International Conference on Biomedical Ontology
Marriott Buffalo Niagara
1340 Millersport Highway â–ª Amherst, New York 14221
Amherst, New York 14221
Ontologies are being used in a variety of ways by researchers in almost every life science discipline, and their use in annotation of both clinical and experimental data is now a common technique in integrative translational research. Principles-based ontologies are being developed for the description of biological and biomedical phenomena of almost every different type. To be maximally effective, such ontologies must work well together. But as ontologies become more commonly used, the problems involved in achieving coordination in ontology development become ever more urgent. To address these problems there is a need for an overarching conference which brings together representatives of all major communities involved in the development and application of ontologies in biomedicine and related areas. ICBO is designed to meet this need.

Schedule of Presentations:

Thursday, July 28, 2011
08:00:00 Registration & Continental Breakfast
08:45:00 Opening Remarks Mark Musen
09:00:00 From Proteins to Diseases
09:10:00 The Integration of Biomedical Knowledge Cathy Wu
09:20:00 Pathways and Complexes: How to Represent What We Know and What We Don't Know Judith Blake
09:30:00 From Protein Complex to Supra-Complex
10:15:00 Refreshment Break
10:40:00 Pathways and Diseases: Towards an Integrated Representation
10:45:00 Gene and Cell Ontologies Judith Blake
10:50:00 Where the GO is Going and What it Means for Ontology Extension
11:10:00 Revising the Cell Ontology Michael J. Meehan
11:20:00 Rapid Development of an Ontology of Coriell Cell Lines Helen Parkinson
11:30:00 Cell Line Ontology | Redesigning the Cell Line Knowledgebase to Aid Integrative Translational Informatics Alexander Diehl, Helen Parkinson
11:40:00 Towards a Semantic Web Application: Ontology-Driven Ortholog Clustering Analysis
12:30:00 Buffet Lunch
14:00:00 Ontology of Biological Mechanisms Lindsay Cowell
14:10:00 HeartCyc | A Cardiac Cycle Process Ontology Based in the Ontology of Physics for Biology J. L. E. Mejino
14:20:00 Composite Annotation for Heart Development Ronald Summers
14:30:00 Ontology-Based Analysis of Event-Related Potentials
15:00:00 Refreshment Break
15:20:00 Symptoms and Disease Maryann Martone
15:30:00 River Flow Model of Diseases
15:40:00 Dispositions and Processes in the Emotion OntologyHastings, Janna Hastings, Werner Ceusters, Barry Smith
16:00:00 Free Time
17:30:00 Poster Session, Software Demonstrations and Cash-Bar Reception
17:35:00 Poster Session
17:40:00 owl_cpp, a C++ Library for Working with OWL Ontologies Alan Ruttenberg, Lindsay Cowell
17:45:00 Towards Ontologies for ‘Textbook’ of the Future in Obstetrics and Gynecology (OB/Gyn)
17:50:00 Gene Ontology Signatures for Immune Cell-Types Inferred by Gene Expression Analysis Christopher Mungall, Judith Blake, Alexander Diehl
17:55:00 Aligning Research Resource and Researcher Representation: The eagle-i and VIVO Use Case
18:00:00 An Ontology-Based Approach to Linking Model Organisms and Resources to Human Diseases
18:05:00 Using RxNorm to Extract Medication Information from Electronic Health Records in the Rochester Epidemiology Project
18:10:00 Towards Desiderata for Provenance Ontologies in Biomedicine
18:15:00 Modeling Issues Encountered from Building a Taxonomy from a Biology Textbook
18:20:00 Biomedical Analyses | OWL Model Based Edition
18:25:00 Ontobee | Serving and Browsing Linked Data for Ontology Terms
18:30:00 Software Demonstrations
18:35:00 Protein-Centric Connection of Biomedical Knowledge: Demo of Protein Ontology (PRO) Research and Annotation Tools
18:40:00 SHIRAZ and CABERNET | Leveraging Automation, Crowdsourcing, and Ontologies to Improve the Accuracy and Throughput of Zebrafish Histological Phenotype Annotations
18:45:00 Biomedical Ontology Matching Using the AgreementMaker System
18:50:00 Bioportal | Ontologies and Integrated Data Resources at the Click of a Mouse
18:55:00 Populous | A Tool for Populating an Ontology
19:00:00 Dinner & Keynote Lecture | Virtual Physiological Human Project Susanna-Assunta Sansone
Friday, July 29, 2011
