ICBO 2011: Buffalo, NY, USA
Olivier Bodenreider, Maryann E. Martone, Alan Ruttenberg (Eds.): Proceedings of the 2nd International Conference on Biomedical Ontology, Buffalo, NY, USA, July 26-30, 2011. CEUR-WS.org 2012 CEUR Workshop Proceedings 833
ICBO Presentations
- Chao Pang, Tomasz Adamusiak, Helen E. Parkinson, James Malone: Rapid Development of an Ontology of Coriell Cell Lines.
- Sirarat Sarntivijai, Zuoshuang Xiang, Terrence F. Meehan, Alexander D. Diehl, Uma Vempati, Stephan C. Schürer, Chao Pang, James Malone, Helen E. Parkinson, Brian D. Athey, Yongqun He: Cell Line Ontology: Redesigning the Cell Line Knowledgebase to Aid Integrative Translational Informatics.
- Yu Lin, Zuoshuang Xiang, Yongqun He: Towards a Semantic Web Application: Ontology-Driven Ortholog Clustering Analysis.
- Daniel L. Cook, Michal Galdzicki, Maxwell Lewis Neal, José L. V. Mejino Jr., John H. Gennari: HeartCyc: A Cardiac Cycle Process Ontology Based in the Ontology of Physics for Biology.
- Tariq Abdulla, Ryan Imms, Jean-Marc Schleich, Ron Summers: Composite Annotation for Heart Development.
- Gwen A. Frishkoff, Robert M. Frank, Paea LePendu: Ontology-Based Analysis of Event-Related Potentials.
- Riichiro Mizoguchi, Kouji Kozaki, Hiroko Kou, Yuki Yamagata, Takeshi Imai, Kayo Waki, Kazuhiko Ohe: River Flow Model of Diseases.
- Janna Hastings, Werner Ceusters, Barry Smith, Kevin Mulligan: Dispositions and Processes in the Emotion Ontology.
- 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: An Advanced Strategy for Integration of Biological Measurement Data.
- Alexander García Castro, Olga L. Giraldo, Jael García: Annotating Experimental Records Using Ontologies.
- Carlo Torniai, Matthew H. Brush, Nicole Vasilevsky, Erik Segerdell, Melanie Wilson, Tenille Johnson, Karen Corday, Chris Shaffer, Melissa Haendel: Developing an Application Ontology for Biomedical Resource Annotation and Retrieval: Challenges and Lessons Learned.
- Anika Gross, Michael Hartung, Toralf Kirsten, Erhard Rahm: Mapping Composition for Matching Large Life Science Ontologies.
- João D. Ferreira, Francisco M. Couto: Generic Semantic Relatedness Measure for Biomedical Ontologies.
- Valerie Cross, Cosmin Stroe, Xueheng Hu, Pramit Silwal, Maryam Panahiazar, Isabel F. Cruz, Priti Parikh, Amit P. Sheth: Aligning the Parasite Experiment Ontology and the Ontology for Biomedical Investigations Using AgreementMaker.
- Guoqian Jiang, Harold R. Solbrig, Robert J. G. Chalmers, Kent A. Spackman, Alan L. Rector, Christopher G. Chute: A Case Study of ICD-11 Anatomy Value Set Extraction from SNOMED CT.
- William R. Hogan, Swetha Garimalla, Shariq A. Tariq: Representing the Reality Underlying Demographic Data.
- Daniel Karlsson, Martin Berzell, Stefan Schulz: Information Models and Ontologies for Representing the Electronic Health Record.
- Luc Schneider, Mathias Brochhausen: The CHRONIOUS Ontology Suite: Methodology and Design Principles.
- Patrice Seyed, Stuart C. Shapiro: Applying Rigidity to Standardizing OBO Foundry Candidate Ontologies.
- Stefan Schulz, Mathias Brochhausen, Robert Hoehndorf: Higgs Bosons, Mars Missions, and Unicorn Delusions: How to Deal with Terms of Dubious Reference in Scientific Ontologies.
- James P. McCusker, Joanne S. Luciano, Deborah L. McGuinness: Towards an Ontology for Conceptual Modeling.
- Janna Hastings, Colin R. Batchelor, Fabian Neuhaus, Christoph Steinbeck: What's in an 'is about' Link? Chemical Diagrams and the Information Artifact Ontology.
- Uma Vempati, Ubbo Visser, Saminda Abeyruwan, Kunie Sakurai, Magdalena Przydzial, Caty Chung, Robin P. Smith, Amar Koleti, Christopher Mader, Vance P. Lemmon, Stephan C. Schürer: Bioassay Ontology to Describe High-Throughput Screening Assays and their Results.
