ICBO 2021
International Conference on Biomedical Ontologies 2021

Table of Contents

• Preface
  Summary: There were 32 papers submitted for peer-review to this conference. Out of these, 27 papers were accepted for this volume: 4 main research track papers, 5 early career contributions, 8 short papers, 8 extended abstracts. Furthermore, 2 papers were accepted for the OntoBess workshop, which also included one invited contribution.

Main Research Track Papers

• 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 77-83
  Eric C. Merrell, Robert M. Kelly

Short Papers

• LUMC Clinical Ontology for Biomedical Research 84-88
  Núria Queralt-Rosinach, César H. Bernabé, Qinqin Long, Rajaram Kaliyaperumal, Marco Roos
• GNOme – Glycan Naming and Subsumption Ontology 89-93
  Wenjin Zhang, Nathan J. Edwards
• HAO: Hearing Aid Ontology 94-98
  Maria Ausilia Napoli-Spatafora
• Analysis of Biomarker Data Towards Development of a Molecular Biomarker Ontology 99-103
  Daniel Lyman, Darren Natale, Lynn Schriml, Kriston Anton, Daniel C. Crichton, Raja Mazumder
• 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, Suyuan Peng, Luxia Zhang, Yongqun He
• A Community Effort for COVID-19 Ontology Harmonization 122-127
  Asiyah Yu Lin, Yuki Yamagata, William D. Duncan, Leigh C. Carmody, Tatsuya Kushida, Hiroshi Masuya, John Beverley, Biswanath Dutta, Michael DeBellis, Zoë May Pendlington, Paola Roncaglia, Yongqun He

Extended Abstracts for Flash Presentations

• Managing Incompleteness and Validating the Content of Nutritional Food Sources using FoodOn as Pivot Ontology 128-130
  Patrice Buche, Julien Cufi, Stéphane Dervaux, Liliana Ibanescu, Alrick Oudot, Magalie Weber
• KG-Microbe: A Reference Knowledge-Graph and Platform for Harmonized Microbial Information 131-133
  Marcin P. Joachimiak, Harshad Hegde, William D. Duncan, Justin T. Reese, Luca Cappelletti, Anne E. Thessen, Christopher J. Mungall
• Horned-OWL: Building Ontologies at Big Data Scale 134-136
  Phillip Lord, Jennifer Warrender
• Expanding the Mammalian Phenotype Ontology to Meet the Needs of COVID-19 Model Curation 137-140
  Susan M. Bello, Anna V. Anagnostopoulos, Cynthia L. Smith
• Leveraging Ontologies within the National Microbiome Data Collaborative 141-143
  William D. Duncan, Faiza Ahmed, Fnu Anubhav, Jeffrey Baumes, Jonathan Beezley, Mark Borkum, Lisa Bramer, Shane Canon, Patrick Chain, Danielle Christianson, Yuri Corilo, Karen Davenport, Brandon Davis, Meghan Drake, Kjiersten Fagnan, Mark Flynn, David Hays, Bin Hu, Marcel Huntemann, Julia Kelliher, Sofya Lebedeva, Po-E Li, Mary Lipton, Chien-Chi Lo, Douglas Mans, Stanton Martin, Lee Ann McCue, David Millard, Kayd Miller, Nigel Mouncey, Paul Piehowski, Elais Player Jackson, Anastasiya Prymolenna, Samuel Purvine, Tbk Reddy, Rachel Richardson, Migun Shakya, Montana Smith, Jagadish Chandrabose Sundaramurthi, Mark A. Miller, Deepak Unni, Pajau Vangay, Bruce Wilson, Donald Winston, Elisha Wood-Charlson, Yan Xu, Emiley Eloe-Fadrosh, Christopher J. Mungall
• Bringing Schemas to the Schemaless 144-147
  Mark A. Miller, Rebecca C. Jackson, Christopher J. Mungall
• The Linked Data Modeling Language (LinkML): A General-Purpose Data Modeling Framework Grounded in Machine-Readable Semantics 148-151
  Sierra Moxon, Harold Solbrig, Deepak Unni, Dazhi Jiao, Richard Bruskiewich, James Balhoff, Gaurav Vaidya, William D. Duncan, Harshad Hegde, Mark Miller, Matthew Brush, Nomi Harris, Melissa Haendel, Christopher J. Mungall
• Recent Refinements of the NeuroPsychological Testing Ontology 152-154
  Alexander P. Cox, Kiernan L. Johnson, Lauren Wishnie, Aaron S. Kemp, Jonathan P. Bona, Alexander D. Diehl

Workshop on Ontologies for the Behavioural and Social Sciences

• Ontologies for the Behavioural and Social Sciences: Opportunities and Challenges 155-161
  Janna Hastings, Robert West, Susan Michie, Caitlin Notley, Sharon Cox
• CIDS: An Ontology for Representing Social and Environmental Impact 162-173
  Mark Fox, Kate Ruff
• Foundations for an Ontology of Nudges 174-183
  Adrien Barton