Accelerating Ontology Curation with Agentic AI and GitHub

Overview

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.

What Participants Will Learn

• Core concepts underlying agentic AI

• How to use an AI coding agent for tasks including

• Simple mechanical edits to individual terms

• Adding terms or batches of terms to an ontology

• Performing complex updates and refactorings that touch multiple terms

Format
A 3-hour tutorial with a mix of short lectures and hands-on walkthroughs. Attendees should have a basic familiarity with ontologies and GitHub. 

Target Audience
Ontology developers, maintainers, and biomedical curators interested in accelerating workflows using agentic AI 

Materials

Slides: ICBO Agent Tutorial 2025

Repo: https://github.com/ai4curation/icbo-ai-tutorial 

Blog: https://monarchinit.medium.com/ai-for-curation-workshop-at-icbo-2025-15007c14d34b 

Recording: 

 https://youtu.be/_9Re39yB7EE?si=1WaUJiKL1U1OssGT