ICBO 2025 conference
About Program¶
- Conference Dates:
- Workshops/tutorials: (see Program page for more detail)
- Annotating Data with Ontologies: LinkML Can Help (11/5/2025, 11 am - 1:30 pm ET/ 8 am - 10:30 am ET )
- 14th Vaccine and Drug Ontology Studies (VDOS) 2025 Workshop (11/7/2025)
- Workshop for PhD Students & Early Career Researchers: (11/10/2025)
- Food, Waste, and Sustainability: Synergizing Ontology Efforts (11/14/2025, 10am - 1pm ET/4pm - 7pm CET)
- Accelerating Ontology Curation with Agentic AI and GitHub: (11/18/2025)
- Main conference: November 9th to November 11th (11/9/2025-11/11/2025)
- ICBO-EAST Satelite: November 1st (11/1/2025)
- online general session: 10:00 - 13:00 JST
Schedule¶
Note that the following schedule is subject to change. Additionally, more detail about presentations days/times will be added as it becomes available.
LinkML Workshop¶
Wednesday, November 5, 2025 Annotating Data with Ontologies: LinkML Can Help
11:00am ET (08:00am PT) Please check details here(zoom link inlucded)
VDOS workshop¶
Friday, November 7, 2025,14th Vaccine and Drug Ontology Studies (VDOS) 2025 Workshop
9:00am-12:40pm ET Please check details here(zoom link included)
Main conference Day 1¶
Sunday, November 9, 2025 - ICBO 2025 Main Conference Day 1
12:00pm-12:15pm Opening Remark by Asiyah Yu Lin
12:15pm-1:00pm ET Kenote: Conspiracy theories: Are ontologies really under attack? Speaker: Mark Musen
1:00pm-1:10pm ET Break
1:10pm-1:40pm ET Ontology Development and Use for Cholangiocarcinoma Risk Factors and Predictions : A Term Enrichment Data Analysis and Machine Learning Classification (Primary Author: Anuwat Penpgut; Corresponding Author: Alexander D. Diehl)
1:40pm-2:10pm ET History in the Basic Formal Ontology (Primary Author: Werner Ceusters)
2:10pm-2:20pm ET Break
2:20pm-3:05pm ET Short Talks Pt. 1
(2:20pm) OntoChimp: A ChatGPT-based document analysis program for identifying key concepts for ontological development and its application in the solitude domain (Primary Author: Samuel Smith)
(2:35pm) Active Animals Ontology (Primary Author: Ditch Townsend)
(2:50pm) Logic-based Yin-Yang Ontology: Top-level Design for Integrating Traditional Chinese and Western Medicine (Primary Author: Yongqun He)
3:05pm-3:15pm ET Break
3:15pm-4:00pm ET Short Talks Pt. 2
(3:15pm) The OntoChoice Community: Answering "How can I choose terms and ontologies?" (Primary Author: John Graybeal)
(3:30pm) Ontology-based Updated Profiling of COVID-19 Vaccine Adverse Events Using VAERS Case Reports (Primary Author: Yongqun He)
(3:45pm) PICO/PECO-Guided Large Language Model Extraction and Ontological Modeling of Structured Occupational Safety and Health Evidence from Biomedical Literature (Primary Author: Junguk Hur)
Workshop: AI, Ontologies, and the Next Generation of Researchers¶
Monday, November 10, 2025, Workshop for PhD Students & Early Career Researchers
09:00am - 11:00am ET Workshop for PhD Students & Early Career Researchers: AI, Ontologies, and the Next Generation of Researchers
Main conference Day 2¶
Monday, November 10, 2025, ICBO 2025 Main Conference Day 2
11:00am-11:05am ET Opening Remark
11:05-11:30am ET Invited Speaker: Giovanni Nisato
11:30am-12:00pm ET Representing Dental Caries and Dysbiosis within the Oral Microbiome in the Oral Health and Disease Ontology (Corresponding Author: William D. Duncan)
12:00pm-12:10pm ET Break
12:10pm-12:40pm ET Utilizing BERTopic Modeling for Concept Discovery in the Domain of Gerotranscendence and Solitude (Presenter: B. Damayanthi Jesudas)
12:40pm-12:50pm ET Break
12:50pm-1:50pm ET Short Talks Pt. 1
(12:50pm) Towards an Integrated Agentic Workflow for Cell Ontology Annotation and Extension (Primary Author: Caroline Eastwood)
(1:05pm) Ontological modeling of the SEA-CDM and its applications for the vaccine domain (Primary Author: Anthony Huffman)
(1:20pm) Immunology Ontology: Filling the Gap (Primary Author: Anna Maria Masci)
(1:35pm) Improvement of vaccine representation in OHDSI Standardized Vocabularies using Vaccine Ontology (Primary Author: Jie Zheng)
