ICBO 2018
International Conference on Biological Ontology

Table of Contents

• Preface
  
  

Full Papers

• Comparison of Natural Language Processing Tools for Automatic Gene Ontology Annotation of Scientific Literature
  Lucas Beasley , Prashanti Manda
• A Quality Assurance Methodology for ChEBI Ontology Focusing on Uncommonly Modeled Concepts
  Hao Liu , Ling Chen , Ling Zheng , Yehoshua Perl , James Geller
• Transforming and Unifying Research with Biomedical Ontologies: The Penn TURBO Project
  Christian J. Stoeckert , David Birtwell , Hayden Freedman , Mark A. Miller , Heather Williams
• The Identity and Mereology of Pathological Dispositions
  Adrien Barton , Olivier Grenier , Jean-Francois Ethier
• Does the Foundational Model of Anatomy Ontology Provide a Knowledgebase for Learning and Assessment in Anatomy Education?
  Melissa D. Clarkson , Mark E. Whipple
• Quality Assurance of Ontology Content Reuse
  Michael Halper , Christopher Ochs , Yehoshua Perl , Sivaram Arabandi , Mark A. Musen
• Taking a Dive: Experiments in Deep Learning for Automatic Ontology-Based Annotation of Scientific Literature
  Prashanti Manda , Lucas Beasley , Somya D. Mohanty
• KTAO: A Kidney Tissue Atlas Ontology to Support Community-Based Kidney Knowledge Base Development and Data Integration
  Yongqun He , Becky Steck , Edison Ong , Laura Mariani , Chrysta Lienczewski , Ulysses Balis , Matthias Kretzler , Jonathan Himmelfarb , John F. Bertram , Evren Azeloglu , Ravi Iyengar , Deborah Hoshizaki , Sean D. Mooney
• Test-Driven Ontology Development in Protégé
  Konstantin Schekotihin , Patrick Rodler , Wolfgang Schmid , Matthew Horridge , Tania Tudorache
• Can a Convolutional Neural Network Support Auditing of NCI Thesaurus Neoplasm Concepts?
  Hao Liu , Ling Zheng , Yehoshua Perl , James Geller , Gai Elhana
• The New SNOMED CT International Medicinal Product Model
  Olivier Bodenreider , Julie James
• Ontology-Enhanced Representations of Non-Image Data in The Cancer Image Archive
  Jonathan Bona , Tracy Nolan , Mathias Brochhausen
• TOCSOC: A Temporal Ontology for Comparing the Survival Outcomes of Clinical Trials in Oncology
  Deendayal Dinakarpandian , Michaela Liedtke , Mark A. Musen , Bhavish Dinakar
• Standardizing Ontology Workflows Using ROBOT
  Rebecca Tauber , James Balhoff , Eric Douglass , Chris Mungall , James A. Overton
• On the Statistical Sensitivity of Semantic Similarity Metrics
  Prashanti Manda , Todd Vision

Short Papers

• Planteome & BisQue: Automating Image Annotation with Ontologies using Deep-Learning Networks
  Dimitrios Trigkakis , Justin Preece , Austin Meier , Justin Elser , Kris Kvilekval , Dmitry Fedorov , B.S. Manjunath , Pankaj Jaiswal , Sinisa Todorovic
• OOPS: The Ontology of Plant Stress, A Semi-Automated Standardization Methodology
  Austin Meier , Marie-Angélique Laporte , Justin Elser , Laurel Cooper , Justin Preece , Pankaj Jaiswal , Jorrit Poelen
• Formalizing the Representation of Immune Exposures for Human Immunology Studies
  Randi Vita , Bjoern Peters , James Overton , Kei-Hoi Cheung , Steven Kleinstein
• Domain Informational Vocabulary Extraction Experiences with Publication Pipeline Integration and Ontology Curation
  Amit Gupta , Weijia Xu , Pankaj Jaiswal , Crispin Taylor , Jennifer Regala
• Ontological Framework for Representation of Tractable Flavor: Food Phenotype, Sensation, Perception
  Tarini Naravane , Matthew Lange
• A Natural Language Processing Pipeline to Extract Phenotypic Data from Formal Taxonomic Descriptions with a Focus on Flagellate Plants
  Lorena Endara , Gordon Burleigh , Laurel Cooper , Pankaj Jaiswal , Marie-Angelique Laporte , Hong Cui

