| Vol-1747 urn:nbn:de:0074-1747-1 Copyright © 2016 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-BioCreative 2016
Food, Nutrition, Health and Environment for the 9 Billion

### Proceedings of the Joint International Conference on Biological Ontology and BioCreative

### Corvallis, Oregon, United States, August 1-4, 2016.

Edited by

### Pankaj Jaiswal *
Robert Hoehndorf **
Cecilia Arighi ***
Austin Meier *

* Oregon State University, College of Agricultural Sciences, Corvallis, Oregon, United States
** King Abdullah University of Science and Technology, Division of Computational Bioscience, KAUST, Saudi Arabia
** University of Delaware, Department of Computer & Information Sciences, Newark, Delaware, United States

## Table of Contents

- Preface and abstract booklet PDF

- bibtex

### BioCreative Plenary Session #1 : Text Mining-facilitated Models of Curation

- SourceData: Making Data Discoverable
  Nancy George, Sara El-Gebali, Thomas Lemberger
- Cycles of Scientific Investigation in Discourse - Machine Reading Methods for the Primary Research Contributions of a Paper
  Gully A. Burns, Anita de Waard, Pradeep Dasigi, Eduard H. Hovy
- Collaborative Workspaces for Pathway Curation
  Funda Durupinar-Babur, Metin Can Siper, Ugur Dogrusoz, Istemi Bahceci, Ozgun Babur, Emek Demir
- Crowdsourcing Protein Family Database Curation
  Matt Jeffryes, Maria Liakata, Alex Bateman
- Opportunities and Challenges Presented by Wikidata in the Context of Biocuration
  Benjamin Good, Sebastian Burgstaller-Muehlbacher, Elvira Mitraka, Timothy Putman, Andrew Su, Andra Waagmeester

### Plenary Session #2 : Text Mining in Precision Medicine

- Text Mining to Enable Routine Personalized Cancer Therapy
  Hua Xu
- MutD - A PubMed Scale Resource for Protein Mutation-Disease Relations through Bio-Medical Literature Mining
  Ravikumar Komandur Elayavilli, Majid Rastegar-Mojarad, Hongfang Liu
- CancerMine: Knowledge Base Construction for Personalised Cancer Treatment
  Jake Lever, Martin Jones, Steven Jm Jones
- Text Mining for Drug Development: Gathering Insights to Support Decision Making
  Sherri Matis-Mitchell

### BioCreative Plenary Session #3 : Domain Portability or Generalizability Across Medical Literature

- NLP for the Institute: Developing and Deploying an NLP Capability to Accelerate Cancer Research
  Aaron Cohen
- Annotations for Biomedical Research and Healthcare - Bridging the Gap
  Olivier Bodenreider
- PubAnnotation: A Public Shared Platform for Scientific Literature Annotation.
  Jin-Dong Kim
- BioCconvert: A Conversion Tool Between BioC and PubAnnotation
  Donald C. Comeau, Rezarta Islamaj Doğan, Sun Kim, Chih-Hsuan Wei, W. John Wilbur, Zhiyong Lu

### ICBO and BioCreative Joint Posters and Demo Session #1 :

- Plant Image Segmentation and Annotation with Ontologies in BisQue
  Justin Preece, Justin Elser, Pankaj Jaiswal, Kris Kvilekval, Dmitry Fedorov, B.S. Manjunath, Ryan Kitchen, Xu Xu, Dmitrios Trigkakis, Sinisa Todorovic, Seth Carbon
- SPARQL2OWL: Towards Bridging the Semantic Gap Between RDF and OWL
  Mona Alsharani, Hussein Almashouq, Robert Hoehndorf
- The Phenoscape Knowledgebase: Tools and APIs for Computing Across Phenotypes from Evolutionary Diversity and Model Organisms
  James Balhoff
- Updates to the AberOWL Ontology Repository
  Miguel Ángel Rodríguez-García, Luke Slater, Imane Boudellioua, Paul Schofield, Georgios Gkoutos, Robert Hoehndorf
- Enhancing Information Accessibility of Publications with Text Mining and Ontology
  Weijia Xu, Amit Gupta, Pankaj Jaiswal, Crispin Taylor, Patti Lockhart

