20 December 2012

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.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:

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.

Makefile




config.mk:

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