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Agenda – Day Two

Sponsored by the University of Southampton. Agenda – Day Two. 08.45-09.00 - Welcome 09.00-10.00 - myExperiment: towards Research Objects - David de Roure 10.00-10.30 - Break 10.30-11.00 - HCLS Strategy 11.00-11.30 - Integration Points across Tasks

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Agenda – Day Two

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  1. Sponsored by the University of Southampton Agenda – Day Two • 08.45-09.00 - Welcome • 09.00-10.00 - myExperiment: towards Research Objects - David de Roure • 10.00-10.30 - Break • 10.30-11.00 - HCLS Strategy • 11.00-11.30 - Integration Points across Tasks • 11.30-12.00 - Conference/Paper Outreach Opportunities • 12.00-12.30 - Grant Opportunities • 12.30-13.30 - Lunch • 13.30-15.30 - Terminology Discussion • 15.30-16.00 - Wrap Up

  2. Strategy for Health Care and Life Sciences Interest Group

  3. Group Activities • Document use cases to aid individuals in understanding the business and technical benefits of using Semantic Web technologies • Document guidelines to accelerate the adoption of the technology • Implement a selection of the use cases as proof-of-concept demonstrations • Develop high-level vocabularies • Disseminate information about the group’s work at government, industry, and academic events

  4. Accomplishments • Technical • HCLS KB hosted at 2 institutes • Linked Open Data contributions • Demonstrator of querying across heterogeneous EHR systems • Integration of SWAN and SIOC ontologies for Scientific Discourse • Outreach • Conference Presentations and Workshops: • Bio-IT World, WWW, ISMB, AMIA, C-SHALS, etc. • Publications: • Proceedings of LOD Workshop at WWW 2009: Enabling Tailored Therapeutics with Linked Data • Proceedings of the ICBO: Pharma Ontology: Creating a Patient-Centric Ontology for Translational Medicine • AMIA Spring Symposium: Clinical Observations Interoperability: A Semantic Web Approach • BMC Bioinformatics. A Journey to Semantic Web Query Federation in Life Sciences

  5. Misc from yesterday • We can also search for workflows (BioRDF) • How do we represent an experiment? • Continued confirmation of a desire to integrate and consolidate across tasks (and projects). • Large number of collaborations and reuse

  6. Semantic Web: Strengths • Business • Trends all require more flexibility, and better integration and sharing of data • Technology • Complimentary technologies are gaining considerable traction • Key Semantic Web standards are mostly in place • Linked Data has raised awareness and understanding of the Semantic Web

  7. Semantic Web: Opportunities • Business • Bridging divide between genomics and the clinic • Interacting with domain focused standards organizations • Technology • Federated query • Easy to use interfaces • Alignment with other technologies

  8. Technology Trends • Cloud computing • Security, Identity • SOA • Web 2.0

  9. Electronic Health Records

  10. Translating across domains • Translational medicine – use cases the cross domains • Link across domains and research: • What are the links? • gene – transcription factor – protein • pathway – molecular interaction – chemical compound • drug – drug side effect – chemical compound

  11. Strategic areas • Translational medicine – use cases the cross domains • Integration points: integrating genomics, proteomics, assay • Biomarkers • Other accomplishments to aim for? • What does your organization want? • What do you want?

  12. Integration across tasks

  13. Current Task Forces • BioRDF – integrated neuroscience knowledge base • Kei Cheung (Yale University) • Clinical Observations Interoperability – patient recruitment in trials • Vipul Kashyap (Cigna Healthcare) • Linking Open Drug Data – aggregation of Web-based drug data • Chris Bizer (Free University Berlin) • Pharma Ontology – high level patient-centric ontology • Christi Denney (Eli Lilly) • Scientific Discourse – building communities through networking • Tim Clark (Harvard University) • Terminology – Semantic Web representation of existing resources • John Madden (Duke University)

  14. ‘Tasks’ in the task forces • Search – How can we share data and *queries*? • Storage – How can we federate across our tasks? • Annotation – How can we share new knowledge that is added (aTags, hypothesis in SWAN, workflows)

  15. What do we want to share and find? • ontologies • terminologies • assertions using (see above) • workflows • ..[fill in]

  16. Conferences/Grants/Outreach • Conferences: SWAT4LS in Amsterdam end Nov, back to back with HCLS F2F?

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