# HG changeset patch
# User jose-minyarro
# Date 1332159959 14400
# Node ID 354aa87772e0ebb78170c843784921e232ef0f0b
# Parent c324108a12cedfbbfe03f0d2dbf77cbfb4ce073a
Uploaded
diff -r c324108a12ce -r 354aa87772e0 NCBO_services/README
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NCBO_services/README Mon Mar 19 08:25:59 2012 -0400
@@ -0,0 +1,82 @@
+
+
+
+ =============
+ NCBO Services
+ =============
+
+
+
+INSTALLATION
+============
+
+1.- Stop Galaxy.
+
+2.- Copy the .jar files to /galaxy-dist/tool-data/shared/jars/
+
+3.- Create directory /galaxy-dist/tools/NCBO_services/
+
+4.- Copy the .xml files to /galaxy-dist/tools/NCBO_services/
+
+5.- Add the following lines to /galaxy-dist/tool_conf.xml:
+
+
+
+6.- Start Galaxy.
+
+
+
+USAGE
+=====
+
+Each tool has a different functionality, but all of them need a
+bioportal API key. The API key can be obtained by creating an account at
+bioportal (http://bioportal.bioontology.org/).
+
+
+
+CONTACT
+=======
+
+Please send any request or comment to mikel.egana.aranguren@gmail.com or
+jose.minya@gmail.com.
+
+
+
+ACKNOWLEDGEMENTS
+================
+
+The work on get_ontology, extract and get_ontology_view is funded by the
+Marie Curie Cofund program of the EU, FP7.
+
+
+
+COPYRIGHT AND LICENSE
+=====================
+
+get_ontology, extract and get_ontology_view are copyright of Mikel
+Egaña Aranguren (2012), and they are distributed under a GPL 3 license
+(http://www.gnu.org/licenses/)
+
+
+
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diff -r c324108a12ce -r 354aa87772e0 NCBO_services/extract.jar
Binary file NCBO_services/extract.jar has changed
diff -r c324108a12ce -r 354aa87772e0 NCBO_services/extract.java
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NCBO_services/extract.java Mon Mar 19 08:25:59 2012 -0400
@@ -0,0 +1,65 @@
+package es.upm.fi.dia.oeg.ncbo.galaxy;
+
+import java.io.BufferedReader;
+import java.io.BufferedWriter;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+import java.io.OutputStreamWriter;
+
+import org.apache.http.HttpEntity;
+import org.apache.http.HttpResponse;
+import org.apache.http.client.ClientProtocolException;
+import org.apache.http.client.HttpClient;
+import org.apache.http.client.methods.HttpGet;
+import org.apache.http.impl.client.DefaultHttpClient;
+
+public class extract {
+
+ /**
+ * @param args
+ * @throws IOException
+ * @throws ClientProtocolException
+ */
+ public static void main(String[] args) throws ClientProtocolException, IOException {
+
+// http://www.bioontology.org/wiki/index.php/View_Extraction
+// ./viewextractor/{ontology version id}[?{args}]&apikey={YourAPIKey}
+
+ String api_key = args [0];
+ String ontologyversionid = args [1]; // 35686
+ String conceptid = args [2]; // E800-E999.9
+ String filterrelations = args [3]; // PAR,isa,CHD,inverse_isa,SUBSETMEMBER,SubClass,SuperClass,[R]SIB,SI
+ String ontologyname = args [4]; // http://who.int/icd9
+
+ HttpClient client = new DefaultHttpClient();
+
+// HttpGet get = new HttpGet("http://rest.bioontology.org/bioportal/viewextractor/35686/" +
+// "?conceptid=E800-E999.9&filterrelations=PAR,isa,CHD,inverse_isa,SUBSETMEMBER,SubClass,SuperClass," +
+// "[R]SIB,SIB&existontology=true&ontologyname=http://who.int/icd9&apikey=74c12fc6-9423-455a-a619-b94f47d1951b");
+
+ HttpGet get = new HttpGet("http://rest.bioontology.org/bioportal/viewextractor/" + ontologyversionid +
