Closes #60

Added missing database names to script, so hopefully these nodes are now converted (will test this with version 66).

src/org/gk/gpml/ReactometoGPML2013.java

@@ -339,6 +339,8 @@ private void addXref(PathwayElement pwyele, Long rId, GKInstance instance)
 
 			/*
 			 * ChEBI and uniprot give errors while searching by full name
+			 * This also happens for PubChem Compound (should be PubChem-Compound)
+			 * And NCBI Nucleotide (which should link to NCBI Protein).
 			 */
 			String identifier = getIdentifierFromReferenceEntity(referenceEntity);
 			if (db.getDisplayName().equalsIgnoreCase("chebi")) {
@@ -350,6 +352,10 @@ private void addXref(PathwayElement pwyele, Long rId, GKInstance instance)
 				pwyele.setDataSource(DataSource.getExistingBySystemCode("En"));
 			} else if (db.getDisplayName().equalsIgnoreCase("miRBase")) {
 				pwyele.setDataSource(DataSource.getExistingBySystemCode("Mbm"));
+			} else if (db.getDisplayName().equalsIgnoreCase("PubChem Compound")) {
+				pwyele.setDataSource(DataSource.getExistingBySystemCode("Cpc"));
+			} else if (db.getDisplayName().equalsIgnoreCase("NCBI Nucleotide")) {
+				pwyele.setDataSource(DataSource.getExistingBySystemCode("Np"));
 			} else {
 				pwyele.setDataSource(DataSource.getExistingByFullName(db
 						.getDisplayName()));