The Gene Ontology Annotation (GOA) Database: sharing knowledge in Uniprot with Gene Ontology
Evelyn Camon,Michele Magrane,Daniel Barrell,Vivian Lee,Emily Dimmer,John Maslen,David Binns,Nicola Harte,Rodrigo Lopez,Rolf Apweiler +9 more
Reads0
Chats0
TLDR
The Gene Ontology Annotation database aims to provide high-quality electronic and manual annotations to the UniProt Knowledgebase (Swiss-Prot, TrEMBL and PIR-PSD) using the standardized vocabulary of theGene Ontology (GO).Abstract:
The Gene Ontology Annotation (GOA) database (http://www.ebi.ac.uk/GOA) aims to provide high-quality electronic and manual annotations to the UniProt Knowledgebase (Swiss-Prot, TrEMBL and PIR-PSD) using the standardized vocabulary of the Gene Ontology (GO). As a supplementary archive of GO annotation, GOA promotes a high level of integration of the knowledge represented in UniProt with other databases. This is achieved by converting UniProt annotation into a recognized computational format. GOA provides annotated entries for nearly 60,000 species (GOA-SPTr) and is the largest and most comprehensive open-source contributor of annotations to the GO Consortium annotation effort. By integrating GO annotations from other model organism groups, GOA consolidates specialized knowledge and expertise to ensure the data remain a key reference for up-to-date biological information. Furthermore, the GOA database fully endorses the Human Proteomics Initiative by prioritizing the annotation of proteins likely to benefit human health and disease. In addition to a non-redundant set of annotations to the human proteome (GOA-Human) and monthly releases of its GO annotation for all species (GOA-SPTr), a series of GO mapping files and specific cross-references in other databases are also regularly distributed. GOA can be queried through a simple user-friendly web interface or downloaded in a parsable format via the EBI and GO FTP websites. The GOA data set can be used to enhance the annotation of particular model organism or gene expression data sets, although increasingly it has been used to evaluate GO predictions generated from text mining or protein interaction experiments. In 2004, the GOA team will build on its success and will continue to supplement the functional annotation of UniProt and work towards enhancing the ability of scientists to access all available biological information. Researchers wishing to query or contribute to the GOA project are encouraged to email: goa@ebi.ac.uk.read more
Citations
More filters
Journal ArticleDOI
The Universal Protein Resource (UniProt)
Amos Marc Bairoch,Rolf Apweiler,Cathy H. Wu,Winona C. Barker,Brigitte Boeckmann,Serenella Ferro,Elisabeth Gasteiger,Hongzhan Huang,Rodrigo Lopez,Michele Magrane,Maria Jesus Martin,Darren A. Natale,Claire O'Donovan,Nicole Redaschi,Lai-Su L. Yeh +14 more
TL;DR: During 2004, tens of thousands of Knowledgebase records got manually annotated or updated; the UniProt keyword list got augmented by additional keywords; the documentation of the keywords and are continuously overhauling and standardizing the annotation of post-translational modifications.
Journal ArticleDOI
High-throughput functional annotation and data mining with the Blast2GO suite.
Stefan Götz,Juan M. García-Gómez,Javier Terol,Tim D. Williams,Shivashankar H. Nagaraj,María José Nueda,Montserrat Robles,Manuel Talon,Joaquín Dopazo,Ana Conesa +9 more
TL;DR: The Blast2GO framework is used to carry out a detailed analysis of annotation behaviour through homology transfer and its impact in functional genomics research to offer biologists useful information to take into account when addressing the task of functionally characterizing their sequence data.
Journal ArticleDOI
Towards a proteome-scale map of the human protein–protein interaction network
Jean François Rual,Kavitha Venkatesan,Tong Hao,Tomoko Hirozane-Kishikawa,Amélie Dricot,Ning Li,Gabriel F. Berriz,Francis D. Gibbons,Matija Dreze,Nono Ayivi-Guedehoussou,Niels Klitgord,Christophe Simon,Mike Boxem,Stuart Milstein,Jennifer Rosenberg,Debra S. Goldberg,Lan V. Zhang,Sharyl L. Wong,Giovanni Franklin,Siming Li,Joanna S. Albala,Joanna S. Albala,Janghoo Lim,Carlene Fraughton,Estelle Llamosas,Sebiha Cevik,Camille Bex,Philippe Lamesch,Robert S. Sikorski,Jean Vandenhaute,Huda Y. Zoghbi,Alex Smolyar,Stephanie Bosak,Reynaldo Sequerra,Lynn Doucette-Stamm,Michael E. Cusick,David E. Hill,Frederick P. Roth,Marc Vidal +38 more
TL;DR: An initial version of a proteome-scale map of human binary protein–protein interactions is described, which increases by ∼70% the set of available binary interactions within the tested space and reveals more than 300 new connections to over 100 disease-associated proteins.
