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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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• 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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• (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
  • File->Save Project->Exit

Configure Protégé Server for a Project

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