### Joint ICBO and BioCreative Plenary Session #1 : Natural Language Processing & Data Mining with Ontologies

- Large-scale Semantic Indexing with Biomedical Ontologies
  Chih-Hsuan Wei, Robert Leaman, Zhiyong Lu
- One Tagger, Many Uses: Illustrating the Power of Ontologies in Dictionary-based Named Entity Recognition
  Lars Juhl Jensen
- Scalable Text Mining Assisted Curation of PTM Proteoforms in the Protein Ontology
  Karen Ross, Darren Natale, Cecilia Arighi, Sheng-Chih Chen, Hongzhan Huang, Gang Li, Jia Ren, Michael Wang, K Vijay-Shanker, Cathy Wu
- Cardiovascular Health and Physical Activity: A Model for Health Promotion and Decision Support Ontologies
  Vimala Ponna, Aaron Baer, Matthew Lange
- A Web Application for Extracting Key Domain Information for Scientific Publications Using Ontology
  Weijia Xu, Amit Gupta, Pankaj Jaiswal, Crispin Taylor, Patti Lockhart
- Use of Text Mining for Experimental Factor Ontology Coverage Expansion in the Scope of Target Validation
  Senay Kafkas, Ian Dunham, Helen Parkinson, Johanna Mcentyre

### ICBO Plenary Session #2 : SDGIO: Sustainable Development Goals Interface Ontology--Semantics for Sustainability

- Environmental Semantics for Sustainable Development in an Interconnected Biosphere
  Pier Luigi Buttigieg, Mark Jensen, Ramona Walls, Christopher Mungall
- Sustainable Development Goals Interface Ontology
  Mark Jensen
- Defining and Sustaining Populations and Communities
  Ramona Walls
- Data-driven Agricultural Research for Development: A Need for Data Harmonization Via Semantics
  Medha Devare, Céline Aubert, Marie-Angélique Laporte, Léo Valette, Elizabeth Arnaud, Pier Luigi Buttigieg
- The UNEP Ontologies and the OBO Foundry
  Barry Smith, Mark Jensen

### ICBO and BioCreative Joint Posters and Demo : Session #2

- Ontobull and BFOConvert: Web-based Programs to Support Automatic Ontology Conversion
  Edison Ong, Zuoshuang Xiang, Jie Zheng, Barry Smith, Yongqun He
- Reusing the NCBO BioPortal Technology for Agronomy to Build AgroPortal
  Clément Jonquet, Anne Toulet, Elizabeth Arnaud, Sophie Aubin, Esther Dzalé Yeumo, Vincent Emonet, John Graybeal, Mark A. Musen, Cyril Pommier, Pierre Larmande
- Humane OWL: RDF and OWL for Humans
  James A. Overton
- Easy Extraction of Terms and Definitions with OWL2TL
  John Judkins, Joseph Utecht, Mathias Brochhausen

