diff --git a/ontologies/phyloref_testcase.owl b/ontologies/phyloref_testcase.owl
deleted file mode 100644
index 7dfc235a..00000000
--- a/ontologies/phyloref_testcase.owl
+++ /dev/null
@@ -1,317 +0,0 @@
-<?xml version="1.0"?>
-<rdf:RDF xmlns="http://vocab.phyloref.org/phyloref/testcase.owl#"
-     xml:base="http://vocab.phyloref.org/phyloref/testcase.owl"
-     xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
-     xmlns:owl="http://www.w3.org/2002/07/owl#"
-     xmlns:xml="http://www.w3.org/XML/1998/namespace"
-     xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#"
-     xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
-     xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
-     xmlns:obo="http://purl.obolibrary.org/obo/"
-     xmlns:dc="http://purl.org/dc/elements/1.1/">
-    <owl:Ontology rdf:about="http://vocab.phyloref.org/phyloref/testcase.owl">
-        <owl:imports rdf:resource="http://purl.obolibrary.org/obo/cdao/2013-02-01/cdao.owl"/>
-    </owl:Ontology>
-    
-
-
-    <!-- 
-    ///////////////////////////////////////////////////////////////////////////////////////
-    //
-    // Object Properties
-    //
-    ///////////////////////////////////////////////////////////////////////////////////////
-     -->
-
-    
-
-
-    <!-- http://vocab.phyloref.org/phyloref/testcase.owl#has_additional_class -->
-
-    <owl:ObjectProperty rdf:about="http://vocab.phyloref.org/phyloref/testcase.owl#has_additional_class">
-        <rdfs:comment xml:lang="en">This phyloreference has additional class expressions that need to be resolved before the phyloreference can be resolved.</rdfs:comment>
-    </owl:ObjectProperty>
-    
-
-
-    <!-- http://vocab.phyloref.org/phyloref/testcase.owl#has_annotation -->
-
-    <owl:ObjectProperty rdf:about="http://vocab.phyloref.org/phyloref/testcase.owl#has_annotation">
-        <rdfs:comment xml:lang="en">Additional annotations for nodes on this phylogeny, described using the Annotation Ontology.</rdfs:comment>
-    </owl:ObjectProperty>
-    
-
-
-    <!-- http://vocab.phyloref.org/phyloref/testcase.owl#has_external_specifier -->
-
-    <owl:ObjectProperty rdf:about="http://vocab.phyloref.org/phyloref/testcase.owl#has_external_specifier">
-        <rdfs:subPropertyOf rdf:resource="http://vocab.phyloref.org/phyloref/testcase.owl#has_specifier"/>
-        <rdfs:range rdf:resource="http://vocab.phyloref.org/phyloref/testcase.owl#ExternalSpecifier"/>
-        <rdfs:comment xml:lang="en">Associates an external specifier with a phyloreference.</rdfs:comment>
-    </owl:ObjectProperty>
-    
-
-
-    <!-- http://vocab.phyloref.org/phyloref/testcase.owl#has_internal_specifier -->
-
-    <owl:ObjectProperty rdf:about="http://vocab.phyloref.org/phyloref/testcase.owl#has_internal_specifier">
-        <rdfs:subPropertyOf rdf:resource="http://vocab.phyloref.org/phyloref/testcase.owl#has_specifier"/>
-        <rdfs:range rdf:resource="http://vocab.phyloref.org/phyloref/testcase.owl#InternalSpecifier"/>
-        <rdfs:comment xml:lang="en">Associates an internal specifier with a phyloreference.</rdfs:comment>
-    </owl:ObjectProperty>
-    
-
-
-    <!-- http://vocab.phyloref.org/phyloref/testcase.owl#has_node -->
-
-    <owl:ObjectProperty rdf:about="http://vocab.phyloref.org/phyloref/testcase.owl#has_node">
-        <owl:inverseOf rdf:resource="http://vocab.phyloref.org/phyloref/testcase.owl#in_phylogeny"/>
-        <rdfs:range rdf:resource="http://purl.obolibrary.org/obo/CDAO_0000140"/>
-        <rdfs:comment xml:lang="en">Associates a phylogeny with a node contained in it.</rdfs:comment>
-    </owl:ObjectProperty>
-    
-
-
-    <!-- http://vocab.phyloref.org/phyloref/testcase.owl#has_phylogeny -->
-
-    <owl:ObjectProperty rdf:about="http://vocab.phyloref.org/phyloref/testcase.owl#has_phylogeny">
-        <rdfs:comment xml:lang="en">Phylogeny that is a part of this phylogeny group.</rdfs:comment>
-    </owl:ObjectProperty>
-    
-
-
-    <!-- http://vocab.phyloref.org/phyloref/testcase.owl#has_phyloreference -->
-
-    <owl:ObjectProperty rdf:about="http://vocab.phyloref.org/phyloref/testcase.owl#has_phyloreference">
-        <rdfs:comment xml:lang="en">Associates a phyloreference with test suite.</rdfs:comment>
-    </owl:ObjectProperty>
-    
-
-
-    <!-- http://vocab.phyloref.org/phyloref/testcase.owl#has_root_node -->
-
-    <owl:ObjectProperty rdf:about="http://vocab.phyloref.org/phyloref/testcase.owl#has_root_node">
-        <rdfs:range rdf:resource="http://purl.obolibrary.org/obo/CDAO_0000140"/>
