AGD data use request
Apply data use request to National Bioscience Database Center (NBDC) with the AGD Study (e.g., AGDS_00000000005) and Dataset (e.g., AGDD_00000000005) IDs.
Approved users should follow the NBDC Security Guidelines for Human Data (for Data Users).
NBDC will notify user ID and password to approved users. The download account will expire in three months after assignment.
This page explains how to use the AGD data.
AGD download tool
Download the AGD download tool (last updated: 2018-11-22，v3.5.0).
Run the tool by clicking the “bat” file in the folder.
Run the tool by executing the sh file in the directory.
Use “Java SE Development Kit 8” and not OpenJDK.
Run the AGD tool and login the AGD system with user ID and password notified by NBDC.
The left window is your local computer and the right window is the secure AGD file server.
In the right window, data sets approved to use are listed. Check the data sets you want to download. Total number of files and size are displayed at below.
Click the [Download] button and the tool download and decrypt the data sets. The number of parallel download can be adusted from 1-5 at “Parallel Download count”.
When this process finishes, decrypted data set are downloaded to your local computer.
In the created directory with data set accession number, the metadata XML and data files have been downloaded.
You can expand the directory tree by clicking the arrowhead left to the dataset directory icon. By selecting each data directory and file, you can download individual files.
Download via a proxy server
To use the tool via the proxy server, you need to set the name and port number of the proxy server.
Edit the “proxy.properties” file in the tool folder and enter the name (server=) and port number (port=) of the proxy server.
# Enter the server name and port number of the proxy server to connect the AGD server via the proxy. # For example: # server=proxy.example.ac.jp # port=8080 server= port=
After login, when the proxy requires user authentication, enter the authentication information in the displayed window. The v3.5.0 (2018-11-21) tool is compatible with the BASIC authentication but not with the Digest authentication.
View metadata in website
Users can view AGD metadata also in website.
From the “AGD studies” page, move to the AGD datasets page.
Select data sets with data use permission.
As in the AGD tool, login the website by using user ID and password notified by NBDC.
Users can view metadata in the website after login.
Logout from the metadata view site
After viewing metadata, do NOT close your browser but logout at right-top “Logout”.
The following error is displayed when access from single account exceeds “1”. Login again after 30 min interval.
Data file transfer by hard disk
For all hard drive request please contact AGD team and let us know the permitted datasets you would like to have transferred.
If you would like the data in hard disk, please prepare the USB hard disk drive (filesystem should be NTFS, ext3 or ext4) with enough space for the approved dataset. Be sure to virus check the entire filesystem and send us the empty drive.
Please send your disk to the following address. Be sure to label your disk.
Postal code: 411-8540
1111 Yata, Mishima, Shizuoka 411-8540, Japan