Integrate and share your data

The EBRAINS data curation process involves several steps to ensure that datasets, computational models, and software are properly annotated with metadata and can be easily discovered and reused by the research community.

Request curation FAIR Guiding Principles

Publish your data in a high-profile online resource for neuroscience data, models and software
Receive metadata management support in line with the FAIR data principles
Integration of the data in the EBRAINS Knowledge Graph via community-driven metadata standards and ontologies
Compatible with other EBRAINS services, including visualisation tools and analysis workflows
Receive a citable DOI for your work

How to integrate and share your data?

EBRAINS ensures the data received is properly annotated throughout the curation process and meets the necessary data sharing and reuse standards. By offering this service, EBRAINS aims to increase the visibility of scientific work and support the advancement of neuroscience research.

The Data Curation team is continuously expanding the metadata ontology to enable registration of more detailed metadata. Therefore, it will be possible to add more in-depth metadata also after data have been released, which again will improve the level of FAIRness.

EBRAINS strive to share data in accordance with the FAIR guiding principles, aiming to make data: Findable, accessible, interoperable and reusable.

learn more

The EBRAINS data curation service

Neuroscientific data - experimental or simulated data, models, or software - are multimodal, heterogeneous, and organised in many ways. Although most of these data use similar terms and concepts, it can be challenging to standardise them without losing each data type's study-specific aspects. The process of organising, categorising and integrating data is called data curation. Data curation allows the data to be found, compared and/or reused by other researchers. The EBRAINS Curation Services support you in this process. Together, we will advance Open Science by making data FAIR.

Open data are shared without restrictions on data reuse to promote transparency, accelerate scientific research, and encourage new collaborations. In some cases, there may be legitimate reasons to shield data from the public, such as protecting sensitive data (e.g., safeguarding subjects' privacy) and reducing the risk of being scooped by others. The “A” in the FAIR Data Guiding Principles (Wilkinson et al., 2016) stands for “Accessible under well-defined conditions”. The goal is to strive to make data “as open as possible, and as closed as necessary”, ensure that the data are safeguarded and prevent misuse without compromising the possibility of reuse.

What is open data and EBRAINS data sharing

EBRAINS has clear guidelines on how data are shared. We ensure that all data are accompanied by licenses to allow for such restrictions; we have several options for releasing data under embargo until a scientific article is accepted for publication; and we safeguard data via our access control solutions for sensitive human data.

The FAIR guiding principles also serve to guide researchers in preparing data for data sharing and managing data and metadata appropriately. The EBRAINS data curation service follows the FAIR principles in the curation of data and supports researchers and scientific publishers in their endeavours to improve the Findability, Accessibility, Interoperability, and Reusability (FAIRness) of their data.

How we make data FAIR

The FAIRness of data depends on the amount of information that is shared, what format it is shared in, and the number of connections that can be made with other existing data. EBRAINS offers two levels of FAIR data curation that meet the needs of any researcher. Regardless of which track the researcher chooses, all data and metadata are integrated into the EBRAINS Knowledge Graph (KG).

The KG is a powerful semantic network developed to bring together information from different fields and illustrate their relationships. The KG is a graph database in which data, models, and software are integrated, and it is a powerful tool for connecting datasets to software, analysis and visualisation tools.

All research products that are shared via EBRAINS are curated, a process in which important information, better known as metadata, is extracted and integrated into the KG. To give structure to metadata, we rely on metadata schemas that describe how metadata relate to each other. EBRAINS has adopted the flexible, scalable and extendable openMINDS metadata framework. openMINDS is grounded in standardised terminologies and ontologies, increasing the interoperability of datasets, models and software in the EBRAINS KG and with resources outside of the EBRAINS research infrastructure. openMINDS is continuously developing to accommodate curation-specific needs for particular research areas. One example of such an extension is SANDS. The SANDS extension was developed to enable the standardisation of anatomical locations of neuroscience data, both semantically using names of brain regions, and spatially via coordinates, allowing datasets to be linked to the atlases hosted by EBRAINS.

