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annotate OPPL/oppl.xml @ 7:756f1f5798bf

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Added (Properly) reasoner option (Pellet or HermiT)
author Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
date Sun, 18 Sep 2011 12:57:22 +0200
parents 3740505b579c
children 40adbcb2a7cc
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1 <tool id="oppl" name="Execute an OPPL file against an ontology" version="1.0.4">
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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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4 <!-- The command execution of the conditional is tacky, I think, but it works! -->
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5 <!-- Galaxy is not happy with OPPL throwing info into stderr, and I have redirected stderr to /dev/null, which is a bad solution since OPPL galaxy does not inform properly when it fails -->
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6 <!-- More info on the stderr issue: http://wiki.g2.bx.psu.edu/Future/Job%20Failure%20When%20stderr -->
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8 <command>
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9 #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 $reasoner > $output 2>/dev/null
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10 #else #java -Xmx7000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/oppl_galaxy_tool.jar $input $OPPL $format $inferred $imports $reasoner > $output 2>/dev/null
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11 #end if
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12 </command>
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14 <!-- For big ontologies use something like java -Xmx7000M -Xms250M -DentityExpansionLimit=1000000000 -jar -->
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16 <inputs>
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17 <param format="text" name="input" type="data" label="Input ontology file"/>
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18 <param format="text" name="OPPL" type="data" label="OPPL file"/>
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19 <conditional name="import_opts">
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20 <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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21 <when value="imports_no"/>
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22 <!--<when value="imports_no">
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23 <param type="hidden" name="imports" value="NoImports"/>
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24 </when>-->
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25 <when value="imports_yes">
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26 <param format="text" name="imports" type="data" label="OWL imports URI mapping file"/>
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27 </when>
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28 </conditional>
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29 <param name="format" type="select" label="Choose ontology output format">
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30 <option value="OWL" selected="true">OWL</option>
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31 <option value="OBO">OBO</option>
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32 </param>
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33 <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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34 <param name="reasoner" type="select" label="Choose reasoner">
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35 <option value="Pellet" selected="true">Pellet</option>
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36 <option value="HermiT">HermiT</option>
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37 </param>
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38
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39 </inputs>
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40 <outputs>
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41 <data format="text" name="output" />
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42 </outputs>
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43 <tests>
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44 <test>
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45 <param name="input" value="test.owl"/>
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46 <param name="OPPL" value="test.oppl"/>
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47 <param name="imports" value="NoImports"/>
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48 <param name="format" value="OWL"/>
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49 <param name="inferred" value="False"/>
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50 <param name="reasoner" value="Pellet"/>
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51 <output name="out_file" file="test_new.owl"/>
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52 </test>
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53 </tests>
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54 <help>
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55
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56 **About OPPL-Galaxy**
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57
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58 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. An OPPL script (See test.oppl) defines a query to be performed against the ontology, and some actions (Adding or removing axioms) 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 an ontology, saving time and effort.
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59
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60 **Formats**
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61
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5255f1333cc4 Version 1.0.1
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62 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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63
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64 **Usage**
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65
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66 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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67
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68 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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69
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70 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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72 http://purl.obolibrary.org/obo/CHEBI_ONTOLOGY_chebi_ontology /home/pik/UPM/OPPL_galaxy/oppl/OPPL/chebi.owl
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73
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74 http://purl.obolibrary.org/obo/UBERON_uberon /home/pik/UPM/OPPL_galaxy/oppl/OPPL/cell.owl
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76 The output ontology can be OBO or OWL (RDF/XML).
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77
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78 The inferred subsumption axioms can be added to the output ontology as asserted axioms.
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79
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80 The reasoner can be Pellet or HermiT. Sometimes, if an execution fails it can be fixed by using a different reasoner.
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81
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82 **More information**
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83
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84 http://oppl.sf.net/
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85
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86 http://owlapi.sourceforge.net/
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87
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88 http://www.w3.org/TR/owl2-manchester-syntax/
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89
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90 http://clarkparsia.com/pellet
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91
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92 http://hermit-reasoner.com/
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93
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94 **Contact**
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95
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96 Please send any request or comment to mikel.egana.aranguren@gmail.com.
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97
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98 </help>
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99
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100 </tool>