[CEUR Workshop Proceedings] Vol-833
urn:nbn:de:0074-833-7

Copyright © 2012 for the individual papers by the papers' authors. Copying permitted for private and academic purposes. This volume is published and copyrighted by its editors. The papers in this volume are also licensed under the terms of Creative Commons Attribution 3.0.





ICBO-2011
International Conference on Biomedical Ontology


Proceedings of the 2nd International Conference on Biomedical Ontology

Buffalo, NY, USA, July 26-30, 2011
Workshops: July 26-27
Conference: July 28-30


Edited by

Olivier Bodenreider *
Maryann E. Martone **
Alan Ruttenberg ***

* National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
** University of California at San Diego, San Diego, CA, USA
*** University at Buffalo, Buffalo, NY, USA



Table of Contents

    ICBO Presentations

  1. Where GO is Going and What it Means for Ontology Extension
    Catia Pesquita, Francisco M. Couto
  2. Revising the Cell Ontology
    Terrence F. Meehan, Christopher J. Mungall, Alexander D. Diehl
  3. Rapid Development of an Ontology of Coriell Cell Lines
    Chao Pang, Tomasz Adamusiak, Helen Parkinson, James Malone
  4. Cell Line Ontology: Redesigning the Cell Line Knowledgebase to Aid Integrative Translational Informatics
    Sirarat Sarntivijai, Zuoshuang Xiang, Terrence F. Meehan, Alexander D. Diehl, Uma Vempati,
    Stephan Schurer, Chao Pang, James Malone, Helen Parkinson, Brian D. Athey, Yongqun He
  5. Towards a Semantic Web Application: Ontology-Driven Ortholog Clustering Analysis
    Yu Lin, Zuoshuang Xiang, Yongqun He
  6. HeartCyc: A Cardiac Cycle Process Ontology Based in the Ontology of Physics for Biology
    Daniel L. Cook, Michal Galdzicki, Maxwell L. Neal, Jose L.V. Mejino, John H. Gennari
  7. Composite Annotation for Heart Development
    Tariq Abdulla, Ryan Imms, Jean-Marc Schleich, Ron Summers
  8. Ontology-Based Analysis of Event-Related Potentials
    Gwen Frishkoff, Robert Frank, Paea LePendu
  9. River Flow Model of Diseases
    Riichiro Mizoguchi, Kouji Kozaki, Hiroko Kou, Yuki Yamagata, Takeshi Imai, Kayo Waki, Kazuhiko Ohe
  10. Dispositions and Processes in the Emotion Ontology
    Janna Hastings, Werner Ceusters, Barry Smith, Kevin Mulligan
  11. An Advanced Strategy for Integration of Biological Measurement Data
    Hiroshi Masuya, Georgios V. Gkoutos, Nobuhiko Tanaka, Kazunori Waki, Yoshihiro Okuda, Tatsuya Kushida,
    Norio Kobayashi, Koji Doi, Kouji Kozaki, Robert Hoehndorf, Shigeharu Wakana, Tetsuro Toyoda, Riichiro Mizoguchi
  12. Annotating Experimental Records Using Ontologies
    Alexander Garcia, Olga Giraldo, Jael García
  13. Ontology Driven Data Collection for EuPathDB
    Jie Zheng, Omar S. Harb, Christian J. Stoeckert Jr.
  14. Developing an Application Ontology for Biomedical Resource Annotation and Retrieval: Challenges and Lessons Learned
    Carlo Torniai, Matt Brush, Nicole Vasilevsky, Erik Segerdell, Melanie Wilson,
    Tenille Johnson, Karen Corday, Chris Shaffer, Melissa Haendel
  15. Mapping Composition for Matching Large Life Science Ontologies
    Anika Gross, Michael Hartung, Toralf Kirsten, Erhard Rahm
  16. Generic Semantic Relatedness Measure for Biomedical Ontologies
    João D. Ferreira, Francisco M. Couto
  17. Aligning the Parasite Experiment Ontology and the Ontology for Biomedical Investigations Using AgreementMaker
    Valerie Cross, Cosmin Stroe, Xueheng Hu, Pramit Silwal, Maryam Panahiazar, Isabel F. Cruz, Priti Parikh, Amit Sheth
  18. A Case Study of ICD-11 Anatomy Value Set Extraction from SNOMED CT
    Guoqian Jiang, Harold R. Solbrig, Robert J.G. Chalmers, Kent Spackman, Alan L. Rector, Christopher G. Chute
  19. The HL7 Approach to Semantic Interoperability
    Jobst Landgrebe, Barry Smith
  20. Representing the Reality Underlying Demographic Data
    William R. Hogan, Swetha Garimalla, Shariq A. Tariq
  21. Information Models and Ontologies for Representing the Electronic Health Record
    Daniel Karlsson, Martin Berzell, Stefan Schulz
  22. The CHRONIOUS Ontology Suite: Methodology and Design Principles
    Luc Schneider, Mathias Brochhausen
  23. Applying Rigidity to Standardizing OBO Foundry Candidate Ontologies
    Patrice Seyed, Stuart C. Shapiro
  24. Higgs Bosons, Mars Missions, and Unicorn Delusions:
    How to Deal with Terms of Dubious Reference in Scientific Ontologies

