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Protégé NCI Thesaurus Admin Guide Cheatsheet v1.0

Servers

Related Programs/Services

• MobaXterm Professional
• Reflection X (using "Direct" or xterm over SSH connection).
• F-Secure SSH Client
• F-Secure SSH Transfer
• Username and password advertised separately

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Dev, QA, Stage File Directory for Builds

• /app/protege/repo

Build Notes

• The automated build script will prompt for various configuration items (for files such as the run scripts, PromptNCIPlugin.properties, etc).
• Do not use the default localhost for any IP addresses. Always use the machine name, and include the port.
• Do not include PromptNCIPlugin.properties with a distributed client.
• Set the max code + 1 in codegen.dat

Production Login and Basic Server Operations

• If the Protégé server is brought down for maintenance, classification, Prompt analysis, and so on, the RMI can continue running. While all the services need to be started (e.g. after a reboot), follow this order (see the following bullets for details):
  • star start RMI
  • start explanation server
  • start Protégé server

• Remote login
  • Use reflection X MobaXterm (or SSH client if running the Protégé client is not required).

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• Shutdown rmiregistry
  • Kill from OS (identify with ps -ef | grep rmiregistry)
  • Run kill -9 [rmi pid]

• Start explanation server
  • From /usr/local/protegeqa/NCIThesaurusGroup/Explanation.Server-x.y.z
  • Run with option to periodically save the reasoner state at a desired time frame: ./start_explanation_server.sh --port 8092 --protege-standalone /path/to/database/project/ --persistence <numeric time value>
  • Run w/out checking for any changes in ontology: ./start_explanation_server.sh --port 8092 --protege-standalone /path/to/database/project/ --no-ontology-sync

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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

Preconditions – Thesaurus running normally

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

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

Configuring a New Project

• (already logged-in in the server box)
• Enable tabs in this order
  
  • NCIEditTab
  • LuceneQueryPlugin
  • OWLProperties
  • OWLMetadataTab
  • ChangesTab
  • ExplanationTab
• Upon enabling the ChangesTab, click OK
  
  • Dialogue will pop up. Select 2nd option 'Create ChAO stored in database' and click enable change tracking. Click OK.
  • Create new DB dialogue table gets "annotation_" prefixed
  • Enter DB credentials
  • Click OK
• File->Save Project
• Configure->Deselect Changes tab, Options tab->Track changes should be checked
• Disable other extra tabs (OWLClasses, OWLInstances, OWLForms)
• Configure URL for explanation service.
• Enable journaling
• Disable redo/undo
• Set OWL Preferences to read 'Manchester Syntax'
• Set transitivity
• Set display slots to read 'Preferred Name' for the NCI Edit tab as well as Property Tag within the Forms Tab for:
  • owl:Class
  • DatatypeProperty
  • code
  • ObjectProperty
• Configure URL for explanation service.
• Goto OWL->Preferences
  
  • Disable
  drag and drop in 'OWL Preferences'
• Disable test of deprecated classes/properties
• Set Visibility tab to uncheck all MetaData items
• • Drag and Drop, verify reasoner URL is correct
  • Visibility->uncheck rdfs:Class, owl:Class, rdf:Property
  • Datatypes->rdf:XMLLiteral should be checked
  • Tests->uncheck 'Find TODO list items' and 'List deprecated classes and properties'
• Reasoning->Select Clark & Parsia
• Reasoner Details->Click Synchronize Changes with Reasoner, Reasoner Behavior select Synchronize on query
• Set OWL Preferences to read 'Manchester Syntax'
• Set transitivity
• Generate Lucene indicesGenerate Lucene indices
  
  • Lucene->Index Ontologies, accept all slots, Use Phoenetic and Standard indexers, click OK (this should take less than 20 minutes in a Production quality envrironment)
  • Move lucene index from /app/protegeqa/data/Protege_x.y.z/NCIThesaurus to the Proege server directory
• Save project
• Exit Protégé

Configuring the Metaproject

• Open the metaproject
• Instance tab->Click User class
  • In the Instance Browser copy an editor (to the number of users needed)
  • Enter full name
  • Change password
• PolicyControlledObject->ProjectClass
  • Verify Thesaurus instance Location is edited to the pprj location
  • Verify Annotation Thesaurus instance Location is edited to the annotation_Thesaurus... location
    • It should be granted the 'GrpOp(World)' instance that does not contain the 'DisplayInList' instance to prevent it from showing as a selectable project on login
    • See 'DisplayInList' Project Setup Instructions for more details.
  • File->Save Project->Exit

Configure Protégé Server for a Project

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• From the client GUI, enable OWLClassesTab (results are shown there)
• From the OWL menu, select 'Classify Taxonomy' it takes about 20 minutes
• Once classification is complete, an inferred hierarchy panel and a list panel are displayed.
• Accept retreeing suggestions in the list panel as per guideline
• Generate table to pass around to editors and mail it
• Process table from previous classification (accept/reject)
• Close project without saving
• Exit the client.

Troubleshooting

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

Image Added

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

Q: I exported an owl file from my project, but now the project loads from a file.  What's up?

A: When exporting an owl file, rename the project and not the owl file by itself.  When renaming the project, your owl export will follow the same naming convention used.

Q: I've started a new project and am trying to enable the Changes tab, but am getting a red box and error similar to 'ncit.

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annotation_thesaurus doesn't exist'

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.

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