The NF Data Portal is a public data repository that stores and shares data generated by multiple collaborative research programs focused on neurofibromatosis (NF) diseases (neurofibromatosis type 1, type 2NF2-related-schwannomatosis, and other forms of schwannomatosis). Collaborators and Sage Bionetworks support the portal, open science, and the NF research community through the effort collectively called the NF Open Science Initiative (NF-OSI). Children’s Tumor Foundation (CTF) and the Neurofibromatosis Therapeutic Acceleration Program (NTAP) participation dates back to 2014. More recent participants include the Gilbert Family Foundation (GFF), the Developmental and Hyperactive Ras Tumor SPORE (DHART-SPORE), and the CDMRP Neurofibromatosis Research Program (NFRP). You can read more about these programs here. Importantly, anyone in the NF research community can join the NF-OSI. Learn more about joining the NF-OSI here.
Because NF diseases are relatively rare, samples and data generated in this area are precious. This is why open science principles are so valuable—data sharing and collaboration maximizes the value and impact of research. The , and the NF Data Portal exists to support this joint effort. Read more about open science and data sharing here. The open access data in the NF Data Portal is generated by studies backed by funding organizations, including Children’s Tumor Foundation (CTF), Neurofibromatosis Therapeutic Acceleration Program (NTAP), and Gilbert Family Foundation (GFF). See our past Hackathon projects to see examples of re-use.
Some studies are funded in conjunction with one another—such a group of funded projects is called an initiative on the portal. Funded studies produce data files, metadata and annotations, publications, and biological tools like cell lines, mouse models, and plasmids. Study products, such as multiple data files, may be bundled into a dataset, or explored and analyzed with computational tools developed by the community.
Learn about the organizational structure and contents of the portal here.
History
The NF Data Portal was built by members of the NF Open Science Initiative (NF-OSI), an alliance that was formed to support open science within the neurofibromatosis and schwannomatosis research community. NF-OSI is the result of a collaboration effort between the Children’s Tumor Foundation (CTF) and the Neurofibromatosis Therapeutic Acceleration Program (NTAP) that dates back to 2014. More recent participants include the Gilbert Family Foundation (GFF), the Developmental and Hyperactive Ras Tumor SPORE (DHART-SPORE), and the CDMRP Neurofibromatosis Research Program (NFRP). You can read more about these programs here. The NF-OSI is an open effort focusing on finding NF treatments by sharing data and analysis results with the broader community—an effort aided by the existence of the NF Data Portal.
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Collaborators and Funding
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The NF Data Portal was built and is maintained thanks to generous support from:
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As a user of the portal, you can engage with as many of these stages as fits your needs. Each stage of the data lifecycle manifests on the portal in different ways.
During the data generation phase, data are uploaded to the data storage platform, Synapse. During this phase, the data are typically not available for download on the portal, but some information is exposed, such as study title, study description, and metadata.
Data curation mostly occurs behind the scenes of the portal on our data storage platform, Synapse, but this stage enables data discovery, powering search and exploration on the portal.
Data analysis surfaces on the portal through biological and computational tools and is boosted through information available on the portal such as metadata and provenance.
Data interpretation is enabled through various Synapse features, including wikis and discussion forums, but can also be explored on the portal via published data, associated publications, and tools.
Data dissemination includes the NF Data Portal, journal publications, and other means of data distribution.
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For an in-depth review of the NF Data Portal’s community engagement and structure, please see our article in Scientific Data. |
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At this point, you know what the NF Data Portal is, and have likely come across the term Synapse - but how do they fit together? Let’s break this down:
Sage Bionetworks |
Sage Bionetworks (also referred to as Sage) is a non-profit organization based out of Seattle, Washington. Sage is dedicated to promoting and advancing open science, as well as engaging patients in the research process. Sage acts as the Data Coordinating Center (DCC) for several different portals, including the NF Data Portal. The scientists, developers, and designers that built the tools you’re using are all employed by Sage. You can learn more about Sage Bionetworks and its initiatives here. | |
Synapse | In line with advocating for open science, Sage developed a software platform called Synapse. This platform is what allows for collaborative data curation and analysis, computational modelling, and more. It allows users to upload, store, analyze, and track data in a private space, before releasing it to the public-facing NF Data Portal. Think of Synapse as the back-end for all the data to live in. |
NF Data Portal | If Synapse is the back-end for data, the NF Data Portal is the front. It’s essentially the user interface (UI) or entry point for you to view data and other shared content. Data gets uploaded into Synapse |
and becomes searchable and accessible in the portal. |
NF Data Standards
Data standards underpin data sharing and make it possible to successfully explore, access, analyze, and reuse data. Data standards involve:
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To allow for data standards, we control the terminology used for values through (meta)data dictionaries and other tools. Using controlled vocabularies and other data standards allows you to find what you’re looking for on the portal, so that you don’t have to search through multiple terms for the same thing. For example, instead of ribonucleic acid sequencing, or RNA-Seq, we use the value rnaSeq RNA-seq.
You can find our full data dictionary here and as regular releases of a JSON-LD file on our nf-osi github hereat our open-source GitHub repository.
Quarterly Newsletter
Looking for NF Portal and NF-OSI news? Register for the NF-OSI newsletter here.
Help & Feedback
If you have questions, suggestions or other feedback about the NF Data Portal, please contact us at nf-osi@sagebionetworks.org.