Gene ontology annotations and resources

J. A. Blake; M. Dolan; H. Drabkin; D. P. Hill; Li Ni; D. Sitnikov; S. Bridges; S. Burgess; T. Buza; F. McCarthy; D. Peddinti; L. Pillai; S. Carbon; H. Dietze; A. Ireland; S. E. Lewis; C. J. Mungall; P. Gaudet; R. L. Chisholm; P. Fey; W. A. Kibbe; S. Basu; D. A. Siegele; B. K. McIntosh; D. P. Renfro; A. E. Zweifel; J. C. Hu; N. H. Brown; S. Tweedie; Y. Alam-Faruque; R. Apweiler; A. Auchinchloss; K. Axelsen; B. Bely; M. C. Blatter; C. Bonilla; L. Bougueleret; E. Boutet; L. Breuza; A. Bridge; W. M. Chan; G. Chavali; E. Coudert; E. Dimmer; A. Estreicher; L. Famiglietti; M. Feuermann; A. Gos; N. Gruaz-Gumowski; R. Hieta; U. Hinz; C. Hulo; R. Huntley; J. James; F. Jungo; G. Keller; K. Laiho; D. Legge; P. Lemercier; D. Lieberherr; M. Magrane; M. J. Martin; P. Masson; P. Mutowo-Muellenet; C. O'Donovan; I. Pedruzzi; K. Pichler; D. Poggioli; P. Porras Millan; S. Poux; C. Rivoire; B. Roechert; T. Sawford; M. Schneider; A. Stutz; S. Sundaram; M. Tognolli; I. Xenarios; R. Foulger; J. Lomax; P. Roncaglia; V. K. Khodiyar; R. C. Lovering; P. J. Talmud; M. Chibucos; M. Gwinn Giglio; H. Y. Chang; S. Hunter; C. McAnulla; A. Mitchell; A. Sangrador; R. Stephan; M. A. Harris; S. G. Oliver; K. Rutherford; V. Wood; J. Bahler; A. Lock; P. J. Kersey; M. D. McDowall; D. M. Staines; M. Dwinell; M. Shimoyama; S. Laulederkind; T. Hayman; S. J. Wang; V. Petri; T. Lowry; P. D'Eustachio; L. Matthews; R. Balakrishnan; G. Binkley; J. M. Cherry; M. C. Costanzo; S. S. Dwight; S. R. Engel; D. G. Fisk; B. C. Hitz; E. L. Hong; K. Karra; S. R. Miyasato; R. S. Nash; J. Park; M. S. Skrzypek; S. Weng; E. D. Wong; T. Z. Berardini; D. Li; E. Huala; H. Mi; P. D. Thomas; J. Chan; R. Kishore; P. Sternberg; K. Van Auken; D. Howe; M. Westerfield

doi:10.1093/nar/gks1050

Gene ontology annotations and resources

J. A. Blake, M. Dolan, H. Drabkin, D. P. Hill, Li Ni, D. Sitnikov, S. Bridges, S. Burgess, T. Buza, F. McCarthy, D. Peddinti, L. Pillai, S. Carbon, H. Dietze, A. Ireland, S. E. Lewis, C. J. Mungall, P. Gaudet, R. L. Chisholm, P. FeyW. A. Kibbe, S. Basu, D. A. Siegele, B. K. McIntosh, D. P. Renfro, A. E. Zweifel, J. C. Hu, N. H. Brown, S. Tweedie, Y. Alam-Faruque, R. Apweiler, A. Auchinchloss, K. Axelsen, B. Bely, M. C. Blatter, C. Bonilla, L. Bougueleret, E. Boutet, L. Breuza, A. Bridge, W. M. Chan, G. Chavali, E. Coudert, E. Dimmer, A. Estreicher, L. Famiglietti, M. Feuermann, A. Gos, N. Gruaz-Gumowski, R. Hieta, U. Hinz, C. Hulo, R. Huntley, J. James, F. Jungo, G. Keller, K. Laiho, D. Legge, P. Lemercier, D. Lieberherr, M. Magrane, M. J. Martin, P. Masson, P. Mutowo-Muellenet, C. O'Donovan, I. Pedruzzi, K. Pichler, D. Poggioli, P. Porras Millan, S. Poux, C. Rivoire, B. Roechert, T. Sawford, M. Schneider, A. Stutz, S. Sundaram, M. Tognolli, I. Xenarios, R. Foulger, J. Lomax, P. Roncaglia, V. K. Khodiyar, R. C. Lovering, P. J. Talmud, M. Chibucos, M. Gwinn Giglio, H. Y. Chang, S. Hunter, C. McAnulla, A. Mitchell, A. Sangrador, R. Stephan, M. A. Harris, S. G. Oliver, K. Rutherford, V. Wood, J. Bahler, A. Lock, P. J. Kersey, M. D. McDowall, D. M. Staines, M. Dwinell, M. Shimoyama, S. Laulederkind, T. Hayman, S. J. Wang, V. Petri, T. Lowry, P. D'Eustachio, L. Matthews, R. Balakrishnan, G. Binkley, J. M. Cherry, M. C. Costanzo, S. S. Dwight, S. R. Engel, D. G. Fisk, B. C. Hitz, E. L. Hong, K. Karra, S. R. Miyasato, R. S. Nash, J. Park, M. S. Skrzypek, S. Weng, E. D. Wong, T. Z. Berardini, D. Li, E. Huala, H. Mi, P. D. Thomas, J. Chan, R. Kishore, P. Sternberg, K. Van Auken, D. Howe, M. Westerfield

