mesh-medical-subject-headings 2.1.0 → 2.2.0

checksums.yaml

@@ -1,7 +1,7 @@
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-  data.tar.gz: 1c3f83c62564d794239a05084b099dd0160da13b
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data/CHANGELOG.md

@@ -1,3 +1,6 @@
+#2.2.0 / 2014-07-10
+* [FEATURE] Headings now have structured_entries which include semantic and lexical information
+
 #2.1.0 / 2014-07-04
 * [FEATURE] Headings matched with Wikipedia, infobox images and abstracts imported
 

data/Gemfile.lock

@@ -1,7 +1,7 @@
 PATH
   remote: .
   specs:
-    mesh-medical-subject-headings (2.1.0)
+    mesh-medical-subject-headings (2.2.0)
 
 GEM
   remote: https://rubygems.org/

data/lib/MESH.rb

@@ -6,3 +6,6 @@ require 'MESH/heading'
 require 'MESH/translator'
 require 'MESH/classifier'
 require 'MESH/semantic_types'
+require 'MESH/lexical_types'
+require 'MESH/semantic_relationship_types'
+require 'MESH/entry'

data/lib/MESH/entry.rb

@@ -0,0 +1,36 @@
+module MESH
+
+  class Entry
+
+    attr_accessor :heading, :term, :semantic_types, :semantic_relationship, :lexical_type
+
+    def initialize(heading, entry_text)
+      @heading = heading
+      @semantic_types = []
+      parts = entry_text.split('|')
+      if entry_text.include? '|'
+        key = parts.pop
+        parts.each_with_index do |part, i|
+          case key[i]
+            when 'a' # the term itself
+              @term = part
+            when 'b' # semantic type*
+              @semantic_types << MESH::SemanticTypes[part]
+            when 'c' # lexical type*
+              @lexical_type = MESH::LexicalTypes[part]
+            when 'd' # semantic relation*
+              @semantic_relationship = MESH::SemanticRelationshipTypes[part]
+            when 'e' # thesaurus id
+            when 'f' # date
+            when 's' # sort version
+            when 'v' # entry version
+          end
+        end
+      else
+        @term = entry_text
+      end
+    end
+
+  end
+
+end

data/lib/MESH/heading.rb

@@ -2,7 +2,7 @@ module MESH
   class Heading
 
     include Comparable
-    attr_accessor :unique_id, :tree_numbers, :roots, :parents, :children, :useful, :descriptor_class, :default_locale, :semantic_types, :wikipedia_links
+    attr_accessor :unique_id, :tree_numbers, :roots, :parents, :children, :useful, :descriptor_class, :default_locale, :semantic_types, :wikipedia_links, :structured_entries
     attr_reader :linkified_summary
 
     def <=> other
@@ -33,7 +33,6 @@ module MESH
       @entries[locale] ||= []
     end
 
-
     def has_ancestor(heading)
       return false if parents.empty?
       return true if parents.include? heading
@@ -112,6 +111,7 @@ module MESH
       @parents = []
       @children = []
       @entries = {}
+      @structured_entries = []
       @original_heading = {}
       @natural_language_name = {}
       @summary = {}

data/lib/MESH/lexical_types.rb

@@ -0,0 +1,21 @@
+module MESH
+  class LexicalTypes
+
+    def self.[](key)
+      Types[key]
+    end
+
+    Types = {
+      'ABB' => :abbreviation,
+      'ABX' => :embedded_abbreviation,
+      'ACR' => :acronym,
+      'ACX' => :embedded_acronym,
+      'EPO' => :eponym,
+      'LAB' => :lab_number,
+      'NAM' => :proper_name,
+      'NON' => nil,
+      'TRD' => :trade_name
+    }
+
+  end
+end

data/lib/MESH/semantic_relationship_types.rb

@@ -0,0 +1,16 @@
+module MESH
+  class SemanticRelationshipTypes
+
+    def self.[](key)
+      Types[key]
+    end
+
+    Types = {
+      'BRD' => :broader,
+      'EQV' => :equivalent,
+      'NRW' => :narrower,
+      'REL' => :related
+    }
+
+  end
+end

data/lib/MESH/tree.rb

@@ -67,9 +67,15 @@ module MESH
             nln = librarian_parts.nil? ? mh : "#{librarian_parts[2]} #{librarian_parts[1]}"
             current_heading.set_natural_language_name(nln)
 
