin to decide Parser also pluggable API as simple as possible IBM OUCL

18 IBM Software Group eDiaMoND API

19 IBM Software Group eDiaMoND - Organisation Development (Mirada) Oxford / Churchill UCL / St Georges Edinburgh JANET Network Development (OUCL)Aberdeen KCL / Guys Development (IBM) Workstation Server T221 Grid Boundary OUCL LAN eDiaMoND LAN VPN & FW Oxford LAN eDiaMoND LAN VPN & FW Edinburgh LAN eDiaMoND LAN VPN & FW Aberdeen LAN eDiaMoND LAN VPN & FW eDiaMoND LAN Mirada LAN VPN & FW eDiaMoND LAN UCL LAN VPN & FW eDiaMoND LAN KCL LAN VPN & FW eDiaMoND LAN IBM LAN VPN & FW

20 IBM Software Group DB=FEDCORE Node=edibm View cis.patient = edibm.patient union edouc.patient Federation setup DB2 Server = edibm Nickname= edibm.patient DB=EDCORE Node=edibm Table=cis.patient DB=EDCORE Node=edouc Table=cis.patient Server = edouc Nickname= edouc.patient Create view over union of nicknames of identical tables No query rewrite necessary

21 IBM Software Group The M Diagram

22 IBM Software Group Non-Repudiation Systems Administration Epidemiology Teaching Diagnosis Screening Epidemiology Teaching Diagnosis Screening eDiaMoND – Non-Functional Grid Ethics Legal Security Performance Manageability …… Scalability Auditability Epidemiology Teaching Diagnosis Screening Epidemiology Training Screening Anonymisation 256MB & 5 secs response Lossless Compression Encryption ~100 Centres

23 IBM Software Group UCL KCL CHU UED Phase 1 Deployment IBM MIR OUCL SCO Digitiser W/S T221 Digit. GEO eDiaMoND Grid Node eDiaMoND W/S T221 UCL LAN eDiaMoND Grid Node eDiaMoND W/S T221 Digitiser W/S T221 Digit. UED LAN JANET / Internet OUCL LAN eDiaMoND LAN eDiaMoND Dev. Grid Node eDiaMoND Test Grid Node eDiaMoND Demo Grid Node CHU LAN GUY LAN eDiaMoND W/S T221 eDiaMoND Demo W/S T221 eDiaMoND Grid Node eDiaMoND Dev. W/S T221 eDiaMoND Dev. Grid Node eDiaMoND W/S T221 eDiaMoND Grid Node MIR LAN eDiaMoND Demo. W/S T221 eDiaMoND Demo. Grid Node IBM LAN Digitiser W/S Digit. eDiaMoND Repository Server IBM Dev. Grid Node eDiaMoND LAN T221 GUY

24 IBM Software Group UK Breast Screening – Challenges 230 - Radiologists (Double Reading) 50% - Workload Increase 2,000,000 - Screened every Year 120,000 - Recalled for Assessment 10,000 - Cancers 1,250 - Lives Saved Began in 1988 Women 50-70 Screened Every 3 Years 2 Views/Breast + Demographic Increase ~100 Breast Screening Programmes - Scotland - Wales - Northern Ireland - England Digital

25 IBM Software Group Breast Cancer Facts 1 in 8 women will develop breast cancer in the course of their lives, 1 in 28 will die of it In the EC breast cancer accounts for 19% of cancer deaths and 24% of cancer cases Diagnosed in 348,000 women in EC+USA and kills 115,000 women annually 1,000,000 new cases world-wide in 1997 Rationale for Screening Early diagnosis = better Prognosis Detection at 0.5cm has favourable outcome in 99% cases; but at 2cm only 50%

26 IBM Software Group UK Breast Screening Programme Call 1000 Missed 1 Interval Cancers Screening Assessment Epidemiology Training ~100 Breast Screening Programmes Recall 40 (86) All Clear 960 (914) All Clear 34 (80) Cancer 6 Previous Current The Recall rate is 86 for First Time Screening as no comparison is possible with a previous Screening

27 IBM Software Group Project Teams Grid Infrastructure Team IBM Oxford University Computing Laboratory Image Analysis Technology Team Dept of Engineering Science Mirada Solutions Image Collection & Clinical Assessment Team St Georges Hospital Guys and St Thomas Hospitals Oxford Radcliffe Hospitals Kings College London University College London University of Edinburgh

28 IBM Software Group Mammograms have very different appearances, depending on image settings and acquisition systems The interesting tissue representation is a surface independent of scanner SMF® - Miradas Patented Standardisation Process

29 IBM Software Group H int Compression Plates 1cm 1.0 cm Fatty Tissue Glandular Tissue Tumour A quantitative representation of breast tissue density Miradas Interesting Tissue Representation

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