1:50pm-2:00pm ET Break
2:00pm-3:00pm ET Short Talks Pt. 2
(2:00pm) Data Model-Based Ingestion Pipeline: Automating Harmonization of Datasets (Primary Author: Corey Cox)
(2:15pm) An Ontology for a Clinical Decision Support System in the Management of COVID‑19–Related Acute Respiratory Failure (Primary Author: Esther Roman)
(2:30pm) Semantic Analysis of SNOMED CT Concept Co-occurrences in Clinical Documentation using MIMIC-IV (Presenter: Prashanti Manda)
(2:45pm) AI-Support in Ontology Construction: A Pilot Targeting SEDOH Factors as Represented by Diverse Data-Collection Instruments (Presenter: Colbie J. Reed)
Main conference Day 3¶
Tuesday, November 11, 2025 ICBO 2025 Main Conference Day 3
11:00am-11:05am ET Opening Remark
11:05am-11:50am ET Kenote: Ontologies for Semantic Interoperability in the Age of AI Speaker: Michel Dumontier
11:50am-12:00pm ET Break
12:00pm-12:30pm ET Advancing the BioAssay Ontology through Integrated PK/PD and Safety Pharmacology Representation (Presenter: Stephan C. Schürer)
12:30pm-1:00pm ET Representing Dental Restoration Materials in the Oral Health and Disease Ontology (Presenter: Nivedita Dutta)
1:00pm-1:10pm ET Break
1:10pm-1:55pm ET Short Talks Pt. 1
(1:10pm) Automated Annotation of Rare Disease Data Dictionaries to Support Semantic Search (Primary Author: Ian Braun)
(1:25pm) Ontology Development Workflows with Progressive Web Apps and Client-Side Processing Browser-Based Tools (Primary Author: Jonathan Vajda)
(1:40pm) Developing semantically-augmented graphics as visual standards for anatomical knowledge representation (Primary Author: Melissa Clarkson)
1:55pm-2:05pm ET Break
2:05pm-3:05pm ET Short Talks Pt. 2
(2:05pm) METPO: A Pragmatic Ontology for Microbial Ecophysiological Traits (Primary Author: Mark Miller)
(2:20pm) Modeling fMRI Analysis in the MRI Ontology (MRIO): Practical Reuse of OBO Foundry Statistical Ontologies (Primary Author: Alexander Bartnik)
(2:35pm) The ROBOKOP Biomedical Knowledge Graph System: Leveraging Ontologies for Data Normalization, Integration, and Query (Primary Author: Karamarie Fecho)
(2:50pm) MCBO: Mammalian Cell Bioprocessing Ontology, A Hub-and-Spoke, IOF-Anchored Application Ontology (Primary Author: Kimberly Robasky)
Food, Waste, and Sustainbitlity Workshop¶
Friday, November 14, 2025
10:00am - 01:00pm ET (04:00pm - 07:00pm CET) Food, Waste, and Sustainability: Synergizing Ontology Efforts
Tuesday, November 18, 2025
10:00am - 01:00pm ET (07:00am - 10:00am PT / 03:00pm - 06:00pm UK / 04:00pm - 07:00pm CET) Accelerating Ontology Curation with Agentic AI and GitHub
ICBO EAST ¶
Saturday, November 1, 2025 JST (*Oct. 30, 2025 in EST) ICBO-EAST
10:00am-10:05am JST Opening Remarks
10:05am-10:45am JST Keynote, Dr. Achille Zappa and Dr. Yukie Akune-Taylor Glycoscience data and ontologies for understanding the expanded central dogma
10:45am-11:10am JST Dr. Fariz Darai Ontology-Driven Prompt Engineering for Text-to-SPARQL: A Case Study on Tuberculosis in Wikidata
11:10am-11:50am JST Invited Speaker, Dr. Bairong Shen Disease-Specific Ontology-Driven Intelligent Medicine
11:50am-12:15pm JST Dr. Tatsuya Kushida Ontology-driven Exploration of RIKEN Bioresources via ChEBI Roles and Gene Ontology
12:15pm-12:55pm JST Keynote, Dr. Jian Du Utilizing Large Language Models to Build Causal Diagrams for Observational Health Research
12:55pm-13:00pm JST Break
13:00pm–13:40pm JST Keynote, Dr. Junguk Hur Unlocking Biomedical Knowledge with LLMs: Literature Mining for Protein Interactions and Vaccine Adjuvant Research
• (12:00pm–12:40pm Beijing Time, 11:00am–11:40am BKK Time)
13:40pm–14:00pm JST Discussion, Announcement of Multi-language sessions, and Break
14:00pm-17:30pm JST Japan on-site session at ISWC venue (Nara Prefectural Convention Center) as a SIG-SWO meeting
Local Hosts: Takanori Ugai (Fujitsu, Japan), Eiichi Sunagawa (Toshiba, Japan), Shusaku Egami (National Institute of Advanced Industrial Science and Technology, Japan), Tetsuya Mihara (Tsukuba University, Japan), Atsuko Yamaguchi (Tokyo City University, Japan)
