diff --git a/pom.xml b/pom.xml
index 61421c4..cc51473 100644
--- a/pom.xml
+++ b/pom.xml
@@ -205,7 +205,7 @@
             <dependency>
                 <groupId>ch.qos.logback</groupId>
                 <artifactId>logback-classic</artifactId>
-                <version>1.4.12</version>
+                <version>1.4.14</version>
             </dependency>
         </dependencies>
     </dependencyManagement>
diff --git a/src/main/java/org/humanmetabolism/ReconxToBiopax.java b/src/main/java/org/humanmetabolism/ReconxToBiopax.java
index 6e05bbe..b360fed 100644
--- a/src/main/java/org/humanmetabolism/ReconxToBiopax.java
+++ b/src/main/java/org/humanmetabolism/ReconxToBiopax.java
@@ -31,14 +31,14 @@ public static void main(String[] args) throws IOException, XMLStreamException {
             makePathway = true;
         }
 
-        log.info("Converting SBML model to BioPAX...");
+        log.info("Converting the SBML model to BioPAX...");
         SbmlToBiopaxConverter sbmlToBiopaxConverter = new SbmlToBiopaxConverter();
         sbmlToBiopaxConverter.setMakePathway(makePathway);
+        sbmlToBiopaxConverter.biopaxModelXmlBase("reconx:");
         Model bpModel = sbmlToBiopaxConverter.convert(new File(sbmlFile));
-
-        log.info("Saving BioPAX model to " + bpFile);
+        log.info("Saving the BioPAX model to " + bpFile);
         SimpleIOHandler bpHandler = new SimpleIOHandler(BioPAXLevel.L3);
         bpHandler.convertToOWL(bpModel, new FileOutputStream(bpFile));
-        log.info("Conversion completed.");
+        log.info("Completed!");
     }
 }
diff --git a/src/main/java/org/humanmetabolism/converter/SbmlToBiopaxConverter.java b/src/main/java/org/humanmetabolism/converter/SbmlToBiopaxConverter.java
index cc6f5e0..6e36d87 100644
--- a/src/main/java/org/humanmetabolism/converter/SbmlToBiopaxConverter.java
+++ b/src/main/java/org/humanmetabolism/converter/SbmlToBiopaxConverter.java
@@ -16,6 +16,10 @@ public class SbmlToBiopaxConverter {
     private final SbmlToBiopaxUtils sbmlToBiopaxUtils = new SbmlToBiopaxUtils();
     private boolean makePathway = false;
 
+    public void biopaxModelXmlBase(String xmlBase) {
+        sbmlToBiopaxUtils.setXmlBase(xmlBase);
+    }
+
     /**
      * Whether to generate the model's root pathway that contains all the interactions.
      *
@@ -43,7 +47,7 @@ public Model convert(SBMLDocument sbmlDocument) {
     private Model convert(org.sbml.jsbml.Model sbmlModel) {
         Model bpModel = sbmlToBiopaxUtils.createModel();
 
-        final Provenance provenance = sbmlToBiopaxUtils.convertProvenance(bpModel,sbmlModel);
+        final Provenance provenance = sbmlToBiopaxUtils.convertProvenance(bpModel, sbmlModel);
 
         // create a Pathway that corresponds to this SBML model (optional)
         Pathway pathway = null;
diff --git a/src/main/java/org/humanmetabolism/converter/SbmlToBiopaxUtils.java b/src/main/java/org/humanmetabolism/converter/SbmlToBiopaxUtils.java
index c79ba56..643c0e9 100644
--- a/src/main/java/org/humanmetabolism/converter/SbmlToBiopaxUtils.java
+++ b/src/main/java/org/humanmetabolism/converter/SbmlToBiopaxUtils.java
@@ -1,5 +1,6 @@
 package org.humanmetabolism.converter;
 
+import org.apache.commons.lang3.StringUtils;
 import org.biopax.paxtools.model.BioPAXFactory;
 import org.biopax.paxtools.model.BioPAXLevel;
 import org.biopax.paxtools.model.Model;
@@ -16,20 +17,24 @@
 public class SbmlToBiopaxUtils {
     private static Logger log = LoggerFactory.getLogger(SbmlToBiopaxUtils.class);
 
