UniProt-GOA - Publications

 

To cite UniProt-GOA, please use the following publication;

Dimmer EC , Huntley RP , Alam-Faruque Y , Sawford T , O'Donovan C , Martin MJ et al. (2012)
The UniProt-GO Annotation database in 2011.
Nucleic Acids Research 2012 40: D565-D570.

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To cite the QuickGO browser, please use the following publication;

Binns D, Dimmer E, Huntley R, Barrell D, O'Donovan C, Apweiler R. (2009)
QuickGO: a web-based tool for Gene Ontology searching.
Bioinformatics. 2009; 25(22):3045-6.

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For more information on UniProt-GOA, please see the following publications;

The Gene Ontology Consortium (2012)
The Gene Ontology: enhancements for 2011.
Nucleic Acids Research 2012 40: D559-564

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Alam-Faruque Y, Huntley RP, Khodiyar VK, Camon EB, Dimmer EC, Sawford T, Martin MJ, O'Donovan C, Talmud PJ, Scambler P, Apweiler R, Lovering RC. (2011)
The impact of focused Gene Ontology curation of specific mammalian systems.
PLoS One. 2011;6(12):e27541.

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Alam-Faruque Y, Dimmer EC, Huntley RP, O'Donovan C, Scambler P, Apweiler R. (2010)
The renal gene ontology annotation initiative.
Organogenesis. 6(2):71-5.

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Deegan JI, Dimmer EC, Mungall CJ. (2010)
Formalization of taxon-based constraints to detect inconsistencies in annotation and ontology development.
BMC Bioinformatics 11(1): 530.

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Huntley RP, Dimmer EC, Apweiler R. (2010)
Practical applications of the Gene Ontology resource.
In: Problem Solving Handbook in Computational Biology and Bioinformatics, LS Heath and N Ramakrishnan, Editors. Springer: New York, NY.

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Khodiyar VK, Dimmer EC, Huntley RP, Lovering RC. (2010)
Fundamentals of gene ontology functional annotation.
In Knowledge-based Bioinformatics, G Alterovitz and M Ramoni, Editors. Wiley: Boston, MA.

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The Gene Ontology Consortium. (2010)
The Gene Ontology in 2010: extensions and refinements.
Nucleic Acids Research 38: D331-D335.

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Barrell D., Dimmer E., Huntley R.P., Binns D., O'Donovan C., Apweiler R. (2009)
The GOA database in 2009--an integrated Gene Ontology Annotation resource.
Nucleic Acids Research 2009 37: D396-D403.

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Huntley RP, Binns D, Dimmer E, Barrell D, O'Donovan C, Apweiler R. (2009)
QuickGO: a user tutorial for the web-based Gene Ontology browser.
Database (Oxford). 2009:bap010.

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Dimmer EC, Huntley RP, Barrell DG, Binns D, Draghici S, Camon EB, Hubank M, Talmud PJ, Apweiler R, Lovering RC. (2008)
The Gene Ontology - Providing a Functional Role in Proteomic Studies.
Proteomics. 2008, 8 Suppl. (Practical Proteomics), DOI 10.1002/pmic.200800002

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The Gene Ontology Consortium. (2008)
The Gene Ontology project in 2008.
Nucleic Acids Research Database Issue Jan 2008 [epub ahead of print]

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Camon E., Barrell D., Dimmer E., Lee V. (2006)
The Gene Ontology Annotation (GOA) Database: Sharing Biological Knowledge with GO.
In: In Silico Genomics and Proteomics: Functional Annotation of Genomes and Proteins. Mulder N., and Apweiler R. (eds); pp 37-54, Nova Science Publishers, Inc, New York (2006).

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Couto F.M., Silva M.J., Lee V., Dimmer E., Camon, E., Apweiler R., Kirsch H., Rebholz-Schuhmann D. (2006)
GOAnnotator: Linking Protein GO Annotations to Evidence Text.
The Journal of Biomedical Discovery and Collaboration 1: 19.