Journal ArticleDOI
The tomato genome sequence provides insights into fleshy fruit evolution
Shusei Sato,Satoshi Tabata,Hideki Hirakawa,Erika Asamizu,Kenta Shirasawa,Sachiko Isobe,Takakazu Kaneko,Yasukazu Nakamura,Daisuke Shibata,Koh Aoki,Michael Egholm,James R. Knight,Robert Bogden,Changbao Li,Yang Shuang,Xun Xu,Shengkai Pan,Shifeng Cheng,Xin Liu,Yuanyuan Ren,Jun Wang,Alessandro Albiero,Francesca Dal Pero,Sara Todesco,Joyce Van Eck,Robert M. Buels,Aureliano Bombarely,Joseph Gosselin,Minyun Huang,Jonathan A. Leto,Naama Menda,Susan R. Strickler,Linyong Mao,Shan Gao,Isaak Y. Tecle,Thomas L. York,Yi Zheng,Julia Vrebalov,Je Min Lee,Silin Zhong,Lukas A. Mueller,Willem J. Stiekema,Paolo Ribeca,Tyler Alioto,Wencai Yang,Sanwen Huang,Yongchen Du,Zhonghua Zhang,Jianchang Gao,Yanmei Guo,Xiaoxuan Wang,Ying Li,Jun He,Chuanyou Li,Zhukuan Cheng,Jianru Zuo,Jianfeng Ren,Jiuhai Zhao,Liuhua Yan,Hongling Jiang,Bao Wang,Hongshuang Li,Zhenjun Li,Fuyou Fu,Bingtang Chen,Bin Han,Qi Feng,Danlin Fan,Ying Wang,Hong-Qing Ling,Yongbiao Xue,Doreen Ware,W. Richard McCombie,Zachary B. Lippman,Jer Ming Chia,Ke Jiang,Shiran Pasternak,Laura Gelley,Melissa Kramer,Lorinda K. Anderson,Song Bin Chang,Suzanne M. Royer,Lindsay A. Shearer,Stephen M. Stack,Jocelyn K. C. Rose,Yimin Xu,Nancy T. Eannetta,Antonio J. Matas,Ryan P. McQuinn,Steven D. Tanksley,Francisco Camara,Roderic Guigó,Stephane Rombauts,Jeffrey A. Fawcett,Yves Van de Peer,Dani Zamir,Chunbo Liang,Manuel Spannagl,Heidrun Gundlach,Rémy Bruggmann,Klaus F. X. Mayer,Zhiqi Jia,Junhong Zhang,Zhibiao Ye,Gerard J. Bishop,Sarah Butcher,Rosa Lopez-Cobollo,Daniel W. A. Buchan,Ioannis Filippis,James Abbott,Manju Singh,Alok Singh,Jitendra Kumar Pal,Awadhesh Pandit,Pradeep Kumar Singh,Ajay Kumar Mahato,Vivek Dogra,Kishor Gaikwad,Tilak Raj Sharma,Trilochan Mohapatra,Nagendra K. Singh,Mathilde Causse,Christophe Rothan,Céline Noirot,Arnaud Bellec,Christophe Klopp,Corinne Delalande,Hélène Bergès,Jérôme Mariette,Pierre Frasse,Sonia Vautrin,Toulouse Mohamed Zouine,Alain Latché,Christine Rousseau,Farid Regad,Jean-Claude Pech,Murielle Philippot,Mondher Bouzayen,Pierre Pericard,Sonia Osorio,Asuncion Fernandez Del Carmen,Antonio J. Monforte,Antonio Granell,Rafael Fernández-Muñoz,Mariana Conte,Gabriel Lichtenstein,Fernando Carrari,Gianluca De Bellis,Fabio Fuligni,Clelia Peano,Silvana Grandillo,Pasquale Termolino,Marco Pietrella,Elio Fantini,Giulia Falcone,Alessia Fiore,Giovanni Giuliano,Loredana Lopez,Paolo Facella,Gaetano Perrotta,Loretta Daddiego,Glenn J. Bryan,Biology Modesto Orozco,Xavier Pastor,David Torrents,Marco G.M. Van Schriek,Richard Feron,Jan van Oeveren,Peter De Heer,Lorena Da Ponte,Saskia Jacobs-Oomen,Mike Cariaso,Marcel Prins,Michael Josephus Theresia Van Eijk,Antoine Janssen,J. J. Van Haaren,Sung HwanJo,Jungeun Kim,Suk-Yoon Kwon,Sangmi Kim,Dal-Hoe Koo,Sanghyeob Lee,Christopher Clouser,Alain Rico,Asis Hallab,Christiane Gebhardt,Kathrin Klee,Anika Jöcker,Jens Warfsmann,Ulrike Göbel,Shingo Kawamura,Kentaro Yano,Jamie