-    private BioPAXFactory bioPAXFactory = BioPAXLevel.L3.getDefaultFactory();
+    private BioPAXFactory bioPAXFactory;
+    private String xmlBase;
 
-    private String XMLBase = "http://www.humanmetabolism.org/#";
+    public SbmlToBiopaxUtils() {
+        this.xmlBase = "";
+        this.bioPAXFactory = BioPAXLevel.L3.getDefaultFactory();
+    }
 
-    public String getXMLBase() {
-        return XMLBase;
+    public String getXmlBase() {
+        return xmlBase;
     }
 
-    public void setXMLBase(String XMLBase) {
-        this.XMLBase = XMLBase;
+    public void setXmlBase(String xmlBase) {
+        this.xmlBase = (StringUtils.isBlank(xmlBase)) ? "" : xmlBase;
     }
 
     public String completeId(String partialId) {
-        return getXMLBase() + partialId;
+        return getXmlBase() + partialId;
     }
 
     public Pathway convertPathway(Model bpModel, org.sbml.jsbml.Model sbmlModel) {
@@ -42,15 +47,12 @@ public Pathway convertPathway(Model bpModel, org.sbml.jsbml.Model sbmlModel) {
 
     public Provenance convertProvenance(Model bpModel, org.sbml.jsbml.Model sbmlModel) {
         Provenance p = createBPEfromSBMLE(bpModel, Provenance.class, sbmlModel,
-                "http://identifiers.org/biomodels.db/" + sbmlModel.getId());
-
+                "bioregistry.io/biomodels.db:" + sbmlModel.getId());
         for (Xref xref : generateXrefsForSBase(bpModel, RelationshipXref.class, sbmlModel)) {
             p.addXref(xref);
         }
-
-        final UnificationXref x = bpModel.addNew(UnificationXref.class,
-                bpModel.getXmlBase() + "xref_biomodels_" + sbmlModel.getId());
-        x.setDb("BioModels Database");
+        final UnificationXref x = bpModel.addNew(UnificationXref.class,"biomodels.db:" + sbmlModel.getId());
+        x.setDb("biomodels.db");
         x.setId(sbmlModel.getId());
         p.addXref(x);
 
@@ -60,7 +62,7 @@ public Provenance convertProvenance(Model bpModel, org.sbml.jsbml.Model sbmlMode
     public Model createModel() {
         Model model = bioPAXFactory.createModel();
         // This could change, would be great to make this configurable
-        model.setXmlBase(getXMLBase());
+        model.setXmlBase(getXmlBase());
         return model;
     }
 
@@ -110,9 +112,11 @@ public Control convertModifier(Model bpModel, ModifierSpeciesReference modifierS
         return control;
     }
 
-    public <T extends SimplePhysicalEntity, S extends EntityReference> T convertSpeciesToSPE(Model bpModel, Class<T> entityClass, Class<S> refClass, Species species) {
+    public <T extends SimplePhysicalEntity, S extends EntityReference> T convertSpeciesToSPE(
+        Model bpModel, Class<T> entityClass, Class<S> refClass, Species species)
+    {
         Set<Xref> xrefs = generateXrefsForSBase(bpModel, UnificationXref.class, species);
-        HashSet<XReferrable> ers = new HashSet<XReferrable>();
+        HashSet<XReferrable> ers = new HashSet<>();
         for (Xref xref : xrefs) {
             for (XReferrable xReferrable : xref.getXrefOf()) {
                 // Only add the entity references
@@ -272,9 +276,9 @@ private <T extends Xref> Set<Xref> generateXrefsForSBase(Model bpModel, Class<T>
     }
 
     public void fillComplexes(Model bpModel) {
-        HashMap<String, ProteinReference> xrefToProtein = new HashMap<String, ProteinReference>();
+        HashMap<String, ProteinReference> xrefToProtein = new HashMap<>();
         // Now let's use xrefs to find the complex components
-        // First, find the proteinrefs and map them with their xrefs
+        // First, find the protein refs and map them with their xrefs
         for (ProteinReference proteinRef : bpModel.getObjects(ProteinReference.class)) {
             for (Xref xref : proteinRef.getXref()) {
                 xrefToProtein.put(xref.toString(), proteinRef);
@@ -282,17 +286,16 @@ public void fillComplexes(Model bpModel) {
         }
 
