The document summarizes a presentation about AIDA, a biological knowledge extraction toolbox used in a Virtual Laboratory for e-Science. The presentation demonstrated how AIDA can be used for life science applications like extracting knowledge from literature on chromatin structure, and for food informatics applications like developing a food thesaurus. It also described components of the AIDA toolbox and examples of biological and food science workflows developed using AIDA services.

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