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comparison NCBO_services/extract.xml @ 18:0078fe4c89e3

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get_ontology interface improved, extract tool added
author Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
date Wed, 18 Jan 2012 16:04:52 +0100
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17:fc4c8a9b3152 18:0078fe4c89e3
1 <tool id="extract" name="Extract a branch from an ontology" version="1.0.1">
2 <description>Retrieves a subtree from an ontology using a root concept</description>
3 <command>java -jar ${__tool_data_path__}/shared/jars/extract.jar $api_key $ontologyversionid $conceptid $filterrelations $ontologyname > $output </command>
4
5 <inputs>
6 <param name="api_key" type="text" size="100" label="BioPortal API key" />
7 <param name="ontologyversionid" type="text" size="100" label="Ontology version ID" />
8 <param name="conceptid" type="text" size="100" label="Concept id" />
9 <param name="filterrelations" type="text" value="None" size="100" label="Filter relations" />
10 <param name="ontologyname" type="text" size="100" label="Ontology name" />
11 </inputs>
12 <outputs>
13 <data format="text" name="output" />
14 </outputs>
15 <tests>
16 <test>
17 <param name="api_key"/>
18 </test>
19 </tests>
20 <help>
21
22 **What it does**
23
24 It extracts a subtree from an ontology contained in BioPortal, and retrieves such subtree as an OWL ontology.
25
26 **Parameters**
27
28 * Bioportal API key: to obtain an API key, open an account in http://bioportal.bioontology.org.
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.
30 * Concept ID: the root term. For example, GO:0051179.
31 * Filter relations: for example "is_a,part_of".
32 * Ontology name: the URI for the new ontology. For example http://go_redux_is_a.owl.
33
34 **Contact**
35
36 Please send any request or comment to mikel.egana.aranguren@gmail.com.
37
38 **More information**
39
40 http://bioportal.bioontology.org
41
42 http://www.bioontology.org/wiki/index.php/BioPortal_REST_services
43
44 </help>
45
46 </tool>