2000 Meeting
Sharing Experiences and Spreading Best Practice
3rd Annual Bio-Ontologies Workshop
24 August 2000
About the Workshop
We would like to invite you to the Third Annual Bio-Ontologies Meeting (Bio-Ontologies 2000), on August 24th in La Jolla, California, USA. This is immediately after the ISMB-00 August 20-23 in La Jolla.
The goal of this consortium is the identification and promotion of a practical set of technologies that will aid in the knowledge management and exchange of concepts and representations in the life sciences. The first meeting took place in Montreal in 1998, and made clear the general interest and support people had for ontologies in the life sciences. The following year in Heidelberg we discussed ontology exchange and presented ontologies currently under development.
Many in the group have been active since our last meeting. The community now has considerable experience in the development and deployment of ontologies in the life sciences, so it is appropriate for us to take stock and reflect. So the theme for this year's meeting is Sharing Experiences and Spreading Best Practice. The idea is that we share not only the results of our labors but how we got there, and what we wished we had known while we did it.
Topics that will be discussed include:
Shared experiences in using ontology tools, development methodologies, comparing ontologies, and reusing others ontologies;
The latest in ontology languages and ontology exchange languages, including an update on eXtensible Ontology Language (XOL) and Ontology Inference Layer (OIL);
Ontologies produced by members from various genomics and life-science efforts;
Specific uses of ontologies in research and drug discovery especially pre-competitive ontologies for the industry;
Updates on the latest developments in ontology development in general.
Venue
The workshop will be held on August 24th on the UCSD campus in the Price Center Theatre. Attendees are expected to make their own arrangements for travel and accommodation (we assume most will simply extend their bookings for ISMB). For more information on hotels with special ISMB conference rates, see http://ismb00.sdsc.edu
Workshop Details
The day-long seminar will be divided into two sections.
A key-note address followed by three invited speakers on the theme of the workshop, followed by
A series of 20 minute talks selected from respondents to this call for abstracts, covering a range of topics that may be wider than the theme of the workshop.
Some intended results of the meeting are:
Establish a user community for sharing experiences with designing and building ontologies for the Life Sciences;
Enlist support from the Knowledge Management community for tools and methodologies to aid our ontology efforts;
Create a permanent portal for the exchange of ontologies, ontology building tools and relationships with other organizations engaged in similar ontology-building tasks;
Establish a consortium for promoting and sharing open-source ontologies in the Life Sciences.
Short Talks/Posters
Deadline: 21 July 2000
Please submit abstracts to
Registration
Admission to the meeting, tea, coffee, and all workshop material will be covered by the registration fee of $35. (Lunch is not covered)
Please remit payment (check made out to InGenuity Systems) with a printout of your completed registration form to:
Bio-Ontology Workshop Registration
InGenuity Systems
2160 Gold Street 2nd Floor
P.O. Box 2199
Alviso, CA 95002
E-mail Sherry Burr for any further registration questions.
Short Talks/Posters
Deadline: 21 July 2000
Please submit abstracts to
Schedule
"Sharing Experiences and Spreading Best Practice"
This year we have Tom Gruber, of Intraspect Software, as our key note speaker. The title for his talk "It Is What It Does: The Pragmatics of Ontology as Language, Contract, and Content".
In the morning we have three invited speakers from well-known developments in the use of bio-ontologies:
"A Report on the Status of the Gene Ontology Consortium" by the GO Consortium, presented by Mike Cherry.
"Early Challenges in Building an Ontology for Pharmacogenomics" by Russ Altman, the Stanford Medical Informatics Group, Stanford University.
"The GKB Editor Ontology Authoring Tool and the EcoCyc Ontology" by Peter Karp , the Bioinformatics Research Group, SRI International.
In the afternoon session we have a demonstration session and selected talks from submitted abstracts. These cover a range of bio-ontologies and ontology development tools:
"Protégé-2000: A flexible and extensible ontology-editing environment" by Natalya Fridman Noy, Monica Crubézy, Ray W. Fergerson, John H. Gennari, William E. Grosso, and Mark A. Musen, Stanford Medical Informatics, Stanford University and Information and Computer Science Department, University of California, Irvine.
"The Ontology Inference Layer (OIL): A Slick way to include Semantics in the Web" by Carole Goble, Ian Horrocks and the OIL Consortium, the Department of Computer Science, University of Manchester, UK.
"A Novel schema to represent `time' in biological events" by Hong Yu and Burkhard Rost, Columbia University.
"Flexible ontologies in neuroanatomy for knowledge sharing" by John H. Gennari and Natalya F. Noy, the Department of Information and Computer Science, University of California Irvine and Stanford Medical Informatics, Stanford University.
"Cell Signaling Ontology" by Takako Takai-Igarashi and Toshihisa Takagi, the National Institute of Health Sciencesand HGC, Institute of Medical Science, University of Tokyo.
"A Knowledge Model for the Analysis and Simulation of Regulatory Networks" by Andrey Rzhetsky, Tomohiro Koike, Sergey Kalachikov, Shawn M. Gomez, Michael Krauthammer, Sabina H. Kaplan, Pauline Kra, James R. Russo and Carol Friedman, Columbia Genome Center and Department of Medical Informatics Columbia University.
"Applying Formal Ontology to Biochemical Pathway Databases" Bill Andersen (Ontology Works).