DOE OSTI · 3484906
The Gene Ontology knowledgebase in 2026
Abstract
Abstract The Gene Ontology (GO) knowledgebase (https://geneontology.org) is a comprehensive resource describing the functions of genes. The GO knowledgebase is regularly updated and improved. We describe here the major updates that have been made in the past 3 years. The ontology and annotations have been expanded and revised, particularly in several areas of biology: cellular metabolism, multi-organism interactions (e.g. host-pathogen), extracellular matrix proteins, chromatin remodeling (e.g. the “histone code”), and noncoding RNA functions. We have released version 2 of a comprehensive set of integrated, reviewed annotations for human genes, which we call the “functionome.” We have also dramatically increased the number of GO-CAM models, with over 1500 models of metabolic and signaling pathways, primarily in human, mouse, budding and fission yeast, and fruit fly. Finally, we discuss our current recommendations and future prospects of AI in the use and development of GO.
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Aleksander, Suzi A (ORCID:0000000167872901), Balhoff, James P (ORCID:0000000286886599), Carbon, Seth (ORCID:0000000182441536), Cherry, J Michael (ORCID:0000000191635180), Ebert, Dustin (ORCID:0000000266590416), Feuermann, Marc (ORCID:0000000241872863), Gaudet, Pascale (ORCID:0000000318136857), Harris, Nomi L (ORCID:0000000163153707), Hill, David P (ORCID:0000000174766306), Kalita, Patrick (ORCID:000000026150307X), Lee, Raymond (ORCID:0000000281517479), Mi, Huaiyu (ORCID:000000018721202X), Moxon, Sierra (ORCID:0000000287197760), Mungall, Christopher J (ORCID:0000000266012165), Muruganujan, Anushya (ORCID:0000000171695864), Mushayahama, Tremayne (ORCID:0000000228746934), Sternberg, Paul W (ORCID:0000000276990173), Thomas, Paul D (ORCID:0000000290743507), Van Auken, Kimberly (ORCID:0000000217064196), Wong, Edith D (ORCID:0000000197995523), Wood, Valerie (ORCID:0000000163307526), Ramsey, Jolene (ORCID:0000000237745896), Siegele, Deborah A (ORCID:0000000189350696), Chisholm, Rex L (ORCID:0000000256383990), Dodson, Robert (ORCID:0000000227575950), Fey, Petra (ORCID:0000000245322703), Aspromonte, Maria Cristina (ORCID:0000000249376952), Nugnes, Maria Victoria (ORCID:0000000183997907), Naser, Ximena Aixa Castro (ORCID:0000000292111255), Tosatto, Silvio C E (ORCID:0000000345257793), Giglio, Michelle (ORCID:0000000176285565), Nadendla, Suvarna (ORCID:000000033643281X), Antonazzo, Giulia (ORCID:0000000300865621), Attrill, Helen (ORCID:0000000332126364), Brown, Nicholas H (ORCID:0000000289587017), dos Santos, Gil (ORCID:0000000335078273), Marygold, Steven (ORCID:000000032759266X), Röper, Katja (ORCID:000000023361766X), Strelets, Victor (ORCID:0000000165569335), Tabone, Christopher J (ORCID:0000000187460680), Thurmond, Jim (ORCID:0000000251422583), Zhou, Pinglei (ORCID:0000000230121044), Zaru, Rossana (ORCID:0000000233584423), Lovering, Ruth C (ORCID:0000000297910064), Logie, Colin (ORCID:0000000285346582), Chen, Daiqing (ORCID:0009000359965181), Naba, Alexandra (ORCID:0000000247965614), Christie, Karen (ORCID:000000015501853X), Corbani, Lori (ORCID:000000022366557X), Ni, Li (ORCID:0000000297967693), Sitnikov, Dmitry (ORCID:0000000333949805), Smith, Cynthia (ORCID:0000000336910324), Seager, James (ORCID:000000017487610X), Cooper, Laurel (ORCID:0000000263798932), Elser, Justin (ORCID:0000000309211982), Jaiswal, Pankaj (ORCID:0000000210058383), Gupta, Parul (ORCID:0000000201908753), Naithani, Sushma (ORCID:0000000178194552), Carme, Pascal (ORCID:0009000390591333), Rutherford, Kim (ORCID:000000016277726X), De Pons, Jeffrey L, Dwinell, Melinda R (ORCID:0000000295283618), Hayman, G Thomas (ORCID:0000000295537227), Kaldunski, Mary L (ORCID:0000000336456803), Kwitek, Anne E (ORCID:0000000310244116), Laulederkind, Stanley J F (ORCID:0000000153564174), Tutaj, Marek A (ORCID:000000021025101X), Vedi, Mahima (ORCID:0000000153616739), Wang, Shur-Jen (ORCID:0000000152568683), D’Eustachio, Peter (ORCID:000000025494626X), Aimo, Lucila (ORCID:0000000309436401), Axelsen, Kristian (ORCID:0000000338892879), Bridge, Alan (ORCID:0000000321489135), Hyka-Nouspikel, Nevila (ORCID:000000017855209X), Morgat, Anne (ORCID:0000000212162969), Goldbold, Gene (ORCID:0000000257024690), Engel, Stacia R (ORCID:000000015472917X), Miyasato, Stuart R (ORCID:0000000152508920), Nash, Robert S (ORCID:0000000237267441), Sherlock, Gavin (ORCID:0000000216924983), Weng, Shuai (ORCID:0000000342330772), Bakker, Erika (ORCID:0000000179333817), Berardini, Tanya Z (ORCID:0000000238378864), Reiser, Leonore (ORCID:0000000300730858), Auchincloss, Andrea (ORCID:0000000252975390), Argoud-Puy, Ghislaine (ORCID:0000000229798613), Blatter, Marie-Claude (ORCID:0000000274741499), Boutet, Emmanuel (ORCID:0000000237434203), Breuza, Lionel (ORCID:0000000280758625), Casals-Casas, Cristina (ORCID:000000018769177X), Coudert, Elisabeth (ORCID:000000018314404X), Estreicher, Anne (ORCID:0000000168282508), Famiglietti, Maria Livia (ORCID:0000000252836593), Gos, Arnaud (ORCID:0000000250181378), Gruaz-Gumowski, Nadine (ORCID:0000000246994907), Hulo, Chantal (ORCID:0000000181767999), Jungo, Florence (ORCID:0000000274568390), Mercier, Philippe Le (ORCID:000000018528090X), Lieberherr, Damien (ORCID:0000000297241710), Masson, Patrick (ORCID:0000000176460052). 2025-12-18. The Gene Ontology knowledgebase in 2026. https://doi.org/10.1093/nar%2Fgkaf1292
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