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. 2001:2:7.
doi: 10.1186/1471-2105-2-7. Epub 2001 Oct 10.

The distributed annotation system

R D Dowell  1 , R M Jokerst, A Day, S R Eddy, L Stein
Affiliations

The distributed annotation system

R D Dowell et al. BMC Bioinformatics. 2001.

Abstract

Background: Currently, most genome annotation is curated by centralized groups with limited resources. Efforts to share annotations transparently among multiple groups have not yet been satisfactory.

Results: Here we introduce a concept called the Distributed Annotation System (DAS). DAS allows sequence annotations to be decentralized among multiple third-party annotators and integrated on an as-needed basis by client-side software. The communication between client and servers in DAS is defined by the DAS XML specification. Annotations are displayed in layers, one per server. Any client or server adhering to the DAS XML specification can participate in the system; we describe a simple prototype client and server example.

Conclusions: The DAS specification is being used experimentally by Ensembl, WormBase, and the Berkeley Drosophila Genome Project. Continued success will depend on the readiness of the research community to adopt DAS and provide annotations. All components are freely available from the project website http://www.biodas.org/.

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Figures

Figure 1
Figure 1
Basic distributed annotation system architecture One server is the designated reference server, in this case the Washington University Genome Sequencing Center. One or more annotation servers, shown above as Ensembl, Whitehead, and the Sean Eddy Laboratory, provide annotations relative to the reference sequence. The client, at Cold Spring Harbor Laboratory in our example, fetches data from multiple servers and automatically generates an integrated view.
Figure 2
Figure 2
Geodesic A screen-shot of the current version of Geodesic. The view is on clone ZK154 using sources from the C. elegans test server set.
Figure 3
Figure 3
DasView A screen-shot of the current version of DasView. The view is on Chromosome II of WormBase.
See this image and copyright information in PMC

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