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Gene Ontology Consortium* (2006)

*Current members of the GO Consortium are: Midori A. Harris, Jennifer I. Clark, Amelia Ireland, Jane Lomax (GO-EBI, Hinxton, UK); Michael Ashburner, Russell Collins (FlyBase, Department of Genetics, University of Cambridge, Cambridge, UK); Karen Eilbeck, Suzanna Lewis, Chris Mungall, John Richter, Gerald M. Rubin, ShengQiang Shu (BDGP, UC-Berkeley, Berkeley, CA, USA), Judith A. Blake, Carol J. Bult, Alexander D. Diehl, Mary E. Dolan, Harold J. Drabkin, Janan T. Eppig, David P. Hill, Li Ni, Martin Ringwald (MGI, The Jackson Laboratory, Bar Harbor, ME, USA); Rama Balakrishnan, Gail Binkley, J. Michael Cherry, Karen R. Christie, Maria C. Costanzo, Qing Dong, Stacia R. Engel, Dianna G. Fisk, Jodi E. Hirschman, Benjamin C. Hitz, Eurie L. Hong, Christopher Lane, Stuart Miyasato, Robert Nash, Anand Sethuraman, Marek Skrzypek, Chandra L. Theesfeld, Shuai Weng (SGD, Department of Genetics, Stanford University, Stanford, CA, USA); David Botstein, Kara Dolinski, Rose Oughtred (Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA); Tanya Berardini, Suparna Mundodi, Seung Y. Rhee (TAIR, Carnegie Institution, Department of Plant Biology, Stanford, CA, USA); Rolf Apweiler, Daniel Barrell, Evelyn Camon, Emily Dimmer, Nicola Mulder (UniProtKB-GOA Database, UniProt, EBI, Hinxton, UK); Rex Chisholm, Petra Fey, Pascale Gaudet, Warren Kibbe, Karen Pilcher (DictyBase, Northwestern University, Chicago, IL, USA); Carol A. Bastiani, Ranjana Kishore, Erich M. Schwarz, Paul Sternberg, Kimberly Van Auken (WormBase, California Institute of Technology, Pasadena, CA, USA); Michelle Gwinn, Linda Hannick, Jennifer Wortman (The Institute for Genome Research, Rockville, MD, USA); Martin Aslett, Matthew Berriman, Valerie Wood (Wellcome Trust Sanger Institute, Hinxton, UK); Susan Bromberg, Cindy Foote, Howard Jacob, Dean Pasko, Victoria Petri, Dorothy Reilly, Kathy Seiler, Mary Shimoyama, Jennifer Smith, Simon Twigger (RGD, Medical College of Wisconsin, Milwaukee, WI, USA); Pankaj Jaiswal (Gramene, Department of Plant Breeding, Cornell University, Ithaca, NY, USA); Trent Seigfried (MaizeGDB, Iowa State University, Ames, IA, USA); Candace Collmer (Wells College, Aurora, NY, USA); Doug Howe, Monte Westerfield (ZFIN, University of Oregon, Eugene, OR, USA).

The Gene Ontology (GO) project in 2006.
Nucleic Acids Research 34: D322-D326 (2006).

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McCarthy F.M. Wang N., Magee G.B., Nanduri B., Lawrence M.L., Camon E.B., Barrell D.G., Hill D.P., Dolan M.E., Williams W.P., Luthe D.S., Bridges S.M., Burgess S.C. (2006)
AgBase: A Functional Genomics Resource for Agriculture.
BMC Genomics 7: 229.

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Camon E., Barrell D., Dimmer E., Lee V., Magrane M., Maslen J., Binns D., Apweiler R. (2005)
An evaluation of GO annotation retrieval for BioCreAtIvE and GOA.
BMC Bioinformatics 6(1): S17.

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Dolan M.E., Li N., Camon E., Blake J.A. (2005)
A procedure for assessing GO annotation consistency.
Bioinformatics 21: i136-i143.

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Lee V., Camon E., Dimmer E., Barrell D., Apweiler R. (2005)
Who tangos with GOA? Use of Gene Ontology Annotation (GOA) for biological interpretation of '-omics' data and for validation of automatic annotation tools.
In Silico Biol. 5: 0002.

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Camon E., Magrane M., Barrell D., Lee V., Dimmer E., Maslen J., Binns D., Harte N., Lopez R., Apweiler R. (2004)
The Gene Ontology Annotation (GOA) Database: sharing knowledge in Uniprot with Gene Ontology.
Nucleic Acids Research 32(1): D262-D266.

