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comparison OPPL/query.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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17:c9e01f86b07c 18:d3616fac4ca5
14 <!-- 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, ...... --> 14 <!-- 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, ...... -->
15 <!-- 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 --> 15 <!-- 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 -->
16 16
17 <!--<command> 17 <!--<command>
18 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/query.jar $ontology $reasoner $answer_type $answer_format "$query" > $output 18 java -Djava.library.path=${__tool_data_path__}/shared/jars/FaCT++-linux-v1.5.2/64bit -Xmx3000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/query.jar $ontology $reasoner $answer_type $answer_format "$query" > $output
19 </commadn>--> 19 </command>-->
20 20
21 21
22 <inputs> 22 <inputs>
23 <param name="ontology" type="data" label="Input ontology file"/> 23 <param name="ontology" type="data" label="Input ontology file"/>
24 <param name="query" type="text" size="100" value="" label="Query" /> 24 <param name="query" type="text" size="100" value="" label="Query" />
25 <param name="reasoner" type="select" label="Choose reasoner"> 25 <param name="reasoner" type="select" label="Choose reasoner">
26 <option value="Pellet" selected="true">Pellet</option> 26 <option value="Pellet" selected="true">Pellet</option>
27 <option value="HermiT">HermiT</option> 27 <option value="HermiT">HermiT</option>
28 <option value="FaCTPlusPlus">FaCT++</option> 28 <option value="FaCTPlusPlus">FaCT++</option>
29 <option value="Elk">Elk (Not all axioms supported)</option>
29 </param> 30 </param>
30 <param name="answer_type" type="select" label="Choose answer type"> 31 <param name="answer_type" type="select" label="Choose answer type">
31 <option value="Descendants">Descendant classes</option> 32 <option value="Descendants">Descendant classes</option>
32 <option value="DirectSubClasses" selected="true">Direct sub-classes</option> 33 <option value="DirectSubClasses" selected="true">Direct sub-classes</option>
33 <option value="Ancestors">Ancestor classes</option> 34 <option value="Ancestors">Ancestor classes</option>
56 </tests>--> 57 </tests>-->
57 <help> 58 <help>
58 59
59 **About Query-Galaxy** 60 **About Query-Galaxy**
60 61
61 Query-Galaxy can be used to execute a DL query against an OWL ontology (e.g. GO_0007049 or part_of some GO_0007049). The result is a list of entities from the target ontology. How those entities relate to the query can be chosen (A DL query is just an anonymous OWL Class). 62 Query-Galaxy can be used to execute a DL query against an OWL ontology. The result is a list of entities from the target ontology.
62 63
63 **Formats** 64 **Usage**
64 65
65 Query-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 output is a list of terms. 66 An ontology is needed as input: load it with Get Data >> Upload File from your computer or redirect the output of another galaxy tool. Query-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, Query-Galaxy will try to resolve them.
67
68 A DL query must be provided, e.g. GO_0007049 or part_of some GO_0007049.
69
70 The reasoner can be Pellet, HermiT, FaCT++ or Elk.
71
72 How the retrieved entities relate to the query can be chosen: a DL query is just an anonymous OWL Class, and the retrieved entities can be descendant classes, direct sub-classes, ancestor classes, direct super-classes, equivalent classes, or member individuals.
73
74 The returned entities can be rendered using their URI, their URI fragment, or OBO type URI fragment (e.g. GO_0000022 to GO:0000022).
66 75
67 **Contact** 76 **Contact**
68 77
69 Please send any request or comment to mikel.egana.aranguren@gmail.com. 78 Please send any request or comment to mikel.egana.aranguren@gmail.com.
70 79