Research output: Contribution to journal › Article › peer-review

461 Scopus citations

Abstract

The Gene Ontology (GO) Consortium (GOC, http://www.geneontology.org) is a community-based bio-informatics resource that classifies gene product function through the use of structured, controlled vocabularies. Over the past year, the GOC has implemented several processes to increase the quantity, quality and specificity of GO annotations. First, the number of manual, literature-based annotations has grown at an increasing rate. Second, as a result of a new 'phylogenetic annotation' process, manually reviewed, homology-based annotations are becoming available for a broad range of species. Third, the quality of GO annotations has been improved through a streamlined process for, and automated quality checks of, GO annotations deposited by different annotation groups. Fourth, the consistency and correctness of the ontology itself has increased by using automated reasoning tools. Finally, the GO has been expanded not only to cover new areas of biology through focused interaction with experts, but also to capture greater specificity in all areas of the ontology using tools for adding new combinatorial terms. The GOC works closely with other ontology developers to support integrated use of terminologies. The GOC supports its user community through the use of e-mail lists, social media and web-based resources.

Original language	English (US)
Pages (from-to)	D530-D535
Journal	Nucleic acids research
Volume	41
Issue number	D1
DOIs	https://doi.org/10.1093/nar/gks1050
State	Published - Jan 1 2013
Externally published	Yes

ASJC Scopus subject areas

Genetics

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10.1093/nar/gks1050

Cite this

Blake, J. A., Dolan, M., Drabkin, H., Hill, D. P., Ni, L., Sitnikov, D., Bridges, S., Burgess, S., Buza, T., McCarthy, F., Peddinti, D., Pillai, L., Carbon, S., Dietze, H., Ireland, A., Lewis, S. E., Mungall, C. J., Gaudet, P., Chisholm, R. L., ... Westerfield, M. (2013). Gene ontology annotations and resources. Nucleic acids research, 41(D1), D530-D535. https://doi.org/10.1093/nar/gks1050

