How can SciLifeLab help you to publish your human data?
Who can get help? If you are a researcher at a Swedish academic institution working in SciLifeLab’s areas of activity, you can get help from SciLifeLab Data Management support team.
What kind of data publishing can we support?
If your data is located on the Bianca server at UPPMAX (or in the future at local EGA), we can help with the publishing and access requests! If your data is located in your own safe environment, we can not help with the handling of access requests but the to-do steps listed below are still valid.
Until local EGA is ready for both storing and sharing data, currently data can only be shared with PIs that can get a project account set up on Bianca.
This is what you need to do:
- Adjust the Data Access Agreement and Data Access request forms (available from email@example.com) to suit your particular case.
- Store your data in your own project account on Bianca at UPPMAX.
- Prepare a metadata record for the dataset with license “Restricted access” and a clear descriptive text in the SciLifeLab Data Repository. More information regarding accounts and submission can be found here. Do not upload the human data, but DO upload other linked data, such as the article itself and supplemental datasets. If you can not republish the article for licensing reasons, please provide a DOI link to the published article at the journal. Set firstname.lastname@example.org as “access request email” and your own email address as “contact email”. Provide as much descriptive meta data as possible to improve the findability.
- In the manuscript add a section on Data Availability and make sure it includes information on where to go for requesting access to the data. The section in the manuscript can include eg. : “The data is deposited on a secure Swedish server and has been assigned a DOI (XXX). Data access requests may be submitted to the Science for Life Laboratory Data Centre through the DOI link.”
- When a user applies for access to email@example.com, the application will be vetted and you will be contacted by us. Then you can make a decision on access approved or denied. Ideally, you can (should) delegate this decision to an independent Data Access Committee (DAC).
- When a user has been approved for access, Data Centre will document the processing and arrange for the physical file access. Until local EGA is up and running, the physical file access will be that you, as a PI, copies the dataset from your Bianca project space, to the specified project space of the approved applicant. Because of SNIC user policy, only PIs at a Swedish academic institution can have a project at Bianca. So to share data with a collaborator outside Sweden, the PI in Sweden needs to have applied for a project at Bianca. Here is information on how to do this: https://www.uppmax.uu.se/support/user-guides/bianca-user-guide/.
- Data Centre will keep track of current and expired approvals.
Sensitive data in a federated EGA solution
We are working on a federated European Genome-phenome Archive (EGA) solution, where sensitive human genomic and phenotypic data can be stored locally e.g. in Sweden, and the metadata stored centrally at EGA to make the data discoverable. The Swedish node is close, but not yet in a production stage (hopefully later this year). In the meantime we suggest to keep the human sequencing data stored locally as outlined in the process above, and make a metadata-only record in the SciLifeLab Data Repository. Once the Swedish EGA node is operational, and the dataset deposited there, the access information can be changed to point at the EGA ID. See https://doi.org/10.17044/scilifelab.12292778.v1, for an example.
For additional information on sensitive data, see here.
Data Availability and Access
The General Data Protection Regulation (GDPR) requires data processing agreements, and the public genomics archives available in Europe do not enter such agreements. The datasets above will be deposited in a GDPR-compliant local EGA-node as soon as this service is available. Until then, the data is deposited on a secure Swedish server, but regulations by the service provider may make access technically restricted to PIs at Swedish organizations. Data access requests may be submitted to the SciLifeLab Data Centre.
SciLifeLab DataCentre provides a number of scientific resources of national interest. Among these are the Swedish allele frequency database, SweFreq, and data access services for large scale genomic data from SciLifeLab supported sequencing projects.
In 2017, the SweGen project published its findings, “SweGen: a whole-genome data resource of genetic variability in a cross-section of the Swedish population“. The data from this project is available to the scientific community, and this includes access both to aggregate allele frequency data (through the SweFreq database) and full whole-genome sequencing data from 1000 individuals, subject to access control arrangements. SciLifeLab Data Centre manages the access, together with NBIS, SNIC and the SweGen project group. The aggregate data in SweFreq comes with specific access terms but is generally available to the public. Please see these terms here.
Can I get access?
Yes, if the requirements above are fulfilled and if the subject of your study where the data will be used is covered by the informed consent given by the individuals sequenced, and if there is an ethical permission that covers the research project.
How do I get access?
Please use the documents below and send them to firstname.lastname@example.org to apply for access to the datasets or contact us at SciLifeLab Data Centre if you have any questions
The data set connected to the publication “RNA Sequencing Provides Novel Insights into the Transcriptome of Aldosterone Producing Adenomas“. It contains RNA-Seq data from fifteen aldosterone producing adenomas, Whole Genome Sequencing data from two aldosterone producing adenomas and one normal peripheral blood sample. SciLifeLab Data Centre manages the access, together with NBIS, SNIC and the AldoRNAseq project group.
GDPR for life science data
On 25 May 2018, the EU General Data Protection Regulation, GDPR, replaced our Swedish Personal Data Act. The biggest changes were that individuals’ rights are now more strongly protected and the Regulation applies in all EU countries.
The General Data Protection Regulation requires a legal basis for all processing of personal data. Individuals are given greater control over their personal data in various ways. Their right to access data that they have submitted themselves is strengthened, as is the possibility of having information corrected or being forgotten and having information erased. All processing of personal data must comply with the fundamental principles specified in the GDPR.