edited by
Janna Hastings and Adrien Barton
1 Otto-von-Guericke University, Department of Computer Science, Magdeburg, Germany; and University College London, Department of Clinical, Educational and Health Psychology, UK 2 IRIT, CNRS, Toulouse, France and GRIIS, Sherbrooke University, Canada
Insititute for Intelligent Interacting Systems, Department of Computer Science, Otto-von-Guericke University Magdeburg, Germany Address: Universitätsplatz 2, 39106 Magdeburg, Germany
Email: hastings@ovgu.de
International Conference on Biomedical Ontologies (ICBO) 2021, part of the Bolzano Summer of Knowledge (BOSK) 2021 Website: https://icbo2021.inf.unibz.it/
Janna Hastings and Adrien Barton (eds.): ICBO 2021 – International Conference on Biomedical Ontologies. Proceedings of the 12th International Conference on Biomedical Ontologies, September 15-18th, 2021. CEUR-WS.org.
It is recommended to include further the CEUR-WS.org volume number and the URL to that volume.
Copyright © 2021 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). Against the backdrop of the ongoing COVID pandemic, the International Conference on Biomedical Ontologies (ICBO) 2021 was held as a hybrid in-person and virtual event, hosted by the Free University of Bozen-Bolzano, Italy and co-located with other Bolzano Summer of Knowledge (BoSK) 2021 events including Formal Ontologies in Information Systems (FOIS), with which ICBO shared a joint keynote. Due to ongoing travel restrictions and healthrelated concerns among the community, the direct in-person attendance of each individual BoSK event was relatively small, but taken together there were a good crowd of persons interested in diverse aspects of ontologies and knowledge representation technologies, which was very welcome after the disruption of community-building activities over the previous 18 months. Furthermore, the event was supplemented by extensive online participation via the Zoom platform, with a significant portion of the presentations being delivered remotely and 75% of the attendees attending remotely. At the same time, a parallel discussion server was held using the Discord platform, which enabled the presentations in the main session to stick to time while additional questions could be answered asynchronously on Discord. It is likely that the hybrid format for conferences will be with us for a long time into the future, and as such it is an opportunity for optimism that this has proven to work for the ICBO community.
Contributions were accepted to three tracks: main research papers, early career abstracts, and flash presentation abstracts (short papers). Each submission to ICBO 2021 was assessed by three reviewers selected from the program committee for the event. Among the topics of contributions to this year’s ICBO were ontologies for coronavirus description and semantic data integration in support of health research, clinical ontologies, ontologies for environmental exposures and accompanying health risks, phenotype ontologies, gender, food-related ontologies and ontologies for the behavioral domain. Furthermore, some technical advances in tooling were presented, such as the introduction of the Horned-OWL scalable OWL programmatic access library, and utilities such as LinkML for representing mappings between ontologies. The two keynotes focused on complementary and topically highly relevant themes: Stefan Schulz spoke about mapping between the medical world of clinical vocabularies and the bio-ontology world by aligning the widely used clinical vocabulary SNOMED with the Basic Formal Ontology, while Chris Mungall gave a whirlwind tour of the history of and recent developments in the OBO Foundry.
The organizers thank everyone involved in making ICBO 2021 happen, in particular the heroic work of the team of local organizers in Bolzano, who successfully pulled together a massively complex series of hybrid events and solved the inevitable technical challenges with astonishing levels of grace, speed and humor. The organizers would furthermore like to thank the keynote speakers, the authors of contributions, the Program Committee members, those who contribute to the organization behind the scenes, as well as those participating in the sessions, with or without their own presentation. Moreover, we appreciate the acknowledgement of the conference by the International Association for Ontology and its Applications (IAOA) as an IAOA Supported Event and we are grateful for the services provided by EasyChair and the free services provided by CEUR-WS.org. Last but not least, we acknowledge the generous hosting of the virtual sessions by the Free University of Bozen-Bolzano, Italy. Adrien Barton Randi Vita Nicole Vasilevsky Robert Hoehndorf
Oliver Kutz Guendalina Righetti Nicolas Troquard
