Claire O’Donovan

Claire O’Donovan

Team Leader: UniProt content

BSc (Hons) in Biochemistry, 1992, University College Cork, Ireland. Diploma in Computer Science, 1993, University College Cork, Ireland. At EMBL since 1993, at EMBL-EBI since 1994. Team Leader since 2009.

ORCID iD: 0000-0001-8051-7429

Tel:+44 (0)1223 494 460 / Fax:+44 (0)1223 494 468

O'Donovan team

The central activity of Claire O'Donovan's team is the biocuration of our UniProt databases. Biocuration involves the interpretation and integration of information relevant to biology into a database or resource that enables integration of the scientific literature as well as large data sets. Accurate and comprehensive representation of biological knowledge, as well as easy access to this data for working scientists and a basis for computational analysis, are primary goals of biocuration.

UniProt manual curation

Manual curation involves a critical review of experimental and predicted data for each protein, as well as manual verification of each protein sequence. The curation methods we apply to UniProtKB/Swiss-Prot include manual extraction and structuring of experimental information from the literature, manual verification of results from computational analyses, quality assessment mining and integration of large-scale data sets and continuous updating as new information becomes available.

UniProt automatic annotation

UniProt has developed two complementary approaches in order to automatically annotate protein sequences with a high degree of accuracy. UniRule is a collection of manually curated annotation rules, which define annotations that can be propagated based on specific conditions. The Statistical Automatic Annotation System (SAAS) is an automatic decision-tree-based rule-generating system. The central components of these approaches are rules based on InterPro classification and the manually curated data in UniProtKB/Swiss-Prot from the experimental literature and InterPro classification.

UniProt GO annotation (GOA)

The UniProt GO annotation (GOA) program aims to add high-quality GO annotations to proteins in the UniProt Knowledgebase (UniProtKB). The assignment of GO terms to UniProt records is an integral part of UniProt biocuration. We supplement UniProt manual and electronic GO annotations are supplemented with manual annotations supplied by external collaborating GO Consortium groups. This ensures that users have a comprehensive GO annotation dataset. UniProt-GOA is a member of the GO consortium.

About UniProt

Claire's team works in a fully complementary fashion with Maria-Jesus Martin's UniProt Development team to provide essential resources to the biological community, as the databases have become an integral part of the tools researchers use on a daily basis for their work. The Universal Protein Resource (UniProt) is a comprehensive resource for protein sequence and functional annotation data. UniProt is comprised of four major components, each optimized for different uses:

  • the UniProt Knowledgebase (UniProtKB) is an expertly curated database, a central access point for integrated protein information with cross-references to multiple sources;
  • the UniProt Archive (UniParc) is a comprehensive sequence repository, reflecting the history of all protein sequences;
  • UniProt Reference Clusters (UniRef) merge closely related sequences based on sequence identity to speed up searches;
  • the UniProt Metagenomic and Environmental Sequences database (UniMES) was created to respond to the expanding area of metagenomic data.

Publications

2015

Analysis of the tryptic search space in UniProt databases.
Alpi E, Griss J, da Silva AW, Bely B, Antunes R, Zellner H, Ríos D, O'Donovan C, Vizcaíno JA, Martin MJ.
Proteomics Volume 15 (2015) p.48-57
DOI: 10.1002/pmic.201400227

The GOA database: gene Ontology annotation updates for 2015.
Huntley RP, Sawford T, Mutowo-Meullenet P, Shypitsyna A, Bonilla C, Martin MJ, O'Donovan C.
Nucleic Acids Res Volume 43 (2015) p.d1057-63
DOI: 10.1093/nar/gku1113

2014

Representing kidney development using the gene ontology.
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.
PLoS One Volume 9 (2014) p.e99864
DOI: 10.1371/journal.pone.0099864

Activities at the Universal Protein Resource (UniProt).
UniProt Consortium.
Nucleic Acids Res Volume 42 (2014) p.d191-8
DOI: 10.1093/nar/gkt1140

Understanding how and why the Gene Ontology and its annotations evolve: the GO within UniProt.
Huntley RP, Sawford T, Martin MJ, O'Donovan C.
Gigascience Volume 3 (2014) p.4
DOI: 10.1186/2047-217x-3-4