-          when matches = line.match(/^(?:PRINT )?ENTRY = ([^|]+)/)
-            entry = matches[1].chomp
-            current_heading.entries << entry unless current_heading.entries.include? entry
+          # when matches = line.match(/^(?:PRINT )?ENTRY = ([^|]+)/)
+          #   entry = matches[1].chomp
+          #   current_heading.entries << entry unless current_heading.entries.include? entry
+          #
+          when matches = line.match(/^(?:PRINT )?ENTRY = (.*)/)
+            entry = matches[1]
+            term = entry.match(/([^|]+)/)
+            current_heading.entries << term[1] unless current_heading.entries.include? term[1]
+            current_heading.structured_entries << MESH::Entry.new(current_heading, entry)
 
         end
 

data/lib/MESH/version.rb

@@ -1,3 +1,3 @@
 module Mesh
-  VERSION = "2.1.0"
+  VERSION = "2.2.0"
 end

data/test/entry_test.rb

@@ -0,0 +1,91 @@
+require_relative 'test_helper'
+
+module MESH
+  class HeadingTest < TestBase
+
+    # PRINT ENTRY = Acetamidophenol|T109|T121|NON|EQV|UNK (19XX)|771118|abbcdef
+    # PRINT ENTRY = Hydroxyacetanilide|T109|T121|NON|EQV|UNK (19XX)|740329|abbcdef
+    # PRINT ENTRY = Paracetamol|T109|T121|NON|EQV|BAN (19XX)|FDA SRS (2014)|INN (19XX)|740329|abbcdeeef
+    # ENTRY = APAP|T109|T121|NON|EQV|BAN (19XX)|FDA SRS (2014)|020515|abbcdeef
+    # ENTRY = Acamol|T109|T121|TRD|NRW|NLM (1995)|930902|abbcdef
+    # ENTRY = Acephen|T109|T121|TRD|NRW|NLM (1991)|900509|abbcdef
+    # ENTRY = Acetaco|T109|T121|TRD|REL|UNK (19XX)|861022|abbcdef
+    # ENTRY = Acetominophen|T109|T121|NON|EQV|UNK (19XX)|810625|abbcdef
+    # ENTRY = Algotropyl|T109|T121|TRD|REL|UNK (19XX)|800825|abbcdef
+    # ENTRY = Anacin-3|T109|T121|TRD|NRW|UNK (19XX)|861119|abbcdef
+    # ENTRY = Datril|T109|T121|NON|NRW|UNK (19XX)|861119|abbcdef
+    # ENTRY = N-(4-Hydroxyphenyl)acetanilide|T109|T121|NON|EQV|NLM (1996)|950330|abbcdef
+    # ENTRY = N-Acetyl-p-aminophenol|T109|T121|NON|EQV|UNK (19XX)|800813|abbcdef
+    # ENTRY = Panadol|T109|T121|TRD|NRW|UNK (19XX)|830915|abbcdef
+    # ENTRY = Tylenol|T109|T121|TRD|NRW|UNK (19XX)|830223|abbcdef
+    # ENTRY = p-Acetamidophenol|T109|T121|NON|EQV|UNK (19XX)|800813|abbcdef
+    # ENTRY = p-Hydroxyacetanilide|T109|T121|NON|EQV|UNK (19XX)|800801|abbcdef
+    # ENTRY = Anacin 3
+    # ENTRY = Anacin3
+
+    def test_has_heading
+      entry = Entry.new(@parent_heading, 'Anacin3')
+      assert_equal @parent_heading, entry.heading
+    end
+
+    def test_construct_from_plain_string
+      entry = Entry.new(@parent_heading, 'Anacin3')
+      assert_equal 'Anacin3', entry.term
+      assert_nil entry.semantic_relationship
+    end
+
+    def test_has_lexical_type
+      entry = Entry.new(@parent_heading, 'Panadol|T109|T121|TRD|NRW|UNK (19XX)|830915|abbcdef')
+      assert_equal 'Panadol', entry.term
+      assert_equal :trade_name, entry.lexical_type
+    end
+
+    def test_has_semantic_relationship
+      entry = Entry.new(@parent_heading, 'Panadol|T109|T121|TRD|NRW|UNK (19XX)|830915|abbcdef')
+      assert_equal 'Panadol', entry.term
+      assert_equal :narrower, entry.semantic_relationship
+    end
+
+    def test_has_semantic_types
+      entry = Entry.new(@parent_heading, 'Panadol|T109|T121|TRD|NRW|UNK (19XX)|830915|abbcdef')
+      assert_equal 'Panadol', entry.term
+      assert_equal ['Organic Chemical', 'Pharmacologic Substance'], entry.semantic_types
+    end
+    
+    def test_datril
+      # ENTRY = 
+      entry = Entry.new(@parent_heading, 'Datril|T109|T121|NON|NRW|UNK (19XX)|861119|abbcdef')
+      assert_equal 'Datril', entry.term
+      assert_equal ['Organic Chemical', 'Pharmacologic Substance'], entry.semantic_types
+      assert_nil entry.lexical_type
+      assert_equal :narrower, entry.semantic_relationship
+    end
+
+    # def test_semantic_relationship
+    #   skip
+    #   # ABB (Abbreviation)
+    #   # ABX (Embedded abbreviation)
+    #   # ACR (Acronym)
+    #   # ACX (Embedded acronym)
+    #   # EPO (Eponym)
+    #   # LAB (Lab number)
+    #   # NAM (Proper name)
+    #   # NON (None)
+    #   # TRD (Trade name)
+    # end
+    #
+    # def test_related_entries
+    #   skip
+    #   # BRD (Broader)
+    #   # EQV (Equivalent)
+    #   # NRW (Narrower)
+    #   # REL (Related)
+    # end
+
+    def setup
+      @mesh_tree = @@mesh_tree
+      @parent_heading = @mesh_tree.find('D000234')
+    end
+
+  end
+end

