Literature DB >> 12654719

The Gene Ontology Annotation (GOA) project: implementation of GO in SWISS-PROT, TrEMBL, and InterPro.

Evelyn Camon1, Michele Magrane, Daniel Barrell, David Binns, Wolfgang Fleischmann, Paul Kersey, Nicola Mulder, Tom Oinn, John Maslen, Anthony Cox, Rolf Apweiler.   

Abstract

Gene Ontology Annotation (GOA) is a project run by the European Bioinformatics Institute (EBI) that aims to provide assignments of terms from the Gene Ontology (GO) resource to gene products in a number of its databases (http://www.ebi.ac.uk/GOA). In the first stage of this project, GO assignments have been applied to a data set representing the complete human proteome by a combination of electronic mappings and manual curation. This vocabulary has also been applied to the nonredundant proteome sets for all other completely sequenced organisms as well as to proteins from a wide range of organisms where the proteome is not yet complete.

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Year:  2003        PMID： 12654719      PMCID： PMC430163          DOI： 10.1101/gr.461403

Source DB:  PubMed          Journal:  Genome Res        ISSN： 1088-9051            Impact factor:   9.043


  29 in total

1.  The ENZYME database in 2000.

Authors:  A Bairoch
Journal:  Nucleic Acids Res       Date:  2000-01-01       Impact factor: 16.971

2.  RefSeq and LocusLink: NCBI gene-centered resources.

Authors:  K D Pruitt; D R Maglott
Journal:  Nucleic Acids Res       Date:  2001-01-01       Impact factor: 16.971

3.  CluSTr: a database of clusters of SWISS-PROT+TrEMBL proteins.

Authors:  E V Kriventseva; W Fleischmann; E M Zdobnov; R Apweiler
Journal:  Nucleic Acids Res       Date:  2001-01-01       Impact factor: 16.971

4.  The PROSITE database, its status in 2002.

Authors:  Laurent Falquet; Marco Pagni; Philipp Bucher; Nicolas Hulo; Christian J A Sigrist; Kay Hofmann; Amos Bairoch
Journal:  Nucleic Acids Res       Date:  2002-01-01       Impact factor: 16.971

5.  The Protein Data Bank: unifying the archive.

Authors:  John Westbrook; Zukang Feng; Shri Jain; T N Bhat; Narmada Thanki; Veerasamy Ravichandran; Gary L Gilliland; Wolfgang Bluhm; Helge Weissig; Douglas S Greer; Philip E Bourne; Helen M Berman
Journal:  Nucleic Acids Res       Date:  2002-01-01       Impact factor: 16.971

6.  Predicting gene ontology functions from ProDom and CDD protein domains.

Authors:  Jonathan Schug; Sharon Diskin; Joan Mazzarelli; Brian P Brunk; Christian J Stoeckert
Journal:  Genome Res       Date:  2002-04       Impact factor: 9.043

7.  Creating the gene ontology resource: design and implementation.

Authors: 
Journal:  Genome Res       Date:  2001-08       Impact factor: 9.043

8.  The EMBL Nucleotide Sequence Database: major new developments.

Authors:  Guenter Stoesser; Wendy Baker; Alexandra van den Broek; Maria Garcia-Pastor; Carola Kanz; Tamara Kulikova; Rasko Leinonen; Quan Lin; Vincent Lombard; Rodrigo Lopez; Renato Mancuso; Francesco Nardone; Peter Stoehr; Mary Ann Tuli; Katerina Tzouvara; Robert Vaughan
Journal:  Nucleic Acids Res       Date:  2003-01-01       Impact factor: 16.971

9.  PROSITE: a documented database using patterns and profiles as motif descriptors.

Authors:  Christian J A Sigrist; Lorenzo Cerutti; Nicolas Hulo; Alexandre Gattiker; Laurent Falquet; Marco Pagni; Amos Bairoch; Philipp Bucher
Journal:  Brief Bioinform       Date:  2002-09       Impact factor: 11.622

10.  The EBI SRS server--recent developments.

Authors:  Evgeni M Zdobnov; Rodrigo Lopez; Rolf Apweiler; Thure Etzold
Journal:  Bioinformatics       Date:  2002-02       Impact factor: 6.937
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  130 in total

