with  AIDA   Biological knowledge extraction for a Virtual Laboratory for e-Science ( Bio AID ) Marco Roos , Scott Marsh...
<ul><li>Outline </li></ul><ul><li>Context </li></ul><ul><ul><li>Virtual Laboratory for e-Science </li></ul></ul><ul><ul><l...
Virtual Laboratory e-Science project
Wet laboratory analogy Data Data handling & Data integration Metadata Data analysis Data storage Expert knowledge
Virtual  laboratory elements <ul><li>Taverna, VLAM, … </li></ul><ul><li>AIDA toolbox </li></ul><ul><li>E-bioscience lab </...
Main elements for experimentation Bioinformaticians point of view Computational experiment Processing Biological knowledge
Virtual laboratory main elements Bioinformaticians point of view Computational experiment Workflow technology Semantic web...
Biological motivation:  Structure and function of chromatin Escherichia coli Mouse fibroblast (skin) cells
components... 08/06/09 BioAID
Biomedical knowledge repository 08/06/09 BioAID PubMed statistics http://www.ncbi.nlm.nih.gov/entrez >17 million citations...
Text mining 08/06/09 BioAID Biology Customized  or  personalized experiment Extracted knowledge I want to do it  my  way, ...
Bioinformatics and e-science 08/06/09 BioAID Single purpose, black box application Customized experiments with reusable co...
The  AIDA  toolbox  for knowledge extraction and knowledge management  in a Virtual Laboratory for e-Science
Components of the  AIDA  toolbox  used for Life Science knowledge extraction
08/06/09 BioAID
08/06/09 BioAID
Bio AID ‘watskeburt’ workflow 08/06/09 BioAID AIDA AIDA OMIM service  (Japan) AIDA ‘ Taverna shim’ Taverna ‘shim’
Bio AID ‘watskeburt’ running 08/06/09 BioAID
Bio AID ‘watskeburt’ results 08/06/09 BioAID
Proto-ontology  (Protégé Jambalaya plugin) 08/06/09 BioAID
Enriched ontology  (snapshot) 08/06/09 BioAID
Generality of AIDA <ul><li>AIDA for food science </li></ul>
08/06/09 BioAID For my research on crispiness of food products I need pictures of bread structure
Components of the  AIDA  toolbox  used for Food Informatics
08/06/09 BioAID RMS>
Food Resource Management System using AIDA services 08/06/09 BioAID
Food Resource Management System using AIDA services 08/06/09 BioAID
Generality of AIDA <ul><li>Prototyping with Taverna </li></ul>
08/06/09 BioAID Taverna RMS>
Food AID thesaurus workflow 08/06/09 BioAID
Food AID thesaurus workflow 08/06/09 BioAID
Generality of AIDA <ul><li>Semantic workflow </li></ul>
08/06/09 BioAID
08/06/09 BioAID
Conclusions <ul><li>We have demonstrated an e-science approach to text mining: </li></ul><ul><ul><li>Application to knowle...
Future ambitions <ul><li>Extend current workflows </li></ul><ul><ul><li>Biology: extend biological ‘cartoon’ models </li><...
Acknowledgements <ul><li>AIDA developers team: Sophia Katrenko, Edgar Meij, Willem van Hage, Frans Verster, (Machiel Janse...
Further information and resources <ul><li>AID information and resources </li></ul><ul><li>http:// adaptivedisclosure.org <...
End of presentation... <ul><li>Thank you </li></ul><ul><li>http://adaptivedisclosure.org </li></ul>08/06/09 BioAID
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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.

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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.
  • myExperiment and AIDA

