Table of Contents

• AEO: A Realism-Based Biomedical Ontology for the Representation of Adverse EventsYongqun He, Zuoshuang Xiang, Sirarat Sarntivijai, Luca Toldo, Werner Ceusters. [doi]
• The Foundational Model of Neuroanatomy Ontology: An Ontology Framework to Support Neuroanatomical Data IntegrationB. Nolan Nichols, José L. V. Mejino Jr., James F. Brinkley. [doi]
• An Advanced Strategy for Integration of Biological Measurement DataHiroshi 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. [doi]
• What's in an 'is about' Link? Chemical Diagrams and the Information Artifact OntologyJanna Hastings, Colin R. Batchelor, Fabian Neuhaus, Christoph Steinbeck. [doi]
• Use of Multiple Ontologies to Characterize the Bioactivity of Small MoleculesYing Yan, Janna Hastings, Jee-Hyub Kim, Stefan Schulz, Christoph Steinbeck, Dietrich Rebholz-Schuhmann. [doi]
• A Framework Ontology for Computer-Based Patient Record SystemsChimezie Ogbuji. [doi]
• Cell Line Ontology: Redesigning the Cell Line Knowledgebase to Aid Integrative Translational InformaticsSirarat 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. [doi]
• Aligning the Parasite Experiment Ontology and the Ontology for Biomedical Investigations Using AgreementMakerValerie Cross, Cosmin Stroe, Xueheng Hu, Pramit Silwal, Maryam Panahiazar, Isabel F. Cruz, Priti Parikh, Amit P. Sheth. [doi]
• Composite Annotation for Heart DevelopmentTariq Abdulla, Ryan Imms, Jean-Marc Schleich, Ron Summers. [doi]
• Ontologies in the Fish Tank: Using the Zebrafish Anatomy Ontology with Other OBO Ontologies to Annotate Expression and PhenotypeYvonne Bradford, Ceri E. Van Slyke. [doi]
• Modeling Issues and Solutions: Building a Taxonomy from a Biology TextbookPatrice Seyed, John Pacheco, Andrew Goldenkranz, Vinay K. Chaudhri. [doi]
• SHIRAZ and CABERNET: Leveraging Automation, Crowdsourcing, and Ontologies to Improve the Accuracy and Throughput of Zebrafish Histological Phenotype AnnotationsBrian A. Canada, Georgia K. Thomas, John Schleicher, James Ze Wang, Keith C. Cheng. [doi]
• The Age of Data-Driven Medicine: Mining the Electronic Health RecordPaea LePendu, Mark A. Musen, Nigam H. Shah. [doi]
• The CHRONIOUS Ontology Suite: Methodology and Design PrinciplesLuc Schneider, Mathias Brochhausen. [doi]
• An Ontology-Based Approach to Linking Model Organisms and Resources to Human DiseasesChris 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. [doi]
• Rapid Development of an Ontology of Coriell Cell LinesChao Pang, Tomasz Adamusiak, Helen E. Parkinson, James Malone. [doi]
• Hyperontology for the Biomedical Ontologist: A Sketch and Some ExamplesOliver Kutz, Till Mossakowski, Janna Hastings, Alexander García Castro, Aleksandra Sojic. [doi]
• Using Failure Modes, Mechanisms, and Effects Analysis in Medical Device Adverse Event InvestigationsShunfeng Cheng, Diganta Das, Michael G. Pecht. [doi]
• Information Models and Ontologies for Representing the Electronic Health RecordDaniel Karlsson, Martin Berzell, Stefan Schulz. [doi]
• A Case Study of ICD-11 Anatomy Value Set Extraction from SNOMED CTGuoqian Jiang, Harold R. Solbrig, Robert J. G. Chalmers, Kent A. Spackman, Alan L. Rector, Christopher G. Chute. [doi]
• Classifying Adverse Events from Clinical TrialsBernard LaSalle, Richard Bradshaw. [doi]
• The Ontology of Microbial Phenotypes (OMP): A Precomposed Ontology Based on Cross Products from Multiple External Ontologies that is Used for Guiding Microbial Phenotype AnnotationMarcus C. Chibucos, Adrienne E. Zweifel, Deborah A. Siegele, Peter Uetz, Michelle Giglio, James C. Hu. [doi]
