Tim Clark
Keynote speakers
- Kenji Doya
- Alon Halevy
- Astrid Prinz
- Andrew Schwartz
- Shankar Subramaniam
- Arthur Toga
Workshop speakers
- Bart ter Haar Romeny
- Uri Eden
- Klaus Linkenkaer-Hansen
- Tim Clark
- Alan Ruttenberg
- Jeffrey Grethe
- Arnd Roth
- Wulfram Gerstner
- Peter Hunter
- Markus Diesmann
- Andrey Semin
- Pietro Liò
- Albert Cardona
- Giorgio Ascoli
- Rolf Kötter
Workshop 2, Ontologies for neuroscience: Applications and advances
Tim Clark
Title: An agile model for semantic integration of biomedical web communities
Harvard Medical School and Massachusetts General Hospital, Cambridge, USA
Abstract: Biomedical web communities are participatory structures on the web in which scientific materials are submitted, published, discussed and shared. They are enabled by "web 2.0" (read-write web) technologies and range from formal to informal. Their contents may include peer-reviewed articles, discussion postings, wiki content, and/or various forms of database entries. The common thread amongst all such communities is the ability to register as members and conduct discussion linked to well-provenanced scientific content.
This evolving form of scientific communication is an advance in terms of agility and rapidity of information exchange. At the same time it raises the very important problem of semantically characterizing and linking related content within and between communities so that information of cross-domain relevance can be discovered and shared.
Semantic annotation, using formalized ontologies or terminologies as a metadata foundation, is one approach to developing the required information links across and within biomedical web communities. Several approaches are being tested to derive such links including structured digital abstracts, automated annotation and semi-automated annotation.
We discuss here a model for creating semantic linkage across biomedical web communities using multiple annotation approaches against various forms of formal vocabularies. We discuss a "spectrum model" for annotation metadata that permits the use of both less-formal terminologies directly accessible to biomedical scientists, and of formal ontologies amenable to deeper automated reasoning. This approach permits the use of valuable legacy terminologies with forward mapping where appropriate to elements of more formal ontologies. We will also review the activity-centric methodology for this approach and present use cases and examples.
Bio sketch: Tim Clark is Director of Informatics at the MassGeneral Institute for Neurodegenerative Disease, Instructor in Neurology at Harvard Medical School, and a member of the Executive Committee of the Massachusetts Alzheimer Disease Research Center. His research program focuses on semantic integration of biomedical web communities, scientific discourse, and experimental results. Before coming to Harvard, Tim was Vice President of Informatics at Millennium Pharmaceuticals, where his team built one of the first integrated bio- and chemi-informatics software platforms in the pharmaceutical industry. Tim is a founding Editorial Board member of the journal Briefings in Bioinformatics and co-founded the Harvard Initiative in Innovative Computing (IIC), where he served as IIC's first Director of Research Programs.