| Vol-897 urn:nbn:de:0074-897-7 Copyright © 2012 for the individual papers by the papers' authors. Copying permitted only for private and academic purposes. This volume is published and copyrighted by its editors.

# KR-MED: ICBO 2012
International Conference on Biomedical Ontology 2012

### Proceedings of the 3rd International Conference on Biomedical Ontology (ICBO 2012), KR-MED Series

### Graz, Austria, July 21-25, 2012.

Edited by

### Ronald Cornet *
Robert Stevens **

* Academic Medical Center, Department of Medical Informatics, Amsterdam, Netherlands
** University of Manchester, Bio and Health Informatics Group, Manchester, UK

## Table of Contents

- Preface

### Session 1: Monday, 23 July, AM

- A plant disease extension of the Infectious Disease Ontology.
  Ramona Walls, Barry Smith, Justin Elser, Albert Goldfain, Dennis W. Stevenson, Pankaj Jaiswal.
- Bringing epidemiology into the Semantic Web.
  João D Ferreira, Catia Pesquita, Francisco Couto, Mario Silva.
- Constructing a Lattice of Infectious Disease Ontologies from a Staphylococcus aureus Isolate Repository.
  Albert Goldfain, Lindsay Cowell, Barry Smith.
- Developing the Animals in Context Ontology.
  Suzanne Santamaria, Maureen Fallon, Julie Green, Stefan Schulz, Jeffrey Wilcke.
- An Ontology of Gene.
  Hiroshi Masuya, Riichiro Mizoguchi.

### Session 2: Monday, 23 July, PM

- Interpreting Patient Data using Medical Background Knowledge.
  Heiner Oberkampf, Sonja Zillner, Bernhard Bauer.
- Discovering Cross-Ontology Subsumption Relationships by Using Ontological Annotations on Biomedical Literature.
  Watson Wei Khong Chua, Jung-Jae Kim.
- Knowledge Acquisition in the construction of ontologies: a case study in the domain of hematology.
  Fabrício Mendonça, Kátia Coelho, André Andrade, Mauricio Almeida.
- Requirements and Strategy for the Development of a Pediatric Drug Ontology.
  Rachel Richesson, Jyotishman Pathak, Wendy McLeod, Ginger Blackmon, Kendra Vehik.
- Checking Class Labels against Naming Conventions: First experiences with the OntoCheck Protégé plugin.
  Daniel Schober, Vojtech Svatek, Martin Boeker.

### Session 3: Tuesday, 24 July, AM

- Representation of Part-Whole Relationships in SNOMED CT.
  Patrice Seyed, Alan Rector, Uli Sattler, Bijan Parsia, Robert Stevens.
- Wanting what we don't want to want: Representing addiction in interoperable bio-ontologies.
  Janna Hastings, Nicolas Le Novère, Werner Ceusters, Kevin Mulligan, Barry Smith.
- Efforts toward a More Consistent and Interoperable Sequence Ontology.
  Michael Bada, Karen Eilbeck.
- Role-based representation and inference of biochemical processes.
  Christian Boelling, Michel Dumontier, Michael Weidlich, Hermann-Georg Holzhütter.
- The CEN ISO Standard Categorial Structure as a Top-Level Set of Constraints for Ontology Disambiguation.
  Jean Marie Rodrigues, Stefan Schulz, Cédric Bousquet, Julien Souvignet.
- Exploitation of ontologies for the management of clinical archetypes in ArchMS.
  María Del Carmen Legaz-García, Catalina Martínez-Costa, Marcos Menárguez-Tortosa, Jesualdo Tomás Fernández-Breis.

### Session 4: Tuesday, 24 July, PM

- Towards an integrated knowledge system for capturing gene expression events.
  Aravind Venkatesan, Vladimir Mironov, Martin Kuiper.
- 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, Mark A. Musen.
- Using a Reference Ontology with Semantic Similarity in Ontology Alignment.
  Valerie Cross, Pramit Silwal, David Morell.
- The SWO Project: A Case Study for Applying Agile Ontology Engineering Methods for Community Driven Ontologies.
  Maria Copeland, Andy Brown, Helen Parkinson, Robert Stevens, James Malone.
- BioMixer: A Web-based Collaborative Ontology Visualization Tool.
  Bo Fu, Lars Grammel, Margaret-Anne Storey.
- Taking a view on bio-ontologies.
  Simon Jupp, Andrew Gibson, James Malone, Robert Stevens.
- Revisiting ontological foundations of the OpenEHR Entry Model.
  André Andrade, Mauricio Almeida, Stefan Schulz.

### Session 5: Wednesday, 25 July, AM

- Waves and fields in bio-ontologies.
  Colin Batchelor, Janna Hastings.
- Teaching Good Biomedical Ontology Design.
  Martin Boeker, Daniel Schober, Djamila Raufie, Niels Grewe, Johannes Röhl, Ludger Jansen, Stefan Schulz.
- Identity Tracking of a Disease as a Causal Chain.
  Kouji Kozaki, Riichiro Mizoguchi, Takeshi Imai, Kazuhiko Ohe.

