New developments on the Encyclopedia of DNA Elements (ENCODE) data portal

Abstract

The Encyclopedia of DNA Elements (ENCODE) is an ongoing collaborative research project aimed at identifying all the functional elements in the human and mouse genomes. Data generated by the ENCODE consortium are freely accessible at the ENCODE portal (https://www.encodeproject.org/), which is developed and maintained by the ENCODE Data Coordinating Center (DCC). Since the initial portal release in 2013, the ENCODE DCC has updated the portal to make ENCODE data more findable, accessible, interoperable and reusable. Here, we report on recent updates, including new ENCODE data and assays, ENCODE uniform data processing pipelines, new visualization tools, a dataset cart feature, unrestricted public access to ENCODE data on the cloud (Amazon Web Services open data registry, https://registry.opendata.aws/encode-project/) and more comprehensive tutorials and documentation.

Figure 1.

Experiment matrix. The ENCODE portal hosts data generated by more than 40 different biochemical assays, listed on the x-axis of the matrix. The y-axis lists various sample types represented on the portal. Each cell in the matrix indicates the number of experiments that are currently available on the portal with a particular sample type and the corresponding assay type. To the left of the matrix are faceted browsing interface bars that can be used to positively select (blue) and negate selection (red) of certain values of specific experimental metadata properties.

Figure 2.

Faceted browsing interface. Four new facet bars were added to the faceted browsing interface: (A) ‘Target category’ facet bar, (B) ‘Target of assay’ facet bar, (C) ‘Cell’ facet bar and (D) ‘Date range selector’ facet bar. The ‘Cell’ and ‘Target of assay’ facet bars that have long lists of values include the typeahead search feature to help users locate terms of interest more quickly.

Figure 3.

Valis genome browser embedded on the portal. Users can find their genomic region of interest by (i) searching for a specific gene, (ii) specifying genomic coordinates or (iii) using the mouse scrolling and zooming features directly to navigate the region. File selectors are available on the left, allowing users to select and visualize tracks for specific genome assembly, specific file format or output type, and files belonging to specific experimental replicate(s). This example can be found by clicking the ‘Genome browser’ tab on the experiment summary page (https://www.encodeproject.org/experiments/ENCSR807BGP/).

Figure 4.

Cart for custom collections of datasets. Experiments can be added to the cart from the experiment search page (A) or by clicking on the cart icon on the experiment summary page (B). Experiments that are no longer needed can be removed from the cart (C). Files that belong to the experiments in the cart can be filtered using the file selectors on the left. For example, users can select only alignments mapped to the GRCh38 genome assembly. The cart allows users to download the data files satisfying specific criteria along with associated metadata. Currently, carts are saved per active browser session and will be erased after closing the web browser or refreshing the page.

Figure 5.

Tutorials, documentation and help on the ENCODE portal. Link to tutorials and examples for ENCODE AWS Registry of Open Data could be found under the ‘Data’ menu on the left-hand side of the top bar. Help information is accessible through the ‘Help’ menu on the top bar of every portal page. Interactive walk-through tutorials and additional help materials are available via the ‘Help’ widget visible in the bottom-right corner of the screen. The ENCODE DCC also supports users directly through the ENCODE help desk at encode-help@lists.stanford.edu.