• Generic Semantic Relatedness Measure for Biomedical OntologiesJoão D. Ferreira, Francisco M. Couto. [doi]
• Higgs Bosons, Mars Missions, and Unicorn Delusions: How to Deal with Terms of Dubious Reference in Scientific OntologiesStefan Schulz, Mathias Brochhausen, Robert Hoehndorf. [doi]
• An Ontological Representation of Adverse Drug EventsGuoqian Jiang, Jon D. Duke, Jyotishman Pathak, Christopher G. Chute. [doi]
• Revising the Cell OntologyTerrence F. Meehan, Christopher J. Mungall, Alexander D. Diehl. [doi]
• Bioportal: Ontologies and Integrated Data Resources at the Click of a MousePatricia 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. [doi]
• Bridging Multiple Ontologies: Representation of the Liver Immune ResponseAnna Maria Masci, Jeffrey Roach, Bernard de Bono, Pierre Grenon, Lindsay G. Cowell. [doi]
• Using RxNorm to Extract Medication Data from Electronic Health Records in the Rochester Epidemiology ProjectJyotishman Pathak, Shawn P. Murphy, Brian N. Willaert, Hilal M. Kremers, Christopher G. Chute, Barbara P. Yawn, Walter A. Rocca. [doi]
• The Vitro Integrated Ontology Editor and Semantic Web ApplicationBrian Lowe, Brian Caruso, Nick Cappadona, Miles Worthington, Stella Mitchell, Jon Corson-Rikert. [doi]
• The NCBO Annotator: Ontology-Based Annotation as a Web ServicePatricia L. Whetzel, Clement Jonquet, Cherie Youn, Michael Dorf, Ray W. Fergerson, Mark A. Musen, Nigam Shah. [doi]
• Towards a Semantic Web Application: Ontology-Driven Ortholog Clustering AnalysisYu Lin, Zuoshuang Xiang, Yongqun He. [doi]
• River Flow Model of DiseasesRiichiro Mizoguchi, Kouji Kozaki, Hiroko Kou, Yuki Yamagata, Takeshi Imai, Kayo Waki, Kazuhiko Ohe. [doi]
• Integrating Anatomy and Phenotype Ontologies with Taxonomic HierarchiesJames P. Balhoff, Peter E. Midford, Hilmar Lapp. [doi]
• Aligning Research Resource and Researcher Representation: The eagle-i and VIVO Use CaseStella Mitchell, Carlo Torniai, Brian Lowe, Jon Corson-Rikert, Melanie Wilson, Mansoor Ahmed, Shanshan Chen, Ying Ding, Nicholas Rejack, Melissa Haendel. [doi]
• Connecting Ontologies for the Representation of Biological PathwaysAnna Maria Masci, Mikhail K. Levin, Alan Ruttenberg, Lindsay G. Cowell. [doi]
• Mouse Anatomy Ontologies and GXDTerry F. Hayamizu, Martin Ringwald. [doi]
• Multiple Ontologies in Healthcare Information Technology: Motivations and Recommendation for Ontology Mapping and AlignmentColin A. Puri, Karthik Gomadam, Prateek Jain 0001, Peter Z. Yeh, Kunal Verma. [doi]
• Ontology-Based Analysis of Event-Related PotentialsGwen A. Frishkoff, Robert M. Frank, Paea LePendu. [doi]
• Modularization for the Cell OntologyChristopher J. Mungall, Melissa Haendel, Amelia Ireland, Shahid Manzoor, Terry Meehan, David Osumi-Sutherland, Carlo Torniai, Alexander D. Diehl. [doi]
• Epistemological Issues in Information Organization Instruments: Ontologies and Health Information ModelsAndré Queiroz de Andrade, Mauricio Barcellos Almeida. [doi]
• Employing Reasoning within the Phenoscape KnowledgebaseJames P. Balhoff, Wasila M. Dahdul, Hilmar Lapp, Peter E. Midford, Todd J. Vision, Monte Westerfield, Paula M. Mabee. [doi]
• Biomedical Analyses: OWL Model Based EditionPierre-Yves Vandenbussche, Ferdinand Dhombres, Sylvie Cormont, Jean Charlet, Eric Lepage. [doi]
• Phenoscape: Use Cases and Anatomy Ontology Requirements for Linking Evolutionary and Model Organism PhenotypesWasila M. Dahdul, James P. Balhoff, Hilmar Lapp, Peter E. Midford, Todd J. Vision, Monte Westerfield, Paula M. Mabee. [doi]
