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Protégé NCI Thesaurus Admin Guide Cheatsheet v1.0
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Servers
Name | Description |
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cbiows501 | Production (protegeqa user) |
cbvapp-s1005 | Stage (protegeadm user) |
cbapp-q1001 | QA (protegeadm user) |
cbvapp-d1012 | Dev (protegeadm user) |
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
- Thesaurus tables exist
- ChaO tables exist
- Metaproject exists
- Prompt.properties exists and configured
- Ncitab.xml exists and configured
- Shell scripts all exist and configured
- Prompt complete (if needed)
- File exported
Steps
- Stop protégé server.
- Stop explanation server.
- Start Protégé, New Project->Check Create from Exisitng Sources, select OWL/RDF Files->Find file->OWL DL->Finish
- Save to temp project Thesaurus_Temp.pprj
- 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(*******)
- Overwrite existing database tables.
- File->Save Project to the temp project
- Close client. Reopen Thesaurus.pprj
- Check that everything is configured correctly and the database can be reached.
- Close client
- Start explanation server and monitor
- Start protégé server
- Start client pointed at server
- Reindex
- Verify it works and returns queries
- 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
- 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?
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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