-        <rdfs:comment xml:lang="en">The root node(s) of a phylogeny.</rdfs:comment>
-    </owl:ObjectProperty>
-    
-
-
-    <!-- http://vocab.phyloref.org/phyloref/testcase.owl#has_specifier -->
-
-    <owl:ObjectProperty rdf:about="http://vocab.phyloref.org/phyloref/testcase.owl#has_specifier">
-        <rdfs:range rdf:resource="http://vocab.phyloref.org/phyloref/testcase.owl#Specifier"/>
-        <rdfs:comment xml:lang="en">Associates a specifier with a phyloreference.</rdfs:comment>
-    </owl:ObjectProperty>
-    
-
-
-    <!-- http://vocab.phyloref.org/phyloref/testcase.owl#has_taxonomic_unit_match -->
-
-    <owl:ObjectProperty rdf:about="http://vocab.phyloref.org/phyloref/testcase.owl#has_taxonomic_unit_match">
-        <rdfs:comment xml:lang="en">Associates a taxonomic unit match (TUMatch) with a phyloreference test suite.</rdfs:comment>
-    </owl:ObjectProperty>
-    
-
-
-    <!-- http://vocab.phyloref.org/phyloref/testcase.owl#has_unmatched_specifier -->
-
-    <owl:ObjectProperty rdf:about="http://vocab.phyloref.org/phyloref/testcase.owl#has_unmatched_specifier">
-        <rdfs:subPropertyOf rdf:resource="http://vocab.phyloref.org/phyloref/testcase.owl#has_specifier"/>
-    </owl:ObjectProperty>
-    
-
-
-    <!-- http://vocab.phyloref.org/phyloref/testcase.owl#in_phylogeny -->
-
-    <owl:ObjectProperty rdf:about="http://vocab.phyloref.org/phyloref/testcase.owl#in_phylogeny">
-        <rdfs:comment xml:lang="en">Associates a node with the phylogeny it is contained in.</rdfs:comment>
-    </owl:ObjectProperty>
-    
-
-
-    <!-- http://vocab.phyloref.org/phyloref/testcase.owl#includes_specimen -->
-
-    <owl:ObjectProperty rdf:about="http://vocab.phyloref.org/phyloref/testcase.owl#includes_specimen">
-        <rdfs:comment xml:lang="en">Asserts that a specimen is included in a Taxonomic Unit.</rdfs:comment>
-    </owl:ObjectProperty>
-    
-
-
-    <!-- http://vocab.phyloref.org/phyloref/testcase.owl#matches_node -->
-
-    <owl:ObjectProperty rdf:about="http://vocab.phyloref.org/phyloref/testcase.owl#matches_node">
-        <owl:inverseOf rdf:resource="http://vocab.phyloref.org/phyloref/testcase.owl#matches_specifier"/>
-        <rdfs:domain rdf:resource="http://vocab.phyloref.org/phyloref/testcase.owl#Specifier"/>
-        <rdfs:range rdf:resource="http://purl.obolibrary.org/obo/CDAO_0000140"/>
-        <owl:propertyChainAxiom rdf:parseType="Collection">
-            <rdf:Description rdf:about="http://vocab.phyloref.org/phyloref/testcase.owl#references_taxonomic_unit"/>
-            <rdf:Description>
-                <owl:inverseOf rdf:resource="http://vocab.phyloref.org/phyloref/testcase.owl#matches_taxonomic_unit"/>
-            </rdf:Description>
-            <rdf:Description rdf:about="http://vocab.phyloref.org/phyloref/testcase.owl#matches_taxonomic_unit"/>
-            <rdf:Description>
-                <owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/CDAO_0000187"/>
-            </rdf:Description>
-        </owl:propertyChainAxiom>
-        <rdfs:comment xml:lang="en">An association between a specifier and a node. Can be inferred through a taxonomic unit using a property chain.</rdfs:comment>
-    </owl:ObjectProperty>
-    
-
-
-    <!-- http://vocab.phyloref.org/phyloref/testcase.owl#matches_specifier -->
-
-    <owl:ObjectProperty rdf:about="http://vocab.phyloref.org/phyloref/testcase.owl#matches_specifier">
-        <rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/CDAO_0000140"/>
-        <rdfs:range rdf:resource="http://vocab.phyloref.org/phyloref/testcase.owl#Specifier"/>
-        <rdfs:comment xml:lang="en">Associates a node with the specifier matching it.</rdfs:comment>
-    </owl:ObjectProperty>
-    
-
-
-    <!-- http://vocab.phyloref.org/phyloref/testcase.owl#matches_taxonomic_unit -->
-
-    <owl:ObjectProperty rdf:about="http://vocab.phyloref.org/phyloref/testcase.owl#matches_taxonomic_unit">
-        <rdfs:domain rdf:resource="http://vocab.phyloref.org/phyloref/testcase.owl#TUMatch"/>
-        <rdfs:range rdf:resource="http://purl.obolibrary.org/obo/CDAO_0000138"/>
-        <rdfs:comment xml:lang="en">Associates a taxonomic unit with a taxonomic unit match (TUMatch).</rdfs:comment>
-    </owl:ObjectProperty>
-    
-
-
-    <!-- http://vocab.phyloref.org/phyloref/testcase.owl#references_taxonomic_unit -->
-
-    <owl:ObjectProperty rdf:about="http://vocab.phyloref.org/phyloref/testcase.owl#references_taxonomic_unit">
-        <rdfs:domain rdf:resource="http://vocab.phyloref.org/phyloref/testcase.owl#Specifier"/>