- Chimezie Ogbuji: A Framework Ontology for Computer-Based Patient Record Systems.
Poster Papers & Abstracts
- Mauricio Barcellos Almeida, Anna Barbara de Freitas Carneiro Proietti, Jiye Ai, Barry Smith: The Blood Ontology: An Ontology in the Domain of Hematology.
- James P. Balhoff, Wasila M. Dahdul, Hilmar Lapp, Peter E. Midford, Todd J. Vision, Monte Westerfield, Paula M. Mabee: Employing Reasoning within the Phenoscape Knowledgebase.
- Susan M. Bello, Allan Peter Davis, Thomas C. Wiegers, Mary E. Dolan, Cynthia L. Smith, Joel E. Richardson, Judith A. Blake, Carolyn J. Mattingly, Janan T. Eppig: Waiting for a Robust Disease Ontology: A Merger of OMIM and MeSH as a Practical Interim Solution.
- Matthew H. Brush, Nicole Vasilevsky, Carlo Torniai, Tenille Johnson, Chris Shaffer, Melissa Haendel: Developing a Reagent Application Ontology within the OBO Foundry Framework.
- Marcus C. Chibucos, Adrienne E. Zweifel, Deborah A. Siegele, Peter Uetz, Michelle Giglio, James C. Hu: 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.
- Ferdinand Dhombres, Pierre-Yves Vandenbussche, Ana Rath, Marc Hanauer, Annie Olry, Bruno Urbero, Rémy Choquet, Jean Charlet: OntoOrpha: An Ontology to Support Edition and Audit of Knowledge of Rare Diseases in ORPHANET.
- Shahim Essaid: An Ontology for Gastrointestinal Endoscopy.
- Chaitanya Guttula, Alok Dhamanaskar, Rui Wang, John A. Miller, Jessica C. Kissinger, Jie Zheng, Christian J. Stoeckert Jr.: Enriching the Ontology for Biomedical Investigations (OBI) to Improve its Suitability for Web Service Annotations.
- Janna Hastings, Paula de Matos, Adriano Dekker, Marcus Ennis, Kenneth Haug, Zara Josephs, Gareth Owen, Steve Turner, Christoph Steinbeck: Recent Developments in the ChEBI Ontology.
- William R. Hogan, Swetha Garimalla, Shariq A. Tariq, Werner Ceusters: Representing Local Identifiers in a Referent-Tracking System.
- Mikhail K. Levin, Alan Ruttenberg, Anna Maria Masci, Lindsay G. Cowell: owl_cpp, a C++ Library for Working with OWL Ontologies.
- Terrence F. Meehan, Christopher J. Mungall, Judith A. Blake, Alexander D. Diehl: Gene Ontology Signatures for Immune Cell-Types Inferred by Gene Expression Analysis.
- Stella Mitchell, Carlo Torniai, Brian Lowe, Jon Corson-Rikert, Melanie Wilson, Mansoor Ahmed, Shanshan Chen, Ying Ding, Nicholas Rejack, Melissa Haendel: Aligning Research Resource and Researcher Representation: The eagle-i and VIVO Use Case.
- Chris Mungall, David Anderson, Anita Bandrowski, Brian A. Canada, Andrew Chatr-aryamontri, Keith C. Cheng, P. Michael Conn, Kara Dolinski, Mark H. Ellisman, Janan T. Eppig, Jeffrey S. Grethe, Joseph Kemnitz, Shawn Iadonato, Stephen D. Larson, Charles Magness, Maryann E. Martone, Mike Tyers, Carlo Torniai, Olga G. Troyanskaya, Judith Turner, Monte Westerfield, Melissa Haendel: An Ontology-Based Approach to Linking Model Organisms and Resources to Human Diseases.
- Jyotishman Pathak, Shawn P. Murphy, Brian N. Willaert, Hilal M. Kremers, Christopher G. Chute, Barbara P. Yawn, Walter A. Rocca: Using RxNorm to Extract Medication Data from Electronic Health Records in the Rochester Epidemiology Project.
- Satya Sanket Sahoo: Towards Desiderata for Provenance Ontologies in Biomedicine.
- Patrice Seyed, John Pacheco, Andrew Goldenkranz, Vinay K. Chaudhri: Modeling Issues and Solutions: Building a Taxonomy from a Biology Textbook.
