Frequently Asked Questions
How do I share my data?
In brief, to share data, you must register your study and the data you intend to share, upload the data to a private workspace in the Synapse data sharing platform, and annotating the data, and releasing the data. Please read the How to Share Data (an Overview) guide for step by step instructions.
Why should I be certified on Synapse, and what does that involve?
If you’ll be uploading data to your project, you must become certified on Synapse before doing so. Certification requires the completion of a short quiz, which ensures you have awareness of privacy and security issues associated with using a platform that stores human subjects research data.
I’ve just added a new person to my research group - how do they get access to modify my Synapse project?
First, they must become a certified Synapse user. As outlined in the previous question, this involves creating an account, taking a short quiz to be certified, and linking your ORCID account to your profile (optional, but recommended).
Once they have created an account, you can either add them to your lab Team (if you have created one), or we can add them individually. Just provide us (nf-osi@sagebionetworks.org) with links to the project(s) they should be added to, and the new person’s Synapse username.
Why do I need to submit a data sharing plan (DSP)?
A DSP helps the NF Data Portal’s data curation team prepare for your data intake, so they can better assist you with your project. DSPs notify us of upcoming deadlines and whether data deposits will include sensitive data requiring access controls. They also indicate whether we need to prepare for new data types by extending our metadata dictionary to accommodate new attributes and terms.
I haven’t published my findings yet, why do I need to upload my data?
During the embargo period (defined in your Data Sharing Plan and/or funder contract, see How to Share Data (an Overview) ), data will only be available to your research team, NF-OSI data curation/support staff at Sage Bionetworks, and project manager(s) from the funder of your project. During this embargo period, all data in your Synapse project will have publicly-visible metadata, but the data itself will remain private. This means that portal users can see metadata terms that indicate type of data is being generated by your project, but they cannot download and use the data. In other words: this allows you to privately “stage” your data and report progress to your funders, without fear of others using it before you’ve had an opportunity to publish your findings.
Will I lose my ability to patent an invention or otherwise protect my intellectual property by uploading data to Synapse?
We recommend you consult with your funder and your institution’s intellectual property experts to ensure that you are sharing data in compliance with the requirements of your institution as well as the requirements of your contract with your funder; we are not able to provide guidance on this.
What does annotation, or annotating your data, mean?
Annotation is the process of labeling your data files with terms from the NF-OSI dictionary. By adding clinical or experimental annotations, you will help make the data easier for others to find and understand things like: what type of data it is, what sort of experiment was performed, what type of biological system it came from, and what format the data is. Metadata/annotation is not a substitute for sharing protocols or methodology; it won’t help someone reproduce an experiment from scratch, but it will help them get a basic understanding of the nature of the data, and can be very helpful to people who aim to reuse the data (or even future you)!
In Synapse and the NF Data Portal, annotations live alongside files. Rather than being in the file itself, these annotations are surfaced in Synapse and the NF Data Portal to allow people looking for data to easily search and filter data by the annotation values.
Please read the How to Annotate Data guide to learn how to annotate your data.
Where can I find definitions for terms in the NF-OSI dictionary?
Versioned releases of our core NF-OSI metadata dictionary are hosted on Github in CSV and JSON format.
The Attribute column lists all NF-OSI terms: concepts (like dataType) and values for those concepts (like geneExpression)
The Description column provides a definition for each Attribute
The Valid Values column lists all of the terms that are allowed for concepts listed in the Attribute column
The remaining columns are out of the scope of this FAQ, but are documented in detail here.
You may also find our https://help.nf.synapse.org/NFdocs/2560131149.html helpful for exploring the metadata dictionary.
My experiment “failed” - do I still need to share the data?
It depends - if “failed” means no difference was observed, then yes. Negative results are valuable to the field, and it may be helpful to people in the future who are considering doing the same or similar experiment.
If “failed” means that the results are unusable or uninterpretable and you plan to re-try the experiment (for example: an in vitro cancer cell line-based assay was contaminated with yeast), then no, it generally is not worth sharing the raw data for these experiments.
I’m about to publish a manuscript, how do I reference my data in my “Data Availability Statement” in the publication?
If your data has been submitted to the NF Data Portal, you should first create a DOI for your project or folder that contains the data. Learn more about creating a DOI: https://help.synapse.org/docs/Digital-Object-Identifiers-(DOIs).1972405096.html.
Then, send us a message at nf-osi@sagebionetworks.org telling us you are ready to release your data. We’ll review the project to make sure the data are properly annotated and to ensure that the permissions settings are correct so that the community can access the data.
Finally, include the DOI in your data availability statement. For example, this statement links to the the Synodos NF2 project:
“Raw data for this manuscript is available on the NF Data Portal (nf.synapse.org) and on Synapse at https://www.doi.org/10.7303/syn2343195.
How do I cite data in the NF Portal?
To reference data from NF Data Portal, you should use the citation/acknowledgement information on the Study page for the data you are using. For example, see the “Acknowledgement Statements” section for the Synodos NF2 study.
We also recommend that you reference the Synapse ID (e.g. syn2343195) or DOI, when available (e.g. 10.7303/syn2343195) for the data or study that you are referencing. These are persistent accession numbers that will help others find the data you used. Both DOIs and Synapse IDs can be found on the portal Study page.
When re-using data from the portal, please acknowledge the NF Data Portal using the following statement: "The results published here are in whole or in part based on data obtained from the NF Data Portal (http://www.nf.synapse.org, RRID:SCR_021683) and made available through the NF Open Science Initiative."
Including this statement in your acknowledgements helps us find your publications and list them on the portal, and helps us track the impact of the portal on the research community.
How do I cite the NF Portal?
If you’d like to cite the portal itself, please cite the following manuscript:
Allaway, R.J., La Rosa, S., Verma, S. et al. Engaging a community to enable disease-centric data sharing with the NF Data Portal. Sci Data 6, 319 (2019). https://doi.org/10.1038/s41597-019-0317-x
We also have a Research Resource ID that you can use to refer to the portal: RRID:SCR_021683.
What are the requirements associated with publications or preprints linked to my study?
For any publications or preprints linked to your study, please send the following information to nf-osi@sagebionetworks.org:
Pubmed ID
DOI (if available)
Disease focus (NF1, NF2 or Schwannomatosis)
Manifestation (disease manifestation(s) under study—for example, the type of tumor)
Funding Agency (the funding organization for the publication)
How do I stay up to date with data releases and other NF-OSI activity?
We post data releases and many other items of interest (open grant opportunities, jobs, events) both on Twitter and in our quarterly(ish) newsletter.
Be sure to follow us on Twitter @nfopensci and sign up for our newsletter!