Mercurial > repos > mikel-egana-aranguren > oppl
annotate OPPL/oppl.xml @ 3:5255f1333cc4
Version 1.0.1
Added output choice: OBO or OWL(RDF/XML)
| author | Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu> |
|---|---|
| date | Wed, 07 Sep 2011 10:46:29 +0200 |
| parents | 46b9d13a44fc |
| children | 4f60202c58d9 |
| rev | line source |
|---|---|
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Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
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1 <tool id="oppl" name="Execute an OPPL file against an ontology" version="1.0.1"> |
| 0 | 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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Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
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3 <command>java -jar ${__tool_data_path__}/shared/jars/oppl_galaxy_tool.jar $input $OPPL $format > $output </command> |
| 0 | 4 <inputs> |
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Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
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5 <param format="text" name="input" type="data" label="Input ontology file"/> |
| 0 | 6 <param format="text" name="OPPL" type="data" label="OPPL file"/> |
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Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
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7 <param name="format" type="select" label="Choose ontology output format"> |
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5255f1333cc4
Version 1.0.1
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
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8 <option value="OWL" selected="true">OWL</option> |
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5255f1333cc4
Version 1.0.1
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
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9 <option value="OBO">OBO</option> |
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5255f1333cc4
Version 1.0.1
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
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10 </param> |
| 0 | 11 </inputs> |
| 12 <outputs> | |
| 13 <data format="text" name="output" /> | |
| 14 </outputs> | |
| 15 | |
| 16 <tests> | |
| 17 <test> | |
| 18 <param name="input" value="test.owl"/> | |
| 19 <param name="OPPL" value="test.oppl"/> | |
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Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
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20 <param name="format" value="OWL"/> |
| 0 | 21 <output name="out_file" file="test_new.owl"/> |
| 22 </test> | |
| 23 </tests> | |
| 24 | |
| 25 <help> | |
| 26 | |
| 27 **About OPPL-Galaxy** | |
| 28 | |
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Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
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29 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. |
| 0 | 30 |
| 31 **Formats** | |
| 32 | |
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3
5255f1333cc4
Version 1.0.1
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
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33 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). |
| 0 | 34 |
| 35 **Usage** | |
| 36 | |
| 37 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. | |
| 38 | |
| 39 Then execute the OPPL file against the OWL file with Ontology Pre Processor Language >> Execute an OPPL file against an OWL file. | |
| 40 | |
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5255f1333cc4
Version 1.0.1
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
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41 This is the OPPL script provided in the bundle, test.oppl (Variables start with ?): |
| 0 | 42 |
| 43 ?whole:CLASS, | |
| 44 ?part:CLASS | |
| 45 SELECT | |
| 46 ?part SubClassOf part_of some ?whole WHERE ?part != Nothing | |
| 47 BEGIN | |
| 48 ADD ?part SubClassOf part_of only ?whole | |
| 49 END; | |
| 50 | |
| 51 **More information** | |
| 52 | |
| 53 http://oppl2.sourceforge.net/ | |
| 54 | |
| 55 http://owlapi.sourceforge.net/ | |
| 56 | |
| 57 http://www.w3.org/TR/owl2-manchester-syntax/ | |
| 58 | |
| 59 http://clarkparsia.com/pellet | |
| 60 | |
| 61 **Features that will be implemented soon** | |
| 62 | |
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3
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Version 1.0.1
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
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63 OWL import closure. |
| 0 | 64 |
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Version 1.0.1
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
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65 Choose reasoner (Right now only Pellet is available). |
| 0 | 66 |
| 67 **Contact** | |
| 68 | |
| 69 Please send any request or comment to mikel.egana.aranguren@gmail.com. | |
| 70 | |
| 71 </help> | |
| 72 | |
| 73 </tool> |