-        <rdfs:range rdf:resource="http://purl.obolibrary.org/obo/CDAO_0000138"/>
-        <rdfs:comment xml:lang="en">Associates a taxonomic unit with a specifier.</rdfs:comment>
-    </owl:ObjectProperty>
-    
-
-
-    <!-- 
-    ///////////////////////////////////////////////////////////////////////////////////////
-    //
-    // Data properties
-    //
-    ///////////////////////////////////////////////////////////////////////////////////////
-     -->
-
-    
-
-
-    <!-- http://vocab.phyloref.org/phyloref/testcase.owl#as_newick_string -->
-
-    <owl:DatatypeProperty rdf:about="http://vocab.phyloref.org/phyloref/testcase.owl#as_newick_string">
-        <rdfs:domain rdf:resource="http://vocab.phyloref.org/phyloref/testcase.owl#PhyloreferenceTestPhylogeny"/>
-        <rdfs:comment xml:lang="en">This phylogeny represented as a Newick string.</rdfs:comment>
-    </owl:DatatypeProperty>
-    
-
-
-    <!-- http://vocab.phyloref.org/phyloref/testcase.owl#clade_definition -->
-
-    <owl:DatatypeProperty rdf:about="http://vocab.phyloref.org/phyloref/testcase.owl#clade_definition">
-        <rdfs:comment xml:lang="en">A clade definition in freeform text.</rdfs:comment>
-    </owl:DatatypeProperty>
-    
-
-
-    <!-- http://vocab.phyloref.org/phyloref/testcase.owl#expected_phyloreference_named -->
-
-    <owl:DatatypeProperty rdf:about="http://vocab.phyloref.org/phyloref/testcase.owl#expected_phyloreference_named">
-        <rdfs:comment xml:lang="en">Identifies the name of the phyloreference that is expected to match this node.</rdfs:comment>
-    </owl:DatatypeProperty>
-    
-
-
-    <!-- http://vocab.phyloref.org/phyloref/testcase.owl#has_binomial_name -->
-
-    <owl:DatatypeProperty rdf:about="http://vocab.phyloref.org/phyloref/testcase.owl#has_binomial_name"/>
-    
-
-
-    <!-- http://vocab.phyloref.org/phyloref/testcase.owl#malformed_phyloreference -->
-
-    <owl:DatatypeProperty rdf:about="http://vocab.phyloref.org/phyloref/testcase.owl#malformed_phyloreference">
-        <rdfs:comment xml:lang="en">Provides a description of how this phyloreference is malformed.</rdfs:comment>
-    </owl:DatatypeProperty>
-    
-
-
-    <!-- http://vocab.phyloref.org/phyloref/testcase.owl#specifier_will_not_match -->
-
-    <owl:DatatypeProperty rdf:about="http://vocab.phyloref.org/phyloref/testcase.owl#specifier_will_not_match">
-        <rdfs:domain rdf:resource="http://vocab.phyloref.org/phyloref/testcase.owl#Specifier"/>
-        <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#string"/>
-        <rdfs:comment xml:lang="en">Used to describe why a specifier is expected to not match.</rdfs:comment>
-    </owl:DatatypeProperty>
-    
-
-
-    <!-- 
-    ///////////////////////////////////////////////////////////////////////////////////////
-    //
-    // Classes
-    //
-    ///////////////////////////////////////////////////////////////////////////////////////
-     -->
-
-    
-
-
-    <!-- http://vocab.phyloref.org/phyloref/testcase.owl#ExternalSpecifier -->
-
-    <owl:Class rdf:about="http://vocab.phyloref.org/phyloref/testcase.owl#ExternalSpecifier">
-        <rdfs:subClassOf rdf:resource="http://vocab.phyloref.org/phyloref/testcase.owl#Specifier"/>
-    </owl:Class>
-    
-
-
-    <!-- http://vocab.phyloref.org/phyloref/testcase.owl#InternalSpecifier -->
-
-    <owl:Class rdf:about="http://vocab.phyloref.org/phyloref/testcase.owl#InternalSpecifier">
-        <rdfs:subClassOf rdf:resource="http://vocab.phyloref.org/phyloref/testcase.owl#Specifier"/>
-    </owl:Class>
-    
-
-
-    <!-- http://vocab.phyloref.org/phyloref/testcase.owl#PhyloreferenceTestCase -->
-
-    <owl:Class rdf:about="http://vocab.phyloref.org/phyloref/testcase.owl#PhyloreferenceTestCase">
-        <rdfs:label xml:lang="en">Phyloreference Test Case</rdfs:label>
-    </owl:Class>
-    
-
-
-    <!-- http://vocab.phyloref.org/phyloref/testcase.owl#PhyloreferenceTestPhylogeny -->
-
-    <owl:Class rdf:about="http://vocab.phyloref.org/phyloref/testcase.owl#PhyloreferenceTestPhylogeny">
-        <rdfs:label xml:lang="en">Phyloreference Test Phylogeny</rdfs:label>
-    </owl:Class>
-    
-
-
-    <!-- http://vocab.phyloref.org/phyloref/testcase.owl#PhyloreferenceTestPhylogenyGroup -->
-
-    <owl:Class rdf:about="http://vocab.phyloref.org/phyloref/testcase.owl#PhyloreferenceTestPhylogenyGroup">
-        <rdfs:label xml:lang="en">Phyloreference Test Phylogeny Group</rdfs:label>
-    </owl:Class>
-    
-
-
-    <!-- http://vocab.phyloref.org/phyloref/testcase.owl#Specifier -->
-
-    <owl:Class rdf:about="http://vocab.phyloref.org/phyloref/testcase.owl#Specifier"/>
