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How to use BioMart, Ensembl's data retrieval site

Getting a count before you retrieve results

When you take time to build a search in Biomart, it's wise to check your numbers of results before you finalize the search and retrieve the results themselves.

  • Your result count is specific to the dataset you begin with: so if you upload a list of genes, the count will be close to the number of genes in your list.
    • The count does not reflect the number of total features/attributes (rows) retrieved in your data. If you upload a list of genes and select variant attributes, you can retrieve thousands of rows, even if you begin with a few genes.
    • If you see 0 results in the result count, you know that you have set too many limits/filters. Try removing some of your filters and re-checking the count.

Screenshot showing the count of results from a BioMart query


Retrieving results

When you're ready to retrieve your results, click on the Results button above the left selection menu.

Results will initially be displayed in your web browser, but you can export results in a few formats: CSV, TSV, HTML or XLS. TSV is the default. 

Viewing the columns of the file in your web browser is another way to double-check to see if the features you want are included in your results. If they are not, you can always click on the left side menu, in the desired category, and add/remove attributes, then click the results button again to get the new set of results.


Depending on the size of your data request, you can choose to export results immediately to a file or a zipped file, or choose a compressed web file, which will be prepared for you, and you will receive a notification by email when it is ready. When you have set your preferred file type and delivery method, click the Go button.

There is an optional checkbox for "Unique results only". Clicking this box may reduce the size of your file, because it will remove duplicated entries (eg. it will only include one line per unique variant ID), but you will still retrieve many lines of results.