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The distributed annotation system.

Dowell RD, Jokerst RM, Day A, Eddy SR, Stein L - BMC Bioinformatics (2001)

Bottom Line: Any client or server adhering to the DAS XML specification can participate in the system; we describe a simple prototype client and server example.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Howard Hughes Medical Institute and Department of Genetics, Washington University, St. Louis, MO 63110 USA. robin@genetics.wustl.edu

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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DasView A screen-shot of the current version of DasView. The view is on Chromosome II of WormBase.
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Figure 3: DasView A screen-shot of the current version of DasView. The view is on Chromosome II of WormBase.

Mentions: We have developed two prototype DAS client programs. One, called Geodesic, is a stand alone Java application. It connects to one or more DAS servers, retrieves annotations, and displays them in an integrated map, as seen in Figure 2. The other, called DasView, is a Perl application that runs as a server-side script. It connects to one or more DAS servers, constructs an integrated image, and serves the image to a web browser as a set of click-able image map, as seen in Figure 3.


The distributed annotation system.

Dowell RD, Jokerst RM, Day A, Eddy SR, Stein L - BMC Bioinformatics (2001)

DasView A screen-shot of the current version of DasView. The view is on Chromosome II of WormBase.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC58584&req=5

Figure 3: DasView A screen-shot of the current version of DasView. The view is on Chromosome II of WormBase.
Mentions: We have developed two prototype DAS client programs. One, called Geodesic, is a stand alone Java application. It connects to one or more DAS servers, retrieves annotations, and displays them in an integrated map, as seen in Figure 2. The other, called DasView, is a Perl application that runs as a server-side script. It connects to one or more DAS servers, constructs an integrated image, and serves the image to a web browser as a set of click-able image map, as seen in Figure 3.

Bottom Line: Any client or server adhering to the DAS XML specification can participate in the system; we describe a simple prototype client and server example.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Howard Hughes Medical Institute and Department of Genetics, Washington University, St. Louis, MO 63110 USA. robin@genetics.wustl.edu

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/.

Show MeSH