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Presentation in support of AIDA demonstration at the ISMB/ECCB conference in Vienna, 2007. We demonstrated the application of AIDA web services for mining associations of proteins and diseases with an ...

Presentation in support of AIDA demonstration at the ISMB/ECCB conference in Vienna, 2007. We demonstrated the application of AIDA web services for mining associations of proteins and diseases with an input query through a text mining workflow implemented as a workflow in Taverna. The AIDA toolkit combines services for information retrieval, information extraction, and Semantic Web modelling and storage. The services are created by experts in different fields collaborating under the name of 'Adaptive Information Disclosure' in the VL-e project (http://www.vl-e.nl).

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  • E-science presentation Manchester September 25 2006 06/10/09 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.

Demo Presentation ISMB/ECCB 2007 Presentation Transcript

  • 1. Bio AID Knowledge extraction for a Virtual Laboratory for e -Science Marco Roos , Scott Marshall , Sophia Katrenko, Edgar Meij, Willem van Hage, Pieter Adriaans ISMB/ECCB2007 – AIDA demonstration 10/06/09 BioAID AIDA = Adaptive Information Disclosure Application
  • 2. components... 10/06/09 BioAID
  • 3. Biomedical knowledge repository 10/06/09 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
  • 4. Text mining 10/06/09 BioAID Biology Customized or personalized experiment Extracted knowledge I want to do it my way, use my models Carole Goble’s me-scientist
  • 5. Bioinformatics and e-science 10/06/09 BioAID Single purpose, black box application Customized experiments with reusable components My component Your component My component Your component My component
  • 6. The AIDA toolbox for knowledge extraction and knowledge management in a Virtual Laboratory for e-Science
  • 7. 10/06/09 BioAID
  • 8. Components of the AIDA toolbox used for Life Science knowledge extraction
  • 9. 10/06/09 BioAID
  • 10. Bio AID ‘watskeburt’ workflow 10/06/09 BioAID AIDA AIDA OMIM service (Japan) AIDA ‘ Taverna shim’ Taverna ‘shim’
  • 11. Bio AID ‘watskeburt’ running 10/06/09 BioAID
  • 12. Bio AID ‘watskeburt’ results 10/06/09 BioAID
  • 13. Proto-ontology (Protégé Jambalaya plugin) 10/06/09 BioAID
  • 14. Enriched ontology (snapshot) 10/06/09 BioAID
  • 15. Components of the AIDA toolbox used for Food Informatics
  • 16. 10/06/09 BioAID
  • 17. Food AID thesaurus workflow 10/06/09 BioAID
  • 18. Food AID thesaurus workflow 10/06/09 BioAID
  • 19. 10/06/09 BioAID For my research on crispiness of food products I need pictures of bread structure RMS
  • 20. 10/06/09 BioAID
  • 21. Food Resource Management System using AIDA services 10/06/09 BioAID
  • 22. Food Resource Management System using AIDA services 10/06/09 BioAID
  • 23. 10/06/09 BioAID
  • 24. 10/06/09 BioAID
  • 25. 10/06/09 BioAID
  • 26. 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 (EZH2++)
    • The use of web services and semantic web:
      • Application by non-text miners
      • Collaboration, information sharing
    10/06/09 BioAID
  • 27. Acknowledgements
    • AIDA developers team: Sophia Katrenko, Edgar Meij, Willem van Hage, Frans Verster,
    • 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
    • http:// adaptivedisclosure.org
    • Work supported by VL-e and BioRange projects (BSIK grants)
    10/06/09 BioAID
  • 28. 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/
    10/06/09 BioAID Workflows available from myExperiment.org going online August 2007
  • 29. On line demo movies
    • Demo movies online (hyperlinks)
    • EZH2 demo (101Mb) [flash version]
    • EZH2 highlights ( 81Mb) [flash version]
    10/06/09 BioAID
  • 30. End of presentation... 10/06/09 BioAID