with AIDA

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AIDA demonstrationUk-AHM, Nottingham, September
10, 2007

• with AIDA
• Biological knowledge extractionfor a Virtual
  Laboratory for e-Science (BioAID)
• Marco Roos, Scott Marshall, Sophia Katrenko,
  Edgar Meij, Willem van Hage, Pieter Adriaans

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AIDA demonstrationUk-AHM, Nottingham, September
10, 2007

• Outline
• Context
• Virtual Laboratory for e-Science
• (my) life science motivation
• Demonstration of AIDA toolbox applications
• Bioinformatics
• Food informatics
• Discussion, questions

BioAID Biological knowledge extraction for a
Virtual Laboratory for e-Science
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Virtual Laboratory e-Science project
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Wet laboratory analogy
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Virtual laboratory elements

• Taverna, VLAM,
• AIDA toolbox
• E-bioscience lab
• BioMoby
• Semantic Web

• PubMed
• WikiProfessional
• OpenWetware.org
• myExperiment.org
• My(OWL)Model.org?

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Main elements for experimentationBioinformatician
s point of view
Computational experiment
Processing
Biological knowledge
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Virtual laboratory main elementsBioinformaticians
point of view
Computational experiment
Workflow technology
Semantic web technology

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Biological motivation Structure and function of
chromatin
Escherichia coli
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components...
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Biomedical knowledge repository
PubMed statistics http//www.ncbi.nlm.nih.gov/entr
ez gt17 million citations gt400,000
added/year 70,000 searches/month

Does not compute
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Text mining
I want to do it my way, use my models
Carole Gobles me-scientist
Biology
Customized or personalizedexperiment
Extracted knowledge
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Bioinformatics and e-science
Customized experiments with reusable components
Single purpose,black box application
My component
Your component
My component
My component
Your component
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The AIDA toolbox for knowledge extraction and
knowledge management in a Virtual Laboratory for
e-Science
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Components of the AIDA toolbox used for Life
Science knowledge extraction
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BioAID watskeburt workflow
AIDA
AIDA
Taverna shim
AIDA
OMIM service (Japan)
Taverna shim
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BioAID watskeburt running
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BioAID watskeburt results
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Proto-ontology (Protégé Jambalaya plugin)
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Enriched ontology (snapshot)
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Generality of AIDA

• AIDA for food science

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For my research on crispiness of food products I
need pictures of bread structure
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Components of the AIDA toolbox used for Food
Informatics
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RMSgt
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Food Resource Management Systemusing AIDA
services
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Food Resource Management Systemusing AIDA
services
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Generality of AIDA

• Prototyping with Taverna

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Taverna RMSgt
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FoodAID thesaurus workflow
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FoodAID thesaurus workflow
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Generality of AIDA

• Semantic workflow

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Conclusions

• We have demonstrated an e-science approach to
  text mining
• Application to knowledge extraction (EZH2)
• Application to rapid prototyping and synonym
  support (Food Informatics)
• Application that logs the trail to evidence via
  semantic models (EZH2)
• The use of web services and semantic web
• Application by non-text miners
• Collaboration, information sharing, modelling

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Future ambitions

• Extend current workflows
• Biology extend biological cartoon models
• Experiment with upper ontologies
• Semantic results part of myExperiment?
• Link to VL-e work on semantic workflow and
  semantic data integration
• Try latest AIDA services (e.g relation
  discovery, concept-learning)
• Help myExperiment.org to reach out to not yet
  enhanced scientists

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Acknowledgements

• AIDA developers team Sophia Katrenko, Edgar
  Meij, Willem van Hage, Frans Verster, (Machiel
  Jansen), Scott Marshall.
• Guus Schreiber, Maarten de Rijke, Pieter Adriaans
• Jan Top, Nicole Koenderink, Food informatics,
  Wageningen University
• Martijn Schuemie, Erasmus University Rotterdam
• myGrid team, especially Katy Wolstencroft, Stian
  Soiland, Stuart Owen, Andy Gibson, Alan Rector,
  Robert Stevens, Carole Goble
• W3C Semantic Web Health Care and Life Sciences
  Interest Group
• Hideaki Sugawara, Center for Information Biology
  and DNA Data Bank of Japan, National Institute of
  Genetics (http//xml.nig.ac.jp)
• This work was supported by the Dutch Ministry of
  Economic Affairs via VL-e and BioRange (BSIK
  grants)

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Further information and resources

• AID information and resources
• http//adaptivedisclosure.org
• W3C Semantic Web Health Care and
• Life Sciences Interest Group
• http//www.w3.org/2001/sw/hcls/
• Workflows available from
• http// .org

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End of presentation...

• Thank you
• http//adaptivedisclosure.org

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