### ICBO Poster Abstracts

- Adverse events following immunization: reporting standardization, automatic case classification and signal detection.
  Mélanie Courtot, Ryan R. Brinkman, Alan Ruttenberg.
- ADO: A formal ontology for understanding structure of information and domain knowledge of Alzheimer’s disease.
  Ashutosh Malhotra, Michaela Gündel, Martin Hofmann-Apitius.
- Using Biomedical Ontologies for Data Representation and Management in the Mouse Genome Informatics (MGI) System.
  Li Ni, Carol J. Bult, Jim A. Kadin, Joel E. Richardson, Martin Ringwald, Janan T. Eppig, Judith A. Blake.
- IDODEN: An Ontology for Dengue.
  Elvira Mitraka, Pantelis Topalis, Emmanuel Dialynas, Vicky Dritsou, Christos Louis.
- miRNAO: An Ontology for microRNAs.
  Vicky Dritsou, Pantelis Topalis, Emmanuel Dialynas, Elvira Mitraka, Christos Louis.
- Mapping of glossary terms from the Flora of North America to the Plant Ontology enhances both resources.
  Ramona Walls, Hong Cui, James A. Macklin, Chris Mungall, Laurel Cooper, Dennis Stevenson, Pankaj Jaiswal.
- Modular Extensions to the ChEBI Ontology.
  Janna Hastings, Paula de Matos, Adriano Dekker, Marcus Ennis, Venkatesh Muthukrishnan, Steve Turner, Gareth Owen, Christoph Steinbeck.
- The ontological challenge of laterality.
  Jörg Niggemann.
- GOCI: An Ontology-Driven Search and Curation Infrastructure for the NHGRI GWAS Catalog.
  Danielle Welter, Tony Burdett, Lucia Hindorff, Heather Junkins, Jackie MacArthur, Helen Parkinson.
- Proposed Ontology for Seizure and Epilepsy.
  Robert Yao, Jeffrey Buchhalter, Graciela Gonzalez.
- Analyzing Tools for Biomedical Text Annotation with Multiple Ontologies.
  Kele T. Belloze, Daniel Igor S. B Monteiro, Tulio F. Lima, Floriano P. Silva-Jr, Maria Claudia Cavalcanti.
- Ontorat web server for automatic generation and annotations of new ontology terms.
  Zuoshuang Xiang, Yu Lin, Yongqun He.
- Ontodog: A Web-based Ontology Community View Generator.
  Jie Zheng, Zuoshuang Xiang, Christian J. Stoeckert Jr, Yongqun He.

### ICBO Software Demonstration Abstracts

- The Epidemic Marketplace Platform: towards semantic characterization of epidemiological resources using biomedical ontologies.
  Francisco M. Couto, João D. Ferreira, João Zamite, Carlos Santos, Tiago Posse, Paulo Graça, Dulce Domingos, Mário J. Silva.
- RIO: The Regularities Inspector for Ontologies Plugin for Protégé-4.
  Eleni Mikroyannidi, Luigi Iannone, Robert Stevens.
- NCBO-Galaxy: bridging the BioPortal web services and the Galaxy platform.
  Jose Antonio Miñarro Giménez, Mikel Egaña Aranguren, Jesualdo Tomás Fernández-Breis, Erick Antezana.
- The Pharmacology Workspace: A Platform for Drug Discovery.
  Alasdair J. G. Gray, Sune Askjaer, Christian Brenninkmeijer, Kees Burger, Christine Chichester, James Eales, Chris T. Evelo, Carole Goble, Paul Groth, Lee Harland, Antonis Loizou, Steve Pettifer, Rishi Ramgolam, Mark Thompson, Andra Waagmeester, Antony J. Williams.
- OntoVerbal: a Protégé plugin for verbalising ontology classes.
  Shao Fen Liang, Robert Stevens, Donia Scott, Alan Rector.
- BioMixer: Visualizing Mappings of Biomedical Ontologies.
  Elena Voyloshnikova, Bo Fu, Lars Grammel, Margaret-Anne Storey.
- Smart Searching System for Biomedical Information.
  Hong-Woo Chun, Chang-Hoo Jeong, Sa-Kwang Song, Yun-Soo Choi, Sung-Pil Choi, Hanmin Jung.
- Identifying Chemical Entities based on ChEBI.
  Tiago Grego, Francisco R. Pinto, Francisco M. Couto.
- ClinicalKey: Terminology driven Semantic Search.
  Sivaram Arabandi, Helen Moran.
- The NEMO Analysis Pipeline: EEG Pattern Extraction and Ontology-based Classification.
  Gwen A. Frishkoff, Robert M. Frank.

### ICBO Early Career Symposium Abstracts

- Knowledge representation in Health Research: the modeling of Adverse Events Following Immunization.
  Mélanie Courtot.
- OWL Representation of Drug Activities on Biological Systems.
  Samuel Croset.
- Nutriknow: a comprehensive foods-for-health knowledge repository.
  Matthew C. Lange.
- Ontology customization for biomedical informatics.
  Pablo López-García.
- An ontologically well-founded framework for modelling Business Organizations, Processes and Services.
  Alessander Botti Benevides.
- The Issue of Perspectivality in Formal Theories of Spatial Representation.
  Marion Haemmerli.
- Representing Core Themes in a Biology E-Textbook.
  Nikhil Dinesh.
- Representing biomedical knowledge: A view from the philosophy of science.
  Aleksandra Sojic, Oliver Kutz.
- An Ontology of Software Evolution.
  Xiaowei Wang.
- Quality ontology engineering based on thesauri.
  Daniel Kless.
- Semantic query expansion for fuzzy proximity information retrieval model.
  Bissan Audeh.
- A Method for Evaluating Ontologies.
  Patrice Seyed.

7-Sep-2012: submitted by Ronald Cornet, Janna Hastings
13-Sep-2012: published on CEUR-WS.org
24-Sep-2012: corrected swapped paper titles