International Conference on Biomedical Ontology: ICBO 2011

[Trish Whetzel <plwhetzel@xxxxxxxxx>]

International Conference on Biomedical Ontology: ICBO 2011

Buffalo, New York

Call for Papers

Important dates:

• February 1: Deadline for submission of workshop and tutorial proposals
• February 20: Notification of acceptance of workshop and tutorial proposals
• March 1: Deadline for submission of papers for the main ICBO conference
• March 24: Notification of acceptance of papers for the main ICBO conference
• April 1: Conference fellowship applications due
• April 1: Deadline for submission of workshop papers
• April 20: Deadline for submission of posters and of extended abstracts for doctoral and postdoctoral consortium
• April 30: Notification of acceptance of workshop papers
• May 1: Software demo proposals due
• May 10: Notification of acceptance of posters
• June 10: Deadline for submission of camera-ready copy

• Workshops and Tutorials: July 26-27, 2011
• Doctoral and Post-Doctoral Colloquium 4pm-7pm July 27, 2011
• ICBO Conference: July 28-30, 2011

Scope of conference

Ontologies are being used in an ever increasing variety of ways by researchers in almost every life science discipline, and their use in annotation of both clinical and experimental data is now a common technique in integrative translational research. Principles-based ontologies are being developed for the description of biological and biomedical phenomena of almost every type. To be maximally effective, such ontologies must work well together. But as ontologies become more commonly used and as their breadth of coverage increases, the problems involved in achieving coordination in ontology development become ever more urgent.

The International Conference on Biomedical Ontologies series was initiated in 2009 to address these problems by providing an overarching forum with the goal of bringing together representatives of all major communities involved in the development and application of ontologies in biomedicine and related areas.

Contributions are welcome on any topic in the broad area of biomedical ontology, with emphasis on the following topics:

• Techniques and technologies for collaborative ontology development
• Reasoning with biomedical ontologies
• Evaluation of biomedical ontologies
• Biomedical ontology and the Semantic Web

Ontologies for :
• Biomedical imaging
• Biochemistry and drug discovery
• Biomedical investigations, experimentation, clinical trials
• Clinical and translational research
• Development and anatomy
• Electronic health records
• Evolution and phylogeny
• Metagenomics
• Neuroscience, psychiatry, cognition

All ontologies described in submissions must be available for open public review.

Papers are to be limited to 2000 words not including abstract or references and can be at most 10 pages inclusive. They must in every case clearly describe how to access the ontologies discussed. Screen shots, when included, should be big enough to read. A submission may take the form of a report on a specific ontology for which thorough documentation has been made available for open public review, ideally as part of the ontology file itself. In such cases the submitter is encouraged to include substantial portions of the ontology document in the body of the paper.

Conference Program

The conference program will be centered around topically organized sessions where papers are presented. The program will include, in addition, software demonstrations, poster sessions, and a panel debate on ontologies and the electronic health record. A keynote lecture on the Virtual Physiological Human Project will be given by Bernard de Bono of the European Bioinformatics Institute.

Tutorials and Workshops

Tutorials are educational events. They may be either for a full day or for a half day. They should focus on one specific topic presented by one or two experts and involve interaction with the audience. Tutorials can include hands-on training, in which case the proposal should specify the exact requirements (laptops, software to install, etc.).

Workshops are full-day or two-day events. They are intended to provide a forum for the discussion of a specific topic through individual paper presentations. The workshop organizers will be responsible for advertising the workshop and reviewing and selecting the contributions.

Papers accepted for workshops will be published together with the ICBO 2011 on-site proceedings.

Workshop and tutorial proposals should include the title of the event, name, affiliation, mailing address and e-mail addresses of the proposers. They should include also a description of the proposed event (maximum 200 words), including an explanation of how the workshop/tutorial will contribute to the field of biomedical ontology. Proposals must include, in addition, a short CV of the proposer explaining their qualifications for the proposed event, including experience in teaching and/or in organizing scientific events.

Workshop proposers should additionally provide names of at least two program committee members who can review their proposal and should describe how they will advertise the workshop in order to receive a sufficient number of submissions and participants. They should also explain the rationale for addressing their specific topic in the workshop rather than in the main conference. One important argument for a workshop would be to attract more people to ICBO.

