Finding orthologues with the Ensembl REST API
In this recipe, we will learn 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 to how to access the Ensembl database using the programmatic API.
In our example, we will try to find any orthologue for the human lactase (LCT) gene on the horse genome.
Getting ready
This recipe will not require any pre-downloaded data, but since we are using web APIs, internet access will be needed. The amount of data that can be 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 in the Chapter05/Orthology.py notebook file.
