ICBO 2022
ICBO 2022: International Conference on Biomedical Ontology

Table of Contents

• Preface
  Summary: There were 39 papers submitted for peer-review to this event. Of these, 34 were accepted for this volume: 15 full papers and 19 poster abstracts. In addition there are 2 papers from invited talks, as well as 3 workshop papers and 1 workshop abstract.

Full Papers

• The Gaps in the Terminological Representation of the ACORN Social Determinants of Health Survey A.1-10
  C. Maria Keet
• Coordinating Coronavirus Research: The Virus Infectious Disease Ontology B.1-14
  John Beverley, Yongqun He, Barry Smith, Shane Babcock, Eric Merrell, Lindsay Cowell, Regina Hurley, Sebastian Deusing
• Classifying Animal Breeds with the Vertebrate Breed Ontology (VBO) C.1-7
  Sabrina Toro, Nicolas Matentzoglu, Kathleen R. Mullen, Nicole Vasilevsky, Halie Rando, Melissa Haendel, Christopher J. Mungall, Zhi-Liang Hu, Gregoire Leroy, Imke Tammen, Frank W. Nicholas
• An Ontological Approach to Developing a Unified and Interdisciplinary Framework for Aging D.1-11
  Fumiaki Toyoshima, Adrien Barton, Jean-Francois Ethier
• Ontology Representation for Cholangiocarcinoma E.1-7
  Anuwat Pengput, Alexander D. Diehl
• The Gaps in the Terminological Representation of the ACORN Social Determinants of Health Survey F.1-10
  Melissa Resnick, Diane Montella, Wilmon McCray, Steven Brown, Keith Campbell, Jonathan Nebeker, Frank LeHouillier, Peter Elkin
• Using Ontologies to Enhance Data on Intimate Partner Violence G.1-6
  S. Clint Dowland, William Hogan
• An Ontology for Healthcare Systems H.1-9
  François Goyer, Paul Fabry, Adrien Barton, Jean-Francois Ethier
• Ubergraph: Integrating OBO Ontologies into a Unified Semantic Graph I.1-9
  James Balhoff, Ugur Bayindir, Anita Caron, Nicolas Matentzoglu, David Osumi-Sutherland, Christopher Mungall
• Development of an Image Data Set Class: Its Role in Biomedical Imaging and Neuroimaging Research J.1-9
  Alexander Bartnik, Lucas Serra, Mackenzie Smith, William Duncan, Alan Ruttenberg, Michael Dwyer, Alexander D. Diehl
• Knowledge of the Ancestors: Intelligent Ontology-aware Annotation of Biological Literature using Semantic Similarity K.1-10
  Pratik Devkota, Somya Mohanty, Prashanti Manda
• Performance Summary Display Ontology: Feedback Intervention Content, Delivery, and Interpreted Information L.1-10
  Zach Landis-Lewis, Cooper Stansbury, John Rincon, Colin Gross
• Environmental Health Language Collaborative (EHLC): a Route to Environmental Health Science Data Harmonization M.1-6
  Anna Maria Masci, Stephanie Holmgren, Charles Schmitt, Rima Habre, Anne E. Thessen, Rebecca Boyles, Carmen J. Marsit
• OMOP-2-OPMI: Ontologization of OMOP CDM Using OPMI to Support Clinical Data interoperability and analysis N.1-11
  Long Tran, Yongqun He
• An Ontological Representation of Money with a View Toward Economic Determinants of Health O.1-9
  Matthew Diller, William Hogan

Invited Talks

• AlphaFold, AI and Ontologies P.1-3
  Barry Smith
• The Coevolution of Ontologies and Knowledge-based Analytics in Bioinformatics Q.1-4
  Robert Hoehndorf

