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Protégé Software Updates and Configuring New Database Project

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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• 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 + Ii" to edit. The code.prefix value can be adjusted, depending on which Protégé Instance is being used (BiomedGT or NCI Thesaurus). BiomedGT uses used a prefix of 'B', while NCI Thesaurus uses 'C'. Keep the seed number at 100000. Save and exit the file by typing 'esc', then ':wq'.

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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.owlthe OWL file, 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.
  
  
• The following few steps reference the deprecated BiomedGT project and may be ignored.

• 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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• Once the window is closed, a pop-up window is displayed prompting you to save the settings and to reload the data into the client. Select the 'Reload' button, and the client should save the settings and reload the client. This step should anywhere from 10-20 minutes, depending on your machine's resources.
• End of steps pertaining to BiomedGT

• Once loaded (the GUI should be visible with the OWL file displayed), the project file can now be converted to a Clark & Parsia OWL/RDF database. Click File, Convert Project to Format, Clark & Parsia OWL / RDF database.

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• After conversion of the project file, you can verify that the database has been created by utilizing a database GUI tool DBMS (such as DB Visualizer) to view if the table has been created. Once verified, the project is now ready to be configured from the client.

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• Next, click the Properties tab, and click the "F" tab on the very right. Click 'OK' for the forms dialogue box. On the left hand menu, click on 'owl:DatatypeProperty, and set it's its display slot drop down to 'rdfs:label'. Next, click on the owl:ObjectProperty on the left hand menu, and set its display slot drop down field to 'rdfs:label' as well.

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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

• Click on the 'options' tab and enable journaling and disable redo/undo.

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• A window will appear requesting all database information, Keep all fields to their default values, except the table name. Another name will need to be assigned to distinguish the annotations table.  It is good practice to prefix the name of this table "annotation_[tablename]". Once the table is renamed, click 'OK'. This process should take a few seconds.

• From the menu bar, select 'LuceneQueryPluginLucene" and select 'Index Ontologies. A window will pop up. Accept all slots. Check both the 'Phonetic Indexer' and the 'Standard Indexer', and and select 'OK'. After indexing has completed (this should take less than 20 minutes on a Production quality machine), a new Lucene folder will be stored in the same directory as your database project file.

• At this point, if a previous version of the Protege and Explanation servers are running, they will need to be shutdown. For best practices, the RMI registry will need to be shutdown as well. Advertise via email that the tier's current Protege instance will be brought down. To shutdown, open another reflection X window SSH connection to the same server. Type 'ps -ef | grep server' to see view the current protege processes running. If both explanation and Protege servers are running, shutdown the explanation server first.

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• Navigate to the previous version Protege server folder by typing 'cd ../Protege.Server-x.x.x'. Once in the directory, type './shutdown_protege_server.sh localhost:<server port>. A message will appear on the console that the server has been shut down. The RMI registry is also shutdown from this directory. Unfortunately, there is no script to shutdown the RMI registry, however, can be killed manually. To determine which port you want to kill, refer to the tier-specific info page. Once the correct port has been determined, type 'ps -ef | grep rmi' to figure out which process ID is running the port that needs to be killed. To kill the process, type '_KILL kill -9 <RMI Process ID>'. _   Once executed, type ps -ef | grep rmi again to see if the process has been terminated.

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• Once in the directory, type './start_explanation_server.sh --protege-standalone --port <port number> /app/protege/data/Protege_x.x/<PROTEGE INSTANCE>/<DB PROEJCT NAME>.pprj. _ After the server has initiated start up, type '_tail -f nohup.out' to view start up status. Within the nohup.out file, the explanation server has started when you see "Jena, Classification, and Extracting' processes all complete, and a "Server started, listening on port xxxx" message.

• Once the server is up and running, go back to the client GUI, click on the 'Reasoning' menu, and ensure that "Clark&Parsia Custom Protege 3.x Reasoner" is selected on the menu list. Click on the 'Reasoning menu again, and scroll down to "Clark&Parsia Custom Protege 3.x Reasoner Details" and ensure that the 'Synchronize Changes with Reasoneron query' box is checked. Click 'OK'.

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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.  There should be a project instance for both the main ontology and annotation ontology.
• 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.
• To add users, select the 'User' class and within the Instance Browser, clone an existing user and modify the username and password.
• Save the metaproject and exit the client.

• Verify that the port numbers in the run_protege_server_nci.sh script correspond to the port numbers in run_rmiregistry.sh. Please refer to Appendix A for tier specific port numbers.

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• Once tested, the client can now be posted up on the GForge website posted to the sFTP to be downloaded by users.

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