|  | Vol-4194 urn:nbn:de:0074-4194-x Copyright © 2025 for the individual papers by the papers' authors. Copyright © 2026 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).

# ICBO 2025
Biological and Biomedical Ontology 2025

## Proceedings of the 16th International Conference on Biological and Biomedical Ontology (ICBO 2025)

### Virtual Event, Bethesda, USA, November 9-11, 2025.

Edited by

### Yuki Yamagata1
Muhammad Tuan Amith2
Giorgio A. Ubbiali3
Ludger Jansen3,4
William D. Duncan5
Asiyah Yu Lin6

1 RIKEN BioResource Research Center, Japan
2 University of Texas Medical Branch, USA
3 PTH Brixen College, Italy
4 University of Rostock, Germany
5 University of Florida College of Dentistry, USA
6 OntoData Research and Solutions, LLC, USA

## Table of Contents

- Preface
  Summary: There were thirteen papers submitted for peer review to the tracks contributing to this volume (Main: 3, ICBO-EAST: 4, Food: 6). Out of these, five peer-reviewed papers were accepted for publication in this volume. Each peer-reviewed paper included in this volume received at least two completed reviews recorded in CMT. The review process was single-blind, and no rebuttal phase was used. In addition, 20 short talks were accepted for presentation (two were reported as no-shows); short talk abstracts are not published in this CEUR volume. This volume also includes two invited reports: a Food workshop report and a panel discussion report. Additionally, ICBO 2025 offered a direct-to-journal track in the Journal of Biomedical Semantics (JBMS) ICBO Thematic Series collection. The track received six submissions, of which five were accepted. Journal-track articles are published by JBMS and are added to the collection as they appear (not republished as CEUR papers in this volume). At the time of finalizing this CEUR volume, one ICBO 2025 journal-track article had been published (doi: 10.1186/s13326-025-00345-2).

### ICBO 2025 (Main Conference)

- History in the Basic Formal Ontology
  Werner Ceusters, Alan Ruttenberg

### ICBO-EAST (Satellite Event)

- Ontology-driven Exploration of RIKEN Bioresources via ChEBI Roles and Gene Ontology
  Tatsuya Kushida, Daiki Usuda, Takatomo Fujisawa, Yasunori Yamamoto, Norio Kobayashi, Hiroshi Masuya
- Ontology-Based Prompt Engineering for Text-to-SPARQL: A Case Study on Tuberculosis in Wikidata
  Fariz Darari

### Workshop: Food, Waste, and Sustainability: Synergizing Ontology Efforts 2025 Workshop

- The “Food, Waste, and Sustainability: Synergizing Ontology Efforts” 2025 Workshop – A Report (invited workshop report)
  Giorgio A. Ubbiali, Ludger Jansen
- Integrated Ontological Framework for Food Waste Prevention, Recovery, and Valorization
  Emily Steliotes, Riley Lawson, Matthew Lange
- Towards a Meta-ontology of Sustainability: An Educational Perspective
  Antonio Lizzadri

### Panel Discussion: AI, Ontologies, and the Next Generation of Researchers

- Panel Discussion Summary: AI, Ontologies, and the Next Generation of Researchers (invited panel report)
  Olga Mashkova, Anthony Huffman

2026-03-03: submitted by Yuki Yamagata, metadata incl. bibliographic data published under Creative Commons CC0
2026-04-17: published on CEUR Workshop Proceedings (CEUR-WS.org, ISSN 1613-0073) |valid HTML5|