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. 2012;7(9):e44180.
doi: 10.1371/journal.pone.0044180. Epub 2012 Sep 13.

MyDas, an extensible Java DAS server

Gustavo A Salazar  1 , Leyla J García, Philip Jones, Rafael C Jimenez, Antony F Quinn, Andrew M Jenkinson, Nicola Mulder, Maria Martin, Sarah Hunter, Henning Hermjakob
Affiliations

MyDas, an extensible Java DAS server

Gustavo A Salazar et al. PLoS One. 2012.

Abstract

A large number of diverse, complex, and distributed data resources are currently available in the Bioinformatics domain. The pace of discovery and the diversity of information means that centralised reference databases like UniProt and Ensembl cannot integrate all potentially relevant information sources. From a user perspective however, centralised access to all relevant information concerning a specific query is essential. The Distributed Annotation System (DAS) defines a communication protocol to exchange annotations on genomic and protein sequences; this standardisation enables clients to retrieve data from a myriad of sources, thus offering centralised access to end-users.We introduce MyDas, a web server that facilitates the publishing of biological annotations according to the DAS specification. It deals with the common functionality requirements of making data available, while also providing an extension mechanism in order to implement the specifics of data store interaction. MyDas allows the user to define where the required information is located along with its structure, and is then responsible for the communication protocol details.

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Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.

Figures

Figure 1
Figure 1. Flow of information in DAS.
Interaction between a DAS client and the different DAS servers (i.e. Registry, Reference and Data Source).
Figure 2
Figure 2. MyDas Architecture.
The requesters can interact with MyDas through the servlet, which communicates the commands to the Controller. The Controller knows which Data Sources have been implemented by querying the Configuration Manager. Data Sources should implement at least one of the provided Interfaces. MyDas internally implements the DAS model.
Figure 3
Figure 3. A MyDas Source as displayed on the Ensembl client.
The data source created during the MyDas tutorials as it is visualised on the Ensembl web browser.
See this image and copyright information in PMC

References

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