2012 Meeting

The Bio-Ontologies SIG provides a forum for discussion of the latest and most innovative research in the application of ontologies and more generally the organisation, presentation and dissemination of knowledge in biomedicine and the life sciences. Bio-Ontologies has existed as a SIG at ISMB for 14 years, making it one of the longest running. In addition to our usual focus on reports on newly developed Bio-Ontologies, and the use of ontologies in data sharing standards; this year we will focus on using ontologies for pre-competitive, translational research as well as data-driven approaches to evaluate ontologies.

The SIG will be held Friday, July 13 and Saturday, July 14, 2012, co-located with ISMB 2012 in Long Beach, CA, USA.

Start time: 8:30 a.m.

Room Location: 201B – Long Beach Convention Center (LBCC) 

Key dates:

Call for Participation

** Submissions Due: April 13th, 2012 (Fri) **

We are interested in innovative approaches to organizing 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 ones, and the use of ontologies in data sharing standards. In addition, we invite submissions on using ontologies for translational research as well as data-driven approaches to evaluate ontologies. We invite submissions on a range of topics including, but not limited to:

 - Discoveries enabled by Scientific Wikis

 - Semantic Web Enabled Applications

 - Hypothesis Testing Platforms

 - Use of Ontologies in Data Standards

 - Role of Bio-Ontologies in Health 2.0

 - Bio-Curation Platforms

 - Collaborative Ontology Authoring and Peer-Review Mechanisms

 - Automated Ontology Learning

 - Automated Annotation Pipelines

 - Ontology Generation From Natural Language

 - Mapping Between Ontologies 

 - Research in Ontology Evaluation

 - "Flash updates" on Newly Developed or Existing 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. Authors of posters can also provide a flash update. Unsuccessful papers will automatically be considered for poster presentation.


Nigam Shah,

Stanford University, USA

Susanna-Assunta Sansone,

University of Oxford, Oxford e-Research Center, UK

Michel Dumontier,

Carleton University, Canada

Larisa Soldatova,

Brunel University, UK



Start time: 8:30 a.m.

Room Location: 201B – Long Beach Convention Center (LBCC) 

Janusz Dutowski—From Networks to Ontologies of Gene Function

Abstract: Ontologies are of key importance to many domains of biological research. The Gene Ontology (GO), in particular, has been instrumental in unifying knowledge about biological processes, cellular components, and molecular functions through a hierarchy of concepts and their interrelationships. However, given only partial biological knowledge and inconsistency in how this knowledge is curated, it has been difficult to construct, extend and validate GO in an unbiased manner. We show that the existing collection of high-throughput network maps for Saccharomyces cerevisiae can be analyzed to automatically assemble an ontology of gene function that is comparable to manually curated efforts. Our systematic computational approach combines evidence from physical, genetic and transcriptional networks to produce an ontology comprised of 4,123 biological concepts and 5,766 hierarchical concept relations. Using a new ontology alignment procedure, we find that the network-based ontology captures the majority of known cellular components in budding yeast and identifies approximately 600 new cellular components and component relations – many of which we were able to validate either experimentally or bioinformatically. By working closely with the GO curators, we were also able to incorporate selected new components and relations into the Gene Ontology.  We demonstrate the many aspects of the multi-scale analysis performed using our framework, including automatically identifying, annotating and visualizing the complete hierarchical structure of biological networks. We also illustrate how it provides a powerful tool to uncover new biological knowledge and errors of manual curation. Finally, based on our results, we suggest a new role for ontologies in bioinformatics: rather than merely being used as a gold-standard for performing functional enrichment, ontologies should serve as evolvable models that are validated, revised, and expanded based on new genomic data.

Robert Hoendorf—My ontology is better than yours!  Building and evaluating ontologies for integrative research

Abstract: Ontologies are now pervasive in all areas of biology and research on biomedical ontologies applies theories and methods from diverse disciplines such as information management, knowledge representation, cognitive science, linguistics and philosophy. With the increasing use of ontologies, it becomes crucial to establish a methodology based on which the ontologies' utility for biomedical research can be evaluated, compared and improved. For ontologies that are intended to facilitate or improve scientific analyses, such a methodology must be based on the scientific results obtained using a particular ontology. I will demonstrate how multiple ontologies can be combined to integrate pharmacogenomics databases and knowledge, and used to reveal significant associations between drugs, pathways and diseases. In this application, different ontology design decisions lead to different results, making a sound evaluation based on real biomedical data a necessity. Ultimately, developing a research methodology based on ontology evaluation with respect to biomedical applications and analyses will improve the utility of ontologies in integrative biology and translational research.

Sean D. Mooney—Using ontologies for hypothesis generation and prediction in translational informatics

Abstract: Diverse ontologies have been developed for the annotation of disease, genome and proteome function, physiology, pharmacology and phenotype.  We have been using automated concept recognition tools to explore ontological concepts present in curated text that describes genes and proteins.  In this talk, we will review how to automatically annotate genes and proteins with a diverse set of ontological terms.  We compare these annotations to gold standard curated annotations from Gene Ontology (GO) and human disease ontologies, and describe the scope of annotations we observe.  I will then describe the use of these annotations to perform enrichment analysis of these concepts and to generate hypotheses from the results of high throughput experimentation, typically lists of genes and/or proteins.  We show that it is possible to map these annotations to an integrated functional network derived from high throughput datasets, such as protein interaction, gene coexpression, shared sequence features, etc.  Using this map, we can evaluate which of these terms can be predicted in humans and other model organisms using semi-supervised classification and cross validation methods.  Finally, we will also discuss species specific gene and protein annotation similarity networks derived from both curated and/or automatically annotated terms and their utility in describing gene and concept similarity.

Friday, July 13th

Presentations from July 13 are at: http://goo.gl/1wkXH

Saturday, July 14th

Presentations from July 14 are at: http://goo.gl/0i96h


Register for the Bio-Ontologies SIG at the ISMB/ECCB 2011 website at: http://www.iscb.org/ismb2012-registration


We thank the program committee for their excellent input and reviews. The program committee, organized alphabetically is:


Please submit via easychair (make sure to use the right template from below)

We are inviting three types of submissions.

 - Short papers, up to 4 pages ... use the template bio-ontologies-paper-2012.dot

 - Poster abstracts, up to 1 page ... use the template bio-ontologies-poster-or-flash-update-2012.dot

 - Flash updates, up to 1 page  ... use the template bio-ontologies-poster-or-flash-update-2012.dot