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Gene Ontology Consortium* (2004)

*Current members of the GO Consortium are: M. A. Harris, J. Clark, A. Ireland, J. Lomax (GO-EBI, Hinxton, UK); M. Ashburner, R. Foulger (FlyBase, Department of Genetics, University of Cambridge, Cambridge, UK); K. Eilbeck, S. Lewis, B. Marshall, C. Mungall, J. Richter, G. M. Rubin (BDGP, UC-Berkeley, Berkeley, CA, USA), J. A. Blake, C. Bult, M. Dolan, H. Drabkin, J. T. Eppig, D. P. Hill, L. Ni, M. Ringwald (MGI, Jackson Laboratory, Bar Harbor, ME, USA); R. Balakrishnan, J. M. Cherry, K. R. Christie, M. C. Costanzo, S. S. Dwight, S. Engel, D. G. Fisk, J. E. Hirschman, E. L. Hong, R. S. Nash, A. Sethuraman, C. L. Theesfeld (SGD, Department of Genetics, Stanford University, Stanford, CA, USA); D. Botstein, K. Dolinski, B. Feierbach (Genomics Institute, Princeton University, Princeton, NJ, USA); T. Berardini, S. Mundodi, S. Y. Rhee (TAIR, Carnegie Institution, Department of Plant Biology, Stanford, CA, USA); R. Apweiler, D. Barrell, E. Camon, E. Dimmer, V. Lee (UniProtKB-GOA database, UniProt, EBI, Hinxton, UK); R. Chisholm, P. Gaudet, W. Kibbe (DictyBase, Northwestern University, Chicago, IL, USA); R. Kishore, E. M. Schwarz, P. Sternberg (WormBase, California Institute of Technology, Pasadena, CA, USA); M. Gwinn, L. Hannick, J. Wortman (Institute for Genome Research, Rockville, MD, USA); M. Berriman, V. Wood (Wellcome Trust Sanger Institute, Hinxton, UK); N. de la Cruz, P. Tonellato (RGD, Medical College of Wisconsin, Milwaukee, WI, USA); P. Jaiswal (Gramene, Department of Plant Breeding, Cornell University, Ithaca, NY, USA); T. Seigfried (Maize DB, Iowa State University, Ames, IA, USA); R. White (Incyte Genomics, Palo Alto, CA, USA).

The Gene Ontology (GO) database and informatics resource.
Nucleic Acids Research 32: D258-D261.

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Brooksbank C., Camon E., Harris M.A., Magrane M., Martin M., Mulder N., O'Donovan C., Parkinson H., Tuli M., Apweiler R., Birney E., Brazma A., Henrick K., Lopez R., Stoesser G., Stoehr P., and Cameron G. (2003)
The European Bioinformatics Institute's data resources.
Nucleic Acids Research 31: 43-50.

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Camon E., Barrell D., Brooksbank C., Magrane M. and Apweiler R. (2003)
The Gene Ontology Annotation (GOA) Project: Application of GO in SWISS-PROT, TrEMBL and InterPro.
Comparative and Functional Genomomics 4: 71-74.

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Camon E., Barrell D., Lee V., Dimmer E. and Apweiler R. (2003)
The Gene Ontology Annotation Database - An integrated resource of GO annotations to UniProt Knowledgebase.
In Silico Biol. 4: 0002.

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Camon E.*, Magrane M.*, Barrell D., Binns D., Fleischmann W., Kersey P., Mulder N., Oinn T., Maslen J., Cox A. and Apweiler R. (2003)
The Gene Ontology Annotation (GOA) project: implementation of GO in Swiss-Prot, TrEMBL and InterPro.
Genome Research Apr 13(4): 662-672.

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Biswas M., O'Rourke J.F.,Camon E.,Karavidopoulou Y., Kersey P., Kriventseva E., Mittard V., Mulder N., Phan I., and Servant F. (2002)
Applications of InterPro in protein annotation and genome analysis.
Briefings in Bioinformatics 3: 285-295.

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N.B. * denotes equal contribution.