### ICBO Plenary Session #4 : Ontology Development and Application

- An Analysis of Differences in Biological Pathway Resources
  Lucy Wang, John Gennari, Neil Abernethy
- Enhancing the Human Phenotype Ontology for Use by the Layperson
  Nicole Vasilevsky, Mark Engelstad, Erin Foster, Chris Mungall, Peter Robinson, Sebastian Köhler, Melissa Haendel
- Dealing with Social and Legal Entities in the Obstetric and Neonatal Domain
  Fernanda Farinelli, Mauricio Almeida, Peter Elkin, Barry Smith
- Ten Simple Rules for Biomedical Ontology Development
  Melanie Courtot, James Malone, Chris Mungall
- Building Concordant Ontologies for Drug Discovery
  Hande Küçük-Mcginty, Saurabh Metha, Yu Lin, Nooshin Nabizadeh, Vasileios Stathias, Dusica Vidovic, Amar Koleti, Christopher Mader, Jianbin Duan, Ubbo Visser, Stephan Schurer
- The Planteome Project
  Laurel Cooper, Austin Meier, Justin Elser, Justin Preece, Xu Xu, Ryan Kitchen, Botong Qu, Eugene Zhang, Sinisa Todorovic, Pankaj Jaiswal, Marie-Angélique Laporte, Elizabeth Arnaud, Seth Carbon, Chris Mungall, Barry Smith, Georgios Gkoutos, John Doonan
- Annotating Germplasm to Planteome Reference Ontologies
  Austin Meier, Laurel Cooper, Justin Elser, Pankaj Jaiswal, Marie-Angélique Laporte

### ICBO Plenary Session #5 : Ontology-based Applications

- A Descriptive Delta for Identifying Changes in SNOMED CT
  Christopher Ochs, Yehoshua Perl, Gai Elhanan, James Case
- Visualizing the "Big Picture" of Change in NCIt's Biological Processes
  Yehoshua Perl, Christopher Ochs, Sherri de Coronado, Nicole Thomas
- Malaria Study Data Integration and Information Retrieval Based on OBO Foundry Ontologies
  Jie Zheng, Jashon Cade, Brian Brunk, David Roos, Chris Stoeckert, San James, Emmanuel Arinaitwe, Bryan Greenhouse, Grant Dorsey, Steven Sullivan, Jane Carlton, Gabriel Carrasco-Escobar, Dionicia Gamboa, Paula Maguina-Mercedes, Joseph Vinetz
- OOSTT: a Resource for Analyzing the Organizational Structures of Trauma Centers and Trauma Systems
  Joseph Utecht, John Judkins, Mathias Brochhausen, Terra Colvin Jr., J. Neil Otte, Nicholas Rogers, Robert Rose, Maria Alvi, Amanda Hicks, Jane Ball, Stephen M. Bowman, Robert T. Maxson, Rosemary Nabaweesi, Rohit Pradhan, Nels D. Sanddal, M. Eduard Tudoreanu, Robert Winchell
- Towards a Standard Ontology Metadata Model
  Hua Min, Stuart Turner, Sherri de Coronado, Brian Davis, Trish Whetzel, Robert R. Freimuth, Harold R. Solbrig, Richard Kiefer, Michael Riben, Grace A. Stafford, Lawrence Wright, Riki Ohira
- An Ontological Framework for Representing Topological Information in Human Anatomy
  Takeshi Imai, Emiko Shinohara, Masayuki Kajino, Ryota Sakurai, Kazuhiko Ohe, Kouji Kozaki, Riichiro Mizoguchi
- Natural Language Definitions for the Leukemia Knowledge Domain
  Amanda Damasceno De Souza, Mauricio Barcellos Almeida

### ICBO Plenary Session #6 : Semantics and Interoperability

- Identifying Missing Hierarchical Relations in SNOMED CT from Logical Definitions Based on the Lexical Features of Concept Names
  Olivier Bodenreider
- A Semantic Web Representation of Entire Populations
  Daniel Welch, Amanda Hicks, Josh Hanna, William Hogan
- Improving the Semantics of Drug Prescriptions with a Realist Ontology
  Jean-Francois Ethier, Ryeyan Taseen, Luc Lavoie, Adrien Barton
- Qualitative Causal Analyses of Biosimulation Models
  Maxwell Neal, John Gennari, Daniel Cook
- SEPIO: A Semantic Model for the Integration and Analysis of Scientific Evidence
  Matthew Brush, Kent Shefchek, Melissa Haendel
- Measuring the Importance of Annotation Granularity to the Detection of Semantic Similarity Between Phenotype Profiles
  Prashanti Manda, James P. Balhoff, Todd J. Vision

