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ICBO 2018: Corvallis, Oregon, USA
- Pankaj Jaiswal, Laurel Cooper, Melissa A. Haendel, Christopher J. Mungall:
Proceedings of the 9th International Conference on Biological Ontology (ICBO 2018), Corvallis, Oregon, USA, August 7-10, 2018. CEUR Workshop Proceedings 2285, CEUR-WS.org 2018
Full Papers
- Lucas Beasley, Prashanti Manda:
Comparison of Natural Language Processing Tools for Automatic Gene Ontology Annotation of Scientific Literature. - Hao Liu, Ling Chen, Ling Zheng, Yehoshua Perl, James Geller:
A Quality Assurance Methodology for ChEBI Ontology Focusing on Uncommonly Modeled Concepts. - Christian J. Stoeckert Jr., David L. Birtwell, Hayden Freedman, Mark A. Miller, Heather Williams:
Transforming and Unifying Research with Biomedical Ontologies: The Penn TURBO Project. - Adrien Barton, Olivier Grenier, Jean-François Ethier:
The Identity and Mereology of Pathological Dispositions. - Melissa D. Clarkson, Mark E. Whipple:
Does the Foundational Model of Anatomy Ontology Provide a Knowledgebase for Learning and Assessment in Anatomy Education? - Michael Halper, Christopher Ochs, Yehoshua Perl, Sivaram Arabandi, Mark A. Musen:
Quality Assurance of Ontology Content Reuse. - Prashanti Manda, Lucas Beasley, Somya D. Mohanty:
Taking a Dive: Experiments in Deep Learning for Automatic Ontology-Based Annotation of Scientific Literature. - Yongqun 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:
KTAO: A Kidney Tissue Atlas Ontology to Support Community-Based Kidney Knowledge Base Development and Data Integration. - Konstantin Schekotihin, Patrick Rodler, Wolfgang Schmid, Matthew Horridge, Tania Tudorache:
Test-Driven Ontology Development in Protégé. - Hao Liu, Ling Zheng, Yehoshua Perl, James Geller, Gai Elhanan:
Can a Convolutional Neural Network Support Auditing of NCI Thesaurus Neoplasm Concepts? - Olivier Bodenreider, Julie James:
The New SNOMED CT International Medicinal Product Model. - Jonathan P. Bona, Tracy S. Nolan, Mathias Brochhausen:
Ontology-Enhanced Representations of Non-Image Data in The Cancer Image Archive. - Deendayal Dinakarpandian, Michaela Liedtke, Mark A. Musen, Bhavish Dinakar:
TOCSOC: A Temporal Ontology for Comparing the Survival Outcomes of Clinical Trials in Oncology. - Rebecca Tauber, James P. Balhoff, Eric Douglass, Chris Mungall, James A. Overton:
Standardizing Ontology Workflows Using ROBOT.
Short Papers
- Dimitrios Trigkakis, Justin Preece, Austin Meier, Justin Elser, Kristian Kvilekval, Dmitry V. Fedorov, B. S. Manjunath, Pankaj Jaiswal, Sinisa Todorovic:
Planteome & BisQue: Automating Image Annotation with Ontologies using Deep-Learning Networks. - Austin Meier, Marie-Angélique Laporte, Justin Elser, Laurel Cooper, Justin Preece, Pankaj Jaiswal, Jorrit H. Poelen:
OOPS: The Ontology of Plant Stress, A Semi-Automated Standardization Methodology. - Randi Vita, Bjoern Peters, James A. Overton, Kei-Hoi Cheung, Steven H. Kleinstein:
Formalizing the Representation of Immune Exposures for Human Immunology Studies. - Amit Gupta, Weijia Xu, Pankaj Jaiswal, Crispin Taylor, Jennifer Regala:
Domain Informational Vocabulary Extraction Experiences with Publication Pipeline Integration and Ontology Curation. - Tarini Naravane, Matthew Lange:
Ontological Framework for Representation of Tractable Flavor: Food Phenotype, Sensation, Perception. - Prashanti Manda, Todd J. Vision:
On the Statistical Sensitivity of Semantic Similarity Metrics. - Lorena Endara, J. Gordon Burleigh, Laurel Cooper, Pankaj Jaiswal, Marie-Angélique Laporte, Hong Cui:
A Natural Language Processing Pipeline to Extract Phenotypic Data from Formal Taxonomic Descriptions with a Focus on Flagellate Plants.
