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Making a copy of a PGDB on the same computer (i.e. change the OrgID)

asked 2013-04-29 16:19:45 -0500

anonymous user


I want to make a copy of one of my PGDBs, so that I can try something out on it that I don’t want to clobber my original version. How do I have both copies of my PGDB loaded into the same Pathway Tools session?

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answered 2013-05-01 13:46:31 -0500

quang777 gravatar image

Sometimes you want to make changes to a PGDB, yet keep an unmodified copy of the PGDB around, so that you can compare the two versions, such as by running Pathway Tools in web mode, and using the Comparative Analysis tools.

If you want to make a copy of any PGDB, including built-in PGDBs like MetaCyc, EcoCyc, or any of the Tier 2 PGDBS, make sure to heed the warning about the default-version file as found in the external documentation about copying a PGDB from one computer to another.

You have to make sure to extend the shell variable PTOOLS_ORG_ROOTS to include the path where you are placing any newly-copied PGDBs.

If you want to have the original PGDB and the newly-copied PGDB to be loaded into the same session of PTools, then you'll need to give the newly-copied PGDB a unique name & org-id. You'll have to:

  1. If the original PGDB is a file KB, make sure that it has been saved to disk recently. If the original PGDB is a RDBMS KB, make sure to run (backup-ekb) via the PTools Lisp API with the original PGDB as the current KB.
  2. Copy the original PGDB's directory structure to the new location
  3. Change the directory name from foocyc to footestcyc.
  4. Change the org-id in the footestcyc/[version]/input/organism.dat file to something unique, such as FOOTEST.
  5. Modify the NAME & ABBREV-NAME attributes in the same file to signify that they are different than the original. This helps avoid confusion.
  6. Don't forget to modify the STORAGE attribute in the same file to be FILE, not MYSQL or ORACLE.
  7. Go into the footestcyc/[version]/kb directory, and move foobase.ocelot file to footestbase.ocelot .
  8. Open up the footestbase.ocelot file, and change the :name attribute in the first s-expression (that starts with :OCELOT-KB) to the org-id (from above, FOOTEST) that you selected earlier.
  9. In the footestbase.ocelot file, look for a top-level s-expression that starts a line with (FOO NIL (, where foo is the old org-id. Change it to the new org-id of the copied PGDB (i.e., FOOTEST).
  10. In the data directory for the PGDB, you'll need to rename some files in order to have the nucleotide and protein sequence data display correctly in PTools. Effectively, whenever you see a file with the prefix foobase, it needs to be replaced with the prefix footestbase. Also, there should be a file with a suffix of .fsa, and a prefix of the Organism ID (i.e., foo). You'll need to change the prefix to the new Organism ID, such as footest.

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Asked: 2013-04-29 16:19:45 -0500

Seen: 10,323 times

Last updated: May 01 '13