From e072d44fc3633247d8eb6d8aa4a17c500a1bf226 Mon Sep 17 00:00:00 2001
From: Chris Want <cjwant@gmail.com>
Date: Mon, 27 Apr 2026 10:54:24 -0600
Subject: [PATCH 1/6] Model concern doesn't need to have an Edam-specific name.

---
 .../{has_edam_terms.rb => has_terms_and_synonyms.rb}      | 8 ++++----
 app/models/event.rb                                       | 2 +-
 app/models/material.rb                                    | 2 +-
 app/models/workflow.rb                                    | 2 +-
 4 files changed, 7 insertions(+), 7 deletions(-)
 rename app/models/concerns/{has_edam_terms.rb => has_terms_and_synonyms.rb} (62%)

diff --git a/app/models/concerns/has_edam_terms.rb b/app/models/concerns/has_terms_and_synonyms.rb
similarity index 62%
rename from app/models/concerns/has_edam_terms.rb
rename to app/models/concerns/has_terms_and_synonyms.rb
index 4c8169f11..96848841a 100644
--- a/app/models/concerns/has_edam_terms.rb
+++ b/app/models/concerns/has_terms_and_synonyms.rb
@@ -1,17 +1,17 @@
-module HasEdamTerms
+module HasTermsAndSynonyms
   extend ActiveSupport::Concern
 
   def scientific_topics_and_synonyms
-    edam_term_names_and_synonyms(scientific_topics)
+    term_names_and_synonyms(scientific_topics)
   end
 
   def operations_and_synonyms
-    edam_term_names_and_synonyms(operations)
+    term_names_and_synonyms(operations)
   end
 
   private
 
-  def edam_term_names_and_synonyms(terms)
+  def term_names_and_synonyms(terms)
     terms.map do |term|
       [term.preferred_label] + term.has_exact_synonym + term.has_narrow_synonym
     end.flatten.uniq
diff --git a/app/models/event.rb b/app/models/event.rb
index 910b5dbd5..571acf006 100644
--- a/app/models/event.rb
+++ b/app/models/event.rb
@@ -17,7 +17,7 @@ class Event < ApplicationRecord
   include HasFriendlyId
   include FuzzyDictionaryMatch
   include WithTimezone
-  include HasEdamTerms
+  include HasTermsAndSynonyms
   include HasLanguage
   include InSpace
   include HasPeople
diff --git a/app/models/material.rb b/app/models/material.rb
index 9663b35fb..f4ac0cb11 100644
--- a/app/models/material.rb
+++ b/app/models/material.rb
@@ -19,7 +19,7 @@ class Material < ApplicationRecord
   include IdentifiersDotOrg
   include HasFriendlyId
   include HasDifficultyLevel
-  include HasEdamTerms
+  include HasTermsAndSynonyms
   include InSpace
   include HasPeople
 
diff --git a/app/models/workflow.rb b/app/models/workflow.rb
index bd135facc..b212a49ff 100644
--- a/app/models/workflow.rb
+++ b/app/models/workflow.rb
@@ -10,7 +10,7 @@ class Workflow < ApplicationRecord
   include HasFriendlyId
   include CurationQueue
   include HasDifficultyLevel
-  include HasEdamTerms
+  include HasTermsAndSynonyms
   include InSpace
   include HasPeople
 

From c022c1dcad4f3fe925bdba41377f1e14d0a1bc95 Mon Sep 17 00:00:00 2001
From: Chris Want <cjwant@gmail.com>
Date: Wed, 29 Apr 2026 09:29:11 -0600
Subject: [PATCH 2/6] Make HasOntologyTerm testable, with small demo test.

---
 app/models/ontology_term_link.rb     |  3 +-
 app/ontologies/ontology.rb           |  9 ++++
 lib/has_ontology_terms.rb            |  8 +++-
 test/unit/has_ontology_terms_test.rb | 69 ++++++++++++++++++++++++++++
 4 files changed, 86 insertions(+), 3 deletions(-)
 create mode 100644 test/unit/has_ontology_terms_test.rb

diff --git a/app/models/ontology_term_link.rb b/app/models/ontology_term_link.rb
index f376fb3aa..d605d98f3 100644
--- a/app/models/ontology_term_link.rb
+++ b/app/models/ontology_term_link.rb
@@ -6,6 +6,7 @@ def ontology_term
   end
 
   def ontology
-    Edam::Ontology.instance
+    @ontology ||= Ontology.subclasses.map(&:instance).\
+                    find { |ontology| ontology.term_uri_matches?(term_uri) }
   end
 end
diff --git a/app/ontologies/ontology.rb b/app/ontologies/ontology.rb
index 649f489d9..3535ca69e 100644
--- a/app/ontologies/ontology.rb
+++ b/app/ontologies/ontology.rb
@@ -6,6 +6,15 @@ def initialize(filename, term_class = OntologyTerm)
     @query_cache = {}
   end
 
