DTA submission

Overview*

Metadata and trace files are required for submission to the DDBJ Trace Archive (DTA). Unique identifiers (TI numbers) are assigned to each traces upon loading to the NCBI Trace Archive. As soon as loading to the NCBI Trace Archive, TI numbers are assigned and the data become public.

Note: TI number assignment and data release are simultaneous events.

Obtain a submission account*

Submitters need an account of the DDBJ submission system. Please apply the account according to the D-way Submission Account Manual.

Create submission files*

The metadata file (TRACEINFO file) describes the submitted data as well as points to the location of the chromatograms. All submissions when extracted should have a top directory. All metadata files should be placed under that directory. In case when the submission should contain trace files at least one more directory should be introduced to the top directory and all trace files should be placed under that directory. The trace files (either in SCF or in ABI format) should not appear in the top level directory, but rather should be in a subdirectory. It is suggested to use the name of the traces or the name of the project for subdirectories. There may be subdirectories within and this is encouraged to group traces. Below are examples of the submission directory hierarchy.

Submission directory hierarchy example

TOP_DIRECTORY/
TOP_DIRECTORY/TRACEINFO
TOP_DIRECTORY/traces
TOP_DIRECTORY/traces/FLJ/
TOP_DIRECTORY/traces/FLJ/FLJA1U0001.scf
TOP_DIRECTORY/traces/FLJ/FLJA1U0002.scf
TOP_DIRECTORY/traces/FLJ/FLJA1U0003.scf

The metadata file can be either in XML or in tab-delimited format. The metadata requirements are in the Validation Table (spreadsheet format) for specific combinations of STRATEGY and TRACE_TYPE_CODE. Both types of metadata files can contain common fields section at the beginning of it. This section defines common for the submission values if any. Below are examples of TRACEINFO metadata files.

TRACEINFO xml example

<?xml version="1.0"?>
<trace_volume>
   <common_fields>
      <center_name>CENTER NAME ACRONYM IS HERE</center_name>
      <center_project>FLJ</center_project>
      <source_type>N</source_type>
      <species_code>HOMO SAPIENS</species_code>
      <strategy>EST</strategy>
      <submission_type>NEW</submission_type>
      <trace_format>SCF</trace_format>
      <trace_type_code>EST</trace_type_code>
   </common_fields>
   <trace>
      <trace_name>F-3NB691000020</trace_name>
      <trace_file>./traces/F-3NB691000020.scf</trace_file>
      <clone_id>3NB691000020</clone_id>
      <library_id>3NB691</library_id>
      <template_id>3NB691000020</template_id>
   </trace>
   <trace>
      <trace_name>F-3NB691000033</trace_name>
      <trace_file>./traces/F-3NB691000033.scf</trace_file>
      <clone_id>3NB691000033</clone_id>
      <library_id>3NB691</library_id>
      <template_id>3NB691000033</template_id>
   </trace>
     --- more information ---
</trace_volume>

TRACEINFO tab-delimited text example

center_name = CENTER NAME ACRONYM IS HERE
center_project = FLJ
source_type = N
species_code = HOMO SAPIENS
strategy = EST
submission_type = NEW
trace_format = SCF
trace_type_code = EST
trace_name	clone_id	library_id	template_id	trace_file
F-3NB691000020	3NB691000020	3NB691	3NB691000020	./traces/F-3NB691000020.scf
F-3NB691000033	3NB691000033	3NB691	3NB691000033	./traces/F-3NB691000033.scf
		               --- more information ---			

Upload submission files*

DTA creates a directory for data submission. Please contact to the DTA team. Transfer files by SCP according to the Chapter 3 of the DRA Submission Manual.

Submission directory example

submission/submitter_id/dta/dta_submitter_id-0001
Note: Directory for the DTA submission is separated from those for the DDBJ Sequence Read Archive.

Completion of submission*

After submission files become complete, DTA can keep the data private until the submitters instruct us to release the data. After instruction of data release, DTA uploads the files to the NCBI Trace Archive. As soon as the data are loaded to the NCBI Trace Archive, TI numbers are assigned and the data become public.

Please note that TI number assignment and data release are concurrent events.

To update the records, please contact to the DTA team.