- Course overview
- Search within this course
- Why Ensembl?
- What is Ensembl?
- When to use Ensembl
- How to access Ensembl
- How to search Ensembl
- How to search Ensembl
- How to search Ensembl
- Exploring sources of biological data
- Navigating Ensembl
- Customise Ensembl
- Manage your data
- Export data
- Download data with BioMart
- Bulk download genome-wide data files with FTP
- Ensembl tools
- Summary
- Guided examples of using Ensembl
- Exercises
- Your feedback
- Get help and support on Ensembl
- Acknowledgements
- Learn more
All materials are free cultural works licensed under a Creative Commons Attribution 4.0 International (CC BY 4.0) license, except where further licensing details are provided.
Download data with BioMart
Much of Ensembl’s data can be quickly exported in text format, as an Excel table, or as FASTA sequences through the BioMart interface (Video 15).
BioMart allows you to:
- ‘Translate’ one ID type into another (for example, an Ensembl gene ID to an NCBI RefSeqID;
- Export data in different formats, including: html, csv, tsv and xls (Excel) file types;
- Quickly generate tables of information.
You can use the ‘Biomart’ link at the top of every Ensembl page to access BioMart (Figure 45).
Database. You can choose the database you are interested in. In our example, we have selected the Ensembl genes database, version 113.
Dataset. You can choose the dataset you want to access. In our example we chose the Human data set.
Options. Apply filters on the data set in order to select a set of genes of interest. Attributes allow you to select output options. Addtional datasets can be combined in your query as an advanced function.
 This tutorial is a good guide for getting started. You can also view the Ensembl FAQs page. |