我有RDF数据,我想形成一个SPARQL查询以获取与特定生物名称匹配的记录。
仅供参考,我使用RDF4J使用可用的JSONLD数据生成RDF记录。我在获取与任何特定的PropertyValue集匹配的记录时遇到问题。例如:所有具有生物的名称为caquus caballus的记录,或所有具有提交标识符为GSB-7331的记录。
非常感谢您的帮助。
数据记录类似于:
中以JSONLD下载示例数据@prefix schema: <http://schema.org/> . @prefix obo: <http://purl.obolibrary.org/obo/> . @prefix ebi-bsd: <https://www.ebi.ac.uk/biosamples/> . @prefix biosamples: <http://identifiers.org/biosample/> . biosamples:SAMEA104496657 a schema:DataRecord ; schema:dateCreated "0002-10-15T00:00:00Z"^^schema:Date ; schema:dateModified "2019-07-23T18:33:14.867Z"^^schema:Date ; schema:identifier "SAMEA104496657" ; schema:isPartOf ebi-bsd:samples ; schema:mainEntity _:b0 . ebi-bsd:samples a schema:Dataset . _:b0 a schema:Sample , obo:OBI_0000747 ; schema:additionalProperty _:b1 , _:b2 , _:b3 , _:b4 ; schema:description "Blood samples N123" ; schema:identifier "SAMEA104496657" ; schema:name "N123" ; schema:sameAs biosamples:SAMEA104496657 . _:b1 a schema:PropertyValue ; schema:name "organism" ; schema:value "Equus caballus" ; schema:valueReference obo:NCBITaxon_9796 . obo:NCBITaxon_9796 a schema:DefinedTerm . _:b2 a schema:PropertyValue ; schema:name "submission description" ; schema:value "ELOAD_294_samples" . _:b3 a schema:PropertyValue ; schema:name "submission identifier" ; schema:value "GSB-7331" . _:b4 a schema:PropertyValue ; schema:name "submission title" ; schema:value "ELOAD_294" . @prefix schema: <http://schema.org/> . @prefix obo: <http://purl.obolibrary.org/obo/> . @prefix ebi-bsd: <https://www.ebi.ac.uk/biosamples/> . @prefix biosamples: <http://identifiers.org/biosample/> . biosamples:SAMEA104625758 a schema:DataRecord ; schema:dateCreated "0014-06-07T00:00:00Z"^^schema:Date ; schema:dateModified "2019-08-06T17:46:01.812Z"^^schema:Date ; schema:identifier "SAMEA104625758" ; schema:isPartOf ebi-bsd:samples ; schema:mainEntity _:b0 . ebi-bsd:samples a schema:Dataset . _:b0 a schema:Sample , obo:OBI_0000747 ; schema:additionalProperty _:b1 , _:b2 , _:b3 ; schema:description "Colorectal Cancer Tumor Sequenced Samaple; schema:identifier "SAMEA104625758" ; schema:name "P-0009062-T01-IM5" ; schema:sameAs biosamples:SAMEA104625758 ; schema:subjectOf "http://www.ebi.ac.uk/ena/data/view/SAMEA104625758" . :b1 a schema:PropertyValue ; schema:name "common name" ; schema:value "Human" ; schema:valueReference obo:NCBITaxon_9606 . obo:NCBITaxon_9606 a schema:DefinedTerm . _:b2 a schema:PropertyValue ; schema:name "organism" ; schema:value "Homo sapiens" ; schema:valueReference obo:NCBITaxon_9606 . _:b3 a schema:PropertyValue ; schema:name "scientific name" ; schema:value "Homo sapiens" ; schema:valueReference obo:NCBITaxon_9606 .
