in the eDiaMoND Project

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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

IBM Software Group

Overview



eDiaMoND the project


Strategies for Virtualisation


How DB2 and CM are used


OGSA
-
DAI enablement of CM


Lessons Learnt

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)

IBM Software Group

eDiaMoND Partners

IBM Software Group

eDiaMoND


Project Deliverables

Breast

Screening

Programmes

eDiaMoND

Phase 0

Prototype

(end
-
2003)

?

(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)

IBM Software Group

eDiaMoND Functional Model

IBM Software Group

Strategies for Virtualisation

Use II & II4C

Expose through

OGSA
-
DAI

Investigate DQP

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 it’s got to be a Grid (eScience project)


OGSA
-
DAI


Distributed Query Processing (QDP) over OGSA
-
DAI




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

IBM Software Group

Query Service

Persistent




OGSA
-
DAI Service

Persistent




Data Layer

Grid 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

2

3

DB2 Instance


Patient ID

DICOM ID

Content Manager Instance


DICOM ID

URL


DICOM ID

Retrieve Service

Persistent




OGSA
-
DAI Service

Persistent




4

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

KCL

UCL

UED

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

IBM Software Group

CM Grid enablement


What it means


Driver Class, e.g.



com.ibm.db2.jcc.DB2Driver



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


com.ibm.mm.sdk.server.DKDatastoreICM



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

IBM Software Group

The Gory details

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


IBM Software Group

Thank You

Manfred Oevers

manfred_oevers@uk.ibm.com

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


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

IBM Software Group

eDiaMoND API

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









IBM Software Group

DB=
FED
CORE

Node=
edibm


View cis.patient =

edibm.patient

union

edouc.patient

Federation setup DB2


Server = edibm

Nickname=


edibm.patient

DB=
ED
CORE

Node=
edibm

Table=cis.patient

DB=
ED
CORE

Node=edouc

Table=cis.patient


Server = edouc

Nickname=

edouc.patient

Create view over

union of

nicknames of

identical tables



No query rewrite

necessary

IBM Software Group

The M Diagram

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

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

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

T221

eDiaMoND
Grid Node

eDiaMoND

Dev.


W/S

T221

T221

eDiaMoND
Dev.

Grid Node

eDiaMoND
W/S

T221

eDiaMoND
Grid Node

MIR LAN

eDiaMoND

Demo.


W/S

T221

T221

eDiaMoND
Demo.

Grid Node

IBM LAN

Digitiser
W/S

Digitiser
W/S

Digit.

Digit.

eDiaMoND
Repository

Server

IBM

Dev.

Grid Node

eDiaMoND LAN

T221

T221

GUY

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

Digital

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%


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

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


Guy’s and St Thomas’ Hospitals


Oxford Radcliffe Hospitals


Kings College London


University College London


University of Edinburgh


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®
-

Mirada’s Patented Standardisation Process

IBM Software Group

H
int

Compression
Plates

1cm

1.0 cm

Fatty
Tissue

Glandular
Tissue

Tumour

A
quantitative

representation of breast tissue density

Mirada’s Interesting Tissue Representation