• Towards Desiderata for Provenance Ontologies in BiomedicineSatya Sanket Sahoo. [doi]
• Representing Local Identifiers in a Referent-Tracking SystemWilliam R. Hogan, Swetha Garimalla, Shariq A. Tariq, Werner Ceusters. [doi]
• Applications for a Translational Biomedical Ontology ModelRobert Yao, Graciela Gonzalez. [doi]
• Towards an Adverse Event Reporting OntologyMélanie Courtot, Ryan R. Brinkman. [doi]
• Populous: A Tool for Populating an OntologySimon Jupp, Matthew Horridge, Luigi Iannone, Julie Klein, Stuart Owen, Joost Schanstra, Katy Wolstencroft, Robert Stevens. [doi]
• Developing a Reagent Application Ontology within the OBO Foundry FrameworkMatthew H. Brush, Nicole Vasilevsky, Carlo Torniai, Tenille Johnson, Chris Shaffer, Melissa Haendel. [doi]
• Ontology Driven Data Collection for EuPathDBJie Zheng, Omar S. Harb, Christian J. Stoeckert Jr.. [doi]
• Supporting Medical Device Adverse Event Analysis in an Interoperable Clinical Environment: Design of a Data Logging and Playback SystemDavid Arney, Sandy Weininger, Susan F. Whitehead, Julian M. Goldman. [doi]
• 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. [doi]
• Where GO is Going and What it Means for Ontology ExtensionCatia Pesquita, Francisco M. Couto. [doi]
• Applying Rigidity to Standardizing OBO Foundry Candidate OntologiesPatrice Seyed, Stuart C. Shapiro. [doi]
• A Case Study in Using ZFA and PATO for Describing Histological Phenotypes in the Larval ZebrafishBrian A. Canada, Georgia K. Thomas, Timothy Cooper, Keith C. Cheng. [doi]
• Quality of Care Domain Modeling in Cancer: A Semantic ApproachSina Madani, Dean F. Sittig, Parsa Mirhaji, Kim Dunn. [doi]
• Developing an Application Ontology for Biomedical Resource Annotation and Retrieval: Challenges and Lessons LearnedCarlo Torniai, Matthew H. Brush, Nicole Vasilevsky, Erik Segerdell, Melanie Wilson, Tenille Johnson, Karen Corday, Chris Shaffer, Melissa Haendel. [doi]
• Gene Ontology Signatures for Immune Cell-Types Inferred by Gene Expression AnalysisTerrence F. Meehan, Christopher J. Mungall, Judith A. Blake, Alexander D. Diehl. [doi]
• OntoOrpha: An Ontology to Support Edition and Audit of Knowledge of Rare Diseases in ORPHANETFerdinand Dhombres, Pierre-Yves Vandenbussche, Ana Rath, Marc Hanauer, Annie Olry, Bruno Urbero, Rémy Choquet, Jean Charlet. [doi]
• Waiting for a Robust Disease Ontology: A Merger of OMIM and MeSH as a Practical Interim SolutionSusan 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. [doi]
• Multi-Species Anatomy Ontology Development Requires a Pluralist Approach to Label-Class MappingIstvén Mikó, Matthew J. Yoder, Matthew A. Bertone, Katja C. Seltmann, Andrew R. Deans. [doi]
• Biomedical Ontology Matching Using the AgreementMaker SystemIsabel F. Cruz, Cosmin Stroe, Catia Pesquita, Francisco M. Couto, Valerie Cross. [doi]
• Refining Ontology for Glucose Metabolism DisordersYu Lin. [doi]
• Toward Answering Time-Related Questions from Adverse Event Reports Using Ontology-Based ApproachesCui Tao, Guoqian Jiang, Kimberly Clark, Deepak K. Sharma, Christopher G. Chute. [doi]
• Mapping Composition for Matching Large Life Science OntologiesAnika Gross, Michael Hartung, Toralf Kirsten, Erhard Rahm. [doi]
• The Biomedical Ontology Applications (BOA) FrameworkBruno Tavares, Hugo P. Bastos, Daniel Faria, João D. Ferreira, Tiago Grego, Catia Pesquita, Francisco M. Couto. [doi]
• Bioassay Ontology to Describe High-Throughput Screening Assays and their ResultsUma Vempati, Ubbo Visser, Saminda Abeyruwan, Kunie Sakurai, Magdalena Przydzial, Caty Chung, Robin P. Smith, Amar Koleti, Christopher Mader, Vance P. Lemmon, Stephan C. Schürer. [doi]
