Bioinformatics with Python Cookbook

Retrieving gene ontology information from Ensembl

In this recipe, we will introduce the usage of gene ontology information again by querying the Ensembl REST API. Gene ontologies are controlled vocabularies to annotate gene and gene products. These are made available as trees of concepts (with more general concepts near the top of the hierarchy). There are three domains for gene ontologies: cellular component, molecular function, and biological process.

Getting ready

As with the previous recipe, we do not require any predownloaded data, but as we are using web APIs, Internet access will be needed. The amount of data transferred will be limited.

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

We will make use of ...