Expert curation in UniProtKB: a case study on dealing with conflicting and erroneous data.
Poux S, Magrane M, Arighi CN, Bridge A, O'Donovan C, Laiho K, UniProt Consortium.
Database (Oxford) Volume 2014 (2014) p.bau016
DOI: 10.1093/database/bau016

Genetic variations and diseases in UniProtKB/Swiss-Prot: the ins and outs of expert manual curation.
Famiglietti ML, Estreicher A, Gos A, Bolleman J, Géhant S, Breuza L, Bridge A, Poux S, Redaschi N, Bougueleret L, Xenarios I, UniProt Consortium.
Hum Mutat Volume 35 (2014) p.927-935
DOI: 10.1002/humu.22594

2013

The COMBREX project: design, methodology, and initial results.
Anton BP, Chang YC, Brown P, Choi HP, Faller LL, Guleria J, Hu Z, Klitgord N, Levy-Moonshine A, Maksad A, Mazumdar V, McGettrick M, Osmani L, Pokrzywa R, Rachlin J, Swaminathan R, Allen B, Housman G, Monahan C, Rochussen K, Tao K, Bhagwat AS, Brenner SE, Columbus L, de Crécy-Lagard V, Ferguson D, Fomenkov A, Gadda G, Morgan RD, Osterman AL, Rodionov DA, Rodionova IA, Rudd KE, Söll D, Spain J, Xu SY, Bateman A, Blumenthal RM, Bollinger JM, Chang WS, Ferrer M, Friedberg I, Galperin MY, Gobeill J, Haft D, Hunt J, Karp P, Klimke W, Krebs C, Macelis D, Madupu R, Martin MJ, Miller JH, O'Donovan C, Palsson B, Ruch P, Setterdahl A, Sutton G, Tate J, Yakunin A, Tchigvintsev D, Plata G, Hu J, Greiner R, Horn D, Sjölander K, Salzberg SL, Vitkup D, Letovsky S, Segrè D, DeLisi C, Roberts RJ, Steffen M, Kasif S.
PLoS Biol Volume 11 (2013) p.e1001638
DOI: 10.1371/journal.pbio.1001638

DATABASE, The Journal of Biological Databases and Curation, is now the official journal of the International Society for Biocuration.
Gaudet P, Munoz-Torres M, Robinson-Rechavi M, Attwood T, Bateman A, Cherry JM, Kania R, O'Donovan C, Yamasaki C.
Database (Oxford) Volume 2013 (2013) p.bat077
DOI: 10.1093/database/bat077

Update on activities at the Universal Protein Resource (UniProt) in 2013.
UniProt Consortium.
Nucleic Acids Res Volume 41 (2013) p.d43-7
DOI: 10.1093/nar/gks1068

The EBI enzyme portal.
Alcántara R, Onwubiko J, Cao H, Matos Pd, Cham JA, Jacobsen J, Holliday GL, Fischer JD, Rahman SA, Jassal B, Goujon M, Rowland F, Velankar S, López R, Overington JP, Kleywegt GJ, Hermjakob H, O'Donovan C, Martín MJ, Thornton JM, Steinbeck C.
Nucleic Acids Res Volume 41 (2013) p.d773-80
DOI: 10.1093/nar/gks1112

HAMAP in 2013, new developments in the protein family classification and annotation system.
Pedruzzi I, Rivoire C, Auchincloss AH, Coudert E, Keller G, de Castro E, Baratin D, Cuche BA, Bougueleret L, Poux S, Redaschi N, Xenarios I, Bridge A, UniProt Consortium.
Nucleic Acids Res Volume 41 (2013) p.d584-9
DOI: 10.1093/nar/gks1157

Use of Gene Ontology Annotation to understand the peroxisome proteome in humans.
Mutowo-Meullenet P, Huntley RP, Dimmer EC, Alam-Faruque Y, Sawford T, Jesus Martin M, O'Donovan C, Apweiler R.
Database (Oxford) Volume 2013 (2013) p.bas062
DOI: 10.1093/database/bas062

A fast Peptide Match service for UniProt Knowledgebase.
Chen C, Li Z, Huang H, Suzek BE, Wu CH, UniProt Consortium.
Bioinformatics Volume 29 (2013) p.2808-2809
DOI: 10.1093/bioinformatics/btt484

