Programmatic Interfaces to Plant Genomic Data

The Ensembl Plants and Gramene resources collaborate to develop a common set of genomic databases, but also utilise a common database infrastructure, which provides access to data in a variety of ways, including SQL databases, a Perl Applications Programming Interface (API), a data mining environment implemented using the BioMart technology.  A recent development is a REST-ful API (specified at http://rest.ensemblgenomes.org) to supplement the existing Perl API.  REST stands for representational state transfer, and defines a clear and simple grammar for the construction of web services.  A REST-ful service is invoked through the reference of a specific URL, and typically will return a data in a simple structural format (e.g. JavaScript Object Notation), which can be remodeled into any programming language for downstream analysis (thus, the REST-ful API is language agnostic).  The interface works consistently over all databases utilizing the Ensembl infrastructure (including plant pathogens, pests, pollinators and symbionts).

The Ensembl Genomes REST-ful API supports access to genes, comparative genomics data, assembly mapping, ontologies and taxonomy, cross-references, sequences and variation.  Methods for lookup allow users to explore the contents of the database programmatically to discover content meeting specifications.  In this talk, I will demonstrate the use of the REST-ful API for plant data, highlighting its simplicity and flexibility.