ACGT: Open Grid Services for Improving Medical Knowledge Discovery - - PowerPoint PPT Presentation

ACGT:

Open Grid Services for Improving Medical Knowledge Discovery

Credit slides: M. Tsiknakis, FORTH

Yannick Legré, CNRS-IN2P3

President of the HealthGrid association

• n behalf of the ACGT consortium

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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.

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Enabling dynamic Virtual Organizations

Ontologies and mediation tools Basic GRID technology and security

D D D U U U D D

Clinical Trials…

U User Data and Public Databases Layer

Knowledge Discovery Tools

D D

Simulation and Visualization Tools

U D D D D Distributed multilevel Biomedical Data The ACGT Integration Layer, the ACGT Tools and Services User Applications and services layer in support of U

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The ACGT Virtual Organizations

Grid Portal

V Virtual O Organizations

Grid Services Infrastructure

(VO Manag., Metadata, Registry, Publishing, Query, Invocation, Security, etc.)

Tool 1 Tool 2 Grid Data Service Analytical Services Clinical data

Research Center

Microarray Grid Data Service Image Tool 2 Tool 3

Research Center

Analytical Services Grid Data Service Grid-Enabled Client

Research Center Gene Database Protein Database

Tool 3 Tool 4 Grid Data Services Analytical Services Grid Data Service

Public data & tools

Tool n

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Discovery and Orchestration of S ervices

2D/3D visualization for in silico models

ACGT experiment topology

Microarray data processing for molecular classification

• f disease

Analytical Services Data access Services DM/KDD and visualization services

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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

• f the project;

Open source bioinformatics 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;

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The ACGT clinical trials

Multicentric TOP trial – Breast Cancer S IOP 2002 – paediatric nephroblastoma In S ilico modeling and simulation of tumor growth & response to treatment

Breast Ca Multicentric Oncogenomic Study

1

Nephroblastoma Multi-centric Oncogenomic Study

2

UoC UoO UoS JBI IEO FORTH In Silico Oncology Study

3

Prolipsis

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In silico modeling and simulation

S eeks to extract information related to tumor growth & response to treatment Requires

access to multi-level clinico-genomic data. implementation of a variety of processing tools and specification of complex analytical workflows

BIOPSY MATERIAL BLOOD SAMPLE GENE EXPRESSION DATA (MICROARRAYS) GENOTYPING GENE/PROTEIN NETWORK RADIOBIOLOGICAL PHARMACODYNAMIC PARAMETERS TUMOR & NORMAL TISSUE RESPONSE SIMULATION IMAGING DATA CANDIDATE THERAPEUTIC SCHEME PREDICTION PREDICTION EVALUATION FURTHER SCHEME? THERAPY DECISION YES NO

SYNOPTIC BLOCK DIAGRAM OF THE ONCOSIMULATOR

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The ACGT master ontology

Priority: Ontology of entities involved in two carcinomas

Nephroblastoma and Breast Carcinoma

Terms from different terminologies & ontologies are integrated together Hierarchy and Relations of terminologies & ontologies NOT incorporated (except FMA) S

• urces used as a dictionary

Deficiencies present in each source in classification and relations: improved

OMIM Swissprot-Uniprot Reactome GO medDRA NCIT FMA ICD 10

Disease - Gene

Protein Annotation

Pathways Bio-processes Cell Anatomy Molecular Function Diseases Anatomy Textbook Information Drug Databases

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End user tools

Clinical trial workflows

– Graphical representation of workflows – Processing modules attached to each other in a workflow

• wnsExperiments

Clinical Trial Templates

– Augmented by the ACGT Master Ontology ACGT Master Ontology – Graphical representation of data elements and processing steps in a clinical trial

Data mining and analytical tools

– A variety of tools and applications

An integrated visual environment An integrated visual environment

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Tools for clinical trials life cycle management

Administrative and Regulatory Management Clinical Research Management Financial Management Study Parameters Development Data mining and De- Identification Patient Enrollment

New Idea Generation Research Development Trial Setup Patient Enrollment Patient Treatment Reporting & Administration Financial & Billing Data Analysis

CT Reporting & Administration Research Development Data mining & Analysis CT Enrollment & Patient care

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Collaborations

ACGT is planning to develop strong links with other proj ects/ initiatives for collaboration – harmonization, in areas such as

Grid middleware HealthGrid Biomedical data analysis In S ilico modelling and simulation Biomedical Ontologies S OA and metadata for biomedical applications eS cience workflows Translational research on cancer

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The ACGT Consortium

Uni Lund SIVECO Uni Oxford Uni Madrid, Uni Malaga Uni Amsterdam, Philips FORTH, Uni Hosp Crete, ICCS- NTU Athens, Biovista Uni Hamburg , Uni Hosp Saarland, IFOMIS Fraunhofer (IBMT, AiS ), Uni Hannover PSNC Poznan

• J. Bordet

Institute, Custodix , Uni Namur INRIA, HealthGrid , ERCIM SIB Lausanne Uni Hokkaido

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

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Thank you for your attention!

4th HealthGrid conference

6th – 9th June Valencia (S pain) http:/ / valencia2006.healthgrid.org