Retrieving gene and genome annotations from BioMart

Once a draft of a genome sequence is prepared, a lot of bioinformatics work goes into finding the genes and other functional features or important loci that are in a genome. These are numerous, difficult to perform and verify, typically take lots of expertise and time, and are not something we would want to repeat. Genome project consortia will typically share their annotations in some way, often through public databases of some sort. BioMart is a common data structure and computational interface through which annotation data is made available. In this recipe, we’ll look at how to programmatically access such databases so we can get annotations for genes that we are interested in.

Getting ready

For this recipe, we’ll need the biomaRt Bioconductor package and a working internet connection. We’ll also need to know the BioMart server to connect to – there are about 40 worldwide, providing information...