bio 1.4.0 → 1.4.1

data/test/unit/bio/db/kegg/test_module.rb

@@ -0,0 +1,246 @@
+#
+# test/unit/bio/db/kegg/test_module.rb - Unit test for Bio::KEGG::MODULE
+#
+# Copyright::  Copyright (C) 2010 Kozo Nishida <kozo-ni@is.naist.jp>
+#              Copyright (C) 2010 Naohisa Goto <ng@bioruby.org>
+# License::    The Ruby License
+
+# loading helper routine for testing bioruby
+require 'pathname'
+load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4,
+                            'bioruby_test_helper.rb')).cleanpath.to_s
+
+# libraries needed for the tests
+require 'test/unit'
+require 'bio/db/kegg/module'
+
+module Bio
+  class TestKeggModule < Test::Unit::TestCase
+
+    def setup
+      filename = File.join(BioRubyTestDataPath, 'KEGG/M00118.module')
+      entry = File.read(filename)
+      @obj = Bio::KEGG::MODULE.new(entry)
+    end
+
+    def test_new
+      assert_instance_of(Bio::KEGG::MODULE, @obj)
+    end
+
+    def test_entry_id
+      assert_equal('M00118', @obj.entry_id)
+    end
+
+    def test_name
+      assert_equal('Pentose interconversion, arabinose/ribulose/xylulose/xylose', @obj.name)
+    end
+
+    def test_definition
+      expected = "K00011 K01804 K00853 (K01786,K03080) K03331 K05351 K00854 K00011 K01805 K01783 (K00853,K00875) K00039"
+      assert_equal(expected, @obj.definition)
+    end
+
+    def test_keggclass
+      assert_equal('Metabolism; Central metabolism; Other carbohydrate metabolism', @obj.keggclass)
+    end
+
+    def test_pathways_as_strings
+      expected = ["ko00040(K00011+K01804+K00853+K01786+K03080+K03331+K05351+K00854+K00011+K01805+K01783+K00853+K00875+K00039)  Pentose and glucuronate interconversions"]
+      assert_equal(expected, @obj.pathways_as_strings)
+    end
+
+    def test_pathways_as_hash
+      expected = { "ko00040(K00011+K01804+K00853+K01786+K03080+K03331+K05351+K00854+K00011+K01805+K01783+K00853+K00875+K00039)" =>
+        "Pentose and glucuronate interconversions" }
+      assert_equal(expected, @obj.pathways_as_hash)
+    end
+
+    def test_pathways
+      expected = { "ko00040(K00011+K01804+K00853+K01786+K03080+K03331+K05351+K00854+K00011+K01805+K01783+K00853+K00875+K00039)" =>
+        "Pentose and glucuronate interconversions" }
+      assert_equal(expected, @obj.pathways)
+    end
+
+    def test_orthologs_as_strings
+      expected =
+        [ "K00011  aldehyde reductase [EC:1.1.1.21] [RN:R01758 R01759]",
+          "K01804  L-arabinose isomerase [EC:5.3.1.4] [RN:R01761]",
+          "K00853  L-ribulokinase [EC:2.7.1.16] [RN:R02439]",
+          "K01786,K03080  L-ribulose-5-phosphate 4-epimerase [EC:5.1.3.4] [RN:R05850]",
+          "K03331  L-xylulose reductase [EC:1.1.1.10] [RN:R01904]",
+          "K05351  D-xylulose reductase [EC:1.1.1.9] [RN:R01896]",
+          "K00854  xylulokinase [EC:2.7.1.17] [RN:R01639]",
+          "K00011  aldehyde reductase [EC:1.1.1.21] [RN:R01431]",
+          "K01805  xylose isomerase [EC:5.3.1.5] [RN:R01432]",
+          "K01783  ribulose-phosphate 3-epimerase [EC:5.1.3.1] [RN:R01529]",
+          "K00853,K00875  ribulokinase [EC:2.7.1.16 2.7.1.47] [RN:R01526]",
+          "K00039  ribitol 2-dehydrogenase [EC:1.1.1.56] [RN:R01895]"
+        ]
+      assert_equal(expected, @obj.orthologs_as_strings)
+    end
+
+    def test_orthologs_as_hash
+      expected = {
+        "K00039" => "ribitol 2-dehydrogenase [EC:1.1.1.56] [RN:R01895]",
+        "K00853" => "L-ribulokinase [EC:2.7.1.16] [RN:R02439]",
+        "K00854" => "xylulokinase [EC:2.7.1.17] [RN:R01639]",
+        "K05351" => "D-xylulose reductase [EC:1.1.1.9] [RN:R01896]",
+        "K00853,K00875" => "ribulokinase [EC:2.7.1.16 2.7.1.47] [RN:R01526]",
+        "K03331" => "L-xylulose reductase [EC:1.1.1.10] [RN:R01904]",
+        "K00011" => "aldehyde reductase [EC:1.1.1.21] [RN:R01431]",
+        "K01786,K03080" =>
+        "L-ribulose-5-phosphate 4-epimerase [EC:5.1.3.4] [RN:R05850]",
+        "K01804" => "L-arabinose isomerase [EC:5.3.1.4] [RN:R01761]",
+        "K01783" => "ribulose-phosphate 3-epimerase [EC:5.1.3.1] [RN:R01529]",
+        "K01805" => "xylose isomerase [EC:5.3.1.5] [RN:R01432]"
+      }
+      assert_equal(expected, @obj.orthologs_as_hash)
+    end
+
+    def test_orthologs
+      expected = {
+        "K00039" => "ribitol 2-dehydrogenase [EC:1.1.1.56] [RN:R01895]",
+        "K00853" => "L-ribulokinase [EC:2.7.1.16] [RN:R02439]",
+        "K00854" => "xylulokinase [EC:2.7.1.17] [RN:R01639]",
+        "K05351" => "D-xylulose reductase [EC:1.1.1.9] [RN:R01896]",
+        "K00853,K00875" => "ribulokinase [EC:2.7.1.16 2.7.1.47] [RN:R01526]",
+        "K03331" => "L-xylulose reductase [EC:1.1.1.10] [RN:R01904]",
+        "K00011" => "aldehyde reductase [EC:1.1.1.21] [RN:R01431]",
+        "K01786,K03080" =>
+        "L-ribulose-5-phosphate 4-epimerase [EC:5.1.3.4] [RN:R05850]",
+        "K01804" => "L-arabinose isomerase [EC:5.3.1.4] [RN:R01761]",
+        "K01783" => "ribulose-phosphate 3-epimerase [EC:5.1.3.1] [RN:R01529]",
+        "K01805" => "xylose isomerase [EC:5.3.1.5] [RN:R01432]"
+      }
+      assert_equal(expected, @obj.orthologs)
+    end
+
+    def test_orthologs_as_array
+      expected =
+        [ "K00011",
+          "K00039",
+          "K00853",
+          "K00854",
+          "K00875",
+          "K01783",
+          "K01786",
+          "K01804",
+          "K01805",
+          "K03080",
+          "K03331",
+          "K05351"
+        ]
+      assert_equal(expected, @obj.orthologs_as_array)
+    end
+
+    def test_reactions_as_strings
+      expected = [ "R01903  C00312 -> C00532",
+                   "R01758,R01759  C00532 -> C00259",
+                   "R01761  C00259 -> C00508",
+                   "R02439  C00508 -> C01101",
+                   "R05850  C01101 -> C00231",
+                   "R01904  C00312 -> C00379",
+                   "R01896  C00379 -> C00310",
+                   "R01639  C00310 -> C00231",
+                   "R01431  C00379 -> C00181",
+                   "R01432  C00181 -> C00310",
+                   "R01529  C00199 -> C00231",
+                   "R01526  C00231 -> C00309",
+                   "R01895  C00309 -> C00474"
+                 ]
+      assert_equal(expected, @obj.reactions_as_strings)
+    end
+
+    def test_reactions_as_hash
+      expected = {
+        "R01529" => "C00199 -> C00231",
+        "R01431" => "C00379 -> C00181",
+        "R01639" => "C00310 -> C00231",
+        "R01761" => "C00259 -> C00508",
+        "R01903" => "C00312 -> C00532",
+        "R01904" => "C00312 -> C00379",
+        "R01432" => "C00181 -> C00310",
+        "R01758,R01759" => "C00532 -> C00259",
+        "R01895" => "C00309 -> C00474",
+        "R01896" => "C00379 -> C00310",
+        "R02439" => "C00508 -> C01101",
+        "R05850" => "C01101 -> C00231",
+        "R01526" => "C00231 -> C00309"
+      }
+      assert_equal(expected, @obj.reactions_as_hash)
+    end
+
+    def test_reactions
+      expected = {
+        "R01529" => "C00199 -> C00231",
+        "R01431" => "C00379 -> C00181",
+        "R01639" => "C00310 -> C00231",
+        "R01761" => "C00259 -> C00508",
+        "R01903" => "C00312 -> C00532",
+        "R01904" => "C00312 -> C00379",
+        "R01432" => "C00181 -> C00310",
+        "R01758,R01759" => "C00532 -> C00259",
