# HG changeset patch
# User Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
# Date 1326899092 -3600
# Node ID 0078fe4c89e3746a05ebda3965ff70fe45ebcf57
# Parent  fc4c8a9b3152202a72e06e020e7a4e979a5c63ff
get_ontology interface improved, extract tool added

diff -r fc4c8a9b3152 -r 0078fe4c89e3 NCBO_services/README
--- a/NCBO_services/README	Wed Jan 18 11:06:11 2012 +0100
+++ b/NCBO_services/README	Wed Jan 18 16:04:52 2012 +0100
@@ -22,6 +22,7 @@
 
   <section name="NCBO services" id="NCBO_services">
     <tool file="NCBO_services/get_ontology.xml"/>
+    <tool file="NCBO_services/extract.xml"/>
     <tool file="NCBO_services/ncbo_annotator.xml"/>
     <tool file="NCBO_services/ncbo_annotator.xml"/>
     <tool file="NCBO_services/ncbo_recommender.xml"/>
diff -r fc4c8a9b3152 -r 0078fe4c89e3 NCBO_services/extract.jar
Binary file NCBO_services/extract.jar has changed
diff -r fc4c8a9b3152 -r 0078fe4c89e3 NCBO_services/extract.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/NCBO_services/extract.xml	Wed Jan 18 16:04:52 2012 +0100
@@ -0,0 +1,46 @@
+<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>
diff -r fc4c8a9b3152 -r 0078fe4c89e3 NCBO_services/get_ontology.xml
--- a/NCBO_services/get_ontology.xml	Wed Jan 18 11:06:11 2012 +0100
+++ b/NCBO_services/get_ontology.xml	Wed Jan 18 16:04:52 2012 +0100
@@ -286,17 +286,26 @@
 	</tests>
 	<help>
 
-**Usage**
+**What it does**
+
+It retrieves an ontology from BioPortal.
 
-  Enter bioportal API key and ontology id (e.g. 1522 for BioPAX), or select from list, and the ontology will be retrieved.
+**Parameters**
+
+* Bioportal API key: to obtain an API key, open an account in http://bioportal.bioontology.org.
+* Ontology ID: provide it by hand (e.g. 1522 for BioPAX), or select from list.
 
 **Contact**
 
-  Please send any request or comment to mikel.egana.aranguren@gmail.com.
-  
+Please send any request or comment to mikel.egana.aranguren@gmail.com.
+    
 **More information**
 
-  http://bioportal.bioontology.org
+http://bioportal.bioontology.org
+  
+http://www.bioontology.org/wiki/index.php/BioPortal_REST_services
+  
+
 
 	</help>