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**NOTE: THIS PLUG-IN IS STILL IN DEVELOPMENT, VERY PROBABLY YOU WILL EXPERIENCE FAULTY AND UNEXPECTED BEHAVIOUR SUCH AS DEADLOCKS**
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# Installation
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## Prerequisites
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#### Prerequisites
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These requirements are necessary in order to run the plugin:
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* Java Runtime Version 8. If you do not have it installed, please download it from [https://www.java.com/de/download/](https://www.java.com/de/download/) and follow the installation instructions there.
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* The most recent Protege Desktop Version. Please download it from [http://protege.stanford.edu/](http://protege.stanford.edu/) and follow the installation instructions. Please not that is recommended to use version 5. The Protégé Debugger Plug-In is not compatible with version 4.
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* The [Protégé Debugger Plug-In](/uploads/14b0041bfa33146eb10283d795b745de/org.exquisite.protege-1.0-SNAPSHOT.jar)
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## Usage
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### Some other plugins are necessary
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Our plugin requires at least one reasoner. Protege 5 comes already with HermiT, but you can also install other reasoners like FaCT++ or Pellet. Installing plugins in Protégé is done by selecting File->Check for plugins... After installing additional reasoner plugins you will have to restart Protégé
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### Install the Protégé Plugin
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#### Some other plugins are necessary
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Our plugin requires at least one reasoner. Protege 5 comes already with HermiT, but you can also install other reasoners like FaCT++ or Pellet. Installing plugins in Protégé is done by selecting *File->Check for plugins...*. After installing additional reasoner plugins you will have to restart Protégé.
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#### Install the Protégé Plugin
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Copy the protege [Protégé plug-in](/uploads/14b0041bfa33146eb10283d795b745de/org.exquisite.protege-1.0-SNAPSHOT.jar) into the plugins subfolder of your Protégé 5 desktop client. If your Protégé client is running, please restart it to load the Plug-In. You should see now a new tab called Exquisite Debugger!
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![ExquisiteDebuggerTab](/uploads/a25cb9d39e0523e0b9ddfdd83928e50e/ExquisiteDebuggerTab.PNG)
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### Exquisite Ontology Debugging
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Now load an ontology. For this document we are using [our example ontology](/uploads/f100242ac5e8c655833a21e3ec9143e6/running_example_annotated.owl) with explicit declaration of axioms that are possibly faulty (we name the m the knowledge base, correct axioms or background knowledge as well as entailed and not entailed examples.
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# How to use the Plug-In
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Let us load an ontology (*File->Open File*)!
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For this document we are using [our example ontology](/uploads/f100242ac5e8c655833a21e3ec9143e6/running_example_annotated.owl) with explicit declaration of axioms (the _diagnoses model_) that are possibly faulty (we name them the _knowledge base_), axioms which are correct (or the _background knowledge_) as well as entailed and not entailed axioms, which must or must not be concluded from the diagnoses model. You will see this explicit declaration in our Ontolgy Debug Tab.
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Open the Exquisite Ontology Debug Tab (*Exquisite Debugger -> Open Exquisite Ontology Debug Tab*) and select the tab.
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#### The Exquisite Ontology Debugging Tab
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Open the Exquisite Ontology Debug Tab (*Exquisite Debugger -> Open Exquisite Ontology Debug Tab*).
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![debugger](/uploads/b18b3ea12f8ee4e7e14b07676abbc080/debugger.PNG)
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### Diagnoses
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# Diagnoses
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With this tool we can search for diagnoses. But first we have to configure which reasoner we want to use for the diagnoses search. Select *Reasoner->and a preferered reasoner*
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### Options for diagnoses
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Next let us see what option do we have for the diagnoses search. Select *Exquisite Debugger->Options*
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#### Options for diagnoses
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Next let us see what option we do have for the diagnoses search. Select *Exquisite Debugger->Options*
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![options_diagnoses](/uploads/085d60225ca537dd5df02a8e543e9086/options_diagnoses.PNG)
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* As diagnoses engine we can choose between Juncker's QuickXPlain (default), HS-DAG and HS-Tree.
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* As diagnoses engine we can choose between Juncker's QuickXPlain (default) and Reiter's HS-Tree and HS-DAG. Please note that with HS-Tree and HS-DAG we can present the minimal conflict set too.
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* Next we can choose how many diagnoses we want to calculate at most (default is 9). Please note that the higher the number the more time is required to calculate depending on the complexity of the ontology.
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* If we have a consistent ontology we can reduce the incoherency to inconsistency and by option can extract star modules for that case.
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### The search for diagnoses
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#### The search for diagnoses
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Once we are happy with our preferences we can start the *Search Diagnoses* button and hopefully we will get some diagnoses in reasonable time.
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In our example we will get these diagnoses:
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![diagnoses](/uploads/216e58d304370983784d2b4d480777e1/diagnoses.PNG)
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_Please note_: when you want to select another reasoner for diagnoses calculation you have to choose *Exquisite Debugger->Options* once to make the reasoner selection effective. |
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_Please note_: when you want to select another reasoner for diagnoses calculation you have to choose *Exquisite Debugger->Options* once to make the reasoner selection effective.
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# Queries
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Using the diagnoses we can interview the expert if some axioms are entailed or not entailed. This interaction is possible with the Exquisite Interactive Debugging Tab
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#### The Exquisite Ontology Interactive Debugging Tab
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**Please note that some functionality in this tab is not implemented yet.**
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Open the Exquisite Ontology Interactive Debug Tab (*Exquisite Debugger -> Open Exquisite Ontology Interactive Debug Tab*). |