iyad031.pdf (800.23 kB)
The Gene Ontology knowledgebase in 2023.
journal contributionposted on 2023-05-05, 11:26 authored by Gene Ontology Consortium, Suzi A Aleksander, James Balhoff, Seth Carbon, J Michael Cherry, Harold J Drabkin, Dustin Ebert, Marc Feuermann, Pascale Gaudet, Nomi L Harris, David P Hill, Raymond Lee, Huaiyu Mi, Sierra Moxon, Christopher J Mungall, Anushya Muruganugan, Tremayne Mushayahama, Paul W Sternberg, Paul D Thomas, Kimberly Van Auken, Jolene Ramsey, Deborah A Siegele, Rex L Chisholm, Petra Fey, Maria Cristina Aspromonte, Maria Victoria Nugnes, Federica Quaglia, Silvio Tosatto, Michelle Giglio, Suvarna Nadendla, Giulia Antonazzo, Helen Attrill, Gil Dos Santos, Steven Marygold, Victor Strelets, Christopher J Tabone, Jim Thurmond, Pinglei Zhou, Saadullah H Ahmed, Praoparn Asanitthong, Diana Luna Buitrago, Meltem N Erdol, Matthew C Gage, Mohamed Ali Kadhum, Kan Yan Chloe Li, Miao Long, Aleksandra Michalak, Angeline Pesala, Armalya Pritazahra, Shirin CC Saverimuttu, Renzhi Su, Kate E Thurlow, Ruth C Lovering, Colin Logie, Snezhana Oliferenko, Judith Blake, Karen Christie, Lori Corbani, Mary E Dolan, Li Ni, Dmitry Sitnikov, Cynthia Smith, Alayne Cuzick, James Seager, Laurel Cooper, Justin Elser, Pankaj Jaiswal, Parul Gupta, Sushma Naithani, Manuel Lera-Ramirez, Kim Rutherford, Valerie Wood, Jeffrey L De Pons, Melinda R Dwinell, G Thomas Hayman, Mary L Kaldunski, Anne E Kwitek, Stanley JF Laulederkind, Marek A Tutaj, Mahima Vedi, Shur-Jen Wang, Peter D'Eustachio, Lucila Aimo, Kristian Axelsen, Alan Bridge, Nevila Hyka-Nouspikel, Anne Morgat, Stacia R Engel, Kalpana Karra, Stuart R Miyasato, Robert S Nash, Marek S Skrzypek, Shuai Weng, Edith D Wong, Erika Bakker, Tanya Z Berardini, Leonore Reiser, Andrea Auchincloss, Ghislaine Argoud-Puy, Marie-Claude Blatter, Emmanuel Boutet, Lionel Breuza, Cristina Casals-Casas, Elisabeth Coudert, Anne Estreicher, Maria Livia Famiglietti, Arnaud Gos, Nadine Gruaz-Gumowski, Chantal Hulo, Florence Jungo, Philippe Le Mercier, Damien Lieberherr, Patrick Masson, Ivo Pedruzzi, Lucille Pourcel, Sylvain Poux, Catherine Rivoire, Shyamala Sundaram, Alex Bateman, Emily Bowler-Barnett, Hema Bye-A-Jee, Paul Denny, Alexandr Ignatchenko, Rizwan Ishtiaq, Antonia Lock, Yvonne Lussi, Michele Magrane, Maria J Martin, Sandra Orchard, Pedro Raposo, Elena Speretta, Nidhi Tyagi, Kate Warner, Rossana Zaru, Alexander D Diehl, Juancarlos Chan, Stavros Diamantakis, Daniela Raciti, Magdalena Zarowiecki, Malcolm Fisher, Christina James-Zorn, Virgilio Ponferrada, Aaron Zorn, Sridhar Ramachandran, Leyla Ruzicka, Monte Westerfield
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.