In a previous post, I've shown that the XALAN XSLT engine can be extended with custom function returning a DOM Document that will be used by the xslt-stylesheet. Here, I'll create an extension for XALAN getting some RDF statements from a Jena/RDF model. The RDF model will be loaded in memory but one can imagine to use a persistent model ( TDB or SDB). I'll download a record from NCBI-gene, transform it to html and use the disease-ontology database as RDF to annotate it.

A Gene record is downloaded as XML from NCBI gene:

curl "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=gene&id=4853&retmode=xml" > notch2.html

The disease ontology is downloaded as RDF/XML:

curl -odoid.owl "http://www.berkeleybop.org/ontologies/doid.owl"

The XSLT Stylesheet

The stylesheet declares the extension jena, loads the RDF model ("$model"), searches for the OMIM identifiers in the Gene record and loads the RDF statements related to that OMIM-ID.
For example the following xpath expression:

jena:query(
   $model,
   $doiid,
   'http://www.geneontology.org/formats/oboInOwl#hasExactSynonym',
   ''
   )

returns a rdf/XML document containing the RDF statements having a subject=$doiid, a property "http://www.geneontology.org/formats/oboInOwl#hasExactSynonym" and any object.

<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
  <rdf:Statement>
    <rdf:subject rdf:resource="http://purl.obolibrary.org/obo/DOID_0050721"/>
    <rdf:predicate rdf:resource="http://www.geneontology.org/formats/oboInOwl#hasExactSynonym"/>
    <rdf:object>Phosphoserine phosphatase deficiency</rdf:object>
  </rdf:Statement>
</rdf:RDF>

The stylesheet:

	<?xml version="1.0" encoding="ISO-8859-1"?>
	<xsl:stylesheet
	xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
	xmlns:xsl="http://www.w3.org/1999/XSL/Transform"
	xmlns:jena="xalan://jena4xalan.Jena4Xalan"
	version="1.0"
	extension-element-prefixes="jena"
	>
	<xsl:output method="html"/>
	<!-- the path to the RDF file -->
	<xsl:param name="doid.path">doid.owl</xsl:param>
	<!-- create a new instance of Jena4Xalan and load the RDF dataset -->
	<xsl:variable name="model" select="jena:new($doid.path)"/>
	<!-- main template -->
	<xsl:template match="/">
	<html>
	<head>
	<style type="text/css">
	dt { font-weight: bold; color: blue;}
	</style>
	</head>
	<body>
	<xsl:apply-templates select="Entrezgene-Set"/>
	</body>
	</html>
	</xsl:template>
	<!--template matching Entrezgene-Set -->
	<xsl:template match="Entrezgene-Set">
	<div>
	<xsl:apply-templates select="Entrezgene"/>
	</div>
	</xsl:template>
	<!--template matching Entrezgene -->
	<xsl:template match="Entrezgene">
	<div>
	<!-- name of this entry -->
	<h1>
	<xsl:value-of select="Entrezgene_gene/Gene-ref/Gene-ref_locus"/>
	</h1>
	<!-- OMIM-ID -->
	<xsl:apply-templates select=".//Gene-commentary[Gene-commentary_heading='OMIM']"/>
	</div>
	</xsl:template>
	<!--template matching Gene-commentary for OMIM -->
	<xsl:template match="Gene-commentary">
	<xsl:for-each select="Gene-commentary_source/Other-source/Other-source_src/Dbtag/Dbtag_tag/Object-id/Object-id_id">
	<div>
	<!-- print URL to omim -->
	<h3>Omim ID <a><xsl:attribute name="href"><xsl:value-of select="concat('http://omim.org/entry/',.)"/></xsl:attribute><xsl:value-of select="."/></a></h3>
	<!-- set the variable 'stmts' with the RDF statements having an object='http://omim.org/entry/xxx' -->
	<xsl:variable name="stmts" select="jena:query($model,'','',concat('http://omim.org/entry/',.))"/>
	<p>
	<!-- loop over the rdf:Statement in $stmts having a dbXref=this OMIM-ID -->
	<xsl:for-each select="jena:query($model,'','http://www.geneontology.org/formats/oboInOwl#hasDbXref',concat('OMIM:',.))/rdf:Statement">
	<!-- the Subject of this rdf:statement is a DOID resource -->
	<xsl:variable name="doiid" select="rdf:subject/@rdf:resource"/>
	<xsl:if test="starts-with($doiid,'http://purl.obolibrary.org/obo/DOID_')">
	<!-- recursive call -->
	<xsl:call-template name="disease">
	<xsl:with-param name="doiid" select="$doiid"/>
	</xsl:call-template>
	</xsl:if>
	</xsl:for-each>
	</p>
	</div>
	</xsl:for-each>
	</xsl:template>
	<!-- method 'disease' -->
	<xsl:template name="disease">
	<!-- param doid: a DOID URI -->
	<xsl:param name="doiid"/>
	<!-- get the rdfs:label -->
	<xsl:variable name="label" select="jena:query($model,$doiid,'http://www.w3.org/2000/01/rdf-schema#label','')/rdf:Statement[1]/rdf:object"/>
	<!-- get the hasExactSynonym -->
	<xsl:variable name="synonym" select="jena:query($model,$doiid,'http://www.geneontology.org/formats/oboInOwl#hasExactSynonym','')/rdf:Statement[1]/rdf:object"/>
	<!-- get the rdfs:subclasses -->
	<xsl:variable name="sublass" select="jena:query($model,$doiid,'http://www.w3.org/2000/01/rdf-schema#subClassOf','')/rdf:Statement/rdf:object"/>
	<div style="margin:5px;padding:5px;border: 1px solid black;">
	<dl>
	<!-- print the label-->
	<xsl:if test="$label">
	<dt>Label</dt>
	<dd>
	<xsl:value-of select="$label"/>
	</dd>
	</xsl:if>
	<!-- print the synonym -->
	<xsl:if test="$synonym">
	<dt>Synonym</dt>
	<dd>
	<xsl:value-of select="$synonym"/>
	</dd>
	</xsl:if>
	<!-- print the subclasses, recursive calls -->
	<xsl:if test="$sublass">
	<dt>Sub-Class Of</dt>
	<dd>
	<xsl:for-each select="$sublass">
	<xsl:call-template name="disease">
	<xsl:with-param name="doiid" select="@rdf:resource"/>
	</xsl:call-template>
	</xsl:for-each>
	</dd>
	</xsl:if>
	</dl>
	</div>
	</xsl:template>
	</xsl:stylesheet>