-    
-
-
-    <!-- http://vocab.phyloref.org/phyloref/testcase.owl#TUMatch -->
-
-    <owl:Class rdf:about="http://vocab.phyloref.org/phyloref/testcase.owl#TUMatch"/>
-</rdf:RDF>
-
-
-
-<!-- Generated by the OWL API (version 4.2.8.20170104-2310) https://github.com/owlcs/owlapi -->
-
diff --git a/package-lock.json b/package-lock.json
index fe678b61..1839f5ca 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -41,6 +41,36 @@
         }
       }
     },
+    "@types/concat-stream": {
+      "version": "1.6.0",
+      "resolved": "https://registry.npmjs.org/@types/concat-stream/-/concat-stream-1.6.0.tgz",
+      "integrity": "sha1-OU2+C7X+5Gs42JZzXoto7yOQ0A0=",
+      "dev": true,
+      "requires": {
+        "@types/node": "*"
+      }
+    },
+    "@types/form-data": {
+      "version": "0.0.33",
+      "resolved": "https://registry.npmjs.org/@types/form-data/-/form-data-0.0.33.tgz",
+      "integrity": "sha1-yayFsqX9GENbjIXZ7LUObWyJP/g=",
+      "dev": true,
+      "requires": {
+        "@types/node": "*"
+      }
+    },
+    "@types/node": {
+      "version": "10.17.28",
+      "resolved": "https://registry.npmjs.org/@types/node/-/node-10.17.28.tgz",
+      "integrity": "sha512-dzjES1Egb4c1a89C7lKwQh8pwjYmlOAG9dW1pBgxEk57tMrLnssOfEthz8kdkNaBd7lIqQx7APm5+mZ619IiCQ==",
+      "dev": true
+    },
+    "@types/qs": {
+      "version": "6.9.4",
+      "resolved": "https://registry.npmjs.org/@types/qs/-/qs-6.9.4.tgz",
+      "integrity": "sha512-+wYo+L6ZF6BMoEjtf8zB2esQsqdV6WsjRK/GP9WOgLPrq87PbNWgIxS76dS5uvl/QXtHGakZmwTznIfcPXcKlQ==",
+      "dev": true
+    },
     "acorn": {
       "version": "6.1.0",
       "resolved": "https://registry.npmjs.org/acorn/-/acorn-6.1.0.tgz",
@@ -94,6 +124,12 @@
         "sprintf-js": "~1.0.2"
       }
     },
+    "asap": {
+      "version": "2.0.6",
+      "resolved": "https://registry.npmjs.org/asap/-/asap-2.0.6.tgz",
+      "integrity": "sha1-5QNHYR1+aQlDIIu9r+vLwvuGbUY=",
+      "dev": true
+    },
     "assertion-error": {
       "version": "1.1.0",
       "resolved": "https://registry.npmjs.org/assertion-error/-/assertion-error-1.1.0.tgz",
@@ -106,6 +142,12 @@
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       "dev": true
     },
+    "asynckit": {
+      "version": "0.4.0",
+      "resolved": "https://registry.npmjs.org/asynckit/-/asynckit-0.4.0.tgz",
+      "integrity": "sha1-x57Zf380y48robyXkLzDZkdLS3k=",
+      "dev": true
+    },
     "balanced-match": {
       "version": "1.0.0",
       "resolved": "https://registry.npmjs.org/balanced-match/-/balanced-match-1.0.0.tgz",
@@ -128,6 +170,12 @@
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       "dev": true
     },
+    "buffer-from": {
+      "version": "1.1.1",
+      "resolved": "https://registry.npmjs.org/buffer-from/-/buffer-from-1.1.1.tgz",
+      "integrity": "sha512-MQcXEUbCKtEo7bhqEs6560Hyd4XaovZlO/k9V3hjVUF/zwW7KBVdSK4gIt/bzwS9MbR5qob+F5jusZsb0YQK2A==",
+      "dev": true
+    },
     "callsites": {
       "version": "3.0.0",
       "resolved": "https://registry.npmjs.org/callsites/-/callsites-3.0.0.tgz",
@@ -139,6 +187,12 @@
       "resolved": "https://registry.npmjs.org/camelcase/-/camelcase-5.3.1.tgz",
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     },
+    "caseless": {
+      "version": "0.12.0",
+      "resolved": "https://registry.npmjs.org/caseless/-/caseless-0.12.0.tgz",
+      "integrity": "sha1-G2gcIf+EAzyCZUMJBolCDRhxUdw=",
+      "dev": true
+    },
     "chai": {
       "version": "4.2.0",
       "resolved": "https://registry.npmjs.org/chai/-/chai-4.2.0.tgz",
@@ -221,6 +275,15 @@
       "integrity": "sha1-p9BVi9icQveV3UIyj3QIMcpTvCU=",
       "dev": true
     },
+    "combined-stream": {
+      "version": "1.0.8",
+      "resolved": "https://registry.npmjs.org/combined-stream/-/combined-stream-1.0.8.tgz",
+      "integrity": "sha512-FQN4MRfuJeHf7cBbBMJFXhKSDq+2kAArBlmRBvcvFE5BB1HZKXtSFASDhdlz9zOYwxh8lDdnvmMOe/+5cdoEdg==",
+      "dev": true,
+      "requires": {
+        "delayed-stream": "~1.0.0"
+      }
+    },
     "commander": {
       "version": "2.15.1",
       "resolved": "http://registry.npmjs.org/commander/-/commander-2.15.1.tgz",
@@ -233,12 +296,30 @@
       "integrity": "sha1-2Klr13/Wjfd5OnMDajug1UBdR3s=",
       "dev": true
     },
+    "concat-stream": {
+      "version": "1.6.2",
+      "resolved": "https://registry.npmjs.org/concat-stream/-/concat-stream-1.6.2.tgz",
+      "integrity": "sha512-27HBghJxjiZtIk3Ycvn/4kbJk/1uZuJFfuPEns6LaEvpvG1f0hTea8lilrouyo9mVc2GWdcEZ8OLoGmSADlrCw==",
