ICBO 2012: Full papers

  • Hiroshi Masuya and Riichiro Mizoguchi. An Ontology of Gene
  • Fabrício Mendonça, Kátia Coelho, André Andrade and Mauricio Almeida. Knowledge Acquisition in the construction of ontologies: a case study in the domain of hematology
  • Watson Wei Khong Chua and Jung-Jae Kim. Discovering Cross-Ontology Subsumption Relationships by Using Ontological Annotations on Biomedical Literature
  • Kouji Kozaki, Riichiro Mizoguchi, Takeshi Imai and Kazuhiko Ohe. Identity Tracking of a Disease as a Causal Chain
  • Simon Walk, Markus Strohmaier, Tania Tudorache, Natalya F. Noy, Csongor Nyulas and Mark A. Musen. Recommending Concepts to Experts: An Exploration of Recommender Techniques for Collaborative Ontology Engineering Platforms in the Biomedical Domain
  • Jean Marie Rodrigues, Stefan Schulz, Cédric Bousquet and Julien Souvignet. The CEN ISO Standard Categorial Structure as a Top-Level Set of Constraints for Ontology Disambiguation
  • María Del Carmen Legaz-García, Catalina Martínez-Costa, Marcos Menárguez-Tortosa and Jesualdo Tomás Fernández-Breis. Exploitation of ontologies for the management of clinical archetypes in ArchMS
  • Patrice Seyed, Alan Rector, Uli Sattler, Bijan Parsia and Robert Stevens. Representation of Part-Whole Relationships in SNOMED CT
  • Janna Hastings, Nicolas Le Novère, Werner Ceusters, Kevin Mulligan and Barry Smith. Wanting what we don't want to want: Representing addiction in interoperable bio-ontologies
  • Joao D Ferreira, Catia Pesquita, Francisco Couto and Mario Silva. Bringing epidemiology into the Semantic Web
  • Heiner Oberkampf, Sonja Zillner and Bernhard Bauer. Interpreting Patient Data using Medical Background Knowledge
  • Colin Batchelor and Janna Hastings. Waves and fields in bio-ontologies
  • Bo Fu, Lars Grammel and Margaret-Anne Storey. BioMixer: A Web-based Collaborative Ontology Visualization Tool
  • Michael Bada and Karen Eilbeck. Efforts toward a More Consistent and Interoperable Sequence Ontology
  • Ramona Walls, Barry Smith, Justin Elser, Albert Goldfain, Dennis W. Stevenson and Pankaj Jaiswal. A plant disease extension of the Infectious Disease Ontology
  • Suzanne Santamaria, Maureen Fallon, Julie Green, Stefan Schulz and Jeffrey Wilcke. Developing the Animals in Context Ontology
  • Albert Goldfain, Lindsay Cowell and Barry Smith. Constructing a Lattice of Infectious Disease Ontologies from a Staphylococcus aureus Isolate Repository
  • Rachel Richesson, Jyotishman Pathak, Wendy McLeod, Ginger Blackmon and Kendra Vehik. Requirements and Strategy for the Development of a Pediatric Drug Ontology
  • Christian Boelling, Michel Dumontier, Michael Weidlich and Hermann-Georg Holzhütter. Role-based representation and inference of biochemical processes
  • Andre Andrade, Mauricio Almeida and Stefan Schulz. Revisiting ontological foundations of the OpenEHR Entry Model
  • Martin Boeker, Daniel Schober, Djamila Raufie, Niels Grewe, Johannes Röhl, Ludger Jansen and Stefan Schulz. Teaching Good Biomedical Ontology Design
  • Valerie Cross, Pramit Silwal and David Morell. Using a Reference Ontology with Semantic Similarity in Ontology Alignment
  • Aravind Venkatesan, Vladimir Mironov and Martin Kuiper. Towards an integrated knowledge system for capturing gene expression events
  • Daniel Schober, Vojtech Svatek and Martin Boeker. Checking Class Labels against Naming Conventions: First experiences with the OntoCheck Protégé plugin
  • Maria Copeland, Andy Brown, Helen Parkinson, Robert Stevens and James Malone. The SWO Project: A Case Study for Applying Agile Ontology Engineering Methods for Community Driven Ontologies
  • Simon Jupp, Andrew Gibson, James Malone and Robert Stevens. Taking a view on bio-ontologies

