Papers and Poster Abstracts

Papers

• The Environmental Conditions, Treatments, and Exposures Ontology (ECTO): Connecting Toxicology and Exposure to Human Health and Beyond (slides)
  Lauren E. Chan, Anne E. Thessen, William D. Duncan, Nicolas Matentzoglu, Charles Schmitt, Cynthia Grondin, Nicole Vasilevsky, Julie A. McMurry, Peter N. Robinson, Christopher J. Mungall, and Melissa A. Haendel
• A Comprehensive Update on CIDO: The Community-based Coronavirus Infectious Disease Ontology (slides)
  Yongqun He, Hong Yu, Anthony Huffman, Asiyah Yu Lin, Darren A. Natale, John Beverley, Ling Zheng, Yehoshua Perl, Zhigang Wang, Yingtong Liu, Edison Ong, Yang Wang, Philip Huang, Long Tran, Jinyang Du, Zalan Shah, Easheta Shah, Roshan Desai, Hsin-hui Huang, Yujia Tian, Eric Merrell, William D. Duncan, Sivaram Arabandi,Lynn M. Schriml, Jie Zheng, Anna Maria Masci, Liwei Wang, Hongfang Liu, Fatima Zohra Smaili, Robert Hoehndorf, Zoë May Pendlington, Paola Roncaglia, Xianwei Ye, Jiangan Xie, Yi-Wei Tang, Xiaolin Yang, Suyuan Peng, Luxia Zhang, Luonan Chen, Junguk Hur, Gilbert S. Omenn, Brian Athey, Barry Smith
• Exploring the Ontology of Pandemic (recording)
  C. Maria Keet
• Coordinating Coronavirus Research: The Virus Infectious Disease Ontology (slides)
  John Beverley, Yongqun He, Barry Smith, Shane Babcock, Eric Merrell, Lindsay Cowell, Regina Hurley and Sebastian Deusing
• Classifying Animal Breeds with the Vertebrate Breed Ontology (slides)
  Sabrina Toro, Nicolas Matentzoglu, Kathleen R. Mullen, Nicole Vasilevsky, Halie Rando, Melissa Haendel, Christopher J. Mungall, Zhi-Liang Hu, Gregoire Leroy, Imke Tammen and Frank W. Nicholas
• An Ontological Approach to Developing a Unified and Interdisciplinary Framework for Aging (slides)
  Fumiaki Toyoshima, Adrien Barton and Jean-Francois Ethier
• Ontology representation for Cholangiocarcinoma (slides)
  Anuwat Pengput and Alexander D. Diehl
• The Gaps in the Terminological Representation of the ACORN Social Determinants of Health Survey (recording)
  Melissa Resnick, Diane Montella, Wilmon McCray, Steven Brown, Keith Campbell, Jonathan Nebeker, Frank LeHouillier and Peter Elkin
• Using Ontologies to Enhance Data on Intimate Partner Violence (slides)
  S. Clint Dowland and William Hogan
• An ontology for healthcare systems (slides)
  François Goyer, Paul Fabry, Adrien Barton and Jean-Francois Ethier
• Ubergraph: integrating OBO ontologies into a unified semantic graph (slides)
  James Balhoff, Ugur Bayindir, Anita Caron, Nicolas Matentzoglu, David Osumi-Sutherland and Christopher Mungall
• Development of an Image Data Set Class: Its Role in Biomedical Imaging and Neuroimaging Research (slides)
  Alexander Bartnik, Lucas Serra, Mackenzie Smith, William Duncan, Alan Ruttenberg, Michael Dwyer and Alexander D. Diehl
• Knowledge of the Ancestors: Intelligent Ontology-aware Annotation of Biological Literature using Semantic Similarity (slides)
  Pratik Devkota, Somya Mohanty and Prashanti Manda
• Performance Summary Display Ontology: Feedback intervention content, delivery, and interpreted information (slides)
  Zach Landis-Lewis, Cooper Stansbury, John Rincon and Colin Gross
• Environmental Health Language Collaborative (EHLC): a route to environmental health science data harmonization (slides)
  Anna Maria Masci, Stephanie Holmgren, Charles Schmitt, Rima Habre, Anne E. Thessen, Rebecca Boyles and Carmen J. Marsit
• Identification of missing hierarchical relations in the vaccine ontology using acquired term pairs (slides)
  Warren Manuel, Rashmie Abeysinghe, Yongqun He, Cui Tao, and Licong Cui
• OMOP-2-OPMI: Ontologization of OMOP CDM using OPMI to support clinical data interoperability and analysi (slides)
  Long Tran and Yongqun He
• An Ontological Representation of Money with a View Toward Economic Determinants of Health (slides)
  Matthew Diller and William Hogan

