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ACGT: Open Grid Services for Improving Medical Knowledge Discovery. Stelios G. Sfakianakis, FORTH. The ACGT vision & principles. The ultimate objective of the ACGT project is the provision of a unified technological infrastructure which will facilitate

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acgt open grid services for improving medical knowledge discovery

ACGT:Open Grid Services for Improving Medical Knowledge Discovery

Stelios G. Sfakianakis, FORTH

the acgt vision principles
The ACGT vision & principles
  • The ultimate objective of the ACGT project is the provision of a unified technological infrastructure which will facilitate
    • integrated access to multi-level biomedical data
    • development or re-use of open source analytical tools, accompanied with the appropriate meta-data allowing their discovery and orchestration into complex workflows.
  • ACGT will deliver a European Biomedical GRID infrastructure offering seamless mediation services for sharing data and data-processing methods and tools, and advanced security;
  • ACGT
    • focuses on clinical trials on Cancer (Wilms tumor, Breast) and
    • is based on the principles of
      • Open access (among trusted partners)
      • Open source
    • is not a standards generating exercise but a standards adopting one.
enabling dynamic virtual organizations

User Applications

and services layer in support of

Clinical Trials

U

U

The ACGT Integration Layer, the ACGT Tools and Services

Simulation and Visualization Tools

U

D

U

D

Knowledge

Discovery Tools

D

U

D

U

D

Ontologies and

mediation tools

D

D

D

D

D

Basic GRID

technology and security

D

User Data

and Public Databases Layer

Distributed multilevel

Biomedical Data

Enabling dynamic Virtual Organizations
the acgt virtual organizations

Analytical

Services

Tool 1

Clinical data

Tool 2

Research

Center

Grid Data Service

Protein Database

Grid Data Service

Public data

& tools

Image

Microarray

Grid Data Service

Analytical Services

Research

Center

Tool 2

Grid Data

Service

Grid Portal

Tool 3

Tool n

The ACGT Virtual Organizations

Grid-Enabled

Client

Gene

Database

Research

Center

VirtualOrganizations

Grid Services Infrastructure

(VO Manag., Metadata, Registry,

Publishing, Query,

Invocation, Security, etc.)

Tool 3

Grid Data

Services

Tool 4

Analytical Services

discovery and orchestration of services
Discovery and Orchestrationof Services

2D/3D visualization for in silico models

DM/KDD and visualization services

Data access Services

Analytical Services

ACGT experiment topology

Microarray data processing for molecular classification

of disease

the acgt clinical trials

UoO

Nephroblastoma

Multi-centric

Oncogenomic Study

JBI

2

UoS

In Silico

Oncology Study

3

IEO

Prolipsis

FORTH

UoC

Breast Ca

Multicentric

Oncogenomic Study

1

The ACGT clinical trials
  • Multicentric TOP trial – Breast Cancer
  • SIOP 2002 – paediatric nephroblastoma
  • In Silico modeling and simulation of tumor growth & response to treatment
main challenges in acgt
Main challenges in ACGT
  • Grid middleware services, enabling large-scale (semantic, structural, and syntactic) interoperation among biomedical resources and services;
  • Master ontology (on Cancer) through semantic modelling of biomedical concepts using existing ontologies and ontologies developed for the needs of the project;
  • Open source bioinformatic tools and other analytical services;
  • Semantic annotation and advertisement of biomedical resources, to allow metadata-based discovery and query of tools, and services;
  • Orchestration of data access and analytical services into complex eScience workflows for post genomic clinical research and trials on cancer;
  • Meta-data descriptions of clinical trials to provide adequate provenance information for future re-use, comparison, and integration of results;
major challenge semantic interoperability
Major Challenge: Semantic Interoperability
  • The bottleneck is not so much about:
    • computational needs,
    • the volume of data, or
    • performance issues in accessing/transferring data;
  • It’s integration and semantic interoperability;
data integration impediments
Data Integration Impediments
  • Heterogeneity
    • Syntactic: Relational (SQL) Databases, web accessible databases, …
    • Structural: Different schemas and formats
    • Semantic: Different vocabularies and semantics
  • Security related:
    • Different access policies: some data sources require authentication, whereas others are public
    • Sensitive and confidential data: patient names or other identifying traits should be hidden (anonymization, pseudonymization)
required services
Required Services
  • The primary services required for supporting the identified scenarios fall into four categories:
    • services for access and retrieval of data , that is: internal phenotypical (clinical and imaging) DBs and other “-omic” DBs, as well as external biomedical databases;
    • services that are the analytical and visualizationtools, that is: computational analysis, simulations, knowledge extraction, exposed as Grid (web) services;
    • services for forming and executing eScience Workflows, that is:
      • workflow management services,
      • information management services, and
      • distributed database query processing;
    • semantic services for discovering services and workflows, and managing metadata, such as:
      • ontologies
      • metadata
      • provenance
the acgt consortium

Uni Lund

Uni Oxford

Uni

Hamburg

, Uni

Hosp

Saarland, IFOMIS

Fraunhofer (IBMT,

AiS

), Uni

Hannover

PSNC

Poznan

Uni Amsterdam, Philips

J. Bordet

Institute

,

Custodix

, Uni Namur

INRIA,

HealthGrid

, ERCIM

SIB Lausanne

SIVECO

Uni Madrid, Uni Malaga

FORTH, Uni

Hosp

Crete

,

ICCS

-

NTU

Athens

,

Biovista

Uni Hokkaido

The ACGT Consortium

Funding: ~18 MEuro, Time plan: 1/2/2006 – 31/1/2010