data/test/heading_test.rb

@@ -0,0 +1,506 @@
+require_relative 'test_helper'
+
+module MESH
+  class HeadingTest < TestBase
+
+    def test_have_the_correct_unique_id
+      mh = @mesh_tree.find('D000001')
+      assert_equal 'D000001', mh.unique_id
+    end
+
+    def test_have_the_correct_tree_number
+      mh = @mesh_tree.find('D000001')
+      assert_equal 1, mh.tree_numbers.length
+      assert_includes mh.tree_numbers, 'D03.438.221.173'
+    end
+
+    def test_have_the_correct_tree_numbers
+      mh = @mesh_tree.find('D000224')
+      assert_equal 2, mh.tree_numbers.length
+      assert_includes mh.tree_numbers, 'C19.053.500.263'
+      assert_includes mh.tree_numbers, 'C20.111.163'
+    end
+
+    def test_have_the_correct_root_letters
+      mh = @mesh_tree.find('D000224')
+      assert_equal ['C'], mh.roots
+      mh = @mesh_tree.find('D064946')
+      assert_equal ['H', 'N'], mh.roots
+    end
+
+    def test_have_the_correct_descriptor_class
+      mh = @mesh_tree.find('D000224')
+      assert_equal :topical_descriptor, mh.descriptor_class
+      mh = @mesh_tree.find('D005260')
+      assert_equal :check_tag, mh.descriptor_class
+    end
+
+    def test_have_the_correct_semantic_type
+      mh = @mesh_tree.find('D000224')
+      assert_equal ['Disease or Syndrome'], mh.semantic_types
+      mh = @mesh_tree.find('D005260')
+      assert_equal ['Organism Attribute'], mh.semantic_types
+      mh = @mesh_tree.find('D014148')
+      assert_equal ['Organic Chemical', 'Pharmacologic Substance'], mh.semantic_types
+
+    end
+
+    def test_have_the_correct_original_heading
+      mh = @mesh_tree.find('D000224')
+      assert_equal 'Addison Disease', mh.original_heading
+      mh = @mesh_tree.find('D000014')
+      assert_equal 'Abnormalities, Drug-Induced', mh.original_heading
+    end
+
+    def test_have_anglicised_original_heading
+      mh = @mesh_tree.find('D001471')
+      assert_equal 'Barrett Esophagus', mh.original_heading
+      assert_equal 'Barrett Oesophagus', mh.original_heading(:en_gb)
+    end
+
+    def test_have_natural_language_name
+      mh = @mesh_tree.find('D000224')
+      assert_equal 'Addison Disease', mh.natural_language_name
+      mh = @mesh_tree.find('D000014')
+      assert_equal 'Drug-Induced Abnormalities', mh.natural_language_name
+    end
+
+    def test_have_anglicised_natural_language_name
+      mh = @mesh_tree.find('D001471')
+      assert_equal 'Barrett Esophagus', mh.natural_language_name
+      assert_equal 'Barrett Oesophagus', mh.natural_language_name(:en_gb)
+    end
+
+    def test_have_the_correct_summary
+      mh = @mesh_tree.find('D000238')
+      assert_equal 'A benign tumor of the anterior pituitary in which the cells do not stain with acidic or basic dyes.', mh.summary
+    end
+
+    def test_have_anglicised_summary
+      mh = @mesh_tree.find('D001471')
+      assert_equal 'A condition with damage to the lining of the lower ESOPHAGUS resulting from chronic acid reflux (ESOPHAGITIS, REFLUX). Through the process of metaplasia, the squamous cells are replaced by a columnar epithelium with cells resembling those of the INTESTINE or the salmon-pink mucosa of the STOMACH. Barrett\'s columnar epithelium is a marker for severe reflux and precursor to ADENOCARCINOMA of the esophagus.', mh.summary
+      assert_equal 'A condition with damage to the lining of the lower OESOPHAGUS resulting from chronic acid reflux (OESOPHAGITIS, REFLUX). Through the process of metaplasia, the squamous cells are replaced by a columnar epithelium with cells resembling those of the INTESTINE or the salmon-pink mucosa of the STOMACH. Barrett\'s columnar epithelium is a marker for severe reflux and precursor to ADENOCARCINOMA of the oesophagus.', mh.summary(:en_gb)
