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annotate OPPL/oppl.xml @ 18:d3616fac4ca5 draft

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Elk support added
author Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
date Thu, 20 Sep 2012 12:46:36 +0200
parents c9e01f86b07c
children
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1 <tool id="oppl" name="Execute an OPPL file against an ontology" version="1.0.8">
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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 <!-- 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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5 <!-- More info on the stderr issue: http://wiki.g2.bx.psu.edu/Future/Job%20Failure%20When%20stderr -->
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6 <!-- Testing with wrapper.sh but no success so far -->
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10 <!-- DEFAULT SETTINGS -->
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12 <!-- For big ontologies I use -Xmx3000M -Xms250M -DentityExpansionLimit=1000000000 If that's too much for your machine simply delete or modify at will, but since Galaxy is usually used in a server setting it makes sense to use a big chunk of memory -->
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14 <!--<command>
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15 java -Xmx3000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/oppl_galaxy.jar $input $reasoner $OPPL $format > $output 2>/dev/null
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16 </command>-->
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18 <!-- FACT++ -->
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20 <!-- If you are planning to use FaCT++ you have to uncomment bellow (And comment the default settings above) and replace the -Djava.library.path with the appropiate JNI library path for your platform:FaCT++-linux-v1.5.2/64bit, FaCT++-linux-v1.5.2/32bit, FaCT++-OSX-v1.5.2/64bit, ...... -->
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21 <!-- Using this setting doesn't upset the rest of the reasoners so you may as well leave it on if you plan to switch between FaCT++, Pellet and HermiT -->
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23 <command>
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24 java -Djava.library.path=${__tool_data_path__}/shared/jars/FaCT++-linux-v1.5.2/64bit -Xmx3000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/oppl_galaxy.jar $input $reasoner $OPPL $format > $output 2>/dev/null
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25 </command>
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30 <!-- DEBUGGING -->
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32 <!-- For debugging simply remove 2>/dev/null Or uncomment bellow (And comment the default settings above). It will fail always (Due to OPPL messages) but at least it will be informative -->
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34 <!--<command>
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35 java -Xmx3000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/oppl_galaxy.jar $input $reasoner $OPPL $format > $output
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36 </command>-->
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41 <inputs>
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42 <param name="input" type="data" label="Input ontology file"/>
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43 <param format="text" name="OPPL" type="data" label="OPPL file"/>
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44 <param name="reasoner" type="select" label="Choose reasoner">
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45 <option value="Pellet" selected="true">Pellet</option>
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46 <option value="HermiT">HermiT</option>
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47 <option value="FaCTPlusPlus">FaCT++</option>
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48 <option value="Elk">Elk (Not all axioms supported)</option>
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49 </param>
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50 <param name="format" type="select" label="Choose ontology output format">
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51 <option value="OWL" selected="true">OWL</option>
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52 <option value="OBO">OBO</option>
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53 </param>
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54 </inputs>
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55 <outputs>
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56 <data format="text" name="output" />
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57 </outputs>
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58 <!--<tests>
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59 <test>
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60 <param name="input" value="test.owl"/>
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61 <param name="OPPL" value="test.oppl"/>
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62 <param name="format" value="OWL"/>
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63 <param name="reasoner" value="Pellet"/>
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64 <output name="out_file" file="test_new.owl"/>
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65 </test>
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66 </tests>-->
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67 <help>
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69 **About OPPL-Galaxy**
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70
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71 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 energy.
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73 **Usage**
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74
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75 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, or redirect from another Galaxy tool. 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. In case the loaded ontology includes OWL imports, OPPL-Galaxy will try to resolve them.
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77 The reasoner can be Pellet, HermiT, FaCT++ or Elk.
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79 The output ontology can be OBO or OWL (RDF/XML).
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80
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81 **More information**
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82
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83 Galaxy public instances with OPPL-Galaxy pre-installed:
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84
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85 http://sele.inf.um.es:9080/
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87 http://linkeddata2.dia.fi.upm.es:8080
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89 OPPL-Galaxy Examples:
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91 http://miuras.inf.um.es/OPPL-Galaxy/
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93 OPPL examples:
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95 http://oppl2.sourceforge.net/taggedexamples/
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97 Links of interest:
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99 http://oppl.sf.net/
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101 http://www.w3.org/TR/owl2-manchester-syntax/
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102
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103 http://clarkparsia.com/pellet
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105 http://hermit-reasoner.com/
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106
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107 http://code.google.com/p/factplusplus/
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108
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109 http://code.google.com/p/elk-reasoner/
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110
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111 http://owlapi.sourceforge.net/
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112
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113 **Citation**
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114
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115 Mikel Egaña Aranguren, Jesualdo Tomás Fernández-Breis, Erick Antezana. OPPL-Galaxy: Enhancing ontology exploitation in Galaxy with OPPL. In Proceedings of the 4th International Workshop on Semantic Web Applications and Tools for the Life Sciences, SWAT4LS 2011, pages 12–19, ACM 2012.
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116
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117 **Contact**
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118
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119 Please send any request or comment to mikel.egana.aranguren@gmail.com.
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120
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121 </help>
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122
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123 </tool>