[Paper Review] Data navigation on the ENCODE portal

Meenakshi S. Kagda, Bonita R. Lam+32 more|arXiv (Cornell University)|Apr 27, 2023

Single-cell and spatial transcriptomics8 citations

TL;DR

The paper describes recent updates to the ENCODE data portal, including a redesigned home page, improved search, new data collections pages, single-cell data, and an enhanced cart interface for data visualization and download.

ABSTRACT

Spanning two decades, the Encyclopaedia of DNA Elements (ENCODE) is a collaborative research project that aims to identify all the functional elements in the human and mouse genomes. To best serve the scientific community, all data generated by the consortium is shared through a web-portal (https://www.encodeproject.org/) with no access restrictions. The fourth and final phase of the project added a diverse set of new samples (including those associated with human disease), and a wide range of new assays aimed at detection, characterization and validation of functional genomic elements. The ENCODE data portal hosts results from over 23,000 functional genomics experiments, over 800 functional elements characterization experiments (including in vivo transgenic enhancer assays, reporter assays and CRISPR screens) along with over 60,000 results of computational and integrative analyses (including imputations, predictions and genome annotations). The ENCODE Data Coordination Center (DCC) is responsible for development and maintenance of the data portal, along with the implementation and utilisation of the ENCODE uniform processing pipelines to generate uniformly processed data. Here we report recent updates to the data portal. Specifically, we have completely redesigned the home page, improved search interface, added several new pages to highlight collections of biologically related data (deeply profiled cell lines, immune cells, Alzheimer's Disease, RNA-Protein interactions, degron matrix and a matrix of experiments organised by human donors), added single-cell experiments, and enhanced the cart interface for visualisation and download of user-selected datasets.

Motivation & Objective

• Explain the purpose and scope of ENCODE data sharing via the portal.
• Describe recent portal redesign and new data organization features.
• Highlight improvements in search, data collections curation, and user data download workflows.
• Show integration with ENCODE processing pipelines for uniformly processed data.

Proposed method

• Redesigned the portal home page to improve navigation.
• Enhanced the search interface for easier data discovery.
• Added pages highlighting biologically related data collections (e.g., deeply profiled cell lines, immune cells).
• Incorporated single-cell experiments into portal content.
• Enhanced the cart interface to visualize and download user-selected datasets.

Experimental results

Research questions

• RQ1 How can the ENCODE portal be redesigned to improve data discovery and navigation?
• RQ2 What new data collections and assay types should be highlighted to users?
• RQ3 How can single-cell data be effectively integrated into the ENCODE portal experience?
• RQ4 What changes to the data cart workflow optimize visualization and download of datasets?

Key findings

• The ENCODE portal home page was completely redesigned.
• The search interface was improved for better data discovery.
• New pages were added to highlight collections of biologically related data.
• Single-cell experiments were added to the portal.
• The cart interface was enhanced for visualization and download of user-selected datasets.