D. Sherman,Hiroyuki Fukuoka,Satomi Negoro,Sarita Bhutty,Parul Chowdhury,Debasis Chattopadhyay,Erwin Datema,Sandra Smit,Elio Schijlen,José van de Belt,Jan C. van Haarst,Sander Peters,Marjo J. van Staveren,Marleen H.C. Henkens,Paul Mooyman,Thamara Hesselink,Roeland C. H. J. van Ham,Guoyong Jiang,Marcus Droege,Doil Choi,Byung Cheol Kang,Byung-Dong Kim,Minkyu Park,Seungill Kim,Seon-In Yeom,Yong-Hwan Lee,Yang Do Choi,Guangcun Li,Jianwei Gao,Yongsheng Liu,Shengxiong Huang,Victoria Fernandez-Pedrosa,Carmen Collado,Sheila Zuñ Iga,Guoping Wang,Rebecca Cade,Robert A. Dietrich,Jane Rogers,Sandra Knapp,Zhangjun Fei,Zhangjun Fei,Ruth White,Ruth White,Theodore W. Thannhauser,Theodore W. Thannhauser,James J. Giovannoni,James J. Giovannoni,Miguel A. Botella,Louise Gilbert,Fabra Ramon Gonzalez,Jose Luis Goicoechea,Yeisoo Yu,David Kudrna,Kristi Collura,Marina Wissotski,Rod A. Wing,Blake C. Meyers,Aishwarya Bala Gurazada,Pamela J. Green,Saloni Mathur,Shailendra Vyas,Amolkumar U. Solanke,Rajesh Kumar,Vikrant Gupta,Arun Sharma,Paramjit Khurana,Jitendra P. Khurana,Akhilesh K. Tyagi,Tamas Dalmay,Irina Mohorianu,Brandon Walts,Srikar Chamala,W. Brad Barbazuk,Jingping Li,Hui Guo,Tae-Ho Lee,Yupeng Wang,Dong Zhang,Andrew H. Paterson,Xiyin Wang,Xiyin Wang,Haibao Tang,Haibao Tang,Amalia Barone,Maria Luisa Chiusano,Maria Raffaella Ercolano,Nunzio D’Agostino,Miriam Di Filippo,Alessandra Traini,Walter Sanseverino,Luigi Frusciante,Graham B. Seymour,Mounir Elharam,Ying Fu,Axin Hua,Steven Kenton,Jennifer Lewis,Shaoping Lin,Fares Z. Najar,Hongshing Lai,Baifang Qin,Ruihua Shi,Chunmei Qu,Douglas White,James R. White,Yanbo Xing,Keqin Yang,Jing Yi,Ziyun Yao,Liping Zhou,Bruce A. Roe,Alessandro Vezzi,Michela D'Angelo,Rosanna Zimbello,Riccardo Schiavon,Elisa Caniato,Chiara Rigobello,Davide Campagna,Nicola Vitulo,Giorgio Valle,David R. Nelson,Emanuele De Paoli,Dóra Szinay,Hans H. De Jong,Yuling Bai,Richard G. F. Visser,Reném Klein Lankhorst,Helen Beasley,Karen McLaren,Christine Nicholson,Claire Riddle,Giulio Gianese +323 more
TL;DR: A high-quality genome sequence of domesticated tomato is presented, a draft sequence of its closest wild relative, Solanum pimpinellifolium, is compared, and the two tomato genomes are compared to each other and to the potato genome.
Journal ArticleDOI
The OBO Foundry : coordinated evolution of ontologies to support biomedical data integration
Barry Smith,Michael Ashburner,Cornelius Rosse,Jonathan Bard,William J. Bug,Werner Ceusters,Louis J. Goldberg,Karen Eilbeck,Amelia Ireland,Christopher J. Mungall,Neocles B. Leontis,Philippe Rocca-Serra,Alan Ruttenberg,Susanna-Assunta Sansone,Richard H. Scheuermann,Nigam H. Shah,Patricia L. Whetzel,Suzanna E. Lewis +17 more
TL;DR: This work describes the OBO Foundry initiative and provides guidelines for those who might wish to become involved and describes an expanding family of ontologies designed to be interoperable and logically well formed and to incorporate accurate representations of biological reality.
