From Genotype to Phenotype - Future Perspectives on Data and Service Integration (Keynote)

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From Genotype to Phenotype Future Perspectives on Data and Service Integration

Pedro Lopes | pedrolopes@ua.pt | PDEI - TAEI Bioinformatics | Jan 16, 2009

Friday, January 16, 2009


Outline • Past • Introduction • Present • GEN2PHEN • Problems • Future • Solutions • Ideas • Conclusion

Friday, January 16, 2009


The beginning Friday, January 16, 2009

Atomic Bomb over Hiroshima


The beginning Friday, January 16, 2009

Atomic Bomb over Hiroshima


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


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


GEN2PHEN •Key goals • Analyze genotype to phenotype field and investigate needs and practices • Develop for theweb genotype to phenotype field Nextstandards generation applications integrating • Create heterogeneous generic database components, services and integration information in a unifying infrastructures state-of-the-art user interface • 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


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?

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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

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Workflows •What? • Sequence of tasks • Information flows

•How? • Input/output mapping

•Where? • Yahoo! Pipes • Taverna • geDynamicFlow

Friday, January 16, 2009


Workflows •What? • Sequence of tasks • Information flows

•How? • Input/output mapping

•Where? • Yahoo! Pipes • Taverna • geDynamicFlow

Friday, January 16, 2009


Workflows •What? • Sequence of tasks • Information flows

•How? • Input/output mapping

•Where? • Yahoo! Pipes • Taverna • geDynamicFlow

Friday, January 16, 2009


Mashups •What? • Apps as gadgets • Customizable UI

•How? • Relations among gadgets • Information sharing

•Where • iGoogle • Netvibes

Friday, January 16, 2009


Mashups •What? • Apps as gadgets • Customizable UI

•How? • Relations among gadgets • Information sharing

•Where • iGoogle • Netvibes

Friday, January 16, 2009


Web Semantics •What? • Ontologies • Resource Description • Data exchange

•How? • XML descriptions • SPARQL queries

•Where? • DBPedia • Nextbio

Friday, January 16, 2009


Web Semantics •What? • Ontologies • Resource Description • Data exchange

•How? • XML descriptions • SPARQL queries

•Where? • DBPedia • Nextbio

Friday, January 16, 2009


Web Desktops •What? • Desktops in the browser

•How? • Desktop interface • Traditional metaphors

•Where? • eyeOS • g.ho.st

Friday, January 16, 2009


Web Desktops •What? • Desktops in the browser

•How? • Desktop interface • Traditional metaphors

•Where? • eyeOS • g.ho.st

Friday, January 16, 2009


Visualizations •What? • New visualizations • More appealing results

•How? • UI technologies: AJAX, Flash, Silverlight

•Where? • Viewzi • Searchme

Friday, January 16, 2009


Visualizations •What? • New visualizations • More appealing results

•How? • UI technologies: AJAX, Flash, Silverlight

•Where? • Viewzi • Searchme

Friday, January 16, 2009


In Bioinformatics... Friday, January 16, 2009

Future applications


In Bioinformatics... Friday, January 16, 2009

Future applications


In Bioinformatics... Friday, January 16, 2009

Future applications


In Bioinformatics... Friday, January 16, 2009

Future applications


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


Conclusions •Bioinformatics problems may be solved using generic web solutions •There is no solution from heaven • (Fully autonomous and dynamic) Integration is “complicated” ...be andlearned Web3.0 is right around the corner! •A lot can from Web2.0...

Friday, January 16, 2009


Conclusions •Bioinformatics problems may be solved using generic web solutions •There is no solution from heaven • (Fully autonomous and dynamic) Integration is “complicated” Now it’s Web2.0... up to YOU! •A lot can be learned from

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Questions?

Friday, January 16, 2009


Thank You

Friday, January 16, 2009


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