Federating access to wheat data services for efficient genome-specific marker design

Lead Research Organisation: Earlham Institute
Department Name: UNLISTED

Abstract

The objectives of this proposal will build on the Grassroots infrastructure that researchers at EI have developed as part of EI's contribution to the Wheat Initiative Wheat Information System (http://wheatis.org/). We will develop this infrastructure as a complement to and aggregator of other wheat data services. We will enhance the ability of researchers and breeders to utilise wheat genomic resources by providing a uniform decentralised access for rigorous discovery of suitable markers for primer design:

API assessment of existing wheat data resources and development of integration code for data querying, retrieval, and processing
We will assess APIs for Ensembl Plants, CerealsDB, Phytozome, GnpIS, and document their input and output data types as a measure of interoperability. We will develop open source code to query and retrieve the raw responses of these services. Secondly, the PolyMarker tool is used to allow researchers to build KASP markers quickly, based on genomic reference sequences. Polymarker has a web interface, but will need extension and improvement to interact with the software layers.

Extending existing tools to handle appropriate API requests and responses for service and data aggregation
We will implement an existing and commonly-used standard JSON interchange format so that we can parse and suitably convert the responses made by the services to automated queries, and therefore link up the services quickly and effectively.

Expose workflow to researchers through Grassroots Genomics
We will integrate outputs of the project into the Grassroots infrastructure, representing a reusable and reproducible framework that others can build on for their own purposes. We will simplify and streamline access to the workflow and primer design tools through a common and intuitive user interface, that we will host through the Grassroots Genomics portal to fulfill the necessary researcher and breeder user requirements for automated marker-guided primer design.

Publications

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