    Stefan Schulz, Mathias Brochhausen, Robert Hoehndorf
  25. Towards an Ontology for Conceptual Modeling
    James P. McCusker, Joanne Luciano, Deborah L. McGuinness
  26. What's in an ‘is about’ Link? Chemical Diagrams and the Information Artifact Ontology
    Janna Hastings, Colin Batchelor, Fabian Neuhaus, Christoph Steinbeck
  27. Bioassay Ontology to Describe High-Throughput Screening Assays and their Results
    Uma Vempati, Ubbo Visser, Saminda Abeyruwan, Kunie Sakurai, Magdalena Przydzial,
    Caty Chung, Robin Smith, Amar Koleti, Christopher Mader, Vance Lemmon, Stephan Schürer
  28. A Framework Ontology for Computer-Based Patient Record Systems
    Chimezie Ogbuji
  29. Poster Papers & Abstracts

  30. The Blood Ontology: An Ontology in the Domain of Hematology
    Mauricio Barcellos Almeida, Anna Barbara de Freitas Carneiro Proietti, Jiye Ai, Barry Smith
  31. Employing Reasoning within the Phenoscape Knowledgebase
    James P. Balhoff, Wasila M. Dahdul, Hilmar Lapp, Peter E. Midford,
    Todd J. Vision, Monte Westerfield, Paula M. Mabee
  32. Waiting for a Robust Disease Ontology: A Merger of OMIM and MeSH as a Practical Interim Solution
    Susan M. Bello, Allan Peter Davis, Thomas C. Wiegers, Mary E. Dolan, Cynthia Smith,
    Joel Richardson, Judith Blake, Carolyn Mattingly, Janan T. Eppig
  33. Developing a Reagent Application Ontology within the OBO Foundry Framework
    Matthew H. Brush, Nicole Vasilevsky, Carlo Torniai, Tenille Johnson, Chris Shaffer, Melissa A. Haendel
  34. The Ontology of Microbial Phenotypes (OMP):
    A Precomposed Ontology Based on Cross Products from Multiple External Ontologies that is Used for Guiding Microbial Phenotype Annotation

