Preparing data

This page provides optional practical guidance for preparing files. You can use it before or after creating a submission request. For repository suitability and supported data types, see Is FEGA Sweden the right repository?.

FEGA Sweden follows the European Genome-phenome Archive (EGA) metadata model and submission structure. You can visit the EGA website to learn more about how to prepare files for different data types.

Start with a file overview

Before you start the technical upload steps, it can be useful to create a simple overview of the files you plan to submit. FEGA Sweden does not require a separate file overview before you create a submission request, but having one can make later submission work and communication with the FEGA Sweden Helpdesk easier.

Useful information to collect

  • a list of the files that should be included
  • the file type or data type for each file
  • stable file names that can be referenced consistently in metadata
  • a short description of each file type or group of similar files
  • information about which samples, experiments, or analyses each file relates to
  • an initial idea of which files should belong to the same dataset

For metadata about the study, samples, experiments, and analyses, see Preparing metadata.

For submissions with many files of the same type, you do not need a separate free-text description for every file. It is often enough to describe the file groups, naming pattern, and how the files relate to samples, experiments, or analyses.

Avoid putting sensitive information in public file names or public metadata. Sensitive phenotype information that cannot be shared openly should be submitted as data rather than entered as public metadata.

Plan your dataset grouping

A dataset is the unit through which access is requested. Files in the same dataset must have compatible access conditions.

Group files so that each dataset can be made available to the widest appropriate range of researchers. For example, data with different disease-specific or ethical restrictions will normally need to be placed in separate datasets.

If you are unsure how to group your files, the FEGA Sweden Helpdesk can advise you during the submission process.