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

Oct 12, 2023 •254 likes •406 views

ACGT: Open Grid Services for Improving Medical Knowledge Discovery Yannick Legr, CNRS-IN2P3 President of the HealthGrid association on behalf of the ACGT consortium Credit slides: M. Tsiknakis, FORTH The ACGT vision & principles The

  1. ACGT: Open Grid Services for Improving Medical Knowledge Discovery Yannick Legré, CNRS-IN2P3 President of the HealthGrid association on behalf of the ACGT consortium Credit slides: M. Tsiknakis, FORTH

  2. 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. I SGC 2 0 0 6 – Taipei – May 1 st – 4 th, 2 0 0 6

  3. Enabling dynamic Virtual Organizations User Applications Clinical Trials … and services layer in support of ACGT Tools and Services The ACGT Integration Layer, the U U Simulation and U D Visualization Tools U D Knowledge D Discovery Tools U D U D Ontologies and mediation tools D D D D D Basic GRID D technology and security User Data Distributed multilevel and Public Biomedical Data Databases Layer I SGC 2 0 0 6 – Taipei – May 1 st – 4 th, 2 0 0 6

  4. The ACGT Virtual Organizations Analytical Tool 1 Grid-Enabled Services Gene Client Database Tool 2 Clinical data Research Research Center Center V irtual O O rganizations V Protein Grid Data Service Database Grid Services Infrastructure Tool 3 Grid Data (VO Manag., Metadata, Registry, Services Publishing, Query, Tool 4 Invocation, Security, etc.) Analytical Services Grid Data Service Grid Portal Image Public data Microarray & tools Grid Data Service Analytical Services Research Grid Data Center Service Tool 2 Tool n Tool 3 I SGC 2 0 0 6 – Taipei – May 1 st – 4 th, 2 0 0 6

  5. Discovery and Orchestration of S ervices 2D/3D visualization for in silico models DM/KDD and visualization Data access services Services Analytical Services ACGT experiment topology Microarray data processing for molecular classification of disease I SGC 2 0 0 6 – Taipei – May 1 st – 4 th, 2 0 0 6

  6. 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 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; I SGC 2 0 0 6 – Taipei – May 1 st – 4 th, 2 0 0 6

  7. The ACGT clinical trials Multicentric TOP trial – Breast Cancer S IOP 2002 – paediatric UoO Nephroblastoma JBI 2 nephroblastoma Multi-centric Oncogenomic Study UoS In Silico 3 IEO Oncology Study In S ilico modeling and simulation of tumor Prolipsis growth & response to FORTH UoC treatment Breast Ca 1 Multicentric Oncogenomic Study I SGC 2 0 0 6 – Taipei – May 1 st – 4 th, 2 0 0 6

  8. In silico modeling and simulation SYNOPTIC BLOCK DIAGRAM OF THE ONCOSIMULATOR S eeks to extract THERAPY DECISION information related to NO tumor growth & YES FURTHER SCHEME? response to treatment PREDICTION EVALUATION Requires PREDICTION access to multi-level clinico-genomic data. TUMOR & NORMAL CANDIDATE IMAGING DATA TISSUE RESPONSE THERAPEUTIC SIMULATION SCHEME implementation of a RADIOBIOLOGICAL PHARMACODYNAMIC variety of processing PARAMETERS tools and GENE/PROTEIN NETWORK specification of GENE EXPRESSION DATA GENOTYPING complex analytical (MICROARRAYS) workflows BIOPSY BLOOD MATERIAL SAMPLE I SGC 2 0 0 6 – Taipei – May 1 st – 4 th, 2 0 0 6

  9. The ACGT master ontology Priority: Ontology of entities involved in two carcinomas OMIM medDRA Nephroblastoma and Breast Swissprot-Uniprot NCIT Carcinoma Reactome FMA GO ICD 10 Terms from different terminologies & ontologies are integrated together Diseases Disease - Gene Hierarchy and Relations of Anatomy terminologies & ontologies NOT Protein incorporated (except FMA) Textbook Annotation Information S ources used as a dictionary Drug Pathways Bio-processes Databases Cell Anatomy Deficiencies present in each Molecular Function source in classification and relations: improved I SGC 2 0 0 6 – Taipei – May 1 st – 4 th, 2 0 0 6

  10. End user tools An integrated visual environment An integrated visual environment Clinical Trial Templates – Augmented by the ACGT Master Ontology ACGT Master Ontology – Graphical representation of data elements and processing steps in a clinical trial COMMENTATOR (LINK) COMMENTATOR (LINK) isMadeBy (LINK) isMadeBy (LINK) EXPERIMENT COMMENT (LINK) Data mining and analytical tools (COPY) COMMENT PROPERTY (COPY) (COPY) hasNextExperiment (NOREUSE) hasComments (COPY) hasComments hasProperties hasPrevExperiment (COPY) (COPY) (NOREUSE) hasSteps hasNextStep isPartOfProject (NOREUSE) (NOREUSE) – A variety of tools and applications (NOREUSE) ARRAY PROJECT EXPERIMENT MEASUREMENT DATA ANALYSIS (LINK) (COPY) (COPY) (COPY) hasExperiments isPartOfExperiment hasPrevStep (NOREUSE) (NOREUSE) (NOREUSE) hasOwner LINK isPerformedBy hasPerformed ownsExperiments (LINK) (NOREUSE) hasContributors (NOREUSE) (LINK) contributedExperiments (NOREUSE) OWNER OWNER (LINK) (LINK) CONTRIBUTOR (LINK) Clinical trial workflows – Graphical representation of workflows – Processing modules attached to each other in a workflow I SGC 2 0 0 6 – Taipei – May 1 st – 4 th, 2 0 0 6

  11. Tools for clinical trials life cycle management Research Administrative and Development Regulatory Management CT Enrollment Research Clinical Research Trial Setup Development & Patient care Management Patient New Idea Financial Management Enrollment Generation Study Parameters Patient Data Development Treatment Analysis Data mining and De- Financial Reporting & Data mining Identification & Billing Administration & Analysis Patient Enrollment CT Reporting & Administration I SGC 2 0 0 6 – Taipei – May 1 st – 4 th, 2 0 0 6

  12. 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 I SGC 2 0 0 6 – Taipei – May 1 st – 4 th, 2 0 0 6

  13. 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 Funding: ~18 MEuro, Time plan: 1/2/2006 – 31/1/2010 I SGC 2 0 0 6 – Taipei – May 1 st – 4 th, 2 0 0 6

  14. Thank you for your attention! 4 th HealthGrid conference 6th – 9th June Valencia (S pain) http:/ / valencia2006.healthgrid.org I SGC 2 0 0 6 – Taipei – May 1 st – 4 th, 2 0 0 6

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