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<<apologies for cross-posting>>
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The Bio-Ontologies SIG (www.bio-ontologies.org.uk) provides a forum for discussion of the latest and most innovative research in the organisation, presentation and dissemination of knowledge in biomedicine and the life sciences. Bio-Ontologies has existed as a SIG at ISMB for 13 years, making it one of the longest running. We invite you to join us on July 15th-16th, 2011 (Fri, Sat) at ISMB/ECCB 2011 in Vienna, Austria.

Key dates:

Submissions Due: April 22th, 2011 (Fri)
Notifications: May 13th, 2011 (Fri)
Final Version Due: May 20th, 2011 (Fri)
Workshop: July 15th-16th, 2011 (Fri, Sat)

Keynote speakers: Andrew Su and Ian Dix

Submissions: http://www.bio-ontologies.org.uk/submissions

We are interested in innovative approaches to organizing, presenting and consuming knowledge in life sciences and biomedicine. We invite papers in traditional areas, such as the biological applications of ontologies, reports on newly developed Bio-Ontologies, and the use of ontologies in data sharing standards. 

In addition, we invite submissions on methods, applications and workflows that bridge the gaps in the acquisition, dissemination and consumption of scientific content in biomedical informatics research. For example, the importance and utility of collaborative content acquisition platforms (such as Wikis) is now widely accepted; however success stories about informatics workflows and discoveries that are specifically enabled by the proliferation of bio-wikis are not yet common. Similarly, there is tremendous excitement around sharing and mining of data for both basic as well as clinical research but real life solutions which bridge that divide are still scarce. We are looking for submissions on solutions that demonstrate the use of ontologies for "bridging the gaps" across research areas in the life sciences.

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. Authors of posters can also indicate a desire to provide a flash update. Unsuccessful paper submissions will automatically be considered for poster presentation; there is no need to submit both on the same topic.

Please submit at: http://www.bio-ontologies.org.uk/submissions

Selected papers from the 2010 SIG are now in press at the Journal of Biomedical Semantics, the special issue will be out soon! The papers are:
  1. Luciano, J.S., Andersson, B., Batchelor, C. et al. The Translational Medicine Ontology and Knowledge Base: Driving personalized medicine by bridging the gap between bench and bedside. 
  2. Ghazvinian, A., Noy, N.F., Musen,M.A. How Orthogonal are the OBO Foundry Ontologies? 
  3. Callahan, A., Dumontier, M., Shah, N. HyQue: Evaluating hypotheses using Semantic Web technologies. 
  4. Ciccarese, P., Ocana, M., Castro, L.J.G. et al. An Open Annotation Ontology for Science on Web 3.0.
  5. Stevens, R., Malone, J., Williams, S. et al. Automating Generation of Textual Class Defnitions from OWL to English.
  6. Schulz, S., Spackman, K., James, A. et al. Scalable Representations of Diseases in Biomedical Ontologies.
  7. Jupp, S., Klein, J., Schanstra, J. et al. Developing a Kidney and Urinary Pathway Knowledge Base. 
  8. Özgür, A., Xiang, Z., Radev, D.R. et al. Mining of vaccine-associated IFN-gamma gene interaction networks using the Vaccine Ontology. 
  9. Soldatova, L.N., Rzhetsky, A., King, R.D.  Representation of research hypotheses. 
  10. Coulet, A., Garten, Y., Dumontier, M. et al. Integration and publication of heterogeneous text-mined relationships on the Semantic Web.
The organisers:
Nigam Shah, Stanford University
Larisa Soldatova, University of Wales, Aberystwyth
Susanna-Assunta Sansone, University of Oxford
Susie Stephens, Johnson & Johnson
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