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. All Much of the data and resources uploaded into the portal are labelled with metadata and 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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Use the image below as a reference as you move through the rest of this page and encounter the different action buttons available. For example, when the search icon (magnifying glass) is mentioned, it will be followed by (1️⃣) to indicate where it is located on the page. Note that buttons found in various places on the page (such as the search icon) will produce the same action, specific to its location on the page. |
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Notice that the page is made up of three sections: visualization graphs charts on top, the data table below, and the filtering tools on the left. There are also a few settings you can use at the top right. Let’s break down each tool on this page, starting with the filtering tools.
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Upon landing on the Files subtab, all files stored in the system that you have permission to view will appear in the table by default (“view” as in seeing the existence of a file, not necessarily having access to download it). In the image shown above, the table and associated graphs incorporate the total of 12,876 files stored (at the time this screenshot was taken). To narrow this data down, use the Filter Data By section on the left.
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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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Notice how, by default, each of the categories have a checkmark in the box labelled All. Before you apply any filters for a category, it will includes include all files within that category until a filter(s) is applied. Next to each filtering option is a number—this indicates how many files will be included in once that specific filter is applied. For example, looking at the image above, if you check the rnaSeq box under the Assay section, the files will be narrowed down to 3,802 results, as seen in the image below.
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You can play around with the filtering options as you wish to narrow down the search and find your data of interest. Each additional filter will appear in the section under the graphs—you charts—you can easily remove individual filters as necessary, or click Clear All (top right) to remove all filters and start over.
Visualizations
This section of graphs charts at the top of the page will display visualizations for each category according to the data you’ve filtered. You can use the filter icon (3️⃣) for any chart to adjust the filters for that category—this will change the results as a whole (not just for that chart), just as it would if you changed the filters under Filter Data By.
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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 does require 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
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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.