我用于生成RDF TURTLE数据的代码如下,我从-https://www.ebi.ac.uk/biosamples/samples/SAMN03177689.ldjson
import org.apache.commons.io.FileUtils;
import org.eclipse.rdf4j.model.Statement;
import org.eclipse.rdf4j.rio.RDFFormat;
import org.eclipse.rdf4j.rio.RDFHandlerException;
import org.eclipse.rdf4j.rio.RDFParser;
import org.eclipse.rdf4j.rio.Rio;
import org.eclipse.rdf4j.rio.helpers.StatementCollector;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import java.io.ByteArrayInputStream;
import java.io.File;
import java.io.InputStream;
import java.io.StringWriter;
import java.net.HttpURLConnection;
import java.net.URL;
import java.nio.charset.StandardCharsets;
import java.util.Collection;
import java.util.Scanner;
import java.util.concurrent.Callable;
public class BioSchemasRdfGenerator implements Callable<Void> {
private Logger log = LoggerFactory.getLogger(getClass());
private static File file;
private static long sampleCount = 0;
private final URL url;
public static void setFilePath(String filePath) {
file = new File(filePath);
}
BioSchemasRdfGenerator(final URL url) {
log.info("HANDLING " + url.toString() + " and the current sample count is: " + ++sampleCount);
this.url = url;
}
@Override
public Void call() throws Exception {
requestHTTPAndHandle(this.url);
return null;
}
private static void requestHTTPAndHandle(final URL url) throws Exception {
final HttpURLConnection conn = (HttpURLConnection) url.openConnection();
int response;
try {
conn.setRequestMethod("GET");
conn.connect();
response = conn.getResponseCode();
if (response == 200) {
handleSuccessResponses(url);
}
} catch (final Exception e) {
throw new RuntimeException(e);
} finally {
conn.disconnect();
}
}
private static void handleSuccessResponses(final URL url) {
try (Scanner sc = new Scanner(url.openStream())) {
final StringBuilder sb = new StringBuilder();
while (sc.hasNext()) {
sb.append(sc.nextLine());
}
try (InputStream in = new ByteArrayInputStream(sb.toString().getBytes(StandardCharsets.UTF_8))) {
String dataAsRdf = readRdfToString(in);
write(dataAsRdf);
} catch (final Exception e) {
throw new RuntimeException(e);
}
} catch (final Exception e) {
throw new RuntimeException(e);
}
}
@SuppressWarnings(value = "deprecation")
private static void write(final String sampleData) throws Exception {
FileUtils.writeStringToFile(file, sampleData, true);
}
/**
* @param in a rdf input stream
* @return a string representation
*/
private static String readRdfToString(final InputStream in) {
return graphToString(readRdfToGraph(in));
}
/**
* @param inputStream an Input stream containing rdf data
* @return a Graph representing the rdf in the input stream
*/
private static Collection<Statement> readRdfToGraph(final InputStream inputStream) {
try {
final RDFParser rdfParser = Rio.createParser(RDFFormat.JSONLD);
final StatementCollector collector = new StatementCollector();
rdfParser.setRDFHandler(collector);
rdfParser.parse(inputStream, "");
return collector.getStatements();
} catch (final Exception e) {
throw new RuntimeException(e);
}
}
/**
* Transforms a graph to a string.
*
* @param myGraph a sesame rdf graph
* @return a rdf string
*/
private static String graphToString(final Collection<Statement> myGraph) {
final StringWriter out = new StringWriter();
final TurtleWriterCustom turtleWriterCustom = new TurtleWriterCustom(out);
return modifyIdentifier(writeRdfInTurtleFormat(myGraph, out, turtleWriterCustom));
}
private static String modifyIdentifier(String rdfString) {
if (rdfString != null)
rdfString = rdfString.replaceAll("biosample:", "");
return rdfString;
}
private static String writeRdfInTurtleFormat(Collection<Statement> myGraph, StringWriter out, TurtleWriterCustom writer) {
try {
writer.startRDF();
handleNamespaces(writer);
for (Statement st : myGraph) {
writer.handleStatement(st);
//below line is commented: for short RDF
//writer.writeValue(st.getObject(),O true);
}
writer.endRDF();
} catch (final RDFHandlerException e) {
throw new RuntimeException(e);
}
return out.getBuffer().toString();
}
private static void handleNamespaces(final TurtleWriterCustom writer) {
writer.handleNamespace("schema", "http://schema.org/");
writer.handleNamespace("obo", "http://purl.obolibrary.org/obo/");
writer.handleNamespace("ebi-bsd", "https://www.ebi.ac.uk/biosamples/");
writer.handleNamespace("biosamples", "http://identifiers.org/biosample/");
}
}
我有RDF数据,我想形成一个SPARQL查询以获取与特定生物名称匹配的记录。仅供参考,我使用RDF4J使用可用的JSONLD数据生成RDF记录。我正在...
您的代码看起来比需要的复杂得多。要使用RDF4J将JSON-LD文件作为RDF模型加载到远程URL上,只需执行以下操作: