# Biological Knowledge Extraction from BioPAX Graphs

Cécile Beust, Emmanuelle Becker, Nathalie Théret, Olivier Dameron

► To cite this version:

Cécile Beust, Emmanuelle Becker, Nathalie Théret, Olivier Dameron. Biological Knowledge Extraction from BioPAX Graphs. DKM 2025 - Data and Knowledge Management days, Mar 2025, Rennes, France. 2025. hal-05433535

HAL Id: hal-05433535

https://inria.hal.science/hal-05433535v1

Submitted on 28 Dec 2025

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# Biological Knowledge Extraction from BioPAX Graphs

Cécile Beust¹, Emmanuelle Becker¹, Nathalie Théret¹,², Olivier Dameron¹

¹Univ Rennes, Inria, CNRS, IRISA - UMR 6074, Rennes, F-35000, France
²Univ Rennes, Inserm, EHESP, Irset, UMR S1085, Rennes, F-35000, France
cecile.beust@univ-rennes.fr

## Introduction

In systems biology, the study of biological pathways is a key to understand the complexity of biological systems. The recent massification of biological pathway data available online through various databases raised an important need of standardization of these data. The BioPAX format (Biological Pathway Exchange) [1], created in 2010, is a semantic web format designed for the standardization and exchange of pathway data. BioPAX is highly expressive but intrinsically complex, limiting its wider adoption. Here we report on the use of the BioPAX format in 2024 and present abstraction methods to simplify knowledge extraction from BioPAX graphs [2].

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