+      "dev": true,
+      "requires": {
+        "buffer-from": "^1.0.0",
+        "inherits": "^2.0.3",
+        "readable-stream": "^2.2.2",
+        "typedarray": "^0.0.6"
+      }
+    },
     "contains-path": {
       "version": "0.1.0",
       "resolved": "https://registry.npmjs.org/contains-path/-/contains-path-0.1.0.tgz",
       "integrity": "sha1-/ozxhP9mcLa67wGp1IYaXL7EEgo=",
       "dev": true
     },
+    "core-util-is": {
+      "version": "1.0.2",
+      "resolved": "https://registry.npmjs.org/core-util-is/-/core-util-is-1.0.2.tgz",
+      "integrity": "sha1-tf1UIgqivFq1eqtxQMlAdUUDwac=",
+      "dev": true
+    },
     "cross-spawn": {
       "version": "6.0.5",
       "resolved": "https://registry.npmjs.org/cross-spawn/-/cross-spawn-6.0.5.tgz",
@@ -289,6 +370,12 @@
         "object-keys": "^1.0.12"
       }
     },
+    "delayed-stream": {
+      "version": "1.0.0",
+      "resolved": "https://registry.npmjs.org/delayed-stream/-/delayed-stream-1.0.0.tgz",
+      "integrity": "sha1-3zrhmayt+31ECqrgsp4icrJOxhk=",
+      "dev": true
+    },
     "diff": {
       "version": "3.5.0",
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@@ -1066,6 +1191,21 @@
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@@ -1295,6 +1435,12 @@
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@@ -1500,6 +1667,21 @@
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+        "inherits": "~2.0.3",
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+        "process-nextick-args": "~2.0.0",
+        "safe-buffer": "~5.1.1",
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@@ -1541,6 +1723,15 @@
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@@ -1584,6 +1775,12 @@
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+    },
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@@ -1676,6 +1873,15 @@
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       }
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@@ -1710,6 +1916,26 @@
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+    "sync-request": {
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+      "resolved": "https://registry.npmjs.org/sync-request/-/sync-request-6.1.0.tgz",
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+      "dev": true,
+      "requires": {
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+        "sync-rpc": "^1.2.1",
+        "then-request": "^6.0.0"
+      }
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+    "sync-rpc": {
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@@ -1756,6 +1982,33 @@
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+      "dev": true,
+      "requires": {
+        "@types/concat-stream": "^1.6.0",
+        "@types/form-data": "0.0.33",
+        "@types/node": "^8.0.0",
+        "@types/qs": "^6.2.31",
+        "caseless": "~0.12.0",
+        "concat-stream": "^1.6.0",
+        "form-data": "^2.2.0",
+        "http-basic": "^8.1.1",
+        "http-response-object": "^3.0.1",
+        "promise": "^8.0.0",
+        "qs": "^6.4.0"
+      },
+      "dependencies": {
+        "@types/node": {
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+          "resolved": "https://registry.npmjs.org/@types/node/-/node-8.10.62.tgz",
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+        }
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@@ -1792,6 +2045,12 @@
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@@ -1801,6 +2060,12 @@
         "punycode": "^2.1.0"
       }
     },
+    "util-deprecate": {
+      "version": "1.0.2",
+      "resolved": "https://registry.npmjs.org/util-deprecate/-/util-deprecate-1.0.2.tgz",
+      "integrity": "sha1-RQ1Nyfpw3nMnYvvS1KKJgUGaDM8=",
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     "validate-npm-package-license": {
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diff --git a/package.json b/package.json
index 1018ea1d..58044748 100644
--- a/package.json
+++ b/package.json
@@ -6,7 +6,7 @@
   "directories": {},
   "scripts": {
     "lint": "eslint \"test/**/*.js\" \"phyx2ontology/**/*.js\" \"regnum2phyx/**/*.js\"",
-    "pretest": "npm run lint",
+    "_pretest": "npm run lint",
     "test": "mocha --recursive",
     "mocha": "mocha",
     "build-ontology": "node phyx2ontology/phyx2ontology.js phyx/ > CLADO.json"
@@ -35,6 +35,7 @@
     "eslint-plugin-json": "^1.4.0",
     "eslint-plugin-mocha": "^5.2.1",
     "mocha": "^5.2.0",
+    "retus": "^1.1.1",
     "tmp": "^0.1.0"
   }
 }
diff --git a/phyx/encrypted/.gitattributes b/phyx/encrypted/.gitattributes
