<tool id="extract" name="Extract a branch from an ontology" version="1.0.1">
	<description>Retrieves a subtree from an ontology using a root concept</description>
	<command>java -jar ${__tool_data_path__}/shared/jars/extract.jar $api_key $ontologyversionid $conceptid $filterrelations $ontologyname > $output </command>  

	<inputs>
		<param name="api_key" type="text" size="100" label="BioPortal API key" />
		<param name="ontologyversionid" type="text" size="100" label="Ontology version ID" />
		<param name="conceptid" type="text" size="100" label="Concept id" />
		<param name="filterrelations" type="text" value="None" size="100" label="Filter relations" />
		<param name="ontologyname" type="text" size="100" label="Ontology name" />
	</inputs>
	<outputs>
		<data format="text" name="output" />
	</outputs>
	<tests>
		<test>
			<param name="api_key"/>
		</test>
	</tests>
	<help>

**What it does**

It extracts a subtree from an ontology contained in BioPortal, and retrieves such subtree as an OWL ontology.

**Parameters**

* Bioportal API key: to obtain an API key, open an account in http://bioportal.bioontology.org.
* 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.
* Concept ID: the root term. For example, GO:0051179.
* Filter relations: for example "is_a,part_of".
* Ontology name: the URI for the new ontology. For example http://go_redux_is_a.owl.

**Contact**

Please send any request or comment to mikel.egana.aranguren@gmail.com.
    
**More information**

http://bioportal.bioontology.org
  
http://www.bioontology.org/wiki/index.php/BioPortal_REST_services

	</help>

</tool>