Claire O’Donovan

Claire O’Donovan

Team leader: Protein Function Content

Claire O’Donovan leads the Protein Function Content team at EMBL-EBI, which comprises biocurators working on the Universal Protein Resource (UniProt), the Gene Ontology Annotation project (GOA) and the Enzyme portal. Biocuration involves the translation 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. The goals of biocuration are achieved thanks to the convergent endeavors of biocurators and software developers, and Claire’s team works in a fully complementary fashion with the Protein Function Development group to provide essential resources to the biological community. Claire has been at EMBL since 1993 and has been integrally involved in the evolution of the biocuration field. Claire is a member of the Executive Committee of the International Society for Biocuration.

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

Creating a specialist protein resource network: a meeting report for the protein bioinformatics and community resources retreat.
Babbitt PC, Bagos PG, Bairoch A, Bateman A, Chatonnet A, Chen MJ, Craik DJ, Finn RD, Gloriam D, Haft DH, Henrissat B, Holliday GL, Isberg V, Kaas Q, Landsman D, Lenfant N, Manning G, Nagano N, Srinivasan N, O'Donovan C, Pruitt KD, Sowdhamini R, Rawlings ND, Saier MH Jr, Sharman JL, Spedding M, Tsirigos KD, Vastermark A, Vriend G.
Database : the journal of biological databases and curation Volume 2015 (2015) p.bav063

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

UniProt: a hub for protein information.
UniProt Consortium.
Nucleic acids research Volume 43 (2015) p.D204-12

Gene Ontology Consortium: going forward.
Gene Ontology Consortium.
Nucleic acids research Volume 43 (2015) p.D1049-56

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 research Volume 43 (2015) p.D1057-63

Searching and Navigating UniProt Databases.
Pundir S, Magrane M, Martin MJ, O'Donovan C, UniProt Consortium.
Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.] Volume 50 (2015) p.1.27.1-10

Key challenges for the creation and maintenance of specialist protein resources.
Holliday GL, Bairoch A, Bagos PG, Chatonnet A, Craik DJ, Finn RD, Henrissat B, Landsman D, Manning G, Nagano N, O'Donovan C, Pruitt KD, Rawlings ND, Saier M, Sowdhamini R, Spedding M, Srinivasan N, Vriend G, Babbitt PC, Bateman A.
Proteins Volume 83 (2015) p.1005-1013

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

Activities at the Universal Protein Resource (UniProt).
UniProt Consortium.
Nucleic acids research Volume 42 (2014) p.D191-8

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

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 : the journal of biological databases and curation Volume 2014 (2014) p.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.
Human mutation Volume 35 (2014) p.927-935

2013

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 research Volume 41 (2013) p.D584-9

Update on activities at the Universal Protein Resource (UniProt) in 2013.
UniProt Consortium.
Nucleic acids research Volume 41 (2013) p.D43-7

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 : the journal of biological databases and curation Volume 2013 (2013) p.bas062

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 research Volume 41 (2013) p.D483-9

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 research Volume 41 (2013) p.D773-80

A fast Peptide Match service for UniProt Knowledgebase.
Chen C, Li Z, Huang H, Suzek BE, Wu CH, UniProt Consortium.
Bioinformatics (Oxford, England) Volume 29 (2013) p.2808-2809

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 biology Volume 11 (2013) p.e1001638

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 : the journal of biological databases and curation Volume 2013 (2013) p.bat077

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 research Volume 41 (2013) p.D530-5

2012

UniProtKB amid the turmoil of plant proteomics research.
Schneider M, UniProt Consortium, Poux S.
Frontiers in plant science Volume 3 (2012) p.270

The Gene Ontology: enhancements for 2011.
Gene Ontology Consortium.
Nucleic acids research Volume 40 (2012) p.D559-64

Reorganizing the protein space at the Universal Protein Resource (UniProt).
UniProt Consortium.
Nucleic acids research Volume 40 (2012) p.D71-5

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 research Volume 40 (2012) p.D565-70

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 : the journal of biological databases and curation Volume 2012 (2012) p.bas003

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 : the journal of biological databases and curation Volume 2012 (2012) p.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 : the journal of biological databases and curation Volume 2012 (2012) p.bas036

