Table of Contents

• Adapting Disease Vocabularies for Curation at the Rat Genome DatabaseStanley J. F. Laulederkind, G. Thomas Hayman, Shur-Jen Wang, Elizabeth Bolton, Jennifer R. Smith, Marek Tutaj, Jeff de Pons, Mary Shimoyama, Melinda R. Dwinell. [doi]
• Standardizing Ontology Workflows Using ROBOTRebecca Tauber, James P. Balhoff, Eric Douglass, Chris Mungall, James A. Overton. [doi]
• eXtensible Ontology Development (XOD) using Web-based Ontoanimal ToolsEdison Ong, Yongqun He, Jie Zheng 0001. [doi]
• Coordinated Evolution of Ontologies of Informed ConsentJ. Neil Otte, Cooper Stansbury, Jonathan Vajda, Frank J. Manion, Elizabeth Umberfield, Yongqun He, Marcelline R. Harris, Jihad Obeid, Mathias Brochhausen, William D. Duncan, Cui Tao. [doi]
• Protégé 5.5 - Improvements for Editing Biomedical OntologiesMatthew Horridge, Rafael S. Gonçalves, Csongor I. Nyulas, Tania Tudorache, Mark A. Musen. [doi]
• A Protégé Plug-In for Test-Driven Ontology DevelopmentKonstantin Schekotihin, Patrick Rodler, Wolfgang Schmid, Matthew Horridge, Tania Tudorache. [doi]
• On the Statistical Sensitivity of Semantic Similarity MetricsPrashanti Manda, Todd J. Vision. [doi]
• The Identity and Mereology of Pathological DispositionsAdrien Barton, Olivier Grenier, Jean-François Ethier. [doi]
• Developing Graphic Libraries to Accompany the Craniofacial Human OntologyMelissa Clarkson. [doi]
• An Expertise Ontology for Cooperative ExtensionAllan Hollander, Christine Geith, Matthew Lange. [doi]
• Comparison of Natural Language Processing Tools for Automatic Gene Ontology Annotation of Scientific LiteratureLucas Beasley, Prashanti Manda. [doi]
• Towards the Development of an Opioid Misuse OntologyCorey Hayes, Jonathan P. Bona, Mathias Brochhausen. [doi]
• A Natural Language Processing Pipeline to Extract Phenotypic Data from Formal Taxonomic Descriptions with a Focus on Flagellate PlantsLorena Endara, J. Gordon Burleigh, Laurel Cooper, Pankaj Jaiswal, Marie-Angélique Laporte, Hong Cui. [doi]
• Human Cell Atlas OntologyDanielle Welter, Simon Jupp, David Osumi-Sutherland. [doi]
• A Quality Assurance Methodology for ChEBI Ontology Focusing on Uncommonly Modeled ConceptsHao Liu, Ling Chen, Ling Zheng, Yehoshua Perl, James Geller. [doi]
• KTAO: A Kidney Tissue Atlas Ontology to Support Community-Based Kidney Knowledge Base Development and Data IntegrationYongqun He, Becky Steck, Edison Ong, Laura Mariani, Chrysta Lienczewski, Ulysses J. Balis, Matthias Kretzler, Jonathan Himmelfarb, John F. Bertram, Evren U. Azeloglu, Ravi Iyengar, Deborah Hoshizaki, Sean D. Mooney. [doi]
• Using the Oral Health and Disease Ontology to Study Dental Outcomes in National Dental PBRN PracticesWilliam D. Duncan, Thankam Thyvalikakath, Zasim Azhar Siddiqui, Michelle LaPradd, Chen Wen, Jim Zheng, Anna Roberts, Daniel Hood, Aparna Manimangala, Donald Rindal, Mark Jurkovich, Tracy Shea, David Bogacz, Terrence Yu, Jeffry Fellows, Valerie Gordan, Gregg Gilbert. [doi]
• TOCSOC: A Temporal Ontology for Comparing the Survival Outcomes of Clinical Trials in OncologyDeendayal Dinakarpandian, Michaela Liedtke, Mark A. Musen, Bhavish Dinakar. [doi]
• An Ontology For Formal Representation Of Medication Adherence-Related Knowledge: Case Study In Breast CancerSuhila A. Sawesi, Josette Jones, William Duncan. [doi]
• Visualization of Gene Expression and Expression as a Phenotype with the XPO, XAO and DO using a Combination of Experimental Data SourcesTroy J. Pells, Malcolm Fisher, Erik Segerdell, Joshua Fortriede, Kevin A. Burns, Stanley Chu, Praneet Chaturvedi, Christina James-Zorn, Vaneet Lotay, Mardi Nenni, Virgilio G. Ponferrada, Dong Zhou Wang, Ying Wang, Kamran Karimi, Peter D. Vize, Aaron M. Zorn. [doi]
• Can a Convolutional Neural Network Support Auditing of NCI Thesaurus Neoplasm Concepts?Hao Liu 0025, Ling Zheng, Yehoshua Perl, James Geller, Gai Elhanan. [doi]