    1. 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. 2. <ul><li>Outline </li></ul><ul><li>Context </li></ul><ul><ul><li>Virtual Laboratory for e-Science </li></ul></ul><ul><ul><li>(my) life science motivation </li></ul></ul><ul><li>Demonstration of AIDA toolbox applications </li></ul><ul><ul><li>Bioinformatics </li></ul></ul><ul><ul><li>Food informatics </li></ul></ul><ul><li>Discussion, questions… </li></ul>AIDA demonstration Uk-AHM, Nottingham, September 10, 2007 Bio AID Biological knowledge extraction for a Virtual Laboratory for e-Science
    3. 3. Virtual Laboratory e-Science project
    4. 4. Wet laboratory analogy Data Data handling & Data integration Metadata Data analysis Data storage Expert knowledge
    5. 5. Virtual laboratory elements <ul><li>Taverna, VLAM, … </li></ul><ul><li>AIDA toolbox </li></ul><ul><li>E-bioscience lab </li></ul><ul><li>BioMoby </li></ul><ul><li>Semantic Web </li></ul><ul><li>PubMed </li></ul><ul><li>WikiProfessional </li></ul><ul><li>OpenWetware.org </li></ul><ul><li>myExperiment.org </li></ul><ul><li>My (OWL) Model.org? </li></ul>
    6. 6. Main elements for experimentation Bioinformaticians point of view Computational experiment Processing Biological knowledge
    7. 7. Virtual laboratory main elements Bioinformaticians point of view Computational experiment Workflow technology Semantic web technology +
    8. 8. Biological motivation: Structure and function of chromatin Escherichia coli Mouse fibroblast (skin) cells
    9. 9. components... 08/06/09 BioAID
    10. 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. 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. 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. 13. The AIDA toolbox for knowledge extraction and knowledge management in a Virtual Laboratory for e-Science
    14. 14. Components of the AIDA toolbox used for Life Science knowledge extraction
    15. 15. 08/06/09 BioAID
    16. 16. 08/06/09 BioAID
    17. 17. Bio AID ‘watskeburt’ workflow 08/06/09 BioAID AIDA AIDA OMIM service (Japan) AIDA ‘ Taverna shim’ Taverna ‘shim’
    18. 18. Bio AID ‘watskeburt’ running 08/06/09 BioAID
    19. 19. Bio AID ‘watskeburt’ results 08/06/09 BioAID
    20. 20. Proto-ontology (Protégé Jambalaya plugin) 08/06/09 BioAID
    21. 21. Enriched ontology (snapshot) 08/06/09 BioAID
    22. 22. Generality of AIDA <ul><li>AIDA for food science </li></ul>
    23. 23. 08/06/09 BioAID For my research on crispiness of food products I need pictures of bread structure
    24. 24. Components of the AIDA toolbox used for Food Informatics
    25. 25. 08/06/09 BioAID RMS>
    26. 26. Food Resource Management System using AIDA services 08/06/09 BioAID
    27. 27. Food Resource Management System using AIDA services 08/06/09 BioAID
    28. 28. Generality of AIDA <ul><li>Prototyping with Taverna </li></ul>
    29. 29. 08/06/09 BioAID Taverna RMS>
    30. 30. Food AID thesaurus workflow 08/06/09 BioAID
    31. 31. Food AID thesaurus workflow 08/06/09 BioAID
    32. 32. Generality of AIDA <ul><li>Semantic workflow </li></ul>
    33. 33. 08/06/09 BioAID
    34. 34. 08/06/09 BioAID
    35. 35. Conclusions <ul><li>We have demonstrated an e-science approach to text mining: </li></ul><ul><ul><li>Application to knowledge extraction (EZH2) </li></ul></ul><ul><ul><li>Application to rapid prototyping and synonym support (Food Informatics) </li></ul></ul><ul><ul><li>Application that logs the trail to evidence via semantic models (EZH2++) </li></ul></ul><ul><li>The use of web services and semantic web: </li></ul><ul><ul><li>Application by non-text miners </li></ul></ul><ul><ul><li>Collaboration, information sharing, modelling </li></ul></ul>08/06/09 BioAID
    36. 36. Future ambitions <ul><li>Extend current workflows </li></ul><ul><ul><li>Biology: extend biological ‘cartoon’ models </li></ul></ul><ul><ul><li>Experiment with upper ontologies </li></ul></ul><ul><ul><li>Semantic results part of myExperiment? </li></ul></ul><ul><li>Link to VL-e work on semantic workflow and semantic data integration </li></ul><ul><li>Try latest AIDA services (e.g relation discovery, concept-learning) </li></ul><ul><li>Help myExperiment.org to reach out to not yet ‘enhanced’ scientists </li></ul>
    37. 37. Acknowledgements <ul><li>AIDA developers team: Sophia Katrenko, Edgar Meij, Willem van Hage, Frans Verster, (Machiel Jansen), Scott Marshall. </li></ul><ul><li>Guus Schreiber, Maarten de Rijke, Pieter Adriaans </li></ul><ul><li>Jan Top, Nicole Koenderink, Food informatics, Wageningen University </li></ul><ul><li>Martijn Schuemie, Erasmus University Rotterdam </li></ul><ul><li>myGrid team, especially Katy Wolstencroft, Stian Soiland, Stuart Owen, Andy Gibson, Alan Rector, Robert Stevens, Carole Goble </li></ul><ul><li>W3C Semantic Web Health Care and Life Sciences Interest Group </li></ul><ul><li>Hideaki Sugawara, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics (http://xml.nig.ac.jp) </li></ul><ul><li>This work was supported by the Dutch Ministry of Economic Affairs via VL-e and BioRange (BSIK grants) </li></ul>08/06/09 BioAID
    38. 38. Further information and resources <ul><li>AID information and resources </li></ul><ul><li>http:// adaptivedisclosure.org </li></ul><ul><li>W3C Semantic Web Health Care and </li></ul><ul><li>Life Sciences Interest Group </li></ul><ul><li>http://www.w3.org/2001/sw/hcls/ </li></ul><ul><li>Workflows available from </li></ul><ul><li>http:// .org </li></ul>08/06/09 BioAID
    39. 39. End of presentation... <ul><li>Thank you </li></ul><ul><li>http://adaptivedisclosure.org </li></ul>08/06/09 BioAID

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