2013 Meeting


The Bio-Ontologies SIG provides a forum for discussion of the latest and most innovative research in the appplication 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 16 years, making it one of the longest running.

The SIG will be held on July 20th, co-located with ISMB/ECCB 2013 in Berlin Germany.

Start time: 8:30 a.m.

Room Location: Hall 5, Look for signs at the registration desk

Key dates:

    • Submissions Due: April 12th, 2013 (Fri)

    • Notifications: May 10th, 2013 (Fri)

    • Final Version Due: May 17th, 2013 (Fri)

Accepted submissions for 2013: Papers, Flash updates, Posters

Detail schedule

Call for Participation

** Submissions Due: April 12th, 2013 (Fri) **

The Bio-Ontologies SIG provides a forum for discussion of the latest research in the application of ontologies and in the organisation, presentation and dissemination of knowledge in the life sciences. In its 16th year, Bio-Ontologies is one of the longest running SIG at ISMB. Papers are invited in areas, such as the applications of bio-ontologies, newly developed bio-ontologies, and the use of ontologies in data sharing standards. Example topics include (but not limited to):

Applications of ontologies in bioinformatics

  • Hypothesis Testing Platforms

  • Use of Ontologies in Data Standards

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

  • Bio-Curation Platforms

  • Automated Annotation Pipelines

  • Efforts using ontologies for Bio-NLP or Information Retrieval

  • Semantic Web Enabled Applications

Advances in development of biomedical ontologies

  • Collaborative Ontology Authoring and Peer-Review Mechanisms

  • Automated Ontology Learning

  • Mapping between Ontologies

  • Research in Ontology Evaluation

  • Using games for Ontology review and evaluation

We invite 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 for a flash update on the poster. Flash updates are for short talks (5 min) giving the salient new developments on existing public ontologies. 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 (soldatova.larisa@gmail.com)


Accepted submissions: Papers, Flash updates, Posters. Download the full handout

Time: 8:30 a.m 6:00 pm

Room Location: Hall 5, Look for signs at the registration desk

Introduction and welcome

The Karyotype Ontology: a computational representation for human cytogenetic patterns. Jennifer Warrender and Phillip Lord

Lexical Analysis and Characterization of the OBOFoundry Ontologies. Manuel Quesada-Martínez, Jesualdo Tomás Fernández-Breis and Robert Stevens

Exomiser: improved exome prioritization of disease genes through cross species phenotype comparison. Peter Robinson, Sebastian Köhler, Anika Oellrich, Kai Wang, Chris Mungall, Suzanna E. Lewis, Sebastian Bauer, Dominik Seelow, Peter Krawitz, Christian Gilissen, Melissa Haendel and Damian Smedley

Coffee (10:15 - 10:45) + Posters [Central Lobby]

Three Flash updates, 10 min each

  1. BioAssay Ontology (BAO): Modularization, Integration and Applications. Uma Vempati, Hande Kucuk, Saminda Abeyruwan, Ubbo Visser, Vance Lemmon, Ahsan Mir and Stephan Schürer

  2. eXframe: A Semantic Web Platform for Genomics Experiments. Emily Merrill, Stephane Corlosquet, Paolo Ciccarese, Tim Clark and Sudeshna Das

  3. Ovopub: Modular data publication with minimal provenance. Alison Callahan and Michel Dumontier

Keynote talk: Jyotishman Pathak – Semantic Web and Translational Medicine: Past, Present and Future

Lunch (Hall 2, tickets required) and Posters [Central lobby]

Zooma – A tool for automated ontology annotation. Tony Burdett, Simon Jupp, James Malone, Helen Parkinson, Eleanor Williams and Adam Faulconbridge

A Probabilistic Framework for Ontology-Based Annotation in Neuroimaging Literature. Chayan Chakrabarti, Thomas B. Jones, Jiawei F. Xu, George F. Luger, Angela R. Laird, Matthew D. Turner and Jessica A. Turner

Preserving sequence annotations across reference sequences. Zuotian Tatum, Andrew Gibson, Marco Roos, Peter E.M. Taschner, Mark Thompson, Erik A. Schultes and Jeroen F. J. Laros

Coffee break (3:30 - 4:00) + Posters [Central Lobby]

A Taxonomy for Immunologists. James A. Overton, Randi Vita, Jason A. Greenbaum, Heiko Dietze, Alessandro Sette and Bjoern Peters

Three Flash updates, 10 min each

  1. Health Data Ontology Trunk: A middle-layer ontology for health- care. Ulf Schwarz, Luc Schneider, Emilio Sanfilippo, Holger Stenzhorn and Nikolina Koleva

  2. Structured representation of scientific evidence using semantic web techniques – a biochemistry use case. Christian Bölling, Michael Weidlich and Hermann-Georg Holzhütter

  3. Synthetic Biology Open Language Visual: an ontological use case. Jacqueline Quinn, Michal Galdzicki, Robert Sidney Cox, Jacob Beal, Kevin Clancy, Nathan Hillson and Larisa Soldatova

Keynote talk: Anita de Waard – Why research data management may save science

Closing remarks and Best paper award from the National Center for Biomedical Ontology


Register for the Bio-Ontologies SIG at the ISMB/ECCB 2013 website at: http://www.iscb.org/ismbeccb2013



Please submit via easychair (make sure to use the right template from below). Yes, the templates are from 2012!

Click on the down pointing arrows at the right, to avoid loading a Google docs preview of the template.

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