Website: https://www.sigswo.org/papers/67cfp
13:00pm-16:30pm Beijing Time China on-site session at Harbin Medical University, Harbin, China
Local Host/Co-Organizer: Dr. Liang Cheng, Harbin Medical University
Other Co-Organizers: Xiaoling Yang (Chinese Academy of Medical Sciences) and Oliver He (University of Michigan)
Website: https://bio-computing.hrbmu.edu.cn/ICBO-EAST/index.html
13:00pm-15:30pm BKK Time Thailand online session - OntoThailand 2025
13:00pm-13:05pm BKK Time Opening Remarks
13:05pm-14:00pm BKK Time Keynote Speaker, Dr. Alexander D. Diehl Introduction to Biomedical Ontology (in English)
14:00pm-14:30pm BKK Time Keynote Speaker, Dr. Supharerk Thawillarp Introduction to Interoperability and Terminology (in Thai)
14:30pm-14:40pm BKK Time Break
14:40am-15:10am BKK Time Invited Speaker, Wiphawee Laochaturapit, MPH Burden of disease analysis for informing public health policy using data standard (in Thai)
15:10am-15:30pm BKK Time Discussion and Closing Remarks
Local Host/Co-Organizer: Dr. Anuwat Pengput, (Sirindhorn College of Public Health Khon Kaen, Khon Kaen, Thailand) and Dr. Chuthamat Sucharit, (Phayakkhaphum Phisai Hospital, Maha Sarakham, Thailand)
Website: https://weddingpb.my.canva.site/icbo-east-and-ontothailand-2025
Workshops Details¶
- Organizers
- Sabrina Toro (University of North Carolina at Chapel Hill)
- Justin Reese (Lawrence Berkeley National Laboratory)
- Nicolas Matentzoglu (Semanticly)
- Melissa Haendel (University of North Carolina at Chapel Hill)
- J Harry Caufield (Lawrence Berkeley National Laboratory)
- Chris Mungall (Lawrence Berkeley National Laboratory)
- Date of Workshop
- November 18
- Time and Timezone of Workshop
- 7am-10am PT
- 10am-1pm ET
- 3pm-6pm United Kingdom
- 4pm-7pm Central Europe
- Abstract
- Artificial Intelligence (AI) technology is having a tremendous impact on science and society. This can be readily observed in fields such as software engineering, where developers are increasingly using AI tools and even ‘vibe coding’ entire projects. However, much of this impact has yet to filter down to curation and ontology development. Many ontology developers report that they are either distrustful of AI, or they don’t know where to start. Additionally, ontology developers may think that parts of their workflow are too complex to use in AI.
In fact, AI is particularly well suited to many complex aspects of ontology development, and if used correctly, can be deployed with high reliability, while giving the human experts full control over tasks. Some ontologies, such as Mondo, Uberon, and the GO, have already successfully incorporated ontology agents into their GitHub-based workflows.
In this tutorial, we will give a practical hands-on guide to ontology developers, showing how to use the latest powerful agent-based AI to support and accelerate their work. At the end of the tutorial, participants will be able to use an AI coding agent as a part of their day-to-day workflow.
- Organizers
- Sierra Moxon (Lawrence Berkeley National Laboratory)
- Kevin Schaper (Translational and Integrative Sciences Lab, University of North Carolina)
- Matt Brush (Translational and Integrative Sciences Lab, University of North Carolina)
- Chris Mungall (Lawrence Berkeley National Laboratory)
- Melissa Haendel (Translational and Integrative Sciences Lab, University of North Carolina
- Date of Workshop
-
- November 5
- Time and Timezone of Workshop
- 8am PT
- Abstract
- This tutorial introduces LinkML (Linked Data Modeling Language), an open framework that simplifies the process of authoring, validating, and sharing data. LinkML offers an approachable syntax that is not tied to any one technical architecture, and can be integrated seamlessly with many existing frameworks. A low barrier to entry enables people from different backgrounds and varying levels of technical expertise to collaborate, forming a shared understanding of the underlying data semantics and contributing to data annotation and ontology integration.