ICBO 2012: Posters

  • Melanie Courtot, Ryan Brinkman and Alan Ruttenberg: Adverse events following immunization: reporting standardization, automatic case classification and signal detection
  • Ashutosh Malhotra, Michaela Gündel and Martin Hofmann-Apitius: ADO: A formal ontology for understanding structure of information and domain knowledge of Alzheimer’s disease
  • Li Ni, Carol Bult, Jim Kadin, Joel Richardson, Martin Ringwald Ringwald, Janan Eppig and Judith Blake: Using Biomedical Ontologies for Data Representation and Man-agement in the Mouse Genome Informatics (MGI) System
  • Elvira Mitraka, Pantelis Topalis, Emmanuel Dialynas, Vicky Dritsou and Christos Louis: IDODEN: An Ontology for Dengue
  • Vicky Dritsou, Pantelis Topalis, Emmanuel Dialynas, Elvira Mitraka and Christos Louis: miRNAO: An Ontology for microRNAs
  • Ramona Walls, Hong Cui, James Macklin, Chris Mungall, Laurel Cooper, Dennis W. Stevenson and Pankaj Jaiswal: Mapping of glossary terms from the Flora of North America to the Plant Ontology enhances both resources
  • Janna Hastings, Paula De Matos, Adriano Dekker, Marcus Ennis, Venkatesh Muthukrishnan, Steve Turner, Gareth Owen and Christoph Steinbeck: Modular Extensions to the ChEBI Ontology
  • Jörg Niggemann: The ontological challenge of laterality
  • Danielle Welter, Tony Burdett, Lucia Hindorff, Heather Junkins, Jacqueline MacArthur and Helen Parkinson: GOCI: An Ontology-Driven Search and Curation Infrastructure for the NHGRI GWAS Catalog
  • Robert Yao, Jeffrey Buchhalter and Graciela Gonzalez: A Proposed Ontology for Seizure and Epilepsy
  • Kele Belloze, Daniel Monteiro, Túlio Lima, Floriano Silva-Junior and Maria Claudia Cavalcanti: Analyzing Tools for Biomedical Text Annotation with Multiple Ontologies
  • Mojgan Haghighi: Development of clinical ontology for mood disorders by combination of psychomedical information.
  • Jie Zheng, Zuoshuang Xiang, Christian Stoeckert and Yongqun He: Ontodog: A web-based tool that generates ontology views with user-specified annotations
  • Zuoshuang Xiang, Lin Yu and Yongqun He: Ontorat Web Server for Automatic Generation of New Ontology Terms

ICBO 2012: Software demos

  • Francisco Couto, Joao D Ferreira, João M. Zamite, Carlos Santos, Tiago Posse, Paulo Graça, Dulce Domingos and Mário J. Silva. The Epidemic Marketplace Platform: towards semantic characterization of epidemiological resources using biomedical ontologies
  • Eleni Mikroyannidi, Luigi Iannone, Robert Stevens and Alan Rector. RIO: The Regularities Inspector for Ontologies Plugin for Prote ´ge ´
  • Jose Antonio Miñarro Giménez, Mikel Egaña Aranguren, Jesualdo Tomás Fernández-Breis and Erick Antezana. NCBO-Galaxy: bridging the BioPortal web services and the Galaxy platform
  • Alasdair J. G. Gray, Sune Askjaer, Christian Brenninkmeijer, Kees Burger, Christine Chichester, James Eales, Chris Evelo, Carole Goble, Paul Groth, Lee Harland, Antonis Loizou, Steve Pettifer, Rishi Ramgolam, Mark Thompson, Andra Waagmeester and Antony Williams. The Pharmacology Workspace: A Platform for Drug Discovery
  • Shao Fen Liang, Robert Stevens, Donia Scott and Alan Rector. OntoVerbal: a Prote ´ge ´ plugin for verbalising ontology classes
  • Elena Voyloshnikova, Bo Fu, Lars Grammel and Margaret-Anne Storey. BioMixer: Visualizing Mappings of Biomedical Ontologies
  • Hong-Woo Chun, Chang-Hoo Jeong, Sa-Kwang Song, Yun-Soo Choi, Sung-Pil Choi and Hanmin Jung. Smart Searching System for Biomedical Information
  • Fengqiong Huang, James Macklin, Paul J. Morris, Partha Pratim Sanyal, Robert A. Morris and Hong Cui. OTO: Ontology Term Organizer
  • Tiago Grego, Francisco R. Pinto and Francisco M. Couto. Identifying Chemical Entities based on ChEBI
  • Sivaram Arabandi and Helen Moran. ClinicalKey: Terminology driven Semantic Search
  • Gwen Frishkoff and Robert Frank. The NEMO Analysis Pipeline: EEG Pattern Extraction and Ontology-based Classification

Local Organizers

Stefan Schulz
Catalina Martínez
Markus Kreuzthaler

Institute for Medical
Informatics, Statistics
and Documentation

Medical University of Graz

Auenbruggerplatz 2
8036 Graz, Austria

stefan.schulz [at] medunigraz.at


Jul 31: ICBO + FOIS photos online

Jul 16: ICBO + FOIS brochure published

Jul 3: FOIS posters published

Jun 25: Preliminary ICBO and FOIS programs online

Mar 21: Online Registration open

Mar 20: Accepted FOIS Papers announced

Mar 5: Accepted ICBO Papers announced

Feb 10: Early Career Symposium announced

Feb 1: ICBO and FOIS workshops and tutorials announced

FOIS deadline extended to Feb 12, 2012 (strict)

Jan 25: ICBO workshops and tutorials online

Jan 6: FOIS call for posters open.

Maintainer: Stefan Schulz