The Gene Ontology in 2010: Extensions and refinements

Tanya Z. Berardini, Donghui Li, Eva Huala, Susan Bridges, Shane Burgess, Fiona McCarthy, Seth Carbon, Suzanna E. Lewis, Christopher J. Mungall, Amina Abdulla, Valerie Wood, Erika Feltrin, Giorgio Valle, Rex L. Chisholm, Petra Fey, Pascale Gaudet, Warren Kibbe, Siddhartha Basu, Yulia Bushmanova, Karen EilbeckDeborah A. Siegele, Brenley McIntosh, Daniel Renfro, Adrienne Zweifel, James C. Hu, Michael Ashburner, Susan Tweedie, Yasmin Alam-Faruque, Rolf Apweiler, Andrea Auchinchloss, Amos Bairoch, Daniel Barrell, David Binns, Marie Claude Blatter, Lydie Bougueleret, Emmanuel Boutet, Lionel Breuza, Alan Bridge, Paul Browne, Wei Mun Chan, Elizabeth Coudert, Louise Daugherty, Emily Dimmer, Ruth Eberhardt, Anne Estreicher, Livia Famiglietti, Serenella Ferro-Rojas, Marc Feuermann, Rebecca Foulger, Nadine Gruaz-Gumowski, Ursula Hinz, Rachael Huntley, Silvia Jimenez, Florence Jungo, Guillaume Keller, Kati Laiho, Duncan Legge, Philippe Lemercier, Damien Lieberherr, Michele Magrane, Claire O'Donovan, Ivo Pedruzzi, Sylvain Poux, Catherine Rivoire, Bernd Roechert, Tony Sawford, Michel Schneider, Eleanor Stanley, Andre Stutz, Shyamala Sundaram, Michael Tognolli, Ioannis Xenarios, Midori A. Harris, Jennifer I. Deegan, Amelia Ireland, Jane Lomax, Pankaj Jaiswal, Marcus Chibucos, Michelle Gwinn Giglio, Jennifer Wortman, Linda Hannick, Ramana Madupu, David Botstein, Kara Dolinski, Michael S. Livstone, Rose Oughtred, Judith A. Blake, Carol Bult, Alexander D. Diehl, Mary Dolan, Harold Drabkin, Janan T. Eppig, David P. Hill, Li Ni, Martin Ringwald, Dmitry Sitnikov, Candace Collmer, Trudy Torto-Alalibo, Stan Laulederkind, Mary Shimoyama, Simon Twigger, Peter D'Eustachio, Lisa Matthews, Rama Balakrishnan, Gail Binkley, J. Michael Cherry, Karen R. Christie, Maria C. Costanzo, Stacia R. Engel, Dianna G. Fisk, Jodi E. Hirschman, Benjamin C. Hitz, Eurie L. Hong, Cynthia J. Krieger, Stuart R. Miyasato, Robert S. Nash, Julie Park, Marek S. Skrzypek, Shuai Weng, Edith D. Wong, Martin Aslett, Juancarlos Chan, Ranjana Kishore, Paul Sternberg, Kimberly Van Auken, Varsha K. Khodiyar, Ruth C. Lovering, Philippa J. Talmud, Doug Howe, Monte Westerfield

Research output: Contribution to journalArticle

342 Citations (Scopus)

Abstract

The Gene Ontology (GO) Consortium (http://www.geneontology.org) (GOC) continues to develop, maintain and use a set of structured, controlled vocabularies for the annotation of genes, gene products and sequences. The GO ontologies are expanding both in content and in structure. Several new relationship types have been introduced and used, along with existing relationships, to create links between and within the GO domains. These improve the representation of biology, facilitate querying, and allow GO developers to systematically check for and correct inconsistencies within the GO. Gene product annotation using GO continues to increase both in the number of total annotations and in species coverage. GO tools, such as OBO-Edit, an ontology-editing tool, and AmiGO, the GOC ontology browser, have seen major improvements in functionality, speed and ease of use.

Original languageEnglish (US)
Pages (from-to)D331-D335
JournalNucleic acids research
Volume38
Issue numberSUPPL.1
DOIs
StatePublished - Jan 1 2010
Externally publishedYes

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Gene Ontology
Molecular Sequence Annotation
Controlled Vocabulary
Genes

ASJC Scopus subject areas

  • Genetics

Cite this

Berardini, T. Z., Li, D., Huala, E., Bridges, S., Burgess, S., McCarthy, F., ... Westerfield, M. (2010). The Gene Ontology in 2010: Extensions and refinements. Nucleic acids research, 38(SUPPL.1), D331-D335. https://doi.org/10.1093/nar/gkp1018

