GOA - Publications
To cite GOA, please use the following publication;
Huntley RP, Sawford T, Mutowo-Muellenet P, Shypitsyna A, Bonilla C, Martin MJ, O'Donovan C. (2014)
The GOA database: Gene Ontology annotation updates for 2015.
Nucleic Acids Research 2014 doi: 10.1093/nar/gku1113.
abstract full-text PDF
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.
abstract full-text
PDF
For more information on GOA, please see the following publications;
Huntley RP, Harris MA, Alam-Faruque Y, Blake JA, Carbon S, Dietze H, Dimmer EC, Foulger RE, Hill
DP, Khodiyar VK, Lock A, Lomax J, Lovering RC, Mutowo-Meullenet P, Sawford T, Van Auken K, Wood V,
Mungall CJ. (2014)
A method for increasing expressivity of Gene Ontology annotations using a compositional approach.
BMC Bioinformatics. 2014;15:155.
abstract
Huntley RP, Sawford T, Martin MJ, O'Donovan C. (2014)
Understanding how and why the Gene Ontology and its annotations evolve: the GO within UniProt.
Gigascience. 2014;3(1):4.
abstract
Chibucos MC, Mungall CJ, Balakrishnan R, Christie KR, Huntley RP, White O, Blake JA, Lewis SE,
Giglio M. (2014)
Standardized description of scientific evidence using the Evidence Ontology (ECO).
Database. 2014;bau075.
abstract
Alam-Faruque Y, Hill DP, Dimmer EC, Harris MA, Foulger RE, Tweedie S, Attrill H, Howe DG, Thomas
SR, Davidson D, Woolf AS, Blake JA, Mungall CJ, O'Donovan C, Apweiler R, Huntley RP. (2014)
Representing kidney development using the gene ontology.
PlosOne. 2014;9(6):e99864.
abstract
Balakrishnan R, Harris MA, Huntley R, Van Auken K, Cherry JM. (2013)
A guide to best practices for Gene Ontology (GO) manual annotation.
Database. 2013;bat054.
abstract
Tripathi S, Christie KR, Balakrishnan R, Huntley R, Hill DP, Thommesen L, Blake JA, Kuiper M,
Lægreid A. (2013)
Gene Ontology annotation of sequence-specific DNA binding transcription factors: setting the stage
for a large-scale curation effort.
Database. 2013;bat062.
abstract
Mutowo-Meullenet P, Huntley RP, Dimmer EC, Alam-Faruque Y, Sawford T, Jesus Martin M, O'Donovan C,
Apweiler R. (2013)
Use of Gene Ontology Annotation to understand the peroxisome proteome in humans.
Database. 2013;bas062.
abstract
Gene Ontology Consortium. (2013)
Gene Ontology annotations and resources.
Nucleic Acids Res. 2013;41:D530-5.
abstract
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.
abstract full-text PDF
The Gene Ontology Consortium (2012)
The Gene Ontology: enhancements for 2011.
Nucleic Acids Research 2012 40: D559-564
abstract full-text PDF
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.
abstract full-text PDF
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.
abstract
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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.
abstract
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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.
more info
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.
more
info
The Gene Ontology Consortium. (2010)
The Gene Ontology in 2010: extensions and refinements.
Nucleic Acids Research 38: D331-D335.
abstract full-text PDF
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.
abstract
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.
abstract
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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
abstract full-text PDF Supplement
The Gene Ontology Consortium. (2008)
The Gene Ontology project in 2008.
Nucleic Acids Research Database Issue Jan 2008 [epub ahead of print]
abstract full-text PDF
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).
more info
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.
abstract
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).
abstract full-text HTML full-text PDF
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.
abstract full-text PDF
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.
abstract
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.
abstract full-text PDF
N.B. * denotes equal contribution.