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How to Import a .ocelot Format PGDB into Pathway Tools

How to Import a .ocelot Format PGDB into Pathway Tools

Introduction

These instructions use notation and terminology that is typically used when manipulating a Windows file system, but will work for UNIX-like operating systems (Solaris, Linux, Mac OS X) as well.

Step-by-Step Guide

  1. Fetch a .ocelot format PGDB from the BioCyc download website.
  2. Unpack the ZIP file or the tar-ball (*.tar.Z).
  3. Locate the ptools-local directory that was created when you installed Pathway Tools.
    This ptools-local directory contains a sub-directory called pgdbs, which in turn contains a sub-directory called user.This is the location for the new PGDB.
  4. Create a new folder inside the ptools-local\pgdbs\user directory, with a name based on the organism ID. It is similar, but not identical, to the name of the Ocelot file, as it ends with "cyc" instead of "base". For example, the Ocelot file aaeo63363base.ocelot, is for a PGDB with an organism ID of aaeo63363. You would create a folder with the name aaeo63363cyc.
  5. Within the ptools-local\pgdbs\user\[organism ID]cyc\ folder, create a folder with the version number of the PGDB as its name (e.g. ptools-local\pgdbs\user\aaeo63363cyc\10.0\).
  6. Within the ptools-local\pgdbs\user\[organism ID]cyc\ folder, create a text file called default-version. This file should contain only the current version number, which is the same as the version number folder described in the previous step. Following the example from the previous step, the file would have one line (followed by a return character) with the text 10.0 in it.
  7. Within the ptools-local\pgdbs\user\[organism ID]cyc\[version number]\ folder, create two sub-folders called input and kb.
  8. Place the *.ocelot file in the kb folder (e.g. ptools-local\pgdbs\user\aaeo63363cyc\10.0\kb\aaeo63363base.ocelot).
  9. In the input folder, create a text file called organism.dat, which contains the following text (once again, the aaeo63363 PGDB is used as an example):
    ID      AAEO63363
    STORAGE FILE
    NAME    Aquifex aeolicus
    ABBREV-NAME     A. aeolicus
    

    The documentation for the format of the organism.dat file can be found in Section 6.6.1 of the Pathway Tools User Guide. It might be helpful to see how the organism.dat file is formatted for other PGDBs to make sure that you follow the correct syntax. Please take extra care that the ID attribute in the organism.dat file is the exact same organism ID that was used as the basis of the Ocelot file name and as the basis for the PGDB folder name.
  10. This should set up the necessary files and folders to allow Pathway Tools to automatically detect the new user PGDB. Exit Pathway Tools if it is currently running, and then restart Pathway Tools for the new PGDBs to be displayed.

Conclusion

To summarize, you will need the following files and folders :

C:\...\ptools-local\pgdbs\user\aaeo63363cyc\10.0\kb\aaeo63363base.ocelot
C:\...\ptools-local\pgdbs\user\aaeo63363cyc\10.0\input\organism.dat
C:\...\ptools-local\pgdbs\user\aaeo63363cyc\default-version

Where "..." is replaced with the path from the C: drive to where ever you created the ptools-local directory during the installation of Pathway Tools.