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New Features in the GUDMAP Data Browser | ATLAS-D2K Center

News

New Features in the GUDMAP Data Browser

Mar 26, 2019

The Hub has updated gudmap.org with some important new features and improvements for users and data submitters. We would love to get your feedback - just use this form!

  • Unified imaging model: We unified the data model for all types of imaging data. This means that when you browse our Specimen data, all related images - ie, in situ hybridization (ISH), immunohistochemical (IH) and histology (H&E) - in our repository will now show up under the appropriate “Specimen” page.

  • Specimen Expression Treeview visualization: You can now visually display the scored expression annotation associated with a mouse specimen. For example, go to the specimen page for the Reln gene and click Specimen Expression in the right “Contents” sidebar. To the left of the treeview is a legend representing different states of Strength, Pattern, Density, Density Change and whether there are further notes available. A camera icon indicates one or more related images. Just scroll through the tree and click a term (in bold) to learn more. Tip: Click the “Treeview (full screen)” link at the very top of the tree to open the treeview to it’s full size in a separate browser tab.

  • Boolean Anatomy Search: The ability to perform boolean anatomy searches is now available. From the navigation bar, click Search, then Boolean Anatomy Search to get to the app. You can find documentation here or click the “i” icon on the app for more information.

  • Support for visualization images and applications: As we mentioned in our previous news post, you can now find visualizations of analyzed single cell RNA-Seq data. Check out these studies with visualization images.

  • User experience improvements:

    • Added a link from the Array heatmap page to the raw array data, so users may download the source data.
    • Changed menu bar navigation from hovering to clicking in order to expand sub menus which will enable touch-screen access.
    • New and expanded Help section. Go to Help from the navigation menu for user documentation on querying the data browser, using the boolean anatomy search, Theiler stage reference guide and more.
    • Soon we will be standardizing the menus between the Data Browser and the rest of the website for a more seamless experience. For this release, you’ll notice that instead of “Data” we now have “Search” as a top-level menu item, and its menu is structured similarly to that in the repository. We’ll be announcing the full integration soon.
    • Fixed bugs related to the “Contents” sidebar on the record detail page and fixed broken URLs.

  • Streamlining efforts for data submitters:

    • Unified data model for scRNA-Seq and bulk RNA-Seq. All sequencing experiments now require Replicates (which capture the information about the bio-specimen). Single_Cell_Metrics will only contain statistic information and will be linked to a specific Replicate.

    • Extended the model to take dbGaP_Accession_ID for human-protected sequencing files.

    • Automatically scroll to the top after creating/updating records.

    • Enabled the repository to accept Antibodies and Protocol data from KPMP.
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