[论文解读] Data navigation on the ENCODE portal

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

Single-cell and spatial transcriptomics被引用 8

一句话总结

该论文描述了 ENCODE 数据门户的最新更新，包括重新设计的主页、改进的搜索、新的数据集合页面、单细胞数据以及用于数据可视化与下载的增强购物车界面。

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.

研究动机与目标

• 通过门户解释 ENCODE 数据共享的目的和范围。
• 描述门户的最近重设计和新数据组织功能。
• 突出搜索、数据集合编排和用户数据下载工作流的改进。
• 展示与 ENCODE 处理流水线的集成，以获得统一处理的数据。

提出的方法

• 重新设计门户主页以改善导航。
• 改进搜索界面以便更易发现数据。
• 新增突出生物学相关数据集合的页面（如深度表型的细胞系、免疫细胞）。
• 将单细胞实验纳入门户内容。
• 增强购物车界面以可视化和下载用户选择的数据集。

实验结果

研究问题

• RQ1 如何重新设计 ENCODE 门户以改善数据发现和导航？
• RQ2 应向用户突出哪些新的数据集合和分析类型？
• RQ3 如何在 ENCODE 门户体验中有效整合单细胞数据？
• RQ4 对数据购物车工作流有哪些改动可以优化数据集的可视化和下载？

主要发现

• ENCODE 门户主页已被彻底重新设计。
• 搜索界面为更好地进行数据发现而得到改进。
• 新增页面以突出生物学相关数据的集合。
• 门户中新增了单细胞实验。
• 购物车界面在可视化和下载用户选择的数据集方面得到增强。