1. The Semantic Web and BioMarkers Benjamin Good Wilkinson Laboratory iCAPTURE http://bioinfo.icapture.ubc.ca/bgood

2. Outline Define Semantic Web Discuss Applications in Progress –Ahab –iCAPTURer Discuss needs from BBM team

3. The Semantic Web “The Semantic Web is not a separate Web but an extension of the current one, in which information is given well-defined meaning, better enabling computers and people to work in cooperation.” Tim Berners-Lee

4. Meaning Through Ontology Animal Mammal Primate LemurHumanGorilla Hair BigMediumSmall has has_size is_a Hair

5. Meaning Through Ontology Web Services Bioinformatics programs Sequence Processing Sequence Alignment http://bioinfo.icapture.ubc.ca/bla123.cgi DNA-ProteinDNA-DNA BLAST-X

6. Meaning Through Ontology BiologicalProcess Response to stimulus Defense response Immune response Interleukin-10 Cellular component Membrane Plasma membrane

7. On a Semantic Web It is easier to find things. It is easier to identify similarity. It is easier to integrate information. UCSC FlyBase Genbank Gene Ontology

8. Gene Ontology (http://geneontology.org) (SW!) Applications listed –6 adding annotations –9 miscellaneous –14 searching and browsing –36 for microarray analysis! Mostly for “summarizing the predominant biological theme of a given gene list”. Validation Hypothesis generation

9. GO analysis

10. My Current Projects Ahab - A Semantic Web Browser iCAPTURer - an experimental system for collective ontology creation.

11. Ahab

13. Ahab RDF

14. iCAPTURer Ontology generation Is hard and takes a lot of time

15. iCAPTURer Divide and Conquer

16. iCAPTURer A website that asks volunteers the questions needed to build an ontology. Deployed with some success at the Young Investigators Forum for Research in Circulatory and Respiratory Health

17. My Needs More interaction with the scientists. –Motivate, clarify, and ultimately enable my research. Participation from team members in future knowledge capture experiments. If possible, data and algorithms provided as BioMoby web services…

18. Thanks http://bioinfo.icapture.ubc.ca/bgood Slides available here under presentations. Wilkinson Laboratory –Mark –Clarence –Nina –Eddie BBM team –Martha –Janet –…