- Organizers
- Sebastian Duesing (La Jolla Institute for Immunology)
- Bjoern Peters (La Jolla Institute for Immunology)
- James Overton (Knocean, Inc.)
- Randi Vita (La Jolla Institute for Immunology)
- Chris Mungall (Lawrence Berkeley National Laboratory)
- Abstract
- The Core Ontology for Biology and Biomedicine (COB) is a BFO-compatible upper-level ontology used by the Open Biomedical Ontologies (OBO) Foundry. COB provides a direct parent for the top-level classes in every OBO ontology, and so OBO ontologies that use COB are interoperable. Therefore, COB adoption makes interoperability measurable within the OBO Foundry, a critical step towards the Foundry's goal of ensuring the testability of all its principles. After a robust development push following the 2024 COB Workshop at the La Jolla Institute for Immunology, the COB development team is focused on making COB adoption faster, easier, and more rewarding. The purpose of this workshop is to engage and train others to adopt COB in their own ontologies and participate in future COB development.
- Organizers
- Olga Mashkova (King Abdullah University of Science and Technology)
- Anthony Huffman (University of Michigan)
- Date of Workshop
- November 10
- Time and Timezone of Workshop
- 9am-11am ET
- Abstract
- This interactive panel discussion brings together senior researchers to share insights and advice with early-career colleagues working in biomedical ontologies and knowledge representation. Panelists will reflect on key career decisions, essential skills beyond technical expertise, and strategies for resilience in research. The discussion will explore the evolving role of artificial intelligence and large language models (LLMs) in ontology development, addressing how these technologies can drive real-world impact, support industry, and tackle global challenges such as public health and climate change. The panel will also consider how to foster community governance, and uphold ethical responsibility in ontology-driven applications. The session aims to inspire the next generation of researchers while promoting dialogue on the future of ontologies for health, science, and sustainability.
- Organizers
- Giorgio Ubbiali (OTH Brixen College)
- Ludger Jansen (PTH Brixen College)
- Date of Workshop
- November 14
- Time and Timezone of Workshop
- 4pm-7pm CET
- Abstract
- To date, food and plastic waste deriving from human consumption and other supply chain activities pose serious challenges to human health and the resilience and sustainability of food systems. Ontologies play an essential role in enhancing interconnections among datasets, data sources, and people, proving to be critical means to deal with complex health and sustainability issues, such as food and plastic waste. If originally, ontology efforts mainly centered on developing resources addressing health and related features, recently, attention has also been dedicated to sustainability issues. It is imperative to enhance interconnectedness among these ontologies and related applications. In particular, it will be important to communicate across different ontology communities to adequately capture the intrinsic connections between health and sustainability. This workshop aims to promote discussions in this direction, focusing on waste as a starting use case. First, we will explore the current conceptualization of waste, especially food and plastic waste in food systems. Then, we will move to discuss the corresponding existing ontologies and models. Finally, we will engage with subject matter experts, conversating on how to synergize sustainability and health ontologies across ontology communities for food systems waste.
- Organizers
- Junguk Hur (University of North Dakota)
- Yongqun He (University of Michigan)
- Cui Tao (Mayo Clinic)
- Date of Workshop
- November 7
- Time and Timezone of Workshop
- tbd
- Abstract
- We propose the 14th Vaccine and Drug Ontology Studies (VDOS) workshop at the 16th International Conference on Biomedical Ontology (ICBO 2025). This year, we extend our focus to encompass artificial intelligence's transformative role in drug and vaccine ontology research. The workshop aims to explore innovative solutions and challenges in representing and analyzing drugs and vaccines, covering administration, immune responses, adverse events, and more. Key topics include the ontological representation of drugs and vaccines, real-world application challenges, drug components, administration, immune responses, drug interactions, and adverse events in clinical and research settings. A special emphasis will be placed on how AI can revolutionize ontology studies, enhancing literature mining, meta-analysis, and complex data interpretation. Despite progress, challenges remain in fully representing and utilizing ontologies for research and clinical issues, such as detailed representation of administration and adverse events, drug interactions, and analysis of immune responses. The workshop will bring together experts from clinical, research, and pharma-biotech sectors to discuss solutions to these challenges, aiming to foster advancements in drug development, administration, and the integration of AI in ontological research. Our goal is to contribute to public health improvement by enhancing the understanding and application of drug and vaccine ontologies.
Contact Information¶
Please direct all further questions to Asiya Yu Lin (ontology.world@gmail.com)