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The Semantic Web and BioMarkers

The Semantic Web and BioMarkers. Benjamin Good Wilkinson Laboratory iCAPTURE http://bioinfo.icapture.ubc.ca/bgood. Outline. Define Semantic Web Discuss Applications in Progress Ahab iCAPTURer Discuss needs from BBM team. The Semantic Web.

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The Semantic Web and BioMarkers

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  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. Hair Hair Hair Hair Meaning Through Ontology Animal has Mammal Hair Primate is_a Gorilla Lemur Human has_size Big Small Medium

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

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

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

  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

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

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