How to Download Records using the ENA Browser API

The ENA Browser API can be used to download ENA Records in EMBL flat file, fasta or XML format dependant on the record type.

File Format

Available Record Types

XML

Study, Sample, Run, Experiment, Analysis, Taxon

EMBL Flat File (text)
Sequences (including coding and non-coding
sequences), WGS sets, TSA sets

Fasta
Sequences

API End-points

The Browser API has three endpoints for each file format available in the table above. Using the XML file format as an example, below is a summary of how to use these end-points to retrieve data.

XML Records contain metadata provided by the submitter as well as injected cross-reference links to other related resources and FTP locations of associated files.

The three endpoints available to access XML records in the Browser API are as follows:

Fetch Records by Accession

https://www.ebi.ac.uk/ena/browser/api/xml/<accession>

This allows direct access to the XML of a provided accession. The XML file will not be downloaded automatically.

Fetch Records by Free-Text Search

https://www.ebi.ac.uk/ena/browser/api/xml/textsearch/<query>

This will return all records in XML format which match your text search. It can be used to perform very broad searches and is great to quickly access records of a particular datatype. However, be aware that text searches can lead to false positives so for extensive complex and comprehensive searches, it is best to perform an advanced search.

Fetch Records Linked to a Sample, Taxon or Study

https://www.ebi.ac.uk/ena/browser/api/xml/links/<data-type>

This allows you to directly download records associated with a specified Sample, Study or Taxon. You just need to specify which one of the three datatypes you want to download records from (sample, study or taxon) as well as the accession then specify which datatype you would like to download that is related to that record.