Gene Ontology annotations and resources.
Gene Ontology Consortium, Blake JA, Dolan M, Drabkin H, Hill DP, Li N, 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, Chrisholm 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 M-, Bonilla C, Bouguerleret 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 C, 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 Millán P, Poux S, Rivoire C, Roechert B, Sawford T, Schneider M, Stutz A, Sundaram S, Tognolli M, Xenarios I, Foulgar R, Lomax J, Roncaglia P, Khodiyar VK, Lovering RC, Talmud PJ, Chibucos M, Giglio MG, Chang H-, 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 DM, Staines DM, Dwinell M, Shimoyama M, Laulederkind S, Hayman T, Wang S-, 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, Huala E, Mi H, Thomas PD, Chan J, Kishore R, Sternberg P, Van Auken K, Howe D, Westerfield M.
Nucleic Acids Res Volume 41 (2013) p.d530-5
DOI: 10.1093/nar/gks1050

SIFTS: Structure Integration with Function, Taxonomy and Sequences resource.
Velankar S, Dana JM, Jacobsen J, van Ginkel G, Gane PJ, Luo J, Oldfield TJ, O'Donovan C, Martin MJ, Kleywegt GJ.
Nucleic Acids Res Volume 41 (2013) p.d483-9
DOI: 10.1093/nar/gks1258

2012

UniProtKB amid the turmoil of plant proteomics research.
Schneider M, UniProt Consortium, Poux S.
Front Plant Sci Volume 3 (2012) p.270
DOI: 10.3389/fpls.2012.00270

Biocurators and biocuration: surveying the 21st century challenges.
Burge S, Attwood TK, Bateman A, Berardini TZ, Cherry M, O'Donovan C, Xenarios L, Gaudet P.
Database (Oxford) Volume 2012 (2012) p.bar059
DOI: 10.1093/database/bar059

Recent advances in biocuration: meeting report from the Fifth International Biocuration Conference.
Gaudet P, Arighi C, Bastian F, Bateman A, Blake JA, Cherry MJ, D'Eustachio P, Finn R, Giglio M, Hirschman L, Kania R, Klimke W, Martin MJ, Karsch-Mizrachi I, Munoz-Torres M, Natale D, O'Donovan C, Ouellette F, Pruitt KD, Robinson-Rechavi M, Sansone SA, Schofield P, Sutton G, Van Auken K, Vasudevan S, Wu C, Young J, Mazumder R.
Database (Oxford) Volume 2012 (2012) p.bas036
DOI: 10.1093/database/bas036

AntiFam: a tool to help identify spurious ORFs in protein annotation.
Eberhardt RY, Haft DH, Punta M, Martin M, O'Donovan C, Bateman A.
Database (Oxford) Volume 2012 (2012) p.bas003
DOI: 10.1093/database/bas003

Reorganizing the protein space at the Universal Protein Resource (UniProt).
UniProt Consortium.
Nucleic Acids Res Volume 40 (2012) p.d71-5
DOI: 10.1093/nar/gkr981

The UniProt-GO Annotation database in 2011.
Dimmer EC, Huntley RP, Alam-Faruque Y, Sawford T, O'Donovan C, Martin MJ, Bely B, Browne P, Mun Chan W, Eberhardt R, Gardner M, Laiho K, Legge D, Magrane M, Pichler K, Poggioli D, Sehra H, Auchincloss A, Axelsen K, Blatter MC, Boutet E, Braconi-Quintaje S, Breuza L, Bridge A, Coudert E, Estreicher A, Famiglietti L, Ferro-Rojas S, Feuermann M, Gos A, Gruaz-Gumowski N, Hinz U, Hulo C, James J, Jimenez S, Jungo F, Keller G, Lemercier P, Lieberherr D, Masson P, Moinat M, Pedruzzi I, Poux S, Rivoire C, Roechert B, Schneider M, Stutz A, Sundaram S, Tognolli M, Bougueleret L, Argoud-Puy G, Cusin I, Duek-Roggli P, Xenarios I, Apweiler R.
Nucleic Acids Res Volume 40 (2012) p.d565-70
DOI: 10.1093/nar/gkr1048

The Gene Ontology: enhancements for 2011.
Gene Ontology Consortium.
Nucleic Acids Res Volume 40 (2012) p.d559-64
DOI: 10.1093/nar/gkr1028

2011

Consequences of the discontinuation of the International Protein Index (IPI) database and its substitution by the UniProtKB "complete proteome" sets.
Griss J, Martín M, O'Donovan C, Apweiler R, Hermjakob H, Vizcaíno JA.
Proteomics Volume 11 (2011) p.4434-4438
DOI: 10.1002/pmic.201100363