+  def uri
+    # Must implement in subclass ...
+    raise NotImplementedError
+  end
+
+  def term_uri_matches?(uri)
+    uri.starts_with?(self.uri)
+  end
+
   def lookup(uri)
     @term_cache[RDF::URI(uri)] ||= fetch(uri)
   end
diff --git a/lib/has_ontology_terms.rb b/lib/has_ontology_terms.rb
index 55db7b553..9c8928e87 100644
--- a/lib/has_ontology_terms.rb
+++ b/lib/has_ontology_terms.rb
@@ -43,8 +43,12 @@ def has_ontology_terms(association_name, ontology: Edam::Ontology.instance, bran
                dependent: :destroy,
                inverse_of: :resource
 
-      cattr_accessor :ontology_term_fields
-      self.ontology_term_fields ||= []
+      # Previously used cattr_accessor, which uses "@@" variables that mess with inheritance.
+      # So we do this instead (use "@" class vars)...
+      def self.ontology_term_fields
+        @ontology_term_fields ||= []
+      end
+
       self.ontology_term_fields << method.to_sym
 
       define_method "#{links_method}=" do |links|
diff --git a/test/unit/has_ontology_terms_test.rb b/test/unit/has_ontology_terms_test.rb
new file mode 100644
index 000000000..4791c162e
--- /dev/null
+++ b/test/unit/has_ontology_terms_test.rb
@@ -0,0 +1,69 @@
+require 'test_helper'
+
+class HasOntologyTermsTest < ActiveSupport::TestCase
+  teardown do
+    DummyMaterial.clear_index!
+  end
+
+  class DummyTerm
+    attr_reader :label, :uri
+    def initialize(term)
+      @label = term
+      @uri = "http://dummy/#{term}"
+    end
+    alias_method :preferred_label, :label
+  end
+
+  class DummyOntology < ::Ontology
+    # A very permissive ontology: it allows any term
+    include Singleton
+
+    def initialize
+    end
+
+    def uri
+      'http://dummy/'
+    end
+
+    def scoped_lookup_by_name(term, subset = :_)
+      return DummyTerm.new(term)
+    end
+
+    def lookup(uri)
+      term = uri[/http:\/\/dummy\/(.*)/,1]
+      return DummyTerm.new(term)
+    end
+  end
+
+  class DummyMaterial < ::Material
+    has_ontology_terms(:test_topics, ontology: DummyOntology.instance)
+
+    # TODO: see similar tests with model subclasses, maybe can be in a module?
+    def self.index
+      (@index ||= Hash.new).values.flatten.uniq
+    end
+
+    def self.add_to_index(m)
+      index
+      @index[m.id] = m.reload.collections.to_a
+    end
+
+    def self.clear_index!
+      @index = Hash.new
+    end
+
+    def solr_index
+      self.class.add_to_index(self)
+    end
+  end
+
+  test 'can create an attribute with ontology terms' do
+    dummy = materials(:good_material).becomes(DummyMaterial)
+    dummy.test_topic_names = ['Bioinformatics']
+    dummy.save!
+
+    assert_equal dummy.test_topics.count, 1
+    assert_equal dummy.test_topic_names, ['Bioinformatics'] 
+    assert_equal dummy.test_topic_uris, ['http://dummy/Bioinformatics'] 
+  end
+end

From eefc8402443a5342bd7956410edd3ce50a30494e Mon Sep 17 00:00:00 2001
From: Chris Want <cjwant@gmail.com>
Date: Wed, 29 Apr 2026 14:56:26 -0600
Subject: [PATCH 3/6] Add support for multiple ontologies for a field.