### ICBO Plenary Session #7 : Data Annotation, Standards and Computational Reasoning

- A Quality-Assurance Study of ChEBI
  Hasan Yumak, Ling Chen, Michael Halper, Ling Zheng, Yehoshua Perl, Gai Elhanan
- To MIREOT or not to MIREOT? A Case Study of the Impact of Using MIREOT in the Experimental Factor Ontology (EFO)
  Luke Slater, Georgios Gkoutos, Paul Schofield, Robert Hoehndorf
- Semantic Digitization of Experimental Data in Biological Sciences
  Saurabh Raghuvanshi
- Representation of Parts within the Foundational Model of Anatomy Ontology
  Melissa Clarkson
- A Realist Representation of Social Identity Data
  Amanda Hicks

### ICBO Flash Talks/Posters :

- Towards a Schistosomiasis Ontology (IDOSCHISTO) Extending the Infectious Disease Ontology
  Gaoussou Camara, Sylvie Despres, Rim Djedidi, Moussa Lo
- Adding Evidence Type Representation to DIDEO
  Mathias Brochhausen, Philip E. Empey, Jodi Schneider, William R. Hogan, Richard D. Boyce
- Multi-species Ontologies of the Craniofacial Musculoskeletal System
  Jose L.V. Mejino, James Brinkley, Timothy Cox, Landon Detwiler
- EGO: A Biomedical Ontology for Integrative Epigenome Representation and Analysis
  Yongqun He, Zhaohui Qin, Jie Zheng
- An Ontological Representation for the Transtheoretical Theory
  Hua Min, Robert H. Friedman, Julie Wright
- Building a Molecular Glyco-phenotype Ontology to Decipher Undiagnosed Diseases
  Jean-Philippe Gourdine, Thomas Metz, David Koeller, Matthew Brush, Melissa Haendel
- The Cell Line Ontology Integration and Analysis of the Knowledge of LINCS Cell Lines
  Edison Ong, Jiangan Xie, Zhaohui Ni, Qingping Liu, Yu Lin, Vasileios Stathias, Caty Chung, Stephan Schurer, Yongqun He
- Gold-Standard Ontology-Based Annotation of Concepts in Biomedical Text in the CRAFT Corpus: Updates and Extensions
  Michael Bada, Nicole Vasilevsky, Melissa Haendel, Lawrence Hunter
- How to Summarize Big Knowledge Subjects
  Ling Zheng, Yehoshua Perl, James Geller, Gai Elhanan
- Analysis of SNOMED "Bleeding" Concepts & Terms
  Jonathan Bona, Selja Seppälä, Werner Ceusters
- Uc_Sense: An Ontology for Scientifically-based Unambiguous Characterization of Sensory Experiences
  Aaron Baer, Matthew Lange
- NAPRALERT, from a Historical Information Silo to a Linked Resource Able to Address the New Challenges in Natural Products Chemistry and Pharmacognosy.
  Jonathan Bisson, James McAlpine, James Graham, Guido Pauli
- uc_Eating: Ontology for Unambiguous Characterization of Eating and Food Habits
  Kimiya Taji, Matthew Lange
- Towards Designing an Ontology Encompassing the Environment-agriculture-food-diet-health Knowledge Spectrum for Food System Sustainability and Resilience.
  Ruthie Musker, Matthew Lange, Allan Hollander, Patrick Huber, Nathaniel Springer, Courtney Riggle, James Quinn, Thomas Tomich
- uc_Milk: An Ontology for Scientifically-based Unambiguous Characterization of Mammalian Milk, their Composition and the Biological Processes Giving Rise to their Creation
  Emeline Colet, Matthew Lange
- Definition Coverage in the OBO Foundry Ontologies: The Big Picture
  Daniel Schlegel, Selja Seppälä, Peter Elkin
- Comparison of Ontology Mapping Techniques to Map Plant Trait Ontologies