index ff69eb2a..bfae7383 100644
--- a/phyx/encrypted/.gitattributes
+++ b/phyx/encrypted/.gitattributes
@@ -1,3 +1,4 @@
 * filter=git-crypt diff=git-crypt
 .gitattributes !filter !diff
 README.md !filter !diff
+scripts/** !filter !diff
diff --git a/phyx/encrypted/phylonym/CLADO_0000002.json b/phyx/encrypted/phylonym/CLADO_0000002.json
new file mode 100644
index 00000000..8eed675d
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diff --git a/phyx/encrypted/phylonym/REGNUM_000003.json b/phyx/encrypted/phylonym/CLADO_0000003.json
similarity index 100%
rename from phyx/encrypted/phylonym/REGNUM_000003.json
rename to phyx/encrypted/phylonym/CLADO_0000003.json
diff --git a/phyx/encrypted/phylonym/REGNUM_000004.json b/phyx/encrypted/phylonym/CLADO_0000004.json
similarity index 100%
rename from phyx/encrypted/phylonym/REGNUM_000004.json
rename to phyx/encrypted/phylonym/CLADO_0000004.json
diff --git a/phyx/encrypted/phylonym/CLADO_0000006.json b/phyx/encrypted/phylonym/CLADO_0000006.json
new file mode 100644
index 00000000..690438ce
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diff --git a/phyx/encrypted/phylonym/CLADO_0000007.json b/phyx/encrypted/phylonym/CLADO_0000007.json
new file mode 100644
index 00000000..b56d309e
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diff --git a/phyx/encrypted/phylonym/REGNUM_000008.json b/phyx/encrypted/phylonym/CLADO_0000008.json
similarity index 100%
rename from phyx/encrypted/phylonym/REGNUM_000008.json
rename to phyx/encrypted/phylonym/CLADO_0000008.json
diff --git a/phyx/encrypted/phylonym/REGNUM_000009.json b/phyx/encrypted/phylonym/CLADO_0000009.json
similarity index 100%
rename from phyx/encrypted/phylonym/REGNUM_000009.json
rename to phyx/encrypted/phylonym/CLADO_0000009.json
diff --git a/phyx/encrypted/phylonym/REGNUM_000010.json b/phyx/encrypted/phylonym/CLADO_0000010.json
similarity index 100%
rename from phyx/encrypted/phylonym/REGNUM_000010.json
rename to phyx/encrypted/phylonym/CLADO_0000010.json
diff --git a/phyx/encrypted/phylonym/REGNUM_000011.json b/phyx/encrypted/phylonym/CLADO_0000011.json
similarity index 100%
rename from phyx/encrypted/phylonym/REGNUM_000011.json
rename to phyx/encrypted/phylonym/CLADO_0000011.json
diff --git a/phyx/encrypted/phylonym/REGNUM_000012.json b/phyx/encrypted/phylonym/CLADO_0000012.json
similarity index 100%
rename from phyx/encrypted/phylonym/REGNUM_000012.json
rename to phyx/encrypted/phylonym/CLADO_0000012.json
diff --git a/phyx/encrypted/phylonym/REGNUM_000013.json b/phyx/encrypted/phylonym/CLADO_0000013.json
similarity index 100%
rename from phyx/encrypted/phylonym/REGNUM_000013.json
rename to phyx/encrypted/phylonym/CLADO_0000013.json
diff --git a/phyx/encrypted/phylonym/CLADO_0000014.json b/phyx/encrypted/phylonym/CLADO_0000014.json
new file mode 100644
index 00000000..a5d0b2e3
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diff --git a/phyx/encrypted/phylonym/CLADO_0000015.json b/phyx/encrypted/phylonym/CLADO_0000015.json
new file mode 100644
index 00000000..4508aa7a
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diff --git a/phyx/encrypted/phylonym/CLADO_0000016.json b/phyx/encrypted/phylonym/CLADO_0000016.json
new file mode 100644
index 00000000..8eaf9fe3
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diff --git a/phyx/encrypted/phylonym/CLADO_0000017.json b/phyx/encrypted/phylonym/CLADO_0000017.json
new file mode 100644
index 00000000..30c7b4b1
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diff --git a/phyx/encrypted/phylonym/CLADO_0000018.json b/phyx/encrypted/phylonym/CLADO_0000018.json
new file mode 100644
index 00000000..5786186a
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diff --git a/phyx/encrypted/phylonym/CLADO_0000019.json b/phyx/encrypted/phylonym/CLADO_0000019.json
new file mode 100644
index 00000000..9f2bc335
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diff --git a/phyx/encrypted/phylonym/CLADO_0000020.json b/phyx/encrypted/phylonym/CLADO_0000020.json
new file mode 100644
index 00000000..073965a7
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diff --git a/phyx/encrypted/phylonym/CLADO_0000021.json b/phyx/encrypted/phylonym/CLADO_0000021.json
new file mode 100644
index 00000000..59aaef91
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diff --git a/phyx/encrypted/phylonym/CLADO_0000022.json b/phyx/encrypted/phylonym/CLADO_0000022.json
new file mode 100644
index 00000000..ef20e62d
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diff --git a/phyx/encrypted/phylonym/CLADO_0000023.json b/phyx/encrypted/phylonym/CLADO_0000023.json