The Knowledge Graph contains heterogeneous data, annotated with extensive domain-specific metadata. Data can be extracted via two ways that are tailored to the ability and preference of the user. The intuitive search user interface (UI) offers a low-threshold option for any researcher. The search UI has filters that allow the user to refine their search based on data type, research modalities, methods, species, data accessibility, and keywords. For the advanced user, data and metadata can be accessed via an Application Programming Interface (API) compatible with many programming languages, enabling a versatile downstream implementation of search queries.

for scientific authors

Publish your dataset alongside a journal publication

More and more journals require a data availability statement on how data can be found and reused. EBRAINS caters to the needs of journal authors wishing to share data related to a manuscript submission to a peer-reviewed journal.

We offer several solutions for sharing your data alongside a manuscript, with various levels of accessibility that can help with the peer-review process whilst keeping the data secure.

For example, we can provide temporary access to the dataset for reviewers, without making the data publicly available until the paper is published. Data can also be released under embargo, which allows others to find the dataset, but restricts them from using the data, until the paper is accepted.

All datasets curated and stored through EBRAINS will receive a DOI and are released to the public, making your dataset a published, citable resource.

If you are in the process of submitting your dataset for publication along with a manuscript for a peer-reviewed journal, you have the three options outlined below. In option 1 (recommended) you publish your dataset via EBRAINS and use the assigned DOI to reference your dataset in your manuscript. However, datasets can be withheld from public access for a specified time period to be determined on a case by case basis (e.g., the review period of a peer-reviewed journal) in options 2 and 3. During this period you may still grant the reviewers of your manuscript access to your dataset through a temporary and private URL. All datasets curated and stored at EBRAINS will be released to the public with a DOI once the article has been accepted for publication.

Select the use case that applies to your data best:

Allow public visibility and access to your dataset (you will receive a DOI) before your paper has been published

You may choose to publish your dataset on EBRAINS before submitting your manuscript to a journal. Submit your dataset using the EBRAINS curation request form. Once your dataset is ready for publication, a DOI will be issued that links to the landing page where the dataset is described and the dataset is accessible to the public. The author must ensure this DOI is referenced in the corresponding publication so the dataset is properly linked to the paper.

Allow the public to view the metadata but not the dataset before your paper has been published

You may choose to make your dataset discoverable - but not accessible - on EBRAINS before submitting your manuscript to a journal. To select this option, submit your dataset using the EBRAINS curation request form and request an embargo period until your publication is accepted. After your dataset is curated and stored at EBRAINS, the metadata for the dataset will be described on a landing page (and thus have a URL during the embargo period). You may request a temporary and private URL to allow reviewers to have access to your dataset during the review process. Your dataset will be released to the public and assigned a DOI after the embargo period ends.

The detailed steps are as follows:

a. Upon completion of the curation process, the metadata for the dataset will be published on its EBRAINS landing page. In addition, the author will be provided with a temporary and private URL (not discoverable for search engines) providing access to the dataset.

b. The author will submit his/her paper to the chosen peer-reviewed journal along with the URL for their landing page and the temporary URL to the dataset. This temporary URL will grant the journal’s editor and reviewers access to the embargoed dataset during the whole review period.

c. During the review process, modifications may be requested by editors and/or reviewers. Modifications must be requested by the author via our ticketing system (curation-support@ebrains.eu).

d. Once the paper is accepted for publication and in the proof-read stage, the author needs to notify the assigned curator that the dataset is ready to be released on EBRAINS together with the (in press) citation details. At this juncture, the embargo will be removed, a DOI will be assigned and the dataset will be accessible to the public via EBRAINS. The author must ensure this DOI is referenced in the corresponding publication so the dataset is properly linked to the paper.

e. Once the paper is published, the author must notify the assigned curator of the full citation for the journal article to be included in their EBRAINS landing page. If the published paper is a data paper (e.g., articles in Scientific Data), it may be used to replace the data descriptor on the EBRAINS landing page.

Neither the dataset nor metadata are visible to the public until your paper has been published

Request that your dataset be withheld from public access until your journal article is published. To select this option, submit your dataset using the EBRAINS curation request form and request an embargo period until your publication is accepted. After your dataset is curated and stored at EBRAINS, you will receive a temporary and private URL to grant the reviewers of your manuscript access to your dataset during the review process. Your dataset will be released to the public and assigned a DOI when your article has been accepted for publication.