view raw gene2html.xsl hosted with ❤ by GitHub

The Java code

This is the java extension: the constructor loads the RDF model in memory. The function query(..) returns a RDF/XML document matching the query.

	package jena4xalan;
	import com.hp.hpl.jena.rdf.model.*;
	import com.hp.hpl.jena.util.*;

	import org.apache.xml.dtm.*;
	import org.apache.xml.dtm.ref.*;
	import org.apache.xalan.extensions.*;
	import javax.xml.parsers.*;
	import org.w3c.dom.*;
	import com.hp.hpl.jena.vocabulary.*;

	/**
	* RDF extension for XALAN
	*/
	public class Jena4Xalan
	{
	/** Jena RDF model */
	private Model model;

	/** constructor, param: path to RDF */
	public Jena4Xalan(String rdfFile) throws Exception
	{
	this.model=FileManager.get().loadModel(rdfFile);
	}





	/* returns a RDF Document containing
	the rdf:Statements for the subject/property/object
	empty strings are 'any'
	object startings with 'http://' are Resources
	*/
	public Element query(ExpressionContext exprContext, String subject,String property,String object)
	{

	/* create a DOM builder */
	Document myDoc=null;

	try
	{
	DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance();
	DocumentBuilder db = dbf.newDocumentBuilder();
	myDoc = db.newDocument();
	}
	catch(ParserConfigurationException pce)
	{
	throw new org.apache.xml.utils.WrappedRuntimeException(pce);
	}

	Element root= myDoc.createElementNS(RDF.getURI(),"rdf:RDF");
	root.setAttributeNS("http://www.w3.org/2000/xmlns/", "xmlns:rdf",RDF.getURI());

	/* get an iterator of the statements */
	StmtIterator iter=model.listStatements(
	isEmpty(subject)?null:ResourceFactory.createResource(subject),
	isEmpty(property)?null:ResourceFactory.createProperty(property),
	isEmpty(object)?null: (isURI(object)?ResourceFactory.createResource(object):model.createLiteral(object))
	);
	/* loop over the statements */
	while(iter.hasNext())
	{

