Mercurial > repos > mikel-egana-aranguren > oppl
comparison OPPL/oppl.xml @ 18:d3616fac4ca5 draft
Elk support added
author | Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu> |
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date | Thu, 20 Sep 2012 12:46:36 +0200 |
parents | c9e01f86b07c |
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17:c9e01f86b07c | 18:d3616fac4ca5 |
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9 | 9 |
10 <!-- DEFAULT SETTINGS --> | 10 <!-- DEFAULT SETTINGS --> |
11 | 11 |
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 --> | 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 --> |
13 | 13 |
14 <command> | 14 <!--<command> |
15 java -Xmx3000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/oppl_galaxy.jar $input $reasoner $OPPL $format > $output 2>/dev/null | 15 java -Xmx3000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/oppl_galaxy.jar $input $reasoner $OPPL $format > $output 2>/dev/null |
16 </command> | 16 </command>--> |
17 | |
18 | |
19 | 17 |
20 <!-- FACT++ --> | 18 <!-- FACT++ --> |
21 | 19 |
22 <!-- If you are planning to use FaCT++ you have to uncomment bellow (And comment the default settings above) and replace the -Djava.library.path with the appropiate JNI library path for your platform:FaCT++-linux-v1.5.2/64bit, FaCT++-linux-v1.5.2/32bit, FaCT++-OSX-v1.5.2/64bit, ...... --> | 20 <!-- If you are planning to use FaCT++ you have to uncomment bellow (And comment the default settings above) and replace the -Djava.library.path with the appropiate JNI library path for your platform:FaCT++-linux-v1.5.2/64bit, FaCT++-linux-v1.5.2/32bit, FaCT++-OSX-v1.5.2/64bit, ...... --> |
23 <!-- Using this setting doesn't upset the rest of the reasoners so you may as well leave it on if you plan to switch between FaCT++, Pellet and HermiT --> | 21 <!-- Using this setting doesn't upset the rest of the reasoners so you may as well leave it on if you plan to switch between FaCT++, Pellet and HermiT --> |
24 | 22 |
25 <!--<command> | 23 <command> |
26 java -Djava.library.path=${__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 > $output 2>/dev/null | 24 java -Djava.library.path=${__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 |
27 </commadn>--> | 25 </command> |
28 | 26 |
29 | 27 |
30 | 28 |
31 | 29 |
32 <!-- DEBUGGING --> | 30 <!-- DEBUGGING --> |
40 | 38 |
41 | 39 |
42 | 40 |
43 <inputs> | 41 <inputs> |
44 <param name="input" type="data" label="Input ontology file"/> | 42 <param name="input" type="data" label="Input ontology file"/> |
43 <param format="text" name="OPPL" type="data" label="OPPL file"/> | |
45 <param name="reasoner" type="select" label="Choose reasoner"> | 44 <param name="reasoner" type="select" label="Choose reasoner"> |
46 <option value="Pellet" selected="true">Pellet</option> | 45 <option value="Pellet" selected="true">Pellet</option> |
47 <option value="HermiT">HermiT</option> | 46 <option value="HermiT">HermiT</option> |
48 <option value="FaCTPlusPlus">FaCT++</option> | 47 <option value="FaCTPlusPlus">FaCT++</option> |
48 <option value="Elk">Elk (Not all axioms supported)</option> | |
49 </param> | 49 </param> |
50 <param format="text" name="OPPL" type="data" label="OPPL file"/> | |
51 <param name="format" type="select" label="Choose ontology output format"> | 50 <param name="format" type="select" label="Choose ontology output format"> |
52 <option value="OWL" selected="true">OWL</option> | 51 <option value="OWL" selected="true">OWL</option> |
53 <option value="OBO">OBO</option> | 52 <option value="OBO">OBO</option> |
54 </param> | 53 </param> |
55 </inputs> | 54 </inputs> |
67 </tests>--> | 66 </tests>--> |
68 <help> | 67 <help> |
69 | 68 |
70 **About OPPL-Galaxy** | 69 **About OPPL-Galaxy** |
71 | 70 |
72 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 efforts. | 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. |
73 | |
74 **Formats** | |
75 | |
76 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). | |
77 | 72 |
78 **Usage** | 73 **Usage** |
79 | 74 |
80 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. | 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. |
76 | |
77 The reasoner can be Pellet, HermiT, FaCT++ or Elk. | |
81 | 78 |
82 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. | 79 The output ontology can be OBO or OWL (RDF/XML). |
83 | |
84 In case the loaded ontology includes OWL imports, OPPL-Galaxy will try to resolve them. | |
85 | |
86 The output ontology can be OBO or OWL (RDF/XML). | |
87 | |
88 The reasoner can be Pellet, HermiT FaCT++. Sometimes, if an execution fails it can be fixed by using a different reasoner. | |
89 | 80 |
90 **More information** | 81 **More information** |
91 | 82 |
92 Galaxy public instances with OPPL-Galaxy pre-installed: | 83 Galaxy public instances with OPPL-Galaxy pre-installed: |
93 | 84 |
94 http://sele.inf.um.es:8080/ | 85 http://sele.inf.um.es:9080/ |
95 | 86 |
96 http://linkeddata2.dia.fi.upm.es:8080 | 87 http://linkeddata2.dia.fi.upm.es:8080 |
97 | 88 |
98 OPPL-Galaxy Examples: | 89 OPPL-Galaxy Examples: |
99 | 90 |
105 | 96 |
106 Links of interest: | 97 Links of interest: |
107 | 98 |
108 http://oppl.sf.net/ | 99 http://oppl.sf.net/ |
109 | 100 |
110 http://owlapi.sourceforge.net/ | |
111 | |
112 http://www.w3.org/TR/owl2-manchester-syntax/ | 101 http://www.w3.org/TR/owl2-manchester-syntax/ |
113 | 102 |
114 http://clarkparsia.com/pellet | 103 http://clarkparsia.com/pellet |
115 | 104 |
116 http://hermit-reasoner.com/ | 105 http://hermit-reasoner.com/ |
117 | 106 |
118 http://code.google.com/p/factplusplus/ | 107 http://code.google.com/p/factplusplus/ |
119 | 108 |
109 http://code.google.com/p/elk-reasoner/ | |
110 | |
111 http://owlapi.sourceforge.net/ | |
112 | |
120 **Citation** | 113 **Citation** |
121 | 114 |
122 Mikel Egaña Aranguren, Jesualdo Tomás Fernández-Breis and Erick Antezana. OPPL-Galaxy: Enhancing ontology exploitation in Galaxy with OPPL. SWAT4LS 2011. | 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. |
123 | 116 |
124 **Contact** | 117 **Contact** |
125 | 118 |
126 Please send any request or comment to mikel.egana.aranguren@gmail.com. | 119 Please send any request or comment to mikel.egana.aranguren@gmail.com. |
127 | 120 |