A Database of Drosophila Genes & Genomes

FB2014_02, released March 18th, 2014
 

A more frequent FlyBase update cycle

This year, we adopted a regular and frequent schedule of database updates. We are happy to report that FlyBase has successfully maintained release cycle intervals between 4-6 weeks and plans to maintain this schedule in the future. We encourage users to make note of the release version when using data from FlyBase, and to facilitate this, have made the current version more conspicuous. You will find it in red at the top as well as centered on the bottom of each page. The current FlyBase version, FB2008_07 (released August 8, 2008), represents the seventh release of 2008.

Since FlyBase now includes genome annotation data for a dozen Drosophila species, this new database release version is no longer equivalent to the D. melanogaster genome/annotation release descriptor. For each of the sequenced genomes, every FlyBase release maintains a single genome assembly and annotation set and these are listed in the Release Notes. The assembly and annotations are denoted in, respectively, the prefix and suffix of a species' release descriptor. For example, FlyBase version FB2008_07 contains a third iteration of annotations on the second assembly of the D. pseudoobscura genome (i.e., Dpse R2.3). D. melanogaster is already on its tenth revised annotation set of genome assembly release 5 (i.e., Dmel R5.10). In GBrowse, the relevant genome annotation release descriptor is displayed in the header and is also indicated in the Data Source menu. Older assemblies and annotation sets can be accessed from the Genomes FTP Archive.

We note that while this higher turnover achieves the goal of providing our users with more immediate access to new data, it also exacerbates issues of subsequent retrieval of web-based data, and can make tracking changes in large data sets more difficult. A quantitative summary of the current database release is found in the Release Notes, accessed from the Documents drop-down menu. Previous release notes (since 2006) can be accessed from the Archived data page, listed under the Files menu. Selected past releases are available for immediate access while access to other releases may be obtained by contacting FlyBase.

While each database release usually includes gene model annotation changes in D. melanogaster, annotations changes in the other species will be much less frequent. For D. melanogaster, updated submissions to GenBank are scheduled at approximately 6-month intervals. Thus, the most recent changes to gene model annotations will not be reflected in data from GenBank. Please contact FlyBase if you have further questions about the content of our regular releases.