The Gene Ontology resource: enriching a GOld mine

Carbon, Seth; Douglass, Eric; Good, Benjamin M.; Unni, Deepak R.; Harris, Nomi L.; Mungall, Christopher J.; Basu, Siddartha; Chisholm, Rex L.; Dodson, Robert J.; Hartline, Eric; Fey, Petra; Thomas, Paul D.; Albou, Laurent-Philippe; Ebert, Dustin; Kesling, Michael J.; Mi, Huaiyu; Muruganujan, Anushya; Huang, Xiaosong; Mushayahama, Tremayne; LaBonte, Sandra A.; Siegele, Deborah A.; Antonazzo, Giulia; Attrill, Helen; Brown, Nick H.; Garapati, Phani; Marygold, Steven J.; Trovisco, Vitor; dos Santos, Gil; Falls, Kathleen; Tabone, Christopher; Zhou, Pinglei; Goodman, Joshua L.; Strelets, Victor B.; Thurmond, Jim; Garmiri, Penelope; Ishtiaq, Rizwan; Rodríguez-López, Milagros; Acencio, Marcio L.; Kuiper, Martin; Lægreid, Astrid; Logie, Colin; Lovering, Ruth C.; Kramarz, Barbara; Saverimuttu, Shirin C.; Pinheiro, Sandra M.; Gunn, Heather; Su, Renzhi; Thurlow, Katherine E.; Chibucos, Marcus; Giglio, Michelle; Nadendla, Suvarna; Munro, James; Jackson, Rebecca; Duesbury, Margaret J.; Del-Toro, Noemi; Meldal, Birgit M.; Paneerselvam, Kalpana; Perfetto, Livia; Porras, Pablo; Orchard, Sandra; Shrivastava, Anjali; Chang, Hsin-Yu; Finn, Robert Daniel; Mitchell, Alexander Lawson; Rawlings, Neil David; Richardson, Lorna; Sangrador-Vegas, Amaia; Blake, Judith A.; Christie, Karen R.; Dolan, Mary E.; Drabkin, Harold J.; Hill, David P.; Ni, Li; Sitnikov, Dmitry M.; Harris, Midori A.; Oliver, Stephen G.; Rutherford, Kim; Wood, Valerie; Hayles, Jaqueline; Bähler, Jürg; Bolton, Elizabeth R.; De Pons, Jeffery L.; Dwinell, Melinda R.; Hayman, G. Thomas; Kaldunski, Mary L.; Kwitek, Anne E.; Laulederkind, Stanley F.; Plasterer, Cody; Tutaj, Marek A.; Vedi, Mahima; Wang, Shur-Jen; D’Eustachio, Peter; Matthews, Lisa; Balhoff, James P.; Aleksander, Suzi A.; Alexander, Michael J.; Cherry, J. Michael; Engel, Stacia R.; Gondwe, Felix; Karra, Kalpana; Miyasato, Stuart R.; Nash, Robert S.; Simison, Matt; Skrzypek, Marek S.; Weng, Shuai; Wong, Edith D.; Feuermann, Marc; Gaudet, Pascale; Morgat, Anne; Bakker, Erica; Berardini, Tanya Z.; Reiser, Leonore; Subramaniam, Shabari; Huala, Eva; Arighi, Cecilia N.; Auchincloss, Andrea; Axelsen, Kristian; Argoud-Puy, Ghislaine; Bateman, Alex; Blatter, Marie-Claude; Boutet, Emmanuel; Bowler, Emily; Breuza, Lionel; Bridge, Alan; Britto, Ramona; Bye-A-Jee, Hema; Casas, Cristina Casals; Coudert, Elisabeth; Denny, Paul; Estreicher, Anne; Famiglietti, Maria Livia; Georghiou, George; Gos, Arnaud; Gruaz-Gumowski, Nadine; Hatton-Ellis, Emma; Hulo, Chantal; Ignatchenko, Alexandr; Jungo, Florence; Laiho, Kati; Le Mercier, Philippe; Lieberherr, Damien; Lock, Antonia; Lussi, Yvonne; MacDougall, Alistair; Magrane, Michele; Martin, Maria J.; Masson, Patrick; Natale, Darren A.; Hyka-Nouspikel, Nevila; Orchard, Sandra; Pedruzzi, Ivo; Pourcel, Lucille; Poux, Sylvain; Pundir, Sangya; Rivoire, Catherine; Speretta, Elena; Sundaram, Shyamala; Tyagi, Nidhi; Warner, Kate; Zaru, Rossana; Wu, Cathy H.; Diehl, Alexander D.; Chan, Juancarlos N.; Grove, Christian; Lee, Raymond N.; Muller, Hans-Michael; Raciti, Daniela; Van Auken, Kimberly; Sternberg, Paul W.; Berriman, Matthew; Paulini, Michael; Howe, Kevin; Gao, Sibyl; Wright, Adam; Stein, Lincoln; Howe, Douglas G.; Toro, Sabrina; Westerfield, Monte; Jaiswal, Pankaj; Cooper, Laurel; Elser, Justin

doi:10.1093/nar/gkaa1113

The Gene Ontology resource: enriching a GOld mine

Journal Article · Tue Dec 08 00:00:00 EST 2020 · Nucleic Acids Research

DOI:https://doi.org/10.1093/nar/gkaa1113· OSTI ID:1828339

Carbon, Seth; Douglass, Eric; Good, Benjamin M.; Unni, Deepak R.; Harris, Nomi L.; Mungall, Christopher J.; Basu, Siddartha; Chisholm, Rex L.; Dodson, Robert J.; Hartline, Eric; Fey, Petra; Thomas, Paul D.; Albou, Laurent-Philippe; Ebert, Dustin; Kesling, Michael J.; Mi, Huaiyu; Muruganujan, Anushya; Huang, Xiaosong; Mushayahama, Tremayne; LaBonte, Sandra A. more »

The Gene Ontology Consortium (GOC) provides the most comprehensive resource currently available for computable knowledge regarding the functions of genes and gene products. Here, we report the advances of the consortium over the past two years. The new GO-CAM annotation framework was notably improved, and we formalized the model with a computational schema to check and validate the rapidly increasing repository of 2838 GO-CAMs. In addition, we describe the impacts of several collaborations to refine GO and report a 10% increase in the number of GO annotations, a 25% increase in annotated gene products, and over 9,400 new scientific articles annotated. As the project matures, we continue our efforts to review older annotations in light of newer findings, and, to maintain consistency with other ontologies. As a result, 20,000 annotations derived from experimental data were reviewed, corresponding to 2.5% of experimental GO annotations. The website (http://geneontology.org) was redesigned for quick access to documentation, downloads and tools. To maintain an accurate resource and support traceability and reproducibility, we have made available a historical archive covering the past 15 years of GO data with a consistent format and file structure for both the ontology and annotations.

View Accepted Manuscript (DOE)

Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: Biotechnology and Biological Sciences Research Council; National Institutes of Health (NIH); National Science Foundation (NSF); UK Medical Research Council; USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23); Wellcome Trust

Contributing Organization:: The Gene Ontology Consortium

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1828339

Journal Information:: Nucleic Acids Research, Journal Name: Nucleic Acids Research Journal Issue: D1 Vol. 49; ISSN 0305-1048

Publisher:: Oxford University PressCopyright Statement

Country of Publication:: United States

Language:: English

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