BioMart
BioMart is a feature of Ensembl that allows users to download table formatted results from all of Ensembl's various source databases. The BioMart is very useful for accessing sequences, variant data, regulation data and gene or protein information without using the browser.
Access BioMart from the top menu of any Ensembl page. Click the BioMart link.
Use the drop-down menus in the page to first
- choose your database (Ensembl Genes, Variants, Regulation or Vega)
- then your dataset (species)
Once you've done that, you're ready to select your filters and your output attributes. Click on the Filters menu on the left. The center portion of the page will populate with expandable menus that allow you to set your filters. Depending on which database you start with, the Filters will be different, as will the Attributes.
Be careful when filtering: if you set too many filters, you will retrieve too few results. If you don't set any filters, the database will take a long time to retrieve your results. When you're done setting your filters, click on the Attributes menu on the left (your filter choices will be entered as you select them).
You have many choices for attributes. These will be the columns of your output file. Enter all the features in which you are interested from the radio buttons at the top and the expandable menus.
After you have selected your attributes, you have the option to select data from a second Database. This is useful for variants, if you want to have more attributes than you are allowed if you start with the Ensembl Variants database.
When you have made all your selections, you can test your query by clicking on the Count button at the top of the left menu. This will tell you how many results you will retrieve from your selected database(s). If they are too many or too few, you can try re-selecting your filters. When you want to see the output, click on the Results button.
- Change the numbers of rows viewable
- Export to a file (CSV, TSV, HTML, XML)
- See your query as Perl, XML, bookmarkable URL
BioMart has a vast array of features, so it may take some time getting used to using it. Try different queries with different types of filters and output attributes. It's immensely useful for getting multi-feature files.