| Vol-1327 urn:nbn:de:0074-1327-1 Copyright © 2014 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 2014
International Conference on Biomedical Ontology

### Proceedings of the 5th International Conference on Biomedical Ontology

### Houston, Texas, USA, October 8-9, 2014.

Edited by

### William R. Hogan *
Sivaram Arabandi **
Mathias Brochhausen ***

* University of Florida, Professor of Health Outcomes and Policy, Clinical and Translational Research Building, Gainesville, USA
** Ontopro, Founder, Houston, USA
*** University of Arkansas for Medical Sciences, Assistant Professor of Biomedical Informatics, Stephens Spine Institute Building, Little Rock, USA

## Table of Contents

- Preface

### Scientific Paper

- Pain Assessment Terminology in the NCBO BioPortal: Evaluation and Recommendations 1-6
  Werner Ceusters
- Towards the Integration of Abnormality in Diseases 7-12
  Yuki Yamagata, Kouji Kozaki, Takeshi Imai, Kazuhiko Ohe, Riichiro Mizoguchi
- OGG: a Biological Ontology for Representing Genes and Genomes in Specific Organisms 13-20
  Yongqun He, Yue Liu, Bin Zhao
- A Novel Representation of Terms Related to Infectious Disease Epidemiology for Epidemic Modeling: The Apollo Structured Vocabulary and Pre-existing Representations 21-26
  Mathias Brochhausen, William Hogan, John Levander, Shawn Brown, Nicholas Millet, Josh Hanna, Michael Wagner
- Clinical Data Wrangling using Ontological Realism and Referent Tracking 27-32
  Werner Ceusters, Chiun Yu Hsu, Barry Smith
- Profiling ICD-11 Terminological Content Using the Common Terminology Services 2 (CTS2) Standard 33-38
  Guoqian Jiang, Harold Solbrig, Can Celik, Bedirhan Ustun, Christopher Chute

### Early-career Track Paper

- The Ontological Treatment of Sight and Blindness 39-42
  Patrick Ray, Alexander Cox, Mark Jensen, Alexander D. Diehl
- Knowledge Representation of Protein PTMs and Complexes in the Protein Ontology: Application to Multi-Faceted Disease Analysis 43-46
  Karen Ross, Catalina Tudor, Gang Li, Ruoyao Ding, Irem Celen, Julie Cowart, Cecilia Arighi, Darren Natale, Cathy Wu
- Quality of Care Metric Reporting from Clinical Narratives: Assessing Ontology Components 47-51
  Sina Madani, Reza Alemy, Dean Sittig, Hua Xu
- An Ontological Representation and Analysis of Patient-reported and Clinical Outcomes for Multiple Sclerosis 52-55
  Mark Jensen, Alexander Cox, Patrick Ray, Barbara E. Teter, Bianca Weinstock-Guttman, Alan Ruttenberg, Alexander D. Diehl
- Post-Traumatic Stress Disorder (PTSD) Ontology and Use Case 56-59
  Bryan Gamble, Samah Fodeh, Kei Cheung
- Representing Modification Sites in PRO 60-63
  Jonathan Bona, Alan Ruttenberg, Jenny Rouleau

### Abstract of Scientifc Paper Subsequently Submitted to, and Appearing in, Journal

- Modeling a Microbial Community and Biodiversity Assay with OBI and PCO OBO Foundry Ontologies: the Interoperability Gains of a Modular Approach 64
  Philippe Rocca-Serra, Ramona Walls, Jacob Parnell, Rachel Gallery, Jie Zheng, Susanna-Assunta Sansone, Alejandra Gonzalez-Beltran
- OBCS: The Ontology of Biological and Clinical Statistics 65
  Jie Zheng, Marcelline R. Harris, Anna Maria Masci, Yu Lin, Alfred Hero, Barry Smith, Yongqun He
- Using Ontology Fingerprints to Disambiguate Gene Name Entities in the Biomedical Literature 66
  Guocai Chen, Jieyi Zhao, Trevor Cohen, Cui Tao, Jingchun Sun, Hua Xu, Elmer Bernstam, Jia Zeng, Amber Johnson, Vijaykumar Holla, Ann Balley, Funda Meric-Bernstam, W. Jim Zheng
- Drug Target Prediction for Colorectal Cancer by Combining Ontology and Network Approaches 67
  Cui Tao, Jingchun Sun, Jim Zheng, Junjie Chen, Hua Xu

### Poster

- Pharmacological Class Data Representation in the Web Ontology Language (OWL) 68-69
  Qian Zhu, Cui Tao
- Developing a Patient Safety Ontology for Knowledge Management, Data Integration, and Decision Making 70-72
  Chen Liang, Yang Gong
- Making Biomedical Data Usable: NIH Community-Based Data and Metadata Standards Efforts 73
  Allen Dearry, Cindy Lawler, Rebecca Boyles, Astrid Haugen, Huerta Michael
- Ontological Representation of CDC Active Bacterial Core Surveillance Case Reports 74-77
  Albert Goldfain, Barry Smith, Lindsay Cowell
- Coverage of Rare Disease Names in Clinical Coding Systems and Ontologies and Implications for Electronic Health Records-Based Research 78-80
  Rachel Richesson, Kin Wah Fung, Olivier Bodenreider
- An Initial Framework for an Ontology-based Mobile Application for Vaccine Information Retrieval and Education 81-83
  Muhammad Amith, Cui Tao
- Development of a BFO-Based Informed Consent Ontology (ICO) 84-86
  Yu Lin, Marcelline R. Harris, Frank J. Manion, Elizabeth Eisenhauer, Bin Zhao, Wei Shi, Alla Karnovsky, Yongqun He
- Ontology-based Normalization for Disease-Lab test Relation Extraction 87-89
  Yaoyun Zhang, Jingqi Wang, Cui Tao, Hua Xu
- A Nanopublication Framework for Biological Networks using Cytoscape.js 90-92
  Jim Mccusker, Rui Yan, Kusum Solanki, John Erickson, Cynthia Chang, Michel Dumontier, Jonathan Dordick, Deborah McGuinness
- Ontobat: An Ontology-based Semantic Web Approach for Linked Data Processing and Analysis 93-95
  Zuoshuang Xiang, Yu Lin, Yongqun He
- Applications of OBI 'assay' 96-98
  Mark Jensen, Alexander P. Cox, Jonathan P. Bona, William Duncan, Patrick L. Ray, Alexander D. Diehl
- Linking LOINC and SNOMED CT: A Cooperative Approach to Enhance Each Terminology and Facilitate Co-usage 99-101
  Suzanne Santamaria, Farzaneh Ashrafi, Kent Spackman

### Software Demonstration Abstract

- SciCrunch: A Cooperative and Collaborative Data and Resource Discovery Platform for Scientific Communities 102-103
  Trish Whetzel
- An Ontologic Approach to Leverage Surgical Training Data Development and Application of a CranioMaxilloFacial Ontology 104-105
  Michael Grove, Jeff Emch
- RxClass – Navigating between Drug Classes and RxNorm Drugs 106-107
  Olivier Bodenreider, Lee Peters, Thang Nguyen
- DREAM 9: An Acute Myeloid Leukemia Prediction Big Data Challenge 108-109
  David Noren, Steven Kornblau, Chenyue W. Hu, Byron Long, Alex Bisberg, Raquel Norel, Gustavo Stolovitzky, Amina Qutub

2015-02-08: submitted by William R. Hogan, metadata incl. bibliographic data published under Creative Commons CC0
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