Download - From Genotype to Phenotype - Future Perspectives on Data and Service Integration (Keynote)
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From Genotype to PhenotypeFuture Perspectives on Data and Service Integration
Pedro Lopes | [email protected] | PDEI - TAEI Bioinformatics | Jan 16, 2009
Friday, January 16, 2009
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Outline
• Past• Introduction
• Present• GEN2PHEN• Problems
• Future• Solutions• Ideas
• Conclusion
Friday, January 16, 2009
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The beginning Atomic Bomb over Hiroshima
Friday, January 16, 2009
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The beginning Atomic Bomb over Hiroshima
Friday, January 16, 2009
![Page 5: From Genotype to Phenotype - Future Perspectives on Data and Service Integration (Keynote)](https://reader031.vdocuments.site/reader031/viewer/2022020503/568c4c5c1a28ab49169fda25/html5/thumbnails/5.jpg)
Introduction
•Nuclear radiation causes mutations• Leveraged first studies on mutation impact in health
•Human Genome Project - HGP• First worlwide genomic project• Decode the human genome
•Human Variome Project - HVP• After HGP• Decode variation effects
•Genotype to Phenotype Databases: A Holistic Solution• 7th European Framework Program
Friday, January 16, 2009
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GEN2PHEN
•Key goals• Analyze genotype to phenotype field and investigate needs and
practices• Develop standards for the genotype to phenotype field• Create generic database components, services and integration
infrastructures• Create data search and presentation solutions for GEN2PHEN
knowledge• Facilitate research and diagnostic GEN2PHEN databases
population• Build major GEN2PHEN Internet portal• Deploy solutions to the community
Friday, January 16, 2009
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GEN2PHEN
•Key goals• Analyze genotype to phenotype field and investigate needs and
practices• Develop standards for the genotype to phenotype field• Create generic database components, services and integration
infrastructures• Create data search and presentation solutions for GEN2PHEN
knowledge• Facilitate research and diagnostic GEN2PHEN databases
population• Build major GEN2PHEN Internet portal• Deploy solutions to the community
Next generation web applications integrating heterogeneous information in a unifying
state-of-the-art user interface
Friday, January 16, 2009
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Problems
•How to integrate heterogeneous data?•How to orchestrate distinct services?•How to correctly map concepts?•How to distribute processing?•How to facilitate machine-machine communication?•How to automize data exchanges?
Friday, January 16, 2009
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Solutions
•Meta Applications• Workflows• Mashups• Web Semantics• Web Desktops• Visualization Interfaces
•Why Meta?• Use existing apps• Integrate data / services
•Goals• Improve
• User satisfaction• User control• Information integration
• Enhance• App design• Custom apps
Friday, January 16, 2009
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Workflows
•What?• Sequence of tasks• Information flows
•How?• Input/output mapping
•Where?• Yahoo! Pipes• Taverna• geDynamicFlow
Friday, January 16, 2009
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Workflows
•What?• Sequence of tasks• Information flows
•How?• Input/output mapping
•Where?• Yahoo! Pipes• Taverna• geDynamicFlow
Friday, January 16, 2009
![Page 12: From Genotype to Phenotype - Future Perspectives on Data and Service Integration (Keynote)](https://reader031.vdocuments.site/reader031/viewer/2022020503/568c4c5c1a28ab49169fda25/html5/thumbnails/12.jpg)
Workflows
•What?• Sequence of tasks• Information flows
•How?• Input/output mapping
•Where?• Yahoo! Pipes• Taverna• geDynamicFlow
Friday, January 16, 2009
![Page 13: From Genotype to Phenotype - Future Perspectives on Data and Service Integration (Keynote)](https://reader031.vdocuments.site/reader031/viewer/2022020503/568c4c5c1a28ab49169fda25/html5/thumbnails/13.jpg)
Mashups
•What?• Apps as gadgets• Customizable UI
•How?• Relations among
gadgets• Information sharing
•Where• iGoogle• Netvibes
Friday, January 16, 2009
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Mashups
•What?• Apps as gadgets• Customizable UI
•How?• Relations among
gadgets• Information sharing
•Where• iGoogle• Netvibes
Friday, January 16, 2009
![Page 15: From Genotype to Phenotype - Future Perspectives on Data and Service Integration (Keynote)](https://reader031.vdocuments.site/reader031/viewer/2022020503/568c4c5c1a28ab49169fda25/html5/thumbnails/15.jpg)
Web Semantics
•What?• Ontologies• Resource Description• Data exchange
•How?• XML descriptions• SPARQL queries
•Where?• DBPedia• Nextbio
Friday, January 16, 2009
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Web Semantics
•What?• Ontologies• Resource Description• Data exchange
•How?• XML descriptions• SPARQL queries
•Where?• DBPedia• Nextbio
Friday, January 16, 2009
![Page 17: From Genotype to Phenotype - Future Perspectives on Data and Service Integration (Keynote)](https://reader031.vdocuments.site/reader031/viewer/2022020503/568c4c5c1a28ab49169fda25/html5/thumbnails/17.jpg)
Web Desktops
•What?• Desktops in the browser
•How?• Desktop interface• Traditional metaphors
•Where?• eyeOS• g.ho.st
Friday, January 16, 2009
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Web Desktops
•What?• Desktops in the browser
•How?• Desktop interface• Traditional metaphors
•Where?• eyeOS• g.ho.st
Friday, January 16, 2009
![Page 19: From Genotype to Phenotype - Future Perspectives on Data and Service Integration (Keynote)](https://reader031.vdocuments.site/reader031/viewer/2022020503/568c4c5c1a28ab49169fda25/html5/thumbnails/19.jpg)
Visualizations
•What?• New visualizations• More appealing results
•How?• UI technologies: AJAX,
Flash, Silverlight
•Where?• Viewzi• Searchme
Friday, January 16, 2009
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Visualizations
•What?• New visualizations• More appealing results
•How?• UI technologies: AJAX,
Flash, Silverlight
•Where?• Viewzi• Searchme
Friday, January 16, 2009
![Page 21: From Genotype to Phenotype - Future Perspectives on Data and Service Integration (Keynote)](https://reader031.vdocuments.site/reader031/viewer/2022020503/568c4c5c1a28ab49169fda25/html5/thumbnails/21.jpg)
In Bioinformatics... Future applications
Friday, January 16, 2009
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In Bioinformatics... Future applications
Friday, January 16, 2009
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In Bioinformatics... Future applications
Friday, January 16, 2009
![Page 24: From Genotype to Phenotype - Future Perspectives on Data and Service Integration (Keynote)](https://reader031.vdocuments.site/reader031/viewer/2022020503/568c4c5c1a28ab49169fda25/html5/thumbnails/24.jpg)
In Bioinformatics... Future applications
Friday, January 16, 2009
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Conclusions
•Bioinformatics problems may be solved using generic web solutions
•There is no solution from heaven• (Fully autonomous and dynamic) Integration is “complicated”•A lot can be learned from Web2.0...
Friday, January 16, 2009
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Conclusions
•Bioinformatics problems may be solved using generic web solutions
•There is no solution from heaven• (Fully autonomous and dynamic) Integration is “complicated”•A lot can be learned from Web2.0...... and Web3.0 is right around the corner!
Friday, January 16, 2009
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Conclusions
•Bioinformatics problems may be solved using generic web solutions
•There is no solution from heaven• (Fully autonomous and dynamic) Integration is “complicated”•A lot can be learned from Web2.0...Now it’s up to YOU!
Friday, January 16, 2009
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Questions?
Friday, January 16, 2009
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Thank You
Friday, January 16, 2009