DS model for Chemspider+ChEMBL queries.

bioclipse · Apr 18, 2012 · a7a115c · a7a115c
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diff --git a/plugins/net.bioclipse.ds.chemspider/.classpath b/plugins/net.bioclipse.ds.chemspider/.classpath
@@ -0,0 +1,7 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<classpath>
+	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.6"/>
+	<classpathentry kind="con" path="org.eclipse.pde.core.requiredPlugins"/>
+	<classpathentry kind="src" path="src"/>
+	<classpathentry kind="output" path="bin"/>
+</classpath>
diff --git a/plugins/net.bioclipse.ds.chemspider/.project b/plugins/net.bioclipse.ds.chemspider/.project
@@ -0,0 +1,28 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<projectDescription>
+	<name>net.bioclipse.ds.chemspider</name>
+	<comment></comment>
+	<projects>
+	</projects>
+	<buildSpec>
+		<buildCommand>
+			<name>org.eclipse.jdt.core.javabuilder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+		<buildCommand>
+			<name>org.eclipse.pde.ManifestBuilder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+		<buildCommand>
+			<name>org.eclipse.pde.SchemaBuilder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+	</buildSpec>
+	<natures>
+		<nature>org.eclipse.pde.PluginNature</nature>
+		<nature>org.eclipse.jdt.core.javanature</nature>
+	</natures>
+</projectDescription>
diff --git a/plugins/net.bioclipse.ds.chemspider/META-INF/MANIFEST.MF b/plugins/net.bioclipse.ds.chemspider/META-INF/MANIFEST.MF
@@ -0,0 +1,23 @@
+Manifest-Version: 1.0
+Bundle-ManifestVersion: 2
+Bundle-Name: Chemspider DS
+Bundle-SymbolicName: net.bioclipse.ds.chemspider;singleton:=true
+Bundle-Version: 0.2.0
+Bundle-Vendor: bioclipse.net
+Bundle-RequiredExecutionEnvironment: JavaSE-1.6
+Require-Bundle: org.eclipse.ui,
+ org.eclipse.core.runtime,
+ org.eclipse.help,
+ net.bioclipse.ds,
+ net.bioclipse.cdk.ui.sdfeditor,
+ net.bioclipse.cdk.business,
+ net.bioclipse.core,
+ net.bioclipse.ds.common,
+ net.bioclipse.ds.ui,
+ org.openscience.cdk.interfaces,
+ org.openscience.cdk.standard,
+ org.openscience.cdk.io,
+ org.openscience.cdk.nonotify,
+ net.bioclipse.chemspider;bundle-version="2.5.0",
+ net.bioclipse.rdf;bundle-version="2.5.0"
+Import-Package: org.apache.log4j
diff --git a/plugins/net.bioclipse.ds.chemspider/build.properties b/plugins/net.bioclipse.ds.chemspider/build.properties
@@ -0,0 +1,6 @@
+source.. = src/
+output.. = bin/
+bin.includes = META-INF/,\
+               .,\
+               plugin.xml,\
+               icons/
diff --git a/plugins/net.bioclipse.ds.chemspider/icons/cs-icon.png b/plugins/net.bioclipse.ds.chemspider/icons/cs-icon.png
diff --git a/plugins/net.bioclipse.ds.chemspider/plugin.xml b/plugins/net.bioclipse.ds.chemspider/plugin.xml
@@ -0,0 +1,26 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<?eclipse version="3.4"?>
+<plugin>
+   <extension
+         point="net.bioclipse.decisionsupport">
+
+         <endpoint
+               id="net.bioclipse.ds.chemspider"
+               description="Chemspider lookup"
+               icon="icons/cs-icon.png"
+               name="Chemspider+ChEMBL">
+         </endpoint>
+
+      <test
+            id="chemspider.nearest"
+            name="Chemspider nearest neighbour"
+            endpoint="net.bioclipse.ds.chemspider"
+            class="net.bioclipse.ds.chemspider.SimilaritySearchModel"
+            consensus="net.bioclipse.ds.consensus.majority.emptyinconclusive">
+
+            <parameter name="distance.tanimoto" value="0.8" />
+
+      </test>
+</extension>
+
+</plugin>
diff --git a/plugins/net.bioclipse.ds.chemspider/src/net/bioclipse/ds/chemspider/ChemblInteraction.java b/plugins/net.bioclipse.ds.chemspider/src/net/bioclipse/ds/chemspider/ChemblInteraction.java
@@ -0,0 +1,71 @@
+package net.bioclipse.ds.chemspider;
+
+public class ChemblInteraction {
+
+	String title;
+	String value;
+	String unit;
+	String targetType;
+	String interactionType;
+	String relation;
+	String description;
+
+	public String getTitle() {
+		return title;
+	}
+	public void setTitle(String title) {
+		this.title = title;
+	}
+	public String getValue() {
+		return value;
+	}
+	public void setValue(String value) {
+		this.value = value;
+	}
+	public String getUnit() {
+		return unit;
+	}
+	public void setUnit(String unit) {
+		this.unit = unit;
+	}
+	public String getTargetType() {
+		return targetType;
+	}
+	public void setTargetType(String targetType) {
+		this.targetType = targetType;
+	}
+	public String getInteractionType() {
+		return interactionType;
+	}
