Frequently asked questions

This FAQ is for researchers, data stewards, research support functions, and Swedish organisations considering whether to use or onboard with FEGA Sweden.

Questions on this page

General

Organisational onboarding

Submission

Data Access

Discovery

General

What is FEGA Sweden?

FEGA Sweden is the Swedish node of the Federated European Genome-phenome Archive (FEGA). It provides infrastructure and support for submission, storage, discovery, and controlled access to sensitive human research data for which Swedish research organisations are responsible.

See About FEGA Sweden for more background.

Is FEGA Sweden only for data from Swedish research organisations?

FEGA Sweden is primarily intended for sensitive human research data for which a Swedish research organisation is responsible.

The researchers involved in a project do not all need to be based in Sweden. International collaborators can be involved, and researchers outside Sweden may request access to datasets. Organisational onboarding and submission are handled with the Swedish organisation responsible for the data and its governance.

Is FEGA Sweden suitable for sensitive personal data?

Yes. FEGA Sweden is designed for sensitive human research data that require controlled access, including data that may constitute personal data or sensitive personal data.

The organisation responsible for the data must still confirm that the planned submission and data sharing are permitted under the relevant legal, ethical, and governance conditions. This includes GDPR requirements, ethical approval, participant information, and any confidentiality rules that apply to the data.

Is FEGA Sweden free to use?

Yes. FEGA Sweden is currently offered free of charge to organisations and researchers.

If this changes in the future, we will update the information on this website and inform affected organisations through the established contact routes.

Why use FEGA Sweden rather than EGA directly?

EGA, the European Genome-phenome Archive, is the European infrastructure for discovery and controlled access to sensitive human research data.

For Swedish organisations, FEGA Sweden is normally the recommended route into the EGA ecosystem for sensitive human research data that require controlled access. FEGA Sweden is not a separate alternative to EGA, but the Swedish national route for submission, storage, metadata support, and support for controlled access.

Using FEGA Sweden means that data are stored within Sweden and handled through legal, administrative, and operational arrangements agreed with the Swedish organisation. Public metadata are still indexed in EGA and made discoverable on the EGA website.

The SUHF guidance on external repositories (in Swedish) does not rule out EGA in all situations, but treats EGA as an example of a repository with an international organisation as its governing body. For research data that include personal data or information subject to confidentiality rules, the guidance points to particular caution with such repositories. This is one reason why FEGA Sweden is usually the more appropriate first route for Swedish organisations.

Why use FEGA Sweden instead of a general institutional repository?

For sensitive human biomedical research data that require controlled access, FEGA Sweden is usually a better fit because it is a domain-specific repository built for this type of data.

Institutional repositories can be useful for many research outputs and datasets, but they are often broad services for many disciplines. FEGA Sweden supports the metadata, review, discovery, and controlled-access workflows expected for sensitive biomedical data. The FEGA Sweden team can support submitters with metadata review, public dataset descriptions, and links between studies, samples, experiments, analyses, and controlled-access files.

Public metadata are indexed in EGA and made discoverable on the EGA website, where many biomedical researchers look for this type of data, as well as on Researchdata.se.

Who should I contact for support?

Please contact the FEGA Sweden Helpdesk for questions about FEGA Sweden, onboarding, submission, or data access.

How quickly can I expect a response?

For general questions and submission requests, you can normally expect an initial response within one week.

The full timeline for a submission or access request may vary depending on the data, documentation, review process, and organisational arrangements.

Organisational onboarding

What does organisational onboarding mean?

Organisational onboarding is the process of establishing the legal, administrative, and operational arrangements needed before a Swedish organisation can complete data submissions through FEGA Sweden in a secure and workable way.

This includes agreeing roles, contacts, procedures, and relevant compliance arrangements ahead of the organisation’s first submission.

See Onboarding organisations for the full overview.

Which organisations should consider organisational onboarding?

Swedish organisations responsible for sensitive human research data should consider organisational onboarding if they want to enable submission and controlled data sharing through FEGA Sweden.

This may include universities, biobanks, healthcare-linked research organisations, and other research organisations that need a controlled-access route for sensitive biomedical data.

What are the benefits for my organisation?

