Transcript Open Innovation

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
Sponsored by the University of
Southampton
Strategy for Health Care and Life
Sciences Interest Group
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
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
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
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
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
Technology Trends
• Cloud computing
• Security, Identity
• SOA
• Web 2.0
Electronic Health Records
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
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?
Integration across tasks
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)
‘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)
What do we want to share and find?
• ontologies
• terminologies
• assertions using (see above)
• workflows
• ..[fill in]
Conferences/Grants/Outreach
• Conferences: SWAT4LS in Amsterdam end Nov,
back to back with HCLS F2F?