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... | @@ -7,11 +7,11 @@ This plug-in is still in development! Very probably you may experience faulty an |
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These steps are necessary in order to run the plug-in:
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These steps are necessary in order to run the plug-in:
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* Download the latest version of Protégé Desktop from [http://protege.stanford.edu/](http://protege.stanford.edu/) and follow the installation instructions. Note that the Debugger Plug-In is not compatible with Protégé version 4 and below.
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* Download the latest version of Protégé Desktop from [http://protege.stanford.edu/](http://protege.stanford.edu/) and follow the installation instructions. Note that the Debugger Plug-In is not compatible with Protégé version 4 and below.
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* Install the Ontology Debugger Plugin with Protégé's Update Function```File->Check for Plugins...``` and select *Ontology Debugger* ![Unbenannt](/uploads/71481d72ac9c72dedebdcef37d042d7f/Unbenannt.PNG)
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* Install the Ontology Debugger Plugin with Protégé's Update Function```File->Check for Plugins...``` and select *Ontology Debugger* ![installation_plugin](/uploads/9efbb55d833eccd784b7559f6e56a7cf/installation_plugin.PNG)
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* **Alternatively** you can also download the [latest jar-file](http://isbi.aau.at/ontodebug/plugin) of the *Ontology Debugger* and copy the jar-File into the ```plugins``` subfolder of your Protégé 5 desktop client.
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* **Alternatively** you can also download the [latest jar-file](http://isbi.aau.at/ontodebug/plugin) of the *Ontology Debugger* and copy the jar-File into the ```plugins``` subfolder of your Protégé 5 desktop client.
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* If your Protégé client is already running, then you have to restart the client to load the plug-In.
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* If your Protégé client is already running, then you have to restart the client to load the plug-In.
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* Once your Protégé client has restarted you will see an additional menu entry in ```Tools->Debug Ontology ...``` as shown here: ![debug_ontology_menuentry](/uploads/bee8628627ac19886a99ffa6cc7d8b55/debug_ontology_menuentry.PNG)
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* Once your Protégé client has restarted you will see an additional menu entry in ```Tools->Debug Ontology ...``` as shown here: ![debug_ontology_menuentry](/uploads/4d52afa2f4c3591f9e408cb193f85de5/debug_ontology_menuentry.png)
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# How to use the Ontology Debugger Plug-In in Protégé
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# How to use the Ontology Debugger Plug-In in 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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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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... | @@ -21,10 +21,10 @@ The Ontology Debugger's main task is to ***support the user*** in the process o |
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- Each axiom given in such a query can then be read in the form of the question: ***Must this axiom be entailed by the desired ontology?*** or ***Does this axiom hold in the domain that should be modeled by the ontology?***
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- Each axiom given in such a query can then be read in the form of the question: ***Must this axiom be entailed by the desired ontology?*** or ***Does this axiom hold in the domain that should be modeled by the ontology?***
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- The user responds with the answer _YES_ if she thinks that this axiom must hold for the ontology or _NO_ otherwise.
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- The user responds with the answer _YES_ if she thinks that this axiom must hold for the ontology or _NO_ otherwise.
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- Note that the ***axioms of a query*** can be either ***explicitly stated axioms in the faulty ontology*** or ***statements inferred from axioms in the ontology and the answers given for previous queries***.
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- Note that the ***axioms of a query*** can be either ***explicitly stated axioms in the faulty ontology*** or ***statements inferred from axioms in the ontology and the answers given for previous queries***.
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- The answers given by the user are also taken into account in the process of narrowing down the set of faulty axiom sets (these faulty axiom sets are also called _diagnoses_).
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- The answers given by the user are also taken into account in the process of narrowing down the set of faulty axiom sets (these faulty axiom sets are also called ***Possible Ontology Repairs*** or _diagnoses_).
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- As long as there are more than one set of faulty axioms that together explain the inconsistency/incoherency, the Ontology Debugger is repeating the dialog and stating further queries to the user.
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- As long as there are more than one set of Possible Ontology Repairs that together explain the inconsistency/incoherency, the Ontology Debugger is repeating the dialog and stating further queries to the user.
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- Once there is only one set of faulty axioms that explain the incoherency/inconsistency the interaction is finished and no more questions are generated.
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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 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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- 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 must or must not hold ***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 (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 must or must not hold ***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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### Step 1: Load the ontology
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### Step 1: Load the ontology
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... | @@ -40,7 +40,7 @@ For our example we must therefore also select a reasoner. Please choose the alr |
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Once you have loaded the *Koala ontology*, you can open the *Ontology Debugger Tab* by selecting ```Tools->Debug Ontology...``` in the menu. You may also activate the tab by enabling the tab with ```Window->Tabs->Debugger```. The initial layout of the *Ontology Debugger* should look similar to this screenshot:
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Once you have loaded the *Koala ontology*, you can open the *Ontology Debugger Tab* by selecting ```Tools->Debug Ontology...``` in the menu. You may also activate the tab by enabling the tab with ```Window->Tabs->Debugger```. The initial layout of the *Ontology Debugger* should look similar to this screenshot:
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![step3](/uploads/4552840330ef1449241f3ef422f4a437/step3.PNG)
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![step3](/uploads/1b7a63618ffc50cd0cd5dc333b50e3ce/step3.png)
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***Note*** if you do not see this layout or if you see errors then the layout has changed with a new version of the debugger. Please select ```Window->Reset selected tab to default state``` in such a case to display the current layout.
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***Note*** if you do not see this layout or if you see errors then the layout has changed with a new version of the debugger. Please select ```Window->Reset selected tab to default state``` in such a case to display the current layout.
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