| Vol-2931 urn:nbn:de:0074-2931-2 Copyright © 2019 for the individual papers by the papers' authors. Copyright © 2021 for the volume as a collection by its editors. This volume and its papers are published under the Creative Commons License Attribution 4.0 International (CC BY 4.0).

# ICBO 2019
International Conference on Biomedical Ontology 2019

### Proceedings of the 10th International Conference on Biomedical Ontology (ICBO 2019)

### Buffalo, New York, USA, July 30 – August 2, 2019.

Edited by

### Alexander D. Diehl *
William D. Duncan **
Gloria Sanso ***

* University at Buffalo Department of Biomedical Informatics
** Lawrence Berkeley National Laboratory Berkeley Bioinformatics Open-source Projects (BBOP)
*** University at Buffalo Department of Philosophy

## Table of Contents

- Preface
  Summary: There were 53 papers submitted for peer-review to this event. Of these, 43 were accepted for this volume: 19 full papers, 23 poster abstracts, and 1 software demonstration extended abstract.

### Full Papers

- TXPO: A Toxic Process Ontology for Better Understanding of Drug-Induced Liver Injury A.1-8
  Yuki Yamagata, Yoshinobu Igarashi, Noriyuki Nakatsu, Hiroshi Yamada
- Ontology as Product-Service System: Lessons Learned from GO, BFO and DOLCE B.1-9
  Barry Smith
- Representing Causation: A Dispositional Perspective C.1-8
  Fumiaki Toyoshima
- Roles and Their Siblings in Basic Formal Ontology D.1-9
  Fumiaki Toyoshima
- Wordified Ontologies: Evaluating a Novel Paradigm for Ontology Editing E.1-7
  Aisha Blfgeh, Phillip Lord
- Comparing the Representation of Medicinal Products in RxNorm and SNOMED CT - Consequences on interoperability F.1-6
  Jean Noel Nikiema, Olivier Bodenreider
- A Classification of Instructions in Drug Prescriptions and Pharmacist Documents G.1-7
  Adrien Barton, Paul Fabry, Jean-François Ethier
- ICEO: a Biological Ontology for Representing and Analyzing the Bacterial Integrative and Conjugative Element H.1-10
  Meng Liu, Hong-Yu Ou, Yongqun He
- Foundation for a Realist Ontology of Cognitive Processes I.1-8
  David Kasmier, David Limbaugh, Barry Smith
- Mental Capabilities J.1-7
  Eric Merrell, David Limbaugh, Alex Anderson, Barry Smith
- Warranted Diagnosis K.1-10
  David Limbaugh, David Kasmier, Werner Ceusters, Barry Smith
- A Collaborative, Realism-Based, Electronic Healthcare Graph: Public Data, Common Data Models, and Practical Instantiation L.1-10
  Mark A. Miller, Christian J. Stoeckert Jr.
- Foundations for a Realism-based Drug Repurposing Ontology M.1-8
  James Schuler, William Mangione, Ram Samudrala, Werner Ceusters
- ICDO: Ontological Representation of the International Classification of Diseases (ICD) and its Application in English and Chinese Healthy Data Standardization N.1-1O
  Ling Wan, Edison Ong, Yongqun He
- The Ontology of Physics for Biology - A Companion to Basic Formal Ontology O.1-9
  Daniel L. Cook, John H. Gennari, Maxwell L. Neal
- Early steps of an Ontology for Magnetic Resonance Imaging: MRIO P.1-5
  Lucas M. Serra, Michael G. Dwyer, William D. Duncan, Alexander D. Diehl
- Visual Representation for Knowledge Representation: Graphics Libraries to Support Anatomy Terminologies and Ontologies Q.1-9
  Melissa Clarkson, Steven Roggenkamp
- OPMI: the Ontology of Precision Medicine and Investigation and its Support for Clinical Data and Metadata Representation and Analysis R.1-10
  Yongqun He, Edison Ong, Jennifer Schaub, Frederick Dowd, John F. O'Toole, Anastasios Siapos, Christian Reich, Sarah Seager, Ling Wan, Hong Yu, Jie Zheng, Christian Stoeckert, Xiaolin Yang, Sheng Yang, Becky Steck, Christopher Park, Laura Barisoni, Matthias Kretzler, Jonathan Himmelfarb, Ravi Iyengar1, Sean D. Mooney
- Building a Shared Ontology Use Patterns Repository S.1-7
  Jonathan P. Bona, Joseph Utecht, Sarah Bost, Corey J. Hayes, Mathias Brochhausen

