NIH | National Cancer Institute | NCI Wiki  

Error rendering macro 'rw-search'

null

Versions Compared

Key

  • This line was added.
  • This line was removed.
  • Formatting was changed.

...

  • 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 101000102000. Save and exit the file.  
  • Open the Protege client from the dev tier, and folder, and click on 'run_protege<PROTEGE-INSTANCE>_' to open the client.  Once open, 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 file. Navigate to /app/protege/data/Protege_x.x/<PROTEGE-INSTANCE>/ and select BiomedGT-Fixed-wNS-DefaultAndPrefix.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 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: 

     _

     _

     _

  • The removed repositories will then be re-added to the list, but referenced locally.  Accessing local copies of an external ontology increases performance as well as dependability of the ontology (the ontology URL might be down).  To readd locally, click on the white plus button located at the top right of the window.
  • Follow the wizard by specifying the location of your local folder. Ensure that the  'Force Read-Only' box is uncheked.
  • 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.
  • Once loaded (the GUI should be visible with the OWL file displayed)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.
  • In the database info window, enter all requested database info and click finish. Give the Project name the following naming convention: <PROTEGE INSTANCE>-YYMMDD-DB.pprj.  Note that the JDBC URL must be in the following format: jdbc:mysql://<databasehostname>:<port>/<database name>  (Please look at the database info for each instance and tier). Give the table name the following naming convention: <PROTEGE-INSTANCE>_<YYMMDD>_<tier>_<release number>.  Conversion can take anywhere up to 2.5 hours.

...

     NCIEditTab
     LuceneQueryPlugin
     OWLPropertiesTab
     OWLMetadataTag
     ChangesTab
     ExplanationTab
     WorkflowTab
 

  • Click on the 'options' tab and enable journaling and disable redo/undo.
  • After closing the configurations window, a changes ontology window will appear prompting you to select how to configure the annotations project.  Currently, all annotations and changes are being stored into a database table. Select the radio option to create a changes ontology to a database table (Should be the 2nd button).
  • 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.  Once renamed, click
    'OK'This process should take a few seconds.
  • From the menu bar, select 'LuceneQueryPlugin" 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.

...

  • 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 Reasoner' box is checked.  Click 'OK'.
  • The Changes tab will now be disabled from the GUI, since all changes will be recorded to the database.  To disable, click on 'Projects', 'Configure' and uncheck the 'ChangesTab' box.  Click 'OK', and the changes tab should now be gone from the GUI.
  • Click File,  Save Project. 

...

  • Close the project WITHOUT saving the file project (the file project automatically gets saved), however, leave the Protégé client open.
  • 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.  To configure the project display listIf this has not already been configured, please view the DisplayInList setup instructions.

...