+    end
+
+    def test_linkify_summary
+      mh = @mesh_tree.find('D001471')
+      original_summary = 'A condition with damage to the lining of the lower ESOPHAGUS resulting from chronic acid reflux (ESOPHAGITIS, REFLUX). Through the process of metaplasia, the squamous cells are replaced by a columnar epithelium with cells resembling those of the INTESTINE or the salmon-pink mucosa of the STOMACH. Barrett\'s columnar epithelium is a marker for severe reflux and precursor to ADENOCARCINOMA of the esophagus.'
+      assert_equal original_summary, mh.summary
+
+      found = {
+        'ESOPHAGUS' => false,
+        'ESOPHAGITIS, REFLUX' => false,
+        'INTESTINE' => false,
+        'STOMACH' => false,
+        'ADENOCARCINOMA' => false
+      }
+
+      linkified_summary = mh.linkify_summary do |text, heading|
+        found[text] = true unless heading.nil?
+        "<foo>#{text.downcase}</foo>"
+      end
+
+      assert_equal 5, found.length
+      assert found['ESOPHAGUS']
+      assert found['ESOPHAGITIS, REFLUX']
+      assert found['INTESTINE']
+      assert found['STOMACH']
+      assert found['ADENOCARCINOMA']
+
+      assert_equal original_summary, mh.summary
+      assert_equal 'A condition with damage to the lining of the lower <foo>esophagus</foo> resulting from chronic acid reflux (<foo>esophagitis, reflux</foo>). Through the process of metaplasia, the squamous cells are replaced by a columnar epithelium with cells resembling those of the <foo>intestine</foo> or the salmon-pink mucosa of the <foo>stomach</foo>. Barrett\'s columnar epithelium is a marker for severe reflux and precursor to <foo>adenocarcinoma</foo> of the esophagus.', linkified_summary
+
+    end
+
+    def test_linkifies_another_summary
+      mh = @mesh_tree.find_by_original_heading('Diabetic Nephropathies')
+      linkified_summary = mh.linkify_summary do |text, heading|
+        "<linky href=\"#{heading.unique_id}\">#{text.downcase}</linky>"
+      end
+
+      expected_summary = 'KIDNEY injuries associated with diabetes mellitus and affecting KIDNEY GLOMERULUS; ARTERIOLES; KIDNEY TUBULES; and the interstitium. Clinical signs include persistent PROTEINURIA, from microalbuminuria progressing to ALBUMINURIA of greater than 300 mg/24 h, leading to reduced GLOMERULAR FILTRATION RATE and END-STAGE RENAL DISEASE.'
+
+      expected_linkified = '<linky href="D007668">kidney</linky> injuries associated with diabetes mellitus and affecting <linky href="D007678">kidney glomerulus</linky>; <linky href="D001160">arterioles</linky>; <linky href="D007684">kidney tubules</linky>; and the interstitium. Clinical signs include persistent <linky href="D011507">proteinuria</linky>, from microalbuminuria progressing to <linky href="D000419">albuminuria</linky> of greater than 300 mg/24 h, leading to reduced <linky href="D005919">glomerular filtration rate</linky> and <linky href="D007676">end-stage renal disease</linky>.'
+
+
+      assert_equal expected_summary, mh.summary
+      assert_equal expected_linkified, linkified_summary
+    end
+
+    def test_to_s
+      mh = @mesh_tree.find('D001471')
+      assert_equal 'D001471, Barrett Esophagus, [C06.198.102,C06.405.117.102]', mh.to_s
+    end
+
+    def test_have_the_correct_entries
+      expected_entries = ['Activity Cycles', 'Ultradian Cycles', 'Activity Cycle', 'Cycle, Activity', 'Cycle, Ultradian', 'Cycles, Activity', 'Cycles, Ultradian', 'Ultradian Cycle']
+      expected_entries.sort!
+      mh = @mesh_tree.find('D000204')
+      assert_equal expected_entries, mh.entries
+    end
+
+    def test_have_anglicised_entries
