2010 Meeting

Introduction

Bio-Ontologies: Knowledge in Biology provides a forum for discussion of the latest and most cutting-edge research in ontologies and more generally the organisation, presentation and dissemination of knowledge in biology. It has existed as a SIG at ISMB for 12 years now, making it one of the longest running.

Key dates:

• Submissions Due: April 16th, 2010 (Fri)

• Notifications: May 7th, 2010 (Fri)

• Final Version Due: May 14th, 2010 (Fri)

• Workshop: July 9th-10th, 2010 (Fri, Sat)

*** NEW and Noteworthy ***

Recognizing the increasing synergy in medical and biological ontology research and development, biomedical Knowledge Representation Working Group (KR-WG) of the American Medical Informatics Association (AMIA) has chosen the Bio-Ontologies SIG as the venue of the KR-WG's biannual knowledge representation in medicine meetings (KR-MED, www.kr-med.org). Bio-Ontologies 2010 will serve as host to KR-MED 2010 in the biannual meeting series. In order to attend the biannual KR-MED meeting, please register for the Bio-Ontology SIG.

Call for Participation

We are interested in approachs to organising, presenting and disseminating knowledge in life sciences. We invite papers in traditional areas, such as the biological applications of ontologies, newly developed Bio-Ontologies, and the use of ontologies in data sharing standards. In addition, We invite submissions on a wide range of topics including, but not limited to:

 - Semantic and/or Scientific Wikis.

 - Collaborative Curation Platforms

 - Collaborative Ontology Authoring and Peer-Review Mechanisms

 - Automated ontology learning

 - Mapping between ontologies 

 - Biological Applications of Ontologies

 - "Flash updates" on Newly Developed or Existing Bio-Ontologies

 - Use of Ontologies in Data Standards

 - Semantic Web enabled applications (such as for enhanced publishing and for capturing scientific discourse)

 - Research in Ontology Languages and its Effect on Bio-Ontologies

We are inviting three types of submissions.

 - Short papers, up to 4 pages.

 - Poster abstracts, up to 1 page.

 - Flash updates, up to 1 page

Following review, successful papers will be presented at the Bio-Ontologies SIG. Poster abstracts will be provided poster space and time will be allocated during the 2 days for at least one poster session. Flash updates are for short talks (5 min) giving the salient new developments on existing public ontologies (e.g. the Foundational Model of Anatomy). Posters authors can also indicate a desire to provide a flash update.

Unsuccessful papers will automatically be considered for poster presentation; there is no need to submit both on the same topic.

Submissions are now closed

Organizers

• Nigam Shah

• Larisa Soldatova

• Susie Stephens

• Susanna Sansone

Programme

The SIG will run for two days this year. On each day, the morning session will have an invited keynote and selected papers; while the afternoon session will have a panel session and selected talks. One of the talks session will have "flash updates" from groups developing bio-ontologies as part of large international, collaborative consortia and from selected poster presenters.

- The accepted papers, flash updates and poster abstract are available in the SIG handout.

   (if the link doesn't work, try the attachment at the bottom of the page)

- See a list of accepted papers, flash updates and posters

- See schedule for July 9th

- See schedule for July 10th

- Submit a question for panel sessions

- recent updates, such as poster board assignments

- import calendar (ics file) into your favorite calendar tool

**Journal of BioMedical Semantics (JBMS) Special Issue on papers from Bio-Ontologies 2009 is out!

Subpages (6): Day-1, July 9th Day-2, July 10th Keynote-abstracts Special issue Submit a question Updates

Keynote-abstracts

Tim Clark -- Collaboratories and Semantics for BioScience

The form of information organization is critical for velocity and bandwidth of knowledge transfer between laboratories and disciplines in biomedical research.   Since biomedical research is continually evolving, and to some extent our models of what constitute "facts" are changing, how can information organization keep up with the contents of the research itself? We will examine the role of web communities ("collaboratories"), ontologies, and annotation in connecting "activity systems" of biomedical researchers in translational medicine.  We will discuss how this process can be made scalable and continuously aligned with the goals of scientists themselves, and outline the ecosystem of ontologies being developed in the HCLS Scientific Discourse Task to support this process. Finally we will review the implications for ontology design and describe some new applications of "hypothesis management" in drug development.

Andrey Rzhetsky -- What ontologists think

We asked a number of prominent ontologists the following questions, such as:

1. What is the optimum use of an ontology?

2. Should we design a unified ontology or let 1,000 flowers bloom?

3. Should we account for theories (potentially conflicting and fluid)?

4. Can an ontology become a straightjacket?

5. How ontology could reflect change in views of the community (as time passes by)?

The surprising diversity and breadth of answers is the main theme of this talk.

Special issue

**Journal of BioMedical Semantics (JBMS) Special Issue on papers from Bio-Ontologies 2009 is out!

The papers for the special issue for Bio-Ontologies 2010 are:

1. Coulet et al - Integrating heterogeneous relationships extracted from natural language sentences

2. Dumontier et al - The Translational Medicine Ontology: Driving personalized medicine by bridging the gap from bedside to bench

3. Callahan et al - HyQue: Evaluating hypotheses using Semantic Web technologies

4. Ciccarese et al - AO: An Open Annotation Ontology for Science on the Web

5. Jupp et al - Developing a Kidney and Urinary Pathway Knowledge Base

6. Soldatova et al - Representation of research hypotheses

7. Stevens et al - Automating Generation of textual Class Definitions From OWL to English

8. Ghazvinian et al - How Orthogonal are the OBO Foundry Ontologies?

9. Schulz et al - Scalable representations of diseases in biomedical ontologies

10. Ozgur et al - Mining of vaccine-associated IFN-gamma gene interaction networks using the Vaccine Ontology

Paper selections are made based on the reviews of the SIG submission, the oral presentation at the SIG, audience feedback and discussions among the organizers to ensure a diversity of topics.

Reviewers

(Listed Alphabetically)

Adrien Coulet

Alan Ruttenberg

Bruce Aronow

Chime Ogbuji

Clement Jonquet

Colin Batchelor

David Shotton

Duncan Davidson

Elgar Pichler

Genevieve Melton-Meaux

Helen Parkinson

Holger Stenzhorn

James Malone

Jane Lomax

Jenna Zhou

John Copen

Judith Blake

Kei Cheung

Lee Harland

Li Zhou

Lindsay Cowell

Mark Wilkinson

Mathias Brochhausen

Matthias Samwald

Michel Dumontier

Mike Bada

Olivier Bodenreider

Onard Mejino

Paea LePendu

Paolo Ciccarese

Parsa Mirhaji

Philippe Rocca-Serra

Phillip Lord

Robert Stevens

Robin McEntire

Ronald Cornet

Rudi Verbeeck

Scott Marshall

Stefan Shutlz

Sudeshna Das

Trish Whetzel

Wacek Kusnierczyk

Weech Lee

Yimin Wang

Submissions

Please submit via easychair at http://www.easychair.org/conferences/?conf=bioontologies2010

Templates

• Short paper bio-ontologies-2010.dot

• Poster        bio-ontologies-poster-2010.dot

• Flash update   bio-ontologies-poster-2010.dot