Solving the Problem: Genome Annotation Standards before the Data Deluge.
Klimke W, O'Donovan C, White O, Brister JR, Clark K, Fedorov B, Mizrachi I, Pruitt KD, Tatusova T.
Stand Genomic Sci Volume 5 (2011) p.168-193
DOI: 10.4056/sigs.2084864

Ongoing and future developments at the Universal Protein Resource.
UniProt Consortium.
Nucleic Acids Res Volume 39 (2011) p.d214-9
DOI: 10.1093/nar/gkq1020

UniProt Knowledgebase: a hub of integrated protein data.
Magrane M, Consortium U.
Database (Oxford) Volume 2011 (2011) p.bar009
DOI: 10.1093/database/bar009

The impact of focused Gene Ontology curation of specific mammalian systems.
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.
PLoS One Volume 6 (2011) p.e27541
DOI: 10.1371/journal.pone.0027541

A guide to UniProt for protein scientists.
O'Donovan C, Apweiler R.
Methods Mol Biol Volume 694 (2011) p.25-35
DOI: 10.1007/978-1-60761-977-2_2

2010

The Gene Ontology in 2010: extensions and refinements.
Gene Ontology Consortium.
Nucleic Acids Res Volume 38 (2010) p.d331-5
DOI: 10.1093/nar/gkp1018

The Universal Protein Resource (UniProt) in 2010.
UniProt Consortium.
Nucleic Acids Res Volume 38 (2010) p.d142-8
DOI: 10.1093/nar/gkp846

From protein sequences to 3D-structures and beyond: the example of the UniProt knowledgebase.
Hinz U, UniProt Consortium.
Cell Mol Life Sci Volume 67 (2010) p.1049-1064
DOI: 10.1007/s00018-009-0229-6

The Renal Gene Ontology Annotation Initiative.
Alam-Faruque Y, Dimmer EC, Huntley RP, O'Donovan C, Scambler P, Apweiler R.
Organogenesis Volume 6 (2010) p.71-75
DOI: 10.4161/org.6.2.11294

2009

The GOA database in 2009--an integrated Gene Ontology Annotation resource.
Barrell D, Dimmer E, Huntley RP, Binns D, O'Donovan C, Apweiler R.
Nucleic Acids Res Volume 37 (2009) p.d396-403
DOI: 10.1093/nar/gkn803

The Universal Protein Resource (UniProt) 2009.
UniProt Consortium.
Nucleic Acids Res Volume 37 (2009) p.d169-74
DOI: 10.1093/nar/gkn664

QuickGO: a web-based tool for Gene Ontology searching.
Binns D, Dimmer E, Huntley R, Barrell D, O'Donovan C, Apweiler R.
Bioinformatics Volume 25 (2009) p.3045-3046
DOI: 10.1093/bioinformatics/btp536

QuickGO: a user tutorial for the web-based Gene Ontology browser.
Huntley RP, Binns D, Dimmer E, Barrell D, O'Donovan C, Apweiler R.
Database (Oxford) Volume 2009 (2009) p.bap010
DOI: 10.1093/database/bap010

2008

The universal protein resource (UniProt).
UniProt Consortium.
Nucleic Acids Res Volume 36 (2008) p.d190-5
DOI: 10.1093/nar/gkm895

The Protein Feature Ontology: a tool for the unification of protein feature annotations.
Reeves GA, Eilbeck K, Magrane M, O'Donovan C, Montecchi-Palazzi L, Harris MA, Orchard S, Jimenez RC, Prlic A, Hubbard TJ, Hermjakob H, Thornton JM.
Bioinformatics Volume 24 (2008) p.2767-2772
DOI: 10.1093/bioinformatics/btn528