---
 app/ontologies/edam/ontology.rb      |  8 +++
 lib/has_ontology_terms.rb            | 42 ++++++++++++--
 test/unit/has_ontology_terms_test.rb | 82 +++++++++++++++++++++++++---
 3 files changed, 119 insertions(+), 13 deletions(-)

diff --git a/app/ontologies/edam/ontology.rb b/app/ontologies/edam/ontology.rb
index 30d35c466..b02342852 100644
--- a/app/ontologies/edam/ontology.rb
+++ b/app/ontologies/edam/ontology.rb
@@ -31,5 +31,13 @@ def scoped_lookup_by_name(name, subset = :_)
       result = graph.query(query).first
       lookup(result.u) if result
     end
+
+    def scoped_lookup_by_name_or_synonym(name, subset = :_)
+      out = scoped_lookup_by_name(name, subset)
+      return out unless out.blank?
+      out = find_by(OBO.hasExactSynonym, name)
+      return out unless out.blank?
+      find_by(OBO.hasNarrowSynonym, name)
+    end
   end
 end
diff --git a/lib/has_ontology_terms.rb b/lib/has_ontology_terms.rb
index 9c8928e87..e8c08be58 100644
--- a/lib/has_ontology_terms.rb
+++ b/lib/has_ontology_terms.rb
@@ -22,7 +22,22 @@ def self.included(mod)
   end
 
   module ClassMethods
-    def has_ontology_terms(association_name, ontology: Edam::Ontology.instance, branch: :_) # :_ is essentially a wildcard, meaning it will match any branch.
+    def has_ontology_terms(association_name,
+                           ontology: nil,
+                           branch: nil,
+                           ontologies: nil)
+      unless ontologies
+        ontology ||= Edam::Ontology.instance
+        # :_ is essentially a wildcard, meaning it will match any branch.
+        branch ||= :_
+      else
+        # ontologies is an array of hashes with keys :ontology and :branch
+        ontologies = ontologies.map do |ontology_specification|
+          { ontology: ontology_specification[:ontology] || Edam::Ontology.instance,
+            branch: ontology_specification[:branch] || :_ }
+        end
+      end
+
       method = association_name.to_s
       singular = association_name.to_s.singularize
       links_method = "#{singular}_links"
@@ -89,13 +104,20 @@ def self.ontology_term_fields
         terms = []
         [names].flatten.each do |name|
           unless name.blank?
-            st = [ontology.scoped_lookup_by_name(name, branch)].compact # FIXME: This is probably too EDAM specific
-            st = ontology.find_by(OBO.hasExactSynonym, name) if st.empty?
-            st = ontology.find_by(OBO.hasNarrowSynonym, name) if st.empty?
+            st = if ontologies
+                   # TODO: if name is found in first ontology, should it skip others?
+                   ontologies.map do |ontology_specification|
+                     [ontology_specification[:ontology].\
+                        scoped_lookup_by_name_or_synonym(name,
+                                                         ontology_specification[:branch])]
+                   end
+                 else
+                   [ontology.scoped_lookup_by_name_or_synonym(name, branch)]
+                 end
             terms += st
           end
         end
-        send("#{method}=", terms.uniq)
+        send("#{method}=", terms.flatten.compact.uniq)
       end
 
       # URIs
@@ -104,7 +126,15 @@ def self.ontology_term_fields
       end
 
       define_method "#{uris_method}=" do |uris|
-        send("#{method}=", uris.map { |uri| ontology.lookup(uri) })
+        terms = if ontologies
+                  ontologies.map do |ontology_specification|
+                    uris.map { |uri| ontology_specification[:ontology].lookup(uri) }
+                  end.flatten
+                else
+                  uris.map { |uri| ontology.lookup(uri) }
+                end
+
+        send("#{method}=", terms)
       end
     end
   end
diff --git a/test/unit/has_ontology_terms_test.rb b/test/unit/has_ontology_terms_test.rb
index 4791c162e..5fa9b0c16 100644
--- a/test/unit/has_ontology_terms_test.rb
+++ b/test/unit/has_ontology_terms_test.rb
@@ -1,6 +1,10 @@
 require 'test_helper'
 
 class HasOntologyTermsTest < ActiveSupport::TestCase
+  # Summary: we create attributes 'test_topics' and 'multi_test_topics' for
+  # the fake model DummyMaterial. 'test_topics' uses DummyOntology,
+  # 'multi_test_topics' uses both DummyOntology and Edam::Ontology
+
   teardown do
     DummyMaterial.clear_index!
   end
@@ -15,7 +19,7 @@ def initialize(term)
   end
 