Poster Abstracts and Software Demos

• From Survey to Ontology, the Challenges and Opportunities in Ontologizing Questions and Answers R.1
  Lauren Chan, Jimmy Phuong, Anne Thessen, Stephanie Hong, Shahim Essaid, Melissa Haendel
• Development of Axiomatization for the Cholangiocarcinoma Ontology Using Common Logic Interchange Format S.1
  Anuwat Pengput, Alexander D. Diehl
• Collaborative Development of a Process Chemistry Domain Ontology, PROCO T.1
  Wes Schafer, Jan Nespor, Vincent Antonucci, Yongqun Oliver He, Anna Dunn, Zachary E.X. Dance
• NIDM-Experiment: An Ontology for Annotating Neuroscientific Data U.1-3
  Karl G. Helmer, Derek Chaplin, Nazek Queder, Satrajit Ghosh, Camille Maumet, JeanBaptiste Poline, Theo van Erp, David Keator
• Shaping the Semantics of Healthy and Sustainable Food Systems: a Participatory Metaframework-based Approach V.1-2
  Giorgio A. Ubbiali, Andrea Borghini, Nicola Piras, Matthew C. Lange
• Ontological Analysis of Collection Improves Classification of Cardinality Phenotypes W.1-2
  Sarah Alghamdi, Robert Hoehndorf
• Enhancing Childhood Nutrition Data with Open Biomedical Ontologies X.1
  Jonathan P. Bona, Alexander D. Diehl, Alexander P. Cox, Aaron S. Kemp, Linda Larson-Prio
• Building a Radiation Therapy Ontology Y.1
  Mark Phillips, Andre Dekker, Charles Mayo, Peter Gabriel, Jonathan P. Bona
• Building an Application Ontology and Knowledge Graph for Rare Disease Patient-Level Data Z.1
  Emily Hartley, Daniel Olson, Ian Braun, Nicolas Matentzoglu, James Overton, Ramona L. Walls
• The Protein Conformation Ontology AA.1
  Morgan Mitchell, Lauren M. Wishnie, Alexander D. Diehl
• Ontological Representation and Analysis of the Molecular Interactions Related to COVID-19-associated Acute Kidney Injury BB.1
  Ghida Arnous, Yongqun He
• Knowledge Systematization for Cellular Senescence Processes by Homeostasis Imbalance Process Ontology CC.1
  Yuki Yamagata, Shuichi Onami, Hiroshi Masuya
• OBO Academy: Training Materials for Bioontologists DD.1
  James Overton, Rebecca Jackson, Sabrina Toro, Shawn Tan, Bradley Varner, David Osumi-Sutherland, Nico Matentzoglu, Nicole Vasilevsky
• The Ontology of Adverse Events in 2022 EE.1
  Qiuyue Yang, Jun Su, Xue Zhang, Yongqun He, Jiangan Xie
• Toward an Occupation Ontology, OccO FF.1
  Sam Smith, Damion Dooley, Eric Merrell, John Beverley, Yongqun He
• Ontology Integration for Discovering Bioresources Contributing to Medical Science Research GG.1
  Tatsuya Kushida, Daiki Usuda, Toyoyuki Takada, Yuki Yamagata, Hiroshi Masuya
• The OntoDev Suite of Ontology and Data Integration Tools HH.1
  James A. Overton
• A Data Structure for the Implementation of Referent Tracking Systems II.1
  Lauren Wishnie, Alexander Diehl
• Translating Medical Vocabularies via the Unified Medical Language Systems JJ.1-2
  William T. Roddy, Daniel Olson, Diane Corey, Ian Braun, Terrence R. McHugh, Emily Hartley, Smith Heavner, Ramona L. Walls

CELLS 2022: The 6th International Cells in Experimental Life Science Workshop

• Summarising scRNAseq Expression Data in FlyBase KK.1-4
  Damien Goutte-Gattat

FOHTI 2022: FAIR Ontology Harmonization and TRUST Data Interoperability Workshop

• COB: A Core Ontology for Biology and Biomedicine LL.1
  James A. Overton, Rebecca Jackson, Nico Matentzoglu, William Duncan, Randi Vita, Nomi L. Harris, OBO Operations Committee members, Christopher J. Mungall, Bjoern Peters
• Data Harmonization through Use of Community Standards in the Common Fund Data Ecosystem MM.1-7
  Michelle Giglio, Suvarna Nadendla, Arthur Brady, Amanda Charbonneau, Karl Czajkowski, Jeremy Yang, Tom Gillespie, Philippe Rocca-Serra, Jeff Grethe, Raja Mazumder, Bernard de Bono, Jonathan Silverstein, Daniel Clark, Mark Musen, Owen White, CFDE Ontology Working Group

ROBI 2022: First Workshop on the Role of Ontologies in Biomedical AI

• Investigating Ontology Use in Artificial Intelligence and Machine Learning for Biomedical Research - A Preliminary Report from A Literature Review NN.1-4
  Asiyah Yu Lin, Andrey Ibrahim Seleznev, Tianming “Danny” Ning, Paulene Grier, Lalisa “Mariam” Lin, Christopher Travieso, Ansu Chatterjee, Jaleal Sanjak