\(GO_3\)

GO3 is a high-performance Python library (Rust backend) for Gene Ontology semantic similarity.

It supports:

• ontology and annotation loading

• term-level similarity

• term-set and gene-level similarity

• high-throughput batch workflows

• distance-matrix and embedding utilities

Start Here

• Installation

• Examples

• Semantic Similarity

• Performance Guide

• Visualization (t-SNE / UMAP)

• Benchmarks

Install

pip install go3

Optional visualization extras:

pip install go3[viz]

Quick example

import go3

go3.load_go_terms("go-basic.obo")
annots = go3.load_gaf("goa_human.gaf")
counter = go3.build_term_counter(annots)

sim = go3.semantic_similarity("GO:0006397", "GO:0008380", "lin", counter)
print(sim)