| Vol-2137 urn:nbn:de:0074-2137-1 Copyright © 2017 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 2017
International Conference on Biomedical Ontology

### Proceedings of the 8th International Conference on Biomedical Ontology (ICBO 2017)

### Newcastle-upon-Tyne, United Kingdom, September 13th - 15th, 2017.

Edited by

### Matthew Horridge *
Phillip Lord **
Jennifer D. Warrender **

* Stanford University, Stanford, California, USA
** Newcastle University, Newcastle-upon-Tyne, United Kingdom

## Table of Contents

- Preface

### Main Conference Papers

- A Literature Based Approach to Define the Scope of Biomedical Ontologies: A Case Study on a Rehabilitation Therapy Ontology
  Mohammad K. Halawani, Rob Forsyth, Phillip Lord
- A Maturity Model for Biomedical Data Curation
  Mariam Alqasab, Suzanne M. Embury, Sandra de F. Mendes Sampaio
- BiPOm: Biological Interlocked Process Ontology for Metabolism. How to Infer Molecule Knowledge from Biological Process?
  Vincent Henry, Fatiha Saïs, Elodie Marchadier, Juliette Dibie, Anne Goelzer, Vincent Fromion
- Causation and the River Flow Model of Diseases
  Fumiaki Toyoshima, Riichiro Mizoguchi, Mitsuru Ikeda
- Classifying Processes and Basic Formal Ontology
  Mustafa Jarrar, Werner Ceusters
- Efficient Construction of a New Ontology for Life Sciences by Sub-classifying Related Terms in the Japan Science, Technology Agency Thesaurus
  Tatsuya Kushida, Kouji Kozaki, Yuka Tateisi, Katsutaro Watanabe, Takeshi Masuda, Katsuji Matsumura, Takahiro Kawamura, Toshihisa Takagi
- Facets, Tiers and Gems: Ontology Patterns for the Hypernormalisation
  Phillip Lord, Robert Stevens
- Integrating an Ontology for RDOC with Existing Biomedical Ontologies
  Mark Jensen, Alexander D. Diehl
- Logical Axiomatization of the Evidence & Conclusion Ontology (ECO) by Integrating External Ontology Classes
  Rebecca Tauber, Marcus C. Chibucos
- Ontology Development in Patients Information System for Stroke Rehabilitation
  Radhi Rafiee Afandi, Abduljalil Radman, Mahadi Bahari, Lailatul Qadri Zakaria, Muzaimi Mustapha, Waidah Ismail
- Scrutinizing the Axiomatic Basis of SNOMED CT: How Confused is it by the Ambiguous Terminology Paradigm?
  Jean Marie Rodrigues, Stefan Schulz, Alan L. Rector
- Scrutinizing the Relationships Between SNOMED CT Concepts and Semantic Tags
  Jonathan Bona, Werner Ceusters
- Similarity Metrics for Determining Overlap Among Biological Pathways
  Lucy L. Wang, John H. Gennari
- Supporting Ontology-Based Standardization of Biomedical Metadata in the CEDAR Workbench
  Marcos Martínez-Romero, Martin J. O'Connor, Michael Dorf, Jennifer Vendetti, Debra Willrett, Attila L. Egyedi, John Graybeal, Mark A. Musen
- User and Developer Interaction with Editable and Readable Ontologies
  Aisha Blfgeh, Phillip Lord
- What is a Risk? A Formal Representation of Risk of Stroke for People with Atrial Fibrillation
  Adrien Barton, Ludger Jansen, Arnaud Rosier, Jean-François Ethier

### Main Conference Poster and Demo Papers

- A Tentative Maturity Model for Biomedical Data Curation
  Mariam Alqasab, Suzanne Embury, Sandra de F. Mendes Sampaio
- Aligning the Human Phenotype and Mammalian Phenotype Ontology using Dead Simple Ontology Design Patterns
  Nicole Vasilevsky, James P. Balhoff, Chris J. Mungall, David Osumi-Sutherland, Sebastian Köhler, Susan Bello, Cynthia Smith, Peter Robinson, Melissa Haendel
- Errors and Artefacts in Histopathological Imaging
  Antony Galton, Shereen Fouad, Gabriel Landini, David Randell
- Extending the Ontology of Physics for Biology with Thermodynamics
  Daniel L. Cook, John H. Gennari, Maxwell L. Neal
- FoodOn: A Semantic Ontology Approach for Mapping Foodborne Disease Metadata
  Dalia A. Alghamdi, Damion M. Dooley, Gurinder Gosal, Emma J. Griffiths, Fiona S.L. Brinkman, William W.L. Hsiao
- Identitas: A Better Way To Be Meaningless
  Nizal Alshammry, Phillip Lord
- OLOBO: A New Ontology for Linking and Integrating Open Biological and Biomedical Ontologies
  Edison Ong, Yongqun He
- Ontology Challenges for the Stem Cell Community: Towards Integrative Data Mining in the Stemformatics Atlas
  Chris Pacheco Rivera, Rowland Mosbergen, Othmar Korn, Tyrone Chen, Isha Nagpal, Christine A. Wells
- Ontology of Cancer Related Social-Ecological Variables
  Dharani K. Balasubramanian, Jamillah Z. Khan, Jiang Bian, Yi Guo, William R. Hogan, Amanda Hicks
- OxO – A Gravy of Ontology Mapping Extracts
  Simon Jupp, Thomas Liener, Sirarat Sarntivijai, Olga Vrousgou, Tony Burdett, Helen Parkinson
- Tawny-SBOL: Using Ontologies to Design and Constrain Genetic Circuits
  Goksel Misirli, Phillip Lord
- The Human Behaviour-Change Project: Developing a Behaviour Change Intervention Ontology
  Emma Norris, Ailbhe Finnerty, Marta Marques, Robert West, James Thomas, Pol Mac Aonghusa, Marie Johnston, Michael P. Kelly, Susan Michie
- Toward Using Ontologies to Improve Results in Searches for Mental Health Information
  Jonathan Bona, John Grohol, Meredith Zozus, Robert Zozus, Mathias Brochhausen

### Oncology Ontology Workshop (ONCONTO 2017) Papers

- Tailoring the NCI Thesaurus for Use in The OBO Library
  James P. Balhoff, Matthew Brush, Laura Christopherson, Sherri de Coronado, Gilberto Fragoso, Melissa A. Haendel, Christopher J. Mungall, Kimberly Robasky, Nicole Vasilevsky, Lawrence W. Wright
- Towards an Ontology for Representing Malignant Neoplasms
  William D. Duncan, Carmelo Gaudioso, Alexander D. Diehl

### The 2nd Workshop on Representing Social and Legal Entities in the Biomedical Domain (SoLe-BD 2017) Papers

- Toward a BFO-Based Deontic Ontology
  Brian Donohue
- That Which we Call a Pediatrician Would by Any Other Name a Child Treat (or not)
  Amanda Hicks, William R. Hogan

2018-07-11: submitted by Matthew Horridge, metadata incl. bibliographic data published under Creative Commons CC0
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