Table 1. Animal QTLdb data release procedures and check items.

Steps Check points Operatioins
Step 0:
  Overview of new data in the curation pipeline
  1. Spot checks of data with admin web tools
  2. Monitor data flow/motion
  3. Monitor data statistics
Overview of data in a web environment similar that for editors with limited number of execusion power in terms of batch processes.

This is part of the routine of the DB admin prior to the database release stage.

Step 1:
  Run check points
  1. Re-populated 'breed' table with QTL/association information.
  2. Update gene info from NCBI (where only Gene ID is curated)
  3. Check for any missing statistics
  4. Check any missing map info.
  5. Check if SNPs are available where coordinates are manually entered.
  6. Fix 1: Populated empty coordinates fields where SNP is available
  7. Fix 2: Convert 'bp' to 'cM' where applicable
  8. Fix 3: Fill 'peak'/'span' by their linkage marker locations
  9. Fix 4: Convert 'cM' to 'bp' where applicable
  10. Fix 5: Fill missing symbols/names in QTLdata table
  11. Fix 6: Find and fix inverted bp locations
  12. Fix 7: Look for 'rs' number of 'ss' SNPs
  13. Fix 8: Find missing or conflict QTL Symbols
Each operation is by running scripts specifically developed for each specific purpose. Operations require human verification of input/output/error report to ensure valid processes, identify new problems, exceptions. Modify scripts for fixes where apply.
Step 2:
  Verify new reference PDF files
  1. Find all physical PDF files, “touch” db
  2. Identify missing PDF files, “touch” db
  3. Move PDF file in place from upload pool; Check for errors.
This is to make the backend links of curated data to their sources (PDF files where the data were published) for future data quality control checkups.
Step 3:
  Do the "release"
  1. Database: List data by curators, species, verification status
  2. Web site: Publish release statistics
  3. Release summary: Compose release data summary
  1. Run scripts; Issue option to release; Log automatically kept
  2. Semi-automated data updates on web
  3. Add tools update descriptions
Step 4:
  Post-release operations
  1. Prepare data for download
    • for NCBI (pre-agreed data format)
    • for Routure (pre-agreed data format)
    • for Public users (with updated format)
  2. GBrowse: Re-set up
  3. JBrowse: Re-set up
  4. Biomart: data re-import
Data refresh on "other" data portals.
Step 5:
  Post-release updates
  1. Update “QTL Gene” IDs from NCBI
To complete the new QTL/association data entries with "Gene IDs" assigned by NCBI GeneDB.