+ "/?conceptid="+ conceptid +"&filterrelations=" + filterrelations +
+ "&existontology=true&ontologyname="+ ontologyname + "&apikey=" + api_key);
+
+ HttpResponse response = client.execute(get);
+ HttpEntity entity = response.getEntity();
+ if (entity != null) {
+ InputStream instream = entity.getContent();
+ InputStreamReader is=new InputStreamReader(instream);
+ BufferedReader br=new BufferedReader(is);
+ String read=br.readLine();
+ BufferedWriter bw = new BufferedWriter(new OutputStreamWriter(System.out));
+ while(read!=null){
+// System.out.println(read);
+ bw.write(read);
+ bw.newLine();
+ read=br.readLine();
+ }
+ bw.close();
+ instream.close();
+ }
+
+ }
+
+}
diff -r c324108a12ce -r 354aa87772e0 NCBO_services/extract.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NCBO_services/extract.xml Mon Mar 19 08:25:59 2012 -0400
@@ -0,0 +1,46 @@
+
diff -r c324108a12ce -r 354aa87772e0 NCBO_services/get_ontology.jar
Binary file NCBO_services/get_ontology.jar has changed
diff -r c324108a12ce -r 354aa87772e0 NCBO_services/get_ontology.java
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NCBO_services/get_ontology.java Mon Mar 19 08:25:59 2012 -0400
@@ -0,0 +1,49 @@
+package es.upm.fi.dia.oeg.ncbo.galaxy;
+
+import java.io.BufferedReader;
+import java.io.BufferedWriter;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+import java.io.OutputStreamWriter;
+
+import org.apache.http.HttpEntity;
+import org.apache.http.HttpResponse;
+import org.apache.http.client.ClientProtocolException;
+import org.apache.http.client.HttpClient;
+import org.apache.http.client.methods.HttpGet;
+import org.apache.http.client.methods.HttpPost;
+import org.apache.http.impl.client.DefaultHttpClient;
+
+public class get_ontology {
+
+ /**
+ * @param args
+ * @throws IOException
+ * @throws ClientProtocolException
+ */
+ public static void main(String[] args) throws ClientProtocolException, IOException {
+ String api_key = args [0];
+ String ontology_id = args [1]; // 1522
+ HttpClient client = new DefaultHttpClient();
+
+ HttpGet get = new HttpGet("http://rest.bioontology.org/bioportal/virtual/download/" + ontology_id + "?apikey=" +api_key);
+ HttpResponse response = client.execute(get);
+ HttpEntity entity = response.getEntity();
+ if (entity != null) {
+ InputStream instream = entity.getContent();
+ InputStreamReader is=new InputStreamReader(instream);
+ BufferedReader br=new BufferedReader(is);
+ String read=br.readLine();
+ BufferedWriter bw = new BufferedWriter(new OutputStreamWriter(System.out));
+ while(read!=null){
+// System.out.println(read);
+ bw.write(read);
+ bw.newLine();
+ read=br.readLine();
+ }
+ bw.close();
+ instream.close();
+ }
+ }
+}
diff -r c324108a12ce -r 354aa87772e0 NCBO_services/get_ontology.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NCBO_services/get_ontology.xml Mon Mar 19 08:25:59 2012 -0400
@@ -0,0 +1,384 @@
+
+ Retrieves an ontology from bioportal using its id
+
+
+ #if $id_opts.id_opts_menu=="id_by_hand" #java -jar ${__tool_data_path__}/shared/jars/get_ontology.jar $api_key $id_opts.ontology_id > $output
+ #else #java -jar ${__tool_data_path__}/shared/jars/get_ontology.jar $api_key $id_opts.ontology_id > $output
+ #end if
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+**What it does**
+
+It retrieves an ontology from BioPortal.
+
+**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.
