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. 2020 Dec;108(1):e105.
doi: 10.1002/cphg.105.

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

Anna K Greenwood  1 , Kelsey S Montgomery  1 , Nicole Kauer  1 , Kara H Woo  1 , Zoe J Leanza  1 , William L Poehlman  1 , Jake Gockley  1 , Solveig K Sieberts  1 , Ljubomir Bradic  1 , Benjamin A Logsdon  1 , Mette A Peters  1 , Larsson Omberg  1 , Lara M Mangravite  1
Affiliations

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

Anna K Greenwood et al. Curr Protoc Hum Genet. 2020 Dec.

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.

Keywords: Alzheimer's disease; database; genomics; open data; transcriptomics.

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Figures

Figure 1
Figure 1
Screenshot of AD Knowledge Portal homepage, found at http://adknowledgeportal.synpase.org/.
Figure 2
Figure 2
Screenshot of the Data Table, found at http://adknowledgeportal.synpase.org/Explore/Data.
Figure 3
Figure 3
Screenshot of the Explore Data Search box, revealed by clicking on the magnifying glass icon.
Figure 4
Figure 4
Screenshot of the Data Table after applying the “MC‐CAA” Study filter.
Figure 5
Figure 5
Screenshot of the MC‐CAA Study Detail page, found at http://adknowledgeportal.synapse.org/Explore/Studies/DetailsPage?Study_Name=MC‐CAA.
Figure 6
Figure 6
Screenshot of Access Request dialog box, revealed after clicking on Request Access in the Data Table.
Figure 7
Figure 7
Screenshot of the Data Subtype and Metadata Type facet selection boxes, two of the facets that can be found to the left of the Data Table.
Figure 8
Figure 8
Screenshot of the download menu found within the Explore Data Page toolbar. Three possible options are: Export Table, Add to Download List, or Programmatic Options.
Figure 9
Figure 9
Screenshot of Explore Data Page after adding files to the Download List; two ways to access the Download List are depicted.
See this image and copyright information in PMC

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