Title: An modular approach to fMRI metadata in a Virtual Laboratory - generic tools for specific problems
1An 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
2Outline
- 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
3Vision 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.
4What 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)
5Common 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.
6The Semantic Gap
Resources
Middleware
Application
User
7The Model in the middle
My Model
Model
Model
Resources
Middleware
Application
User
8RDF a web format for knowledge
- RDF is a W3C language to express
- statements.
- RDF Triple
- Subject Predicate Object
- Graph of Knowledge
- Node Edge Node
9Adaptive Information Disclosure
(AID)participating in the VL-e project
10The AIDA toolbox for knowledge extraction and
knowledge management in a Virtual Laboratory for
e-Science
11Example scenario of Taverna application
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13Components of the AIDA toolbox used for Life
Science knowledge extraction
14BioAID Disease Discovery workflow
AIDA
AIDA
Taverna shim
AIDA
OMIM service (Japan)
Taverna shim
15BioAID Disease Discovery results
16Enriched ontology (snapshot)
17Example scenario on Web platform
Looking at custom terminologies, ontologies for
search in personalized index http//aida.science.u
va.nl9999/search/
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19VBrowser 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
20VBrowser Resource Overview
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22MRI more than structural information
anatomical
perfusion MRI
functional MRI
23Functional 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.
24fMRI
25fMRI Paradigms in clinical fMRI
- Motor area
- Language regions (Broca, Wernicke)
- Visual cortex
26fMRI in ClinicalPreparation of Neurosurgery
27Neurosurgery Planning
28Functional MRI Analysis
Stimulus System
Brain activation maps
29fMRI 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.
30Metadata for fMRI data search
31A quick peek at the VBrowser
- A look at fMRI parameters (browsing RDF), RDF
queries, SRB access - http//staff.science.uva.nl/ptdeboer/vlet/
32Acknowledgements
- 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)