Chado controller: advanced annotation management with a community annotation system.

TitleChado controller: advanced annotation management with a community annotation system.
Publication TypeJournal Article
Year of Publication2012
AuthorsGuignon, Valentin, Droc Gaëtan, Alaux Michael, Baurens Franc-Christophe, Garsmeur Olivier, Poiron Claire, Carver Tim, Rouard Mathieu, and Bocs Stéphanie
JournalBioinformatics (Oxford, England)
Volume28
Pagination1054-6
Date Published2012 Apr 1
ISSN1367-4811
KeywordsComputational Biology, Database Management Systems, Genomics, Molecular Sequence Annotation, Software, Vocabulary, Controlled
Abstract

SUMMARY: We developed a controller that is compliant with the Chado database schema, GBrowse and genome annotation-editing tools such as Artemis and Apollo. It enables the management of public and private data, monitors manual annotation (with controlled vocabularies, structural and functional annotation controls) and stores versions of annotation for all modified features. The Chado controller uses PostgreSQL and Perl.

AVAILABILITY: The Chado Controller package is available for download at http://www.gnpannot.org/content/chado-controller and runs on any Unix-like operating system, and documentation is available at http://www.gnpannot.org/content/chado-controller-doc The system can be tested using the GNPAnnot Sandbox at http://www.gnpannot.org/content/gnpannot-sandbox-form

CONTACT: valentin.guignon@cirad.fr; stephanie.sidibe-bocs@cirad.fr

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

DOI10.1093/bioinformatics/bts046
Alternate JournalBioinformatics