ICBO Presentations

CEUR-WS paper

Monday Morning, 23 July
08:30 Opening Remarks
Stefan Schulz, Local Organizer
Andrea Berghold, Head of Institute of Medical Informatics, Statistics and Documentation
08:50 Welcome Robert Stevens
09:00 Workshop Reports
Mélanie Courtot / workshop organizers
Session 1. Chair: Mélanie Courtot
09:10 A plant disease extension of the Infectious Disease Ontology
Ramona Walls, Barry Smith, Justin Elser, Albert Goldfain, Dennis W. Stevenson and Pankaj Jaiswal
09:30 Bringing epidemiology into the Semantic Web
João D Ferreira, Catia Pesquita, Francisco Couto and Mario Silva
09:50 Constructing a Lattice of Infectious Disease Ontologies from a Staphylococcus aureus Isolate Repository
Albert Goldfain, Lindsay Cowell and Barry Smith
RIO: The Regularities Inspector for Ontologies Plugin for Protégé
Eleni Mikroyannidi, Luigi Iannone, Robert Stevens and Alan Rector
Session 2. Chair: Trish Whetzel
10:50 Developing the Animals in Context Ontology
Suzanne Santamaria, Maureen Fallon, Julie Green, Stefan Schulz and Jeffrey Wilcke
11:10 An Ontology of Gene
Hiroshi Masuya and Riichiro Mizoguchi
Truth or consequences? The case for evidence-based ontology development
Alan Rector

Monday Afternoon, 23 July
Session 3. Chair: Ludger Jansen
13:30 How to deal with sectarianism in biomedical ontology/ontologies
Chair: Robert Stevens
Panelists: Alan Rector, Barry Smith, Chris Stoeckert and James Malone
14:30 Interpreting Patient Data using Medical Background Knowledge
Heiner Oberkampf, Sonja Zillner and Bernhard Bauer
14:50 Discovering Cross-Ontology Subsumption Relationships by Using Ontological Annotations on Biomedical Literature
Watson Wei Khong Chua and Jung-Jae Kim
Session 4. Chair: Mike Bada
15:40 Knowledge Acquisition in the construction of ontologies: a case study in the domain of hematology
Fabrício Mendonça, Kátia Coelho, André Andrade and Mauricio Almeida
16:00 Requirements and Strategy for the Development of a Pediatric Drug Ontology
Rachel Richesson, Jyotishman Pathak, Wendy McLeod, Ginger Blackmon and Kendra Vehik
16:20 Checking Class Labels against Naming Conventions: First experiences with the OntoCheck Protégé plugin
Daniel Schober, Vojtech Svatek and Martin Boeker
Identifying Chemical Entities based on ChEBI
Tiago Grego, Francisco R. Pinto and Francisco M. Couto
16:50 Poster Flash Talks

Tuesday Morning, 24 July
08:30 Opening Remarks (Ronald Cornet)
Session 5. Chair: Jie Zheng
08:40 Representation of Part-Whole Relationships in SNOMED CT
Patrice Seyed, Alan Rector, Uli Sattler, Bijan Parsia and Robert Stevens
09:00 Wanting what we don't want to want: Representing addiction in interoperable bio-ontologies
Janna Hastings, Nicolas Le Novère, Werner Ceusters, Kevin Mulligan and Barry Smith
09:20 Efforts toward a More Consistent and Interoperable Sequence Ontology
Michael Bada and Karen Eilbeck
Smart Searching System for Biomedical Information
Hong-Woo Chun, Chang-Hoo Jeong, Sa-Kwang Song, Yun-Soo Choi, Sung-Pil Choi and Hanmin Jung
ClinicalKey: Terminology driven Semantic Search
Sivaram Arabandi and Helen Moran
Session 6. Chair: James Malone
10:30 Role-based representation and inference of biochemical processes
Christian Boelling, Michel Dumontier, Michael Weidlich and Hermann-Georg Holzhütter
10:40 The CEN ISO Standard Categorial Structure as a Top-Level Set of Constraints for Ontology Disambiguation
Jean Marie Rodrigues, Stefan Schulz, Cédric Bousquet and Julien Souvignet
11:00 Exploitation of ontologies for the management of clinical archetypes in ArchMS
María Del Carmen Legaz-García, Catalina Martínez-Costa, Marcos Menárguez-Tortosa and Jesualdo Tomás Fernández-Breis
The Pharmacology Workspace: A Platform for Drug Discovery
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
Formal Knowledge Representation and Automated Reasoning for Explanation of Genome-Scale Data
Larry Hunter