The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts.
Genome Information Integration Project And H-Invitational 2, Yamasaki C, Murakami K, Fujii Y, Sato Y, Harada E, Takeda J, Taniya T, Sakate R, Kikugawa S, Shimada M, Tanino M, Koyanagi KO, Barrero RA, Gough C, Chun HW, Habara T, Hanaoka H, Hayakawa Y, Hilton PB, Kaneko Y, Kanno M, Kawahara Y, Kawamura T, Matsuya A, Nagata N, Nishikata K, Noda AO, Nurimoto S, Saichi N, Sakai H, Sanbonmatsu R, Shiba R, Suzuki M, Takabayashi K, Takahashi A, Tamura T, Tanaka M, Tanaka S, Todokoro F, Yamaguchi K, Yamamoto N, Okido T, Mashima J, Hashizume A, Jin L, Lee KB, Lin YC, Nozaki A, Sakai K, Tada M, Miyazaki S, Makino T, Ohyanagi H, Osato N, Tanaka N, Suzuki Y, Ikeo K, Saitou N, Sugawara H, O'Donovan C, Kulikova T, Whitfield E, Halligan B, Shimoyama M, Twigger S, Yura K, Kimura K, Yasuda T, Nishikawa T, Akiyama Y, Motono C, Mukai Y, Nagasaki H, Suwa M, Horton P, Kikuno R, Ohara O, Lancet D, Eveno E, Graudens E, Imbeaud S, Debily MA, Hayashizaki Y, Amid C, Han M, Osanger A, Endo T, Thomas MA, Hirakawa M, Makalowski W, Nakao M, Kim NS, Yoo HS, De Souza SJ, Bonaldo Mde F, Niimura Y, Kuryshev V, Schupp I, Wiemann S, Bellgard M, Shionyu M, Jia L, Thierry-Mieg D, Thierry-Mieg J, Wagner L, Zhang Q, Go M, Minoshima S, Ohtsubo M, Hanada K, Tonellato P, Isogai T, Zhang J, Lenhard B, Kim S, Chen Z, Hinz U, Estreicher A, Nakai K, Makalowska I, Hide W, Tiffin N, Wilming L, Chakraborty R, Soares MB, Chiusano ML, Suzuki Y, Auffray C, Yamaguchi-Kabata Y, Itoh T, Hishiki T, Fukuchi S, Nishikawa K, Sugano S, Nomura N, Tateno Y, Imanishi T, Gojobori T.
Nucleic Acids Res Volume 36 (2008) p.d793-9
DOI: 10.1093/nar/gkm999

The Rice Annotation Project Database (RAP-DB): 2008 update.
Rice Annotation Project, Tanaka T, Antonio BA, Kikuchi S, Matsumoto T, Nagamura Y, Numa H, Sakai H, Wu J, Itoh T, Sasaki T, Aono R, Fujii Y, Habara T, Harada E, Kanno M, Kawahara Y, Kawashima H, Kubooka H, Matsuya A, Nakaoka H, Saichi N, Sanbonmatsu R, Sato Y, Shinso Y, Suzuki M, Takeda J, Tanino M, Todokoro F, Yamaguchi K, Yamamoto N, Yamasaki C, Imanishi T, Okido T, Tada M, Ikeo K, Tateno Y, Gojobori T, Lin YC, Wei FJ, Hsing YI, Zhao Q, Han B, Kramer MR, McCombie RW, Lonsdale D, O'Donovan CC, Whitfield EJ, Apweiler R, Koyanagi KO, Khurana JP, Raghuvanshi S, Singh NK, Tyagi AK, Haberer G, Fujisawa M, Hosokawa S, Ito Y, Ikawa H, Shibata M, Yamamoto M, Bruskiewich RM, Hoen DR, Bureau TE, Namiki N, Ohyanagi H, Sakai Y, Nobushima S, Sakata K, Barrero RA, Sato Y, Souvorov A, Smith-White B, Tatusova T, An S, An G, OOta S, Fuks G, Fuks G, Messing J, Christie KR, Lieberherr D, Kim H, Zuccolo A, Wing RA, Nobuta K, Green PJ, Lu C, Meyers BC, Chaparro C, Piegu B, Panaud O, Echeverria M.
Nucleic Acids Res Volume 36 (2008) p.d1028-33
DOI: 10.1093/nar/gkm978

2007

The Universal Protein Resource (UniProt).
UniProt Consortium.
Nucleic Acids Res Volume 35 (2007) p.d193-7
DOI: 10.1093/nar/gkl929

Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana.
Rice Annotation Project, Itoh T, Tanaka T, Barrero RA, Yamasaki C, Fujii Y, Hilton PB, Antonio BA, Aono H, Apweiler R, Bruskiewich R, Bureau T, Burr F, Costa de Oliveira A, Fuks G, Habara T, Haberer G, Han B, Harada E, Hiraki AT, Hirochika H, Hoen D, Hokari H, Hosokawa S, Hsing YI, Ikawa H, Ikeo K, Imanishi T, Ito Y, Jaiswal P, Kanno M, Kawahara Y, Kawamura T, Kawashima H, Khurana JP, Kikuchi S, Komatsu S, Koyanagi KO, Kubooka H, Lieberherr D, Lin YC, Lonsdale D, Matsumoto T, Matsuya A, McCombie WR, Messing J, Miyao A, Mulder N, Nagamura Y, Nam J, Namiki N, Numa H, Nurimoto S, O'Donovan C, Ohyanagi H, Okido T, Oota S, Osato N, Palmer LE, Quetier F, Raghuvanshi S, Saichi N, Sakai H, Sakai Y, Sakata K, Sakurai T, Sato F, Sato Y, Schoof H, Seki M, Shibata M, Shimizu Y, Shinozaki K, Shinso Y, Singh NK, Smith-White B, Takeda J, Tanino M, Tatusova T, Thongjuea S, Todokoro F, Tsugane M, Tyagi AK, Vanavichit A, Wang A, Wing RA, Yamaguchi K, Yamamoto M, Yamamoto N, Yu Y, Zhang H, Zhao Q, Higo K, Burr B, Gojobori T, Sasaki T.
Genome Res Volume 17 (2007) p.175-183
DOI: 10.1101/gr.5509507

2006

The Universal Protein Resource (UniProt): an expanding universe of protein information.
Wu CH, Apweiler R, Bairoch A, Natale DA, Barker WC, Boeckmann B, Ferro S, Gasteiger E, Huang H, Lopez R, Magrane M, Martin MJ, Mazumder R, O'Donovan C, Redaschi N, Suzek B.
Nucleic Acids Res Volume 34 (2006) p.d187-91
DOI: 10.1093/nar/gkj161

Curator driven protein sequence analysis and annotation
Magrane M, O'Donovan C.
Volume (2006) p.55-70

2005

The Universal Protein Resource (UniProt).
Bairoch A, Apweiler R, Wu CH, Barker WC, Boeckmann B, Ferro S, Gasteiger E, Huang H, Lopez R, Magrane M, Martin MJ, Natale DA, O'Donovan C, Redaschi N, Yeh LS.
Nucleic Acids Res Volume 33 (2005) p.d154-9
DOI: 10.1093/nar/gki070

2004

Protein sequence database methods.
Martin MJ, O'Donovan C, Apweiler R.
Genet Eng (N Y) Volume 26 (2004) p.13-17
DOI: 10.2478/v10050-008-0057-3

Integrative annotation of 21,037 human genes validated by full-length cDNA clones.
Imanishi T, Itoh T, Suzuki Y, O'Donovan C, Fukuchi S, Koyanagi KO, Barrero RA, Tamura T, Yamaguchi-Kabata Y, Tanino M, Yura K, Miyazaki S, Ikeo K, Homma K, Kasprzyk A, Nishikawa T, Hirakawa M, Thierry-Mieg J, Thierry-Mieg D, Ashurst J, Jia L, Nakao M, Thomas MA, Mulder N, Karavidopoulou Y, Jin L, Kim S, Yasuda T, Lenhard B, Eveno E, Suzuki Y, Yamasaki C, Takeda J, Gough C, Hilton P, Fujii Y, Sakai H, Tanaka S, Amid C, Bellgard M, Bonaldo Mde F, Bono H, Bromberg SK, Brookes AJ, Bruford E, Carninci P, Chelala C, Couillault C, de Souza SJ, Debily MA, Devignes MD, Dubchak I, Endo T, Estreicher A, Eyras E, Fukami-Kobayashi K, Gopinath GR, Graudens E, Hahn Y, Han M, Han ZG, Hanada K, Hanaoka H, Harada E, Hashimoto K, Hinz U, Hirai M, Hishiki T, Hopkinson I, Imbeaud S, Inoko H, Kanapin A, Kaneko Y, Kasukawa T, Kelso J, Kersey P, Kikuno R, Kimura K, Korn B, Kuryshev V, Makalowska I, Makino T, Mano S, Mariage-Samson R, Mashima J, Matsuda H, Mewes HW, Minoshima S, Nagai K, Nagasaki H, Nagata N, Nigam R, Ogasawara O, Ohara O, Ohtsubo M, Okada N, Okido T, Oota S, Ota M, Ota T, Otsuki T, Piatier-Tonneau D, Poustka A, Ren SX, Saitou N, Sakai K, Sakamoto S, Sakate R, Schupp I, Servant F, Sherry S, Shiba R, Shimizu N, Shimoyama M, Simpson AJ, Soares B, Steward C, Suwa M, Suzuki M, Takahashi A, Tamiya G, Tanaka H, Taylor T, Terwilliger JD, Unneberg P, Veeramachaneni V, Watanabe S, Wilming L, Yasuda N, Yoo HS, Stodolsky M, Makalowski W, Go M, Nakai K, Takagi T, Kanehisa M, Sakaki Y, Quackenbush J, Okazaki Y, Hayashizaki Y, Hide W, Chakraborty R, Nishikawa K, Sugawara H, Tateno Y, Chen Z, Oishi M, Tonellato P, Apweiler R, Okubo K, Wagner L, Wiemann S, Strausberg RL, Isogai T, Auffray C, Nomura N, Gojobori T, Sugano S.
PLoS Biol Volume 2 (2004) p.e162
DOI: 10.1371/journal.pbio.0020162