+	public void setInteractionType(String interactionType) {
+		this.interactionType = interactionType;
+	}
+	public String getRelation() {
+		return relation;
+	}
+	public void setRelation(String relation) {
+		this.relation = relation;
+	}
+	public String getDescription() {
+		return description;
+	}
+	public void setDescription(String description) {
+		this.description = description;
+	}
+
+	public ChemblInteraction(String value, String unit, String interactionType) {
+		super();
+		this.value = value;
+		this.unit = unit;
+		this.interactionType = interactionType;
+	}
+	@Override
+	public String toString() {
+		return "ChemblInteraction [title=" + title + ", value=" + value
+				+ ", unit=" + unit + ", targetType=" + targetType
+				+ ", interactionType=" + interactionType + ", relation="
+				+ relation + ", description=" + description + "]";
+	}
+
+
+}
diff --git a/plugins/net.bioclipse.ds.chemspider/src/net/bioclipse/ds/chemspider/ChemblLookup.java b/plugins/net.bioclipse.ds.chemspider/src/net/bioclipse/ds/chemspider/ChemblLookup.java
@@ -0,0 +1,98 @@
+package net.bioclipse.ds.chemspider;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import net.bioclipse.core.business.BioclipseException;
+import net.bioclipse.core.domain.IStringMatrix;
+import net.bioclipse.rdf.Activator;
+import net.bioclipse.rdf.business.IRDFManager;
+
+/**
+ * Look up interactions in ChEMBL-rdf for a given Chemspider ID
+ *  
+ * @author Ola Spjuth
+ *
+ */
+public class ChemblLookup {
+
+	public static List<ChemblInteraction> lookupCSID(Integer csid) throws BioclipseException{
+
+		IRDFManager rdf = Activator.getDefault().getJavaManager();
+		String endpoint = "http://rdf.farmbio.uu.se/chembl/sparql";
+
+		//10368587 is one example
+
+		String query =			
+		"PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>"+
+		"PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>"+
+		"PREFIX owl: <http://www.w3.org/2002/07/owl#>"+
+		"PREFIX dc: <http://purl.org/dc/elements/1.1/>"+
+		"PREFIX foaf: <http://xmlns.com/foaf/0.1/>"+
+		"PREFIX chembl: <http://rdf.farmbio.uu.se/chembl/onto/#>"+
+		"PREFIX bo: <http://www.blueobelisk.org/chemistryblogs/>"+
+		"PREFIX bibo: <http://purl.org/ontology/bibo/>"+
+		"PREFIX cito: <http://purl.org/spar/cito/>"+
+		"PREFIX cheminf: <http://semanticscience.org/resource/>"+
+		"PREFIX pro: <http://purl.obolibrary.org/obo/>"+
+		"PREFIX skos: <http://www.w3.org/2004/02/skos/core#>"+
+
+		"SELECT ?val ?units ?targetType ?title ?interactionType ?relation ?description ?assay WHERE {"+
+		"?csid <http://semanticscience.org/resource/SIO_000300> " + csid + " ."+
+		"?chembl cheminf:CHEMINF_000200 ?csid ."+
+		"?mol owl:equivalentClass ?chembl ."+
+		"?act chembl:forMolecule ?mol ."+
+		"?act chembl:standardValue ?val ."+
+		"FILTER (?val < 100000)"+
+		"?act chembl:standardUnits ?units ."+
+		"?act chembl:onAssay ?assay ."+
+		"?act chembl:type ?interactionType ."+
+		"?assay chembl:hasTarget ?target ."+
+		 "?assay chembl:hasDescription ?description ."+
+		"?target dc:title ?title ."+
+		"OPTIONAL { ?target chembl:classL1 ?targetType . }"+
+		"OPTIONAL { ?act chembl:relation ?relation . }"+
+		"}";		
+
+		IStringMatrix res = rdf.sparqlRemote(endpoint, query);
+
+//		System.out.println(res);
+
+		if (res.getColumnCount()<=0)
+			return null;
+
+		System.out.println("Got " + res.getRowCount() + " hits for CSID=" + csid);
+
+		List<ChemblInteraction> interactions = new ArrayList<ChemblInteraction>();
+		for (int i=0; i < res.getRowCount(); i++){
+			String value = res.getColumn("val").get(i);
+			String unit = res.getColumn("units").get(i);
+			String inttype = res.getColumn("interactionType").get(i);
+			String targetType = res.getColumn("targetType").get(i);
+			String title = res.getColumn("title").get(i);
+			String interactionType = res.getColumn("interactionType").get(i);
+			String relation = res.getColumn("relation").get(i);
+			String description = res.getColumn("description").get(i);
+			String assay = res.getColumn("assay").get(i);
+
+			value=value.substring(0,value.indexOf("^^"));
+			if (null==title || title.length()<=0)
+				title=assay.substring(assay.lastIndexOf("/")+1);
+
+			ChemblInteraction interaction = new ChemblInteraction(value, unit, inttype);
+
+			interaction.setTitle(title);
+			interaction.setRelation(relation);
+			interaction.setTargetType(targetType);
+			interaction.setInteractionType(interactionType);
+			interaction.setDescription(description);
+
+			interactions.add(interaction);
+//			System.out.println(interaction);
+
+		}
+
+		return interactions;
+	}
+
+}