The Gene Ontology knowledgebase in 2023-Reference-Cited by-同舟云学术

The Gene Ontology knowledgebase in 2023

Published:2023-03-03 Issue:1 Volume:224 Page:
ISSN:1943-2631
Container-title:GENETICS
language:en
Short-container-title:

Author:

,Aleksander Suzi A^ORCID,Balhoff James^ORCID,Carbon Seth^ORCID,Cherry J Michael^ORCID,Drabkin Harold J^ORCID,Ebert Dustin^ORCID,Feuermann Marc^ORCID,Gaudet Pascale^ORCID,Harris Nomi L^ORCID,Hill David P^ORCID,Lee Raymond^ORCID,Mi Huaiyu^ORCID,Moxon Sierra^ORCID,Mungall Christopher J^ORCID,Muruganugan Anushya^ORCID,Mushayahama Tremayne^ORCID,Sternberg Paul W^ORCID,Thomas Paul D^ORCID,Van Auken Kimberly^ORCID,Ramsey Jolene^ORCID,Siegele Deborah A^ORCID,Chisholm Rex L^ORCID,Fey Petra^ORCID,Aspromonte Maria Cristina^ORCID,Nugnes Maria Victoria^ORCID,Quaglia Federica^ORCID,Tosatto Silvio^ORCID,Giglio Michelle^ORCID,Nadendla Suvarna^ORCID,Antonazzo Giulia^ORCID,Attrill Helen^ORCID,dos Santos Gil^ORCID,Marygold Steven^ORCID,Strelets Victor^ORCID,Tabone Christopher J^ORCID,Thurmond Jim^ORCID,Zhou Pinglei^ORCID,Ahmed Saadullah H,Asanitthong Praoparn^ORCID,Luna Buitrago Diana^ORCID,Erdol Meltem N^ORCID,Gage Matthew C^ORCID,Ali Kadhum Mohamed,Li Kan Yan Chloe^ORCID,Long Miao,Michalak Aleksandra,Pesala Angeline^ORCID,Pritazahra Armalya,Saverimuttu Shirin C C^ORCID,Su Renzhi^ORCID,Thurlow Kate E^ORCID,Lovering Ruth C^ORCID,Logie Colin^ORCID,Oliferenko Snezhana^ORCID,Blake Judith^ORCID,Christie Karen^ORCID,Corbani Lori^ORCID,Dolan Mary E^ORCID,Drabkin Harold J^ORCID,Hill David P^ORCID,Ni Li^ORCID,Sitnikov Dmitry^ORCID,Smith Cynthia^ORCID,Cuzick Alayne^ORCID,Seager James^ORCID,Cooper Laurel^ORCID,Elser Justin^ORCID,Jaiswal Pankaj^ORCID,Gupta Parul^ORCID,Jaiswal Pankaj^ORCID,Naithani Sushma^ORCID,Lera-Ramirez Manuel^ORCID,Rutherford Kim^ORCID,Wood Valerie^ORCID,De Pons Jeffrey L,Dwinell Melinda R^ORCID,Hayman G Thomas^ORCID,Kaldunski Mary L^ORCID,Kwitek Anne E^ORCID,Laulederkind Stanley J F^ORCID,Tutaj Marek A^ORCID,Vedi Mahima^ORCID,Wang Shur-Jen^ORCID,D’Eustachio Peter^ORCID,Aimo Lucila^ORCID,Axelsen Kristian^ORCID,Bridge Alan^ORCID,Hyka-Nouspikel Nevila^ORCID,Morgat Anne^ORCID,Aleksander Suzi A^ORCID,Cherry J Michael^ORCID,Engel Stacia R^ORCID,Karra Kalpana^ORCID,Miyasato Stuart R^ORCID,Nash Robert S^ORCID,Skrzypek Marek S^ORCID,Weng Shuai^ORCID,Wong Edith D^ORCID,Bakker Erika^ORCID,Berardini Tanya Z^ORCID,Reiser Leonore^ORCID,Auchincloss Andrea^ORCID,Axelsen Kristian^ORCID,Argoud-Puy Ghislaine^ORCID,Blatter Marie-Claude^ORCID,Boutet Emmanuel^ORCID,Breuza Lionel^ORCID,Bridge Alan^ORCID,Casals-Casas Cristina^ORCID,Coudert Elisabeth^ORCID,Estreicher Anne^ORCID,Livia Famiglietti Maria^ORCID,Feuermann Marc^ORCID,Gos Arnaud^ORCID,Gruaz-Gumowski Nadine^ORCID,Hulo Chantal^ORCID,Hyka-Nouspikel Nevila^ORCID,Jungo Florence^ORCID,Le Mercier Philippe^ORCID,Lieberherr Damien^ORCID,Masson Patrick^ORCID,Morgat Anne^ORCID,Pedruzzi Ivo^ORCID,Pourcel Lucille^ORCID,Poux Sylvain^ORCID,Rivoire Catherine^ORCID,Sundaram Shyamala^ORCID,Bateman Alex^ORCID,Bowler-Barnett Emily^ORCID,Bye-A-Jee Hema^ORCID,Denny Paul^ORCID,Ignatchenko Alexandr^ORCID,Ishtiaq Rizwan^ORCID,Lock Antonia^ORCID,Lussi Yvonne^ORCID,Magrane Michele^ORCID,Martin Maria J^ORCID,Orchard Sandra^ORCID,Raposo Pedro^ORCID,Speretta Elena^ORCID,Tyagi Nidhi^ORCID,Warner Kate^ORCID,Zaru Rossana^ORCID,Diehl Alexander D^ORCID,Lee Raymond^ORCID,Chan Juancarlos^ORCID,Diamantakis Stavros^ORCID,Raciti Daniela^ORCID,Zarowiecki Magdalena^ORCID,Fisher Malcolm^ORCID,James-Zorn