2003

The European Bioinformatics Institute's data resources.
Brooksbank C, Camon E, Harris MA, Magrane M, Martin MJ, Mulder N, O'Donovan C, Parkinson H, Tuli MA, Apweiler R, Birney E, Brazma A, Henrick K, Lopez R, Stoesser G, Stoehr P, Cameron G.
Nucleic Acids Res Volume 31 (2003) p.43-50
DOI: 10.1093/nar/gkg066

Managing core resources for genomics and proteomics.
Apweiler R, Martin MJ, O'Donovan C, Pruess M.
Pharmacogenomics Volume 4 (2003) p.343-350
DOI: 10.1517/phgs.4.3.343.22689

The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003.
Boeckmann B, Bairoch A, Apweiler R, Blatter MC, Estreicher A, Gasteiger E, Martin MJ, Michoud K, O'Donovan C, Phan I, Pilbout S, Schneider M.
Nucleic Acids Res Volume 31 (2003) p.365-370
DOI: 10.1093/nar/gkg095

2002

High-quality protein knowledge resource: SWISS-PROT and TrEMBL.
O'Donovan C, Martin MJ, Gattiker A, Gasteiger E, Bairoch A, Apweiler R.
Brief Bioinform Volume 3 (2002) p.275-284
DOI: 10.1093/bib/3.3.275

2001

The human proteomics initiative (HPI).
O'Donovan C, Apweiler R, Bairoch A.
Trends Biotechnol Volume 19 (2001) p.178-181
DOI: 10.1016/s0167-7799(01)01598-0

2000

The role SWISS-PROT and TrEMBL play in the genome research environment.
Junker V, Contrino S, Fleischmann W, Hermjakob H, Lang F, Magrane M, Martin MJ, Mitaritonna N, O'Donovan C, Apweiler R.
J Biotechnol Volume 78 (2000) p.221-234
DOI: 10.1016/s0168-1656(00)00198-x

1999

Removing redundancy in SWISS-PROT and TrEMBL.
O'Donovan C, Martin MJ, Glemet E, Codani JJ, Apweiler R.
Bioinformatics Volume 15 (1999) p.258-259
DOI: 10.1093/bioinformatics/15.3.258

1998

Glycosyltransferases in SWISS-PROT.
O'Donovan C, Mitaritonna N.
Glycoconj J Volume 15 (1998) p.507-509
DOI: 10.1023/a:1006991121281

1997

Protein sequence annotation in the genome era: the annotation concept of SWISS-PROT+TREMBL.
Apweiler R, Gateau A, Contrino S, Martin MJ, Junker V, O'Donovan C, Lang F, Mitaritonna N, Kappus S, Bairoch A.
Proc Int Conf Intell Syst Mol Biol Volume 5 (1997) p.33-43

Services

Team members

Joanna Argasinska
Ramona Britto
Hema Bye-A-Jee
Amy Cottage
Rebecca Foulger
Penelope Garmiri
Daniel Gonzalez
Emma Hatton-Ellis
Alistair MacDougall
Michele Magrane
Barbara Palka
Klemens Pichler
Lorna Richardson
Aleksandra Shypitsyna
Elena Speretta
Kate Warner
Rossana Zaru