+      expected_entries = ['Barrett Esophagus', 'Barrett Syndrome', 'Esophagus, Barrett', 'Barrett Epithelium', 'Barrett Metaplasia', 'Barrett\'s Esophagus', 'Barrett\'s Syndrome', 'Barretts Esophagus', 'Barretts Syndrome', 'Epithelium, Barrett', 'Esophagus, Barrett\'s', 'Syndrome, Barrett', 'Syndrome, Barrett\'s']
+      expected_entries_en = ['Barrett Oesophagus', 'Barrett Syndrome', 'Oesophagus, Barrett', 'Barrett Epithelium', 'Barrett Metaplasia', 'Barrett\'s Oesophagus', 'Barrett\'s Syndrome', 'Barretts Oesophagus', 'Barretts Syndrome', 'Epithelium, Barrett', 'Oesophagus, Barrett\'s', 'Syndrome, Barrett', 'Syndrome, Barrett\'s']
+
+      expected_entries.sort!
+      expected_entries_en.sort!
+      mh = @mesh_tree.find('D001471')
+      assert_equal expected_entries.sort, mh.entries
+      assert_equal expected_entries_en.sort, mh.entries(:en_gb)
+    end
+
+    def test_has_structured_entries
+
+      mh = @mesh_tree.find_by_original_heading('Acetaminophen')
+      assert_equal 19, mh.structured_entries.length
+
+      expected_terms = ['Acetamidophenol', 'Hydroxyacetanilide', 'Paracetamol', 'APAP', 'Acamol', 'Acephen', 'Acetaco', 'Acetominophen', 'Algotropyl', 'Anacin-3', 'Datril', 'N-(4-Hydroxyphenyl)acetanilide', 'N-Acetyl-p-aminophenol', 'Panadol', 'Tylenol', 'p-Acetamidophenol', 'p-Hydroxyacetanilide', 'Anacin 3', 'Anacin3']
+
+      actual_terms = mh.structured_entries.map { |tn| tn.term }
+
+      assert_equal actual_terms, expected_terms
+
+
+# PRINT ENTRY = Acetamidophenol|T109|T121|NON|EQV|UNK (19XX)|771118|abbcdef
+# PRINT ENTRY = Hydroxyacetanilide|T109|T121|NON|EQV|UNK (19XX)|740329|abbcdef
+# PRINT ENTRY = Paracetamol|T109|T121|NON|EQV|BAN (19XX)|FDA SRS (2014)|INN (19XX)|740329|abbcdeeef
+# ENTRY = APAP|T109|T121|NON|EQV|BAN (19XX)|FDA SRS (2014)|020515|abbcdeef
+# ENTRY = Acamol|T109|T121|TRD|NRW|NLM (1995)|930902|abbcdef
+# ENTRY = Acephen|T109|T121|TRD|NRW|NLM (1991)|900509|abbcdef
+# ENTRY = Acetaco|T109|T121|TRD|REL|UNK (19XX)|861022|abbcdef
+# ENTRY = Acetominophen|T109|T121|NON|EQV|UNK (19XX)|810625|abbcdef
+# ENTRY = Algotropyl|T109|T121|TRD|REL|UNK (19XX)|800825|abbcdef
+# ENTRY = Anacin-3|T109|T121|TRD|NRW|UNK (19XX)|861119|abbcdef
+# ENTRY = Datril|T109|T121|NON|NRW|UNK (19XX)|861119|abbcdef
+# ENTRY = N-(4-Hydroxyphenyl)acetanilide|T109|T121|NON|EQV|NLM (1996)|950330|abbcdef
+# ENTRY = N-Acetyl-p-aminophenol|T109|T121|NON|EQV|UNK (19XX)|800813|abbcdef
+# ENTRY = Panadol|T109|T121|TRD|NRW|UNK (19XX)|830915|abbcdef
+# ENTRY = Tylenol|T109|T121|TRD|NRW|UNK (19XX)|830223|abbcdef
+# ENTRY = p-Acetamidophenol|T109|T121|NON|EQV|UNK (19XX)|800813|abbcdef
+# ENTRY = p-Hydroxyacetanilide|T109|T121|NON|EQV|UNK (19XX)|800801|abbcdef
+# ENTRY = Anacin 3
+# ENTRY = Anacin3
+
+    end
+
+    def test_have_a_single_wikipedia_link
+
+      expected = {
+        'D000001' => 'http://en.wikipedia.org/wiki/A23187',
+        'D000005' => 'http://en.wikipedia.org/wiki/Abdomen',
+        'D000082' => 'http://en.wikipedia.org/wiki/Paracetamol'
+      }
+
+      expected.each do |id, expected_link|
+        mh = @mesh_tree.find(id)
+        assert_equal 1, mh.wikipedia_links.length
+        assert_equal expected_link, mh.wikipedia_links[0][:link]
+      end
+
+    end
+
+    def test_have_a_single_wikipedia_score
+      expected = {
+        'D000001' => 0.5,
+        'D000005' => 1.0,
+        'D000082' => 0.35
+      }
+
+      expected.each do |id, expected_score|
+        mh = @mesh_tree.find(id)
+        assert_equal 1, mh.wikipedia_links.length
+        assert_equal expected_score, mh.wikipedia_links[0][:score]
+      end
+
+    end
+
+    def test_have_a_single_wikipedia_image
+      expected = {
+        'D000001' => 'http://upload.wikimedia.org/wikipedia/commons/thumb/1/17/A23187.png/220px-A23187.png',
+        'D000005' => 'http://upload.wikimedia.org/wikipedia/commons/thumb/3/3b/Abdomen_%28PSF%29.jpg/250px-Abdomen_%28PSF%29.jpg',