Christina^ORCID,Ponferrada Virgilio^ORCID,Zorn Aaron^ORCID,Ramachandran Sridhar^ORCID,Ruzicka Leyla^ORCID,Westerfield Monte^ORCID,Aleksander Suzi A^ORCID,Balhoff James^ORCID,Carbon Seth^ORCID,Cherry J Michael^ORCID,Drabkin Harold J^ORCID,Ebert Dustin^ORCID,Feuermann Marc^ORCID,Gaudet Pascale^ORCID,Harris Nomi L^ORCID,Hill David P^ORCID,Lee Raymond^ORCID,Mi Huaiyu^ORCID,Moxon Sierra^ORCID,Mungall Christopher J^ORCID,Muruganugan Anushya^ORCID,Mushayahama Tremayne^ORCID,Sternberg Paul W^ORCID,Thomas Paul D^ORCID,Van Auken Kimberly^ORCID,Ramsey Jolene^ORCID,Siegele Deborah A^ORCID,Chisholm Rex L^ORCID,Fey Petra^ORCID,Aspromonte Maria Cristina^ORCID,Nugnes Maria Victoria^ORCID,Quaglia Federica^ORCID,Tosatto Silvio^ORCID,Giglio Michelle^ORCID,Nadendla Suvarna^ORCID,Antonazzo Giulia^ORCID,Attrill Helen^ORCID,dos Santos Gil^ORCID,Marygold Steven^ORCID,Strelets Victor^ORCID,Tabone Christopher J^ORCID,Thurmond Jim^ORCID,Zhou Pinglei^ORCID,Ahmed Saadullah H,Asanitthong Praoparn^ORCID,Luna Buitrago Diana^ORCID,Erdol Meltem N^ORCID,Gage Matthew C^ORCID,Ali Kadhum Mohamed,Li Kan Yan Chloe^ORCID,Long Miao,Michalak Aleksandra,Pesala Angeline^ORCID,Pritazahra Armalya,Saverimuttu Shirin C C^ORCID,Su Renzhi^ORCID,Thurlow Kate E^ORCID,Lovering Ruth C^ORCID,Logie Colin^ORCID,Oliferenko Snezhana^ORCID,Blake Judith^ORCID,Christie Karen^ORCID,Corbani Lori^ORCID,Dolan Mary E^ORCID,Drabkin Harold J^ORCID,Hill David P^ORCID,Ni Li^ORCID,Sitnikov Dmitry^ORCID,Smith Cynthia^ORCID,Cuzick Alayne^ORCID,Seager James^ORCID,Cooper Laurel^ORCID,Elser Justin^ORCID,Jaiswal Pankaj^ORCID,Gupta Parul^ORCID,Jaiswal Pankaj^ORCID,Naithani Sushma^ORCID,Lera-Ramirez Manuel^ORCID,Rutherford Kim^ORCID,Wood Valerie^ORCID,De Pons Jeffrey L,Dwinell Melinda R^ORCID,Hayman G Thomas^ORCID,Kaldunski Mary L^ORCID,Kwitek Anne E^ORCID,Laulederkind Stanley J F^ORCID,Tutaj Marek A^ORCID,Vedi Mahima^ORCID,Wang Shur-Jen^ORCID,D’Eustachio Peter^ORCID,Aimo Lucila^ORCID,Axelsen Kristian^ORCID,Bridge Alan^ORCID,Hyka-Nouspikel Nevila^ORCID,Morgat Anne^ORCID,Aleksander Suzi A^ORCID,Cherry J Michael^ORCID,Engel Stacia R^ORCID,Karra Kalpana^ORCID,Miyasato Stuart R^ORCID,Nash Robert S^ORCID,Skrzypek Marek S^ORCID,Weng Shuai^ORCID,Wong Edith D^ORCID,Bakker Erika^ORCID,Berardini Tanya Z^ORCID,Reiser Leonore^ORCID,Auchincloss Andrea^ORCID,Axelsen Kristian^ORCID,Argoud-Puy Ghislaine^ORCID,Blatter Marie-Claude^ORCID,Boutet Emmanuel^ORCID,Breuza Lionel^ORCID,Bridge Alan^ORCID,Casals-Casas Cristina^ORCID,Coudert Elisabeth^ORCID,Estreicher Anne^ORCID,Livia Famiglietti Maria^ORCID,Feuermann Marc^ORCID,Gos Arnaud^ORCID,Gruaz-Gumowski Nadine^ORCID,Hulo Chantal^ORCID,Hyka-Nouspikel Nevila^ORCID,Jungo Florence^ORCID,Le Mercier Philippe^ORCID,Lieberherr Damien^ORCID,Masson Patrick^ORCID,Morgat Anne^ORCID,Pedruzzi Ivo^ORCID,Pourcel Lucille^ORCID,Poux Sylvain^ORCID,Rivoire Catherine^ORCID,Sundaram Shyamala^ORCID,Bateman Alex^ORCID,Bowler-Barnett Emily^ORCID,Bye-A-Jee Hema^ORCID,Denny Paul^ORCID,Ignatchenko Alexandr^ORCID,Ishtiaq Rizwan^ORCID,Lock Antonia^ORCID,Lussi Yvonne^ORCID,Magrane Michele^ORCID,Martin Maria J^ORCID,Orchard Sandra^ORCID,Raposo Pedro^ORCID,Speretta Elena^ORCID,Tyagi Nidhi^ORCID,Warner Kate^ORCID,Zaru Rossana^ORCID,Diehl Alexander D^ORCID,Lee Raymond^ORCID,Chan Juancarlos^ORCID,Diamantakis Stavros^ORCID,Raciti Daniela^ORCID,Zarowiecki Magdalena^ORCID,Fisher Malcolm^ORCID,James-Zorn Christina^ORCID,Ponferrada Virgilio^ORCID,Zorn Aaron^ORCID,Ramachandran Sridhar^ORCID,Ruzicka Leyla^ORCID,Westerfield Monte^ORCID