+        "R01895" => "C00309 -> C00474",
+        "R01896" => "C00379 -> C00310",
+        "R02439" => "C00508 -> C01101",
+        "R05850" => "C01101 -> C00231",
+        "R01526" => "C00231 -> C00309"
+      }
+      assert_equal(expected, @obj.reactions)
+    end
+
+    def test_compounds_as_strings
+      expected = [ "C00312  L-Xylulose",
+                   "C00532  L-Arabitol",
+                   "C00259  L-Arabinose",
+                   "C00508  L-Ribulose",
+                   "C01101  L-Ribulose 5-phosphate",
+                   "C00231  D-Xylulose 5-phosphate",
+                   "C00379  Xylitol",
+                   "C00310  D-Xylulose",
+                   "C00181  D-Xylose",
+                   "C00199  D-Ribulose 5-phosphate",
+                   "C00309  D-Ribulose",
+                   "C00474  Ribitol"
+                 ]
+      assert_equal(expected, @obj.compounds_as_strings)
+    end
+
+    def test_compounds_as_hash
+      expected = {
+        "C00231" => "D-Xylulose 5-phosphate",
+        "C00474" => "Ribitol",
+        "C00309" => "D-Ribulose",
+        "C00199" => "D-Ribulose 5-phosphate",
+        "C01101" => "L-Ribulose 5-phosphate",
+        "C00310" => "D-Xylulose",
+        "C00508" => "L-Ribulose",
+        "C00532" => "L-Arabitol",
+        "C00312" => "L-Xylulose",
+        "C00181" => "D-Xylose",
+        "C00379" => "Xylitol",
+        "C00259" => "L-Arabinose"
+      }
+      assert_equal(expected, @obj.compounds_as_hash)
+    end
+
+    def test_compounds
+      expected = {
+        "C00231" => "D-Xylulose 5-phosphate",
+        "C00474" => "Ribitol",
+        "C00309" => "D-Ribulose",
+        "C00199" => "D-Ribulose 5-phosphate",
+        "C01101" => "L-Ribulose 5-phosphate",
+        "C00310" => "D-Xylulose",
+        "C00508" => "L-Ribulose",
+        "C00532" => "L-Arabitol",
+        "C00312" => "L-Xylulose",
+        "C00181" => "D-Xylose",
+        "C00379" => "Xylitol",
+        "C00259" => "L-Arabinose"
+      }
+      assert_equal(expected, @obj.compounds)
+    end
+
+  end
+end

data/test/unit/bio/db/kegg/test_orthology.rb

@@ -11,6 +11,7 @@ load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4,
 
 # libraries needed for the tests
 require 'test/unit'
+require 'bio/reference'
 require 'bio/db/kegg/orthology'
 
 module Bio
@@ -42,8 +43,102 @@ module Bio
       assert_equal({"COG"=>["COG0592"], "RN"=>["R00375", "R00376", "R00377", "R00378"], "GO"=>["0003887"]}, @obj.dblinks_as_hash)
     end
 
+    def test_dblinks
+      expected = {
+        "COG" => ["COG0592"],
+        "RN"  => ["R00375", "R00376", "R00377", "R00378"],
+        "GO"  => ["0003887"]
+      }
+      assert_equal(expected, @obj.dblinks)
+    end
+
     def test_genes_as_hash
+      assert_equal(1000, @obj.genes_as_hash.size)
       assert_equal(["BSU00020"], @obj.genes_as_hash["bsu"])
+      assert_equal(["SynWH7803_0001"], @obj.genes_as_hash["syx"])
+    end
+
+    def test_modules_as_hash
+      expected = {"M00597"=>"DNA polymerase III complex"}
+      assert_equal(expected, @obj.modules_as_hash)
+    end
+
+    def test_modules
+      expected = {"M00597"=>"DNA polymerase III complex"}
+      assert_equal(expected, @obj.modules)
+    end
+
+    def test_references
+      data = 
+        [ { "authors" => [ "Stillman B." ],
+            "journal" => "Cell",
+            "pages"   => "725-8",
+            "pubmed"  => "8087839",
+            "title"   => "Smart machines at the DNA replication fork.",
+            "volume"  => "78",
+            "year"    => "1994"
+          } ]
+      expected = data.collect { |h| Bio::Reference.new(h) }
+      assert_equal(expected, @obj.references)
+    end
+
+    def test_keggclass
+      expected = "Metabolism; Nucleotide Metabolism; Purine metabolism [PATH:ko00230] Metabolism; Nucleotide Metabolism; Pyrimidine metabolism [PATH:ko00240] Genetic Information Processing; Replication and Repair; DNA replication [PATH:ko03030] Genetic Information Processing; Replication and Repair; DNA replication proteins [BR:ko03032] Genetic Information Processing; Replication and Repair; Mismatch repair [PATH:ko03430] Genetic Information Processing; Replication and Repair; Homologous recombination [PATH:ko03440] Genetic Information Processing; Replication and Repair; DNA repair and recombination proteins [BR:ko03400]"
+      assert_equal(expected, @obj.keggclass)
+    end
+
+    def test_keggclasses
+      expected =
+        [ "Metabolism; Nucleotide Metabolism; Purine metabolism",
+          "Metabolism; Nucleotide Metabolism; Pyrimidine metabolism",
+          "Genetic Information Processing; Replication and Repair; DNA replication",
+          "Genetic Information Processing; Replication and Repair; DNA replication proteins",
+          "Genetic Information Processing; Replication and Repair; Mismatch repair",
+          "Genetic Information Processing; Replication and Repair; Homologous recombination",
+          "Genetic Information Processing; Replication and Repair; DNA repair and recombination proteins"
+        ]
+      assert_equal(expected, @obj.keggclasses)
+    end
+
+    def test_pathways_as_strings
+      expected = ["ko00230  Purine metabolism",
+ "ko00240  Pyrimidine metabolism",
+ "ko03030  DNA replication",
+ "ko03430  Mismatch repair",
+ "ko03440  Homologous recombination"]
+      assert_equal(expected, @obj.pathways_as_strings)
+    end
+
+    def test_pathways_in_keggclass
+      expected = ["ko00230", "ko00240", "ko03030", "ko03430", "ko03440"]
+      assert_equal(expected, @obj.pathways_in_keggclass)
+    end
+
+    def test_modules_as_strings
+      expected = ["M00597  DNA polymerase III complex"]
+      assert_equal(expected, @obj.modules_as_strings)
+    end
+
+    def test_dblinks_as_strings
+      expected = [ "RN: R00375 R00376 R00377 R00378",
+                   "COG: COG0592", "GO: 0003887" ]
+      assert_equal(expected, @obj.dblinks_as_strings)
+    end
+
+    def test_genes_as_strings
+      assert_equal(1000, @obj.genes_as_strings.size)
+      assert_equal("ECO: b3701(dnaN)", @obj.genes_as_strings[0])
+      assert_equal("BPN: BPEN_015(dnaN)", @obj.genes_as_strings[100])
+      assert_equal("SVO: SVI_0032(dnaN)", @obj.genes_as_strings[200])
+      assert_equal("RFR: Rfer_0002 Rfer_4311", @obj.genes_as_strings[300])
+      assert_equal("OTS: OTBS_0002(dnaN)", @obj.genes_as_strings[400])
+      assert_equal("ACR: Acry_1437", @obj.genes_as_strings[500])
+      assert_equal("SPD: SPD_0002(dnaN)", @obj.genes_as_strings[600])
+      assert_equal("TEX: Teth514_0002", @obj.genes_as_strings[700])
+      assert_equal("FAL: FRAAL0004(dnaN) FRAAL1257",
+                   @obj.genes_as_strings[800])
+      assert_equal("AMU: Amuc_0816", @obj.genes_as_strings[900])
+      assert_equal("DAP: Dacet_2869", @obj.genes_as_strings[-1])
     end
 
   end

data/test/unit/bio/db/kegg/test_pathway.rb

@@ -0,0 +1,1250 @@
+#
+# test/unit/bio/db/kegg/test_pathway.rb - Unit test for Bio::KEGG::PATHWAY
+#
+# Copyright::  Copyright (C) 2010 Kozo Nishida <kozo-ni@is.naist.jp>
+#              Copyright (C) 2010 Naohisa Goto <ng@bioruby.org>
+# License::    The Ruby License
+
+# loading helper routine for testing bioruby
+require 'pathname'
+load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4,
