rCAD Taxonomy Updater Utility

Purpose

Update the Taxonomy existing mappings for sequence alignments loaded in an rCAD database. Taxonomy relationships are obtained from NCBI Taxonomy http://www.ncbi.nlm.nih.gov/Taxonomy/.

This utility is not capable of assigning missing Taxonomy relationships to sequences in a sequence alignment.

Note: This utility requires SQL Server Integration Services (SSIS), and an Internet connection (to download Taxonomy data from the NCBI FTP site). This utility will not work rCAD databases installed in SQL Server 2008 Express, or SQL Server Standard or higher without SSIS.

Table of Contents

1. Launch the Utility (Back to Top)

  • Shortcut in Start Menu: All Programs\Gutell Lab\rCAD\Utilities: rCAD Taxonomy Updater
rCAD Taxonomy Updater Main Window

2. Identify the target SQL Server Instance (Back to Top)

  • Enter the name of the SQL Server Instance with the rCAD database to update Taxonomy.
  • Can leave the Instance field blank if the rCAD database to be updated is installed on a Default SQL Server instance.
  • Note: SSIS is required. The rCAD database to be updated must be installed in SQL Server Standard or higher with SSIS installed. SQL Express is not compatible with the rCAD Taxonomy Updater Utility.
rCAD Taxonomy Updater Main Window

3. Test the SQL Server Connection and Identify the rCAD Database (Back to Top)

  • Note: Login for the Taxonomy Updater is by Windows Authentication, Trusted Connection only. Please ensure that your Windows Login has Create, Insert and Update privileges on the target rCAD database.
  • Click the Test button to test the SQL Server Connection. (A)
  • On a successful test, you will be prompted to select the rCAD Database to update. (B)
rCAD Taxonomy Updater Main Window

4. Run the Taxonomy Update (Back to Top)

  • Once the connection is tested and the rCAD database selected in Step 3, the Update Taxonomy button will appear. Click the Update Taxonomy button to start the update process.
rCAD Taxonomy Updater Main Window
  • The NCBI taxonomy download, as well as output files from the update can be found at: [System Root\GutellLab\rCAD\Utilities\TaxonomyUpdater\Data
    • The Dumps Directory contains output files identifying the number of sequences:
      • Merged into a different branch of the tree (RNAJOINMergedSequences.dmp). This would be when two nodes in the tree are collapsed into one.
      • Moved to a different branch of the tree (RNAJOINMovedSequences.dmp).
      • Orphaned (_RNAJOINOrphanedSequences.dmp).
    • The SavedTaxonomyDownloads Directory contains the compressed NCBI Taxonomy downloads.
rCAD Taxonomy Updater Dump Files

Last edited Nov 30, 2009 at 10:54 PM by kjdoshi, version 5

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