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annotate NCBO_services/extract.xml @ 20:1910c878378c

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get_ontology menu improved (Automatically generated), source added, readme improved
author Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
date Wed, 25 Jan 2012 19:49:20 +0100
parents 0078fe4c89e3
children
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0078fe4c89e3 get_ontology interface improved, extract tool added
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1 <tool id="extract" name="Extract a branch from an ontology" version="1.0.1">
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2 <description>Retrieves a subtree from an ontology using a root concept</description>
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3 <command>java -jar ${__tool_data_path__}/shared/jars/extract.jar $api_key $ontologyversionid $conceptid $filterrelations $ontologyname > $output </command>
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5 <inputs>
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6 <param name="api_key" type="text" size="100" label="BioPortal API key" />
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7 <param name="ontologyversionid" type="text" size="100" label="Ontology version ID" />
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8 <param name="conceptid" type="text" size="100" label="Concept id" />
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9 <param name="filterrelations" type="text" value="None" size="100" label="Filter relations" />
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10 <param name="ontologyname" type="text" size="100" label="Ontology name" />
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11 </inputs>
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12 <outputs>
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13 <data format="text" name="output" />
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14 </outputs>
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15 <tests>
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16 <test>
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17 <param name="api_key"/>
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18 </test>
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19 </tests>
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20 <help>
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22 **What it does**
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24 It extracts a subtree from an ontology contained in BioPortal, and retrieves such subtree as an OWL ontology.
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26 **Parameters**
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28 * Bioportal API key: to obtain an API key, open an account in http://bioportal.bioontology.org.
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29 * Ontology version ID: it can be obtained from BioPortal, in the Ontology page, on the versions column, by looking at the version URL. For example, it is 46754 for the Gene Ontology.
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30 * Concept ID: the root term. For example, GO:0051179.
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31 * Filter relations: for example "is_a,part_of".
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32 * Ontology name: the URI for the new ontology. For example http://go_redux_is_a.owl.
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34 **Contact**
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36 Please send any request or comment to mikel.egana.aranguren@gmail.com.
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38 **More information**
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40 http://bioportal.bioontology.org
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42 http://www.bioontology.org/wiki/index.php/BioPortal_REST_services
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44 </help>
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46 </tool>