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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.
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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
*
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
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Where GO is Going and What it Means for Ontology Extension
Catia Pesquita, Francisco M. Couto
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Revising the Cell Ontology
Terrence F. Meehan, Christopher J. Mungall, Alexander D. Diehl
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Rapid Development of an Ontology of Coriell Cell Lines
Chao Pang, Tomasz Adamusiak, Helen Parkinson, James Malone
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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
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Towards a Semantic Web Application: Ontology-Driven Ortholog Clustering Analysis
Yu Lin, Zuoshuang Xiang, Yongqun He
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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
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Composite Annotation for Heart Development
Tariq Abdulla, Ryan Imms, Jean-Marc Schleich, Ron Summers
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Ontology-Based Analysis of Event-Related Potentials
Gwen Frishkoff, Robert Frank, Paea LePendu
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River Flow Model of Diseases
Riichiro Mizoguchi, Kouji Kozaki, Hiroko Kou, Yuki Yamagata, Takeshi Imai, Kayo Waki, Kazuhiko Ohe
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Dispositions and Processes in the Emotion Ontology
Janna Hastings, Werner Ceusters, Barry Smith, Kevin Mulligan
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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
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Annotating Experimental Records Using Ontologies
Alexander Garcia, Olga Giraldo, Jael García
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Ontology Driven Data Collection for EuPathDB
Jie Zheng, Omar S. Harb, Christian J. Stoeckert Jr.
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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
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Mapping Composition for Matching Large Life Science Ontologies
Anika Gross, Michael Hartung, Toralf Kirsten, Erhard Rahm
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Generic Semantic Relatedness Measure for Biomedical Ontologies
João D. Ferreira, Francisco M. Couto
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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
-
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
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The HL7 Approach to Semantic Interoperability
Jobst Landgrebe, Barry Smith
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Representing the Reality Underlying Demographic Data
William R. Hogan, Swetha Garimalla, Shariq A. Tariq
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Information Models and Ontologies for Representing the Electronic Health Record
Daniel Karlsson, Martin Berzell, Stefan Schulz
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The CHRONIOUS Ontology Suite: Methodology and Design Principles
Luc Schneider, Mathias Brochhausen
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Applying Rigidity to Standardizing OBO Foundry Candidate Ontologies
Patrice Seyed, Stuart C. Shapiro
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Higgs Bosons, Mars Missions, and Unicorn Delusions:
How to Deal with Terms of Dubious Reference in Scientific Ontologies
Stefan Schulz, Mathias Brochhausen, Robert Hoehndorf
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Towards an Ontology for Conceptual Modeling
James P. McCusker, Joanne Luciano, Deborah L. McGuinness
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What's in an ‘is about’ Link? Chemical Diagrams and the Information Artifact Ontology
Janna Hastings, Colin Batchelor, Fabian Neuhaus, Christoph Steinbeck
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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
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A Framework Ontology for Computer-Based Patient Record Systems
Chimezie Ogbuji
Poster Papers & Abstracts
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The Blood Ontology: An Ontology in the Domain of Hematology
Mauricio Barcellos Almeida, Anna Barbara de Freitas Carneiro Proietti, Jiye Ai, Barry Smith
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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
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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
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Developing a Reagent Application Ontology within the OBO Foundry Framework
Matthew H. Brush, Nicole Vasilevsky, Carlo Torniai, Tenille Johnson, Chris Shaffer, Melissa A. Haendel
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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
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Towards an Adverse Event Reporting Ontology
Mélanie Courtot, Ryan R. Brinkman
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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
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An Ontology for Gastrointestinal Endoscopy
Shahim Essaid
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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.