Stefan Schulz Chris Mungall
Sivaram Arabandi Leyla Garcia James P. Balhoff Jonathan Bona Tiffany Callahan Lauren Chan Melanie Courtot Francisco Couto Alexander D. Diehl S. Clint Dowland William Duncan Michel Dumontier Paul Fabry Jesualdo Tomás FernándezBreis Yongqun He Amanda Hicks William Hogan Rebecca C. Jackson Mark Jensen Senay Kafkas Kouji Kozaki Phillip Lord Otto-von-Guericke University Magdeburg, Germany & University College London, UK IRIT, CNRS, France & Sherbrooke University, Canada La Jolla Institute for Immunology, USA Translational and Integrative Sciences Laboratory, University of Colorado Center for Health AI, Colorado, USA King Abdullah University of Science and Technology, Saudi Arabia Free University of Bozen-Bolzano, Italy Free University of Bozen-Bolzano, Italy Free University of Bozen-Bolzano, Italy Medical University of Graz, Austria Berkeley, California, USA Intelligent Medical Objects, USA ZB MED Information Centre for Life Sciences, Germany University of North Carolina at Chapel Hill, USA University of Arkansas, USA University of Colorado Anschutz Medical Campus, USA TISLab, University of Colorado Center for Health AI, USA EMBL-EBI, UK University of Lisbon, Portugal University at Buffalo, USA University of Florida, USA Lawrence Berkeley National Laboratory, USA Maastricht University, NL GRIIS, Université de Sherbrooke, Canada University of Murcia, Spain University of Michigan, USA University of Florida, USA University of Florida, USA Knocean, inc., Canada University at Buffalo, USA King Abdullah University of Science and Technology, Saudi Arabia Osaka Electro-Communication University, Japan Newcastle University, UK University of Lisbon, Portugal La Jolla Institute for Immunology, USA The Jackson Laboratory for Genomic Medicine, USA Leiden University Medical Center, NL Medical University of Vienna, Austria University of Cambridge, UK University of Maryland, USA University at Buffalo, USA University of Manchester, UK GRIIS, Université de Sherbrooke, Canada University of Pennsylvania, USA
SNOMED CT x BFO: can the gap between legacy terminology and foundational ontology be bridged? Stefan Schulz The Human Behaviour-Change Project and the Behaviour Change Intervention Ontology Susan Michie
Representing Gender in Ontologies: A Dispositional Perspective 1-12 Fumiaki Toyoshima, Adrien Barton, Paul Fabry, Jean-François Ethier Assessing the consistency of modeling in complex ontologies: A study of the musculoskeletal system of the Foundational Model of Anatomy 13-23 Melissa D. Clarkson, Landon T. Detwiler, Kristen M. Platt, Steven Roggenkamp Toward A Dairy Ontology to Support Precision Farming 24-35 Victor Fuentes, Tomas Martin, Petko Valtchev, Abdoulaye Baniré Diallo, René Lacroix, Maxime Leduc An ontological analysis of health procedure information 36-47
Paul Fabry, Francois Goyer, Adrien Barton, Jean-Francois Ethier Early Career Papers • A semantic model leveraging pattern-based ontology terms to bridge environmental exposures and health outcomes 48-55 Lauren E. Chan, Nicole A. Vasilevsky, Anne Thessen, Nicolas Matentzoglu, William D. Duncan, Christopher J. Mungall, Melissa A. Haendel • Modeling Logical Definitions in Biomedical Ontologies by Reusing Ontology Design Patterns 56-62 Mirna El Ghosh, Fethi Ghazouani, Benjamin Birene, Elise Akan, Jean Charlet, Ferdinand Dhombres • Challenges in Realism-Based Ontology Design: a Case Study on Creating an Ontology for Motivational Learning Theories 63-69
Irshad Ally, Werner Ceusters • Ontology-based modeling, representation, and analysis of biomarkers in healthy and disease kidney tissue 70-76
Yingtong Liu, Wenjun Ju, Becky Steck, Sanjay Jain, Matthias Kretzler, Yongqun He • Improving Biomedical Data by Improving the Information Artifact Ontology 7783
Eric C. Merrell, Robert M. Kelly Short Papers • • • • • • • • • Reclassification of Infectious Disease in the Mondo Disease Ontology 104-109 Nicole Vasilevsky, Sabrina Toro, Nico Matentzoglu, Dazhi Jiao, Melissa Haendel, Peter N. Robinson, Christopher J. Mungall • Identification and ontology term enrichment analysis of genes associated with COVID-19 and acute kidney disease 110-115
Guirui Huang, Suyuan Peng, Luxia Zhang, Yongqun He • Ontology modeling and analysis of COVID-19-associated Acute Kidney Injury and its underlying molecular mechanisms 116-121
Easheta Shah, Roshan Desai, Yongqun He, Suyuan Peng, Luxia Zhang • A community effort for COVID-19 Ontology Harmonization 122-127 Asiyah Lin, Yuki Yamagata, William D. Duncan, Leigh Carmody, Tatsuya Kushida, Hiroshi Masuya, ohn Beverley, Biswanath Dutta, Michael DeBellis, Zoë May Pendlington, Paola Roncaglia, Yongqun He Extended Abstracts for Flash Presentations Workshop on Ontologies for the Behavioural and Social Sciences