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comparison OPPL/oppl.xml @ 0:46b9d13a44fc

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First commit (1.0.0)
author mikel-egana-aranguren
date Tue, 06 Sep 2011 14:53:59 -0400
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1 <tool id="oppl" name="Execute an OPPL file against an OWL file" version="1.0.0">
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>
3 <command>java -jar ${__tool_data_path__}/shared/jars/oppl_galaxy_tool.jar $input $OPPL > $output </command>
4 <inputs>
5 <param format="text" name="input" type="data" label="Source OWL file"/>
6 <param format="text" name="OPPL" type="data" label="OPPL file"/>
7 </inputs>
8 <outputs>
9 <data format="text" name="output" />
10 </outputs>
11
12 <tests>
13 <test>
14 <param name="input" value="test.owl"/>
15 <param name="OPPL" value="test.oppl"/>
16 <output name="out_file" file="test_new.owl"/>
17 </test>
18 </tests>
19
20 <help>
21
22 **About OPPL-Galaxy**
23
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.
25
26 **Formats**
27
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.
29
30 **Usage**
31
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.
33
34 Then execute the OPPL file against the OWL file with Ontology Pre Processor Language >> Execute an OPPL file against an OWL file.
35
36 This is the OPPL script provided in the bundle, test.oppl. Variables start with ?:
37
38 ?whole:CLASS,
39 ?part:CLASS
40 SELECT
41 ?part SubClassOf part_of some ?whole WHERE ?part != Nothing
42 BEGIN
43 ADD ?part SubClassOf part_of only ?whole
44 END;
45
46 **More information**
47
48 http://oppl2.sourceforge.net/
49
50 http://owlapi.sourceforge.net/
51
52 http://www.w3.org/TR/owl2-manchester-syntax/
53
54 http://clarkparsia.com/pellet
55
56 **Features that will be implemented soon**
57
58 OWL import closure
59
60 Choose output format (Right now only OWL RDF/XML is available)
61
62 Choose reasoner (Right now only Pellet is available)
63
64 **Contact**
65
66 Please send any request or comment to mikel.egana.aranguren@gmail.com.
67
68 </help>
69
70 </tool>