The Gene Ontology knowledgebase in 2023

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ID: 291323
2023
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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.
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Authors Suzi Aleksander, James P. Balhoff, Seth Carbon, J. Michael Cherry, Harold Drabkin, Dustin Ebert, Marc Feuermann, Pascale Gaudet, Nomi L. Harris, David P. Hill, Raymond Lee, Huaiyu Mi, Sierra Moxon, Chris 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, María Victoria Nugnes, Federica Quaglia, Silvio C. E. Tosatto, Michelle Giglio, Suvarna Nadendla, Giulia Antonazzo, Helen Attrill, Gil dos Santos, Steven J Marygold, Victor Strelets, Christopher J Tabone, Jim Thurmond, Pinglei Zhou, Saadullah H. Ahmed, Praoparn Asanitthong, Diana Luna Buitrago, Meltem N Erdol, Matthew Gage, Mohamed Ali Kadhum, Kan Yan Chloe Li, Miao Long, Aleksandra Michalak, Angeline Pesala, Armalya Pritazahra, Shirin C C Saverimuttu, Renzhi Su, Kate E. Thurlow, Ruth C. Lovering, Colin Logie, Snezhana Oliferenko, Judith A. Blake, Karen Christie, Lori E Corbani, M. Eileen Dolan, Li Ni, Dmitry Sitnikov, Cynthia L. Smith, Alayne Cuzick, James Seager, Laurel Cooper, Justin Elser, Pankaj Jaiswal, Parul Gupta, Sushma Naithani, Manuel Lera-Ramírez, Kim Rutherford, Valerie Wood, Jeffrey L De Pons, Melinda R. Dwinell, G. Thomas Hayman, Mary L. Kaldunski, Anne E. Kwitek, Stanley J. F. Laulederkind, Marek Tutaj, Mahima Vedi, Shur‐Jen Wang, Peter D'Eustachio, Lucila Aimo, Kristian B. 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 Berardini
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Journal current genetics
Year 2023
DOI
10.1093/genetics/iyad031
URL
https://academic.oup.com/genetics/advance-article-pdf/doi/10.1093/genetics/iyad031/49407834/iyad031.pdf
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