	Statement stmt= iter.nextStatement();
	/* create a new rdf:Statement and append to the element rdf:RDF */
	Element S=myDoc.createElementNS(RDF.getURI(),"rdf:Statement");
	root.appendChild(S);
	/* create subject */
	Element f=myDoc.createElementNS(RDF.getURI(),"rdf:subject");
	S.appendChild(f);
	f.setAttributeNS(RDF.getURI(),"rdf:resource",stmt.getSubject().getURI());

	/* create predicate */
	f=myDoc.createElementNS(RDF.getURI(),"rdf:predicate");
	S.appendChild(f);
	f.setAttributeNS(RDF.getURI(),"rdf:resource",stmt.getPredicate().getURI());

	/* create object */
	f=myDoc.createElementNS(RDF.getURI(),"rdf:object");
	S.appendChild(f);
	if(stmt.getObject().isLiteral())
	{
	f.appendChild(myDoc.createTextNode(""+stmt.getLiteral().getValue()));
	}
	else
	{
	f.setAttributeNS(RDF.getURI(),"rdf:resource",stmt.getResource().getURI());
	}
	}

	iter.close();
	/* return the document element */
	return root;
	}

	private static boolean isEmpty(String s)
	{
	return s==null \|\| s.isEmpty();
	}

	private static boolean isURI(String s)
	{
	return s.startsWith("http://");
	}

	}

view raw Jena4Xalan.java hosted with ❤ by GitHub

Makefile

	include config.mk
	.PHONY: transform

	transform: result.html

	result.html : notch2.xml doid.owl gene2html.xsl lib/jena4xalan.jar
	java -cp ${xalan.libs}:${jena.libs}:lib/jena4xalan.jar org.apache.xalan.xslt.Process \
	-IN notch2.xml \
	-XSL gene2html.xsl -EDUMP -OUT $@

	lib/jena4xalan.jar: src/jena4xalan/Jena4Xalan.java
	mkdir -p tmp
	mkdir -p $(dir $@)
	javac -d tmp -cp ${xalan.libs}:${jena.libs} -sourcepath src $<
	jar cvf $@ -C tmp .

	notch2.xml:
	curl "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=gene&id=4853&retmode=xml" \|\
	sed 's/<!DOCTYPE [^>]*>//' > $@

	doid.owl :
	curl -o$@ "http://www.berkeleybop.org/ontologies/doid.owl"

view raw Makefile hosted with ❤ by GitHub

config.mk:

	xalan.dir=/home/lindenb/package/exist/lib/endorsed
	xalan.libs=${xalan.dir}/xalan-2.7.1.jar:${xalan.dir}/serializer-2.9.1.jar:${xalan.dir}/xercesImpl-2.9.1.jar
	ivy.cache=/home/lindenb/.ivy2/cache
	jena.libs=${ivy.cache}/org.apache.jena/jena-core/jars/jena-core-2.7.3.jar:${ivy.cache}/org.apache.jena/jena-iri/jars/jena-iri-0.9.3.jar:${ivy.cache}/org.slf4j/slf4j-log4j12/jars/slf4j-log4j12-1.6.4.jar:${ivy.cache}/org.slf4j/slf4j-api/jars/slf4j-api-1.6.4.jar:${ivy.cache}/log4j/log4j/bundles/log4j-1.2.16.jar

view raw config.mk hosted with ❤ by GitHub

Result

java -cp ${class.path} org.apache.xalan.xslt.Process \
 -IN notch2.xml \
 -XSL gene2html.xsl -EDUMP -OUT result.html

NOTCH2

Omim ID 610205

Label

Alagille syndrome

Synonym

Arteriohepatic dysplasia (disorder)

Sub-Class Of

Label

gastrointestinal system disease

Synonym

gastrointestinal disease

Sub-Class Of

Label

disease of anatomical entity

Sub-Class Of

Label: disease

Omim ID 102500

Label

Hajdu-Cheney syndrome

Synonym

Hajdu-Cheney syndrome (disorder)

Sub-Class Of

Label

autosomal dominant disease

Sub-Class Of

Label

autosomal genetic disease

Sub-Class Of

Label

monogenic disease

Sub-Class Of

Label

genetic disease

Sub-Class Of

Label: disease

That's it,

Pierre

YOKOFAKUN

20 December 2012

RDF/Jena: a simple extension for XSLT/XALAN. Testing with NCBI-Gene

The XSLT Stylesheet

The Java code

Makefile

Result

NOTCH2

Omim ID 610205

Omim ID 102500

About Me

Feeds

Blog Archive

Web2.0

Labels