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myExperiment and AIDA

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One of my favorites given by Marco, who also gave a similar talk in Oxford Zoology in 2008.

One of my favorites given by Marco, who also gave a similar talk in Oxford Zoology in 2008.

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  • We will demonstrate a biological application of the ‘Adaptive Information Disclosure Application’ toolbox, a toolbox that is of general purpose, but can be used for specific applications, such as life science.
  • Transcript

    • 1. with AIDA Biological knowledge extraction for a Virtual Laboratory for e-Science ( Bio AID ) Marco Roos , Scott Marshall, Sophia Katrenko, Edgar Meij, Willem van Hage, Pieter Adriaans AIDA demonstration Uk-AHM, Nottingham, September 10, 2007
    • 2.
      • Outline
      • Context
        • Virtual Laboratory for e-Science
        • (my) life science motivation
      • Demonstration of AIDA toolbox applications
        • Bioinformatics
        • Food informatics
      • Discussion, questions…
      AIDA demonstration Uk-AHM, Nottingham, September 10, 2007 Bio AID Biological knowledge extraction for a Virtual Laboratory for e-Science
    • 3. Virtual Laboratory e-Science project
    • 4. Wet laboratory analogy Data Data handling & Data integration Metadata Data analysis Data storage Expert knowledge
    • 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 experimentation Bioinformaticians point of view Computational experiment Processing Biological knowledge
    • 7. Virtual laboratory main elements Bioinformaticians point of view Computational experiment Workflow technology Semantic web technology +
    • 8. Biological motivation: Structure and function of chromatin Escherichia coli Mouse fibroblast (skin) cells
    • 9. components... 08/06/09 BioAID
    • 10. Biomedical knowledge repository 08/06/09 BioAID PubMed statistics http://www.ncbi.nlm.nih.gov/entrez >17 million citations >400,000 added/year ~70,000 searches/month … Does not compute Does not fit
    • 11. Text mining 08/06/09 BioAID Biology Customized or personalized experiment Extracted knowledge I want to do it my way, use my models Carole Goble’s me -scientist
    • 12. Bioinformatics and e-science 08/06/09 BioAID Single purpose, black box application Customized experiments with reusable components My component Your component My component Your component My component
    • 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. 08/06/09 BioAID
    • 16. 08/06/09 BioAID
    • 17. Bio AID ‘watskeburt’ workflow 08/06/09 BioAID AIDA AIDA OMIM service (Japan) AIDA ‘ Taverna shim’ Taverna ‘shim’
    • 18. Bio AID ‘watskeburt’ running 08/06/09 BioAID
    • 19. Bio AID ‘watskeburt’ results 08/06/09 BioAID
    • 20. Proto-ontology (Protégé Jambalaya plugin) 08/06/09 BioAID
    • 21. Enriched ontology (snapshot) 08/06/09 BioAID
    • 22. Generality of AIDA
      • AIDA for food science
    • 23. 08/06/09 BioAID For my research on crispiness of food products I need pictures of bread structure
    • 24. Components of the AIDA toolbox used for Food Informatics
    • 25. 08/06/09 BioAID RMS>
    • 26. Food Resource Management System using AIDA services 08/06/09 BioAID
    • 27. Food Resource Management System using AIDA services 08/06/09 BioAID
    • 28. Generality of AIDA
      • Prototyping with Taverna
    • 29. 08/06/09 BioAID Taverna RMS>
    • 30. Food AID thesaurus workflow 08/06/09 BioAID
    • 31. Food AID thesaurus workflow 08/06/09 BioAID
    • 32. Generality of AIDA
      • Semantic workflow
    • 33. 08/06/09 BioAID
    • 34. 08/06/09 BioAID
    • 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
      08/06/09 BioAID
    • 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)
      08/06/09 BioAID
    • 38. 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
      08/06/09 BioAID
    • 39. End of presentation...
      • Thank you
      • http://adaptivedisclosure.org
      08/06/09 BioAID