Blake, JA, Dolan, M, Drabkin, H, Hill, DP, Ni, L, Sitnikov, D, Bridges, S, Burgess, S, Buza, T, McCarthy, F, Peddinti, D, Pillai, L, Carbon, S, Dietze, H, Ireland, A, Lewis, SE, Mungall, CJ, Gaudet, P, Chisholm, RL, Fey, P, Kibbe, WA, Basu, S, Siegele, DA, McIntosh, BK, Renfro, DP, Zweifel, AE, Hu, JC, Brown, NH, Tweedie, S, Alam-Faruque, Y, Apweiler, R, Auchinchloss, A, Axelsen, K, Bely, B, Blatter, MC, Bonilla, C, Bougueleret, L, Boutet, E, Breuza, L, Bridge, A, Chan, WM, Chavali, G, Coudert, E, Dimmer, E, Estreicher, A, Famiglietti, L, Feuermann, M, Gos, A, Gruaz-Gumowski, N, Hieta, R, Hinz, U, Hulo, C, Huntley, R, James, J, Jungo, F, Keller, G, Laiho, K, Legge, D, Lemercier, P, Lieberherr, D, Magrane, M, Martin, MJ, Masson, P, Mutowo-Muellenet, P, O'Donovan, C, Pedruzzi, I, Pichler, K, Poggioli, D, Porras Millan, P, Poux, S, Rivoire, C, Roechert, B, Sawford, T, Schneider, M, Stutz, A, Sundaram, S, Tognolli, M, Xenarios, I, Foulger, R, Lomax, J, Roncaglia, P, Khodiyar, VK, Lovering, RC, Talmud, PJ, Chibucos, M, Gwinn Giglio, M, Chang, HY, Hunter, S, McAnulla, C, Mitchell, A, Sangrador, A, Stephan, R, Harris, MA, Oliver, SG, Rutherford, K, Wood, V, Bahler, J, Lock, A, Kersey, PJ, McDowall, MD, Staines, DM, Dwinell, M, Shimoyama, M, Laulederkind, S, Hayman, T, Wang, SJ, Petri, V, Lowry, T, D'Eustachio, P, Matthews, L, Balakrishnan, R, Binkley, G, Cherry, JM, Costanzo, MC, Dwight, SS, Engel, SR, Fisk, DG, Hitz, BC, Hong, EL, Karra, K, Miyasato, SR, Nash, RS, Park, J, Skrzypek, MS, Weng, S, Wong, ED, Berardini, TZ, Li, D, Huala, E, Mi, H, Thomas, PD, Chan, J, Kishore, R, Sternberg, P, Van Auken, K, Howe, D & Westerfield, M 2013, 'Gene ontology annotations and resources', Nucleic acids research, vol. 41, no. D1, pp. D530-D535. https://doi.org/10.1093/nar/gks1050

@article{bb3cfb8758264fd0b7ba752d305578b7,

title = "Gene ontology annotations and resources",

abstract = "The Gene Ontology (GO) Consortium (GOC, http://www.geneontology.org) is a community-based bio-informatics resource that classifies gene product function through the use of structured, controlled vocabularies. Over the past year, the GOC has implemented several processes to increase the quantity, quality and specificity of GO annotations. First, the number of manual, literature-based annotations has grown at an increasing rate. Second, as a result of a new 'phylogenetic annotation' process, manually reviewed, homology-based annotations are becoming available for a broad range of species. Third, the quality of GO annotations has been improved through a streamlined process for, and automated quality checks of, GO annotations deposited by different annotation groups. Fourth, the consistency and correctness of the ontology itself has increased by using automated reasoning tools. Finally, the GO has been expanded not only to cover new areas of biology through focused interaction with experts, but also to capture greater specificity in all areas of the ontology using tools for adding new combinatorial terms. The GOC works closely with other ontology developers to support integrated use of terminologies. The GOC supports its user community through the use of e-mail lists, social media and web-based resources.",

author = "Blake, {J. A.} and M. Dolan and H. Drabkin and Hill, {D. P.} and Li Ni and D. Sitnikov and S. Bridges and S. Burgess and T. Buza and F. McCarthy and D. Peddinti and L. Pillai and S. Carbon and H. Dietze and A. Ireland and Lewis, {S. E.} and Mungall, {C. J.} and P. Gaudet and Chisholm, {R. L.} and P. Fey and Kibbe, {W. A.} and S. Basu and Siegele, {D. A.} and McIntosh, {B. K.} and Renfro, {D. P.} and Zweifel, {A. E.} and Hu, {J. C.} and Brown, {N. H.} and S. Tweedie and Y. Alam-Faruque and R. Apweiler and A. Auchinchloss and K. Axelsen and B. Bely and Blatter, {M. C.} and C. Bonilla and L. Bougueleret and E. Boutet and L. Breuza and A. Bridge and Chan, {W. M.} and G. Chavali and E. Coudert and E. Dimmer and A. Estreicher and L. Famiglietti and M. Feuermann and A. Gos and N. Gruaz-Gumowski and R. Hieta and U. Hinz and C. Hulo and R. Huntley and J. James and F. Jungo and G. Keller and K. Laiho and D. Legge and P. Lemercier and D. Lieberherr and M. Magrane and Martin, {M. J.} and P. Masson and P. Mutowo-Muellenet and C. O'Donovan and I. Pedruzzi and K. Pichler and D. Poggioli and {Porras Millan}, P. and S. Poux and C. Rivoire and B. Roechert and T. Sawford and M. Schneider and A. Stutz and S. Sundaram and M. Tognolli and I. Xenarios and R. Foulger and J. Lomax and P. Roncaglia and Khodiyar, {V. K.} and Lovering, {R. C.} and Talmud, {P. J.} and M. Chibucos and {Gwinn Giglio}, M. and Chang, {H. Y.} and S. Hunter and C. McAnulla and A. Mitchell and A. Sangrador and R. Stephan and Harris, {M. A.} and Oliver, {S. G.} and K. Rutherford and V. Wood and J. Bahler and A. Lock and Kersey, {P. J.} and McDowall, {M. D.} and Staines, {D. M.} and M. Dwinell and M. Shimoyama and S. Laulederkind and T. Hayman and Wang, {S. J.} and V. Petri and T. Lowry and P. D'Eustachio and L. Matthews and R. Balakrishnan and G. Binkley and Cherry, {J. M.} and Costanzo, {M. C.} and Dwight, {S. S.} and Engel, {S. R.} and Fisk, {D. G.} and Hitz, {B. C.} and Hong, {E. L.} and K. Karra and Miyasato, {S. R.} and Nash, {R. S.} and J. Park and Skrzypek, {M. S.} and S. Weng and Wong, {E. D.} and Berardini, {T. Z.} and D. Li and E. Huala and H. Mi and Thomas, {P. D.} and J. Chan and R. Kishore and P. Sternberg and {Van Auken}, K. and D. Howe and M. Westerfield",