+        'D000082' => 'http://upload.wikimedia.org/wikipedia/commons/thumb/2/29/Paracetamol-skeletal.svg/150px-Paracetamol-skeletal.svg.png'
+      }
+
+      expected.each do |id, expected_image|
+        mh = @mesh_tree.find(id)
+        assert_equal 1, mh.wikipedia_links.length
+        assert_equal expected_image, mh.wikipedia_links[0][:image]
+      end
+    end
+
+    def test_have_a_single_wikipedia_abstract
+      expected = {
+        'D000001' => '| CAS_number = 52665-69-7',
+        'D000005' => 'The abdomen (less formally called the belly, stomach, or tummy), in vertebrates such as mammals, constitutes the part of the body between the thorax (chest) and pelvis. The region enclosed by the abdomen is termed the abdominal cavity.',
+        'D000082' => '| MedlinePlus = a681004'
+      }
+
+      expected.each do |id, expected_abstract|
+        mh = @mesh_tree.find(id)
+        assert_equal 1, mh.wikipedia_links.length
+        assert_equal expected_abstract, mh.wikipedia_links[0][:abstract]
+      end
+    end
+
+    def test_have_more_than_one_wikipedia_link
+      mh = @mesh_tree.find('D000100')
+      expected = %w(
+        http://en.wikipedia.org/wiki/Sodium_acetrizoate
+        http://en.wikipedia.org/wiki/Acetrizoic_acid
+      )
+      assert_equal expected, mh.wikipedia_links.map { |l| l[:link] }
+    end
+
+    def test_have_more_than_one_wikipedia_score
+      mh = @mesh_tree.find('D000100')
+      expected = [0.09, 0.09]
+      assert_equal expected, mh.wikipedia_links.map { |l| l[:score] }
+    end
+
+    def test_have_more_than_one_wikipedia_image
+      mh = @mesh_tree.find('D000100')
+      expected = %w(
+        http://upload.wikimedia.org/wikipedia/commons/thumb/4/4d/Sodium_acetrizoate.svg/150px-Sodium_acetrizoate.svg.png
+        http://upload.wikimedia.org/wikipedia/commons/thumb/2/26/Acetrizoic_acid.png/220px-Acetrizoic_acid.png
+      )
+      assert_equal expected, mh.wikipedia_links.map { |l| l[:image] }
+    end
+
+    def test_have_more_than_one_wikipedia_abstract
+      mh = @mesh_tree.find('D000100')
+      expected = ['| CAS_number = 129-63-5', '| CAS_number = 85-36-9']
+      assert_equal expected, mh.wikipedia_links.map { |l| l[:abstract] }
+    end
+
+    def test_have_the_correct_parent
+      mh = @mesh_tree.find('D000001')
+      assert_equal 1, mh.parents.length
+      assert_equal 'D001583', mh.parents[0].unique_id
+    end
+
+    def test_have_the_correct_parents
+      mh = @mesh_tree.find('D000224')
+      p1 = @mesh_tree.find('D000309')
+      p2 = @mesh_tree.find('D001327')
+      assert_equal 2, mh.parents.length
+      assert_includes mh.parents, p1
+      assert_includes mh.parents, p2
+    end
+
+    def test_have_the_correct_parents_again
+      child = @mesh_tree.find_by_original_heading('Questionnaires')
+      assert_equal 1, child.parents.length
+      expected_parent = @mesh_tree.find_by_original_heading('Data Collection')
+      assert_includes child.parents, expected_parent
+    end
+
+    def test_have_the_correct_children
+      parent = @mesh_tree.find_by_tree_number('C19.053.500')
+      child1 = @mesh_tree.find_by_tree_number('C19.053.500.263')
+      child2 = @mesh_tree.find_by_tree_number('C19.053.500.270')
+      child3 = @mesh_tree.find_by_tree_number('C19.053.500.480')
+      child4 = @mesh_tree.find_by_tree_number('C19.053.500.740')
+
+      assert_equal 4, parent.children.length
+      assert_includes parent.children, child1
+      assert_includes parent.children, child2
+      assert_includes parent.children, child3
+      assert_includes parent.children, child4
+    end
+
+    def test_have_the_correct_children_again
+      parent = @mesh_tree.find_by_original_heading('Data Collection')
+