08:00:00 Continental Breakfast
08:30:00 Ontologies for Biomedical Investigations Melanie Courtot, Bjoern Peters
08:35:00 An Advanced Strategy for Integration of Biological Measurement Data
08:40:00 Annotating Experimental Records Using Ontologies
08:45:00 Ontology Driven Data Collection for EuPathDB
08:50:00 Developing an Application Ontology for Biomedical Resource Annotation and Retrieval: Challenges and Lessons Learned
09:50:00 Refreshment Break
10:20:00 Ontology Mapping and Integration Christopher Mungall
10:25:00 Mapping Composition for Matching Large Life Science Ontologies
10:30:00 A Generic Semantic Relatedness Measure for Biomedical Ontologies
10:35:00 Aligning the Parasite Experiment Ontology and the Ontology for Biomedical Investigations
10:40:00 A Case Study of ICD-11 Anatomy Value Set Extraction from SNOMED CT Harold Solbrig
10:50:00 The HL7 Approach to Semantic Interoperability Barry Smith
12:00:00 Buffet Lunch
13:30:00 NCBO Technology in Support of Clinical and Translational Science
15:00:00 Refreshment Break
15:30:00 Parallel Sessions on Special Topics
15:35:00 The OBO Foundry, featuring discussions of the Infectious Disease Ontology, the Ontology for Biomedical Investigations, the Ontology for General Medical Sciences, and the Plant Ontology
15:55:00 Further sessions to be announced
17:30:00 Poster Session, Software Demonstrations and Cash-Bar Reception
17:35:00 The Blood Ontology | An Ontology in the Domain of Hematology Barry Smith
17:40:00 An Analysis of Gene Ontology Concepts in the Biomedical Journal Articles
17:45:00 Employing Reasoning within the Phenoscape Knowledgebase
17:50:00 Waiting for a Robust Disease Ontology | A Mashup of OMIM and MeSH as a Practical Interim Solution Judith Blake
18:00:00 Developing a Reagent Application Ontology within the OBO Foundry Framework Christopher L. Shaffer
18:05:00 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 Deborah Siegele
18:10:00 Towards an Adverse Event Reporting Ontology Melanie Courtot
18:15:00 OntoOrpha | An Ontology to Support Edition and Audit of Rare Diseases Knowledge in Orphanet
18:20:00 An Ontology for Gastrointestinal Endoscopy
18:25:00 Enriching the Ontology for Biomedical Investigations (OBI) to Improve its Suitability for Web Service Annotations John Miller, Chris Stoeckert
18:30:00 Recent developments in the ChEBI Ontology Janna Hastings
18:35:00 Representing Local Identifiers in a Referent-Tracking System Werner Ceusters
18:40:00 Software Demonstrations
18:45:00 The Vitro Integrated Ontology Editor and Semantic Web Application
18:50:00 The BioPortal Import Plugin for Protégé
18:55:00 The Biomedical Ontology Applications (BOA) Framework
18:55:00 The NCBO Annotator: Ontology-Based Annotation as a Web Service
19:00:00 OntoFox and its Application in Development of Brucellosis Ontology
19:05:00 Dinner & Keynote Lecture | Practical Applications of Ontologies in Clinical Systems Olivier Bodenreider
Saturday, July 30, 2011
08:00:00 Continental Breakfast
08:30:00 Ontology and the Electronic Health Record Christopher G. Chute, Kent Spackman
08:35:00 Representing the Reality Underlying Demographic Data
08:40:00 Information Models and Ontologies for Representing the Electronic Health Record Stefan Schulz
08:45:00 Ontology-based Mammography Annotation with SQWRL
08:50:00 The CHRONIOUS Ontology Suite | Methodology and Design Principles
10:00:00 Refreshment Break
10:30:00 Panel | Problems with Existing EHR Paradigms and How Ontology Can Solve Them Christopher G. Chute
11:45:00 Buffet Lunch
13:00:00 Principles of Ontology Development Alexander Diehl
13:05:00 Applying Rigidity to Standardizing OBO Foundry Candidate Ontologies
13:10:00 Higgs Bosons, Mars Missions, and Unicorn Delusions: How to Deal with Terms of Unclear Reference in Scientific Ontologies Stefan Schulz, Robert Hoehndorf
13:15:00 Towards an Ontology for Conceptual Modeling
13:20:00 What's in an Is About Link? Chemical Diagrams and the Information Artifact Ontology Janna Hastings, Colin Batchelor
14:30:00 Refreshment Break
15:00:00 Panel | Collaborative Ontology Development: Why? and How? Chimezie Ogbuji, Bjoern Peters, Barry Smith
16:00:00 Closing Remarks Barry Smith
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