• Towards an Ontology for Conceptual ModelingJames P. McCusker, Joanne S. Luciano, Deborah L. McGuinness. [doi]
• The HL7 Approach to Semantic InteroperabilityJobst Landgrebe, Barry Smith. [doi]
• Adverse Events from Clinical Studies in Pharmaceutical Research and DevelopmentPia Emilsson, Kerstin Forsberg. [doi]
• Ontobee: A Linked Data Server and Browser for Ontology TermsZuoshuang Xiang, Chris Mungall, Alan Ruttenberg, Yongqun He. [doi]
• Annotating Experimental Records Using OntologiesAlexander García Castro, Olga L. Giraldo, Jael García. [doi]
• owl_cpp, a C++ Library for Working with OWL OntologiesMikhail K. Levin, Alan Ruttenberg, Anna Maria Masci, Lindsay G. Cowell. [doi]
• HeartCyc: A Cardiac Cycle Process Ontology Based in the Ontology of Physics for BiologyDaniel L. Cook, Michal Galdzicki, Maxwell Lewis Neal, José L. V. Mejino Jr., John H. Gennari. [doi]
• Towards a Body Fluids Ontology: A Unified Application Ontology for Basic and Translational ScienceJiye Ai, Mauricio Barcellos Almeida, André Queiroz de Andrade, Alan Ruttenberg, David Tai Wai Wong, Barry Smith. [doi]
• CARO 2.0David Osumi-Sutherland. [doi]
• Workflows and Framework for Nutritional/Metabolic Phenotype/Genotype and Foods-for-Health Knowledge IntegrationMatthew Lange, J. Bruce German, Jim Kaput. [doi]
• Dispositions and Processes in the Emotion OntologyJanna Hastings, Werner Ceusters, Barry Smith, Kevin Mulligan. [doi]
• The Vertebrate Bridging Ontology (VBO)Ravensara S. Travillian, James Malone, Chao Pang, John M. Hancock, Peter W. H. Holland, Paul N. Schofield, Helen E. Parkinson. [doi]
• Reporting Adverse Events: Basis for a Common RepresentationMélanie Courtot, Ryan R. Brinkman, Alan Ruttenberg. [doi]
• Representing the Reality Underlying Demographic DataWilliam R. Hogan, Swetha Garimalla, Shariq A. Tariq. [doi]
• Enriching the Ontology for Biomedical Investigations (OBI) to Improve its Suitability for Web Service AnnotationsChaitanya Guttula, Alok Dhamanaskar, Rui Wang, John A. Miller, Jessica C. Kissinger, Jie Zheng, Christian J. Stoeckert Jr.. [doi]
• NIFSTD and NeuroLex: Comprehensive Neuroscience Ontology Development Based on Multiple Biomedical Ontologies and Community InvolvementFahim T. Imam, Stephen D. Larson, Jeffrey S. Grethe, Amarnath Gupta, Anita Bandrowski, Maryann E. Martone. [doi]
• Philosophy, Ontology, and Scientific ExplanationJames A. Overton. [doi]
• A Meta-Data Approach to Querying Multiple Biomedical OntologiesRavi Palla, Dan Tecuci, Vinay Shet, Mathäus Dejori. [doi]
• The BioPortal Import Plugin for ProtégéJithun Nair, Tania Tudorache, Trish Whetzel, Natalya Fridman Noy, Mark A. Musen. [doi]
• Recent Developments in the ChEBI OntologyJanna Hastings, Paula de Matos, Adriano Dekker, Marcus Ennis, Kenneth Haug, Zara Josephs, Gareth Owen, Steve Turner, Christoph Steinbeck. [doi]
• OntoFox and its Application in Development of Brucellosis OntologyZuoshuang Xiang, Yu Lin, Yongqun He. [doi]
• An Ontology for Gastrointestinal EndoscopyShahim Essaid. [doi]
• The Blood Ontology: An Ontology in the Domain of HematologyMauricio Barcellos Almeida, Anna Barbara de Freitas Carneiro Proietti, Jiye Ai, Barry Smith. [doi]
• Building the OBO Foundry - One Policy at a TimeMélanie Courtot, Chris Mungall, Ryan R. Brinkman, Alan Ruttenberg. [doi]
• Protein-Centric Connection of Biomedical Knowledge: Protein Ontology (PRO) Research and Annotation ToolsCecilia 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. [doi]
• FUNCARO: A Functional Extension to CARODavid Osumi-Sutherland. [doi]