ICBO 2024
Biological and Biomedical Ontology 2024

Table of Contents

• Preface
  Summary: Nine papers were submitted for peer-review to this conference. Out of these, seven papers were accepted for this volume, four as regular papers and three as short papers. Additionally, we offered authors the option to submit manuscripts to the ICBO Thematic Series of the Journal of Biomedical Semantics. There were three papers submitted to this track, of which two were accepted. Thirteen poster abstracts were submitted, with twelve of them included in this volume. We have also included two works (one abstract and one paper) that were reviewed and presented at the CELLS 2024 workshop.

ICBO Thematic Series of the Journal of Biomedical Semantics

• Empowering Standardization of Cancer Vaccines Through Ontology: Enhanced Modeling and Data Analysis
  Jie Zheng, Xingxian Li, Anna Maria Masci, Hayleigh Kahn, Anthony Huffman, Eliyas Asfaw, Yuanyi Pan, Jinjing Guo, Virginia He, Justin Song, Andrey I. Seleznev, Asiyah Yu Lin, Yongqun He
• Concretizing Plan Specifications as Realizables Within the OBO Foundry
  William D. Duncan, Matthew Diller, Damion Dooley, William R. Hogan, John Beverley

Full Papers

• Modeling Biomedical Burdens in Basic Formal Ontology
  Paul Smart, Nic Fair, Michael Boniface
• Exploring the Evolution of the Gene Ontology and its Impact on Enrichment Analysis
  Yi Chen, Frank W Takes, Fons J Verbeek, Katherine J Wolstencroft
• Grounding Realizable Entities
  Michael Rabenberg, Carter Benson, Federico Donato, Yongqun He, Anthony Huffman, Shane Babcock, John Beverley
• Credentials in the Occupation Ontology
  John Beverley, Robin McGill, Sam Smith, Jie Zheng, Giacomo De Colle, Finn Wilson, Matthew A. Diller, William D. Duncan, William R. Hogan, Yongqun He

Short Papers

• (Re-)bridging the Anatomy Ontologies with SSSOM
  Damien Goutte-Gattat,
• Semantic Representation of Preclinical Data in Radiation Oncology
  Olga Giraldo, Abumansur Sabyrrakhim, Mareike Roscher, Rosemarie Euler-Lange, Michael Baumann, Ina Kurth, Wahyu Wijaya Hadiwikarta
• Expanding the Ontology of Organizational Structures of Trauma Centers and Trauma Systems
  Diya Mehta, Justin M. Whorton, Reza Shahriari, Eric D Ragan, Jonathan P. Bona, William R. Hogan, Kevin W. Sexton, Mathias Brochhausen

Poster Abstracts

• OLS4: New Features for Exploring Ontologies
  Haider Iqbal, James McLaughlin, Helen Parkinson, Henriette Harmse
• Bridging the Gap: Integrating Public Bio-Ontologies into Enterprise Data Management Strategies
  Shawn Zheng Kai Tan, Joshua Daniel Valdez, Saritha Vettikunnel Kuriakose
• Standardising Biological Trait Representation with the Ontology of Biological Attributes (OBA)
  Arwa Ibrahim, Ray Stefancsik, Vinicius de Souza, Anita R. Caron, Nicolas Matentzoglu, James McLaughlin, Zoë M. Pendlington
• Representing Bionic-vision Devices in the Neural Electronic Interface Ontology
  Jisoo Seo, Alexander D. Diehl, Daniel L. Rathbun, Gopikrishnan M. Chandrasekharan, Callie McGrath, William D. Duncan
• Initial Steps in Developing an Ontology of Dental Care-Related Fear, Anxiety, and Phobia
  William D. Duncan, Astha Singhal, Olga S. Enz, Alexander D. Diehl, Brenda Heaton, Daniel W. McNeil
• An Ontological Representation of Oral Dysbiosis
  Gopikrishnan M. Chandrasekharan, Alexander D. Diehl, Nivedita Dutta, William D. Duncan
• Classification of Genetic Developmental Disorders in the Peer-Reviewed Literature using biomedical ontologies
  T. Michael Yates, T. Ian Simpson
• Building an Ontology of Pain
  Finn D. Wilson, Gopikrishnan M. Chandrasekharan, Matthew Diller, Jisoo Seo, Alexander Diehl, William D. Duncan
• Building An Ecological Mental Functioning Ontology: An Informatics Perspective
  Guy Divita, Maryanne Sacco, Kathleen Coale, Rebecca Parks, Elizabeth Rasch
• Universal-Particular Distinction in Biomedical Ontologies
  Steven Chun Tak Wong, Vojtĕch Svátek
• ON TO A Better Path to Choose Your Best Ontologies
  Asiyah Yu Lin, John Graybeal, Anna Maria Masci, Juliane Schneider, Ruth Duerr, Eric G. Stephan, Hande Kuçük McGinty
• Compare the OBO Foundry Principles with the FAIR and TRUST Principles
  Anna Maria Masci, Daniela Rosu, Asiyah Yu Lin

CELLS 2024 Workshop

• CellCards: Development of a Dynamic Ontology-Derived ETL Pipeline for Automatic Cell Information Extraction and Analysis
  Mary Czelusniak, Emily Tran, Fatima Oudeif, Jie Zheng, William D. Duncan, Alexander D. Diehl, Yongqun He