+                            'bioruby_test_helper.rb')).cleanpath.to_s
+
+# libraries needed for the tests
+require 'test/unit'
+require 'bio/db/kegg/pathway'
+
+module Bio
+  class TestKeggPathway_map00052 < Test::Unit::TestCase
+
+    def setup
+      testdata_kegg = Pathname.new(File.join(BioRubyTestDataPath, 'KEGG')).cleanpath.to_s
+      entry = File.read(File.join(testdata_kegg, "map00052.pathway"))
+      @obj = Bio::KEGG::PATHWAY.new(entry)
+    end
+
+    def test_entry_id
+      assert_equal('map00052', @obj.entry_id)
+    end
+
+    def test_name
+      assert_equal('Galactose metabolism', @obj.name)
+    end
+
+    def test_keggclass
+      assert_equal('Metabolism; Carbohydrate Metabolism', @obj.keggclass)
+    end
+
+    def test_modules_as_hash
+      expected = {
+        "M00097"=>"UDP-glucose and UDP-galactose biosynthesis, Glc-1P/Gal-1P => UDP-Glc/UDP-Gal",
+        "M00614"=>"PTS system, N-acetylgalactosamine-specific II component",
+        "M00616"=>"PTS system, galactitol-specific II component",
+        "M00618"=>"PTS system, lactose-specific II component",
+        "M00624"=>"PTS system, galactosamine-specific II component"
+      }
+      assert_equal(expected, @obj.modules_as_hash)
+      assert_equal(expected, @obj.modules)
+    end
+
+    def test_modules_as_strings
+      expected =
+        [ "M00097  UDP-glucose and UDP-galactose biosynthesis, Glc-1P/Gal-1P => UDP-Glc/UDP-Gal",
+          "M00614  PTS system, N-acetylgalactosamine-specific II component",
+          "M00616  PTS system, galactitol-specific II component",
+          "M00618  PTS system, lactose-specific II component",
+          "M00624  PTS system, galactosamine-specific II component"
+        ]
+      assert_equal(expected, @obj.modules_as_strings)
+    end
+
+    def test_rel_pathways_as_strings
+      expected = [ "map00010  Glycolysis / Gluconeogenesis",
+                   "map00040  Pentose and glucuronate interconversions",
+                   "map00051  Fructose and mannose metabolism",
+                   "map00520  Amino sugar and nucleotide sugar metabolism"
+                 ]
+      assert_equal(expected, @obj.rel_pathways_as_strings)
+    end
+
+    def test_rel_pathways_as_hash
+      expected = {
+        "map00010"=>"Glycolysis / Gluconeogenesis",
+        "map00040"=>"Pentose and glucuronate interconversions",
+        "map00051"=>"Fructose and mannose metabolism",
+        "map00520"=>"Amino sugar and nucleotide sugar metabolism"
+      }
+      assert_equal(expected, @obj.rel_pathways_as_hash)
+      assert_equal(expected, @obj.rel_pathways)
+    end
+
+    def test_references
+      assert_equal([], @obj.references)
+    end
+
+    def test_dblinks_as_strings
+      assert_equal([], @obj.dblinks_as_strings)
+    end
+
+    def test_dblinks_as_hash
+      assert_equal({}, @obj.dblinks_as_hash)
+    end
+
+    def test_pathways_as_strings
+      expected = ["map00052  Galactose metabolism"]
+      assert_equal(expected, @obj.pathways_as_strings)
+    end
+
+    def test_pathways_as_hash
+      expected = {"map00052"=>"Galactose metabolism"}
+      assert_equal(expected, @obj.pathways_as_hash)
+    end
+
+    def test_orthologs_as_strings
+      assert_equal([], @obj.orthologs_as_strings)
+    end
+
+    def test_orthologs_as_hash
+      assert_equal({}, @obj.orthologs_as_hash)
+    end
+
+    def test_genes_as_strings
+      assert_equal([], @obj.genes_as_strings)
+    end
+
+    def test_genes_as_hash
+      assert_equal({}, @obj.genes_as_hash)
+    end
+
+    def test_diseases_as_strings
+      assert_equal([], @obj.diseases_as_strings)
+    end
+
+    def test_diseases_as_hash
+      assert_equal({}, @obj.diseases_as_hash)
+    end
+
+    def test_enzymes_as_strings
+      assert_equal([], @obj.enzymes_as_strings)
+    end
+
+    def test_reactions_as_strings
+      assert_equal([], @obj.reactions_as_strings)
+    end
+
+    def test_reactions_as_hash
+      assert_equal({}, @obj.reactions_as_hash)
+    end
+
+    def test_compounds_as_strings
+      assert_equal([], @obj.compounds_as_strings)
+    end
+
+    def test_compounds_as_hash
+      assert_equal({}, @obj.compounds_as_hash)
+    end
+
+    def test_description
+      assert_equal("", @obj.description)
+    end
+
+    def test_organism
+      assert_equal("", @obj.organism)
+    end
+
+    def test_ko_pathway
+      assert_equal("", @obj.ko_pathway)
+    end
+
+  end #class TestKeggPathway_map00052
+
+  class TestBioKEGGPATHWAY_map00030 < Test::Unit::TestCase
+
+    def setup
+      filename = File.join(BioRubyTestDataPath, 'KEGG/map00030.pathway')
+      @obj = Bio::KEGG::PATHWAY.new(File.read(filename))
+    end
+
+    def test_references
+      data =
+        [ { "authors"  => [ "Nishizuka Y (ed)." ],
+            "comments" => [ "(map 3)" ],
+            "journal"  => "Tokyo Kagaku Dojin",
+            "title"    => "[Metabolic Maps] (In Japanese)",
+            "year"     => "1980"
+          },
+          { "authors"  => [ "Nishizuka Y", "Seyama Y", "Ikai A",
+                            "Ishimura Y", "Kawaguchi A (eds)." ],
+            "comments" => [ "(map 4)" ],
+            "journal"  => "Tokyo Kagaku Dojin",
+            "title"=>"[Cellular Functions and Metabolic Maps] (In Japanese)",
+            "year"     => "1997"
+          },
+          { "authors" => [ "Michal G." ],
+            "journal" => "Wiley",
+            "title"   => "Biochemical Pathways",
+            "year"    => "1999"
+          },
+          { "authors" => [ "Hove-Jensen B", "Rosenkrantz TJ",
+                           "Haldimann A", "Wanner BL." ],
+            "journal" => "J Bacteriol",
+            "pages"   => "2793-801",
+            "pubmed"  => "12700258",
+            "title"   => "Escherichia coli phnN, encoding ribose 1,5-bisphosphokinase activity (phosphoribosyl diphosphate forming): dual role in phosphonate degradation and NAD biosynthesis pathways.",
+            "volume"  => "185",
+            "year"    => "2003"
+          }
+        ]
+      expected = data.collect { |h| Bio::Reference.new(h) }
+      assert_equal(expected, @obj.references)
+    end
+
+    def test_new
+      assert_instance_of(Bio::KEGG::PATHWAY, @obj)
+    end
+
+    def test_entry_id
+      assert_equal("map00030", @obj.entry_id)
+    end
+
+    def test_name
+      assert_equal("Pentose phosphate pathway", @obj.name)
+    end
+
+    def test_description
+      expected = "The pentose phosphate pathway is a process of glucose turnover that produces NADPH as reducing equivalents and pentoses as essential parts of nucleotides. There are two different phases in the pathway. One is irreversible oxidative phase in which glucose-6P is converted to ribulose-5P by oxidative decarboxylation, and NADPH is generated [MD:M00006]. The other is reversible non-oxidative phase in which phosphorylated sugars are interconverted to generate xylulose-5P, ribulose-5P, and ribose-5P [MD:M00007]. Phosphoribosyl pyrophosphate (PRPP) formed from ribose-5P [MD:M00005] is an activated compound used in the biosynthesis of histidine and purine/pyrimidine nucleotides. This pathway map also shows the Entner-Doudoroff pathway where 6-P-gluconate is dehydrated and then cleaved into pyruvate and glyceraldehyde-3P [MD:M00008]."
