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

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

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.

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)

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.

The Semantic Gap User ResourcesMiddlewareApplication

The Model in the middle User ResourcesMiddlewareApplication My Model Model

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

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

Example scenario of Taverna application myModel myExtended Model

05/12/2015BioAID12

Components of the AIDA toolbox used for Life Science knowledge extraction

05/12/2015BioAID14 BioAID Disease Discovery workflow AIDA OMIM service (Japan) AIDA ‘Taverna shim’ Taverna ‘shim’

05/12/2015BioAID15 BioAID Disease Discovery results

05/12/2015BioAID16 Enriched ontology (snapshot)

Example scenario on Web platform Looking at custom terminologies, ontologies for search in personalized index

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

VBrowser: Resource Overview Location Bar Grid Resources Grid FTPReliable File Transfer SRB (SARA) Local Resources

MRI: more than structural information perfusion MRI functional MRI anatomical

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.

fMRI

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

fMRI in Clinical: Preparation of Neurosurgery

Neurosurgery Planning

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

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.

Metadata for fMRI data search

A quick peek at the VBrowser A look at fMRI parameters (browsing RDF), RDF queries, SRB access:

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 Work supported by VL-e and BioRange projects (BSIK grants)