note = "Funding Information: National Human Genome Research Institute (NHGRI) [U41HG002273 to the Gene Ontology Consortium, 1U41HG006104-03 to the European Bioinformatics Institute]; British Heart Foundation [SP/07/007/23671]. Funding for open access charge: NHGRI.",

year = "2013",

month = jan,

day = "1",

doi = "10.1093/nar/gks1050",

language = "English (US)",

volume = "41",

pages = "D530--D535",

journal = "Nucleic acids research",

issn = "0305-1048",

publisher = "Oxford University Press",

number = "D1",

}

TY - JOUR

T1 - Gene ontology annotations and resources

AU - Blake, J. A.

AU - Dolan, M.

AU - Drabkin, H.

AU - Hill, D. P.

AU - Ni, Li

AU - Sitnikov, D.

AU - Bridges, S.

AU - Burgess, S.

AU - Buza, T.

AU - McCarthy, F.

AU - Peddinti, D.

AU - Pillai, L.

AU - Carbon, S.

AU - Dietze, H.

AU - Ireland, A.

AU - Lewis, S. E.

AU - Mungall, C. J.

AU - Gaudet, P.

AU - Chisholm, R. L.

AU - Fey, P.

AU - Kibbe, W. A.

AU - Basu, S.

AU - Siegele, D. A.

AU - McIntosh, B. K.

AU - Renfro, D. P.

AU - Zweifel, A. E.

AU - Hu, J. C.

AU - Brown, N. H.

AU - Tweedie, S.

AU - Alam-Faruque, Y.

AU - Apweiler, R.

AU - Auchinchloss, A.

AU - Axelsen, K.

AU - Bely, B.

AU - Blatter, M. C.

AU - Bonilla, C.

AU - Bougueleret, L.

AU - Boutet, E.

AU - Breuza, L.

AU - Bridge, A.

AU - Chan, W. M.

AU - Chavali, G.

AU - Coudert, E.

AU - Dimmer, E.

AU - Estreicher, A.

AU - Famiglietti, L.

AU - Feuermann, M.

AU - Gos, A.

AU - Gruaz-Gumowski, N.

AU - Hieta, R.

AU - Hinz, U.

AU - Hulo, C.

AU - Huntley, R.

AU - James, J.

AU - Jungo, F.

AU - Keller, G.

AU - Laiho, K.

AU - Legge, D.

AU - Lemercier, P.

AU - Lieberherr, D.

AU - Magrane, M.

AU - Martin, M. J.

AU - Masson, P.

AU - Mutowo-Muellenet, P.

AU - O'Donovan, C.

AU - Pedruzzi, I.

AU - Pichler, K.

AU - Poggioli, D.

AU - Porras Millan, P.

AU - Poux, S.

AU - Rivoire, C.

AU - Roechert, B.

AU - Sawford, T.

AU - Schneider, M.

AU - Stutz, A.

AU - Sundaram, S.

AU - Tognolli, M.

AU - Xenarios, I.

AU - Foulger, R.

AU - Lomax, J.

AU - Roncaglia, P.

AU - Khodiyar, V. K.

AU - Lovering, R. C.