Poster Abstracts

• From Survey to Ontology, the challenges and opportunities of ontologizing questions and answers
  Flash Talk
  Lauren Chan, Jimmy Phuong, Anne Thessen, Stephanie Hong, Shahim Essaid and Melissa Haendel
• Development of Axiomatization for the Cholangiocarcinoma Ontology Using Common Logic Interchange Format
  Flash Talk
  Anuwat Pengput and Alexander D. Diehl
• Collaborative Development of a Process Chemistry Domain Ontology, PROCO
  Flash Talk
  Wes Schafer, Jan Nespor, Vincent Antonucci, Oliver He, Anna Dunn and Zachary E.X. Dance
• NIDM-Experiment: An Ontology for Annotating Neuroscientific Data
  Flash Talk
  Karl Helmer, Derek Chaplin, Nazek Queder, Satrajit Ghosh, Camille Maumet, Jean-Baptiste Poline, Theo van Erp and David Keator
• Shaping the semantics of healthy and sustainable food systems: a participatory meta-framework- based approach
  Flash Talk
  Giorgio Alberto Ubbiali, Andrea Borghini, Nicola Piras and Matthew C. Lange
• Ontological analysis of collection improves classification of cardinality phenotypes
  Flash Talk
  Sarah Alghamdi and Robert Hoehndorf
• Enhancing childhood nutrition data with open biomedical ontologies
  Flash Talk
  Jonathan Bona, Aaron Kemp, Alexander D. Diehl, Alexander P. Cox and Linda Larson-Prior
• Building a Radiation Therapy Ontology
  Flash Talk
  Mark Phillips, Andre Dekker, Charles Mayo, Peter Gabriel and Jonathan Bona
• Building an Application Ontology and Knowledge Graph for Rare Disease Patient-Level Data
  Flash Talk
  Emily Hartley, Daniel Olson, Ian Braun, Nicolas Matentzoglu, James Overton and Ramona Walls
• The Protein Conformation Ontology
  Flash Talk
  Morgan Mitchell, Lauren Wishnie and Alexander D. Diehl
• Ontological representation and analysis of the molecular interactions related to COVID-19-associated Acute Kidney Injury
  Flash Talk
  Ghida Arnous and Yongqun He
• Knowledge Systematization for Cellular Senescence Processes by Homeostasis Imbalance Process Ontology
  Flash Talk
  Yuki Yamagata, Shuichi Onami and Hiroshi Masuya
• OBO Academy: Training materials for bioontologists
  Flash Talk
  James A. Overton, Rebecca Jackson, Sabrina Toro, Shawn Tan, Bradley Varner, David Osumi-Sutherland, Nicolas Matentzoglu and Nicole Vasilevsky
• The Ontology of Adverse Events in 2022
  Flash Talk
  Qiuyue Yang, Jun Su, Xue Zhang, Yongqun He and Jiangan Xie
• Toward an Occupation Ontology, OccO
  Flash Talk
  Sam Smith, Yongqun He, Damion Dooley, Eric Merrell and John Beverley
• Ontology Integration for Discovering Bioresources Contributing to Medical Science Research
  Flash Talk
  Tatsuya Kushida, Daiki Usuda, Toyoyuki Takada, Yuki Yamagata and Hiroshi Masuya
• The OntoDev Suite of Ontology and Data Integration Tools
  Flash Talk
  James A. Overton
• The Ontology for Avida digital evolution platform (OntoAvida)
  Flash Talk
  Raul Ortega, Enrique Wulff and Miguel A. Fortuna
• Investigating Ontology Use in Artificial Intelligence and Machine Learning for Biomedical Research - A Preliminary Report from A Comprehensive Literature Review
  Flash Talk
  Asiyah Lin, Tianming Ning, Paulene Grier, Lalisa Mariam Lin and Andrey Ibrahim Seleznev
• A data structure for the implementation of referent tracking systems
  Flash Talk
  Lauren Wishnie and Alexander D. Diehl
• Translating medical vocabularies via the Unified Medical Language System
  William T. Roddy, Daniel Olson, Diane Corey, Ian Braun, Terrence R. McHugh, Emily Hartley, Smith Heavner, Ramona L. Walls