• Standardization of the Histopathology Cancer Report: An Ontological ApproachAnna Maria Masci, Shannon McCall, Alessandro Racioppi, Helena Judge Ellis, Jihad S. Obeid, Barry Smith 0001, Christian J. Stoeckert Jr., Jie Zheng 0001. [doi]
• Planteome & BisQue: Automating Image Annotation with Ontologies using Deep-Learning NetworksDimitrios Trigkakis, Justin Preece, Austin Meier, Justin Elser, Kristian Kvilekval, Dmitry Fedorov, B. S. Manjunath, Pankaj Jaiswal, Sinisa Todorovic. [doi]
• A Falsification Approach to Create and Check Ontology DefinitionsCitlalli Mejía, Julio Collado-Vides. [doi]
• Ontology-Enhanced Representations of Non-Image Data in The Cancer Image ArchiveJonathan P. Bona, Tracy S. Nolan, Mathias Brochhausen. [doi]
• Domain Informational Vocabulary Extraction Experiences with Publication Pipeline Integration and Ontology CurationAmit Gupta, Weijia Xu, Pankaj Jaiswal, Crispin Taylor, Jennifer Regala. [doi]
• Ontological Framework for Representation of Tractable Flavor: Food Phenotype, Sensation, PerceptionTarini Naravane, Matthew Lange. [doi]
• Current Development in the Evidence and Conclusion Ontology (ECO)Rebecca Tauber, James B. Munro, Suvarna Nadendla, Binika Chunara, Marcus C. Chibucos, Michelle G. Giglio. [doi]
• Expanding the Molecular Glycophenotype Ontology to include model organisms and acquired diseasesJean-Philippe Gourdine, Nicole Vasilevsky, Lilly Winfree, Matthew H. Brush, Melissa Haendel. [doi]
• OOPS: The Ontology of Plant Stress, A Semi-Automated Standardization MethodologyAustin Meier, Marie-Angélique Laporte, Justin Elser, Laurel Cooper, Justin Preece, Pankaj Jaiswal, Jorrit H. Poelen. [doi]
• Reconciling Ontology Definitions using the Ontology Pattern Reconciliation Workbench and the DOSDP FrameworkNicolas Matentzoglu, David Osumi-Sutherland. [doi]
• Transforming and Unifying Research with Biomedical Ontologies: The Penn TURBO ProjectChristian J. Stoeckert Jr., David L. Birtwell, Hayden Freedman, Mark A. Miller, Heather Williams. [doi]
• Using Equivalence Axioms from the Mammalian Phenotype Ontology to Facilitate Phenotype and Expression ComparisonsSusan M. Bello, Terry F. Hayamizu, Cynthia L. Smith, Martin Ringwald. [doi]
• Formalizing the Representation of Immune Exposures for Human Immunology StudiesRandi Vita, Bjoern Peters, James A. Overton, Kei-Hoi Cheung, Steven H. Kleinstein. [doi]
• Reasoning over Anatomical Homology in the Phenoscape KBPaula M. Mabee, James P. Balhoff, Wasila M. Dahdul, Hilmar Lapp, Christopher J. Mungall, Todd J. Vision. [doi]
• Ontology Based Data Architecture to Promote Data Sharing in ElectrophysiologyBrenda Farrell, Jason Bengtson. [doi]
• The Integrative use of Anatomy Ontology and Protein-protein Interaction Networks to Study Evolutionary Phenotypic TransitionsPasan Fernando, Erliang Zeng Paula Mabee. [doi]
• The New SNOMED CT International Medicinal Product ModelOlivier Bodenreider, Julie James. [doi]
• Does the Foundational Model of Anatomy Ontology Provide a Knowledgebase for Learning and Assessment in Anatomy Education?Melissa D. Clarkson, Mark E. Whipple. [doi]
• Taking a Dive: Experiments in Deep Learning for Automatic Ontology-Based Annotation of Scientific LiteraturePrashanti Manda, Lucas Beasley, Somya D. Mohanty. [doi]
• Computational Classification of Phenologs Across Biological DiversityIan Braun, Carolyn J. Lawrence-Dill. [doi]
• Quality Assurance of Ontology Content ReuseMichael Halper, Christopher Ochs, Yehoshua Perl, Sivaram Arabandi, Mark A. Musen. [doi]
• Enhancing Semantic Analysis of Pathology ReportsWilliam D. Duncan, Philip Whalen, Aditya Muralidharan, Jonathan Kiddy. [doi]
• Test-Driven Ontology Development in ProtégéKonstantin Schekotihin, Patrick Rodler, Wolfgang Schmid, Matthew Horridge, Tania Tudorache. [doi]