ICBO 2015
International Conference on Biomedical Ontology

Table of Contents

Frontmatter

• Preface
  
• Organisation
  

Regular Papers

• TNM-O an ontology for the Tumor-Node-Metastasis classification of malignant tumors: a study on rectal cancer
  Martin Boeker, Fábio França, Peter Bronsert, Stefan Schulz
• An ontological analysis of diagnostic assertions in electronic healthcare records
  Werner Ceusters, William R. Hogan
• A UML profile for functional modeling applied to the Molecular Function Ontology
  Patryk Burek, Frank Loebe, Heinrich Herre
• An ontology-based approach for SNOMED CT translation
  Mário J. Silva, Tiago Chaves, Bárbara Simões
• Formalization of indicators of diagnostic performance in a realist ontology
  Adrien Barton, Régis Duvauferrier, Anita Burgun
• Formal representation of disorder associations in SNOMED CT
  Edward Cheetham, Yongsheng Gao, Bruce Goldberg, Robert Hausam, Stefan Schulz
• Can SNOMED CT be squeezed without losing its shape?
  Pablo López-García, Stefan Schulz
• BIM: an open ontology for the annotation of biomedical images
  Ahmad C. Bukhari, Mate Levente Nagy, Michael Krauthammer, Paolo Ciccarese, Christopher J. O. Baker
• Investigating term reuse and overlap in biomedical ontologies
  Maulik R. Kamdar, Tania Tudorache, Mark A. Musen
• Aboutness: towards foundations for the Information Artifact Ontology
  Barry Smith, Werner Ceusters
• Medical and transmission vector vocabulary alignment with Schema.org
  William Smith, Alan Chappell, Courtney Corley
• Scaffolding the mitochondrial Disease Ontology from extant knowledge sources
  Jennifer D. Warrender, Phillip Lord
• Analysis of the evolution of ontologies using OQuaRE: application to EDAM
  Manuel Quesada-Martínez, Astrid Duque-Ramos, Jesualdo Tomás Fernández-Breis
• Structured data acquisition with ontology-based web forms
  Rafael S. Gonçalves, Samson W. Tu, Csongor I. Nyulas, Michael J. Tierney, Mark A. Musen
• Using Aber-OWL for fast and scalable reasoning over BioPortal ontologies
  Luke Slater, Georgios V. Gkoutos, Paul N. Schofield, Robert Hoehndorf
• Disease Compass – a navigation system for disease knowledge based on ontology and linked data techniques
  Kouji Kozaki, Yuki Yamagata, Riichiro Mizoguchi, Takeshi Imai, Kazuhiko Ohe

Early Career Papers

• Annotating biomedical ontology terms in electronic health records using crowd-sourcing
  Andre Lamurias, Vasco Pedro, Luka Clarke, Francisco M. Couto
• Replacing EHR structured data with explicit representations
  Jonathan Bona, Werner Ceusters
• Compound matching of biomedical ontologies
  Daniela Oliveira, Catia Pesquita
• Towards visualizing the mapping incoherences in Bioportal
  Catarina Martins, Ernesto Jimenez-Ruiz, Emanuel Santos, Catia Pesquita
• Ontology-driven patient history questionnaires
  Jonathan Bona, Gunther Kohn, Alan Ruttenberg

Poster abstracts

• Development of a discharge ontology to support postanesthesia discharge decision making
  Lucy L. Wang, Yong Choi
• Improvements to the Drosophila anatomy ontology
  Marta Costa, David Osumi-Sutherland, Steven Marygold, Nick Brown
• Ontoanimal tools for reusing ontologies, generating and editing ontology terms, and dereferencing ontology terms
  Yongqun He, Jie Zheng, Yu Lin
• Bridging Vaccine Ontology and NCIt vaccine domain for cancer vaccine data integration and analysis
  Yongqun He, Guoqian Jiang
• 2015 Disease Ontology update: DO's expanded curation activities to connect disease-related data
  Elvira Mitraka, Lynn M. Schriml
• Using Semantics and NLP in the SMART Protocols Repository
  Olga Giraldo, Alexander Garcia, Oscar Corcho
• ChEBI for systems biology and metabolic modelling
  Janna Hastings, Neil Swainston, Venkatesh Muthukrishnan, Namrata Kale, Adriano Dekker, Gareth Owen, Steve Turner, Pedro Mendes, Christoph Steinbeck
• Mapping WordNet to the Basic Formal Ontology using the KYOTO ontology
  Selja Seppälä
• Representing bioinformatics datatypes using the OntoDT ontology
  Panče Panov, Larisa Soldatova, Sašo Džeroski
• Visualization and editing of biomedical ontology alignments in AgreementMakerLight
  Catarina Martins, Daniel Faria, Catia Pesquita
• Inferring logical definitions using compound ontology matching
  Daniela Oliveira, Catia Pesquita
• Modeling and tools for supporting post-coordination in ICD-11
  Csongor I. Nyulas, Samson W. Tu, Tania Tudorache, Mark A. Musen
• FAIRDOM approach for semantic interoperability of systems biology data and models
  Olga Krebs, Katy Wolstencroft, Natalie Stanford, Norman Morrison, Martin Golebiewski, Stuart Owen, Quyen Nguyen, Jacky Snoep, Wolfgang Mueller, Carole Goble
• Mapping a database schema to the structure of an existing ontology
  Anahita Nafissi, Fabio Fiorani, Björn Usadel

Demonstrations abstracts

• GOfox: Semantics-based simplified hierarchical classification and interactive visualization to support GO enrichment analysis
  Edison Ong, Yongqun He
• Ontorat: Automatic generation and editing of ontology terms
  Yongqun He, Jie Zheng, Yu Lin
• OnToology, a tool for collaborative development of ontologies
  Ahmad Alobaid, Daniel Garijo, María Poveda-Villalón, Idafen Santana-Perez, Oscar Corcho
• AberOWL: an ontology portal with OWL EL reasoning
  Luke Slater, Georgios V. Gkoutos, Paul N. Schofield, Robert Hoehndorf
• EDN-LD: A simple linked data tool
  James A. Overton
• ROBOT: A command-line tool for ontology development
  James A. Overton, Heiko Dietze, Shahim Essaid, David Osumi-Sutherland, Christopher J. Mungall
• Highly literate ontologies
  Phillip Lord, Jennifer D. Warrender
• NCBO BioPortal version 4
  Ray W. Fergerson, Paul R. Alexander, Michael Dorf, Rafael S. Gonçalves, Manuel Salvadores, Alex Skrenchuk, Jennifer Vendetti, Mark A. Musen
• OWL-based form generation and structured data acquisition
  Rafael S. Gonçalves, Csongor I. Nyulas, Samson W. Tu, Mark A. Musen