1.  Genome evolution reveals biochemical networks and functional modules.

Authors:  Christian von Mering; Evgeny M Zdobnov; Sophia Tsoka; Francesca D Ciccarelli; Jose B Pereira-Leal; Christos A Ouzounis; Peer Bork
Journal:  Proc Natl Acad Sci U S A       Date:  2003-12-12       Impact factor: 11.205

2.  E-MSD: an integrated data resource for bioinformatics.

Authors:  A Golovin; T J Oldfield; J G Tate; S Velankar; G J Barton; H Boutselakis; D Dimitropoulos; J Fillon; A Hussain; J M C Ionides; M John; P A Keller; E Krissinel; P McNeil; A Naim; R Newman; A Pajon; J Pineda; A Rachedi; J Copeland; A Sitnov; S Sobhany; A Suarez-Uruena; G J Swaminathan; M Tagari; S Tromm; W Vranken; K Henrick
Journal:  Nucleic Acids Res       Date:  2004-01-01       Impact factor: 16.971

3.  The Gene Ontology (GO) database and informatics resource.

Authors:  M A Harris; J Clark; A Ireland; J Lomax; M Ashburner; R Foulger; K Eilbeck; S Lewis; B Marshall; C Mungall; J Richter; G M Rubin; J A Blake; C Bult; M Dolan; H Drabkin; J T Eppig; D P Hill; L Ni; M Ringwald; 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; D Botstein; K Dolinski; B Feierbach; T Berardini; S Mundodi; S Y Rhee; R Apweiler; D Barrell; E Camon; E Dimmer; V Lee; R Chisholm; P Gaudet; W Kibbe; R Kishore; E M Schwarz; P Sternberg; M Gwinn; L Hannick; J Wortman; M Berriman; V Wood; N de la Cruz; P Tonellato; P Jaiswal; T Seigfried; R White
Journal:  Nucleic Acids Res       Date:  2004-01-01       Impact factor: 16.971

4.  TrSDB: a proteome database of transcription factors.

Authors:  Antoni Hermoso; Daniel Aguilar; Francesc X Aviles; Enrique Querol
Journal:  Nucleic Acids Res       Date:  2004-01-01       Impact factor: 16.971

5.  OntoBlast function: From sequence similarities directly to potential functional annotations by ontology terms.

Authors:  Günther Zehetner
Journal:  Nucleic Acids Res       Date:  2003-07-01       Impact factor: 16.971

6.  Divergence in the spatial pattern of gene expression between human duplicate genes.

Authors:  Kateryna D Makova; Wen-Hsiung Li
Journal:  Genome Res       Date:  2003-07       Impact factor: 9.043

7.  PANDORA: keyword-based analysis of protein sets by integration of annotation sources.

Authors:  Noam Kaplan; Avishay Vaaknin; Michal Linial
Journal:  Nucleic Acids Res       Date:  2003-10-01       Impact factor: 16.971

8.  GOblet: a platform for Gene Ontology annotation of anonymous sequence data.

Authors:  Detlef Groth; Hans Lehrach; Steffen Hennig
Journal:  Nucleic Acids Res       Date:  2004-07-01       Impact factor: 16.971

9.  Functional annotation of the Arabidopsis genome using controlled vocabularies.

Authors:  Tanya Z Berardini; Suparna Mundodi; Leonore Reiser; Eva Huala; Margarita Garcia-Hernandez; Peifen Zhang; Lukas A Mueller; Jungwoon Yoon; Aisling Doyle; Gabriel Lander; Nick Moseyko; Danny Yoo; Iris Xu; Brandon Zoeckler; Mary Montoya; Neil Miller; Dan Weems; Seung Y Rhee
Journal:  Plant Physiol       Date:  2004-06-01       Impact factor: 8.340

10.  The Gene Ontology Annotation (GOA) Database: sharing knowledge in Uniprot with Gene Ontology.

Authors:  Evelyn Camon; Michele Magrane; Daniel Barrell; Vivian Lee; Emily Dimmer; John Maslen; David Binns; Nicola Harte; Rodrigo Lopez; Rolf Apweiler
Journal:  Nucleic Acids Res       Date:  2004-01-01       Impact factor: 16.971
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