Example Query

The following picture shows a total ion chromatogram and the spectra that belong to it. Assume that we want to query the data highlighted in the following figure:

Representation of the Query in SPARQL

To keep it simple, the example uses human readable identifiers surrounded by guillemets (« ») instead of artificial identifiers.

PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX qudt: <http://qudt.org/schema/qudt#>
PREFIX af-r: <http://purl.allotrope.org/ontologies/result#>
PREFIX af-x: <http://purl.allotrope.org/ontologies/propert#>
SELECT ?scan ?scanTimeValue ?scanTimeUnit ?totalIonCurrent ?basePeakPosValue ?basePeakPosUnit ?basePeakHeightValue ?basePeakHeightUnit
WHERE {
	?spectrum a «af-r:MS1 spectrum» ;
	«af-x:total ion current» ?totalIonCurrent ;
	«af-x:base peak» ?basePeak .
	?basePeak a «af-r:peak» ;
	«af-x:total retention time» [
		qudt:numericValue ?basePeakPosValue ;
		qudt:unit ?basePeakPosUnit ;
	] ;
	«af-x:intensity» [
		qudt:numericValue ?basePeakHeightValue ;
		qudt:unit ?basePeakHeightUnit ;
	] ;
	?scan a «af-x:scan» ;
	«af-x:scanned spectrum» ?spectrum ;
	«af-x:start time» [
		qudt:numericValue ?scanTimeValue ;
		qudt:unit ?scanTimeUnit ;
	] .
}					

A short query with artificial identifiers could look like this:

PREFIX qudt: <http://qudt.org/schema/qudt#>
PREFIX af-r: <http://purl.allotrope.org/ontologies/result#>
PREFIX af-x: <http://purl.allotrope.org/ontologies/propert#>
SELECT ?spectrum ?basePeakHeightValue ?basePeakHeightUnit
WHERE {
	?spectrum a af-r:AFR_0000472 ;
	af-x:AFX_0000361 [
		qudt:numericValue ?basePeakHeightValue ;
		qudt:unit ?basePeakHeightUnit ;
	] .
}					

Execution of the SPARQL Query

Given a SPARQL query as queryString and a Jena Model, we can execute the query on the model as follows, using the Jena ARQ API [[JENA-ARQ]]:

JAVA:
Query query = QueryFactory.create(queryString);
try (QueryExecution qexec = QueryExecutionFactory.create(query, dataDescription)) {
	ResultSet resultSet = qexec.execSelect();
	while (resultSet.hasNext()) {
		QuerySolution solution = resultSet.nextSolution();
		// extract the queried information via solution.get("variable name")
		// and do something with the result
	}
}

C#:
Query query = QueryFactory.create(queryString);
QueryExecution qexec = QueryExecutionFactory.create(query, dataDescription);
try
{
	ResultSet results = qexec.execSelect();
	while (results.MoveNext())
	{
		QuerySolution solution = resultSet.Current;
		// extract the queried information via solution.getResource("variable name");
		// and do something with the result
	}
}
finally
{
	qexec.close();
}
					

In this example, we first create a Query out of the given query string. Then we execute it and finally iterate over the results.

Resuming the example from above, the execution of the query looks like this:

JAVA:
// Iterate over the ResultSet
while (resultSet.hasNext()) {
	QuerySolution soln = resultSet.nextSolution();

	// Get the Scan Time, the Total Ion Current and the Base Peak of the spectrum
	String scanTime = soln.get("scanTimeValue") + " " + soln.get("scanTimeUnit");
	String tic = soln.get("tic");
	String basePeakMZ = soln.get("basePeakPosValue") + " " + soln.get("basePeakPosUnit");
	String basePeakint = soln.get("basePeakHeightValue") + " " + soln.get("basePeakHeightUnit");
}

C#:
// Iterate over the ResultSet
while (results.MoveNext())
{
	com.hp.hpl.jena.query.QuerySolution soln = results.Current;

	// Get the Scan Time, the Total Ion Current and the Base Peak of the spectrum
	String = soln.get("scanTimeValue") + " " + soln.get("scanTimeUnit");
	String tic = soln.get("tic");
	String basePeakMZ = soln.get("basePeakPosValue") + " " + soln.get("basePeakPosUnit");
	String basePeakint = soln.get("basePeakHeightValue") + " " + soln.get("basePeakHeightUnit");
}
					

Please refer to [[JENA-ARQ]] for more details and additional examples on SPARQL queries with the Jena ARQ API.