GOTaxon: Representing the evolution of biological functions in the Gene Ontology

TL;DR

This paper introduces GOTaxon, a method to represent the evolutionary gain and loss of biological functions in the Gene Ontology, significantly expanding the annotation of taxon constraints across GO terms.

Contribution

It presents a novel approach to encode evolutionary dynamics of functions within the Gene Ontology, enhancing the understanding of functional evolution across species.

Findings

Almost tripled the number of GO terms with taxon constraints

Covered 76% of GO terms with evolutionary gain/loss annotations

Significantly improved representation of functional evolution in GO

Abstract

The Gene Ontology aims to define the universe of functions known for gene products, at the molecular, cellular and organism levels. While the ontology is designed to cover all aspects of biology in a "species independent manner", the fact remains that many if not most biological functions are restricted in their taxonomic range. This is simply because functions evolve, i.e. like other biological characteristics they are gained and lost over evolutionary time. Here we introduce a general method of representing the evolutionary gain and loss of biological functions within the Gene Ontology. We then apply a variety of techniques, including manual curation, logical reasoning over the ontology structure, and previously published "taxon constraints" to assign evolutionary gain and loss events to the majority of terms in the GO. These gain and loss events now almost triple the number of terms with taxon constraints, and currently cover a total of 76% of GO terms, including 40% of molecular function terms, 78% of cellular component terms, and 89% of biological process terms. Database URL: GOTaxon is freely available at https://github.com/haimingt/GOTaxonConstraint