2011

Ongoing and future developments at the Universal Protein Resource.
UniProt Consortium.
Nucleic acids research Volume 39 (2011) p.D214-9

A guide to UniProt for protein scientists.
O'Donovan C, Apweiler R.
Methods in molecular biology (Clifton, N.J.) Volume 694 (2011) p.25-35

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

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.
Standards in genomic sciences Volume 5 (2011) p.168-193

UniProt Knowledgebase: a hub of integrated protein data.
Magrane M, UniProt Consortium.
Database : the journal of biological databases and curation Volume 2011 (2011) p.bar009

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

2010

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

From protein sequences to 3D-structures and beyond: the example of the UniProt knowledgebase.
Hinz U, UniProt Consortium.
Cellular and molecular life sciences : CMLS Volume 67 (2010) p.1049-1064

The Universal Protein Resource (UniProt) in 2010.
UniProt Consortium.
Nucleic acids research Volume 38 (2010) p.D142-8

The Gene Ontology in 2010: extensions and refinements.
Gene Ontology Consortium.
Nucleic acids research Volume 38 (2010) p.D331-5

2009

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

The Universal Protein Resource (UniProt) 2009.
UniProt Consortium.
Nucleic acids research Volume 37 (2009) p.D169-74

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 research Volume 37 (2009) p.D396-403

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 : the journal of biological databases and curation Volume 2009 (2009) p.bap010

2008

The universal protein resource (UniProt).
UniProt Consortium.
Nucleic acids research Volume 36 (2008) p.D190-5

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 (Oxford, England) Volume 24 (2008) p.2767-2772

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 research Volume 36 (2008) p.D1028-33

The Universal Protein Resource. A Growing Online Protein Database.
O'Donovan C, Martin MJ, Apweiler R.
BIOforum Europe Volume 12 (2008) p.32-33

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 research Volume 36 (2008) p.D793-9

2007

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 research Volume 17 (2007) p.175-183

The Universal Protein Resource (UniProt).
UniProt Consortium.
Nucleic acids research Volume 35 (2007) p.D193-7

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 research Volume 34 (2006) p.D187-91

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 research Volume 33 (2005) p.D154-9

2004

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 biology Volume 2 (2004) p.e162

Protein sequence database methods.
Martin MJ, O'Donovan C, Apweiler R.
Genetic engineering Volume 26 (2004) p.13-17

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 research Volume 31 (2003) p.43-50

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

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 research Volume 31 (2003) p.365-370

2002

High-quality protein knowledge resource: SWISS-PROT and TrEMBL.
O'Donovan C, Martin MJ, Gattiker A, Gasteiger E, Bairoch A, Apweiler R.
Briefings in bioinformatics Volume 3 (2002) p.275-284

2001

The human proteomics initiative (HPI).
O'Donovan C, Apweiler R, Bairoch A.
Trends in biotechnology Volume 19 (2001) p.178-181

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.
Journal of biotechnology Volume 78 (2000) p.221-234

1999

Removing redundancy in SWISS-PROT and TrEMBL.
O'Donovan C, Martin MJ, Glemet E, Codani JJ, Apweiler R.
Bioinformatics (Oxford, England) Volume 15 (1999) p.258-259

1998

Glycosyltransferases in SWISS-PROT.
O'Donovan C, Mitaritonna N.
Glycoconjugate journal Volume 15 (1998) p.507-509

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.
Proceedings / ... International Conference on Intelligent Systems for Molecular Biology ; ISMB. International Conference on Intelligent Systems for Molecular Biology Volume 5 (1997) p.33-43

0

Curator driven protein sequence analysis and annotation
Magrane M, O'Donovan C.
Volume (0) p.55-70

Services

Team members

Ramona Britto
Hema Bye-A-Jee
Amy Cottage
Melanie Courtot
Rebecca Foulger
Penelope Garmiri
Daniel Gonzalez
Emma Hatton-Ellis
Alex Holmes
Alistair MacDougall
Michele Magrane
Barbara Palka
Klemens Pichler
Aleksandra Shypitsyna
Elena Speretta
Nidhi Tyagi
Kate Warner
Rossana Zaru