    Marcus Chibucos, Adrienne Zweifel, Deborah Siegele, Peter Uetz, Michelle Giglio, James Hu
  35. Towards an Adverse Event Reporting Ontology
    Mélanie Courtot, Ryan R. Brinkman
  36. OntoOrpha: An Ontology to Support Edition and Audit of Knowledge of Rare Diseases in ORPHANET
    Ferdinand Dhombres, Pierre-Yves Vandenbussche, Ana Rath, Marc Hanauer,
    Annie Olry, Bruno Urbero, Rémy Choquet, Jean Charlet
  37. An Ontology for Gastrointestinal Endoscopy
    Shahim Essaid
  38. Enriching the Ontology for Biomedical Investigations (OBI) to Improve its Suitability for Web Service Annotations
    Chaitanya Guttula, Alok Dhamanaskar, Rui Wang, John A. Miller, Jessica C. Kissinger, Jie Zheng, Christian J. Stoeckert, Jr.
  39. Recent Developments in the ChEBI Ontology
    Janna Hastings, Paula de Matos, Adriano Dekker, Marcus Ennis, Kenneth Haug, Zara Josephs, Gareth Owen, Steve Turner, Christoph Steinbeck
  40. Representing Local Identifiers in a Referent-Tracking System
    William R. Hogan, Swetha Garimalla, Shariq A. Tariq, Werner Ceusters
  41. owl_cpp, a C++ Library for Working with OWL Ontologies
    Mikhail K. Levin, Alan Ruttenberg, Anna Maria Masci, Lindsay G. Cowell
  42. Gene Ontology Signatures for Immune Cell-Types Inferred by Gene Expression Analysis
    Terrence F. Meehan, Christopher J. Mungall, Judith A. Blake, Alexander D. Diehl
  43. Aligning Research Resource and Researcher Representation: The eagle-i and VIVO Use Case
    Stella Mitchell, Carlo Torniai, Brian Lowe, Jon Corson-Rikert, Melanie Wilson, Mansoor Ahmed,
    Shanshan Chen, Ying Ding, Nicholas Rejack, Melissa Haendel, the eagle-i Consortium, the VIVO Collaboration
  44. An Ontology-Based Approach to Linking Model Organisms and Resources to Human Diseases
    Chris J. Mungall, David Anderson, Anita Bandrowski, Brian Canada, Andrew Chatr-Aryamontri,
    Keith Cheng, P. Michael Conn, Kara Dolinski, Mark Ellisman, Janan Eppig, Jeffrey S. Grethe,
    Joseph Kemnitz, Shawn Iadonato, Stephen D. Larson, Charles Magness, Maryann E. Martone,
    Mike Tyers, Carlo Torniai, Olga Troyanskaya, Judith Turner, Monte Westerfield, Melissa A. Haendel
  45. Using RxNorm to Extract Medication Data from Electronic Health Records in the Rochester Epidemiology Project
    Jyotishman Pathak, Shawn P. Murphy, Brian N. Willaert, Hilal M. Kremers, Christopher G. Chute, Barbara P. Yawn, Walter A. Rocca
  46. Towards Desiderata for Provenance Ontologies in Biomedicine
    Satya S. Sahoo
  47. Modeling Issues and Solutions: Building a Taxonomy from a Biology Textbook
    Patrice Seyed, John Pacheco, Andrew Goldenkranz, Vinay Chaudhri
  48. Biomedical Analyses: OWL Model Based Edition
    Pierre-Yves Vandenbussche, Ferdinand Dhombres, Sylvie Cormont, Jean Charlet, Eric Lepage
  49. Ontobee: A Linked Data Server and Browser for Ontology Terms
    Zuoshuang Xiang, Chris Mungall, Alan Ruttenberg, Yongqun He
  50. Software Demonstrations

  51. Protein-Centric Connection of Biomedical Knowledge: Protein Ontology (PRO) Research and Annotation Tools
    Cecilia N. Arighi, Darren A. Natale, Judith A. Blake, Carol J. Bult, Michael Caudy, Alexander D. Diehl,
    Harold J. Drabkin, Peter D'Eustachio, Alexei Evsikov, Hongzhan Huang, Natalia V. Roberts, Alan Ruttenberg,
    Barry Smith, Jian Zhang, Cathy H. Wu
  52. SHIRAZ and CABERNET:
    Leveraging Automation, Crowdsourcing, and Ontologies to Improve the Accuracy and Throughput of Zebrafish Histological Phenotype Annotations.

