The AD Knowledge Portal: A Repository for Multi-Omic Data on Alzheimer's Disease and Aging

Current Protocols in Human Genetics Pub Date : 2020-10-21 DOI:10.1002/cphg.105

Anna K. Greenwood, Kelsey S. Montgomery, Nicole Kauer, Kara H. Woo, Zoe J. Leanza, William L. Poehlman, Jake Gockley, Solveig K. Sieberts, Ljubomir Bradic, Benjamin A. Logsdon, Mette A. Peters, Larsson Omberg, Lara M. Mangravite

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引用次数: 26

Abstract

The AD Knowledge Portal (adknowledgeportal.org) is a public data repository that shares data and other resources generated by multiple collaborative research programs focused on aging, dementia, and Alzheimer's disease (AD). In this article, we highlight how to use the Portal to discover and download genomic variant and transcriptomic data from the same individuals. First, we show how to use the web interface to browse and search for data of interest using relevant file annotations. We demonstrate how to learn more about the context surrounding the data, including diagnostic criteria and methodological details about sample preparation and data analysis. We present two primary ways to download data—using a web interface, and using a programmatic method that provides access using the command line. Finally, we show how to merge separate sources of metadata into a comprehensive file that contains factors and covariates necessary in downstream analyses. © 2020 The Authors.

Basic Protocol 1: Find and download files associated with a selected study

Basic Protocol 2: Download files in bulk using the command line client

Basic Protocol 3: Working with file annotations and metadata

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AD知识门户:关于阿尔茨海默病和衰老的多组学数据储存库

AD知识门户(adknowledgeportal.org)是一个公共数据存储库，共享由多个专注于衰老、痴呆和阿尔茨海默病(AD)的合作研究项目生成的数据和其他资源。在本文中，我们重点介绍如何使用Portal来发现和下载来自同一个体的基因组变体和转录组数据。首先，我们展示了如何使用web界面浏览和搜索相关文件注释感兴趣的数据。我们演示了如何更多地了解数据周围的环境，包括诊断标准和关于样本准备和数据分析的方法细节。我们介绍了下载数据的两种主要方式——使用web界面，以及使用使用命令行提供访问的编程方法。最后，我们将展示如何将独立的元数据源合并到包含下游分析所需的因素和协变量的综合文件中。©2020作者。基本协议1:查找并下载与选定的研究相关的文件基本协议2:使用命令行批量下载文件client基本协议3:处理文件注释和元数据

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Current Protocols in Human Genetics Biochemistry, Genetics and Molecular Biology-Genetics

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期刊介绍： Current Protocols in Human Genetics is the resource for designing and running successful research projects in all branches of human genetics.