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Added OWL imports closure
author Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
date Sat, 17 Sep 2011 13:41:28 +0200
parents 4f60202c58d9
children 3740505b579c
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1 <tool id="oppl" name="Execute an OPPL file against an ontology" version="1.0.3">
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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
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4 <!-- The conditional is tacky, I think, but it works! -->
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5
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6 <command>
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7 #if $import_opts.imports_select==False #java -Xmx7000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/oppl_galaxy_tool.jar $input $OPPL $format $inferred NoImports > $output 2>/dev/null
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8 #else #java -Xmx7000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/oppl_galaxy_tool.jar $input $OPPL $format $inferred $imports > $output 2>/dev/null
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9 #end if
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10 </command>
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12 <!--<command>java -Xmx7000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/oppl_galaxy_tool.jar $input $OPPL $format $inferred $imports > $output 2>/dev/null</command>-->
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14 <inputs>
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15 <param format="text" name="input" type="data" label="Input ontology file"/>
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16 <param format="text" name="OPPL" type="data" label="OPPL file"/>
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17 <conditional name="import_opts">
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18 <param name="imports_select" type="boolean" value="False" truevalue="imports_yes" falsevalue="imports_no" label="Tick the box if the loaded ontology includes OWL imports"/>
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19 <when value="imports_no"/>
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20 <!--<when value="imports_no">
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21 <param type="hidden" name="imports" value="NoImports"/>
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22 </when>-->
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23 <when value="imports_yes">
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24 <param format="text" name="imports" type="data" label="OWL imports URI mapping file"/>
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25 </when>
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26 </conditional>
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27 <param name="format" type="select" label="Choose ontology output format">
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28 <option value="OWL" selected="true">OWL</option>
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29 <option value="OBO">OBO</option>
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30 </param>
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31 <param name="inferred" type="boolean" value="False" truevalue="Add_inferred" falsevalue="Gora_ni" label="Add inferred subsumption axioms to output ontology"/>
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33 </inputs>
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34 <outputs>
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35 <data format="text" name="output" />
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36 </outputs>
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37 <tests>
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38 <test>
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39 <param name="input" value="test.owl"/>
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40 <param name="OPPL" value="test.oppl"/>
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41 <param name="format" value="OWL"/>
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42 <param name="inferred" value="False"/>
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43 <param name="imports" value="NoImports"/>
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44 <output name="out_file" file="test_new.owl"/>
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45 </test>
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46 </tests>
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47 <help>
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48
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49 **About OPPL-Galaxy**
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50
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5255f1333cc4 Version 1.0.1
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51 OPPL-Galaxy can be used to execute an OPPL script against an 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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52
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53 **Formats**
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54
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55 OPPL-Galaxy uses the OWL API, and therefore it can load any ontology format that such API is able to load: OBO flat file, OWL (RDF/XML, OWL/XML, Functional, Manchester), turtle, and KRSS. The available output formats are OBO flat file and OWL (RDF/XML).
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56
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57 **Usage**
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58
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59 An ontology and an OPPL file are needed (test.owl and test.oppl can be used as samples, both available in the bundle). Load both with Get Data >> Upload File from your computer.
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61 Then execute the OPPL file against the OWL file with Ontology Pre Processor Language >> Execute an OPPL file against an OWL file. A new output ontology will be generated.
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63 In case the loaded ontology includes OWL imports, a file that maps the imported ontologies' URIs to actual physical URIs is needed. The file (See the file test_URI_mappings provided in the bundle) follows the convention URI-tab-physical URI:
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64
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65 http://purl.obolibrary.org/obo/CHEBI_ONTOLOGY_chebi_ontology /home/pik/UPM/OPPL_galaxy/oppl/OPPL/chebi.owl
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66
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67 http://purl.obolibrary.org/obo/UBERON_uberon /home/pik/UPM/OPPL_galaxy/oppl/OPPL/cell.owl
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68
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69 The output ontology can be OBO or OWL (RDF/XML).
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71 The inferred subsumption axioms can be added to the output ontology as asserted axioms.
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72
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73 **More information**
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74
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75 http://oppl.sf.net/
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77 http://owlapi.sourceforge.net/
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78
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79 http://www.w3.org/TR/owl2-manchester-syntax/
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81 http://clarkparsia.com/pellet
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82
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83 **Contact**
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84
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85 Please send any request or comment to mikel.egana.aranguren@gmail.com.
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86
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87 </help>
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88
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89 </tool>