Abstract

Abstract The Gene Ontology (GO) knowledgebase (http://geneontology.org) is a comprehensive resource concerning the functions of genes and gene products (proteins and noncoding RNAs). GO annotations cover genes from organisms across the tree of life as well as viruses, though most gene function knowledge currently derives from experiments carried out in a relatively small number of model organisms. Here, we provide an updated overview of the GO knowledgebase, as well as the efforts of the broad, international consortium of scientists that develops, maintains, and updates the GO knowledgebase. The GO knowledgebase consists of three components: (1) the GO—a computational knowledge structure describing the functional characteristics of genes; (2) GO annotations—evidence-supported statements asserting that a specific gene product has a particular functional characteristic; and (3) GO Causal Activity Models (GO-CAMs)—mechanistic models of molecular “pathways” (GO biological processes) created by linking multiple GO annotations using defined relations. Each of these components is continually expanded, revised, and updated in response to newly published discoveries and receives extensive QA checks, reviews, and user feedback. For each of these components, we provide a description of the current contents, recent developments to keep the knowledgebase up to date with new discoveries, and guidance on how users can best make use of the data that we provide. We conclude with future directions for the project.

Funder

National Human Genome Research Institute

UK Medical Research Council

Wellcome Trust

Eunice Kennedy Shriver National Institute of Child Health and Human Development

National Institute for Health Research

National Science Foundation

Alliance of Genome Resources Central

National Institute of Allergy and Infectious Diseases

National Institute on Aging

National Institute of General Medical Sciences

National Institute of Diabetes and Digestive and Kidney Diseases