{"about":{"site":"https://codewithpapers.app","non_affiliation":"Code with Papers and Syntology are not affiliated with, endorsed by, or sponsored by Papers with Code, Meta, or the pwc-archive mirror.","licence":"CC BY-SA 4.0","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","attribution":"https://codewithpapers.app/attribution","modified":"archive material modified by Syntology; see the attribution page"},"url":"/paper/gotaxon-representing-the-evolution-of","title":"GOTaxon: Representing the evolution of biological functions in the Gene Ontology","arxiv_id":"1802.06004","date":"2018-02-16","proceeding":null,"authors":[],"abstract":"The Gene Ontology aims to define the universe of functions known for gene\nproducts, at the molecular, cellular and organism levels. While the ontology is\ndesigned to cover all aspects of biology in a \"species independent manner\", the\nfact remains that many if not most biological functions are restricted in their\ntaxonomic range. This is simply because functions evolve, i.e. like other\nbiological characteristics they are gained and lost over evolutionary time.\nHere we introduce a general method of representing the evolutionary gain and\nloss of biological functions within the Gene Ontology. We then apply a variety\nof techniques, including manual curation, logical reasoning over the ontology\nstructure, and previously published \"taxon constraints\" to assign evolutionary\ngain and loss events to the majority of terms in the GO. These gain and loss\nevents now almost triple the number of terms with taxon constraints, and\ncurrently cover a total of 76% of GO terms, including 40% of molecular function\nterms, 78% of cellular component terms, and 89% of biological process terms.\n  Database URL: GOTaxon is freely available at\nhttps://github.com/haimingt/GOTaxonConstraint","url_abs":"http://arxiv.org/abs/1802.06004v1","url_pdf":"http://arxiv.org/pdf/1802.06004v1.pdf","source":{"archive":"pwc-archive (Hugging Face), CC BY-SA 4.0","snapshot":"2025-07-28","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","row_kind":"abstracts"},"code_links":[{"paper_slug":"gotaxon-representing-the-evolution-of","repo_url":"https://github.com/haimingt/GOTaxonConstraint","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":0,"framework":"none","reach":null}],"tasks":[{"task_slug":"logical-reasoning","task_name":"Logical Reasoning"}],"methods":[],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"atlas_url":null,"mcp":null,"developers":"https://syntology.ai/developers"},"arxiv_metadata":null,"syntology_extracted_results":null}