Ensembl Genomes provides a RESTful web service, giving language-independent programmatic access to data including sequences, genes and gene trees, and tools including assembly conversion and variant effect predictors. Full documentation, including extensive code samples, is available at http://rest.ensemblgenomes.org. For vertebrate genomes, use the Ensembl REST service at http://rest.ensembl.org.
This service uses the same code-base (v3.0.0) as the equivalent Ensembl REST service but provides additional endpoints which are described in more detail here. REST (Representational State Transfer) is an increasingly popular paradigm for accessing data remotely over HTTP. For more information, this Wikipedia article is a good place to start.
Note on accessing Compara Data through the Ensembl REST API
Note when using the REST API with Compara end-points such as genetree or homology , the particular compara database to use can be selected using the appropriate compara argument (metazoa, protists, plants, fungi, pan_homology).
For example, to select homologies for a given metazoan gene in the default metazoan compara:
To select gene trees for a given fungal gene in the default fungal compara, use the following form of URL:
To select gene trees for a plant gene in the pan-taxonomic compara, use the following form of URL:
The compara argument applies for any compara-related endpoint.