Extended Abstracts for Posters and Demonstrations

• Adapting Disease Vocabularies for Curation at the Rat Genome Database
  Stan Laulederkind , G. Thomas Hayman , Shur-Jen Wang , Elizabeth Bolton , Jennifer R. Smith , Marek Tutaj , Jeff De Pons , Mary Shimoyama , Melinda Dwinell
• Ontology Based Data Architecture to Promote Data Sharing in Electrophysiology
  Brenda Farrell , Jason Bengtson
• Using Equivalence Axioms from the Mammalian Phenotype Ontology to Facilitate Phenotype and Expression Comparisons
  Susan M. Bello , Terry F. Hayamizu , Cynthia L. Smith , Martin Ringwald , The MGI Software Group
• A Protégé Plug-In for Test-Driven Ontology Development
  Konstantin Schekotihin , Patrick Rodler , Wolfgang Schmid , Matthew Horridge , Tania Tudorache
• Standardization of the Histopathology Cancer Report: An Ontological Approach
  Anna Maria Masci , Shannon McCall , Alessandro Racioppi , Helena Judge Ellis , Jihad S. Obeid , Barry Smith , Christian Stoeckert , Jie Zheng
• A Falsification Approach to Create and Check Ontology Definitions
  Citlalli Mejía , Julio Collado-Vides
• Current Development in the Evidence and Conclusion Ontology (ECO)
  Rebecca Tauber , James B. Munro , Suvarna Nadendla , Binika Chunara , Marcus C. Chibucos , Michelle Giglio
• Reconciling Ontology Definitions using the Ontology Pattern Reconciliation Workbench and the DOSDP Framework
  Nicolas Matentzoglu , David Osumi-Sutherland
• Protégé 5.5 – Improvements for Editing Biomedical Ontologies
  Matthew Horridge , Rafael S Gonçalves , Csongor I Nyulas , Tania Tudorache , Mark Musen
• eXtensible Ontology Development (XOD) using Web-based Ontoanimal Tools
  Edison Ong , Yongqun He , Jie Zheng
• An Expertise Ontology for Cooperative Extension
  Allan Hollander , Christine Geith , Matthew Lange
• Expanding the Molecular Glycophenotype Ontology to include model organisms and acquired diseases
  Jean-Philippe Gourdine , Nicole Vasilevsky , Lilly Winfree , Matthew Brush , Melissa Haendel
• Human Cell Atlas Ontology
  Danielle Welter , Simon Jupp , David Osumi-Sutherland
• The Integrative use of Anatomy Ontology and Protein-protein Interaction Networks to Study Evolutionary Phenotypic Transitions
  Pasan Fernando , Erliang Zeng Paula Mabee
• Visualization of Gene Expression and Expression as a Phenotype with the XPO, XAO and DO using a Combination of Experimental Data Sources
  Troy Pells , Malcolm Fisher , Erik Segerdell , Joshua Fortriede , Kevin Burns , Stanley Chu , Praneet Chaturvedi , Christina James-Zorn , Vaneet Lotay , Mardi Nenni , V.G. Ponferrada , Dong Zhou Wang , Ying Wang , Kamran Karimi , Peter Vize , Aaron Zorn
• Developing Graphic Libraries to Accompany the Craniofacial Human Ontology
  Melissa Clarkson
• Towards the Development of an Opioid Misuse Ontology
  Corey Hayes , Jonathan Bona , Mathias Brochhausen
• An Ontology For Formal Representation Of Medication Adherence-Related Knowledge: Case Study In Breast Cancer
  Suhila Sawesi , Josette Jones , William Duncan
• Computational Classification of Phenologs Across Biological Diversity
  Ian Braun , Carolyn Lawrence-Dill
• Coordinated Evolution of Ontologies of Informed Consent
  J. Neil Otte , Cooper Stansbury , Jonathan Vajda , Frank Manion , Elizabeth Umberfield , Yongqun He , Marcelline Harris , Jihad Obeid , Mathias Brochhausen William Duncan , Cui Tao
• Enhancing Semantic Analysis of Pathology Reports
  William Duncan , Philip Whalen , Aditya Muralidharan , Jonathan Kiddy
• Using the Oral Health and Disease Ontology to Study Dental Outcomes in National Dental PBRN Practices
  William Duncan , Thankam Thyvalikakath , Zasim 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
• Reasoning over Anatomical Homology in the Phenoscape KB
  Paula Mabee , James Balhoff , Wasila Dahdul , Hilmar Lapp , Christopher Mungall , Todd Vision