Doctoral and Post-Doctoral Consortium

The Doctoral and Postdoctoral Consortium is designed to provide an opportunity for PhDs and postdoctoral researchers to network with other early career scientists and to receive direct mentorship from experts in the field. Intending participants should submit a 1-page extended abstract, which may be a description of their current or planned research, an abstract of their PhD proposal, or a description of a related issue such as methodology. Please contact Albert Goldfain (albertgoldfain@xxxxxxxxx) for further information.

Software Demonstrations

Those wishing to submit proposals for software demonstrations should contact Trish Whetzel (whetzel@xxxxxxxxxxxx) before May 1, 2011.

Student fellowships

A number of fellowships will be available to support participation by students and by early-career researchers (less than 5 years from award of PhD). Submission details will be made available in due course.

Details Regarding Submission and Publication

All papers for both the main ICBO conference and the associated workshops will be published in a set of proceedings made available to all workshop and conference participants at the time of the meeting.

In addition, a number of papers will be selected for further refereeing for publication in the open access Journal of Biomedical Semantics.

Submit workshop, proposals, conference papers, posters, and workshop papers to http://www.easychair.org/conferences/?conf=icbo2011. All submissions should be PDF files formatted according to LNCS. See: Information for LNCS Authors.

Details of the ICBO conference and of its co-located tutorials and courses can be found at http://icbo.buffalo.edu.

Participation in this meeting by women, minorities, and persons with disabilities is strongly encouraged.

Organizing Committee

• Barry Smith, University at Buffalo (Conference Chair)
• Judith Blake, The Jackson Laboratory
• Suzanna E. Lewis, Berkeley National Laboratory
• Mark Musen, Stanford University
• Susanna-Assunta Sansone, University of Oxford
• Chris Stoeckert, University of Pennsylvania
• Dagobert Soergel, University at Buffalo

Scientific Committee

• Alan Ruttenberg, University at Buffalo (Chair)
• Olivier Bodenreider, National Library of Medicine (Co-Chair)
• Maryanne Martone, University of California at San Diego (Co-Chair)
• Stefan Schulz, University of Freiburg (Workshop and Tutorials Chair)
• Albert Goldfain, University at Buffalo (Doctoral and Postdoctoral Colloquium Chair)
• Trish Whetzel, Stanford University (Software Demonstrations Chair)

Program committee will include, in addition to the above:

• Colin Batchelor, Royal Society of Chemistry
• Sebastian Brandt, University of Manchester
• Werner Ceusters, University at Buffalo
• Rex Chisholm, Northwestern University
• Melanie Courtot, British Columbia Cancer Research Centre
• Lindsay Cowell, University of Texas Southwestern Medical Center
• Alexander Diehl, University at Buffalo
• Michel Dumontier, Carleton University
• Louis J. Goldberg, University at Buffalo
• Janna Hastings, European Bioinformatics Institute
• Pascal Hitzler, Wright State University
• Robert Hoehndorf, University of Cambridge
• Jobst Landgrebe, International Institute for the Safety of Medicines Ltd.
• Phillip Lord, Newcastle University
• Alexa McCray, Harvard Medical School
• J. L. E. Mejino, Jr., University of Washington
• Christopher Mungall, Lawrence Berkeley National Laboratory
• Darren Natale, Georgetown University
• Chimezie Ogbuji, Cleveland Clinic
• Helen Parkinson, European Bioinformatics Institute
• Bjoern Peters, La Jolla Institute for Allergy and Immunology
• Daniel Rubin, Stanford University
• Peter Robinson, Charité Hospital, Berlin
• Ulrike Sattler, University of Manchester
• Richard Scheuermann, University of Texas Southwestern Medical Center
• Robert Stevens, University of Manchester
• Ida Sim, University of California at San Francisco
• Harold Solbrig, Mayo Clinic
• Kent Spackman, International Health Terminology Standards Development Organization
• Cathy Wu, Georgetown University / University of Delaware

Trish Whetzel, PhD
Outreach Coordinator
The National Center for Biomedical Ontology
Ph: 650-721-2378
whetzel@xxxxxxxxxxxx
www.bioontology.org

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