The Gene Ontology in 2010 : Extensions and refinements. / Berardini, Tanya Z.; Li, Donghui; Huala, Eva; Bridges, Susan; Burgess, Shane; McCarthy, Fiona; Carbon, Seth; Lewis, Suzanna E.; Mungall, Christopher J.; Abdulla, Amina; Wood, Valerie; Feltrin, Erika; Valle, Giorgio; Chisholm, Rex L.; Fey, Petra; Gaudet, Pascale; Kibbe, Warren; Basu, Siddhartha; Bushmanova, Yulia; Eilbeck, Karen; Siegele, Deborah A.; McIntosh, Brenley; Renfro, Daniel; Zweifel, Adrienne; Hu, James C.; Ashburner, Michael; Tweedie, Susan; Alam-Faruque, Yasmin; Apweiler, Rolf; Auchinchloss, Andrea; Bairoch, Amos; Barrell, Daniel; Binns, David; Blatter, Marie Claude; Bougueleret, Lydie; Boutet, Emmanuel; Breuza, Lionel; Bridge, Alan; Browne, Paul; Chan, Wei Mun; Coudert, Elizabeth; Daugherty, Louise; Dimmer, Emily; Eberhardt, Ruth; Estreicher, Anne; Famiglietti, Livia; Ferro-Rojas, Serenella; Feuermann, Marc; Foulger, Rebecca; Gruaz-Gumowski, Nadine; Hinz, Ursula; Huntley, Rachael; Jimenez, Silvia; Jungo, Florence; Keller, Guillaume; Laiho, Kati; Legge, Duncan; Lemercier, Philippe; Lieberherr, Damien; Magrane, Michele; O'Donovan, Claire; Pedruzzi, Ivo; Poux, Sylvain; Rivoire, Catherine; Roechert, Bernd; Sawford, Tony; Schneider, Michel; Stanley, Eleanor; Stutz, Andre; Sundaram, Shyamala; Tognolli, Michael; Xenarios, Ioannis; Harris, Midori A.; Deegan, Jennifer I.; Ireland, Amelia; Lomax, Jane; Jaiswal, Pankaj; Chibucos, Marcus; Giglio, Michelle Gwinn; Wortman, Jennifer; Hannick, Linda; Madupu, Ramana; Botstein, David; Dolinski, Kara; Livstone, Michael S.; Oughtred, Rose; Blake, Judith A.; Bult, Carol; Diehl, Alexander D.; Dolan, Mary; Drabkin, Harold; Eppig, Janan T.; Hill, David P.; Ni, Li; Ringwald, Martin; Sitnikov, Dmitry; Collmer, Candace; Torto-Alalibo, Trudy; Laulederkind, Stan; Shimoyama, Mary; Twigger, Simon; D'Eustachio, Peter; Matthews, Lisa; Balakrishnan, Rama; Binkley, Gail; Cherry, J. Michael; Christie, Karen R.; Costanzo, Maria C.; Engel, Stacia R.; Fisk, Dianna G.; Hirschman, Jodi E.; Hitz, Benjamin C.; Hong, Eurie L.; Krieger, Cynthia J.; Miyasato, Stuart R.; Nash, Robert S.; Park, Julie; Skrzypek, Marek S.; Weng, Shuai; Wong, Edith D.; Aslett, Martin; Chan, Juancarlos; Kishore, Ranjana; Sternberg, Paul; Auken, Kimberly Van; Khodiyar, Varsha K.; Lovering, Ruth C.; Talmud, Philippa J.; Howe, Doug; Westerfield, Monte.

In: Nucleic acids research, Vol. 38, No. SUPPL.1, 01.01.2010, p. D331-D335.