Extended Abstracts for Posters and Demonstrations
- Stanley J. F. Laulederkind, G. Thomas Hayman, Shur-Jen Wang, Elizabeth R. Bolton, Jennifer R. Smith, Marek Tutaj, Jeff de Pons, Mary Shimoyama, Melinda R. Dwinell:
Adapting Disease Vocabularies for Curation at the Rat Genome Database. - Brenda Farrell, Jason Bengtson:
Ontology Based Data Architecture to Promote Data Sharing in Electrophysiology. - Susan M. Bello, Terry F. Hayamizu, Cynthia L. Smith, Martin Ringwald:
Using Equivalence Axioms from the Mammalian Phenotype Ontology to Facilitate Phenotype and Expression Comparisons. - Konstantin Schekotihin, Patrick Rodler, Wolfgang Schmid, Matthew Horridge, Tania Tudorache:
A Protégé Plug-In for Test-Driven Ontology Development. - Anna Maria Masci, Shannon McCall, Alessandro Racioppi, Helena Judge Ellis, Jihad S. Obeid, Barry Smith, Christian J. Stoeckert Jr., Jie Zheng:
Standardization of the Histopathology Cancer Report: An Ontological Approach. - Citlalli Mejía, Julio Collado-Vides:
A Falsification Approach to Create and Check Ontology Definitions. - Rebecca Tauber, James B. Munro, Suvarna Nadendla, Binika Chunara, Marcus C. Chibucos, Michelle G. Giglio:
Current Development in the Evidence and Conclusion Ontology (ECO). - Nicolas Matentzoglu, David Osumi-Sutherland:
Reconciling Ontology Definitions using the Ontology Pattern Reconciliation Workbench and the DOSDP Framework. - Matthew Horridge, Rafael S. Gonçalves, Csongor I. Nyulas, Tania Tudorache, Mark A. Musen:
Protégé 5.5 - Improvements for Editing Biomedical Ontologies. - Edison Ong, Yongqun He, Jie Zheng:
eXtensible Ontology Development (XOD) using Web-based Ontoanimal Tools. - Allan Hollander, Christine Geith, Matthew Lange:
An Expertise Ontology for Cooperative Extension. - Jean-Philippe F. Gourdine, Nicole A. Vasilevsky, Lilly Winfree, Matthew H. Brush, Melissa A. Haendel:
Expanding the Molecular Glycophenotype Ontology to include model organisms and acquired diseases. - Danielle Welter, Simon Jupp, David Osumi-Sutherland:
Human Cell Atlas Ontology. - Pasan Fernando, Erliang Zeng Paula Mabee:
The Integrative use of Anatomy Ontology and Protein-protein Interaction Networks to Study Evolutionary Phenotypic Transitions. - Troy J. Pells, Malcolm E. Fisher, Erik Segerdell, Joshua D. Fortriede, Kevin A. Burns, Stanley Chu, Praneet Chaturvedi, Christina James-Zorn, Vaneet Lotay, Mardi J. Nenni, Virgilio G. Ponferrada, Dong Zhou Wang, Ying Wang, Kamran Karimi, Peter D. Vize, Aaron M. Zorn:
Visualization of Gene Expression and Expression as a Phenotype with the XPO, XAO and DO using a Combination of Experimental Data Sources. - Melissa D. Clarkson:
Developing Graphic Libraries to Accompany the Craniofacial Human Ontology. - Corey J. Hayes, Jonathan P. Bona, Mathias Brochhausen:
Towards the Development of an Opioid Misuse Ontology. - Suhila A. Sawesi, Josette Jones, William Duncan:
An Ontology For Formal Representation Of Medication Adherence-Related Knowledge: Case Study In Breast Cancer. - Ian Braun, Carolyn J. Lawrence-Dill:
Computational Classification of Phenologs Across Biological Diversity. - J. Neil Otte, Cooper Stansbury, Jonathan Vajda, Frank J. Manion, Elizabeth Umberfield, Yongqun He, Marcelline R. Harris, Jihad S. Obeid, Mathias Brochhausen, William D. Duncan, Cui Tao:
Coordinated Evolution of Ontologies of Informed Consent. - William D. Duncan, Philip Whalen, Aditya Muralidharan, Jonathan Kiddy:
Enhancing Semantic Analysis of Pathology Reports. - William 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 H. Gilbert:
Using the Oral Health and Disease Ontology to Study Dental Outcomes in National Dental PBRN Practices. - Paula M. Mabee, James P. Balhoff, Wasila M. Dahdul, Hilmar Lapp, Christopher J. Mungall, Todd J. Vision:
Reasoning over Anatomical Homology in the Phenoscape KB.
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