Finding orthologues with the Ensembl REST API

Here, we will see how to look for orthologues for a certain gene. This simple recipe will not only introduce orthology retrieval, but also how to use REST APIs on the Web to access biological data. Last but surely not least, it will serve as an introduction on how to access the Ensembl database using the programmatic API.

In our example, we will try to find any orthologue for the human lactase gene (LCT) on the horse genome.

Getting ready

This recipe will not require any pre-downloaded data, but as we are using the web APIs, Internet access will be needed. The amount of data transferred will be limited.

We will also make use of the requests library to access Ensembl. The request API is an easy-to-use wrapper for web requests. Of course, you can use the standard Python libraries, but these are much more cumbersome.

As usual, you can find this content on the 02_Genomes/Orthology.ipynb notebook.

How to do it...

Let's take a look at the following steps...