Organisational onboarding gives a Swedish organisation a practical and consistent route for making sensitive human research data available for controlled reuse while retaining control over access conditions and access decisions.

Benefits include:

  • secure national infrastructure for large volumes of sensitive research data
  • a domain-specific repository for biomedical data, with metadata support that general institutional repositories usually do not provide
  • public metadata indexed in EGA and made discoverable on the EGA website and Researchdata.se
  • agreed roles and processes for submission and access handling
  • better organisational oversight of submissions and access workflows

Using FEGA Sweden can help an organisation offer researchers a consistent way to handle controlled data sharing instead of setting up separate solutions for each project.

How is information security handled?

FEGA Sweden is designed for sensitive human research data that require controlled access.

Before an organisation can complete submissions through FEGA Sweden, legal, administrative, and operational arrangements need to be in place. Submitted files are encrypted before upload and stored and backed up on secure servers in Sweden.

Public metadata can be made findable through EGA, but access to sensitive data files is controlled and requires approval by the depositing institution. Approved files are made available for secure download and encrypted so that only the approved recipient can decrypt them.

If your organisation needs to assess FEGA Sweden from an information security, legal, or compliance perspective, please contact the FEGA Sweden Helpdesk. We can help identify the relevant documentation and contacts.

What does organisational onboarding cover?

Organisational onboarding usually covers:

  • roles and points of contact for submission and access handling
  • governance and operational procedures
  • legal and compliance alignment, including a Data Processing Agreement (DPA) where applicable
  • practical support for a first submission

The exact setup depends on the organisation, the data, and the local governance process.

What responsibilities remain with the organisation?

The organisation responsible for the data remains responsible for data governance, ethical and legal compliance, access conditions, and access decisions.

FEGA Sweden provides infrastructure, support, and operational processes for submission, storage, discovery, and controlled access. However, FEGA Sweden does not take over the organisation’s responsibility for ensuring that the data can be shared under the relevant ethical approval, participant information, legal basis, confidentiality rules, and local governance procedures.

Does having a Data Processing Agreement mean that an organisation is onboarded?

Not necessarily. A Data Processing Agreement is often part of organisational onboarding, but it does not by itself mean that the organisation is ready to complete submissions through FEGA Sweden.

Full onboarding also requires agreed roles, contacts, and operational procedures for submission and access handling.

See Onboarding organisations and Complying with GDPR.

Who should contact FEGA Sweden about onboarding?

A suitable first contact is usually someone at the Swedish organisation with responsibility for research data management, legal coordination, data protection, infrastructure, or support for researchers who need to share sensitive human data.

Individual researchers are also welcome to contact us. If organisational onboarding is needed, we can help identify the relevant next steps and contacts.

Can a researcher create a submission request before the organisation is onboarded?

Yes. A researcher can contact us or create a submission request before organisational onboarding has been completed.

This can help clarify whether FEGA Sweden is the right archive, what preparations are needed, and whether onboarding needs to be started with the organisation responsible for the data.

Research data can only be uploaded if onboarding is in progress and the Swedish organisation responsible for the data approves the upload. The organisation still needs to be onboarded before a full submission workflow can be completed.

How can an organisation get started with onboarding?

Contact the FEGA Sweden team to discuss organisational onboarding.

It is helpful to include what type of organisation you represent, what kind of data or submissions you expect, and whether there is a concrete first submission that can be used as a practical starting point.

Contact the team

Submission

What data can I submit to FEGA Sweden?

FEGA Sweden is intended for sensitive human research data that require controlled access.

This includes genetic, genomic, phenotypic, and related biomedical research data. If you are unsure whether FEGA Sweden is suitable for your data, see Is FEGA Sweden the right archive? for guidance.

Can I submit data that does not require controlled access?

Usually not. If your data can be shared openly, another repository may be a better fit. FEGA Sweden is designed for data where access needs to be reviewed and approved before files are made available.

Will my data be made available to other researchers when I submit it?

Not immediately. Submitting data to FEGA Sweden does not by itself make the research data available to other researchers.

