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A new project file will need to be created using the raw OWL file located in /app/protégé/data/Protégé_x.x/<PROTÉGÉ INSTANCE>. Usually newer, more fresher data is available by the editors after performing a PROMPT of production data. Each baseline file that is created after each session can be used as test data. If however, for some reason, an OWL file must be created manually, instructions are available on how to export data from the production database.

• As long as no changes have been made to the behavior of the startup scripts, the following files and scripts should be copied over from the old Protégé.Server version to the new folder:

  Code Block
  run_rmiregistry.sh run_protege\_ server_nci.sh shutdown_protege_server.sh codegen.properties codegen.dat

• 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 displays 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.

• As long as no changes have been made to the behavior of the startup scripts, navigate to the Protégé.Client folder and transfer the following script:

  Code Block
  run_protege_BGT.sh (BiomedGT) or run_protege_NCIT.sh (NCIThesaurus)

• If you do need to use a new script, make sure the -Xmx memory is adjusted upwards from the default from the table.

• As long as no changes have been made to the behavior of the startup scripts, navigate to the Explanation.Server directory and transfer the following files:

  Code Block
  restart_explanation_server.sh stop_explanation_server.sh start_explanation_server.sh

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• A window will open requesting the address of the source of the OWL file. Navigate to /app/protege/data/Protege_x.x/<PROTEGE-INSTANCE>/ and select BiomedGT.owl, and click next. Leave the next two windows to their default values, then click Finish. Loading the file to the client will take approximately 5-10 minutes.

• Once the file is loaded, the ontology repository settings will need to be changed if configuring a BiomedGT project. From the menu bar, click 'OWL', and 'Ontology Repositories'. The Repository Manager window is now displayed with a list of default project repository locations underneath the 'Project repository' tab. Remove the following URL repositories:

  Code Block
  http://ncicb.nih.gov/xml/owl/EVS/BGTCommonWords.owl http://ncicb.nih.gov/xml/owl/EVS/BGTThesaurusNodes.owl http://ncicb.nih.gov/xml/owl/EVS/External.owl

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• Click 'EditTab' on the menu bar, and select 'preferences'. Click on the 'panels' tab, and ensure that all four checkboxes are checked (Retire, Split, Merge, and Copy). Click the close button.

• Click 'Project' on the menu bar, and select 'configure'. On the Tab Widgets tab, enable only the following boxes from the Widgets tab and put in the following order:

  Code Block
  NCIEditTab LuceneQueryPlugin OWLPropertiesTab OWLMetadataTag ChangesTab ExplanationTab WorkflowTab

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• From the menu bar, select 'LuceneQueryPluginLucene" and select 'Index Ontologies. A window will pop up. Check both the 'Phonetic Indexer' and the 'Standard Indexer', and and select 'OK'. After indexing has completed, a new Lucene folder will be stored in the same directory as your database project file.

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• Open the nci_metaproject.pprj located at /app/protégé/data/<PROTÉGÉ INSTACE>/meta/. Click on the project tab underneath the SYSTEM-CLASS tab on the left-hand side menu. Select the 'Instances' tab at the top of the page. You will notice an 'Instance Browser' section, and an 'Instance Editor' section. The instance browser specifies the display name of your project, and the Instance Editor specifies the path of your database project. Click on the display project name and set the correct path to your project files.
• Within the nci_metaproject, the changes ontology projects (annotation files) should also not be made visible to users when trying to access a project on the server. If this has not already been configured, please view the DisplayInList setup instructions.

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