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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
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Representing Local Identifiers in a Referent-Tracking System
William R. Hogan, Swetha Garimalla, Shariq A. Tariq, Werner Ceusters
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owl_cpp, a C++ Library for Working with OWL Ontologies
Mikhail K. Levin, Alan Ruttenberg, Anna Maria Masci, Lindsay G. Cowell
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Gene Ontology Signatures for Immune Cell-Types Inferred by Gene Expression Analysis
Terrence F. Meehan, Christopher J. Mungall, Judith A. Blake, Alexander D. Diehl
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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
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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
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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
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Towards Desiderata for Provenance Ontologies in Biomedicine
Satya S. Sahoo
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Modeling Issues and Solutions: Building a Taxonomy from a Biology Textbook
Patrice Seyed, John Pacheco, Andrew Goldenkranz, Vinay Chaudhri
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Biomedical Analyses: OWL Model Based Edition
Pierre-Yves Vandenbussche, Ferdinand Dhombres, Sylvie Cormont, Jean Charlet, Eric Lepage
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Ontobee: A Linked Data Server and Browser for Ontology Terms
Zuoshuang Xiang, Chris Mungall, Alan Ruttenberg, Yongqun He
Software Demonstrations
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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
-
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
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Biomedical Ontology Matching Using the AgreementMaker System
Isabel F. Cruz, Cosmin Stroe, Catia Pesquita, Francisco M. Couto, Valerie Cross
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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
-
Populous: A Tool for Populating an Ontology
Simon Jupp, Matthew Horridge, Luigi Iannone, Julie Klein, Stuart Owen, Joost Schanstra, Katy Wolstencroft, Robert Stevens
-
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
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The BioPortal Import Plugin for Protégé
Jithun Nair, Tania Tudorache, Trish Whetzel, Natalya Noy, Mark Musen
-
The Biomedical Ontology Applications (BOA) Framework
Bruno Tavares, Hugo P. Bastos, Daniel Faria, Jo�o D. Ferreira, Tiago Grego, Catia Pesquita, Francisco M. Couto
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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
-
OntoFox and its Application in Development of Brucellosis Ontology
Zuoshuang Xiang, Yu Lin, Yongqun He
Pre-ICBO Workshops
Representing Adverse Events
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AEO: A Realism-Based Biomedical Ontology for the Representation of Adverse Events
Yongqun He, Zuoshuang Xiang, Sirarat Sarntivijai, Luca Toldo, Werner Ceusters
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Reporting Adverse Events: Basis for a Common Representation
Mélanie Courtot, Ryan R. Brinkman, Alan Ruttenberg
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Adverse Events from Clinical Studies in Pharmaceutical Research and Development
Pia Emilsson, Kerstin Forsberg
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Classifying Adverse Events from Clinical Trials
Bernard LaSalle, Richard Bradshaw
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An Ontological Representation of Adverse Drug Events
Guoqian Jiang, Jon D. Duke, Jyotishman Pathak, Christopher G. Chute
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Toward Answering Time-Related Questions from Adverse Event Reports Using Ontology-Based Approaches
Cui Tao, Guoqian Jiang, Kim Clark, Deepak Sharma, Christopher G. Chute
-
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
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Using Failure Modes, Mechanisms, and Effects Analysis in Medical Device Adverse Event Investigations
Shunfeng Cheng, Diganta Das, Michael Pecht
Working with Multiple Biomedical Ontologies
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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
-
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
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A Meta-Data Approach to Querying Multiple Biomedical Ontologies
Ravi Palla, Dan Tecuci, Vinay Shet, Mathaeus Dejori
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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
-
Modularization for the Cell Ontology
Christopher J. Mungall, Melissa Haendel, Amelia Ireland, Shahid Manzoor,
Terry Meehan, David Osumi-Sutherland, Carlo Torniai, Alexander D. Diehl
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Building the OBO Foundry - One Policy at a Time
Mélanie Courtot, Chris Mungall, Ryan R. Brinkman, Alan Ruttenberg
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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
-
Connecting Ontologies for the Representation of Biological Pathways
Anna Maria Masci, Mikhail Levin, Alan Ruttenberg, Lindsay G. Cowell
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Bridging Multiple Ontologies: Representation of the Liver Immune Response
Anna Maria Masci, Jeffrey Roach, Bernard de Bono, Pierre Grenon, Lindsay Cowell
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Hyperontology for the Biomedical Ontologist: A Sketch and Some Examples
Oliver Kutz, Till Mosskowski, Janna Hastings, Alexander Garcia Castro, Aleksandra Sojic
Facilitating Anatomy Ontology Interoperability
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Mouse Anatomy Ontologies and GXD
Terry F. Hayamizu, Martin Ringwald
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FUNCARO: A Functional Extension to CARO
David Osumi-Sutherland
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The Vertebrate Bridging Ontology (VBO)
Ravensara Travillian, James Malone, Chao Pang, John Hancock, Peter W.H. Holland, Paul Schofield, Helen Parkinson
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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
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CARO 2.0
David Osumi-Sutherland
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Integrating Anatomy and Phenotype Ontologies with Taxonomic Hierarchies
James P. Balhoff, Peter E. Midford, Hilmar Lapp
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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
-
Ontologies in the Fish Tank: Using the Zebrafish Anatomy Ontology
with Other OBO Ontologies to Annotate Expression and Phenotype
Yvonne Bradford, Ceri Van Slyke
Doctoral and Post-Doctoral Consortium
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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
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The Age of Data-Driven Medicine: Mining the Electronic Health Record
Paea LePendu, Mark A. Musen, Nigam H. Shah
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Quality of Care Domain Modeling in Cancer: A Semantic Approach
Sina Madani, Dean F. Sittig, Parsa Mirhaji, Kim Dunn
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Philosophy, Ontology, and Scientific Explanation
James A. Overton
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Refining Ontology for Glucose Metabolism Disorders
Yu Lin
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A Case Study in Using ZFA and PATO for Describing Histological Phenotypes in the Larval Zebrafish
Brian Canada, Georgia Thomas, Timothy Cooper, Keith Cheng
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Epistemological Issues in Information Organization Instruments: Ontologies and Health Information Models
André Queiroz Andrade, Mauricio Barcellos Almeida
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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
-
Workflows and Framework for Nutritional/Metabolic Phenotype/Genotype
and Foods-for-Health Knowledge Integration
Matthew Lange, J. Bruce German, Jim Kaput
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Applications for a Translational Biomedical Ontology Model
Robert Yao, Graciela Gonzalez
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