RDF/Jena: a simple extension for XSLT/XALAN. Testing with NCBI-Gene
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.htmlThe 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:
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| <?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> |
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.
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| 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://"); | |
| } | |
| } |
Makefile
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| 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" |
config.mk:
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| 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 |
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
