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Nucleic Acids Research Advance Access published online on November 15, 2007
Nucleic Acids Research, doi:10.1093/nar/gkm967
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© 2007
The Author(s) This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Database Issue

ORegAnno: an open-access community-driven resource for regulatory annotation

Obi L. Griffith1,*, Stephen B. Montgomery2, Bridget Bernier1, Bryan Chu1, Katayoon Kasaian1, Stein Aerts3, Shaun Mahony4, Monica C. Sleumer1, Mikhail Bilenky1, Maximilian Haeussler5, Malachi Griffith1, Steven M. Gallo6, Belinda Giardine7, Bart Hooghe8, Peter Van Loo3, Enrique Blanco9, Amy Ticoll10, Stuart Lithwick10, Elodie Portales-Casamar10, Ian J. Donaldson11, Gordon Robertson1, Claes Wadelius12, Pieter De Bleser8, Dominique Vlieghe8, Marc S. Halfon6, Wyeth Wasserman10, Ross Hardison7, Casey M. Bergman11, Steven J.M. Jones1 and The Open Regulatory Annotation Consortium{dagger}

1Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 4S6, Canada, 2Wellcome Trust Sanger Institute, CB10 1SA Hinxton, UK, 3VIB Department of Molecular and Developmental Genetics, Katholieke Universiteit Leuven, 3000 Leuven, Belgium, 4Department of Computational Biology, School of Medicine, 3501 Fifth Avenue, University of Pittsburgh, Pittsburgh, PA 15213, USA, 5DEPSN, Institut Alfred Fessard, CNRS, 91198 Gif-sur-Yvette, France, 6New York State Center of Excellence in Bioinformatics and the Life Sciences, Buffalo, NY 14203, 7Center for Comparative Genomics and Bioinformatics, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA, 8VIB Department for Molecular Biomedical Research, Ghent University, 9052 Ghent, Belgium, 9Bioinformatics and Genomics Program, Centre de Regulació Genòmica. Dr Aiguader 88, 08003 Barcelona, Catalonia, Spain, 10Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, BC V5Z 4H4, Canada, 11Faculty of Life Sciences, University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK and 12Department of genetics and pathology, Uppsala University, SE-75185 Uppsala, Sweden

*To whom correspondence should be addressed. Tel: +1 604 707 5900 x. 5401; Fax: +1 604 876 3561; Email: obig{at}bcgsc.ca Correspondence may also be addressed to Stephen Montgomery. Tel: +44 1223 834244 (ext 7297); Fax: +44 1223 494919; Email: sm8{at}sanger.ac.uk; Steven J.M. Jones. Tel: +1 604 877 6083; Fax: +1 604 876 3561; Email: sjones{at}bcgsc.ca

Received September 15, 2007. Revised October 16, 2007. Accepted October 17, 2007.

ORegAnno is an open-source, open-access database and literature curation system for community-based annotation of experimentally identified DNA regulatory regions, transcription factor binding sites and regulatory variants. The current release comprises 30 145 records curated from 922 publications and describing regulatory sequences for over 3853 genes and 465 transcription factors from 19 species. A new feature called the ‘publication queue’ allows users to input relevant papers from scientific literature as targets for annotation. The queue contains 4438 gene regulation papers entered by experts and another 54 351 identified by text-mining methods. Users can enter or ‘check out’ papers from the queue for manual curation using a series of user-friendly annotation pages. A typical record entry consists of species, sequence type, sequence, target gene, binding factor, experimental outcome and one or more lines of experimental evidence. An evidence ontology was developed to describe and categorize these experiments. Records are cross-referenced to Ensembl or Entrez gene identifiers, PubMed and dbSNP and can be visualized in the Ensembl or UCSC genome browsers. All data are freely available through search pages, XML data dumps or web services at: http://www.oreganno.org.

{dagger}The complete list of The Open Regulatory Annotation Consortium members has been listed at the end of the article.

The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors.


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