+      assert_equal(expected, @obj.description)
+    end
+
+    def test_keggclass
+      expected = "Metabolism; Carbohydrate Metabolism"
+      assert_equal(expected, @obj.keggclass)
+    end
+
+    def test_modules_as_strings
+      expected =
+        [ "M00004  Pentose phosphate pathway (Pentose phosphate cycle) [PATH:map00030]",
+          "M00005  PRPP biosynthesis, ribose 5P -> PRPP [PATH:map00030]",
+          "M00006  Pentose phosphate pathway, oxidative phase, glucose 6P => ribulose 5P [PATH:map00030]",
+          "M00007  Pentose phosphate pathway, non-oxidative phase, fructose 6P => ribose 5P [PATH:map00030]",
+          "M00008  Entner-Doudoroff pathway, glucose-6P => glyceraldehyde-3P + pyruvate [PATH:map00030]",
+          "M00680  Semi-phosphorylative Entner-Doudoroff pathway, gluconate => glyceraldehyde-3P + pyruvate [PATH:map00030]",
+          "M00681  Non-phosphorylative Entner-Doudoroff pathway, gluconate => glyceraldehyde + pyruvate [PATH:map00030]"
+        ]
+      assert_equal(expected, @obj.modules_as_strings)
+    end
+
+    def test_modules_as_hash
+      expected = {
+        "M00008" => "Entner-Doudoroff pathway, glucose-6P => glyceraldehyde-3P + pyruvate [PATH:map00030]",
+        "M00680" => "Semi-phosphorylative Entner-Doudoroff pathway, gluconate => glyceraldehyde-3P + pyruvate [PATH:map00030]",
+        "M00681" => "Non-phosphorylative Entner-Doudoroff pathway, gluconate => glyceraldehyde + pyruvate [PATH:map00030]",
+        "M00004" => "Pentose phosphate pathway (Pentose phosphate cycle) [PATH:map00030]",
+        "M00005" => "PRPP biosynthesis, ribose 5P -> PRPP [PATH:map00030]",
+        "M00006" => "Pentose phosphate pathway, oxidative phase, glucose 6P => ribulose 5P [PATH:map00030]",
+        "M00007" => "Pentose phosphate pathway, non-oxidative phase, fructose 6P => ribose 5P [PATH:map00030]"
+      }
+      assert_equal(expected, @obj.modules_as_hash)
+      assert_equal(expected, @obj.modules)
+    end
+
+    def test_rel_pathways_as_strings
+      expected = [ "map00010  Glycolysis / Gluconeogenesis",
+                   "map00040  Pentose and glucuronate interconversions",
+                   "map00230  Purine metabolism",
+                   "map00240  Pyrimidine metabolism",
+                   "map00340  Histidine metabolism" ]
+      assert_equal(expected, @obj.rel_pathways_as_strings)
+    end
+
+    def test_rel_pathways_as_hash
+      expected = {
+        "map00240" => "Pyrimidine metabolism",
+        "map00340" => "Histidine metabolism",
+        "map00230" => "Purine metabolism",
+        "map00010" => "Glycolysis / Gluconeogenesis",
+        "map00040" => "Pentose and glucuronate interconversions"
+      }
+      assert_equal(expected, @obj.rel_pathways_as_hash)
+      assert_equal(expected, @obj.rel_pathways)
+    end
+
+    def test_dblinks_as_strings
+      assert_equal(["GO: 0006098"], @obj.dblinks_as_strings)
+    end
+
+    def test_dblinks_as_hash
+      assert_equal({"GO"=>["0006098"]}, @obj.dblinks_as_hash)
+    end
+
+    def test_pathways_as_strings
+      expected = ["map00030  Pentose phosphate pathway"]
+      assert_equal(expected, @obj.pathways_as_strings)
+    end
+
+    def test_pathways_as_hash
+      expected = {"map00030"=>"Pentose phosphate pathway"}
+      assert_equal(expected, @obj.pathways_as_hash)
+    end
+
+    def test_orthologs_as_strings
+      assert_equal([], @obj.orthologs_as_strings)
+    end
+
+    def test_orthologs_as_hash
+      assert_equal({}, @obj.orthologs_as_hash)
+    end
+
+    def test_genes_as_strings
+      assert_equal([], @obj.genes_as_strings)
+    end
+
+    def test_genes_as_hash
+      assert_equal({}, @obj.genes_as_hash)
+    end
+
+    def test_diseases_as_strings
+      expected = ["H00196  Phosphoribosylpyrophosphate synthetase I superactivity"]
+      assert_equal(expected, @obj.diseases_as_strings)
+    end
+
+    def test_diseases_as_hash
+      expected = {"H00196"=>"Phosphoribosylpyrophosphate synthetase I superactivity"}
+      assert_equal(expected, @obj.diseases_as_hash)
+    end
+
+    def test_enzymes_as_strings
+      assert_equal([], @obj.enzymes_as_strings)
+    end
+
+    def test_reactions_as_strings
+      assert_equal([], @obj.reactions_as_strings)
+    end
+
+    def test_reactions_as_hash
+      assert_equal({}, @obj.reactions_as_hash)
+    end
+
+    def test_compounds_as_strings
+      assert_equal([], @obj.compounds_as_strings)
+    end
+
+    def test_compounds_as_hash
+      assert_equal({}, @obj.compounds_as_hash)
+    end
+
+    def test_organism
+      assert_equal("", @obj.organism)
+    end
+
+    def test_ko_pathway
+      assert_equal("ko00030", @obj.ko_pathway)
+    end
+
+  end #class TestBioKEGGPATHWAY
+
+  class TestBioKeggPathway_rn00250 < Test::Unit::TestCase
+
+    def setup
+      filename = File.join(BioRubyTestDataPath, 'KEGG', 'rn00250.pathway')
+      @obj = Bio::KEGG::PATHWAY.new(File.read(filename))
+    end
+
+    def test_dblinks_as_hash
+      expected = {"GO"=>["0006522", "0006531", "0006536"]}
+      assert_equal(expected, @obj.dblinks_as_hash)
+    end
+
+    def test_pathways_as_hash
+      expected = {"rn00250"=>"Alanine, aspartate and glutamate metabolism"}
+      assert_equal(expected, @obj.pathways_as_hash)
+    end
+
+    def test_orthologs_as_hash
+      assert_equal({}, @obj.orthologs_as_hash)
+    end
+
+    def test_genes_as_hash
+      assert_equal({}, @obj.genes_as_hash)
+    end
+
+    def test_references
+      data =
+        [ { "authors"  => [ "Nishizuka Y", "Seyama Y", "Ikai A",
+                            "Ishimura Y", "Kawaguchi A (eds)." ],
+            "journal"  => "Tokyo Kagaku Dojin",
+            "title"=>"[Cellular Functions and Metabolic Maps] (In Japanese)",
+            "year"     => "1997"
+          },
+          { "authors" => [ "Wu G" ],
+            "journal" => "J Nutr",
+            "pages"   => "1249-52",
+            "pubmed"  => "9687539",
+            "title"   => "Intestinal mucosal amino acid catabolism.",
+            "volume"  => "128",
+            "year"    => "1998"
+          }
+        ]
+      expected = data.collect { |h| Bio::Reference.new(h) }
+      assert_equal(expected, @obj.references)
+    end
+
+    def test_modules_as_hash
+      expected = {
+        "M00019"=>
+        "Glutamate biosynthesis, oxoglutarete => glutamate (glutamate synthase) [PATH:rn00250]",
+        "M00021"=>
+        "Aspartate biosynthesis, oxaloacetate => aspartate [PATH:rn00250]",
+        "M00044"=>
+        "Aspartate degradation, aspartate => fumarate [PATH:rn00250]",
+        "M00022"=>
+        "Asparagine biosynthesis, aspartate => asparagine [PATH:rn00250]",
+        "M00045"=>
+        "Aspartate degradation, aspartate => oxaloacetate [PATH:rn00250]",
+        "M00046"=>
+        "Asparagine degradation, asparagine => aspartate +NH3 [PATH:rn00250]",
+        "M00026"=>
+        "Alanine biosynthesis, pyruvate => alanine [PATH:rn00250]",
+        "M00038"=>
+        "Glutamine degradation, glutamine => glutamate + NH3 [PATH:rn00250]",
