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 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.
Is all data equally accessible?
Anyone can browse public content on the NF Data Portal, but you need a Synapse account in order to download data. Learn how to do so here. If you’re new to Synapse, you may want to explore our Synapse documentation for more information and instructions.
Some data on the portal is considered controlled use and requires you to request access by reading and electronically agreeing to data-specific terms. Learn how to do so here.
Get started exploring data
In the portal’s Explore tab, the various subtabs correspond to how the data is categorized for your filtering purposes. To demonstrate the best practices for finding data, let’s look at the Files subtab.
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.
Notice that the page is made up of three sections: visualization graphs 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.
Please note: The data and numbers displayed in the screenshot above reflects the portal at that moment in time—this will likely be different than what you see when exploring the portal yourself, since the portal is dynamic and changes as new data is uploaded and processed.
Filtering tools
Upon landing on the Files subtab, all files stored in the system will appear in the table by default. In the image shown above, the table and associated graphs incorporate the total of 12,876 files stored. To narrow this data down, use the Filter Data By section on the left.
Filter Data By is broken into sections that will differ depending on the subtab that you’re exploring.
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
For example, when exploring the File subtab, the following Filter By sections appear by default: Assay, Data Type, and Tumor Type. Then, there are more than a dozen additional categories that you can expand and filter by as well. Click the plus sign next to any of these (File Format, Individual ID, Species, etc.) to reveal its filtering options. At the end of each category, click on Show more to reveal all filters for that category.
Notice how by default, each of the categories have a checkmark in the box labelled All—since no filters have been applied for that category, it includes 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 that specific filter. For example, looking at the image above, if you check the rnaSeq box under Assay, the files will be narrowed down to 3,802 results, as seen in the image below.
Selecting filters from more than one category will quickly narrow the results down more. For example, if I also check the geneExpression box from the Data Type section and Schwannoma fro the Assay section, I’m left with only 4 results of data.
You can mix and match filtering options as you wish to narrow the search down to your data of interest. Each filter will appear in the section under the graphs—you can easily remove individual filters as necessary, or click Clear All to remove all filters and start over.
Continue reading about how the resulting data is displayed in the visualizations and table, or visit this page for information on how to download data.
Visualizations
This section of graphs 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 graph to adjust the filters for that category—this will change the results as a whole (not just for that graph), just as it would if you changed the filters under Filter Data By.
Use the expand icon (6️⃣) to make that specific graph bigger and the contract icon (inverse of 6️⃣) to return back to normal size.
Click the X is (7️⃣) to temporarily remove that graph from view.
By default, the graphs displayed are for the categories Study, Data Type, and Assay. Click Show All Graphs to display graphs for all categories, and Hide Optional Graphs to restore the default display.
Data table
The data that you’ve filtered for will appear in the data table below the visualizations section. Notice how it’s organized by category—you can use the filter icon (3️⃣) next to any category header to change the filters, just as it would if you changed the filters under Filter Data By. Use the reorder icon (8️⃣) next to any of the category headers to rearrange the table data in reverse based on that category.
Use the horizontal scroll bar below the table to reveal extra category columns.
The table will only fit 25 rows of data—click Next or Previous to shuffle through more rows as needed.
Additional settings
At the top of the page, above the visualization section, there are several icons you can use to adjust the page settings.
The search icon (1️⃣) allows you to search for specific terms to filter for instead of going through all the categories in the Filter Data By section. You can select a certain category to search within. Click the icon again to hide the search bar.
The graph icon (2️⃣) allows you to hide/show the Visualizations section.
The filter icon (3️⃣) allows you to hide/show the Filter Data By section.
The download icon (4️⃣) allows you to export the currently displayed table in .csv or .tsv format. To do so, click Export Table, select your settings, click Next, and finally click Download once the prompt indicates your file is ready. From the download icon, you can click Add to Download List to save the table to a list for later. You also have the option to click Programmatic Options, which allows you to download the table via the Synapse command line client.
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
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 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 Detail pages 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.
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