2018/02/16 by Haiming Tang, Christopher J Mungall, Chris Mungall +7 · 1 citation
Biochemistry, Genetics and Molecular Biology · #Artificial intelligence #Bioinformatics #Bioinformatics and Genomic Networks #Biological database #Biological materials #Biological organism #Biology #Biomedical Text Mining and Ontologies #Computational biology #Computer science #Cover (algebra) #Epistemology #Evolutionary biology #FOS: Biological sciences #Function (biology) #Gene #Gene ontology #Genetics #Genomics (q-bio.GN) #Genomics and Phylogenetic Studies #Ontology #Organism #Populations and Evolution (q-bio.PE) #Variety (cybernetics) #q-bio.GN #q-bio.PE
paper · pdf · doi:10.48550/arxiv.1802.06004
published in arXiv (Cornell University) (Cornell University) · 23 pages, 2 figures, 6 tables
arxiv created 2018/02/16 · openalex publication_date 2018/02/16 · arxiv updated 2018/02/19 · openalex created_date 2025/10/10 · openalex updated_date 2026/08/06
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