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comparison OPPL/oppl.xml @ 3:5255f1333cc4

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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
comparison
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2:0a374d0b7759 3:5255f1333cc4
1 <tool id="oppl" name="Execute an OPPL file against an OWL file" version="1.0.0"> 1 <tool id="oppl" name="Execute an OPPL file against an ontology" version="1.0.1">
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> 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>
3 <command>java -jar ${__tool_data_path__}/shared/jars/oppl_galaxy_tool.jar $input $OPPL > $output </command> 3 <command>java -jar ${__tool_data_path__}/shared/jars/oppl_galaxy_tool.jar $input $OPPL $format > $output </command>
4 <inputs> 4 <inputs>
5 <param format="text" name="input" type="data" label="Source OWL file"/> 5 <param format="text" name="input" type="data" label="Input ontology file"/>
6 <param format="text" name="OPPL" type="data" label="OPPL file"/> 6 <param format="text" name="OPPL" type="data" label="OPPL file"/>
7 <param name="format" type="select" label="Choose ontology output format">
8 <option value="OWL" selected="true">OWL</option>
9 <option value="OBO">OBO</option>
10 </param>
7 </inputs> 11 </inputs>
8 <outputs> 12 <outputs>
9 <data format="text" name="output" /> 13 <data format="text" name="output" />
10 </outputs> 14 </outputs>
11 15
12 <tests> 16 <tests>
13 <test> 17 <test>
14 <param name="input" value="test.owl"/> 18 <param name="input" value="test.owl"/>
15 <param name="OPPL" value="test.oppl"/> 19 <param name="OPPL" value="test.oppl"/>
20 <param name="format" value="OWL"/>
16 <output name="out_file" file="test_new.owl"/> 21 <output name="out_file" file="test_new.owl"/>
17 </test> 22 </test>
18 </tests> 23 </tests>
19 24
20 <help> 25 <help>
21 26
22 **About OPPL-Galaxy** 27 **About OPPL-Galaxy**
23 28
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. 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.
25 30
26 **Formats** 31 **Formats**
27 32
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. 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).
29 34
30 **Usage** 35 **Usage**
31 36
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. 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.
33 38
34 Then execute the OPPL file against the OWL file with Ontology Pre Processor Language >> Execute an OPPL file against an OWL file. 39 Then execute the OPPL file against the OWL file with Ontology Pre Processor Language >> Execute an OPPL file against an OWL file.
35 40
36 This is the OPPL script provided in the bundle, test.oppl. Variables start with ?: 41 This is the OPPL script provided in the bundle, test.oppl (Variables start with ?):
37 42
38 ?whole:CLASS, 43 ?whole:CLASS,
39 ?part:CLASS 44 ?part:CLASS
40 SELECT 45 SELECT
41 ?part SubClassOf part_of some ?whole WHERE ?part != Nothing 46 ?part SubClassOf part_of some ?whole WHERE ?part != Nothing
53 58
54 http://clarkparsia.com/pellet 59 http://clarkparsia.com/pellet
55 60
56 **Features that will be implemented soon** 61 **Features that will be implemented soon**
57 62
58 OWL import closure 63 OWL import closure.
59 64
60 Choose output format (Right now only OWL RDF/XML is available) 65 Choose reasoner (Right now only Pellet is available).
61
62 Choose reasoner (Right now only Pellet is available)
63 66
64 **Contact** 67 **Contact**
65 68
66 Please send any request or comment to mikel.egana.aranguren@gmail.com. 69 Please send any request or comment to mikel.egana.aranguren@gmail.com.
67 70