The Gene Ontology knowledgebase in 2023

作者：Suzi A Aleksander, J. Balhoff, S. Carbon, J. Cherry, H. Drabkin, Dustin Ebert, M. Feuermann, P. Gaudet, N. Harris, D. Hill, Raymond Lee, H. Mi, S. Moxon, C. Mungall, Anushya Muruganugan, Tremayne Mushayahama, P. Sternberg, Paul D. Thomas, K. V. Van Auken, Jolene Ramsey, D. Siegele, R. Chisholm, P. Fey, M. C. Aspromonte, María Victoria Nugnes, F. Quaglia, Silvio C. E. Tosatto, M. Giglio, Suvarna Nadendla, Giulia Antonazzo, H. Attrill, Gilberto dos Santos, Steven J. Marygold, V. Strelets, C. Tabone, Jim Thurmond, Pinglei Zhou, Saadullah H Ahmed, Praoparn Asanitthong, Diana Luna Buitrago, Meltem N. Erdol, M. 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, R. Lovering, C. Logie, S. Oliferenko, J. Blake, K. Christie, L. Corbani, M. E. Dolan, H. Drabkin, D. Hill, L. Ni, D. Sitnikov, Cynthia L. Smith, A. Cuzick, James Seager, L. Cooper, J. Elser, P. Jaiswal, Parul Gupta, P. Jaiswal, Sushma Naithani, Manuel Lera-Ramírez, Kim M Rutherford, V. Wood, J. D. De Pons, M. Dwinell, G. Hayman, M. Kaldunski, A. Kwitek, S. Laulederkind, M. Tutaj, M. Vedi, Shur-Jen Wang, P. D’Eustachio, L. Aimo, K. Axelsen, A. Bridge, Nevila Hyka-Nouspikel, A. Morgat, Suzi A Aleksander, J. Cherry, S. Engel, K. Karra, S. Miyasato, R. Nash, M. Skrzypek, S. Weng, E. Wong, E. Bakker, T. Berardini, L. Reiser, A. Auchincloss, K. Axelsen, Ghislaine Argoud-Puy, M. Blatter, E. Boutet, L. Breuza, A. Bridge, Cristina Casals-Casas, E. Coudert, A. Estreicher, M. Famiglietti, M. Feuermann, A. Gos, N. Gruaz-Gumowski, C. Hulo, Nevila Hyka-Nouspikel, F. Jungo, Philippe le Mercier, D. Lieberherr, P. Masson, A. Morgat, I. Pedruzzi, L. Pourcel, S. Poux, C. Rivoire, S. Sundaram, A. Bateman, E. Bowler-Barnett, Hema Bye-A-Jee, Paul Denny, A. Ignatchenko, Rizwan Ishtiaq, A. Lock, Yvonne Lussi, M. Magrane, M. Martin, S. Orchard, Pedro Raposo, Elena Speretta, N. Tyagi, Kate Warner, Rossana Zaru, A. Diehl, Raymond Lee, J. Chan, Stavros Diamantakis, Daniela Raciti, M. Zarowiecki, M. Fisher, Christina James-Zorn, V. Ponferrada, A. Zorn, S. Ramachandran, Leyla Ruzicka, M. Westerfield · 发表于：Genetics · 年份：2023 · DOI：10.1093/genetics/iyad031 · 被引用次数：2468 · 研究领域：Medicine

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 direct...