Publish your COVID-19 research data to make it available for the rest of the research community. The data should be deposited in a public repository together with descriptive metadata. For many biological datatypes, there are international databases that can be considered de facto standards.
SciLifeLab (email@example.com) or NBIS (firstname.lastname@example.org) can provide personal consultations for where and how to share data in a public database. Do not hesitate to get in touch with us if you have any questions. Your research group does not have to be affiliated with any particular institution to get our help, we are available to help everyone affiliated with a university in Sweden.
The European Bioinformatics Institute (EBI) hosts many different international data repositories which should be used if appropriate. For further information, see their COVID-19 Data Portal data submission page. For data types where no suitable international repository is available, your data can be deposited to the SciLifeLab Data Repository which is run by the SciLifeLab Data Centre. For human data which needs to be stored in a safe environment with controlled access, SciLifeLab can help with publishing and access control.
Here are our data submission guidelines for each specific data type:
Genomics & transcriptomics data
We suggest that raw virus sequence data as well as assembled and annotated genomes are submitted to ENA. See documentation about submission at SARS-CoV-2 submission. Before submission of raw sequence data (e.g. shotgun sequencing) it is necessary to remove contaminating human reads.
Host (human) sequence data requires restricted access, and NBIS is building a local federated version of the European Genome-phenome Archive (EGA) in Sweden (EGA-SE), allowing for the publication of sensitive personal data within a legal framework. Until local EGA is available, the dataset should remain in the secure analysis environment (e.g., at Bianca on Uppmax). SciLifeLab can help with publishing and access control. In any case, we recommend to make a metadata-only record in the SciLifeLab Data Repository with contact details on how to get access, and for which a DOI (i.e., a persistent identifier) can be issued. The DOI can then be used in the article to refer to the dataset. Once the Swedish EGA is operational, and the dataset is deposited there, the access information can be changed to point to the EGA ID. See DOI: 10.17044/NBIS/G000014 for an example.
- The European Nucleotide Archive (ENA)
- ENA SARS-CoV-2 submission guildelines
- SciLifeLab Data Repostory for metadata records of sequence data with restricted access
We recommend to use the PRIDE repository provided by the ProteomeXchange Consortium. The repository admits protein and peptide identification/quantification data with the accompanying mass spectra evidence and any other related data types. Submission is done using the PX Submission Tool.
Other types of proteomics data should also be made available, we recommend SciLifeLab Data Repository. In order to make the data useful and ready for analyses and integration, a detailed description of the data format and how the variables are organized should be provided. Each protein variable should come with a unique identifier such as UniProt ID or ENGS ID (and stating the versions used to link the data).
- PRIDE repository and PX Submission Tool
- SciLifeLab Data Repository for other types of proteomics data
Depending on the type of image data you have, different public repositories are available, please see the table at BioImage Archive.
We suggest that users submit data to ChEMBL which is a manually curated database of bioactive molecules with drug-like properties run by EMBL-EBI. It brings together chemical, bioactivity and genomic data to aid the translation of genomic information into effective new drugs.
In cases where data cannot be deposited into a public repository due to privacy restrictions we suggest creating a metadata-only record on the SciLifeLab Data Repository with information about what data is available upon request and how such a request can be made. The repository is managed locally by the SciLifeLab Data Centre, and it allows to obtain a DOI which can then be referred to in the publication.
Support for data management planning
SciLifeLab and NBIS can support you with Data Management Planning early on in the project to make data sharing more efficient, both through personal consultations and by providing a customised tool to create Data Management Plans. We can also assist you in identifying relevant repositories and common international standards for describing and publishing your data, as well as guide you through the submission process.
Depositing data in a public repository
By depositing data in a public repository, you accept that the data will be published and may be used and redistributed according to specific terms set by yourself or the repository in question. Data deposition is considered important and you may get credit and acknowledgement for sharing data. A publication often results in getting a unique identifier for your dataset, which is often required for a journal to accept a manuscript for publication. Data sharing is often required by funders.
If required, data can often be published with a set moratorium, which means that data will not go public until a date that you set.
Note that data from human individuals might need special considerations when it comes to publishing.
Storing the data at your university or SNIC
In Sweden, raw measurement data that is generated in a project belongs to the university, while the results are owned by the researcher - the so called teacher’s exception. Unless the data needs protection because of contractual obligations or personal privacy, for example in sensitive personal data such as biomedical measurements of humans, data is considered public.
The university has the legal responsibility to archive the data. Data publishing as supported here is important for the research process, but does not replace the legal responsibility of the university. As a researcher, you are recommended to ensure long term storage of your data in facilities provided by your university. While a project is active, compute and storage services can be provided by Swedish National Infrastructure for Computing, SNIC.