  Marie-Angélique Laporte, Léo Valette, Laurel Cooper, Chris Mungall, Austin Meier, Pankaj Jaiswal, Elizabeth Arnaud
- The ImmPort Antibody Ontology
  William Duncan, Travis Allen, Jonathan Bona, Olivia Helfer, Barry Smith, Alan Ruttenberg, Alexander D. Diehl
- Opportunities and Challenges Presented by Wikidata in the Context of Biocuration
  Benjamin Good, Timothy Putman, Andrew Su, Andra Waagmeester, Sebastian Burgstaller-Muehlbacher, Elvira Mitraka
- Growth of the Zebrafish Anatomy Ontology: Expanded to Support Adult Morphology and Dynamic Changes in the Early Embryo
  Ceri Van Slyke, Yvonne Bradford, Christian Pich
- FoodON: A Global Farm-to-Fork Food Ontology
  Emma Griffiths, Damion Dooley, Pier Luigi Buttigieg, Robert Hoehndorf, Fiona Brinkman, William Hsiao
- SourceData: Making Data Discoverable
  Nancy George, Sara El-Gebali, Thomas Lemberger
- Towards an Ontology of Schizophrenia
  Fumiaki Toyoshima
- An OBI Ontology Datum Proof Sheet
  Damion Dooley, Emma Griffiths, Fiona Brinkman, William Hsiao
- The Zebrafish Experimental Conditions Ontology Systemizing Experimental Descriptions in ZFIN
  Yvonne Bradford, Ceri Van Slyke, Sabrina Toro, Sridhar Ramachandran
- Performance Evaluation Clinical Task Ontology(PECTO)
  Jose F Florez-Arango, Santiago Patiño-Giraldo, Jack W Smith, Sriram Iyengar
- Dealing with Elements of Medical Encounters: an Approach Based on the Ontological Realism
  Fernanda Farinelli, Mauricio Almeida, Peter Elkin, Barry Smith
- uc_FIDO: Unambiguous Characterization of Food Interactions with Drugs Ontology
  Constantine Spyrou, Matthew Lange
- Global Agricultural Concept Scheme: A Hub for Agricultural Vocabularies
  Caterina Caracciolo, Tom Baker, Elizabeth Arnaud
- Supporting Database Annotations and Beyond with the Evidence & Conclusion Ontology (ECO)
  Marcus Chibucos, Suvarna Nadendla, James Munro, Elvira Mitraka, Dustin Olley, Nicole Vasilevsky, Matthew Brush, Michelle Giglio
- Planteome Gene Annotation Enrichment Analysis
  Botong Qu, Jaden Diefenbaugh, Eugene Zhang, Justin Elser, Pankaj Jaiswal, Seth Carbon, Christopher Mungall
- Enhancing SciENcv through Semantic Research Profile Integration with the VIVO-ISF Ontology
  Marijane White, Matthew Brush, Shahim Essaid, Robin Champieux, Adrienne Zell, Melissa Haendel, Colin Grove, Syeda Momina Tabish, David Eichmann
- Ignet: A Centrality and INO-based Web System for Analyzing and Visualizing Literature-mined Networks
  Arzucan Ozgur, Junguk Hur, Zuoshuang Xiang, Edison Ong, Dragomir Radev, Yongqun He
- Disease Named Entity Recognition Using NCBI Corpus
  Thomas Hahn, Hidayat Ur Rahman, Richard Segall
- Label Embedding Approach for Transfer Learning
  Rasha Obeidat, Xiaoli Fern, Prasad Tadepalli

- The Biological Collections Ontology links traditional and contemporary biodiversity data
  Ramona L. Walls, Robert P. Guralnick
- The Plant Phenology Ontology - Integrating plant phenology data across diverse spatial and temporal scales
  Brian J. Stucky, Ellen G. Denny, Ramona L. Walls, John Deck, Robert P. Guralnick, Jennifer Yost

2016-11-29: submitted by Austin Meier, metadata incl. bibliographic data published under Creative Commons CC0
2016-11-29: published on CEUR-WS.org |valid HTML5|