GO3: a Rust-backed Python library for Gene Ontology semantic similarity analysis

[Mellandd]

Hi everyone,

We recently published GO3, an open-source Python library for semantic similarity analysis in the Gene Ontology.

GO3 is built with a Rust backend exposed through a Python API, with the goal of making GO semantic similarity workflows faster and easier to use directly from Python.

Links:

GitHub: https://github.com/Mellandd/GO3
Documentation: https://go3.readthedocs.io/en/latest/
SoftwareX paper: https://www.sciencedirect.com/science/article/pii/S2352711026002475

The library supports several common workflows around GO semantic similarity, including:

• term-level semantic similarity
• comparison of sets of GO terms
• gene-level and gene-set similarity
• batch and all-vs-all comparisons
• distance matrix generation
• downstream embeddings and visualization workflows

The main idea behind GO3 is to provide a practical, Python-friendly tool that covers more than just pairwise GO term similarity. We wanted to make it easier to go from GO annotations to gene/gene-set comparisons, distance matrices, and downstream analyses without writing a lot of custom glue code.

It currently includes multiple term-level similarity methods, groupwise comparison strategies, and parallelized batch operations through the Rust backend.

We would be very happy to hear any feedback from the GO community, especially regarding use cases, documentation, terminology, or anything that could make the library more useful for people working with GO annotations.

Thanks!