| Vol-2285 urn:nbn:de:0074-2285-4 Copyright © 2018 for the individual papers by the papers' authors. Copying permitted for private and academic purposes. This volume is published and copyrighted by its editors.

# ICBO 2018
International Conference on Biological Ontology

### Proceedings of the 9th International Conference on Biological Ontology (ICBO 2018)

### Corvallis, Oregon, USA, August 7-10, 2018.

Edited by:

### Pankaj Jaiswal *
Laurel Cooper *
Melissa A. Haendel *
Christopher J. Mungall **

* Oregon State University, Corvallis, Oregon 97331, USA
** Lawrence Berkeley National Lab, Berkeley, California 94720, USA

## 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

2018-12-20: submitted by Pankaj Jaiswal and Laurel Cooper, metadata incl. bibliographic data published under Creative Commons CC0
2018-12-22: published on CEUR-WS.org |valid HTML5|