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WormBase in the era of comparative genomics: Model Organism Databases and the challenges of multiple species
Todd W. Harris1 and Lincoln D. Stein1.
2005. International C. elegans meeting, UCLA.
1 Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
WormBase offers many features that make it an attractive system for comparative genomics: periodic referential software and data freezes, scriptable access through feature-rich programming interfaces, a publically accessible data mining server, and user-friendly graphical interfaces. With the addition of three additional genomes in 2005, the case for WormBase as a platform for comparative genomics is even more compelling.

Research areas such as comparative genomics are fueling requests for genome-wide data. To meet these requests, WormBase has added new graphical tools, released a new programmatic interface, and simplified the process of building a local installation.

Graphical data mining tools at WormBase continue to evolve in response to user requests. For example, the RNAi phenotype search is now limitable by data set or by genetic or physical map position and the Batch Genes script can fetch orthology data. The most significant new graphical tool at WormBase is the recent introduction of WormMart, a highly flexible interface for retrieving annotations and sequences.

We continue to expand options for users wising to programmatically access the resource, most recently with the release of the Perl Bio::GMOD module. Bio::GMOD aims to provide a unified programmatic interface to model organism databases. Thus, scripts written to fetch all of the genes from WormBase can seamlessly execute the same task at FlyBase regardless of differences in the data model or naming conventions. Furthermore, Bio::GMOD insulates end users from the complexity of the data model by translating common queries into one appropriate for the current schema. WormBase continues to offer direct programmatic access to the underlying databases through the AcePerl and Bio::DB::GFF modules, as well as providing a publically accessible data mining server at aceserver.cshl.org.

We have also made it possible to run WormBase locally in your lab or university through a greatly simplified installation and update procedure. Local installations do not suffer from network latency, are less susceptible to server load, can be accessed with the WormBase data mining modules, and support viewing of local annotations side-by-side with the core WormBase data.