DDBJ Curators' Assistant

The system consists of:

• A set of tools designed to automate and standardize, in a fast and easy way, the curation of Sequence Datasets submitted to DDBJ. It comprises four steps: validation (ddbj_mss_validation); auto-correction (ddbj_autofix); auto upload files to DDBJ Databases (ddbj_sakura2DB); and update work tracking spreadsheet (ddbj_kaeru, "kaeru 帰る" means "leave, go home" in Japanese language, in the sense that the work is done).
• A database, named dblink_ddbj, that contains the most relevant information from DDBJ Database, designed specially for DDBJ curators.
• An easy-to-use search engine tool, search_dblink, for quickly and simultaneously retrieving data from a wide range of accession IDs.

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Mass Dataset Documentation

1. DDBJ Mass Validation
   • An easy command line that identifies submitted files (annotation and fasta) and checks inconsistencies based on DDBJ rules.
   • Requirement: BioSample
   • Command line (production)

   bash /home/andrea/scripts/ddbj_mss_validation
   

   • Command line beta

   bash /home/andrea/scripts/ddbj_mss_validation_beta
   

2. DDBJ Autofix
   • A simple command line that interactively suggests corrections that have been detected by DDBJ Mss Validation and automatically fixes them.
   • Command line

   bash /home/andrea/scripts/ddbj_autofix
   

   • Command line beta (CAUTION! Use this version when running ddbj_mss_validation_beta)

   bash /home/andrea/scripts/ddbj_autofix_beta
   

3. DDBJ Sakura2DB
   • Interactive command line that automatically: a) identifies the file type; b) runs sakura2db (test and actual) for the corrected files to upload the files to their respective databases at DDBJ (Tsunami); c) moves the files to DONE directory.
   • Command line

     bash /home/andrea/scripts/ddbj_sakura2DB
     

     • Command line beta

     bash /home/andrea/scripts/ddbj_sakura2DB_beta
     

4. DDBJ Kaeru
   • Update work tracking spreadsheet, after running DDBJ Sakura2DB.
   • Command line

   bash /home/andrea/scripts/ddbj_kaeru
   

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DBLink DDBJ and Search DBLink Documentation

1. DBLink DDBJ
   • Comprises essential data (dblink dataset) from the major DDBJ databases: BioProject, BioSample, Sequence Read Archive (DRA), Assembled Sequences (Mass Data) and GEA.
2. Search DBLINK
   • A simple command line tool that accesses the DBLink-DDBJ database and correlates the major DBLink dataset from DDBJ using one file with different accession IDs.