ICBO 2013
International Conference on Biomedical Ontology 2013

Table of Contents

• Preface
  
  

Research Papers

• Exploring the use of ontologies and automated reasoning to manage selection of reportable condition lab tests from LOINC 12-15
  Karen Eilbeck, Jason Jacobs, Sunanda McGarvey, Cynthia Vinion, Catherine Staes
• An OWL knowledge base for classifying and querying collections of physiological models: A prototype human physiome 16-21
  Maxwell Lewis Neal, Daniel L. Cook, John H. Gennari
• Ontological Model of Abnormal States and its Application in the Medical Domain 22-27
  Yuki Yamagata, Hiroko Kou, Kouji Kozaki, Riichiro Mizoguchi, Takeshi Imai, Kazuhiko Ohe
• Ontology Based Annotation of Contextualized Vital Signs 28-33
  Albert Goldfain, Min Xu, Jonathan Bona, Barry Smith
• Visualizing ontology mappings to help ontology engineers identify relevant ontologies for their reuse 34-39
  Simon Kocbek, Jin-Dong Kim, Jean-Luc Perret, Patricia L. Whetzel
• Crowdsourcing Ontology Verification 40-45
  Jonathan M. Mortensen, Paul R. Alexander, Mark A. Musen, Natalya F. Noy
• Finding common ground: integrating the eagle-i and VIVO ontologies 46-49
  Carlo Torniai, Shahim Essaid, Brian Lowe, Jon Corson-Rikert, Melissa Haendel
• Enabling semantic search in a bio-specimen repository 50-53
  Shahim Essaid, Carlo Torniai, Melissa A. Haendel
• ONSTR: The Ontology for Newborn Screening Follow-up and Translational Research 54-61
  Snezana Nikolic, Prabhu Shankar, Sivaram Arabandi, Akshaye Dhawan, Rajshekhar Sunderraman, Sham Navathe, Kunal Malhotra, Rani H. Singh
• Development of an Application Ontology for Beta Cell Genomics Based On the Ontology for Biomedical Investigations 62-67
  Jie Zheng, Elisabetta Manduchi, Christian J. Stoeckert Jr
• Towards a Consistent and Scientifically Accurate Drug Ontology 68-73
  William R. Hogan, Josh Hanna, Eric Joseph, Mathias Brochhausen
• Human Development Domain of the Ontology of Craniofacial Development and Malformation 74-77
  Jose LV Mejino Jr, Ravensara S Travillian, Timothy C Cox, Linda G Shapiro, James F Brinkley
• Measuring Cognitive Functions: Hurdles in the Development of the NeuroPsychological Testing Ontology 78-83
  Alexander P. Cox, Mark Jensen, Alan Ruttenberg, Kinga Szigeti, Alexander D. Diehl
• Choosing the Granularity of Abstraction Networks for Orientation and Quality Assurance of the Sleep Domain Ontology 84-89
  Christopher Ochs, Zhe He, Yehoshua Perl, Sivaram Arabandi, Michael Halper, James Geller
• Ontology-based reinterpretation of the SNOMED CT context model 90-95
  Catalina Martínez-Costa, Stefan Schulz

Early Career Symposium

• An OGMS-based Model for Clinical Information (MCI) 97-100
  Heiner Oberkampf, Sonja Zillner, Bernhard Bauer, Matthias Hammon
• Diagnostic criteria and clinical guidelines standardization to automate case classification 101-104
  Mélanie Courtot, Jie Zheng, Christian J. Stoeckert Jr., Ryan R. Brinkman, Alan Ruttenberg
• What's in a Genotype?: An Ontological Characterization for Integration of Genetic Variation Data 105-108
  Matthew H. Brush, Chris Mungall, Nicole Washington, Melissa A. Haendel
• Representing Intracoronal Tooth Restorations in the Ontology for Oral Health and Disease 109-112
  William Duncan, Titus Schleyer, Alan Ruttenberg
• The Web as a Distributed Biochemical Reactor: Semantically Enabled Metabolic Fate Prediction 113-116
  Leonid L. Chepelev, Michel Dumontier

Poster Abstracts

• PopHR: An Integrated Semantic Framework for Population Health Surveillance 118
  Arash Shaban-Nejad, Christian Jauvin, Maxime Lavigne, Masoumeh T. Izadi, Luke Mondor, Anya Okhmatovskaia, David L. Buckeridge
• The Ocular Disease Ontology 119
  Patrick Ray, Alexander Diehl
• Alignment of Cultured Cell Modeling Across OBO Foundry Ontologies: Key Outcomes, Insights 120
  Matthew H. Brush, Jie Zheng, Yongqun He, Sirarat Sarntivijai, Bjoern Peters, Alexander D. Diehl, Christian J. Stoeckert, Melissa A. Haendel
• Representing Disease Courses: An Application of the Neurological Disease Ontology to Multiple Sclerosis Typology 121
  Mark Jensen, Alexander P. Cox, Barry Smith, Alexander D. Diehl
• HINO: BFO-aligned ontology representation of human molecular interactions and pathways 122
  Zoushuang Xiang, Yongqun He
• HyQue: A Semantic Web tool for evaluating scientific hypotheses 123
  Allison Callahan, Michel Dumontier
• A Taxonomy for Immunologists 124
  James A. Overton, Randi Vita, Jason A. Greenbaum, Heiko Dietze, Alessandro Sette, Bjoern Peters
• Brain, Biomedical Knowledge Manipulation 125
  Samuel Croset, John P. Overington, Dietrich Rebholz-Schuhmann
• The Functional Therapeutic Chemical Classification System 125
  Samuel Croset, John P. Overington , Dietrich Rebholz-Schuhmann
• OncoCL: A Cancer Cell Ontology 126
  Karen E. Rasmussen, Mary E. Dolan

Software Demonstration Abstracts

• BLUSNO: A System for Orientation, Visualization, and Quality Assurance of SNOMED CT Using Abstraction Networks 128-129
  Christopher Ochs, Yehoshua Perl, James Geller
• eagle-i: ontology-driven federated search and data entry tools for discovering biomedical research resources 130-131
  Melissa Haendel, Carlo Torniai, Nicole Vasilevsky, Scott Hoffmann, Daniela Bourges-Waldegg
• Next generation ontology browser 132-133
  Tomasz Adamusiak, Naoki Shimoyama, Marek Tutaj, Mary Shimoyama
• A method for semi-automatic extension of a middle-layer ontology 134-135
  Ulf Schwarz, Holger Stenzhorn, Nikolina Koleva, Luc Schneider, Emilio M. Sanfilippo
• A Demonstration of Entity Identity Information Management Applied to Demographic Data in a Referent Tracking System 136-137
  Cheng Chen, Josh Hanna, John R. Talburt, Mathias Brochhausen, William R. Hogan
• Introducing WebProtégé 2 as a Collaborative Platform for Editing Biomedical Ontologies 138-139
  Matthew Horridge, Jonathan Mortensen, Tania Tudorache, Jennifer Vendetti, Csongor Nyulas, Mark A. Musen, Natalya F. Noy