References
More filters
Journal ArticleDOI
Gene Ontology: tool for the unification of biology
M Ashburner,Catherine A. Ball,Judith A. Blake,David Botstein,Heather Butler,J. M. Cherry,Allan Peter Davis,Kara Dolinski,Selina S. Dwight,J.T. Eppig,Midori A. Harris,David P. Hill,Laurie Issel-Tarver,Andrew Kasarskis,Suzanna E. Lewis,John C. Matese,Joel E. Richardson,M. Ringwald,Gerald M. Rubin,Gavin Sherlock +19 more
TL;DR: The goal of the Gene Ontology Consortium is to produce a dynamic, controlled vocabulary that can be applied to all eukaryotes even as knowledge of gene and protein roles in cells is accumulating and changing.
Journal ArticleDOI
The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003
Brigitte Boeckmann,Amos Marc Bairoch,Rolf Apweiler,Marie-Claude Blatter,Anne Estreicher,Elisabeth Gasteiger,Maria Jesus Martin,Karine Michoud,Claire O'Donovan,Isabelle Phan,Sandrine Pilbout,Michel Schneider +11 more
TL;DR: The SWISS-PROT protein knowledgebase connects amino acid sequences with the current knowledge in the Life Sciences by providing an interdisciplinary overview of relevant information by bringing together experimental results, computed features and sometimes even contradictory conclusions.
Journal ArticleDOI
ArrayExpress—a public repository for microarray gene expression data at the EBI
Helen Parkinson,Ugis Sarkans,Mohammadreza Shojatalab,Niran Abeygunawardena,Sergio Contrino,Richard M.R. Coulson,Anna Farne,Gonzalo Garcia Lara,Ele Holloway,Misha Kapushesky,P. Lilja,Gaurab Mukherjee,Ahmet Oezcimen,Tim F. Rayner,Philippe Rocca-Serra,Anjan Sharma,Susanna-Assunta Sansone,Alvis Brazma +17 more
TL;DR: ArrayExpress is a public repository for microarray data that supports the MIAME (Minimum Informa-tion About a Microarray Experiment) requirements and stores well-annotated raw and normalized data.
Journal ArticleDOI
RefSeq and LocusLink: NCBI gene-centered resources.
Kim D. Pruitt,Donna Maglott +1 more
TL;DR: Together, RefSeq and LocusLink provide a non-redundant view of genes and other loci to support research on genes and gene families, variation, gene expression and genome annotation.
Journal ArticleDOI
The InterPro Database, 2003 brings increased coverage and new features
Nicola Mulder,Rolf Apweiler,Teresa K. Attwood,Amos Marc Bairoch,Daniel Barrell,Alex Bateman,David Binns,Margaret Biswas,Paul Bradley,Peer Bork,Phillip Bucher,Richard R. Copley,Emmanuel Courcelle,Ujjwal Das,Richard Durbin,Laurent Falquet,Wolfgang Fleischmann,Sam Griffiths-Jones,Daniel H. Haft,Nicola Harte,Nicolas Hulo,Daniel Kahn,Alexander Kanapin,Maria Krestyaninova,Rodrigo Lopez,Ivica Letunic,David M. Lonsdale,Ville Silventoinen,Sandra Orchard,Marco Pagni,David Peyruc,Chris P. Ponting,Jeremy D. Selengut,Florence Servant,Christian J. A. Sigrist,Robert M. Vaughan,Evgeny M. Zdobnov +36 more
TL;DR: The latest release of InterPro contains 5629 entries describing 4280 families, 1239 domains, 95 repeats and 15 post-translational modifications, an increase of nearly 15% since the inception of Inter pro.
Related Papers (5)
Gene Ontology: tool for the unification of biology
M Ashburner,Catherine A. Ball,Judith A. Blake,David Botstein,Heather Butler,J. M. Cherry,Allan Peter Davis,Kara Dolinski,Selina S. Dwight,J.T. Eppig,Midori A. Harris,David P. Hill,Laurie Issel-Tarver,Andrew Kasarskis,Suzanna E. Lewis,John C. Matese,Joel E. Richardson,M. Ringwald,Gerald M. Rubin,Gavin Sherlock +19 more