- Pierre-Yves Vandenbussche, Ferdinand Dhombres, Sylvie Cormont, Jean Charlet, Eric Lepage: Biomedical Analyses: OWL Model Based Edition.
- Zuoshuang Xiang, Chris Mungall, Alan Ruttenberg, Yongqun He: Ontobee: A Linked Data Server and Browser for Ontology Terms.
Software Demonstrations
- Cecilia N. Arighi, Darren A. Natale, Judith A. Blake, Carol J. Bult, Michael Caudy, Alexander D. Diehl, Harold J. Drabkin, Peter D'Eustachio, Alexei V. Evsikov, Hongzhan Huang, Natalia V. Roberts, Alan Ruttenberg, Barry Smith, Jian Zhang, Cathy H. Wu: Protein-Centric Connection of Biomedical Knowledge: Protein Ontology (PRO) Research and Annotation Tools.
- Brian A. Canada, Georgia K. Thomas, John Schleicher, James Ze Wang, Keith C. Cheng: SHIRAZ and CABERNET: Leveraging Automation, Crowdsourcing, and Ontologies to Improve the Accuracy and Throughput of Zebrafish Histological Phenotype Annotations.
- Isabel F. Cruz, Cosmin Stroe, Catia Pesquita, Francisco M. Couto, Valerie Cross: Biomedical Ontology Matching Using the AgreementMaker System.
- Patricia L. Whetzel, Natasha F. Noy, Nigam Shah, Paul R. Alexander, Michael Dorf, Ray W. Fergerson, Margaret-Anne D. Storey, Barry Smith, Christopher G. Chute, Mark A. Musen: Bioportal: Ontologies and Integrated Data Resources at the Click of a Mouse.
- Simon Jupp, Matthew Horridge, Luigi Iannone, Julie Klein, Stuart Owen, Joost Schanstra, Katy Wolstencroft, Robert Stevens: Populous: A Tool for Populating an Ontology.
- Brian Lowe, Brian Caruso, Nick Cappadona, Miles Worthington, Stella Mitchell, Jon Corson-Rikert: The Vitro Integrated Ontology Editor and Semantic Web Application.
- Jithun Nair, Tania Tudorache, Trish Whetzel, Natalya Fridman Noy, Mark A. Musen: The BioPortal Import Plugin for Protégé.
- Bruno Tavares, Hugo P. Bastos, Daniel Faria, João D. Ferreira, Tiago Grego, Catia Pesquita, Francisco M. Couto: The Biomedical Ontology Applications (BOA) Framework.
- Patricia L. Whetzel, Clement Jonquet, Cherie Youn, Michael Dorf, Ray W. Fergerson, Mark A. Musen, Nigam Shah: The NCBO Annotator: Ontology-Based Annotation as a Web Service.
- Zuoshuang Xiang, Yu Lin, Yongqun He: OntoFox and its Application in Development of Brucellosis Ontology.
Representing Adverse Events
- Yongqun He, Zuoshuang Xiang, Sirarat Sarntivijai, Luca Toldo, Werner Ceusters: AEO: A Realism-Based Biomedical Ontology for the Representation of Adverse Events.
- Mélanie Courtot, Ryan R. Brinkman, Alan Ruttenberg: Reporting Adverse Events: Basis for a Common Representation.
- Pia Emilsson, Kerstin Forsberg: Adverse Events from Clinical Studies in Pharmaceutical Research and Development.
- Guoqian Jiang, Jon D. Duke, Jyotishman Pathak, Christopher G. Chute: An Ontological Representation of Adverse Drug Events.
- Cui Tao, Guoqian Jiang, Kimberly Clark, Deepak K. Sharma, Christopher G. Chute: Toward Answering Time-Related Questions from Adverse Event Reports Using Ontology-Based Approaches.
- David Arney, Sandy Weininger, Susan F. Whitehead, Julian M. Goldman: Supporting Medical Device Adverse Event Analysis in an Interoperable Clinical Environment: Design of a Data Logging and Playback System.
- Shunfeng Cheng, Diganta Das, Michael G. Pecht: Using Failure Modes, Mechanisms, and Effects Analysis in Medical Device Adverse Event Investigations.
Working with Multiple Biomedical Ontologies
- Fahim T. Imam, Stephen D. Larson, Jeffrey S. Grethe, Amarnath Gupta, Anita Bandrowski, Maryann E. Martone: NIFSTD and NeuroLex: Comprehensive Neuroscience Ontology Development Based on Multiple Biomedical Ontologies and Community Involvement.
