Metadata submission: EGA Webin

EGA Webin

This online tool should be used to submit metadata affiliated to sequence files and should be used to register study, Data Access Committee (DAC) and policy for all array based submissions.

EGA Webin should be sufficient for most submitters.  Large scale submitters of sequence data may wish to submit metadata using XMLS to our REST server.

 

 

Make a complete metadata submission 

Register study, samples, experiments, runs, DAC, policy and dataset/s after file upload.

 

Register components of your metadata submission 

Register study, samples, DAC or policy before uploading files.

 

Edit existing submission metadata

Change or update previously submitted metadata.

 

Make a complete metadata submission (sequences only) 

Ensure that all sequence files have been uploaded to your submission account using the EGA Webin Data Uploader.

Go to the EGA Webin page and log in using your submission account name and password.

 

Register components of your metadata submission

Study - Samples - Data Access Committee (DAC) - Data access policy - Dataset

**Study, Samples, Data Access Committee (DAC) and Data access policy may all be registered BEFORE file upload**

 

Register your Study

  • Go to the New Submission tab
  • Choose Register study (project), click Next and follow the online prompts

To use the study accession number in a publication, we suggest the following format:

"Sequence data has been deposited at the European Genome-phenome Archive (EGA, http://www.ebi.ac.uk/ega/), which is hosted by the EBI, under accession number EGASXXXXXXXXXXX."

 

Register your Samples

All samples should have 'Gender', 'Donor id (Subject id)' and 'Phenotype' attributes.

Gender should be described as 'male', 'female' or 'unknown'.  If 'unknown' due to a known sex chromosome aneuploidy, please create a user defined attribute called 'Sex chromosome karyotype' and add the appropriate value, for example, 'XXY'.

Donor id (Subject id) should be a de-identified subject handle.  If unknown, please add 'unknown' to the field.

Phenotypes should, where possible, be an Experimental Factor Ontology accession.  If a term cannot be found to describe your phenotype please use free text.  All sample phenotypes considered important for further analysis of the data should be provided (for example, tumour type), additional phenotype attributes can be created by defining your own attributes; use the notion 'phenotype2', 'phenotype3', etc.

  • Go to the New Submission tab
  • Choose Register samples and click Next

 

 

 

 

 

  

Register your Data Access Committee (DAC)

Further information on the role of your DAC can be found here.

  • Go to the New Submission tab
  • Choose Register Data Access Committee (DAC)and click Next and follow the online prompts 

 

Register your Data access policy

Your Data access policy provides the terms and conditions of data use, this is also referred to as the Data Access Agreement (DAA).

Completion of a DAA by the applicant/s should form part of the application process to the Data Access Committee (DAC).

  • Go to the New Submission tab
  • Choose Register Data access policy and click Next and follow the online prompts 

 

Submitting your Dataset

The dataset describes the data files, defined by the run (EGARXXXXXXXXXXX) and analysis (EGAZ00000000000) accessions that make up the dataset and links the collection of data files to a specified Data Access Committee and Data access policy.

As a result, you must have registered your Reads and experiments, Data Access Committee (DAC) and Data access policy before submitting your Dataset. 

Please consider the number of datasets that your submission consists of, for example, a case control study is likely to consist of at least two datasets.  In addition, we suggest that multiple datasets should be

described for studies using the same samples but different sequence technologies.  Please contact EGA Helpdesk for further assistance.

  • Go to the New Submission tab
  • Choose Submit Datasetand click Next
  • Select/Register Data Access Committee (DAC) and Data access policy
  • Register your dataset

  • After submitting your dataset you should contact the EGA Helpdesk to provide a release date for your dataset.


Datasets are automatically held (i.e. not released) unless they are affiliated to a study that has already been released.

  

Edit/update existing submission metadata

 

 Please contact the EGA helpdesk if you require further assistance.