DRA submission

DRA Handbook combining following manuals is now available (27 Mar., 2014)

D-way Submission Account Manual
DRA/BioProject/BioSample Submission Manual

Overview*

Metadata and run data files are required for submission to DRA. For details, please see the DRA Submission Manual.

The data can be kept private until your paper is published. You can set the hold date for a maximum of 2 years and can change it. Registered records are released according to the Data Release Policy.

Important: Human subject data
The JGA accepts only de-identified data with a National Bioscience Database Center (NBDC) of Japan Science and Technology Agency approved access plan. The users apply for data submission directly to the NBDC and the JGA will only accept and process submissions once the information of a successful application process has been passed from the NBDC to the JGA. Prior to data submission, approved submitters should contact the JGA. A separate notification will then be sent to the submitter including the instructions of how to upload the data into JGA.
Submission of Patent Related Sequences
Please read "Submission of Patent Related Sequences" and "Patent Priority and Other Priority" before submitting patent related sequences.

Please submit the analyzed sequence data to the DDBJ. The DDBJ Mass Submission System (MSS) accepts the genomic or abundant sequence data generated by massively parallel sequencing platforms.

Workflow of DDBJ submission
Workflow of DDBJ submission

Users can analyze raw reads by using the DDBJ Read Annotation Pipeline. The MiGAP automatically annotates uploaded bacterial genome.

Submission of genome data to DDBJ
Submission of genome data to DDBJ

Create a submission account*

To submit the data, you need to create an account for the DDBJ Submission System in advance. An account should be applied by the Principal Investigator (PI) responsible for submissions.
Please register a center name and public key to an account for submission to DRA.

Never submit or update data without the permission of the PI.

Create metadata*

After logging into submission system, you can create metadata by using web-based tool. Please see MetaDefine Manual for details. When metadata have many objects, it may be difficult to create metadata by using the tool. In such a case, metadata can be registered by uploading metadata XML files in the "XML Upload" area.

You can use MetaDefine (public version) without login. You can create XML files but cannnot submit them from the public version.

Upload run data files*

After submitting metadata, upload run data files to your private directory on the DRA file server. Please see DRA Submission Manual for details.

Login submission system and validate uploaded run data files. This validation process checks formats of data files, consistency between data files and metadata.

Completion of submission*

DRA issues the accession numbers with the prefix DR (Submission (DRA), Study (DRP), Sample (DRS), Experiment (DRX), Run (DRR) and Analysis (DRZ) objects) to the completed data. You can view the status and accession numbers in your submission account.

Data release*

In principle, DRA release data when one of the following conditions is met.

  1. Submitter requests to release their data.
  2. Submitter has published their accession number(s) and it has been confirmed.
    We do not release the data when its accession number(s) has been published wrongly by other than the submitter.
    "publish" means to disclose accession number(s) to the public through paper, thesis, academic meeting, internet, press report etc.
  3. Specified hold-date has come.
  4. DDBJ/EMBL-Bank/GenBank records (e.g., TSA, WGS, CON etc.) citing DRA Run (DRR) accession number(s) have been made public.

In cases B, C and D, data will be released with no exception and no permission from the submitter.

When the data is released, in a few days, the released data will become searchable at DRASearch and the data will be mirrored to the NCBI SRA.

In the case of large files, generation of fastq and data mirroring may delay.

Update*

Change hold date

You can set the hold date for a maximum of 2 years and can change it in submission system.

Update metadata

It is possible to update metadata after registration. Please login to the submission system and directly edit metadata.

In the following cases, submission cannot be updated in the submission system. Please contact to DRA in these cases.

  • Update data files in Run
  • Update fields blocked by metadata creation tool
  • Add or delete metadata objects