+      expected_children = [
+        'Health Surveys',
+        'Interviews as Topic',
+        'Questionnaires',
+        'Records as Topic',
+        'Registries',
+        'Vital Statistics',
+        'Geriatric Assessment',
+        'Nutrition Assessment',
+        'Health Care Surveys',
+        'Narration',
+        'Lot Quality Assurance Sampling',
+        'Checklist',
+        'Health Impact Assessment',
+        'Crowdsourcing'
+      ].map { |oh| @mesh_tree.find_by_original_heading(oh) }
+
+
+      assert_equal expected_children.length, parent.children.length
+      expected_children.each do |ec|
+        assert_includes parent.children, ec
+      end
+    end
+
+    def test_have_the_correct_siblings
+      skip
+    end
+
+    def test_match_on_conditions_for_original_heading
+      mh = @mesh_tree.find('D001471')
+      assert mh.matches(original_heading: /^Barrett Esophagus$/)
+    end
+
+    def test_not_match_on_incorrect_condition_for_original_heading
+      mh = @mesh_tree.find('D001471')
+      refute mh.matches(original_heading: /^Foo$/)
+    end
+
+    def test_match_on_conditions_for_entries
+      mh = @mesh_tree.find('D001471')
+      assert mh.matches(entries: /Metaplasia/)
+    end
+
+    def test_not_match_on_incorrect_conditions_for_entries
+      mh = @mesh_tree.find('D001471')
+      refute mh.matches(entries: /Foo/)
+    end
+
+    def test_match_on_descriptor_class
+      mh = @mesh_tree.find('D000224')
+      assert mh.matches(descriptor_class: :topical_descriptor)
+      refute mh.matches(descriptor_class: :check_tag)
+      mh = @mesh_tree.find('D005260')
+      assert mh.matches(descriptor_class: :check_tag)
+      refute mh.matches(descriptor_class: :topical_descriptor)
+    end
+
+    def test_match_on_conditions_for_tree_numbers
+      mh = @mesh_tree.find('D001471')
+      assert mh.matches(tree_numbers: /C06\.198\.102/)
+      assert mh.matches(tree_numbers: /^C06\.198\.102$/)
+      assert mh.matches(tree_numbers: /^C06/)
+      assert mh.matches(tree_numbers: /\.198\./)
+      assert mh.matches(tree_numbers: /^C06\.405\.117\.102$/)
+    end
+
+    def test_not_match_on_incorrect_conditions_for_tree_numbers
+      mh = @mesh_tree.find('D001471')
+      refute mh.matches(tree_numbers: /Foo/)
+    end
+
+    def test_match_on_conditions_for_summary
+      mh = @mesh_tree.find('D001471')
+      assert mh.matches(summary: /the lower ESOPHAGUS resulting from chronic acid reflux \(ESOPHAGITIS, REFLUX\)\./)
+    end
+
+    def test_not_match_on_incorrect_conditions_for_summary
+      mh = @mesh_tree.find('D001471')
+      refute mh.matches(summary: /Foo/)
+    end
+
+    def test_match_on_conditions_for_useful
+      mh = @mesh_tree.find('D001471')
+      begin
+        mh.useful = true
+        assert mh.matches(useful: true)
+        refute mh.matches(useful: false)
+        mh.useful = false
+        assert mh.matches(useful: false)
+        refute mh.matches(useful: true)
+      ensure
+        mh.useful = true
+      end
+    end
+
+    def test_match_on_multiple_conditions
+      mh = @mesh_tree.find('D001471')
+      assert mh.matches(original_heading: /^Barrett Esophagus$/, summary: /the lower ESOPHAGUS/)
+    end
+
+    def test_not_match_on_incorrect_multiple_conditions
+      mh = @mesh_tree.find('D001471')
+      refute mh.matches(original_heading: /^Barrett Esophagus$/, summary: /Foo/)
+      refute mh.matches(original_heading: /^Foo/, summary: /the lower ESOPHAGUS/)
+    end
+
+    def test_allow_headings_to_be_marked_as_not_useful
+      mh = @mesh_tree.find('D055550')
+      mh.useful = true
+      assert mh.useful
+      mh.useful = false
+      refute mh.useful
+      mh.useful = true
+      assert mh.useful
+    end
+