    Brian Canada, Georgia Thomas, John Schleicher, James Z. Wang, Keith C. Cheng
  53. Biomedical Ontology Matching Using the AgreementMaker System
    Isabel F. Cruz, Cosmin Stroe, Catia Pesquita, Francisco M. Couto, Valerie Cross
  54. Bioportal: Ontologies and Integrated Data Resources at the Click of a Mouse
    Patricia L. Whetzel, Natasha Noy, Nigam Shah, Paul Alexander, Michael Dorf,
    Ray Fergerson, Margaret-Anne Storey, Barry Smith, Chris Chute, Mark Musen
  55. Populous: A Tool for Populating an Ontology
    Simon Jupp, Matthew Horridge, Luigi Iannone, Julie Klein, Stuart Owen, Joost Schanstra, Katy Wolstencroft, Robert Stevens
  56. The Vitro Integrated Ontology Editor and Semantic Web Application
    Brian Lowe, Brian Caruso, Nick Cappadona, Miles Worthington, Stella Mitchell, Jon Corson-Rikert, and VIVO Collaboration
  57. The BioPortal Import Plugin for Protégé
    Jithun Nair, Tania Tudorache, Trish Whetzel, Natalya Noy, Mark Musen
  58. The Biomedical Ontology Applications (BOA) Framework
    Bruno Tavares, Hugo P. Bastos, Daniel Faria, Jočo D. Ferreira, Tiago Grego, Catia Pesquita, Francisco M. Couto
  59. The NCBO Annotator: Ontology-Based Annotation as a Web Service
    Patricia L. Whetzel, Clement Jonquet, Cherie Youn, Michael Dorf, Ray Fergerson, Mark Musen, Nigam Shah
  60. OntoFox and its Application in Development of Brucellosis Ontology
    Zuoshuang Xiang, Yu Lin, Yongqun He
  61. Pre-ICBO Workshops

    Representing Adverse Events

  62. AEO: A Realism-Based Biomedical Ontology for the Representation of Adverse Events
    Yongqun He, Zuoshuang Xiang, Sirarat Sarntivijai, Luca Toldo, Werner Ceusters
  63. Reporting Adverse Events: Basis for a Common Representation
    Mélanie Courtot, Ryan R. Brinkman, Alan Ruttenberg
  64. Adverse Events from Clinical Studies in Pharmaceutical Research and Development
    Pia Emilsson, Kerstin Forsberg
  65. Classifying Adverse Events from Clinical Trials
    Bernard LaSalle, Richard Bradshaw
  66. An Ontological Representation of Adverse Drug Events
    Guoqian Jiang, Jon D. Duke, Jyotishman Pathak, Christopher G. Chute
  67. Toward Answering Time-Related Questions from Adverse Event Reports Using Ontology-Based Approaches
    Cui Tao, Guoqian Jiang, Kim Clark, Deepak Sharma, Christopher G. Chute
  68. Supporting Medical Device Adverse Event Analysis in an Interoperable Clinical Environment: Design of a Data Logging and Playback System
    David Arney, Sandy Weininger, Susan F. Whitehead, Julian M. Goldman
  69. Using Failure Modes, Mechanisms, and Effects Analysis in Medical Device Adverse Event Investigations
    Shunfeng Cheng, Diganta Das, Michael Pecht
  70. Working with Multiple Biomedical Ontologies

  71. NIFSTD and NeuroLex:
    Comprehensive Neuroscience Ontology Development Based on Multiple Biomedical Ontologies and Community Involvement

    Fahim T. Imam, Stephen D. Larson, Jeffrey S. Grethe, Amarnath Gupta, Anita Bandrowski, Maryann E. Martone
  72. Use of Multiple Ontologies to Characterize the Bioactivity of Small Molecules
    Ying Yan, Janna Hastings, Jee-Hyub Kim, Stefan Schulz, Christoph Steinbeck, Dietrich Rebholz-Schuhmann
  73. A Meta-Data Approach to Querying Multiple Biomedical Ontologies
    Ravi Palla, Dan Tecuci, Vinay Shet, Mathaeus Dejori
  74. Multiple Ontologies in Healthcare Information Technology: Motivations and Recommendation for Ontology Mapping and Alignment
    Colin Puri, Karthik Gomadam, Prateek Jain, Peter Z. Yeh, Kunal Verma
  75. Modularization for the Cell Ontology
    Christopher J. Mungall, Melissa Haendel, Amelia Ireland, Shahid Manzoor,
    Terry Meehan, David Osumi-Sutherland, Carlo Torniai, Alexander D. Diehl
  76. Building the OBO Foundry - One Policy at a Time
    Mélanie Courtot, Chris Mungall, Ryan R. Brinkman, Alan Ruttenberg
  77. Towards a Body Fluids Ontology: A Unified Application Ontology for Basic and Translational Science
    Jiye Ai, Mauricio Barcellos Almeida, André Queiroz de Andrade, Alan Ruttenberg, David Tai Wai Wong, Barry Smith
  78. Connecting Ontologies for the Representation of Biological Pathways
    Anna Maria Masci, Mikhail Levin, Alan Ruttenberg, Lindsay G. Cowell
  79. Bridging Multiple Ontologies: Representation of the Liver Immune Response
    Anna Maria Masci, Jeffrey Roach, Bernard de Bono, Pierre Grenon, Lindsay Cowell
  80. Hyperontology for the Biomedical Ontologist: A Sketch and Some Examples
    Oliver Kutz, Till Mosskowski, Janna Hastings, Alexander Garcia Castro, Aleksandra Sojic
  81. Facilitating Anatomy Ontology Interoperability

