Whether you’re a scientist, a bioinformatician, a data scientist, or a member of the general public looking for data, data on the NF Portal can be explored and accessed in multiple ways. The portal offers helpful filtering tools to help you find data of interest. Much of the data and resources uploaded into the portal are labelled with annotations, so they can be easily used to help query the list of resources in each page. You can find a detailed breakdown of metadata definitions and explanations in our metadata dictionary.
Data Status Definitions
Data Pending: Data has not been uploaded yet to Synapse.
Under Embargo: The project is either in progress or complete, but data is not released. After the grant ends, data contributors typically are provided an embargo period of 12-18 months to publish results. (This varies by funder).
Available: Data that is ready for public use. The data still might have access controls on it due to the sensitivity of data, but otherwise, data can be downloaded.
Data Not Expected: Data that was not originally planned or anticipated in a dataset.
Partially Available: Data for which only some portions are accessible, while others are still being prepared or restricted.
Rolling Release: A continuous and ongoing process of making new data available. An example of this might be a continuous generation of the same type of data collected from cohorts over a period of time.
Is all data equally accessible?
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To help explain how to use these sections, refer to the following bullet points and the corresponding image below:
red arrows → When exploring the Files subtab, the Filter Data By sections that appear by default are: Assay, Data Type, and Tumor Type
red rectangle → There are various other categories that you can expand and filter by as well—click the plus sign next to any of these (File Format, Funding Agency, Individual ID, NF1 Genotype, NF2 Genotype, etc.) to reveal its filtering options
red circles → At the end of each category, click on Show more to reveal all filters for that category
search icons → Notice that there is a search icon within each category—use this to search for specific filters within the category
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Finally, the columns icon (5️⃣) allows you to customize the table by adding or removing specific columns.
Downloading data
While exploring and accessing data is done directly in the portal, downloading data is done in Synapse.
You can download data from the Synapse web interface, which has a maximum download size of 5 GB or 100 files. Find instructions on how to download files from the web here.
Alternatively, you can download data using programmatic clients (Python, R, and command line). This method requires some technical knowledge, but you can learn the basic commands to do this in Synapse Docs. Find instructions on how to download files programmatically here.
Data exploration tips
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Data Exploration Tips: Here are a few tips to help make the most of your data exploration: |
When using the search function, type exact terms—unlike Google or other search engines, our search function requires exact matches in order to find terms (it may not return accurate results for misspelled or incomplete terms)
For a high-level view of the kinds of data available in the portal, browse the visualizations (mentioned earlier on this page) that are located on every Explore page.
Most initiatives, studies, publications, hackathons, and organizations have associated detailpages where you can drill down into its associated details and related data. For example, if you visit the Children’s Tumor Foundation detail page, you can view all of its associated studies, data, and publications.
Downloading data
You can download data from the Synapse web interface, which has a maximum download size of 5 GB or 100 files. Find instructions on how to download files from the web here.
Alternatively, you can download data using programmatic clients (Python, R, and command line). This method requires some technical knowledge, but you can learn the basic commands to do this in Synapse Docs. Find instructions on how to download files programmatically here.
Accessing data with Access Restrictions
For a walkthrough of how to access data that has access restrictions, see this guide which uses The Johns Hopkins Biospecimen Repository data as an example.