ICBO|ODLS 2020
International Conference on Biomedical Ontologies 2020

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