arXiv subjects

Pascale Gaudet

Publications and source records attributed to Pascale Gaudet.

4 recordsLinked to original sources

arXiv2026

Agents for Everyone: A Workshop Framework for Building Agentic AI Capabilities in a Distributed Curation Community

Agentic AI has the potential to accelerate curation of biological databases and knowledge bases. However, uptake has been hindered by a number of challenges and obstacles, including access to agents and appropriate training. Here we describe how we have attempted to address and mitigate these challenges and obstacles through the deployment of a cloud-based agentic environment, and the development of an interactive training workshop for the Gene Ontology Consortium. Our cloud environment for agentic-assisted curation was based on the JupyterHub platform, and utilized Claude Code as a universal harness. This allows curators to interact with an agent session through a terminal running in the browser, and has additional benefits such as centralization of access through a single API gateway, removing the need for participants to manage subscriptions or install software locally. We created four training modules, walking participants through basic agentic tool use first and then working up to agentic biological pathway curation using the existing GO-CAM (GO Causal Activity Model) curation tool. Thirty-seven participants took part in the four-hour workshop. Our key takeaway from this workshop is that building community capability with agentic AI is primarily a problem of access, workflow design, and training. Removing technical barriers, introducing capabilities gradually, grounding exercises in familiar curation tasks, and giving curators direct experience evaluating agent output can provide a practical route toward building shared agentic AI capability in distributed scientific communities.

cs.AI↗

arXiv2024

Dynamic Retrieval Augmented Generation of Ontologies using Artificial Intelligence (DRAGON-AI)

Background: Ontologies are fundamental components of informatics infrastructure in domains such as biomedical, environmental, and food sciences, representing consensus knowledge in an accurate and computable form. However, their construction and maintenance demand substantial resources and necessitate substantial collaboration between domain experts, curators, and ontology experts. We present Dynamic Retrieval Augmented Generation of Ontologies using AI (DRAGON-AI), an ontology generation method employing Large Language Models (LLMs) and Retrieval Augmented Generation (RAG). DRAGON-AI can generate textual and logical ontology components, drawing from existing knowledge in multiple ontologies and unstructured text sources. Results: We assessed performance of DRAGON-AI on de novo term construction across ten diverse ontologies, making use of extensive manual evaluation of results. Our method has high precision for relationship generation, but has slightly lower precision than from logic-based reasoning. Our method is also able to generate definitions deemed acceptable by expert evaluators, but these scored worse than human-authored definitions. Notably, evaluators with the highest level of confidence in a domain were better able to discern flaws in AI-generated definitions. We also demonstrated the ability of DRAGON-AI to incorporate natural language instructions in the form of GitHub issues. Conclusions: These findings suggest DRAGON-AI's potential to substantially aid the manual ontology construction process. However, our results also underscore the importance of having expert curators and ontology editors drive the ontology generation process.

cs.AI↗

arXiv2016

Gene Ontology: Pitfalls, Biases, Remedies

The Gene Ontology (GO) is a formidable resource but there are several considerations about it that are essential to understand the data and interpret it correctly. The GO is sufficiently simple that it can be used without deep understanding of its structure or how it is developed, which is both a strength and a weakness. In this chapter, we discuss some common misinterpretations of the ontology and the annotations. A better understanding of the pitfalls and the biases in the GO should help users make the most of this very rich resource. We also review some of the misconceptions and misleading assumptions commonly made about GO, including the effect of data incompleteness, the importance of annotation qualifiers, and the transitivity or lack thereof associated with different ontology relations. We also discuss several biases that can confound aggregate analyses such as gene enrichment analyses. For each of these pitfalls and biases, we suggest remedies and best practices.

q-bio.GN↗

arXiv2016

Primer on the Gene Ontology

The Gene Ontology (GO) project is the largest resource for cataloguing gene function. The combination of solid conceptual underpinnings and a practical set of features have made the GO a widely adopted resource in the research community and an essential resource for data analysis. In this chapter, we provide a concise primer for all users of the GO. We briefly introduce the structure of the ontology and explain how to interpret annotations associated with the GO.

q-bio.GN↗