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M. Scott Marshall, Kasper van den Berg, Kamel Boulebiar, Piter de Boer, Marco Roos, Tristan

An modular approach to fMRI metadata in a Virtual Laboratory - generic tools for specific problems. M. Scott Marshall, Kasper van den Berg, Kamel Boulebiar, Piter de Boer, Marco Roos, Tristan Glatard, Silvia Olabarriaga Virtual Laboratory for e-science (VL-e) University of Amsterdam.

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M. Scott Marshall, Kasper van den Berg, Kamel Boulebiar, Piter de Boer, Marco Roos, Tristan

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  1. An modular approach to fMRI metadata in a Virtual Laboratory-generic tools for specific problems M. Scott Marshall, Kasper van den Berg, Kamel Boulebiar, Piter de Boer, Marco Roos, Tristan Glatard, Silvia Olabarriaga Virtual Laboratory for e-science (VL-e) University of Amsterdam

  2. Outline • Vision – an e-science virtual laboratory • Everything is a Resource - Explicit Metadata Support • Components – AIDA web services • Platforms – Taverna, Web, Vbrowser • What we did to manage fMRI data

  3. Vision: Concept-based interfaces • The scientist should be able to work in terms of commonly used concepts. • The scientist should be able to work in terms of personal concepts and hypotheses. - Not be forced to map concepts to the terms that have been chosen for a given application.

  4. What is metadata (in this talk)? • Metadata: data about data • Metadata can be syntactic such as a data type, e.g. Integer. • Metadata can be semantic such as chromosome number. • Note: not always ontology, but metadata can be stored in the Web Ontology Language (OWL)

  5. Common approaches to metadata • Code it into the GUI or application (in datastructures, object types, etc.) • Create special tables or fields for it in a relational database • Map it into substrings of filenames • Mix it in with data in proprietary file formats • Let the user figure it out • Conclusion: There is a need for semantic disclosure.

  6. The Semantic Gap Application Middleware Resources User

  7. The Model in the middle My Model Model Model Application Middleware Resources User

  8. RDF : a web format for knowledge RDF is a W3C language to express statements. RDF Triple: Subject Predicate Object Graph of Knowledge: Node Edge Node

  9. Adaptive Information Disclosure (AID)participating in the VL-e project

  10. The AIDA toolbox for knowledge extraction and knowledge management in a Virtual Laboratory for e-Science

  11. myExtendedModel myModel Example scenario of Taverna application

  12. BioAID

  13. Components of the AIDA toolbox used for Life Science knowledge extraction

  14. BioAID Disease Discovery workflow AIDA AIDA Taverna ‘shim’ AIDA OMIM service (Japan) ‘Taverna shim’ BioAID

  15. BioAID Disease Discovery results BioAID

  16. Enriched ontology (snapshot) BioAID

  17. Example scenario on Web platform Looking at custom terminologies, ontologies for search in personalized index http://aida.science.uva.nl:9999/search/

  18. VBrowser + AIDA • VBrowser provides locators, viewers, access to grid storage and transport, a resource-oriented interface • AIDA provides services for search, annotation, storage, and metadata extraction

  19. Location Bar Local Resources Grid Resources Grid FTP Reliable File Transfer SRB (SARA) VBrowser: Resource Overview

  20. MRI: more than structural information anatomical perfusion MRI functional MRI

  21. Functional MRI (fMRI): What do we do? • Goal: observe brain function during cognitive or physical activity. • Combination of stimulation and imaging. • Based on the increase in blood flow to the local vasculature that accompanies neural activity in the brain.

  22. fMRI

  23. fMRI Paradigms in clinical fMRI • Motor area • Language regions (Broca, Wernicke) • Visual cortex

  24. fMRI in Clinical:Preparation of Neurosurgery

  25. Neurosurgery Planning

  26. Group Activation Map fMRI scan MR scanner Functional MRI: Analysis Stimulus System Brain activation maps

  27. fMRI use case • Feature Extraction parameter sweeps are performed on the fMRI data on the grid. • The desire is to study the results due to different combinations of parameters. • Each parameter set serves as metadata associated with a particular result set location.

  28. Metadata for fMRI data search

  29. A quick peek at the VBrowser A look at fMRI parameters (browsing RDF), RDF queries, SRB access: http://staff.science.uva.nl/~ptdeboer/vlet/

  30. Acknowledgements • AIDA team: Marco Roos, Sophia Katrenko, Edgar Meij, Willem van Hage, Kasper van den Berg • Vbrowser: Piter de Boer • VL-e Medical Imaging: Silvia Olabarriaga, Kamel Boulebiar,Tristan Glatard • Guus Schreiber, Maarten de Rijke, Pieter Adriaans • Food Informatics partners: Wageningen University, TNO, Unilever, • Martijn Schuemie, Erasmus University Rotterdam • myGrid team, especially Katy Wolstencroft, Stian Soiland, Stuart Owen, Andrew Gibson, Alan Rector, Robert Stevens, Carole Goble • Science Commons – Alan Ruttenberg • W3C Semantic Web Health Care and Life Sciences Interest Group • http://adaptivedisclosure.org • Work supported by VL-e and BioRange projects (BSIK grants)

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