- Ying Yan, Janna Hastings, Jee-Hyub Kim, Stefan Schulz, Christoph Steinbeck, Dietrich Rebholz-Schuhmann: Use of Multiple Ontologies to Characterize the Bioactivity of Small Molecules.
- Ravi Palla, Dan Tecuci, Vinay Shet, Mathäus Dejori: A Meta-Data Approach to Querying Multiple Biomedical Ontologies.
- Colin A. Puri, Karthik Gomadam, Prateek Jain, Peter Z. Yeh, Kunal Verma: Multiple Ontologies in Healthcare Information Technology: Motivations and Recommendation for Ontology Mapping and Alignment.
- Christopher J. Mungall, Melissa Haendel, Amelia Ireland, Shahid Manzoor, Terry Meehan, David Osumi-Sutherland, Carlo Torniai, Alexander D. Diehl: Modularization for the Cell Ontology.
- Mélanie Courtot, Chris Mungall, Ryan R. Brinkman, Alan Ruttenberg: Building the OBO Foundry - One Policy at a Time.
- Jiye Ai, Mauricio Barcellos Almeida, André Queiroz de Andrade, Alan Ruttenberg, David Tai Wai Wong, Barry Smith: Towards a Body Fluids Ontology: A Unified Application Ontology for Basic and Translational Science.
- Anna Maria Masci, Mikhail K. Levin, Alan Ruttenberg, Lindsay G. Cowell: Connecting Ontologies for the Representation of Biological Pathways.
- Anna Maria Masci, Jeffrey Roach, Bernard de Bono, Pierre Grenon, Lindsay G. Cowell: Bridging Multiple Ontologies: Representation of the Liver Immune Response.
- Oliver Kutz, Till Mossakowski, Janna Hastings, Alexander García Castro, Aleksandra Sojic: Hyperontology for the Biomedical Ontologist: A Sketch and Some Examples.
Facilitating Anatomy Ontology Interoperability
- David Osumi-Sutherland: FUNCARO: A Functional Extension to CARO.
- Ravensara S. Travillian, James Malone, Chao Pang, John M. Hancock, Peter W. H. Holland, Paul N. Schofield, Helen E. Parkinson: The Vertebrate Bridging Ontology (VBO).
- Istvén Mikó, Matthew J. Yoder, Matthew A. Bertone, Katja C. Seltmann, Andrew R. Deans: Multi-Species Anatomy Ontology Development Requires a Pluralist Approach to Label-Class Mapping.
- David Osumi-Sutherland: CARO 2.0.
- James P. Balhoff, Peter E. Midford, Hilmar Lapp: Integrating Anatomy and Phenotype Ontologies with Taxonomic Hierarchies.
- Wasila M. Dahdul, James P. Balhoff, Hilmar Lapp, Peter E. Midford, Todd J. Vision, Monte Westerfield, Paula M. Mabee: Phenoscape: Use Cases and Anatomy Ontology Requirements for Linking Evolutionary and Model Organism Phenotypes.
- Yvonne Bradford, Ceri E. Van Slyke: Ontologies in the Fish Tank: Using the Zebrafish Anatomy Ontology with Other OBO Ontologies to Annotate Expression and Phenotype.
Doctoral and Post-Doctoral Consortium
- Mila Petrova: 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'.
- Paea LePendu, Mark A. Musen, Nigam H. Shah: The Age of Data-Driven Medicine: Mining the Electronic Health Record.
- Sina Madani, Dean F. Sittig, Parsa Mirhaji, Kim Dunn: Quality of Care Domain Modeling in Cancer: A Semantic Approach.
- James A. Overton: Philosophy, Ontology, and Scientific Explanation.
- Yu Lin: Refining Ontology for Glucose Metabolism Disorders.
- Brian A. Canada, Georgia K. Thomas, Timothy Cooper, Keith C. Cheng: A Case Study in Using ZFA and PATO for Describing Histological Phenotypes in the Larval Zebrafish.
- André Queiroz de Andrade, Mauricio Barcellos Almeida: Epistemological Issues in Information Organization Instruments: Ontologies and Health Information Models.
- B. Nolan Nichols, José L. V. Mejino Jr., James F. Brinkley: The Foundational Model of Neuroanatomy Ontology: An Ontology Framework to Support Neuroanatomical Data Integration.
- Matthew Lange, J. Bruce German, Jim Kaput: Workflows and Framework for Nutritional/Metabolic Phenotype/Genotype and Foods-for-Health Knowledge Integration.
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