   class DummyOntology < ::Ontology
-    # A very permissive ontology: it allows any term
+    # A very permissive ontology: it allows any term as long as it doesn't have Chemistry in it
     include Singleton
 
     def initialize
@@ -26,17 +30,22 @@ def uri
     end
 
     def scoped_lookup_by_name(term, subset = :_)
-      return DummyTerm.new(term)
+      return DummyTerm.new(term) unless term =~ /chemistry/i
     end
+    alias_method :scoped_lookup_by_name_or_synonym, :scoped_lookup_by_name
 
     def lookup(uri)
       term = uri[/http:\/\/dummy\/(.*)/,1]
-      return DummyTerm.new(term)
+      return DummyTerm.new(term) unless term.blank?
     end
   end
 
   class DummyMaterial < ::Material
     has_ontology_terms(:test_topics, ontology: DummyOntology.instance)
+    has_ontology_terms(:multi_test_topics,
+                       ontologies: [{ ontology: Edam::Ontology.instance,
+                                      branch: EDAM.topics},
+                                    { ontology: DummyOntology.instance}])
 
     # TODO: see similar tests with model subclasses, maybe can be in a module?
     def self.index
@@ -57,13 +66,72 @@ def solr_index
     end
   end
 
-  test 'can create an attribute with ontology terms' do
+  test 'can create an attribute with terms from a single ontology' do
+    # See the Event/Material model tests for many examples of this ...
     dummy = materials(:good_material).becomes(DummyMaterial)
+
+    # This is found in the ontology ...
     dummy.test_topic_names = ['Bioinformatics']
     dummy.save!
-
     assert_equal dummy.test_topics.count, 1
-    assert_equal dummy.test_topic_names, ['Bioinformatics'] 
-    assert_equal dummy.test_topic_uris, ['http://dummy/Bioinformatics'] 
+    assert_equal dummy.test_topic_names, ['Bioinformatics']
+    assert_equal dummy.test_topic_uris, ['http://dummy/Bioinformatics']
+
+    # This is not
+    dummy.test_topic_names = ['Biochemistry']
+    dummy.save!
+    assert_equal dummy.test_topics.count, 0
+    assert_equal dummy.test_topic_names, []
+    assert_equal dummy.test_topic_uris, []
+  end
+
+  test 'can create an attribute with terms from multiple ontologies' do
+    dummy = materials(:good_material).becomes(DummyMaterial)
+
+    # This is found in both ontologies ...
+    dummy.multi_test_topic_names = ['Bioinformatics']
+    dummy.save!
+    assert_equal dummy.multi_test_topics.count, 2
+    assert_equal Set.new(dummy.multi_test_topic_uris),
+                 Set.new(['http://edamontology.org/topic_0091', 'http://dummy/Bioinformatics'])
+    # The two exact names collapse into one ...
+    assert_equal dummy.multi_test_topic_names, ['Bioinformatics']
+
+    # This is found in only in Edam ...
+    dummy.multi_test_topic_names = ['Biochemistry']
+    dummy.save!
+    assert_equal dummy.multi_test_topics.count, 1
+    assert_equal dummy.multi_test_topic_names, ['Biochemistry']
+    assert_equal dummy.multi_test_topic_uris, ['http://edamontology.org/topic_3292']
+
+    # This is found only in DummyOntology ...
+    dummy.multi_test_topic_names = ['Poodles']
+    dummy.save!
+    assert_equal dummy.multi_test_topics.count, 1
+    assert_equal dummy.multi_test_topic_names, ['Poodles']
+    assert_equal dummy.multi_test_topic_uris, ['http://dummy/Poodles']
+
+    # This is found in neither ...
+    dummy.multi_test_topic_names = ['Poodle Chemistry']
+    dummy.save!
+    assert_equal dummy.multi_test_topics.count, 0
+    assert_equal dummy.multi_test_topic_names, []
+    assert_equal dummy.multi_test_topic_uris, []
+
+    # Set via URIs
+    dummy.multi_test_topic_uris = ['http://dummy/Poodles',
+                                   'http://edamontology.org/topic_3292']
+    dummy.save!
+    assert_equal dummy.multi_test_topics.count, 2
+    assert_equal Set.new(dummy.multi_test_topic_names),
+                 Set.new(['Biochemistry', 'Poodles'])
+    assert_equal Set.new(dummy.multi_test_topic_uris),
+                 Set.new(['http://dummy/Poodles',
+                          'http://edamontology.org/topic_3292'])
+    assert_equal dummy.ontology_term_links.map(&:field), ["multi_test_topics",
+                                                          "multi_test_topics"]
+    assert_equal Set.new(dummy.ontology_term_links.map(&:term_uri)),
+                 Set.new(['http://dummy/Poodles',
+                          'http://edamontology.org/topic_3292'])
   end
 end

