The new JGA system

New JGA system

The new Japanese Genotype-phenotype Archive (JGA) and NBDC data submission and use application systems (https://humandbs.ddbj.nig.ac.jp/nbdc/application) will be released on 29th, September, 2020. The change points are summarized in this page.

Account integration to D-way

We have been operated the D-way account for BioProject/BioSample/DRA/GEA submission and the JGA account for the JGA data submission and download. After 29th, September, 2020, the JGA account will be merged to the D-way and users will be able to use the BioProject/BioSample/DRA/JGA/NBDC Application systems in the D-way account.

If you want to submit data to JGA or use JGA data, please create your D-way account if you do not have it. You can use the JGA system after your application is approved by NBDC. If you already have a D-way account, you can apply applications to NBDC in your D-way account. For details, please see this page.

Group

In the new account system, submissions and NBDC data submission and use applications are managed through ‘group’. By using group, a principal investigator and a researcher are able to edit submitted records collaboratively, and limit submitters by adding and removing group members without sharing account credentials. When an account holder is sole submitter, submission is linked to default group having one member, the account holder. For details, please see this page.

The owner can send an invitation email to another account holder. If the holder accepts invitation, he/she is added to the group.

The owner can remove a member without his/her permission.

Data submitter group

The submission application (for example, J-DS000001) to NBDC is managed by submission group (for example, subgrp1). NBDC creates JGA submissions (for example, JSUB000001) linked to approved applications and applicants can submit their data.

Update request (for example, J-DS000001-002) should be applied from the same group which applied the initial submission application. The submitter can add data to a new submission linked to approved update application. The initial data submission and update applications are assigned branch numbers such as J-DS000001-002.

The owner can remove a member without his/her permission. However, you need to request member addition to NBDC.

Include all submitters as members. Emails regarding submissions are sent to members only.

Data user group

Data use application to NBDC (for example, J-DU000001) is linked to data use group (for example, usergrp1). After the data use application is approved, you can download JGA Dataset (for example, JGAD000001) approved in the application.

Please include only those who actually download the data as group member. Researcher uses the downloaded data should be listed as a collaborator but should not be included as a group member.

The owner can remove a member without his/her permission. However, you need to request member addition to NBDC.

Data submission and download steps

The NBDC application system and the JGA system will be integrated by the common account and group. In the same account, users can “Apply data submission application - submit data to JGA” and “Apply data use application - download data from JGA”. Please see each page for the data submission and download.

Data transfer by sftp

The JGA upload and download toos will be replaced by scp. In the new JGA system, data files will be uploaded and downloaded by scp.
At 22th April 2021, scp was switched to sftp to improve usability and security.

Data encryption flow

For the data submission, upload unencrypted data files (transfer channel is encrypted by sstp). After issuing accession numbers, the JGA system will store data files in encrypted form as before.

For data use, approved datasets will be encrypted by a public key registered by a user during the data use application to NBDC. Users need to decrypt the data files by using a private key after sftp download. Please see this page for details.

Search system renewal

The JGA Study/Dataset browser provided at https://ddbj.nig.ac.jp/jga/viewer/view/studies will be replaced by the new “DDBJ Search” at https://ddbj.nig.ac.jp/search. We will further develop the DDBJ Search.

Accession number digits

For future addition of version nubmers, the digits of the JGA accession numbers will be changed. The DDBJ Search will respond new accessions when accessed by the old 11-digit numbers.

Incorporation of past data submission and use applications

The NBDC application system does not have past applications. We will incorporate past data submission and use applications linked to groups.