The detailed steps are as follows:

a. Upon completion of the curation process, the author will be provided with a temporary and private URL (not discoverable for search engines) providing access to the dataset.

b. The author will submit his/her paper to the chosen peer-reviewed journal along with the** temporary URL** to the dataset. This temporary URL will grant the journal’s editor and reviewers access to the embargoed dataset during the whole review period.

c. During the review process, modifications may be requested by editors and/or reviewers. Modifications must be requested by the author via our ticketing system (curation-support@ebrains.eu).

d. Once the paper is accepted for publication and in the proof-read stage, the author needs to notify the assigned curator that the dataset can be released on EBRAINS together with the (in press) citation details. At this juncture, a DOI will be assigned and the dataset will be accessible to the public via EBRAINS. The author must ensure this DOI is referenced in the corresponding publication so the dataset is properly linked to the paper.

Leverage EBRAINS to help create your data paper

Data papers are citable scientific papers that describe scientifically valuable datasets in more detail to promote the sharing and reuse of these resources. Many journals, such as Nature Scientific Data and Frontiers, now offer the possibility to publish data papers.

Data papers require datasets to be structured and annotated with enough metadata to make them understandable to others. They also require a unique URL, preferably a DOI, that points directly to the published data files and requires a license that outlines the terms and conditions for reuse.

All datasets that have gone through the EBRAINS curation process meet these requirements, making EBRAINS a suitable repository for datasets related to data papers. EBRAINS is also listed as a recommended repository for Springer Nature journals.

Data governance and ethics

EBRAINS is committed to conducting responsible research and innovation. Part of that commitment is ensuring that any data shared through our platforms meets national, local and European Union ethical, social and legal requirements. All data providers looking to share data on the EBRAINS platform must complete the EBRAINS ethical compliance survey. The evaluation performed by the EBRAINS Ethics Compliance Management team ensures that we can legally and ethically share your data on our platform. Please note that this process is not an ethics review; EBRAINS does not provide ethical approval or seek to replace your local approval processes.

For identifiable data obtained from living human subjects, compliance with the EU General Data Protection Regulation (GDPR) must also be assured. De-identified, anonymised and strongly pseudonymised human data is additionally safeguarded via the Human Data Gateway (HDG) service. For the access to GDPR-sensitive data in the EBRAINS Knowledge Graph, users need to comply with a set of conditions, including the acceptance of an additional Data Use Agreement. We are also developing a service for sensitive data (SSD) that makes the sharing of pseudonymous and raw data possible. This service will be launched in 2023.

For questions or assistance, contact: hbp.compliance@dmu.ac.uk

Long-term storage

To maximise the benefits of data sharing, data should be stored in a sustainable long-term repository. Following the FAIR data guidelines, EBRAINS offers such a repository. EBRAINS uses the OpenStack Object Storage (swift) system, provided by the Swiss National Supercomputing Centre (CSCS) as a part of the FENIX infrastructure. Researchers who are sharing their data through the EBRAINS curation services will be able to store their data free of charge for at least 10 years via the long-term data storage service.

If your data is already stored at a different sustainable data repository, you can still get your data indexed on EBRAINS and enjoy the benefits of increased visibility and data reuse. Metadata accompanying externally stored data can be integrated into the Knowledge Graph and linked to the data via a persistent identifier (e.g. a DOI) once the external repository has been validated by the EBRAINS curation service.

Increasing numbers of researchers are joining the EBRAINS sharing platform

Our international team of curation scientists and software developers, situated in Oslo, Jülich, Paris and Geneva, integrates neuroscience data, models and software across various modalities and levels of granularity and makes them available to the community via the EBRAINS Knowledge Graph.

Each team member contributes valuable insights and hands-on experience from their Master’s or PhD studies in neuroscience, biology or informatics. Curators are matched with your specific needs.

Get in touch with the openMINDS community at INCF Neurostars or GitHub.

openMINDS INCF Forum openMINDS documentation

How to integrate and share your data?

Submission

Review

Acceptance

Integration

Publication

In-depth integration

The EBRAINS data curation service

What is open data and EBRAINS data sharing

How we make data FAIR

Publish your dataset alongside a journal publication

Option 1

Option 2

Option 3

Leverage EBRAINS to help create your data paper

Data governance and ethics

Long-term storage

Increasing numbers of researchers are joining the EBRAINS sharing platform

Make the most out of EBRAINS