| Vol-2807 urn:nbn:de:0074-2807-4 Copyright © 2020 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|ODLS 2020
International Conference on Biomedical Ontologies 2020

### Proceedings of the 11th International Conference on Biomedical Ontologies (ICBO)
joint with the 10th Workshop on Ontologies and Data in Life Sciences (ODLS) and part of the Bolzano Summer of Knowledge (BoSK 2020)

### Virtual conference hosted in Bolzano, Italy, September 17, 2020.

Edited by

### Janna Hastings *, **
Frank Loebe ***

* University College London, Department of Clinical, Educational and Health Psychology, London, UK
** Otto-von-Guericke University Magdeburg, Department of Computer Science, Magdeburg, Germany
*** University of Leipzig, Computer Science Institute, Leipzig, Germany

## Table of Contents

- Preface
  Summary: There were 35 papers submitted for peer-review to this event. Of these, 26 were accepted for this volume: 11 regular papers, 3 tools and applications papers, 3 early career extended abstracts, and 9 poster abstracts.

### Research Track

- Clinical Documents and Their Parts A.1-11
  Adrien Barton, Fumiaki Toyoshima, Jean-François Ethier
- QUESTO – An Ontology for Questionnaires B.1-12
  Paul Fabry, Adrien Barton, Jean-François Ethier
- Scaling and Querying a Semantically Rich, Electronic Healthcare Graph C.1-11
  Hayden Freedman, Mark A. Miller, Heather Williams, Christian J. Stoeckert Jr.
- Towards a Framework for Meaning Negotiation and Conflict Resolution in Ontology Authoring D.1-12
  Rolf Grütter, C. Maria Keet
- CIDO: The Community-Based Coronavirus Infectious Disease Ontology E.1-10
  Yongqun He, Hong Yu, Edison Ong, Yang Wang, Yingtong Liu, Anthony Huffman, Hsin-hui Huang, John Beverley, Asiyah Yu Lin, William D. Duncan, Sivaram Arabandi, Jiangan Xie, Junguk Hur, Xiaolin Yang, Luonan Chen, Gilbert S. Omenn, Brian Athey, Barry Smith
- Corpora as Evolving Entities: Embedding Corpora in Biomedical Ontologies F.1-11
  Elizabeth T. Hobbs, Stephen M. Goralski, Ashley Mitchell, Andrew Simpson, Dorjan Leka, Emmanuel Kotey, Matt Sekira, James B. Munro, Suvarna Nadendla, Rebecca Jackson, Aitor Gonzalez-Agirre, Martin Krallinger, Michelle Giglio, Ivan Erill
- Investigating One Million XRefs in Thirthy Ontologies from the OBO World G.1-12
  Amir Laadhar, Elcio Abrahão, Clement Jonquet
- CTO: A Community-Based Clinical Trial Ontology and Its Applications in PubChemRDF and SCAIView H.1-12
  Asiyah Yu Lin, Stephan Gebel, Qingliang Leon Li, Sumit Madan, Johannes Darms, Evan Bolton, Barry Smith, Martin Hofmann-Apitius, Yongqun Oliver He, Alpha Tom Kodamullil
- A Robust, Self-Training Classifier for Medication Strings, with Quantitative and Semantic Confidence Metrics I.1-12
  Mark A. Miller, Hayden Freedman, Christian J. Stoeckert Jr.
- A BioSequence Ontology from Molecular Structure J.1-12
  Jona Thai, Michael Grüninger
- Foundations for a Realism-Based Ontology of Protein Aggregates K.1-10
  Lauren Wishnie, Alexander P. Cox, Alexander D. Diehl, Werner Ceusters

### Tools & Applications Track

- FIDEO: Food Interactions with Drugs Evidence Ontology L.1-10
  Georgeta Bordea, Jean Nöel Nikiema, Romain Griffier, Thierry Hamon, Fleur Mougin
- The ARK Platform: Enabling Risk Management Through Semantic Web Technologies M.1-10
  Ademar Crotti Jr., Maryam Basereh, Yalemisew Abgaz, Junli Liang, Natalia Duda, Nick McDonald, Rob Brennan
- Ontology-Based Classification of Radiological Procedures for Consistent Sharing in Clinical Data Warehouses N.1-11
  Pierre Lemordant, Bernard Gibaud, Cyril Garde, Sébastien Delarche, Didier Goudet, Marc Cuggia

### Early Career Symposium

- An Ontological Representation of Sex and Gender Information (short paper) O.1-5
  Paul Fabry, Adrien Barton, Jean-François Ethier
- OGG-CoV: Ontology Representation and Analysis of Genes and Genomes of Coronaviruses (short paper) P.1-5
  Anthony Huffman, Yongqun He
- Best-Practice Patterns for Biomedical Ontologies: Moving Under the Meta-Modeling Hood (short paper) Q.1-5
  Jana Vataščinová, Viet Bach Nguyen, Vojtěch Svátek, Ondřej Zamazal

### Posters

- A Python Utility for Working with OBO Foundry Terms (short paper) R.1-2
  Jonathan P. Bona
- A New Alignment Method Based on FoodOn as Pivot Ontology to Manage Incompleteness in Nutritional Legacy Data Sources (short paper) S.1-2
  Patrice Buche, Cufi Julien, Stéphane Dervaux, Juliette Dibie, Liliana Ibanescu, Alrick Oudot, Magalie Weber
- The Plant Trait Ontology Links Wheat Traits for Crop Improvement and Genomics (short paper) T.1-2
  Laurel Cooper, Marie-Angélique Laporte, Justin Elser, Victoria Carollo Blake, Taner Z. Sen, Chris Mungall, Elizabeth Arnaud, Pankaj Jaiswal
- Wikidata WikiProject COVID-19: Modelling the Pandemic in Real Time (short paper) U.1-2
  Tiago Lubiana
- Current OBO Ontologies Are Not Sufficient to Annotate COVID-19-Related Cell Types (short paper) V.1-2
  Tiago Lubiana
- An Insight into Food Semantics: Review, Analysis, and Lessons Learnt over Food-Related Studies (short paper) W.1-2
  Gorjan Popovski, Gordana Ispirova, Eva Valenčič, Riste Stojanov, Tome Eftimov, Barbara Koroušić Seljak
- An Ontological Model for the (Digital) Patient (short paper) X.1-2
  Louis P. Ter Meer, Jan Hazelzet, Marleen de Mul
- Mondo Disease Ontology: Harmonizing Disease Concepts Across the World (short paper) Y.1-2
  Nicole Vasilevsky, Shahim Essaid, Nico Matentzoglu, Nomi L. Harris, Melissa Haendel, Peter Robinson, Christopher J. Mungall
- Expanding the eNanoMapper Ontology (short paper) Z.1-2
  Laurent A. Winckers, Egon L. Willighagen

2021-01-15: submitted by Janna Hastings, metadata incl. bibliographic data published under Creative Commons CC0
2021-02-02: published on CEUR Workshop Proceedings (CEUR-WS.org, ISSN 1613-0073) |valid HTML5|