+
+**More information**
+
+http://bioportal.bioontology.org
+
+http://www.bioontology.org/wiki/index.php/BioPortal_REST_services
+
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diff -r c324108a12ce -r 354aa87772e0 NCBO_services/get_ontology_view.jar
Binary file NCBO_services/get_ontology_view.jar has changed
diff -r c324108a12ce -r 354aa87772e0 NCBO_services/get_ontology_view.java
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NCBO_services/get_ontology_view.java Mon Mar 19 08:25:59 2012 -0400
@@ -0,0 +1,54 @@
+package es.upm.fi.dia.oeg.ncbo.galaxy;
+
+import java.io.BufferedReader;
+import java.io.BufferedWriter;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+import java.io.OutputStreamWriter;
+
+import org.apache.http.HttpEntity;
+import org.apache.http.HttpResponse;
+import org.apache.http.client.ClientProtocolException;
+import org.apache.http.client.HttpClient;
+import org.apache.http.client.methods.HttpGet;
+import org.apache.http.client.methods.HttpPost;
+import org.apache.http.impl.client.DefaultHttpClient;
+
+public class get_ontology_view {
+
+ /**
+ * @param args
+ * @throws IOException
+ * @throws ClientProtocolException
+ */
+ public static void main(String[] args) throws ClientProtocolException, IOException {
+// http://www.bioontology.org/wiki/index.php/BioPortal_REST_services#Download_a_specific_ontology_view_based_on_the_ontology_view_version_id
+// Download a specific ontology view based on the ontology view version id
+
+ String api_key = args [0];
+ String ontology_view_id = args [1];
+
+ HttpClient client = new DefaultHttpClient();
+// http://rest.bioontology.org/bioportal/ontologies/download/43072?apikey=YourAPIKey
+ HttpGet get = new HttpGet("http://rest.bioontology.org/bioportal/ontologies/download/" + ontology_view_id + "?apikey=" + api_key);
+
+ HttpResponse response = client.execute(get);
+ HttpEntity entity = response.getEntity();
+ if (entity != null) {
+ InputStream instream = entity.getContent();
+ InputStreamReader is=new InputStreamReader(instream);
+ BufferedReader br=new BufferedReader(is);
+ String read=br.readLine();
+ BufferedWriter bw = new BufferedWriter(new OutputStreamWriter(System.out));
+ while(read!=null){
+// System.out.println(read);
+ bw.write(read);
+ bw.newLine();
+ read=br.readLine();
+ }
+ bw.close();
+ instream.close();
+ }
+ }
+}
diff -r c324108a12ce -r 354aa87772e0 NCBO_services/get_ontology_view.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NCBO_services/get_ontology_view.xml Mon Mar 19 08:25:59 2012 -0400
@@ -0,0 +1,40 @@
+
+ Retrieves a view of an ontology using the view id
+ java -jar ${__tool_data_path__}/shared/jars/get_ontology_view.jar $api_key $ontologyviewid > $output
+
+
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+
+**What it does**
+
+It retrieves a view from an ontology contained in BioPortal.
+
+**Parameters**
+
+* Bioportal API key: to obtain an API key, open an account in http://bioportal.bioontology.org.
+* Ontology view ID: it can be obtained from BioPortal, in the Ontology page, on the views section, by looking at the view URL. For example, it is 41014 for the generic Gene Ontology slim.
+
+**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
+
+
+
+
diff -r c324108a12ce -r 354aa87772e0 NCBO_services/ncbo_annotator.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NCBO_services/ncbo_annotator.xml Mon Mar 19 08:25:59 2012 -0400
@@ -0,0 +1,704 @@
+
+ Annotates biological texts with the terms of the bio-ontologies from BioPortal
+ java -jar ${__tool_data_path__}/shared/jars/ncbo_annotator_galaxy.jar $longestOnly $wholeWordOnly $filterNumber $stopWords $withDefaultStopWords $isTopWordsCaseSensitive $mintermSize $scored $withSynonyms $ontologiesToExpand $ontologiesToKeepInResult $semanticTypes $levelMax $mappingTypes $textToAnnotate $format $apikey > $output
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+**Usage**
+ Enter bioportal API key, a text to annotate and specify the parameters, and the annotations will be retrieved.