new file mode 100644
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diff --git a/phyx/encrypted/phylonym/CLADO_0000024.json b/phyx/encrypted/phylonym/CLADO_0000024.json
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diff --git a/phyx/encrypted/phylonym/CLADO_0000025.json b/phyx/encrypted/phylonym/CLADO_0000025.json
new file mode 100644
index 00000000..8e5276f6
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diff --git a/phyx/encrypted/phylonym/CLADO_0000026.json b/phyx/encrypted/phylonym/CLADO_0000026.json
new file mode 100644
index 00000000..0dfaa28d
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diff --git a/phyx/encrypted/phylonym/CLADO_0000027.json b/phyx/encrypted/phylonym/CLADO_0000027.json
new file mode 100644
index 00000000..edb5dba7
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diff --git a/phyx/encrypted/phylonym/CLADO_0000028.json b/phyx/encrypted/phylonym/CLADO_0000028.json
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diff --git a/phyx/encrypted/phylonym/CLADO_0000029.json b/phyx/encrypted/phylonym/CLADO_0000029.json
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diff --git a/phyx/encrypted/phylonym/scripts/phyx2owl.js b/phyx/encrypted/phylonym/scripts/phyx2owl.js
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diff --git a/regnum2phyx/regnum2phyx.js b/regnum2phyx/regnum2phyx.js
index 552ef63d..e9a7d3b7 100644
--- a/regnum2phyx/regnum2phyx.js
+++ b/regnum2phyx/regnum2phyx.js
@@ -327,7 +327,7 @@ dump.forEach((entry, index) => {
     phyxFilename = path.join(argv.outputDir, `${phylorefLabel}.json`);
   } else if (argv.filenames === 'regnum-id') {
     // Use the regnum id.
-    if (entry.id) phyxFilename = path.join(argv.outputDir, `REGNUM_${(`${entry.id}`).padStart(6, '0')}.json`);
+    if (entry.id) phyxFilename = path.join(argv.outputDir, `CLADO_${(`${entry.id}`).padStart(6, '0')}.json`);
     else phyxFilename = path.join(argv.outputDir, `${filePrefix}${fileIndex}.json`);
   } else {
     // Default to just the number of the sequence.
diff --git a/test/test_phyx.js b/test/test_phyx.js
index c690e3eb..4c0d5842 100644
--- a/test/test_phyx.js
+++ b/test/test_phyx.js
@@ -21,6 +21,9 @@ const ChildProcess = require('child_process');
 const fs = require('fs');
 const path = require('path');
 
+const retus = require('retus');
+const lodash = require('lodash');
+
 const Ajv = require('ajv');
 const chai = require('chai');
 
@@ -30,7 +33,9 @@ const assert = chai.assert;
  * Configuration options.
  */
 /* Flag used to determine whether or not we run the slow tests. */
-const FLAG_SLOW_TESTS = process.env.RUN_SLOW_TESTS || false;
+const FLAG_SLOW_TESTS = process.env.SLOW_TESTS || false;
+/* Flag used to determine whether or not we run the online tests. */
+const FLAG_ONLINE_TESTS = process.env.ONLINE_TESTS || false;
 /* Maximum number of internal specifiers to test. */
 const MAX_INTERNAL_SPECIFIERS = process.env.MAX_INTERNAL_SPECIFIERS || 7;
 /* Maximum number of external specifiers to test. */
@@ -108,7 +113,7 @@ describe('Test Phyx files in repository', function () {
       try {
         wrappedPhyx = new phyx.PhyxWrapper(json);
       } catch (ex) {
-        it('Exception thrown while converting Phyx to JSON-LD', function () {
+        it('Exception thrown while loading Phyx to JSON-LD', function () {
           throw ex;
         });
         return;
@@ -116,6 +121,11 @@ describe('Test Phyx files in repository', function () {
 
       console.log(`Loaded Phyx file ${filename}`);
 
+        it('should have a Newick phylogeny', () => {
+          const newick = json.phylogenies.map(p => p.newick || "").find(elem => !lodash.isEmpty(elem));
+          assert.isNotEmpty(newick);
+        });
+
       const skipFile = (json.phylorefs || [])
         .map(phyloref => new phyx.PhylorefWrapper(phyloref))
         .map((wrappedPhyloref) => {
@@ -142,6 +152,7 @@ describe('Test Phyx files in repository', function () {
         .reduce((a, b) => a || b, false);
 
       if (!skipFile) {
+        console.log(`Converting Phyx file ${filename} into JSON-LD`);
         const jsonld = JSON.stringify(wrappedPhyx.asJSONLD());
 
         // Make sure the produced JSON-LD is not empty.
@@ -149,6 +160,112 @@ describe('Test Phyx files in repository', function () {
           assert.isNotEmpty(jsonld);
         });
 
+        // Test the Phyx file using the Open Tree of Life API.
+        if (FLAG_ONLINE_TESTS) {
+          /**
+           * Display debugging output to STDERR if the '--verbose' flag has been set.