AU - Talmud, P. J.

AU - Chibucos, M.

AU - Gwinn Giglio, M.

AU - Chang, H. Y.

AU - Hunter, S.

AU - McAnulla, C.

AU - Mitchell, A.

AU - Sangrador, A.

AU - Stephan, R.

AU - Harris, M. A.

AU - Oliver, S. G.

AU - Rutherford, K.

AU - Wood, V.

AU - Bahler, J.

AU - Lock, A.

AU - Kersey, P. J.

AU - McDowall, M. D.

AU - Staines, D. M.

AU - Dwinell, M.

AU - Shimoyama, M.

AU - Laulederkind, S.

AU - Hayman, T.

AU - Wang, S. J.

AU - Petri, V.

AU - Lowry, T.

AU - D'Eustachio, P.

AU - Matthews, L.

AU - Balakrishnan, R.

AU - Binkley, G.

AU - Cherry, J. M.

AU - Costanzo, M. C.

AU - Dwight, S. S.

AU - Engel, S. R.

AU - Fisk, D. G.

AU - Hitz, B. C.

AU - Hong, E. L.

AU - Karra, K.

AU - Miyasato, S. R.

AU - Nash, R. S.

AU - Park, J.

AU - Skrzypek, M. S.

AU - Weng, S.

AU - Wong, E. D.

AU - Berardini, T. Z.

AU - Li, D.

AU - Huala, E.

AU - Mi, H.

AU - Thomas, P. D.

AU - Chan, J.

AU - Kishore, R.

AU - Sternberg, P.

AU - Van Auken, K.

AU - Howe, D.

AU - Westerfield, M.

N1 - Funding Information: National Human Genome Research Institute (NHGRI) [U41HG002273 to the Gene Ontology Consortium, 1U41HG006104-03 to the European Bioinformatics Institute]; British Heart Foundation [SP/07/007/23671]. Funding for open access charge: NHGRI.

PY - 2013/1/1

Y1 - 2013/1/1

N2 - The Gene Ontology (GO) Consortium (GOC, http://www.geneontology.org) is a community-based bio-informatics resource that classifies gene product function through the use of structured, controlled vocabularies. Over the past year, the GOC has implemented several processes to increase the quantity, quality and specificity of GO annotations. First, the number of manual, literature-based annotations has grown at an increasing rate. Second, as a result of a new 'phylogenetic annotation' process, manually reviewed, homology-based annotations are becoming available for a broad range of species. Third, the quality of GO annotations has been improved through a streamlined process for, and automated quality checks of, GO annotations deposited by different annotation groups. Fourth, the consistency and correctness of the ontology itself has increased by using automated reasoning tools. Finally, the GO has been expanded not only to cover new areas of biology through focused interaction with experts, but also to capture greater specificity in all areas of the ontology using tools for adding new combinatorial terms. The GOC works closely with other ontology developers to support integrated use of terminologies. The GOC supports its user community through the use of e-mail lists, social media and web-based resources.

AB - The Gene Ontology (GO) Consortium (GOC, http://www.geneontology.org) is a community-based bio-informatics resource that classifies gene product function through the use of structured, controlled vocabularies. Over the past year, the GOC has implemented several processes to increase the quantity, quality and specificity of GO annotations. First, the number of manual, literature-based annotations has grown at an increasing rate. Second, as a result of a new 'phylogenetic annotation' process, manually reviewed, homology-based annotations are becoming available for a broad range of species. Third, the quality of GO annotations has been improved through a streamlined process for, and automated quality checks of, GO annotations deposited by different annotation groups. Fourth, the consistency and correctness of the ontology itself has increased by using automated reasoning tools. Finally, the GO has been expanded not only to cover new areas of biology through focused interaction with experts, but also to capture greater specificity in all areas of the ontology using tools for adding new combinatorial terms. The GOC works closely with other ontology developers to support integrated use of terminologies. The GOC supports its user community through the use of e-mail lists, social media and web-based resources.

UR - http://www.scopus.com/inward/record.url?scp=84874253819&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84874253819&partnerID=8YFLogxK

U2 - 10.1093/nar/gks1050

DO - 10.1093/nar/gks1050

M3 - Article

C2 - 23161678

AN - SCOPUS:84874253819

SN - 0305-1048

VL - 41

SP - D530-D535

JO - Nucleic acids research

JF - Nucleic acids research

IS - D1

ER -

Gene ontology annotations and resources

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