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Bovine Genome Database: supporting community annotation and analysis of the Bos taurus genome

Justin T Reese12, Christopher P Childers2, Jaideep P Sundaram2, C Michael Dickens1, Kevin L Childs13, Donald C Vile2 and Christine G Elsik12*

Author Affiliations

1 Department of Animal Science, Texas A&M University, College Station, TX 77843 USA

2 Department of Biology, Georgetown University, Washington, DC 20057 USA

3 Department of Plant Biology, Michigan State University, 166 Plant Biology Building, East Lansing, MI 48824, USA

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BMC Genomics 2010, 11:645  doi:10.1186/1471-2164-11-645

Published: 19 November 2010

Abstract

Background

A goal of the Bovine Genome Database (BGD; http://BovineGenome.org webcite) has been to support the Bovine Genome Sequencing and Analysis Consortium (BGSAC) in the annotation and analysis of the bovine genome. We were faced with several challenges, including the need to maintain consistent quality despite diversity in annotation expertise in the research community, the need to maintain consistent data formats, and the need to minimize the potential duplication of annotation effort. With new sequencing technologies allowing many more eukaryotic genomes to be sequenced, the demand for collaborative annotation is likely to increase. Here we present our approach, challenges and solutions facilitating a large distributed annotation project.

Results and Discussion

BGD has provided annotation tools that supported 147 members of the BGSAC in contributing 3,871 gene models over a fifteen-week period, and these annotations have been integrated into the bovine Official Gene Set. Our approach has been to provide an annotation system, which includes a BLAST site, multiple genome browsers, an annotation portal, and the Apollo Annotation Editor configured to connect directly to our Chado database. In addition to implementing and integrating components of the annotation system, we have performed computational analyses to create gene evidence tracks and a consensus gene set, which can be viewed on individual gene pages at BGD.

Conclusions

We have provided annotation tools that alleviate challenges associated with distributed annotation. Our system provides a consistent set of data to all annotators and eliminates the need for annotators to format data. Involving the bovine research community in genome annotation has allowed us to leverage expertise in various areas of bovine biology to provide biological insight into the genome sequence.