         // Now let's go to the complexes and see what xrefs they have
-        Set<Complex> complexes = new HashSet<Complex>(bpModel.getObjects(Complex.class));
+        Set<Complex> complexes = new HashSet<>(bpModel.getObjects(Complex.class));
         for (Complex complex : complexes) {
-            HashSet<String> names = new HashSet<String>(Arrays.asList(complex.getDisplayName().split(":")));
+            HashSet<String> names = new HashSet<>(Arrays.asList(complex.getDisplayName().split(":")));
 
             // Let's try to capture proteins from the model first
-            HashSet<Protein> components = new HashSet<Protein>();
+            HashSet<Protein> components = new HashSet<>();
             for (Xref xref : complex.getXref()) {
                 ProteinReference proteinRef = xrefToProtein.get(xref.toString());
                 if(proteinRef != null) {
                     String cProteinId = completeId(complex.getUri() + "_" + proteinRef.getUri());
-                    //TODO: make sure refactoring has gone correct here (compare, test vs. prev. revision...)
                     if(!bpModel.containsID(cProteinId)) {
                         Protein protein = bpModel.addNew(Protein.class, cProteinId);
                         protein.setDisplayName(proteinRef.getDisplayName());
@@ -308,7 +311,6 @@ public void fillComplexes(Model bpModel) {
             // Let's create proteins for them
             for (String name : names) {
                 final String nameBasedURI = completeId("protein_" + name);
-                //TODO: make sure refactoring here was correct (removed 'newBPEs' intermediate map)
                 Protein protein = (Protein) bpModel.getByID(nameBasedURI);
                 if(protein == null) {
                     protein = bpModel.addNew(Protein.class, nameBasedURI);
@@ -324,15 +326,15 @@ public void fillComplexes(Model bpModel) {
                     proteinReference.setStandardName(name);
                 }
 
-                String xrefId = completeId("symbol_" + name);
-                UnificationXref unificationXref = (UnificationXref) bpModel.getByID(xrefId);
-                if(unificationXref == null) {
-                    unificationXref = bpModel.addNew(UnificationXref.class, xrefId);
-                    unificationXref.setDb("HGNC Symbol");
-                    unificationXref.setId(name);
+                String u = completeId("symbol_" + name);
+                RelationshipXref rx = (RelationshipXref) bpModel.getByID(u);
+                if(rx == null) {
+                    rx = bpModel.addNew(RelationshipXref.class, u);
+                    rx.setDb("hgnc.symbol");
+                    rx.setId(name);
                 }
 
-                proteinReference.addXref(unificationXref);
+                proteinReference.addXref(rx);
                 protein.setEntityReference(proteinReference);
                 components.add(protein);
             }
@@ -349,18 +351,18 @@ public void fillComplexes(Model bpModel) {
 
     public void assignOrganism(Model bpModel) {
         // Since this is RECON2, everything is human
-        BioSource bioSource = bpModel.addNew(BioSource.class, "http://identifiers.org/taxonomy/9606");
+        BioSource bioSource = bpModel.addNew(BioSource.class, "bioregistry.io/ncbitaxon:9606");
         bioSource.setDisplayName("Homo sapiens");
         bioSource.setStandardName("Homo sapiens");
-        UnificationXref unificationXref = bpModel.addNew(UnificationXref.class, completeId("xref_taxonomy_9606"));
-        unificationXref.setDb("Taxonomy");
+        UnificationXref unificationXref = bpModel.addNew(UnificationXref.class, "ncbitaxon:9606");
+        unificationXref.setDb("ncbitaxon");
         unificationXref.setId("9606");
         bioSource.addXref(unificationXref);
 
         for (SequenceEntityReference ser : bpModel.getObjects(SequenceEntityReference.class)) {
             ser.setOrganism(bioSource);
         }
-        for (Gene g : bpModel.getObjects(Gene.class)) { //but, there're probably no Gene objects...
+        for (Gene g : bpModel.getObjects(Gene.class)) { //but, there are probably no Gene objects...
             g.setOrganism(bioSource);
         }
         for (Pathway p : bpModel.getObjects(Pathway.class)) {