During submission, uploaded research data are transferred to and stored by FEGA Sweden’s host organisation, Uppsala University. In this context, Uppsala University acts as a data processor on behalf of the depositing institution, which is typically the data controller.

Access to the data is provided only later, if an access request is approved by the depositing institution.

See Complying with GDPR and the Data access overview.

Does my organisation need to be onboarded before data can be uploaded?

Not necessarily before you contact us or create a submission request. Research data can only be uploaded if onboarding is in progress and the Swedish organisation responsible for the data approves the upload.

The organisation still needs to be onboarded before a full submission workflow can be completed.

See Onboarding organisations and Is my organisation onboarded?.

How do I get started with a submission?

Start with the Pre-submission checklist to see what you need before submitting data.

When you are ready, create a submission request so that the FEGA Sweden team can assess your case and guide you through the next steps.

When should I start the submission process?

Start as early as possible once you know that the data will need to be deposited under controlled access. You do not need to wait until a journal asks for accession numbers.

Early contact gives time to confirm that FEGA Sweden is the right archive, check organisational onboarding, prepare metadata, upload files, and handle any revisions needed before the submission can be finalised in the Submitter Portal.

If you expect to need accession numbers for a manuscript, it is best to create a submission request well before journal submission or acceptance.

What should I prepare before submitting data?

You should identify the files to submit, confirm that FEGA Sweden is the right archive, check organisational onboarding, review GDPR and ethics requirements, prepare your data files, and collect the required metadata.

The Pre-submission checklist links to the detailed preparation pages.

What if my ethical approval or participant information does not mention FEGA Sweden?

If your existing ethics documentation was written without data sharing through FEGA Sweden in mind, the responsible organisation should assess whether the planned submission and future data sharing are covered by the existing documentation.

This assessment may depend on how access to the data will be handled, who may receive access, and whether data may be shared with recipients in Sweden or in another country. FEGA Sweden can help identify issues that may need attention, but the research project and the organisation responsible for the research need to decide what measures are required.

Depending on the situation, this may involve consulting local legal, data protection, or research support functions, or applying for a renewal of the ethical approval.

See Ethical approval for more information.

What can I write in participant information about data sharing and FEGA Sweden?

Participant information should explain that research data may be made available for future research under controlled access, and that each access request will be assessed before access to data is granted.

For Swedish ethical review applications, FEGA Sweden provides example wording that can be adapted for the section describing what will happen to participants’ data. The wording should be reviewed in the context of the specific research project, the planned data sharing, and the responsible organisation’s local requirements.

See Ethical approval for example wording and important limitations.

How long does a submission take?

The time needed for a submission can vary a lot. In straightforward cases, where the data are well documented, the data controller is clear, and it is clear how the data should be organised into datasets, a submission can normally be processed within a few weeks.

It can take longer if metadata or documentation need to be clarified, if the dataset structure or access conditions need further discussion, or if legal or organisational arrangements are not yet in place. FEGA Sweden can only complete submissions for onboarded organisations, so submissions that require organisational onboarding can take considerably longer.

Large data volumes can also affect the process, but upload time is normally not the main factor determining the overall timeline.

When you create a submission request, FEGA Sweden will normally send an initial response within one week.

When will I get accession numbers for my submitted data?

EGA accession numbers for the Study and Dataset become available when the descriptive metadata are complete and the submission has been finalised in the Submitter Portal.

Public metadata can remain on hold until the agreed metadata release date. During this period, the accession numbers can be used in a manuscript, but other researchers cannot yet request access through EGA. Access requests become possible only after the public metadata have been published and the data are findable on the EGA website.

If you need accession numbers for a manuscript or journal deadline, please mention this in your submission request or contact the FEGA Sweden Helpdesk.

Does FEGA Sweden provide DOIs for submitted data?

No. FEGA Sweden does not provide DOIs for submitted data. Instead, submitted studies and datasets receive EGA accession numbers.

EGA accession numbers can be used as persistent identifiers to cite and refer to submitted data. Persistent URLs can also be created through identifiers.org, for example:

  • https://identifiers.org/ega.study:{insert EGA Study ID}
  • https://identifiers.org/ega.dataset:{insert EGA Dataset ID}

For example, the dataset accession EGAD50000002120 can be written as:

https://identifiers.org/ega.dataset:EGAD50000002120

Some journals or funders may use the term DOI when they mean a persistent identifier more generally. If a journal specifically requires a DOI, we recommend checking with the journal whether an EGA accession number and identifiers.org URL are acceptable.

