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ArkDB Web Service Access

About ArkDB Web Services

The Genomic Data in the Ark Database Web Application may be downloaded in bulk in XML format using these Web Services. Downloaded XML Data conforms to a simple XML schema GenomicMappingData.xsd. Documentation for this data exchange format is available at GMD schema documentation. A related schema GenomicDataRelationships.xsd that defines relationship types that are imported into gmd DataSets is documented at GDR schema documentation. We are hosting an interactive WIKI where documentation of our Genomic Mapping Data transfer schema can be found and where interested users in the mapping community can discuss and suggest evolution or extension of the schema. We have published a description of the GMD schema and the use of ArkDB Web Services in Taverna workflows (BMC Bioinformatics 2009, 10:252).

A number of WebServices are available, with autogenerated individual service WSDLs exposed here. The service ArkWebServices.wsdl aggregates all the individual services in a single service descriptor. The methods called via these WebServices allow data to be retrieved using query by species name, chromosome name or object id etc.

These autogenerated service WSDLs do not specify that the returned data conforms to the XML schema. A further WSDL aggregating all of the services, and specifying that the data returned is XSD Conformant is found at ArkWebServicesTyped.wsdl. This WSDL can be used in preference to the autogenerated WSDLs in order to facilitate programmatic parsing of the retuned Data.

For example ArkWebServicesTyped.wsdl can be scavenged by the Taverna Workflow WSDL Scavenger, and the XSD-typed output parsed using Taverna's XML Parser ("XML Splitter"). This allows workflows to be assembled using the result from one query (i.e. the database identifier of a genomic object) as the query input of a subsequent WebService query in a workflow. Taverna workflows can also be constructed allowing integration of the ArkDB data with third party services (such as NCBI PubMed and GenBank).

The ArkDB WebServices are exposed via Codehaus XFire and the ArkDB service class JAR is available to provide the service interfaces for WebService Client Development. Please note that some queries retrieving large amounts of data may take a long time to run, and service requests should be sent using HTTP1.1.

We are now providing ArkMAP a desktop java application for drawing maps that you can download from our Roslin Bioinformatics site. ArkMAP connects to both the ArkDB and ENSEMBL databases (Ensembl and EnsemblGenomes) to retrieve and draw available maps, allowing users to explore the links (e.g. gene orthologies) between markers on different maps.

the GMD transfer schema GenomicMappingData.xsd (v1.0)
the GDR schema defining data relationships GenomicDataRelationships.xsd (v1.0)
GMD schema documentation v1.0 doc
GMD reference BMC Bioinformatics 2009, 10:252
GDR schema documentation v1.0 doc
GMD Transfer Schema WIKI WIKI
webervices access point ArkDB webservice WSDLs
aggregated service WSDL ArkWebServices.wsdl
GMD conformant aggregated WSDL ArkWebServicesTyped.wsdl
ArkDB service classes for developers Java jar library
ArkDB Map Drawing Application ArkMAP
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