+        "M00040"=>
+        "GABA (gamma-Aminobutyrate) shunt [PATH:rn00250]",
+        "M00017"=>
+        "Glutamate biosynthesis, oxoglutarate => glutamate (glutamate dehydrogenase) [PATH:rn00250]",
+        "M00018"=>
+        "Glutamine biosynthesis, glutamate => glutamine [PATH:rn00250]"
+      }
+      assert_equal(expected, @obj.modules_as_hash)
+    end
+
+    def test_new
+      assert_kind_of(Bio::KEGG::PATHWAY, @obj)
+    end
+
+    def test_entry_id
+      assert_equal("rn00250", @obj.entry_id)
+    end
+
+    def test_name
+      expected = "Alanine, aspartate and glutamate metabolism"
+      assert_equal(expected, @obj.name)
+    end
+
+    def test_description
+      assert_equal("", @obj.description)
+    end
+
+    def test_keggclass
+      expected = "Metabolism; Amino Acid Metabolism"
+      assert_equal(expected, @obj.keggclass)
+    end
+
+    def test_pathways_as_strings
+      expected = ["rn00250  Alanine, aspartate and glutamate metabolism"]
+      assert_equal(expected, @obj.pathways_as_strings)
+    end
+
+    def test_modules_as_strings
+      expected =
+        [ "M00017  Glutamate biosynthesis, oxoglutarate => glutamate (glutamate dehydrogenase) [PATH:rn00250]",
+          "M00018  Glutamine biosynthesis, glutamate => glutamine [PATH:rn00250]",
+          "M00019  Glutamate biosynthesis, oxoglutarete => glutamate (glutamate synthase) [PATH:rn00250]",
+          "M00021  Aspartate biosynthesis, oxaloacetate => aspartate [PATH:rn00250]",
+          "M00022  Asparagine biosynthesis, aspartate => asparagine [PATH:rn00250]",
+          "M00026  Alanine biosynthesis, pyruvate => alanine [PATH:rn00250]",
+          "M00038  Glutamine degradation, glutamine => glutamate + NH3 [PATH:rn00250]",
+          "M00040  GABA (gamma-Aminobutyrate) shunt [PATH:rn00250]",
+          "M00044  Aspartate degradation, aspartate => fumarate [PATH:rn00250]",
+          "M00045  Aspartate degradation, aspartate => oxaloacetate [PATH:rn00250]",
+          "M00046  Asparagine degradation, asparagine => aspartate +NH3 [PATH:rn00250]"
+        ]
+      assert_equal(expected, @obj.modules_as_strings)
+    end
+
+    def test_diseases_as_strings
+      expected = [ "H00074  Canavan disease (CD)",
+                   "H00185  Citrullinemia (CTLN)",
+                   "H00197  Adenylosuccinate lyase deficiency" ]
+      assert_equal(expected, @obj.diseases_as_strings)
+    end
+
+    def test_diseases_as_hash
+      expected = {
+        "H00197"=>"Adenylosuccinate lyase deficiency",
+        "H00074"=>"Canavan disease (CD)",
+        "H00185"=>"Citrullinemia (CTLN)"
+      }
+      assert_equal(expected, @obj.diseases_as_hash)
+    end
+
+    def test_dblinks_as_strings
+      expected = ["GO: 0006522 0006531 0006536"]
+      assert_equal(expected, @obj.dblinks_as_strings)
+    end
+
+    def test_orthologs_as_strings
+      assert_equal([], @obj.orthologs_as_strings)
+    end
+
+    def test_organism
+      assert_equal("", @obj.organism)
+    end
+
+    def test_genes_as_strings
+      assert_equal([], @obj.genes_as_strings)
+    end
+
+    def test_enzymes_as_strings
+      assert_equal([], @obj.enzymes_as_strings)
+    end
+
+    def test_reactions_as_strings
+      expected =
+        [ "R00093  L-glutamate:NAD+ oxidoreductase (transaminating)",
+          "R00114  L-Glutamate:NADP+ oxidoreductase (transaminating)",
+          "R00149  Carbon-dioxide:ammonia ligase (ADP-forming,carbamate-phosphorylating)",
+          "R00243  L-Glutamate:NAD+ oxidoreductase (deaminating)",
+          "R00248  L-Glutamate:NADP+ oxidoreductase (deaminating)",
+          "R00253  L-Glutamate:ammonia ligase (ADP-forming)",
+          "R00256  L-Glutamine amidohydrolase",
+          "R00258  L-Alanine:2-oxoglutarate aminotransferase",
+          "R00261  L-glutamate 1-carboxy-lyase (4-aminobutanoate-forming)",
+          "R00269  2-Oxoglutaramate amidohydrolase",
+          "R00348  2-Oxosuccinamate amidohydrolase",
+          "R00355  L-Aspartate:2-oxoglutarate aminotransferase",
+          "R00357  L-Aspartic acid:oxygen oxidoreductase (deaminating)",
+          "R00359  D-Aspartate:oxygen oxidoreductase (deaminating)",
+          "R00369  L-Alanine:glyoxylate aminotransferase",
+          "R00396  L-Alanine:NAD+ oxidoreductase (deaminating)",
+          "R00397  L-aspartate 4-carboxy-lyase (L-alanine-forming)",
+          "R00400  L-alanine:oxaloacetate aminotransferase",
+          "R00483  L-aspartate:ammonia ligase (AMP-forming)",
+          "R00484  N-Carbamoyl-L-aspartate amidohydrolase",
+          "R00485  L-Asparagine amidohydrolase",
+          "R00487  Acetyl-CoA:L-aspartate N-acetyltransferase",
+          "R00488  N-Acetyl-L-aspartate amidohydrolase",
+          "R00490  L-Aspartate ammonia-lyase",
+          "R00491  aspartate racemase",
+          "R00575  hydrogen-carbonate:L-glutamine amido-ligase (ADP-forming, carbamate-phosphorylating)",
+          "R00576  L-Glutamine:pyruvate aminotransferase",
+          "R00578  L-aspartate:L-glutamine amido-ligase (AMP-forming)",
+          "R00707  (S)-1-pyrroline-5-carboxylate:NAD+ oxidoreductase",
+          "R00708  (S)-1-pyrroline-5-carboxylate:NADP+ oxidoreductase",
+          "R00713  Succinate-semialdehyde:NAD+ oxidoreductase",
+          "R00714  Succinate-semialdehyde:NADP+ oxidoreductase",
+          "R00768  L-glutamine:D-fructose-6-phosphate isomerase (deaminating)",
+          "R01072  5-phosphoribosylamine:diphosphate phospho-alpha-D-ribosyltransferase (glutamate-amidating)",
+          "R01083  N6-(1,2-dicarboxyethyl)AMP AMP-lyase (fumarate-forming)",
+          "R01086  2-(Nomega-L-arginino)succinate arginine-lyase (fumarate-forming)",
+          "R01135  IMP:L-aspartate ligase (GDP-forming)",
+          "R01346  L-Asparagine:2-oxo-acid aminotransferase",
+          "R01397  carbamoyl-phosphate:L-aspartate carbamoyltransferase",
+          "R01648  4-Aminobutanoate:2-oxoglutarate aminotransferase",
+          "R01954  L-Citrulline:L-aspartate ligase (AMP-forming)"
+        ]
+      assert_equal(expected, @obj.reactions_as_strings)
+    end
+
+    def test_reactions_as_hash
+      expected = {
+        "R01648"=>"4-Aminobutanoate:2-oxoglutarate aminotransferase",
+        "R00485"=>"L-Asparagine amidohydrolase",
+        "R00397"=>"L-aspartate 4-carboxy-lyase (L-alanine-forming)",
+        "R00243"=>"L-Glutamate:NAD+ oxidoreductase (deaminating)",
+        "R01397"=>"carbamoyl-phosphate:L-aspartate carbamoyltransferase",
+        "R00707"=>"(S)-1-pyrroline-5-carboxylate:NAD+ oxidoreductase",
+        "R00575"=>
+        "hydrogen-carbonate:L-glutamine amido-ligase (ADP-forming, carbamate-phosphorylating)",
+        "R00487"=>"Acetyl-CoA:L-aspartate N-acetyltransferase",
+        "R00355"=>"L-Aspartate:2-oxoglutarate aminotransferase",
+        "R00256"=>"L-Glutamine amidohydrolase",
+        "R01135"=>"IMP:L-aspartate ligase (GDP-forming)",
+        "R00708"=>"(S)-1-pyrroline-5-carboxylate:NADP+ oxidoreductase",