Tuesday Afternoon, 24 July
Session 7. Chair: Janna Hastings
13:30 Biomedical ontologies, where is the use / user?
Chair: Ronald Cornet
Panelists: Jeff Wilcke, Larry Hunter, Mark Musen, Rachel Richesson
14:30 Towards an integrated knowledge system for capturing gene expression events
Aravind Venkatesan, Vladimir Mironov and Martin Kuiper
14:50 Recommending Concepts to Experts: An Exploration of Recommender Techniques for Collaborative Ontology Engineering Platforms in the Biomedical Domain
Simon Walk, Markus Strohmaier, Tania Tudorache, Natalya F. Noy, Csongor Nyulas and Mark A. Musen
Session 8. Chair: Ronald Cornet
15:40 Using a Reference Ontology with Semantic Similarity in Ontology Alignment
Valerie Cross, Pramit Silwal and David Morell
16:00 The SWO Project: A Case Study for Applying Agile Ontology Engineering Methods for Community Driven Ontologies
Maria Copeland, Andy Brown, Helen Parkinson, Robert Stevens and James Malone
16:20 BioMixer: A Web-based Collaborative Ontology Visualization Tool
Bo Fu, Lars Grammel and Margaret-Anne Storey
NCBO-Galaxy: bridging the BioPortal web services and the Galaxy platform
Jose Antonio Miñarro Giménez, Mikel Egaña Aranguren, Jesualdo Tomás Fernández-Breis and Erick Antezana
OntoVerbal: a Protégé plugin for verbalising ontology classes
Shao Fen Liang, Robert Stevens, Donia Scott and Alan Rector
17:00 Taking a view on bio-ontologies
Simon Jupp, Andrew Gibson, James Malone and Robert Stevens
17:20 Revisiting ontological foundations of the OpenEHR Entry Model
André Andrade, Mauricio Almeida and Stefan Schulz
The Epidemic Marketplace Platform: towards semantic characterization of epidemiological resources using biomedical ontologies
Francisco Couto, Joao D Ferreira, João M. Zamite, Carlos Santos, Tiago Posse, Paulo Graça, Dulce Domingos and Mário J. Silva
The NEMO Analysis Pipeline: EEG Pattern Extraction and Ontology-based Classification
Gwen Frishkoff and Robert Frank

Wednesday Morning, 25 July
Joint ICBO FOIS Session. Chair: Alan Ruttenberg
08:30 Waves and fields in bio-ontologies
Colin Batchelor and Janna Hastings
08:50 Teaching Good Biomedical Ontology Design
Martin Boeker, Daniel Schober, Djamila Raufie, Niels Grewe, Johannes Röhl, Ludger Jansen and Stefan Schulz
09:10 Identity Tracking of a Disease as a Causal Chain
Kouji Kozaki, Riichiro Mizoguchi, Takeshi Imai and Kazuhiko Ohe
Observing Formal Ontology from the Street
Steve Ray
Joint ICBO FOIS Session. Chair: Barry Smith
10:50 Probability assignments to dispositions in ontologies
Adrien Barton, Anita Burgun and Régis Duvauferrier
11:20 Maturation of Neuroscience Information Framework: An Ontology Driven Information System for Neuroscience
Fahim Imam, Stephen Larson, Anita Bandrowski, Jeffrey Grethe, Amarnath Gupta and Mary Ann Martone
11:50 Suggestions for Galaxy Workflow Design Using Semantically Annotated Services
Alok Dhamanaskar, Michael Cotterell, Jie Zheng, Jessie Kissinger, Christian Stoeckert and John Miller

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 .

Maintainer: Stefan Schulz