### Poster Abstracts and Software Demos

- Ontology-based Semantic Mapping of Adverse Outcome Pathways T.1
  Rong-Lin Wang
- Integrating and Maintaining OMIM Cross-references in the Disease Ontology U.1-2
  Susan M Bello, Cynthia L Smith, Lynn M Schriml
- Ontological Derivation of Mendeleev's Periodic Table of Chemical Elements V.1
  Kaiyong Liu, Yongqun He
- Alignment of the Ontology of Host-Microbiome Interactions (OHMI) High Level Terms with Existing OBO Ontologies W.1
  Yongqun He, Jie Zheng, Anna Maria Masci, Jihad Obeid
- Ontological Modeling of Two-Component Regulatory Systems X.1
  Hsin-Hui Huang, Meng Liu, Yongqun He
- Representation of Protein Aggregates in an Ontological Framework Y.1
  Lauren Wishnie, Alexander Cox, Alexander Diehl
- Towards an Ontology-Driven Machine Learning Approach to the Diagnosis Classification Problem in Autism Spectrum Disorder Z.1
  Fumiaki Toyoshima
- Where Does an Ontology Start? AA.1
  Henriette Harmse, Melanie Courtot, Warren Read, Nico Matentzoglu, David Osumi-Sutherland, Simon Jupp
- LABO: an Ontology for Laboratory Test Prescription and Reporting BB.1
  Paul Fabry, Adrien Barton, Jean-François Ethier
- OGG-Bac: Ontological Representation of Orthologous Bacterial Genes CC.1
  Meng Liu, Hong-Yu Ou, Yongqun He
- Reconstruction of Hierarchical Structures in a Thesaurus-based Ontology through Curation by Domain Experts DD.1
  Tatsuya Kushida, Kouji Kozaki, Yasunori Yamamoto, Atsuko Yamaguchi, Takahiro Kawamura, Takako Nakagawa, Yuka Tateisi, Toshihisa Takagi
- Ontolion: A Web-based Integrative Ontology Development Platform EE.1
  Edison Ong, Yongqun He
- Catalog for Ontologies Towards Semantic Integration Across Environmental Health Science Research Data FF.1
  Resham Kulkarni, Mike Conway, Deep Patel, Maria Shatz, Stephanie Holmgren, Charles Schmitt
- Mapping Data Annotated with the Minimum Information About BIobank data Sharing (MIABIS) 2.0 to the Ontology for Biobanking (OBIB) GG.1-2
  Sarah Bost, Niina Eklund, Kaisa Silander, Jie Zheng, Christian J. Stoeckert, Mathias Brochhausen
- Using Stases to Enrich Queries for When and Where Regulations Are in Force HH.1
  Jonathan M. Vajda, J. Neil Otte, Cooper Stansbury, Frank J. Manion, Marcelline R. Harris, Cui Tao
- OWLmaker: An Application for Generating OWL Files from Tabular Text II.1-3
  Jie Zheng, John Judkins, Christian Stoeckert
- Semantic Integration of Neuroinformatics Data in the Arkansas Image Enterprise System with Open Biomedical Ontologies JJ.1
  Jonathan P. Bona, Aaron S. Kemp, Tracy Nolan, Linda Larson-Prior, Aparna Das, Tuhin Virmani, Lakshmi Pillai, Mathias Brochhausen, Fred Prior
- NGBO: Introducing -omics Data into Biobanking Ontology KK.1
  Dalia Alghamdi, Damion M. Dooley, Gurinder Gosal, Emma J. Griffiths, William W.L. Hsiao
- An Ontology-Driven Web Platform for Publishing Data Specifications to Support Data Sharing LL.1
  Damion M. Dooley, Ivan S. Gill, Emma J. Griffiths, William L. Hsiao
- Opportunities for Ontologies in Medical Device Total Product Life Cycle (TPLC) Evaluation MM.1
  Asiyah Yu Lin
- Medical Action Ontology (MAxO) NN.1
  Leigh C. Carmody, Xingmin A. Zhang, Nicole A. Vasilevsky, Chris J. Mungall, Nico Matentzoglu, Peter N. Robinson
- Tibb-Med-Linking-Onto: Knowledge Representation of Linking Prophetic Medicine with Current Medical practices OO.1
  Muna Al-Razgan, Salwa Ali, Sarah Mohamed Hassan, Asiyah Yu Lin
- Tripartite Term Enrichment Analysis of Multiple Sclerosis Patient Reported Outcomes PP.1
  Mackenzie T. Smith, Lauren M. Wishnie, William D. Duncan, Mark Jensen, Alexander D. Diehl
- Biomedical Informatics Investigator QQ.1-5
  Peter L. Elkin, Sarah Mullin, Sylvester Sakilay

2021-08-13: submitted by Alexander D. Diehl, metadata incl. bibliographic data published under Creative Commons CC0
2021-08-19: published on CEUR Workshop Proceedings (CEUR-WS.org, ISSN 1613-0073) |valid HTML5|