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1 <tool id="oppl" name="Execute an OPPL file against an OWL file" version="1.0.0">
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2 <description>It executes an OPPL script against the input ontology and generates a new ontology with the changes described in the OPPL script</description>
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3 <command>java -jar ${__tool_data_path__}/shared/jars/oppl_galaxy_tool.jar $input $OPPL > $output </command>
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4 <inputs>
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5 <param format="text" name="input" type="data" label="Source OWL file"/>
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6 <param format="text" name="OPPL" type="data" label="OPPL file"/>
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7 </inputs>
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8 <outputs>
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9 <data format="text" name="output" />
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10 </outputs>
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11
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12 <tests>
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13 <test>
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14 <param name="input" value="test.owl"/>
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15 <param name="OPPL" value="test.oppl"/>
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16 <output name="out_file" file="test_new.owl"/>
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17 </test>
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18 </tests>
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19
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20 <help>
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21
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22 **About OPPL-Galaxy**
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23
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24 OPPL-Galaxy can be used to execute an OPPL script against an (OWL) ontology, generating a new ontology. OPPL (Ontology Pre Processor Language) is a high level scripting language, based in the Manchester OWL Syntax, to automate the manipulation of an ontology (Adding or removing axioms). An OPPL script (See bellow or test.oppl) defines a query to be performed against the ontology, and some actions that affect the entities that will be retrieved. Those entities can be named or defined by a variable. OPPL is a powerful method for defining and executing modelling patterns that are repeated in a given ontology, saving time and effort.
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25
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26 **Formats**
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27
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28 OPPL-Galaxy uses the OWL API, and therefore can work with any ontology format that such API is able to load. That includes: OBO flat file, OWL (RDF/XML, OWL/XML, Functional, Manchester), turtle, and KRSS.
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29
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30 **Usage**
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31
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32 An ontology and an OPPL file are needed (test.owl and test.oppl can be used as samples). Load both with Get Data >> Upload File from your computer.
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33
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34 Then execute the OPPL file against the OWL file with Ontology Pre Processor Language >> Execute an OPPL file against an OWL file.
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35
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36 This is the OPPL script provided in the bundle, test.oppl. Variables start with ?:
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37
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38 ?whole:CLASS,
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39 ?part:CLASS
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40 SELECT
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41 ?part SubClassOf part_of some ?whole WHERE ?part != Nothing
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42 BEGIN
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43 ADD ?part SubClassOf part_of only ?whole
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44 END;
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45
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46 **More information**
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47
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48 http://oppl2.sourceforge.net/
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49
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50 http://owlapi.sourceforge.net/
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51
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52 http://www.w3.org/TR/owl2-manchester-syntax/
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53
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54 http://clarkparsia.com/pellet
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55
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56 **Features that will be implemented soon**
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57
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58 OWL import closure
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59
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60 Choose output format (Right now only OWL RDF/XML is available)
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61
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62 Choose reasoner (Right now only Pellet is available)
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63
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64 **Contact**
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65
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66 Please send any request or comment to mikel.egana.aranguren@gmail.com.
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67
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68 </help>
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69
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70 </tool>
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