ArkDB arose initially from the needs of a project co-ordinated at Roslin Institute to map the pig genome. The original intention was to utilise the Jackson Laboratory's then current mouseGBASE database design, and this was actually implemented for pigs, chickens and sheep. However, it soon became clear that the nature of genome mapping in farmed animal Species differed significantly from the methods and population types employed in mouse genetics. These differences meant that the schema we had didn't fit our data requirements and the decision was taken to develop our own database system.
Because we needed a system that would work for all of the Species that we work with at Roslin, we tried to make the design as generic as possible. We believe that we managed to strike a balance between generalisation and utility. However, the technologies that were available to us then were not as advanced or as maintainable as we might have liked. In addition, genetics and genomics research continued to develop and we found that we had a system that had reached the end of its useful life.
The decision was taken to redesign and rewrite the entire system in a more flexible fashion. The new system is written in java with a well-defined object model and clean separation between the database schema and the model. Consequently, our map Drawing code is independent of the underlying schema and can be used to draw data from other systems. The ArkDB code is open source and available on request.
We have also sought to model the relationships between markers and sequences in a more flexible fashion. This will allow us to extend the system to operate across multiple data sources pertainng to multiple Species and to utilise the power of comparative genomics to address the challenges of identifying candidate genes for trait and disease phenotypes.
Recently we have made the ArkDB data accessible using web services, which provide data according to a well defined XML schema. For more information on the ArkDB webservices, and our data transfer schema please visit ArkDBWS.
We are using these web services as the datasource for ArkMAP our new downloadable Map Drawing application. This tool is being developed to allow integration of mapping data from other web service providers, beginning with ENSEMBL Biomart.
For more information on the ArkDB database system, please contact us using the link at the bottom of this page.