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Literature DB >> 20885853

The Renal Gene Ontology Annotation Initiative.

Yasmin Alam-Faruque¹, Emily C Dimmer, Rachael P Huntley, Claire O'Donovan, Peter Scambler, Rolf Apweiler.

Abstract

The gene ontology (go) resource provides dynamic controlled vocabularies to aid in the description of the functional attributes and subcellular locations of gene products from all taxonomic groups (www.geneontology.org). A renal-focused curation initiative, funded by Kidney Research UK and supported by the GO Consortium, has started at the European Bioinformatics Institute and aims to provide a detailed GO resource for mammalian proteins implicated in renal development and function. This report outlines the aims of this initiative and explains how the renal community can become involved to help improve the availability, quality and quantity of GO terms and their association to specific proteins.

Entities: Species

Keywords: annotation; biocuration; gene ontology; kidney; renal

Mesh：

Substances：
Proteins

Year: 2010 PMID： 20885853 PMCID： PMC2901810 DOI： 10.4161/org.6.2.11294

Source DB: PubMed Journal: Organogenesis ISSN： 1547-6278 Impact factor: 2.500

24 in total

1. 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

2. A panoramic view of gene expression in the human kidney.

Authors: Danielle Chabardès-Garonne; Arnaud Mejéan; Jean-Christophe Aude; Lydie Cheval; Antonio Di Stefano; Marie-Claude Gaillard; Martine Imbert-Teboul; Monika Wittner; Chanth Balian; Véronique Anthouard; Catherine Robert; Beatrice Ségurens; Patrick Wincker; Jean Weissenbach; Alain Doucet; Jean-Marc Elalouf
Journal: Proc Natl Acad Sci U S A Date: 2003-10-31 Impact factor: 11.205

3. Definition and spatial annotation of the dynamic secretome during early kidney development.

Authors: Gemma Martinez; Kylie Georgas; Grant A Challen; Bree Rumballe; Melissa J Davis; Darrin Taylor; Rohan D Teasdale; Sean M Grimmond; Melissa H Little
Journal: Dev Dyn Date: 2006-06 Impact factor: 3.780

4. Database for renal collecting duct regulatory and transporter proteins.

Authors: John Legato; Mark A Knepper; Robert A Star; Raymond Mejia
Journal: Physiol Genomics Date: 2003-04-16 Impact factor: 3.107

5. Pirfenidone is renoprotective in diabetic kidney disease.

Authors: Satish P RamachandraRao; Yanqing Zhu; Timothy Ravasi; Tracy A McGowan; Irene Toh; Stephen R Dunn; Shinichi Okada; Michael A Shaw; Kumar Sharma
Journal: J Am Soc Nephrol Date: 2009-07-02 Impact factor: 10.121

Review 6. Gene expression profiling analysis in nephrology: towards molecular definition of renal disease.

Authors: Yoshinari Yasuda; Clemens D Cohen; Anna Henger; Matthias Kretzler
Journal: Clin Exp Nephrol Date: 2006-06 Impact factor: 2.617

7. The mouse Gene Expression Database (GXD): 2007 update.

Authors: Constance M Smith; Jacqueline H Finger; Terry F Hayamizu; Ingeborg J McCright; Janan T Eppig; James A Kadin; Joel E Richardson; Martin Ringwald
Journal: Nucleic Acids Res Date: 2006-11-27 Impact factor: 16.971

8. An ontology for cell types.

Authors: Jonathan Bard; Seung Y Rhee; Michael Ashburner
Journal: Genome Biol Date: 2005-01-14 Impact factor: 13.583

9. The Gene Ontology's Reference Genome Project: a unified framework for functional annotation across species.

Authors:
Journal: PLoS Comput Biol Date: 2009-07-03 Impact factor: 4.475

10. QuickGO: a web-based tool for Gene Ontology searching.

Authors: David Binns; Emily Dimmer; Rachael Huntley; Daniel Barrell; Claire O'Donovan; Rolf Apweiler
Journal: Bioinformatics Date: 2009-09-10 Impact factor: 6.937

8 in total

1. The UniProt-GO Annotation database in 2011.

Authors: Emily C Dimmer; Rachael P Huntley; Yasmin Alam-Faruque; Tony Sawford; Claire O'Donovan; Maria J Martin; Benoit Bely; Paul Browne; Wei Mun Chan; Ruth Eberhardt; Michael Gardner; Kati Laiho; Duncan Legge; Michele Magrane; Klemens Pichler; Diego Poggioli; Harminder Sehra; Andrea Auchincloss; Kristian Axelsen; Marie-Claude Blatter; Emmanuel Boutet; Silvia Braconi-Quintaje; Lionel Breuza; Alan Bridge; Elizabeth Coudert; Anne Estreicher; Livia Famiglietti; Serenella Ferro-Rojas; Marc Feuermann; Arnaud Gos; Nadine Gruaz-Gumowski; Ursula Hinz; Chantal Hulo; Janet James; Silvia Jimenez; Florence Jungo; Guillaume Keller; Phillippe Lemercier; Damien Lieberherr; Patrick Masson; Madelaine Moinat; Ivo Pedruzzi; Sylvain Poux; Catherine Rivoire; Bernd Roechert; Michael Schneider; Andre Stutz; Shyamala Sundaram; Michael Tognolli; Lydie Bougueleret; Ghislaine Argoud-Puy; Isabelle Cusin; Paula Duek-Roggli; Ioannis Xenarios; Rolf Apweiler
Journal: Nucleic Acids Res Date: 2011-11-28 Impact factor: 16.971

2. The impact of focused Gene Ontology curation of specific mammalian systems.

Authors: Yasmin Alam-Faruque; Rachael P Huntley; Varsha K Khodiyar; Evelyn B Camon; Emily C Dimmer; Tony Sawford; Maria J Martin; Claire O'Donovan; Philippa J Talmud; Peter Scambler; Rolf Apweiler; Ruth C Lovering
Journal: PLoS One Date: 2011-12-09 Impact factor: 3.240

3. AIGO: towards a unified framework for the analysis and the inter-comparison of GO functional annotations.

Authors: Michael Defoin-Platel; Matthew M Hindle; Artem Lysenko; Stephen J Powers; Dimah Z Habash; Christopher J Rawlings; Mansoor Saqi
Journal: BMC Bioinformatics Date: 2011-11-03 Impact factor: 3.169

4. Representing kidney development using the gene ontology.

Authors: Yasmin Alam-Faruque; David P Hill; Emily C Dimmer; Midori A Harris; Rebecca E Foulger; Susan Tweedie; Helen Attrill; Douglas G Howe; Stephen Randall Thomas; Duncan Davidson; Adrian S Woolf; Judith A Blake; Christopher J Mungall; Claire O'Donovan; Rolf Apweiler; Rachael P Huntley
Journal: PLoS One Date: 2014-06-18 Impact factor: 3.240