From 9a6dea60437484cd2aa8d73ebe202e6ce94a735f Mon Sep 17 00:00:00 2001
From: Chris Want <cjwant@gmail.com>
Date: Tue, 5 May 2026 07:52:05 -0600
Subject: [PATCH 4/6] Suggestion from Co-pilot to make the
 `ontology_term_fields` class variable work better with STI (have not really
 tested the STI part). Seems to work (in the "test suite passes" sense), and
 does not suffer from the same inheritance problems that the cattr_accessor
 code had (the specific problem is that fields added to `ontology_term_fields`
 would infect the superclass!).

---
 lib/has_ontology_terms.rb | 12 ++++++++++--
 1 file changed, 10 insertions(+), 2 deletions(-)

diff --git a/lib/has_ontology_terms.rb b/lib/has_ontology_terms.rb
index e8c08be58..bdad8dbe2 100644
--- a/lib/has_ontology_terms.rb
+++ b/lib/has_ontology_terms.rb
@@ -59,12 +59,20 @@ def has_ontology_terms(association_name,
                inverse_of: :resource
 
       # Previously used cattr_accessor, which uses "@@" variables that mess with inheritance.
-      # So we do this instead (use "@" class vars)...
+      # So we do this instead (use "@" class vars), while explicitly merging inherited
+      # values so STI subclasses still see ontology term fields declared on parent classes.
       def self.ontology_term_fields
+        inherited_fields = superclass.respond_to?(:ontology_term_fields) ? superclass.ontology_term_fields : []
+        own_fields = @ontology_term_fields ||= []
+        (inherited_fields + own_fields).uniq
+      end
+
+      def self.add_ontology_term_field(field)
         @ontology_term_fields ||= []
+        @ontology_term_fields << field unless ontology_term_fields.include?(field)
       end
 
-      self.ontology_term_fields << method.to_sym
+      self.add_ontology_term_field(method.to_sym)
 
       define_method "#{links_method}=" do |links|
         send(links_method).reset

From 4a26db54e4e974d8592cd9711eaf04138a5739f2 Mon Sep 17 00:00:00 2001
From: Chris Want <cjwant@gmail.com>
Date: Tue, 5 May 2026 08:03:13 -0600
Subject: [PATCH 5/6] From Co-pilot: ensure `scoped_lookup_by_name_or_synonym`
 is defined in superclass.

---
 app/ontologies/ontology.rb | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/app/ontologies/ontology.rb b/app/ontologies/ontology.rb
index 3535ca69e..f7117c2ea 100644
--- a/app/ontologies/ontology.rb
+++ b/app/ontologies/ontology.rb
@@ -11,6 +11,11 @@ def uri
     raise NotImplementedError
   end
 
+  def scoped_lookup_by_name_or_synonym(name, subset = :_)
+    # Must implement in subclass ...
+    raise NotImplementedError
+  end
+
   def term_uri_matches?(uri)
     uri.starts_with?(self.uri)
   end

From 586ab52cc55756515ac53f9053e496e6ad6a9da6 Mon Sep 17 00:00:00 2001
From: Chris Want <cjwant@gmail.com>
Date: Tue, 5 May 2026 10:53:16 -0600
Subject: [PATCH 6/6] Make code more robust when term URIs aren't found in any
 ontology.

---
 app/models/ontology_term_link.rb     |  2 +-
 lib/has_ontology_terms.rb            |  6 ++--
 test/unit/has_ontology_terms_test.rb | 51 ++++++++++++++++++++++++++++
 3 files changed, 55 insertions(+), 4 deletions(-)

diff --git a/app/models/ontology_term_link.rb b/app/models/ontology_term_link.rb
index d605d98f3..d55c7d448 100644
--- a/app/models/ontology_term_link.rb
+++ b/app/models/ontology_term_link.rb
@@ -2,7 +2,7 @@ class OntologyTermLink < ApplicationRecord
   belongs_to :resource, polymorphic: true
 
   def ontology_term
-    ontology.lookup(term_uri)
+    ontology&.lookup(term_uri)
   end
 
   def ontology
diff --git a/lib/has_ontology_terms.rb b/lib/has_ontology_terms.rb
index bdad8dbe2..94a71594f 100644
--- a/lib/has_ontology_terms.rb
+++ b/lib/has_ontology_terms.rb
@@ -96,7 +96,7 @@ def self.add_ontology_term_field(field)
 
