Protégé NCI Thesaurus Admin Guide Cheatsheet v1.0

Servers

Related Programs/Services

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• Configure project (see below, include Save, but don't Exit).
• Exit Protégé without saving (the Save gets done automatically during the conversion)

Database reload into an existing project

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1. Thesaurus tables exist
2. ChaO tables exist
3. Metaproject exists
4. Prompt.properties exists and configured
5. Ncitab.xml exists and configured
6. Shell scripts all exist and configured
7. Prompt complete (if needed)
8. File exported

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Steps

1. Stop protégé server.
2. Stop explanation server.
3. Start Protégé, New Project->Check Create from Exisitng Sources, select OWL/RDF Files->Find file->OWL DL->Finish
4. Save to temp project Thesaurus_Temp.pprj
5. Change to database project File->Convert Project to Format-> Select Clark-Parsia Protégé OWL/RDF Database->Enter the JDBC URL using the database ->Table (Thesaurus)-> Username (********)->Password(*******)
   1. Overwrite existing database tables.
6. File->Save Project to the temp project
7. Close client.  Reopen Thesaurus.pprj
   1. Check that everything is configured correctly and the database can be reached.
8. Close client
9. Start explanation server and monitor
10. Start protégé server
11. Start client pointed at server
12. Reindex
13. Verify it works and returns queries
14. Classify

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Configuring a New Project

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Q: After building the database, why am I getting this weird warning and Java RuntimeException?

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A: You accidentally selected the 'Clark & Parsia Database' option.  Start over and select the 'Clark & Parsia OWL/RDF Database' instead.

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A: This is due to a hard-coding where the application will attempt to find a project file named annotation_PROJECTNAME.pprj.  Rename this project file if it exists so Protege can create a new one and is no longer trying to reference the old file.