+        "R00576"=>"L-Glutamine:pyruvate aminotransferase",
+        "R00488"=>"N-Acetyl-L-aspartate amidohydrolase",
+        "R00400"=>"L-alanine:oxaloacetate aminotransferase",
+        "R00114"=>"L-Glutamate:NADP+ oxidoreductase (transaminating)",
+        "R00093"=>"L-glutamate:NAD+ oxidoreductase (transaminating)",
+        "R00490"=>"L-Aspartate ammonia-lyase",
+        "R00357"=>"L-Aspartic acid:oxygen oxidoreductase (deaminating)",
+        "R00269"=>"2-Oxoglutaramate amidohydrolase",
+        "R00258"=>"L-Alanine:2-oxoglutarate aminotransferase",
+        "R01346"=>"L-Asparagine:2-oxo-acid aminotransferase",
+        "R01083"=>"N6-(1,2-dicarboxyethyl)AMP AMP-lyase (fumarate-forming)",
+        "R01072"=>
+        "5-phosphoribosylamine:diphosphate phospho-alpha-D-ribosyltransferase (glutamate-amidating)",
+        "R00578"=>"L-aspartate:L-glutamine amido-ligase (AMP-forming)",
+        "R00491"=>"aspartate racemase",
+        "R00369"=>"L-Alanine:glyoxylate aminotransferase",
+        "R00248"=>"L-Glutamate:NADP+ oxidoreductase (deaminating)",
+        "R00149"=>
+        "Carbon-dioxide:ammonia ligase (ADP-forming,carbamate-phosphorylating)",
+        "R00359"=>"D-Aspartate:oxygen oxidoreductase (deaminating)",
+        "R00348"=>"2-Oxosuccinamate amidohydrolase",
+        "R00261"=>"L-glutamate 1-carboxy-lyase (4-aminobutanoate-forming)",
+        "R01954"=>"L-Citrulline:L-aspartate ligase (AMP-forming)",
+        "R01086"=>"2-(Nomega-L-arginino)succinate arginine-lyase (fumarate-forming)",
+        "R00768"=>"L-glutamine:D-fructose-6-phosphate isomerase (deaminating)",
+        "R00713"=>"Succinate-semialdehyde:NAD+ oxidoreductase",
+        "R00483"=>"L-aspartate:ammonia ligase (AMP-forming)",
+        "R00714"=>"Succinate-semialdehyde:NADP+ oxidoreductase",
+        "R00484"=>"N-Carbamoyl-L-aspartate amidohydrolase",
+        "R00396"=>"L-Alanine:NAD+ oxidoreductase (deaminating)",
+        "R00253"=>"L-Glutamate:ammonia ligase (ADP-forming)"
+      }
+      assert_equal(expected, @obj.reactions_as_hash)
+    end
+
+    def test_compounds_as_strings
+      expected =
+        [ "C00014  NH3",
+          "C00022  Pyruvate",
+          "C00025  L-Glutamate",
+          "C00026  2-Oxoglutarate",
+          "C00036  Oxaloacetate",
+          "C00041  L-Alanine",
+          "C00042  Succinate",
+          "C00049  L-Aspartate",
+          "C00064  L-Glutamine",
+          "C00122  Fumarate",
+          "C00152  L-Asparagine",
+          "C00169  Carbamoyl phosphate",
+          "C00232  Succinate semialdehyde",
+          "C00334  4-Aminobutanoate",
+          "C00352  D-Glucosamine 6-phosphate",
+          "C00402  D-Aspartate",
+          "C00438  N-Carbamoyl-L-aspartate",
+          "C00940  2-Oxoglutaramate",
+          "C01042  N-Acetyl-L-aspartate",
+          "C02362  2-Oxosuccinamate",
+          "C03090  5-Phosphoribosylamine",
+          "C03406  N-(L-Arginino)succinate",
+          "C03794  N6-(1,2-Dicarboxyethyl)-AMP",
+          "C03912  (S)-1-Pyrroline-5-carboxylate"
+        ]
+      assert_equal(expected, @obj.compounds_as_strings)
+    end
+
+    def test_compounds_as_hash
+      expected = {
+        "C02362"=>"2-Oxosuccinamate",
+        "C01042"=>"N-Acetyl-L-aspartate",
+        "C00041"=>"L-Alanine",
+        "C03912"=>"(S)-1-Pyrroline-5-carboxylate",
+        "C03406"=>"N-(L-Arginino)succinate",
+        "C00438"=>"N-Carbamoyl-L-aspartate",
+        "C00152"=>"L-Asparagine",
+        "C00064"=>"L-Glutamine",
+        "C00042"=>"Succinate",
+        "C00352"=>"D-Glucosamine 6-phosphate",
+        "C00022"=>"Pyruvate",
+        "C03794"=>"N6-(1,2-Dicarboxyethyl)-AMP",
+        "C03090"=>"5-Phosphoribosylamine",
+        "C00232"=>"Succinate semialdehyde",
+        "C00122"=>"Fumarate",
+        "C00036"=>"Oxaloacetate",
+        "C00025"=>"L-Glutamate",
+        "C00014"=>"NH3",
+        "C00334"=>"4-Aminobutanoate",
+        "C00169"=>"Carbamoyl phosphate",
+        "C00026"=>"2-Oxoglutarate",
+        "C00940"=>"2-Oxoglutaramate",
+        "C00049"=>"L-Aspartate",
+        "C00402"=>"D-Aspartate"
+      }
+      assert_equal(expected, @obj.compounds_as_hash)
+    end
+
+    def test_rel_pathways_as_strings
+      expected =
+        [ "rn00010  Glycolysis / Gluconeogenesis",
+          "rn00020  Citrate cycle (TCA cycle)",
+          "rn00230  Purine metabolism",
+          "rn00240  Pyrimidine metabolism",
+          "rn00253  Tetracycline biosynthesis",
+          "rn00260  Glycine, serine and threonine metabolism",
+          "rn00300  Lysine biosynthesis",
+          "rn00330  Arginine and proline metabolism",
+          "rn00340  Histidine metabolism",
+          "rn00410  beta-Alanine metabolism",
+          "rn00460  Cyanoamino acid metabolism",
+          "rn00471  D-Glutamine and D-glutamate metabolism",
+          "rn00473  D-Alanine metabolism",
+          "rn00480  Glutathione metabolism",
+          "rn00650  Butanoate metabolism",
+          "rn00660  C5-Branched dibasic acid metabolism",
+          "rn00760  Nicotinate and nicotinamide metabolism",
+          "rn00770  Pantothenate and CoA biosynthesis",
+          "rn00860  Porphyrin and chlorophyll metabolism",
+          "rn00910  Nitrogen metabolism"
+        ]
+      assert_equal(expected, @obj.rel_pathways_as_strings)
+    end
+
+    def test_rel_pathways_as_hash
+      expected = {
+        "rn00770"=>"Pantothenate and CoA biosynthesis",
+        "rn00660"=>"C5-Branched dibasic acid metabolism",
+        "rn00473"=>"D-Alanine metabolism",
+        "rn00330"=>"Arginine and proline metabolism",
+        "rn00253"=>"Tetracycline biosynthesis",
+        "rn00760"=>"Nicotinate and nicotinamide metabolism",
+        "rn00650"=>"Butanoate metabolism",
+        "rn00860"=>"Porphyrin and chlorophyll metabolism",
+        "rn00410"=>"beta-Alanine metabolism",
+        "rn00300"=>"Lysine biosynthesis",
+        "rn00480"=>"Glutathione metabolism",
+        "rn00260"=>"Glycine, serine and threonine metabolism",
+        "rn00910"=>"Nitrogen metabolism",
+        "rn00471"=>"D-Glutamine and D-glutamate metabolism",
+        "rn00460"=>"Cyanoamino acid metabolism",
+        "rn00240"=>"Pyrimidine metabolism",
+        "rn00020"=>"Citrate cycle (TCA cycle)",
+        "rn00340"=>"Histidine metabolism",
+        "rn00230"=>"Purine metabolism",
+        "rn00010"=>"Glycolysis / Gluconeogenesis"}
+      assert_equal(expected, @obj.rel_pathways_as_hash)
+    end
+
+    def test_ko_pathway
+      assert_equal("ko00250", @obj.ko_pathway)
+    end
+
+  end #class TestBioKeggPathway_rn00250
+
+  class TestBioKEGGPATHWAY_ec00072 < Test::Unit::TestCase
+
+    def setup
+      filename = File.join(BioRubyTestDataPath, 'KEGG', 'ec00072.pathway')
+      @obj = Bio::KEGG::PATHWAY.new(File.read(filename))
+    end
+
+    def test_dblinks_as_hash
+      assert_equal({}, @obj.dblinks_as_hash)
+    end
+
+    def test_pathways_as_hash
+      expected = {"ec00072"=>"Synthesis and degradation of ketone bodies"}
+      assert_equal(expected, @obj.pathways_as_hash)
+    end
+
