Structural Changes in Gene Ontology Reveal Modular and Complex Representations of Biological Function

This repository contains the data, code, and supplementary materials for the manuscript:

Valverde S., et al. (2025). Structural Changes in Gene Ontology Reveal Modular and Complex Representations of Biological Function. Molecular Biology and Evolution

Read the paper here: https://academic.oup.com/mbe/article/doi/10.1093/molbev/msaf148/8159018

Overview

This study uses network-based methods to analyze fifteen years of Gene Ontology (GO) evolution. We show that GO evolves not only through incremental growth, but also via curator-driven restructuring. In particular, we document a major semantic modularization in the Cellular Component branch in 2019, aligning GO with frameworks such as CARO and GO-CAM. Our results highlight the need for version-aware, multi-layer representations of ontological knowledge in computational biology.

Repository Structure

Repository Structure

gene-ontology-evolution/
├── data/                     # Network files
│   ├── go_versions/          # Individual GO snapshots (in OBO graph format)
│   ├── processed_networks/   # Processed network data (in Pajek graph format)
├── scripts/                  # Python scripts used in the analysis
├── results/                  # Figures and summary outputs
├── README.md                 # Project overview (this file)
├── LICENSE                   # Open source license

Scripts

Figures can be reproduced using the scripts provided in the /scripts folder and the input data under /data. For instructions:

1. Clone this repository
2. Ensure dependencies are installed (Python ≥ 3.8, NetworkX, Matplotlib, etc.)

Licensing

•    Code: MIT License
•    Data: CC-BY 4.0 International

See LICENSE file for details.

Contact

For questions, please contact:

Sergi Valverde Evolution of Networks Lab, Barcelona s.valverde@csic.es