       # OntologyTerm objects
       define_method method do
-        send(links_method).map(&:ontology_term).uniq
+        send(links_method)&.compact&.map(&:ontology_term)&.uniq&.compact
       end
 
       define_method "#{method}=" do |terms|
@@ -105,7 +105,7 @@ def self.add_ontology_term_field(field)
 
       # Names/Labels
       define_method names_method do
-        send(method).map(&:preferred_label).uniq
+        send(method)&.compact&.map(&:preferred_label)&.uniq
       end
 
       define_method "#{names_method}=" do |names|
@@ -130,7 +130,7 @@ def self.add_ontology_term_field(field)
 
       # URIs
       define_method uris_method do
-        send(method).map(&:uri).uniq
+        send(method)&.compact&.map(&:uri)&.uniq
       end
 
       define_method "#{uris_method}=" do |uris|
diff --git a/test/unit/has_ontology_terms_test.rb b/test/unit/has_ontology_terms_test.rb
index 5fa9b0c16..7f30e17e7 100644
--- a/test/unit/has_ontology_terms_test.rb
+++ b/test/unit/has_ontology_terms_test.rb
@@ -134,4 +134,55 @@ def solr_index
                  Set.new(['http://dummy/Poodles',
                           'http://edamontology.org/topic_3292'])
   end
+
+  test "Ignores attributes that don't come from any ontology" do
+    dummy = materials(:good_material).becomes(DummyMaterial)
+    dummy.ontology_term_links.create(field: :test_topics, term_uri: 'http://not-a-term.com')
+    dummy.ontology_term_links.create(field: :multi_test_topics, term_uri: 'http://also-not-a-term.com')
+
+    assert_equal dummy.ontology_term_links.count, 2
+
+    assert_equal dummy.test_topics, []
+    assert_equal dummy.test_topic_names, []
+    assert_equal dummy.test_topic_uris, []
+
+    assert_equal dummy.multi_test_topics, []
+    assert_equal dummy.multi_test_topic_names, []
+    assert_equal dummy.multi_test_topic_uris, []
+
+    # Setting URI manually wipes out the ontology_term_links
+    dummy.test_topic_uris = ['http://not-a-term.com']
+    dummy.multi_test_topic_uris = ['http://also-not-a-term.com']
+
+    assert_equal dummy.ontology_term_links.count, 0
+
+    # What if there is a term in here already, plus a bogus term link?
+    # (perhaps bogus because a previous ontology was take out).
+    dummy.test_topic_names = ['Bioinformatics']
+    dummy.multi_test_topic_names = ['Biochemistry', 'Bioinformatics', 'Poodles']
+    assert_equal dummy.ontology_term_links.count, 5
+    assert_equal dummy.test_topic_links.count, 1
+    assert_equal dummy.multi_test_topic_links.count, 4
+
+    dummy.ontology_term_links.create(field: :test_topics, term_uri: 'http://not-a-term.com')
+    dummy.ontology_term_links.create(field: :multi_test_topics, term_uri: 'http://also-not-a-term.com')
+    assert_equal dummy.ontology_term_links.count, 7
+    assert_equal dummy.test_topic_links.count, 2
+    assert_equal dummy.multi_test_topic_links.count, 5
+
+    # Terms with bogus URIs don't appear here
+    assert_equal dummy.test_topics.count, 1
+    assert_equal dummy.test_topic_names, ['Bioinformatics']
+    assert_equal dummy.test_topic_uris, ['http://dummy/Bioinformatics']
+
+    assert_equal dummy.multi_test_topics.count, 4
+    # Bioinformatics is in both ontologies
+    assert_equal Set.new(dummy.multi_test_topic_names), Set.new(['Biochemistry', 'Bioinformatics', 'Poodles'])
+    assert_equal Set.new(dummy.multi_test_topic_uris),
+                 Set.new(['http://edamontology.org/topic_3292',
+                          'http://edamontology.org/topic_0091',
+                          'http://dummy/Bioinformatics',
+                          'http://dummy/Poodles'])
+  end
+
 end