Research output: Contribution to journalArticle

Berardini, TZ, Li, D, Huala, E, Bridges, S, Burgess, S, McCarthy, F, Carbon, S, Lewis, SE, Mungall, CJ, Abdulla, A, Wood, V, Feltrin, E, Valle, G, Chisholm, RL, Fey, P, Gaudet, P, Kibbe, W, Basu, S, Bushmanova, Y, Eilbeck, K, Siegele, DA, McIntosh, B, Renfro, D, Zweifel, A, Hu, JC, Ashburner, M, Tweedie, S, Alam-Faruque, Y, Apweiler, R, Auchinchloss, A, Bairoch, A, Barrell, D, Binns, D, Blatter, MC, Bougueleret, L, Boutet, E, Breuza, L, Bridge, A, Browne, P, Chan, WM, Coudert, E, Daugherty, L, Dimmer, E, Eberhardt, R, Estreicher, A, Famiglietti, L, Ferro-Rojas, S, Feuermann, M, Foulger, R, Gruaz-Gumowski, N, Hinz, U, Huntley, R, Jimenez, S, Jungo, F, Keller, G, Laiho, K, Legge, D, Lemercier, P, Lieberherr, D, Magrane, M, O'Donovan, C, Pedruzzi, I, Poux, S, Rivoire, C, Roechert, B, Sawford, T, Schneider, M, Stanley, E, Stutz, A, Sundaram, S, Tognolli, M, Xenarios, I, Harris, MA, Deegan, JI, Ireland, A, Lomax, J, Jaiswal, P, Chibucos, M, Giglio, MG, Wortman, J, Hannick, L, Madupu, R, Botstein, D, Dolinski, K, Livstone, MS, Oughtred, R, Blake, JA, Bult, C, Diehl, AD, Dolan, M, Drabkin, H, Eppig, JT, Hill, DP, Ni, L, Ringwald, M, Sitnikov, D, Collmer, C, Torto-Alalibo, T, Laulederkind, S, Shimoyama, M, Twigger, S, D'Eustachio, P, Matthews, L, Balakrishnan, R, Binkley, G, Cherry, JM, Christie, KR, Costanzo, MC, Engel, SR, Fisk, DG, Hirschman, JE, Hitz, BC, Hong, EL, Krieger, CJ, Miyasato, SR, Nash, RS, Park, J, Skrzypek, MS, Weng, S, Wong, ED, Aslett, M, Chan, J, Kishore, R, Sternberg, P, Auken, KV, Khodiyar, VK, Lovering, RC, Talmud, PJ, Howe, D & Westerfield, M 2010, 'The Gene Ontology in 2010: Extensions and refinements', Nucleic acids research, vol. 38, no. SUPPL.1, pp. D331-D335. https://doi.org/10.1093/nar/gkp1018
Berardini, Tanya Z. ; Li, Donghui ; Huala, Eva ; Bridges, Susan ; Burgess, Shane ; McCarthy, Fiona ; Carbon, Seth ; Lewis, Suzanna E. ; Mungall, Christopher J. ; Abdulla, Amina ; Wood, Valerie ; Feltrin, Erika ; Valle, Giorgio ; Chisholm, Rex L. ; Fey, Petra ; Gaudet, Pascale ; Kibbe, Warren ; Basu, Siddhartha ; Bushmanova, Yulia ; Eilbeck, Karen ; Siegele, Deborah A. ; McIntosh, Brenley ; Renfro, Daniel ; Zweifel, Adrienne ; Hu, James C. ; Ashburner, Michael ; Tweedie, Susan ; Alam-Faruque, Yasmin ; Apweiler, Rolf ; Auchinchloss, Andrea ; Bairoch, Amos ; Barrell, Daniel ; Binns, David ; Blatter, Marie Claude ; Bougueleret, Lydie ; Boutet, Emmanuel ; Breuza, Lionel ; Bridge, Alan ; Browne, Paul ; Chan, Wei Mun ; Coudert, Elizabeth ; Daugherty, Louise ; Dimmer, Emily ; Eberhardt, Ruth ; Estreicher, Anne ; Famiglietti, Livia ; Ferro-Rojas, Serenella ; Feuermann, Marc ; Foulger, Rebecca ; Gruaz-Gumowski, Nadine ; Hinz, Ursula ; Huntley, Rachael ; Jimenez, Silvia ; Jungo, Florence ; Keller, Guillaume ; Laiho, Kati ; Legge, Duncan ; Lemercier, Philippe ; Lieberherr, Damien ; Magrane, Michele ; O'Donovan, Claire ; Pedruzzi, Ivo ; Poux, Sylvain ; Rivoire, Catherine ; Roechert, Bernd ; Sawford, Tony ; Schneider, Michel ; Stanley, Eleanor ; Stutz, Andre ; Sundaram, Shyamala ; Tognolli, Michael ; Xenarios, Ioannis ; Harris, Midori A. ; Deegan, Jennifer I. ; Ireland, Amelia ; Lomax, Jane ; Jaiswal, Pankaj ; Chibucos, Marcus ; Giglio, Michelle Gwinn ; Wortman, Jennifer ; Hannick, Linda ; Madupu, Ramana ; Botstein, David ; Dolinski, Kara ; Livstone, Michael S. ; Oughtred, Rose ; Blake, Judith A. ; Bult, Carol ; Diehl, Alexander D. ; Dolan, Mary ; Drabkin, Harold ; Eppig, Janan T. ; Hill, David P. ; Ni, Li ; Ringwald, Martin ; Sitnikov, Dmitry ; Collmer, Candace ; Torto-Alalibo, Trudy ; Laulederkind, Stan ; Shimoyama, Mary ; Twigger, Simon ; D'Eustachio, Peter ; Matthews, Lisa ; Balakrishnan, Rama ; Binkley, Gail ; Cherry, J. Michael ; Christie, Karen R. ; Costanzo, Maria C. ; Engel, Stacia R. ; Fisk, Dianna G. ; Hirschman, Jodi E. ; Hitz, Benjamin C. ; Hong, Eurie L. ; Krieger, Cynthia J. ; Miyasato, Stuart R. ; Nash, Robert S. ; Park, Julie ; Skrzypek, Marek S. ; Weng, Shuai ; Wong, Edith D. ; Aslett, Martin ; Chan, Juancarlos ; Kishore, Ranjana ; Sternberg, Paul ; Auken, Kimberly Van ; Khodiyar, Varsha K. ; Lovering, Ruth C. ; Talmud, Philippa J. ; Howe, Doug ; Westerfield, Monte. / The Gene Ontology in 2010 : Extensions and refinements. In: Nucleic acids research. 2010 ; Vol. 38, No. SUPPL.1. pp. D331-D335.
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AU - Bridges, Susan

