OK, also use the cryptic SIO URI

bioclipse · Jan 7, 2013 · cee5fa0 · cee5fa0
1 parent 0a5adcf
commit cee5fa0
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Showing 2 changed files with 27 additions and 13 deletions.
diff --git a/plugins/net.bioclipse.icebear/src/net/bioclipse/icebear/business/IcebearManager.java b/plugins/net.bioclipse.icebear/src/net/bioclipse/icebear/business/IcebearManager.java
@@ -187,6 +187,7 @@ private void findInfoForOneURI(IcebearWorkload workload, IReturner<IRDFStore> re
 				nextURI.toString()
 			);
 			rdf.importURL(store, nextURIString, extraHeaders, monitor);
+			System.out.println(rdf.asTurtle(store));
 			for (INextURIExtractor spider : spiders) {
 				for (String uri : spider.extractURIs(store, nextURI.toString())) {
 					workload.addNewURI(uri);

diff --git a/...s/net.bioclipse.icebear/src/net/bioclipse/icebear/extractors/properties/SioExtractor.java b/...s/net.bioclipse.icebear/src/net/bioclipse/icebear/extractors/properties/SioExtractor.java
@@ -20,23 +20,36 @@
 
 public class SioExtractor extends AbstractExtractor implements IPropertyExtractor {
 
+	private final static String[] SIO_PREDICATES = {
+		"http://semanticscience.org/resource/has-attribute",
+		"http://semanticscience.org/resource/SIO_000008"
+	};
+
 	@Override
 	public List<Entry> extractProperties(IRDFStore store, String resource) {
 		List<Entry> props = new ArrayList<Entry>();
 
-		// get SIO properties
-		String sparql =
-			"PREFIX sio: <http://semanticscience.org/resource/>\n" +
-			"PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>\n" +
-			"SELECT ?type ?value WHERE {" +
-			"  <" + resource + "> sio:has-attribute ?property ." +
-			"  ?property rdfs:label ?value ;" +
-			"    a ?desc . " +
-			"  ?desc rdfs:label ?type" +
-			"}";
-		StringMatrix results = sparql(store, sparql);
-		for (int i=1; i<=results.getRowCount(); i++) {
-			props.add(new Entry(resource, results.get(i, "type"), results.get(i, "value")));			
+		for (String predicate : SIO_PREDICATES) {
+			// get SIO properties
+			String sparql =
+				"PREFIX sio: <http://semanticscience.org/resource/>\n" +
+				"PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>\n" +
+				"SELECT ?label ?desc ?value WHERE {" +
+				"  <" + resource + "> <" + predicate + "> ?property ." +
+				"  ?property sio:SIO_000300 ?value ." +
+				"  OPTIONAL { ?property a ?desc . } " +
+				"  OPTIONAL { ?property rdfs:label ?label . }" +
+				"}";
+			StringMatrix results = sparql(store, sparql);
+			for (int i=1; i<=results.getRowCount(); i++) {
+				String type = "NA";
+				if (results.get(i, "label") != null) {
+					type = results.get(i, "label");
+				} else if (results.get(i, "desc") != null) {
+					type = results.get(i, "desc");
+				}
+				props.add(new Entry(resource, type, results.get(i, "value")));			
+			}
 		}
 		return props;
 	}