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 Eilbeck; Deborah 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

doi:10.1093/nar/gkp1018

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 journal › Article › peer-review

397 Scopus citations

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 language	English (US)
Pages (from-to)	D331-D335
Journal	Nucleic acids research
Volume	38
Issue number	SUPPL.1
DOIs	https://doi.org/10.1093/nar/gkp1018
State	Published - Jan 1 2010
Externally published	Yes

ASJC Scopus subject areas

Genetics

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10.1093/nar/gkp1018

Cite this

Berardini, T. Z., Li, D., Huala, E., Bridges, S., Burgess, S., McCarthy, F., Carbon, S., Lewis, S. E., Mungall, C. J., Abdulla, A., Wood, V., Feltrin, E., Valle, G., Chisholm, R. L., Fey, P., Gaudet, P., Kibbe, W., Basu, S., Bushmanova, Y., ... 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

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

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title = "The Gene Ontology in 2010: Extensions and refinements",

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.",

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

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doi = "10.1093/nar/gkp1018",

language = "English (US)",

volume = "38",

pages = "D331--D335",

journal = "Nucleic acids research",

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number = "SUPPL.1",

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TY - JOUR

T1 - The Gene Ontology in 2010

T2 - Extensions and refinements

AU - Berardini, Tanya Z.

AU - Li, Donghui

AU - Huala, Eva

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

AU - Laiho, Kati

AU - Legge, Duncan

AU - Lemercier, Philippe

AU - Lieberherr, Damien

AU - Magrane, Michele

AU - O'Donovan, Claire

AU - Pedruzzi, Ivo

AU - Poux, Sylvain

AU - Rivoire, Catherine

AU - Roechert, Bernd

AU - Sawford, Tony

AU - Schneider, Michel

AU - Stanley, Eleanor

AU - Stutz, Andre

AU - Sundaram, Shyamala

AU - Tognolli, Michael

AU - Xenarios, Ioannis

AU - Harris, Midori A.

AU - Deegan, Jennifer I.

AU - Ireland, Amelia

AU - Lomax, Jane

AU - Jaiswal, Pankaj

AU - Chibucos, Marcus

AU - Giglio, Michelle Gwinn

AU - Wortman, Jennifer

AU - Hannick, Linda

AU - Madupu, Ramana

AU - Botstein, David

AU - Dolinski, Kara

AU - Livstone, Michael S.

AU - Oughtred, Rose

AU - Blake, Judith A.

AU - Bult, Carol

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

AU - Westerfield, Monte

PY - 2010/1/1

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N2 - 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.

AB - 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.

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DO - 10.1093/nar/gkp1018

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SP - D331-D335

JO - Nucleic acids research

JF - Nucleic acids research

IS - SUPPL.1

ER -

The Gene Ontology in 2010: Extensions and refinements

Abstract

ASJC Scopus subject areas

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