JEnsembl: ArkMAP WebStart Application for Drawing Genetic Maps
The original ArkMAP application using Biomart web services
The ArkMAP desktop application was originally developed to allow users to draw genetic maps held in the ArkDB database system. These maps are provided by web services at ArkDB, which serve up genetic mapping data according to a standard transfer schema. The original ArkMAP application could also download mapping information for Ensembl (vertebrate) gene annotated genome assemblies using the web services hosted at Biomart; it was also possible to query Biomart to retrieve maps for regions of conserved synteny between Ensembl genomes, and information about interspecies homologies. This original application is no longer available.
A refactored ArkMAP application using JEnsembl data access
In order to demonstrate how the JEnsembl API can be integrated directly into Java applications to allow retrieval of mapping data from any Ensembl datasource, we have refactored ArkMAP incorporating JEnsembl. Further details of ArkMAP are available at Roslin Bioinformatics, full user documentation is provided here and the application is available as a Web Start download.
The currently available version of ArkMAP is configured to use the most recent version of the ensembl-config jar artifact to connect to the current datasources available at Ensembl or EnsemblGenomes, giving access to a wider range of Vertebrate, Plant, Fungi, Protist, Metazoan and Bacterial genomes than provided by Biomart web service access. The backwards compatibility of this configuration also allows the application to be modified to retrieve data from releases back to schema version 50. The JEnsembl architecture also allows for updating the ensembl-config artifact as new releases become available. Because the configuration artifact maps release version, data schema, data queries and Java model objects, ArkMAP is protected from schema changes in the datasources. In contrast the original ArkMAP(Biomart) application was vulnerable to any changes in the Biomart schema or web services, and could only provide data from a single (current) Ensembl vertebrates release.
As with the original application, ArkMAP, can query the data source for interspecies homologues of a selected gene, and also now intraspecies homologues. The behaviour to find and draw regions of conserved synteny across genomes is also replicated using the Java API. The implementation of these homology search features in JEnsembl demonstrate the integration of access across both the core and compara datasources to retrieve the homology pair mappings between genes. Furthermore, JEnsembl integration of variation datasources allows maps of dbSNP variants to be aligned with the assembly maps.
Examples in the user documentation illustrate exploration of gene maps downloaded from Ensembl datasources, the discovery of inter-species gene orthologies and the alignment of chromosomes exhibiting regions of conserved synteny as well as the retrieval of SNP variation data. Code snips demonstrating use of the integrated JEnsembl API within ArkMAP are presented here (using an earlier version of ArkMAP).