AU - Burgess, Shane

AU - McCarthy, Fiona

AU - Carbon, Seth

AU - Lewis, Suzanna E.

AU - Mungall, Christopher J.

AU - Abdulla, Amina

AU - Wood, Valerie

AU - Feltrin, Erika

AU - Valle, Giorgio

AU - Chisholm, Rex L.

AU - Fey, Petra

AU - Gaudet, Pascale

AU - Kibbe, Warren

AU - Basu, Siddhartha

AU - Bushmanova, Yulia

AU - Eilbeck, Karen

AU - Siegele, Deborah A.

AU - McIntosh, Brenley

AU - Renfro, Daniel

AU - Zweifel, Adrienne

AU - Hu, James C.

AU - Ashburner, Michael

AU - Tweedie, Susan

AU - Alam-Faruque, Yasmin

AU - Apweiler, Rolf

AU - Auchinchloss, Andrea

AU - Bairoch, Amos

AU - Barrell, Daniel

AU - Binns, David

AU - Blatter, Marie Claude

AU - Bougueleret, Lydie

AU - Boutet, Emmanuel

AU - Breuza, Lionel

AU - Bridge, Alan

AU - Browne, Paul

AU - Chan, Wei Mun

AU - Coudert, Elizabeth

AU - Daugherty, Louise

AU - Dimmer, Emily

AU - Eberhardt, Ruth

AU - Estreicher, Anne

AU - Famiglietti, Livia

AU - Ferro-Rojas, Serenella

AU - Feuermann, Marc

AU - Foulger, Rebecca

AU - Gruaz-Gumowski, Nadine

AU - Hinz, Ursula

AU - Huntley, Rachael

AU - Jimenez, Silvia

AU - Jungo, Florence

AU - Keller, Guillaume

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AU - Legge, Duncan

AU - Lemercier, Philippe

AU - Lieberherr, Damien

AU - Magrane, Michele

AU - O'Donovan, Claire

AU - Pedruzzi, Ivo

AU - Poux, Sylvain

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AU - Sawford, Tony

AU - Schneider, Michel

AU - Stanley, Eleanor

AU - Stutz, Andre

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AU - Tognolli, Michael

AU - Xenarios, Ioannis

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AU - Jaiswal, Pankaj

AU - Chibucos, Marcus

AU - Giglio, Michelle Gwinn

AU - Wortman, Jennifer

AU - Hannick, Linda

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AU - Livstone, Michael S.

AU - Oughtred, Rose

AU - Blake, Judith A.

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AU - Diehl, Alexander D.

AU - Dolan, Mary

AU - Drabkin, Harold

AU - Eppig, Janan T.

AU - Hill, David P.

AU - Ni, Li

AU - Ringwald, Martin

AU - Sitnikov, Dmitry

AU - Collmer, Candace

AU - Torto-Alalibo, Trudy

AU - Laulederkind, Stan

AU - Shimoyama, Mary

AU - Twigger, Simon

AU - D'Eustachio, Peter

AU - Matthews, Lisa

AU - Balakrishnan, Rama

AU - Binkley, Gail

AU - Cherry, J. Michael

AU - Christie, Karen R.

AU - Costanzo, Maria C.

AU - Engel, Stacia R.

AU - Fisk, Dianna G.

AU - Hirschman, Jodi E.

AU - Hitz, Benjamin C.

AU - Hong, Eurie L.

AU - Krieger, Cynthia J.

AU - Miyasato, Stuart R.

AU - Nash, Robert S.

AU - Park, Julie

AU - Skrzypek, Marek S.

AU - Weng, Shuai

AU - Wong, Edith D.

AU - Aslett, Martin

AU - Chan, Juancarlos

AU - Kishore, Ranjana

AU - Sternberg, Paul

AU - Auken, Kimberly Van

AU - Khodiyar, Varsha K.

AU - Lovering, Ruth C.

AU - Talmud, Philippa J.

AU - Howe, Doug

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