Online Research Information Environment for the Life Sciences

E-BioSci/ORIEL Joint Summer Meeting

21-24 June 2002, Wiesloch, Germany

Background | Meeting Information | Programme

E-BioSci and ORIEL Project partners and other participants were joined by speakers from Europe and North America for a series of presentations and discussions on the following themes: Ontologies, knowledge representation, data transformation; Database integration; Language processing, text analysis, information retrieval and Image databases and image information retrieval systems.

Background

E-BioSci is EMBO's initiative to provide a federated network of European platforms for a wide range of high quality electronic services relating to information access and retrieval in the life sciences.

The ORIEL project, which is the research arm of E-BioSci, will develop tools and procedures to promote access to and integration of these services.

Both projects build on the complementary expertises and strengths of partner institutions in different locations in Europe. They aim to foster optimal pooling and use of European biological archives and data collections, and will involve the development of common protocols for efficient searching and retrieval of different types of information (including images, sequence data and full text published literature) held in different locations and in different formats.

Meeting Information

The Joint Summer Meeting focused on a number of themes that are common to both projects and attempted to bring together a number of experts to address these.

In addition to consortium members, speakers included: Paul Bain (Harvard University, Boston, USA); Graham Cameron (EBI-EMBL, Cambridge, UK); Carol Friedman (Columbia University, NY, USA); Udo Hahn (Freiburg, DE); Midori Harris (EBI-EMBL, Cambridge, UK); Jerry Hobbs (SRI, California, USA); Barend Mons (Collexis, Rotterdam, NL); Jasmin Saric (University of Stuttgart, DE); Stephan Schneider (TECMATH, Kaiserslautern, DE); Robert Stevens (Manchester, UK); John Wilbur (NCBI, Maryland, USA) and Alfonso Valencia (UAM, Spain).

Programme

Friday, June 21, 2002

13.00 - 16.00 Meeting of ORIEL Partners (Hohenhardt Room, Palatin Hotel)

16.00 - 18.00 Summer Meeting Arrival/registration

18.00 - 19.00 Welcoming Remarks (Frank Gannon, EMBO) and

Opening Presentation (Barend Mons, (Collexis, Rotterdam, NL)

19.00 - 20.00 Informal get together

20.00 - 22.00 Dinner

Saturday, June 22, 2002

09.00 - 10.30 Ontologies, knowledge representation, data transformation

Session Chairperson: Jerry Hobbs

Udo Hahn (Freiburg) - "Massive Biomedical Ontology Engineering"

Midori Harris (EBI) - "The Gene Ontology vocabularies: scope and usage"

10.30 - 11.00 Break

11.00 - 12.30 Ontologies, knowledge representation, data transformation (cont'd)

Session Chairperson: Jerry Hobbs

Barend Mons (Rotterdam) - "How to connect the best of different worlds"

David Durand (Brown Univ.) - "Evolving schemas, document transformations, and the semantics of markup"

Isabelle Mougenot (LIRMM) - "Development of adaptive interfaces"

12.30 - 14.00 Lunch

14.00 - 16.00 Database integration

Session Chairperson: Carol Friedman

Robert Stevens (Manchester) - "Knowledge Driven E-Science Upon The Grid Using myGrid"

Mark Wilkinson (PBI) - "BioMOBY: Open Source Biological Data Integration"

Graham Cameron (EBI) - "Data integration: strategies and examples from
bioinformatics"

16.00 - 16.30 Break

16.30 - 19.00 Free Time for informal discussions/partner technical group meetings

19.00 - 21.00 Dinner

Sunday, June 23, 2002

09.00 - 10.30 Language processing, text analysis, information retrieval

Session Chairperson: Les Grivell

Carol Friedman (Columbia) - "Automated Acquisition of Biomolecular Knowledge from Journal Articles"

John Wilbur (NCBI) - "The Synergy between PAV and AdaBoost"

10.30 - 11.00 Break

11.00 - 12.30 Language processing, text analysis, information retrieval (cont'd)

Session Chairperson: Les Grivell

Alfonso Valencia (Madrid) - "IE tasks in the annotation of Databases in Molecular Biology and Biomedicine"

Christian Blaschke (Madrid) - "Interaction networks from the IE point of view"

12.30 - 14.00 Lunch

14.00 - 16.00 Language processing, text analysis, information retrieval (cont'd)

Session Chairperson: David Durand

Jerry Hobbs (SRI) - "Information Extraction from Biomedical Text"

Jasmin Saric (University of Stuttgart) - "Genome Information Extraction"

16.00 - 16.30 Break

16.30 - 19.00 Free Time for informal discussions/partner technical group meetings

16.30 - 19.00 Meeting of the Technical Group (Restaurant, Palatin Hotel)

19.00 - 22.00 Dinner

Monday, June 24, 2002

09.00 - 10.30 Image databases, image information retrieval systems

Session Chairperson: David Shotton

David Shotton (Oxford) - "The evolution of the BioImage Database: where we are going, why, and with whom"

Chris Catton (Oxford) - "Revising the BioImage Data Model in conformity with international multimedia standards"

Simon Sparks (Oxford) - "The development of Ontology Organiser, a Jena based DAML+OIL ontology design and constraint management system, and its application to the BioImage Data Model"

Steffen Lindek (Oxford) - "Metadata for intellectual property rights: <indecs>, MPEG-21 and the Rights Data Dictionary (RDD) project"

10.30 - 11.00 Break

11.00 - 12.30 Image databases, image information retrieval systems (cont'd)

Session Chairperson: David Shotton

Paul Bain (Harvard) - "The Biomedical Image Library: a Data Repository for Biological Images"

Stephan Schneider (Kaiserslautern) - "Content Based Access to a Large Scale Video Archive"

12.30 - 13.30 Lunch, departure

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This project is funded by the European Commission as ORIEL, contract no. IST-2001-32688, under Key Action 3 of the IST Programme (Multimedia Content and Tools).

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