About ArkDB

The ArkDB database system aims to provide a comprehensive public repository for genome mapping data from farmed and other animal Species. In doing so, we aim to provide a route in to genomic and other sequence from the initial viewpoint of linkage mapping, RH mapping, physical mapping or - possibly more importantly - QTL mapping data.

This system represents a complete rewrite of the original version with the code migrated to java and the underlying database targeted at postgres (although any standards-compliant database engine should suffice). The ArkDB code is open source and available and documented at arkdb/code.

ArkDB records details of maps and the markers that they contain. There are alternative entry points that target either a chromosome or a specific mapping analysis as the starting point (via the Species table or Maps menu respectively). Limited relationships between markers are recorded and displayed.

As with our previous version, all maps are drawn using data extracted from the database "on the fly". In this version, the maps are drawn using Java Applet technology. You will therefore need a java-enabled web browser in order to view maps. We are now also providing ArkMAP a downloadable map drawing application for your desktop - that can connect directly to both ArkDB and Ensembl. ArkMAP provides a more fully featured and flexible drawing interface than the Applet, and allows links between maps in ArkDB and those in the Ensembl genome projects to be visualized.

The ArkMAP application uses Web Services that we have implemented for ArkDB, which are available and documented at ArkDBWS, and the Ensembl Biomart Web Services.

We are working to extend the functionality of the system, particularly the ArkMAP tool, adding further details about the markers and adding relationships between markers and genomic sequences. If you have specific features that you would like us to implement sooner rather than later or to ask for more information on the ArkDB database system, please contact us using the link at the bottom of this page.