  82. Mouse Anatomy Ontologies and GXD
    Terry F. Hayamizu, Martin Ringwald
  83. FUNCARO: A Functional Extension to CARO
    David Osumi-Sutherland
  84. The Vertebrate Bridging Ontology (VBO)
    Ravensara Travillian, James Malone, Chao Pang, John Hancock, Peter W.H. Holland, Paul Schofield, Helen Parkinson
  85. Multi-Species Anatomy Ontology Development Requires a Pluralist Approach to Label-Class Mapping
    Istvén Mikó, Matthew J. Yoder, Matthew A. Bertone, Katja C. Seltmann, Andrew R. Deans
  86. CARO 2.0
    David Osumi-Sutherland
  87. Integrating Anatomy and Phenotype Ontologies with Taxonomic Hierarchies
    James P. Balhoff, Peter E. Midford, Hilmar Lapp
  88. Phenoscape: Use Cases and Anatomy Ontology Requirements for Linking Evolutionary and Model Organism Phenotypes
    Wasila Dahdul, James Balhoff, Hilmar Lapp, Peter Midford, Todd Vision, Monte Westerfield, Paula Mabee
  89. Ontologies in the Fish Tank: Using the Zebrafish Anatomy Ontology with Other OBO Ontologies to Annotate Expression and Phenotype
    Yvonne Bradford, Ceri Van Slyke
  90. Doctoral and Post-Doctoral Consortium

  91. One Empirical Study, Three Tests of Translation, Many Questions on Biomedical Ontologies:
    Limited Contribution of MeSH Terms to Effective Literature Searches on ‘Health-Related Values’

    Mila Petrova
  92. The Age of Data-Driven Medicine: Mining the Electronic Health Record
    Paea LePendu, Mark A. Musen, Nigam H. Shah
  93. Quality of Care Domain Modeling in Cancer: A Semantic Approach
    Sina Madani, Dean F. Sittig, Parsa Mirhaji, Kim Dunn
  94. Philosophy, Ontology, and Scientific Explanation
    James A. Overton
  95. Refining Ontology for Glucose Metabolism Disorders
    Yu Lin
  96. A Case Study in Using ZFA and PATO for Describing Histological Phenotypes in the Larval Zebrafish
    Brian Canada, Georgia Thomas, Timothy Cooper, Keith Cheng
  97. Epistemological Issues in Information Organization Instruments: Ontologies and Health Information Models
    André Queiroz Andrade, Mauricio Barcellos Almeida
  98. The Foundational Model of Neuroanatomy Ontology: An Ontology Framework to Support Neuroanatomical Data Integration
    B. Nolan Nichols, Jose L.V. Mejino Jr., James F. Brinkley
  99. Workflows and Framework for Nutritional/Metabolic Phenotype/Genotype and Foods-for-Health Knowledge Integration
    Matthew Lange, J. Bruce German, Jim Kaput
  100. Applications for a Translational Biomedical Ontology Model
    Robert Yao, Graciela Gonzalez

Complete Proceedings available as PDF


Citing the Proceedings

The proceedings are usually cited as follows:

Olivier Bodenreider, Maryann E. Martone, Alan Ruttenberg (eds.): Proceedings of the 
2nd International Conference on Biomedical Ontology (ICBO-2011), Buffalo, NY, USA, 
July, 26-30, 2011. CEUR Workshop Proceedings, ISSN 1613-0073, available online at CEUR-WS.org/Vol-833/.

23-Feb-2012: submitted by Alan Ruttenberg
26-Feb-2012: published on CEUR-WS.org