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with AIDA

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Martijn Schuemie, Erasmus University Rotterdam ... Sugawara, Center for Information Biology and DNA Data Bank of Japan, National ... – PowerPoint PPT presentation

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Title: with AIDA


1
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

2
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
3
Virtual Laboratory e-Science project
4
Wet laboratory analogy
5
Virtual laboratory elements
  • Taverna, VLAM,
  • AIDA toolbox
  • E-bioscience lab
  • BioMoby
  • Semantic Web
  • PubMed
  • WikiProfessional
  • OpenWetware.org
  • myExperiment.org
  • My(OWL)Model.org?

6
Main elements for experimentationBioinformatician
s point of view
Computational experiment
Processing
Biological knowledge
7
Virtual laboratory main elementsBioinformaticians
point of view
Computational experiment
Workflow technology
Semantic web technology

8
Biological motivation Structure and function of
chromatin
Escherichia coli
9
components...
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BioAID
9
10
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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BioAID
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11
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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BioAID
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12
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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BioAID
12
13
The AIDA toolbox for knowledge extraction and
knowledge management in a Virtual Laboratory for
e-Science
14
Components of the AIDA toolbox used for Life
Science knowledge extraction
15
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BioAID
15
16
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BioAID
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17
BioAID watskeburt workflow
AIDA
AIDA
Taverna shim
AIDA
OMIM service (Japan)
Taverna shim
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BioAID
17
18
BioAID watskeburt running
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BioAID
18
19
BioAID watskeburt results
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BioAID
19
20
Proto-ontology (Protégé Jambalaya plugin)
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BioAID
20
21
Enriched ontology (snapshot)
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BioAID
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22
Generality of AIDA
  • AIDA for food science

23
For my research on crispiness of food products I
need pictures of bread structure
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BioAID
23
24
Components of the AIDA toolbox used for Food
Informatics
25
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BioAID
25
RMSgt
26
Food Resource Management Systemusing AIDA
services
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BioAID
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27
Food Resource Management Systemusing AIDA
services
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BioAID
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28
Generality of AIDA
  • Prototyping with Taverna

29
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BioAID
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Taverna RMSgt
30
FoodAID thesaurus workflow
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BioAID
30
31
FoodAID thesaurus workflow
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BioAID
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32
Generality of AIDA
  • Semantic workflow

33
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BioAID
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34
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35
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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36
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

37
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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