+    def test_orthologs_as_hash
+      assert_equal({}, @obj.orthologs_as_hash)
+    end
+
+    def test_genes_as_hash
+      assert_equal({}, @obj.genes_as_hash)
+    end
+
+    def test_references
+      assert_equal([], @obj.references)
+    end
+
+    def test_modules_as_hash
+      expected = { "M00177" =>
+        "Ketone body biosynthesis, acetyl-CoA => acetoacetate/3-hydroxybutyrate/acetone [PATH:ec00072]" }
+      assert_equal(expected, @obj.modules_as_hash)
+    end
+
+    def test_new
+      assert_kind_of(Bio::KEGG::PATHWAY, @obj)
+    end
+
+    def test_entry_id
+      assert_equal("ec00072", @obj.entry_id)
+    end
+
+    def test_name
+      expected = "Synthesis and degradation of ketone bodies"
+      assert_equal(expected, @obj.name)
+    end
+
+    def test_description
+      assert_equal("", @obj.description)
+    end
+
+    def test_keggclass
+      expected = "Metabolism; Lipid Metabolism"
+      assert_equal(expected, @obj.keggclass)
+    end
+
+    def test_pathways_as_strings
+      expected = ["ec00072  Synthesis and degradation of ketone bodies"]
+      assert_equal(expected, @obj.pathways_as_strings)
+    end
+
+    def test_modules_as_strings
+      expected = ["M00177  Ketone body biosynthesis, acetyl-CoA => acetoacetate/3-hydroxybutyrate/acetone [PATH:ec00072]"]
+      assert_equal(expected, @obj.modules_as_strings)
+    end
+
+    def test_diseases_as_strings
+      assert_equal([], @obj.diseases_as_strings)
+    end
+
+    def test_diseases_as_hash
+      assert_equal({}, @obj.diseases_as_hash)
+    end
+
+    def test_dblinks_as_strings
+      assert_equal([], @obj.dblinks_as_strings)
+    end
+
+    def test_orthologs_as_strings
+      assert_equal([], @obj.orthologs_as_strings)
+    end
+
+    def test_organism
+      assert_equal("", @obj.organism)
+    end
+
+    def test_genes_as_strings
+      assert_equal([], @obj.genes_as_strings)
+    end
+
+    def test_enzymes_as_strings
+      expected = [ "1.1.1.30", "2.3.1.9", "2.3.3.10", "2.8.3.5",
+                   "4.1.1.4", "4.1.3.4" ]
+      assert_equal(expected, @obj.enzymes_as_strings)
+    end
+
+    def test_reactions_as_strings
+      assert_equal([], @obj.reactions_as_strings)
+    end
+
+    def test_reactions_as_hash
+      assert_equal({}, @obj.reactions_as_hash)
+    end
+
+    def test_compounds_as_strings
+      expected =
+        [ "C00024  Acetyl-CoA",
+          "C00164  Acetoacetate",
+          "C00207  Acetone",
+          "C00332  Acetoacetyl-CoA",
+          "C00356  (S)-3-Hydroxy-3-methylglutaryl-CoA",
+          "C01089  (R)-3-Hydroxybutanoate"
+        ]
+      assert_equal(expected, @obj.compounds_as_strings)
+    end
+
+    def test_compounds_as_hash
+      expected = {
+        "C00207"=>"Acetone",
+        "C00164"=>"Acetoacetate",
+        "C01089"=>"(R)-3-Hydroxybutanoate",
+        "C00332"=>"Acetoacetyl-CoA",
+        "C00024"=>"Acetyl-CoA",
+        "C00356"=>"(S)-3-Hydroxy-3-methylglutaryl-CoA"
+      }
+      assert_equal(expected, @obj.compounds_as_hash)
+    end
+
+    def test_rel_pathways_as_strings
+      expected =
+        [ "ec00010  Glycolysis / Gluconeogenesis",
+          "ec00071  Fatty acid metabolism",
+          "ec00620  Pyruvate metabolism",
+          "ec00650  Butanoate metabolism"
+        ]
+      assert_equal(expected, @obj.rel_pathways_as_strings)
+    end
+
+    def test_rel_pathways_as_hash
+      expected = {
+        "ec00620"=>"Pyruvate metabolism",
+        "ec00071"=>"Fatty acid metabolism",
+        "ec00010"=>"Glycolysis / Gluconeogenesis",
+        "ec00650"=>"Butanoate metabolism"
+      }
+      assert_equal(expected, @obj.rel_pathways_as_hash)
+    end
+
+    def test_ko_pathway
+      assert_equal("ko00072", @obj.ko_pathway)
+    end
+
+  end #class TestBioKEGGPATHWAY_ec00072
+
+  class TestBioKEGGPATHWAY_hsa00790 < Test::Unit::TestCase
+
+    def setup
+      filename = File.join(BioRubyTestDataPath, 'KEGG', 'hsa00790.pathway')
+      @obj = Bio::KEGG::PATHWAY.new(File.read(filename))
+    end
+
+    def test_dblinks_as_hash
+      assert_equal({"GO"=>["0046656"]}, @obj.dblinks_as_hash)
+    end
+
+    def test_pathways_as_hash
+      expected = {"hsa00790"=>"Folate biosynthesis"}
+      assert_equal(expected, @obj.pathways_as_hash)
+    end
+
+    def test_orthologs_as_hash
+      assert_equal({}, @obj.orthologs_as_hash)
+    end
+
+    def test_genes_as_hash
+      expected = {
+        "248"  => "ALPI, IAP [KO:K01077] [EC:3.1.3.1]",
+        "6697" => "SPR, SDR38C1 [KO:K00072] [EC:1.1.1.153]",
+        "249"  =>
+        "ALPL, AP-TNAP, APTNAP, FLJ40094, FLJ93059, HOPS, MGC161443, MGC167935, TNAP, TNSALP [KO:K01077] [EC:3.1.3.1]",
+        "2356" => "FPGS [KO:K01930] [EC:6.3.2.17]",
+        "250"  => "ALPP, ALP, FLJ61142, PALP, PLAP [KO:K01077] [EC:3.1.3.1]",
+        "1719" => "DHFR, DHFRP1, DYR [KO:K00287] [EC:1.5.1.3]",
+        "251"  => "ALPPL2, ALPG, ALPPL, GCAP [KO:K01077] [EC:3.1.3.1]",
+        "2643" =>
+        "GCH1, DYT14, DYT5, DYT5a, GCH, GTP-CH-1, GTPCH1, HPABH4B [KO:K01495] [EC:3.5.4.16]",
+        "8836" => "GGH, GH [KO:K01307] [EC:3.4.19.9]",
+        "5860" =>
+        "QDPR, DHPR, FLJ42391, PKU2, SDR33C1 [KO:K00357] [EC:1.5.1.34]",
+        "5805" => "PTS, FLJ97081, PTPS [KO:K01737] [EC:4.2.3.12]"
+      }
+      assert_equal(expected, @obj.genes_as_hash)
+    end
+
+    def test_references
+      assert_equal([], @obj.references)
+    end
+
+    def test_modules_as_hash
+      expected = {
+        "M00251"=>"Folate biosynthesis, GTP => THF [PATH:hsa00790]",
+        "M00304"=>"Methanogenesis [PATH:hsa00790]"
+      }
+      assert_equal(expected, @obj.modules_as_hash)
+    end
+
+    def test_new
+      assert_instance_of(Bio::KEGG::PATHWAY, @obj)
+    end
+
+    def test_entry_id
+      assert_equal("hsa00790", @obj.entry_id)
+    end
+
+    def test_name
+      expected = "Folate biosynthesis - Homo sapiens (human)"
+      assert_equal(expected, @obj.name)
+    end
+
+    def test_description
+      assert_equal("", @obj.description)
+    end
+
+    def test_keggclass
+      expected = "Metabolism; Metabolism of Cofactors and Vitamins"
+      assert_equal(expected, @obj.keggclass)
+    end
+
+    def test_pathways_as_strings
+      expected = ["hsa00790  Folate biosynthesis"]
+      assert_equal(expected, @obj.pathways_as_strings)
+    end
+
+    def test_modules_as_strings
+      expected = ["M00251  Folate biosynthesis, GTP => THF [PATH:hsa00790]",
+ "M00304  Methanogenesis [PATH:hsa00790]"]
+      assert_equal(expected, @obj.modules_as_strings)
+    end
+
+    def test_diseases_as_strings
+      expected = [ "H00167  Phenylketonuria (PKU)",
+                   "H00213  Hypophosphatasia" ]
+      assert_equal(expected, @obj.diseases_as_strings)
+    end
+
+    def test_diseases_as_hash
+      expected = {
+        "H00167"=>"Phenylketonuria (PKU)",
+        "H00213"=>"Hypophosphatasia"
+      }
+      assert_equal(expected, @obj.diseases_as_hash)
+    end
+
+    def test_dblinks_as_strings
+      assert_equal(["GO: 0046656"], @obj.dblinks_as_strings)
