Programmatic submissions (XML based)

EGA supports programmatic sequence and analysis (vcf/phenotype/aligned BAM) metadata submissions. Metadata validation and accessioning takes place immediately during the submission. A receipt with corresponding accessions is provided upon successful submission.

The production service is available here:

https://www.ebi.ac.uk/ena/submit/webin/

The test service is available here:

https://wwwdev.ebi.ac.uk/ena/submit/webin/

Submitters are advised to explore the test service before submitting for the first time. The test service is identical to the production service except that all submissions will be discarded on the following day.

Authentication

Submitters are authenticated each time a submission is made. The submission service uses HTTPS protocol for metadata encryption and secure identification to provide a confidential submission environment.

Data file upload

Data files must be uploaded to your submission account before they may be validated using this servlce. More information on uploading your read data is available by here.

The metadata model contains the following xml objects:

Study: information about the sequencing study

Samples: Information about the sequencing samples

Experiment: information about the libraries, platform; associated with study, sample(s) and run(s)

Analysis: contains the analysis data files; associated with study and sample objects

Run: The run submission holds information about the files containing the raw reads generated in a run of sequencing

DAC: contains information about the Data Access Committee (DAC)

Policy: contains the Data Access Agreement (DAA); associated with DAC

Dataset: contains the collection of runs/analysis data files to be subject to controlled access; associated with Policy

Submission: information about the submission actions (such as ADD or VALIDATE and PROTECT to specify an EGA submission)

The Submission, Study, Sample, Experiment, Run and Analysis objects share the same schema as those used by the European Nucleotide Archive (ENA) for open and public submissions.

DAC, policy and dataset are objects that are unique to the EGA and are used to define and describe the submission controlled access requirements.

Link to the latest xml object schemas and documentation 

Further information about working with XML

Further information on preparing your EGA xmls

Programmatic Submission Tutorial Video

Please take a look at the Programmatic Submission Tutorial Video, which explains the workflow of a programmatic submission and goes over an example metadata submission.