<<apologies for cross-posting>>
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.
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
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
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.
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:
- 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.
- Ghazvinian, A., Noy, N.F., Musen,M.A. How Orthogonal are
the OBO Foundry Ontologies?
- Callahan, A., Dumontier, M., Shah, N. HyQue: Evaluating
hypotheses using Semantic Web technologies.
- Ciccarese, P., Ocana, M., Castro, L.J.G. et al. An Open
Annotation Ontology for Science on Web 3.0.
- Stevens, R., Malone, J., Williams, S. et al. Automating
Generation of Textual Class Defnitions from OWL to
- Schulz, S., Spackman, K., James, A. et al. Scalable
Representations of Diseases in Biomedical Ontologies.
- Jupp, S., Klein, J., Schanstra, J. et al. Developing a
Kidney and Urinary Pathway Knowledge Base.
- Özgür, A., Xiang, Z., Radev, D.R. et al. Mining of
vaccine-associated IFN-gamma gene interaction networks
using the Vaccine Ontology.
- Soldatova, L.N., Rzhetsky, A., King, R.D.
Representation of research hypotheses.
- Coulet, A., Garten, Y., Dumontier, M. et al. Integration
and publication of heterogeneous text-mined relationships
on the Semantic Web.
Nigam Shah, Stanford University
Larisa Soldatova, University of Wales, Aberystwyth
Susanna-Assunta Sansone, University of Oxford
Susie Stephens, Johnson & Johnson