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run_rmiregistry.sh
run_protege_ server_nci.sh
shutdown_protege_server.sh
codegen.properties
codegen.dat(the seed number will also need to be changed to 101000.  This can be accomplished by typing 'vi codegen.dat.'Once in the vi editor, type 'shift + insert' and modify the seed number.  Press 'esc', then ':wq' to save and exit the vi editor).

• If you do need to use new scripts, make sure to adjust the memory upwards from the default in the run_protege_server_nci.sh script.  The following table dsisplays how much memory to allocate for each script, per tier.  You will also need to adjust the rmi.registry and rmi.server ports, the hostname and the metaproject location in this same file.  Please view Appendix A for port information for each tier.

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• Navigate to the Protégé server, and open the 'codegen.properties' file using a vi editor. To do this, type 'vi codegen.properties".  Once the file .   is viewable from vi, type "shift + I" to edit.   The code.prefix value will can be adjusted, depending on which Protégé Instance is being used (BiomedGT or NCI Thesaurus).  BiomedGT uses a prefix of 'B', while NCI Thesaurus uses 'C'.   Modify Keep the seed number so that is is one number higher than the number in the at 100000. Save and exit the file by typing 'esc', then ':wq.

• Open the  'codegen.dat' file in the vi editor. You will notice a number which represents a code that will be assigned to the concept code created in the database project. Set this number to 101000. Save and exit the file.  

• Open the Protege client from the dev tier, and click on "Create New Project".  Select OWL/RDF File, and check "Create from existing source".  Click Next.

• A window will display requesting the address of the source of the .owl OWL file. Navigate to where the .owl file is stored and /app/protege/data/Protege_1.4/BiomedGT/ and select BiomedGT-Fixed-wNS-DefaultAndPrefix.owl, and click next. Leave the next two windows to their default values, then click Finish.  Creating the project Loading the file to the client will take approximately 5-10 -20 minutes.

• The One loaded, the project file can now be converted to an Clark & Parsia OWL/RDF database.   Click File, Convert Project to Format, Clark & Parsia OWL / RDF database.

• Enter In the database window, enter all requested database info and click finish.  BiomedGT and NCIThesaurus data are stored in different databases (Please view Appendix A to view specific    (Please look at the database info for each instance). Conversion can take anywhere up to 2 hours, if a file from production is being used 

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