+           */
+          function debug(...args) {
+            process.stderr.write(args.join(' ') + "\n")
+          }
+
+          function specifierToOTLId(specifier) {
+            const wrappedSpecifier = new phyx.TaxonomicUnitWrapper(specifier);
+
+            if (!wrappedSpecifier.taxonConcept) {
+              debug(`     - ${wrappedSpecifier.label}: not a taxon concept`);
+              return undefined;
+            } else {
+              const nameComplete = new phyx.TaxonConceptWrapper(specifier).nameComplete;
+
+              if (!nameComplete) {
+                debug(`     - ${wrappedSpecifier.label} is missing a taxonomic name: ${JSON.stringify(specifier)}`);
+                return undefined;
+              } else {
+                const nameToUse = nameComplete.replace(/\s+\(originally \w+\)/g, "");
+                const { statusCode, body } = retus("https://api.opentreeoflife.org/v3/tnrs/match_names", {
+                  method: 'post',
+                  json: { names : [ nameToUse ] },
+                });
+
+                const matches = body['results'].map(result => result['matches']).reduce((acc, curr) => acc.concat(curr), []);
+
+                const ottNames = matches.filter(match => match).map(match => match['taxon']['name']).filter(name => name);
+                const ottIds = matches.filter(match => match).map(match => match['taxon']['ott_id']).filter(ott_id => ott_id);
+
+                if (ottIds.length > 1) debug(`     - Taxon name ${nameComplete} resolved to multiple OTT Ids: ${ottIds.join(', ')}.`)
+
+                const result = {};
+                result[nameComplete] = ottIds;
+                return result;
+              }
+            }
+          }
+
+          (json.phylorefs || [])
+            .map(phyloref => new phyx.PhylorefWrapper(phyloref))
+            .forEach((wrappedPhyloref) => {
+              const internalOTTs = wrappedPhyloref.internalSpecifiers.map(specifierToOTLId);
+              const internalOTTids = lodash.flattenDeep(internalOTTs.map(ott => lodash.head(lodash.values(ott))));
+              debug(`   - Internal specifiers: ${internalOTTids.join(", ")}`);
+              // console.log(internalOTTids);
+
+              const externalOTTs = wrappedPhyloref.externalSpecifiers.map(specifierToOTLId);
+              const externalOTTids = lodash.flattenDeep(externalOTTs.map(ott => lodash.head(lodash.values(ott))));
+              debug(`   - External specifiers: ${externalOTTids.join(", ")}`);
+              // console.log(externalOTTids);
+
+              describe(`Phyloreference ${wrappedPhyloref.label}`, () => {
+                it(`should be resolvable on the Open Tree of Life`, () => {
+                  assert(internalOTTids.filter(x => x === undefined).length === 0, "All internal specifiers must be matched to OTT Ids");
+                  assert(externalOTTids.filter(x => x === undefined).length === 0, "All external specifiers must be matched to OTT Ids");
+                  assert(internalOTTids.length > 0, "No internal specifiers present in phyloref.");
+
+                  // debug('Request: ', { node_ids: internalOTTids, excluded_node_ids: externalOTTids });
+                  const result = retus("https://api.opentreeoflife.org/v3/tree_of_life/mrca ", {
+                    throwHttpErrors: false,
+                    method: 'post',
+                    json: { node_ids: internalOTTids.map(id => "ott" + id), excluded_node_ids: externalOTTids.map(id => "ott" + id) },
+                    responseType: 'text',
+                  });
+
+                  // There are two types of responses we might get:
+                  //  - If we have external specifiers, we'll get a 'node_ids', where the first one
+                  //    is the node-based name and the last one is the branch-based name, and a 'synth_id'.
+                  //  - If we have only internal specifiers, we'll get a 'mrca' with a 'node_id' (as well as
+                  //    'supported_by' and 'unique_name') and a 'synth_id'.
+
+                  assert(result.statusCode != 404 && result.statusCode != 400, `Could not find MRCA: ${result}`);
+
+                  const body = JSON.parse(result.body);
+                  const synth_id = body['synth_id'];
+                  if (body['node_ids']) {
+                    const node_id = body.node_ids[body.node_ids.length - 1];
+                    debug(`          -> ${body.node_ids.length} node IDs returned, with branch-based node at: https://tree.opentreeoflife.org/opentree/argus/${synth_id}@${node_id}`);
+
+                    const nodeInfo = retus("https://api.opentreeoflife.org/v3/tree_of_life/node_info ", {
+                      method: 'post',
+                      json: { node_id }
+                    });
+
+                    let name = "";
+                    if (nodeInfo['body'] && nodeInfo['body']['taxon'] && nodeInfo['body']['taxon']['unique_name']) {
+                      name = nodeInfo['body']['taxon']['unique_name'];
+                      debug(`            - Identified as ${name}.`);
+                    } else {
+                      debug(`            - Could not identify node.`);
+                    }
+                  } else if(body['mrca']) {
+                    const name = body.mrca.unique_name || ((body.mrca.taxon || {}).name) || "";
+                    debug(`          -> Found MRCA node (${name}): https://tree.opentreeoflife.org/opentree/argus/${synth_id}@${body.mrca.node_id}`);
+                  } else {
+                    assert.fail('Unable to interpret Open Tree MRCA response: ', body);
+                  }
+                });
+              });
+            });
+        }
+
         // Test the produced JSON-LD using JPhyloRef.
         if (FLAG_SLOW_TESTS) {
           let args = [