Submitting to ENA

SeqDesk automates the submission process to the European Nucleotide Archive. This page covers the step-by-step submission workflow.

Submission Process

Prepare the study

Ensure all validation requirements are met. Mark the study as ready for submission.

Submit the study

The facility admin initiates submission from the study page or the ENA Submissions page (/submissions). The system:

Generates Study XML with title, description, and project attributes
Generates Submission XML (the wrapper for ENA’s API)
Sends a multipart POST to ENA’s submit endpoint
Parses the receipt XML for accession numbers

On success, the study receives a studyAccessionId (format: PRJEB...).

Submit samples

After the study is registered, each sample is submitted:

Sample XML is generated with alias, title, taxonomy, and MIxS metadata
The XML includes all required sample attributes with values and units
Each sample is submitted to ENA
Accession numbers are stored:
- sampleAccessionNumber (format: ERS...)
- biosampleNumber (format: SAMEA...)

Track accession numbers

All accession numbers are stored on the corresponding records and visible in the study detail page.

XML Generation

SeqDesk generates ENA-compliant XML for each entity type:

Study XML


<PROJECT_SET>
  <PROJECT alias="my-study-alias">
    <TITLE>Study Title</TITLE>
    <DESCRIPTION>Study description...</DESCRIPTION>
    <SUBMISSION_PROJECT>
      <SEQUENCING_PROJECT/>
    </SUBMISSION_PROJECT>
  </PROJECT>
</PROJECT_SET>

Sample XML


<SAMPLE_SET>
  <SAMPLE alias="HG001">
    <TITLE>Human Gut Sample 1</TITLE>
    <SAMPLE_NAME>
      <TAXON_ID>408170</TAXON_ID>
      <SCIENTIFIC_NAME>human gut metagenome</SCIENTIFIC_NAME>
    </SAMPLE_NAME>
    <SAMPLE_ATTRIBUTES>
      <SAMPLE_ATTRIBUTE>
        <TAG>geographic location (country)</TAG>
        <VALUE>Germany</VALUE>
      </SAMPLE_ATTRIBUTE>
      <!-- Additional MIxS fields -->
    </SAMPLE_ATTRIBUTES>
  </SAMPLE>
</SAMPLE_SET>

ENA API Endpoints

Environment	URL
Test	`https://wwwdev.ebi.ac.uk/ena/submit/drop-box/submit/`
Production	`https://www.ebi.ac.uk/ena/submit/drop-box/submit/`

Requests use HTTP Basic authentication with your Webin credentials and multipart form data containing the XML files.

Submission Tracking

Each submission creates a record in the Submission table:

Field	Description
Submission Type	STUDY, SAMPLE, READ, ASSEMBLY, or BIN
Status	PENDING, SUBMITTING, ACCEPTED, REJECTED, or ERROR
XML Content	The generated XML for debugging
Response	ENA’s response for reference
Receipt XML	The full receipt from ENA
Accession Numbers	Returned accession IDs (JSON)
Error Message	Human-readable error if submission failed

Bulk Submission

For studies with many samples, SeqDesk supports bulk submission:

All samples are validated first
Samples are submitted in batches
Progress is tracked per sample
Failed samples can be retried individually

Test vs Production

Feature	Test Mode	Production
Server	wwwdev.ebi.ac.uk	www.ebi.ac.uk
Data persistence	24 hours	Permanent
Accession numbers	Valid format but temporary	Permanent public accessions
Purpose	Validation and testing	Real submissions

Always validate with test mode before submitting to production. Test submissions expire after 24 hours and do not create permanent records.