+
+**Contact**
+
+ Please send any request or comment to jose.minyarro@um.es
+
+**More information**
+
+ http://bioportal.bioontology.org
+
+
+
+
\ No newline at end of file
diff -r c324108a12ce -r 354aa87772e0 NCBO_services/ncbo_annotator_galaxy.jar
Binary file NCBO_services/ncbo_annotator_galaxy.jar has changed
diff -r c324108a12ce -r 354aa87772e0 NCBO_services/ncbo_recommender.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NCBO_services/ncbo_recommender.xml Mon Mar 19 08:25:59 2012 -0400
@@ -0,0 +1,286 @@
+
+ Provides a bio-ontology as a recommendation depending on the annotations from a biological text
+ java -jar ${__tool_data_path__}/shared/jars/ncbo_recommender_galaxy.jar $text $format $ontologyId $apikey > $output
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+**Usage**
+ Enter bioportal API key, a text, the output format and a list of bioontolgies Ids and the recommender retrieves the bioontology with the best annotations.
+
+**Contact**
+
+ Please send any request or comment to jose.minyarro@um.es
+
+**More information**
+
+ http://bioportal.bioontology.org
+
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\ No newline at end of file
diff -r c324108a12ce -r 354aa87772e0 NCBO_services/ncbo_recommender_galaxy.jar
Binary file NCBO_services/ncbo_recommender_galaxy.jar has changed
diff -r c324108a12ce -r 354aa87772e0 NCBO_services/ncbo_resourceIndex.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NCBO_services/ncbo_resourceIndex.xml Mon Mar 19 08:25:59 2012 -0400
@@ -0,0 +1,320 @@
+
+ Search for resources matched up with terms in bio-ontologies depending on the given text
+ java -jar ${__tool_data_path__}/shared/jars/ncbo_resourceIndex_galaxy.jar $query $ontologyids $resourceId $mode $elementDetails $format $apikey > $output
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+**Usage**
+ Enter bioportal API key, a text, a list of bioontolgies Ids,a list of resources to search for, the mode, tick if you want detailed element and the format of the results, and the Resource Index interface retrieves the resources matched up with the bioontology terms associated with the text provided.
+ Example of search text: Melanoma
+
+**Contact**
+
+ Please send any request or comment to jose.minyarro@um.es
+
+**More information**
+
+ http://bioportal.bioontology.org
+
+
+
+
\ No newline at end of file
diff -r c324108a12ce -r 354aa87772e0 NCBO_services/ncbo_resourceIndex_galaxy.jar
Binary file NCBO_services/ncbo_resourceIndex_galaxy.jar has changed
diff -r c324108a12ce -r 354aa87772e0 NCBO_services/ncbo_search.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/NCBO_services/ncbo_search.xml Mon Mar 19 08:25:59 2012 -0400
@@ -0,0 +1,281 @@
+
+ Search for terms in bio-ontologies depending on the text provided
+ java -jar ${__tool_data_path__}/shared/jars/ncbo_search_galaxy.jar $query $ontologyids $apikey > $output
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+**Usage**
+ Enter bioportal API key, a text, and the list of bioontolgies Ids to search for and the search interface retrieves the bioontology terms associated with the text provided.
+ Example of search text: Breast cancer
+
+**Contact**
+
+ Please send any request or comment to jose.minyarro@um.es
+
+**More information**
+
+ http://bioportal.bioontology.org
+
+
+
+
\ No newline at end of file
diff -r c324108a12ce -r 354aa87772e0 NCBO_services/ncbo_search_galaxy.jar
Binary file NCBO_services/ncbo_search_galaxy.jar has changed