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