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* There are still many features missing that we plan to implement ([see the list of open issues](https://git-ainf.aau.at/interactive-KB-debugging/debugger/issues)). If you have ideas for features that would be nice to have [we](http://isbi.aau.at/ontodebug/team) would be pleased if you [send us your request](http://isbi.aau.at/ontodebug/feedback).
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* Please note that this plugin is a BETA ! **If you experience a faulty behaviour of your Protégé instance** (for example your Protege cannot start), it *may* be that this plugin causes the error. You can test this in the following way: delete the file called "*org.exquisite.protege-\<x.y.z>.BETA.jar*" in the "*plugins*" subdirectory of your Protege installation directory and restart Protégé (the *\<x.y.z>* represents the current version such as 0.1.3). In the same way you can also check other plugins if they are responsible for the fault. If this plugin is not causing the error you can later reinstall it.
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<br><br>
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# Installation
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These steps are necessary in order to run the plug-in:
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* If your Protégé client is already running, you will have to restart the client to load the plugin.
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* After your Protégé client has restarted you will see the additional menu entry ```Tools->Debug Ontology ...```
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![debug_ontology_menuentry](/uploads/4d52afa2f4c3591f9e408cb193f85de5/debug_ontology_menuentry.png)
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*These three menu items in the Tools menu show that the Ontology Debugger is installed correctly*
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<br><br>
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# About the Ontology Debugger Plug-In for Protégé
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The Ontology Debugger's main task is to ***support the user*** in the process of ***finding the faulty axioms*** in [inconsistent and/or incoherent ontologies](http://ontogenesis.knowledgeblog.org/1329).
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- As long as there is more than one possible ontology repair, the Ontology Debugger is repeating the dialog and states further queries to the user.
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- Once there is only one repair set of faulty axioms that explain the incoherency/inconsistency, the interaction is finished and no more questions are generated.
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- Note that once a possible ontology repair set of faulty axioms (or diagnosis) is found this means that ***every axiom*** in this set is responsible for the inconsistency/incoherency in the ontology.
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- **Remark**: The user of the Ontology Debugger is ***not*** required to analyze (1) which entailments (or statements) do or do not hold or why certain entailments (or statements) do or do not hold ***in the faulty input ontology*** or (2) ***why exactly the input ontology is faulty***. The user is just assumed to answer questions about what should be true or not true ***in the intended ontology or domain model***, respectively. Given the answers, the Ontology Debugger will return what must be repaired in the faulty input ontology.
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- **Remark**: The user of the Ontology Debugger is ***not*** required to analyze
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1. which entailments (or statements) do or do not hold or why certain entailments (or statements) do or do not hold ***in the faulty input ontology*** or
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2. ***why exactly the input ontology is faulty***.
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- The user is just assumed to answer questions about what should be true or not true ***in the intended ontology or domain model***, respectively. Given the answers, the Ontology Debugger will return what must be repaired in the faulty input ontology.
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<br><br>
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# Tutorial
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In the following tutorial we want to show you
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The search can be either *case sensitive*, or restricted to have *whole words* or *ignoring white spaces* or a combination of these.
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<br><br>
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# Preference settings for the Ontology Debugger Plug-In in Protégé
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In the above debugging session the default settings and the *HermiT* reasoner were used. You can change these settings in the debugger preferences in ```File->Preferences```
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