What can I write in my manuscript’s data availability statement?

Many journals require a data availability statement explaining where the data are stored and how researchers can request access.

If your data have been submitted to FEGA Sweden and assigned an EGA Study ID, you can state that the data have been submitted to FEGA Sweden and are findable through the European Genome-phenome Archive website. The statement should also explain that access is controlled and granted only after approval according to the applicable access conditions.

If your submission is still in progress, you can state that work on submitting the data to FEGA Sweden has been initiated. In that case, it can also be useful to create a public metadata record describing the data.

See Data availability statement for suggested wording.

Data Access

How do I request access to a dataset?

To request access, go to the relevant dataset page on the EGA website and follow the instructions there. The depositing institution reviews the request and decides whether access should be granted, using the decision process it has established for the dataset.

See the Data access overview for the full process.

Do I need an EGA account to request access?

It depends on the access procedure chosen by the organisation that deposited the data.

The dataset landing page on the EGA website should explain how to request access. If the organisation uses EGA’s system for handling access requests, the person requesting access needs to create an EGA account.

Can access be granted to researchers outside Sweden?

It depends on the access conditions and review process set by the organisation that deposited the data.

Researchers outside Sweden may request access to datasets in FEGA Sweden, but access is granted only if the request is approved by the organisation that deposited the data. Some organisations or datasets may have access conditions that limit where data can be shared.

How long does it take to process an access request?

The time needed to process an access request can vary. In straightforward cases, it may take a few weeks.

Access decisions are made by the depositing institution, not by FEGA Sweden. The timeline depends on the organisation’s access review process, the documentation needed for the request, and whether any legal, ethical, or practical questions need to be clarified before access can be granted.

Once access has been approved and the requester has sent us their public Crypt4GH key, FEGA Sweden can normally make the approved files available for secure download within a few days.

What is a Data Access Committee in a Swedish context?

In the EGA system, a Data Access Committee (DAC) is the function associated with a dataset that handles access requests. In Sweden, however, DAC is not a specific legal concept.

FEGA Sweden leaves it to the depositing institution to decide how access requests should be assessed and decided. The decision does not have to be made by a formal committee, even though the term Data Access Committee includes the word “committee”.

At Swedish public authorities, such as Swedish universities, disclosure decisions are normally made according to the organisation’s delegation of authority. If a request concerns disclosure of confidential information containing sensitive personal data, an individual confidentiality and harm assessment must be made before access to data can be granted.

Who decides whether access is granted?

Access decisions are made by the depositing institution, not by FEGA Sweden. The depositing institution decides which internal function or role is responsible for assessing access requests and making disclosure decisions. Access requests can be rejected if they do not meet the access conditions or cannot be approved under the organisation’s review process.

FEGA Sweden supports the secure delivery of approved data once the access process has been completed.

How do I download approved files?

After access has been approved, FEGA Sweden prepares encrypted copies of the approved files. Before downloading them, you need to prepare your system by installing the required download tool and generating a Crypt4GH key pair.

See Prepare for download for step by step instructions.

Who should I contact if I have problems downloading or decrypting files?

If your access request has been approved but you have problems downloading or decrypting the approved files, please contact the FEGA Sweden Helpdesk.

Discovery

Where can I find datasets available through FEGA Sweden?

The most common way for researchers to find data in FEGA Sweden is through the EGA website, where researchers can search and browse studies and datasets.

Datasets are also described on the FEGA Sweden catalogue, where dataset pages link onward to the corresponding EGA record on the EGA website where applicable. In addition, FEGA Sweden datasets are listed on Researchdata.se, the national research data portal, where public metadata can also be discovered.

Can I see metadata before requesting access?

Yes. Public metadata can be viewed before requesting access and can help you assess whether a dataset is relevant for your research.

The sensitive data files themselves are not available for direct download; access to files requires an approved access request according to the access conditions for the dataset.