+    def test_know_its_deepest_position_in_the_tree
+      #single tree numbers
+      assert_equal 1, @mesh_tree.find('D002319').deepest_position
+      assert_equal 2, @mesh_tree.find('D001808').deepest_position
+      assert_equal 3, @mesh_tree.find('D001158').deepest_position
+      assert_equal 4, @mesh_tree.find('D001981').deepest_position
+    end
+
+    def test_know_its_shallowest_position_in_the_tree
+      #single tree numbers
+      assert_equal 1, @mesh_tree.find('D002319').shallowest_position
+      assert_equal 2, @mesh_tree.find('D001808').shallowest_position
+      assert_equal 3, @mesh_tree.find('D001158').shallowest_position
+      assert_equal 4, @mesh_tree.find('D001981').shallowest_position
+    end
+
+    def test_know_if_one_heading_is_the_descendant_of_another
+      parent = @mesh_tree.find('D002319')
+      child = @mesh_tree.find('D001808')
+      grandchild = @mesh_tree.find('D001158')
+      great_grandchild = @mesh_tree.find('D001981')
+      unrelated = @mesh_tree.find('D008091')
+
+      refute parent.has_descendant(parent), 'should not consider itself a desecendant'
+      assert parent.has_descendant(child), "should consider child #{child.inspect} a descendant of #{parent.inspect} in #{parent.children}"
+      assert parent.has_descendant(grandchild), "should consider grandchild #{grandchild.inspect} a descendant #{parent.inspect}"
+      assert parent.has_descendant(great_grandchild), "should consider great grandchild #{great_grandchild.inspect} a descendant #{parent.inspect}"
+      refute parent.has_descendant(unrelated), 'should not consider an unrelated heading a descendant'
+    end
+
+    def test_know_if_one_heading_is_the_ancestor_of_another
+      child = @mesh_tree.find('D001981')
+      parent = @mesh_tree.find('D001158')
+      grandparent = @mesh_tree.find('D001808')
+      great_grandparent = @mesh_tree.find('D002319')
+      unrelated = @mesh_tree.find('D008091')
+
+      refute child.has_ancestor(child), 'should not consider itself an ancestor'
+      assert child.has_ancestor(parent), "should consider parent #{parent.inspect} an ancestor of #{child.inspect} in #{child.parents}"
+      assert child.has_ancestor(grandparent), "should consider grandparent #{grandparent.inspect} an ancestor #{child.inspect}"
+      assert child.has_ancestor(great_grandparent), "should consider great grandparent #{great_grandparent.inspect} an ancestor #{child.inspect}"
+      refute child.has_ancestor(unrelated), 'should not consider an unrelated heading an ancestor'
+    end
+
+    def test_know_if_headings_are_siblings_at_the_same_level_below_a_common_parent
+      parent = @mesh_tree.find_by_tree_number('C19.053.500')
+      child1 = @mesh_tree.find_by_tree_number('C19.053.500.263')
+      child2 = @mesh_tree.find_by_tree_number('C19.053.500.270')
+      child3 = @mesh_tree.find_by_tree_number('C19.053.500.480')
+      child4 = @mesh_tree.find_by_tree_number('C19.053.500.740')
+      unrelated = @mesh_tree.find('D008091')
+      children = [child1, child2, child3, child4]
+
+      children.each { |c| refute parent.sibling?(c) }
+      children.each { |c| refute c.sibling?(parent) }
+
+      children.each { |c| assert child1.sibling?(c) unless c == child1 }
+      children.each { |c| assert c.sibling?(child1) unless c == child1 }
+
+      children.each { |c| refute unrelated.sibling?(c) }
+      children.each { |c| refute c.sibling?(unrelated) }
+    end
+
+    def test_override_inspect_to_prevent_issues_in_test_diagnostics
+      mh = @mesh_tree.find('D001471')
+      expected = "#{mh.unique_id}, #{mh.original_heading}, [#{mh.tree_numbers.join(',')}]"
+      assert_equal expected, mh.inspect
+    end
+
+    def setup
+      @mesh_tree = @@mesh_tree
+    end
+
+  end
+end
+