+    end
+
+    def test_orthologs_as_strings
+      assert_equal([], @obj.orthologs_as_strings)
+    end
+
+    def test_organism
+      expected = "Homo sapiens (human) [GN:hsa]"
+      assert_equal(expected, @obj.organism)
+    end
+
+    def test_genes_as_strings
+      expected =
+        [ "2643  GCH1, DYT14, DYT5, DYT5a, GCH, GTP-CH-1, GTPCH1, HPABH4B [KO:K01495] [EC:3.5.4.16]",
+          "248  ALPI, IAP [KO:K01077] [EC:3.1.3.1]",
+          "249  ALPL, AP-TNAP, APTNAP, FLJ40094, FLJ93059, HOPS, MGC161443, MGC167935, TNAP, TNSALP [KO:K01077] [EC:3.1.3.1]",
+          "250  ALPP, ALP, FLJ61142, PALP, PLAP [KO:K01077] [EC:3.1.3.1]",
+          "251  ALPPL2, ALPG, ALPPL, GCAP [KO:K01077] [EC:3.1.3.1]",
+          "1719  DHFR, DHFRP1, DYR [KO:K00287] [EC:1.5.1.3]",
+          "2356  FPGS [KO:K01930] [EC:6.3.2.17]",
+          "8836  GGH, GH [KO:K01307] [EC:3.4.19.9]",
+          "5805  PTS, FLJ97081, PTPS [KO:K01737] [EC:4.2.3.12]",
+          "6697  SPR, SDR38C1 [KO:K00072] [EC:1.1.1.153]",
+          "5860  QDPR, DHPR, FLJ42391, PKU2, SDR33C1 [KO:K00357] [EC:1.5.1.34]"
+        ]
+      assert_equal(expected, @obj.genes_as_strings)
+    end
+
+    def test_enzymes_as_strings
+      assert_equal([], @obj.enzymes_as_strings)
+    end
+
+    def test_reactions_as_strings
+      assert_equal([], @obj.reactions_as_strings)
+    end
+
+    def test_reactions_as_hash
+      assert_equal({}, @obj.reactions_as_hash)
+    end
+
+    def test_compounds_as_strings
+      expected =
+        [ "C00044  GTP",
+          "C00101  Tetrahydrofolate",
+          "C00251  Chorismate",
+          "C00266  Glycolaldehyde",
+          "C00268  Dihydrobiopterin",
+          "C00272  Tetrahydrobiopterin",
+          "C00415  Dihydrofolate",
+          "C00504  Folate",
+          "C00568  4-Aminobenzoate",
+          "C00921  Dihydropteroate",
+          "C01217  5,6,7,8-Tetrahydromethanopterin",
+          "C01300  2-Amino-4-hydroxy-6-hydroxymethyl-7,8-dihydropteridine",
+          "C03541  Tetrahydrofolyl-[Glu](n)",
+          "C03684  6-Pyruvoyltetrahydropterin",
+          "C04244  6-Lactoyl-5,6,7,8-tetrahydropterin",
+          "C04807  2-Amino-7,8-dihydro-4-hydroxy-6-(diphosphooxymethyl)pteridine",
+          "C04874  2-Amino-4-hydroxy-6-(D-erythro-1,2,3-trihydroxypropyl)-7,8-dihydropteridine",
+          "C04895  2-Amino-4-hydroxy-6-(erythro-1,2,3-trihydroxypropyl)dihydropteridine triphosphate",
+          "C05922  Formamidopyrimidine nucleoside triphosphate",
+          "C05923  2,5-Diaminopyrimidine nucleoside triphosphate",
+          "C05924  Molybdopterin",
+          "C05925  Dihydroneopterin phosphate",
+          "C05926  Neopterin",
+          "C05927  7,8-Dihydromethanopterin",
+          "C06148  2,5-Diamino-6-(5'-triphosphoryl-3',4'-trihydroxy-2'-oxopentyl)-amino-4-oxopyrimidine",
+          "C06149  6-(3'-Triphosphoryl-1'-methylglyceryl)-7-methyl-7,8-dihydrobiopterin",
+          "C09332  Tetrahydrofolyl-[Glu](2)",
+          "C11355  4-Amino-4-deoxychorismate"
+        ]
+      assert_equal(expected, @obj.compounds_as_strings)
+    end
+
+    def test_compounds_as_hash
+      expected = {
+        "C05925"=>"Dihydroneopterin phosphate",
+        "C04244"=>"6-Lactoyl-5,6,7,8-tetrahydropterin",
+        "C01217"=>"5,6,7,8-Tetrahydromethanopterin",
+        "C00568"=>"4-Aminobenzoate",
+        "C05926"=>"Neopterin",
+        "C00921"=>"Dihydropteroate",
+        "C00415"=>"Dihydrofolate",
+        "C00272"=>"Tetrahydrobiopterin",
+        "C05927"=>"7,8-Dihydromethanopterin",
+        "C04895"=>
+        "2-Amino-4-hydroxy-6-(erythro-1,2,3-trihydroxypropyl)dihydropteridine triphosphate",
+        "C04807"=>"2-Amino-7,8-dihydro-4-hydroxy-6-(diphosphooxymethyl)pteridine",
+        "C00504"=>"Folate",
+        "C00251"=>"Chorismate",
+        "C06148"=>
+        "2,5-Diamino-6-(5'-triphosphoryl-3',4'-trihydroxy-2'-oxopentyl)-amino-4-oxopyrimidine",
+        "C04874"=>
+        "2-Amino-4-hydroxy-6-(D-erythro-1,2,3-trihydroxypropyl)-7,8-dihydropteridine",
+        "C06149"=>
+        "6-(3'-Triphosphoryl-1'-methylglyceryl)-7-methyl-7,8-dihydrobiopterin",
+        "C00044"=>"GTP",
+        "C03684"=>"6-Pyruvoyltetrahydropterin",
+        "C03541"=>"Tetrahydrofolyl-[Glu](n)",
+        "C01300"=>"2-Amino-4-hydroxy-6-hydroxymethyl-7,8-dihydropteridine",
+        "C00266"=>"Glycolaldehyde",
+        "C00101"=>"Tetrahydrofolate",
+        "C05922"=>"Formamidopyrimidine nucleoside triphosphate",
+        "C00268"=>"Dihydrobiopterin",
+        "C11355"=>"4-Amino-4-deoxychorismate",
+        "C05923"=>"2,5-Diaminopyrimidine nucleoside triphosphate",
+        "C09332"=>"Tetrahydrofolyl-[Glu](2)",
+        "C05924"=>"Molybdopterin"
+      }
+      assert_equal(expected, @obj.compounds_as_hash)
+    end
+
+    def test_rel_pathways_as_strings
+      expected =
+        [ "hsa00230  Purine metabolism",
+          "hsa00400  Phenylalanine, tyrosine and tryptophan biosynthesis",
+          "hsa00670  One carbon pool by folate",
+          "hsa00680  Methane metabolism"
+        ]
+      assert_equal(expected, @obj.rel_pathways_as_strings)
+    end
+
+    def test_rel_pathways_as_hash
+      expected = {
+        "hsa00680"=>"Methane metabolism",
+        "hsa00670"=>"One carbon pool by folate",
+        "hsa00230"=>"Purine metabolism",
+        "hsa00400"=>"Phenylalanine, tyrosine and tryptophan biosynthesis"
+      }
+      assert_equal(expected, @obj.rel_pathways_as_hash)
+    end
+
+    def test_ko_pathway
+      assert_equal("ko00790", @obj.ko_pathway)
+    end
+
+  end #class TestBioKEGGPATHWAY_hsa00790
+
+  class TestBioKEGGPATHWAY_ko00312 < Test::Unit::TestCase
+
+    def setup
+      filename = File.join(BioRubyTestDataPath, 'KEGG', 'ko00312.pathway')
+      @obj = Bio::KEGG::PATHWAY.new(File.read(filename))
+    end
+
+    def test_dblinks_as_hash
+      assert_equal({}, @obj.dblinks_as_hash)
+    end
+
+    def test_pathways_as_hash
+      expected = {"ko00312"=>"beta-Lactam resistance"}
+      assert_equal(expected, @obj.pathways_as_hash)
+    end
+
+    def test_orthologs_as_hash
+      expected = {
+        "K02545"=>"penicillin-binding protein 2 prime",
+        "K02172"=>"bla regulator protein blaR1",
+        "K02546"=>"methicillin resistance regulatory protein",
+        "K02547"=>"methicillin resistance protein",
+        "K02352"=>"drp35",
+        "K01467"=>"beta-lactamase [EC:3.5.2.6]",
+        "K02171"=>"penicillinase repressor"
+      }
+      assert_equal(expected, @obj.orthologs_as_hash)
+    end
+
+    def test_genes_as_hash
+      assert_equal({}, @obj.genes_as_hash)
+    end
+
+    def test_references
+      assert_equal([], @obj.references)
+    end
+
+    def test_modules_as_hash
+      assert_equal({}, @obj.modules_as_hash)
+    end
+
+    def test_new
+      assert_instance_of(Bio::KEGG::PATHWAY, @obj)
+    end
+
+    def test_entry_id
+      assert_equal("ko00312", @obj.entry_id)
+    end
+
+    def test_name
+      assert_equal("beta-Lactam resistance", @obj.name)
+    end
+
+    def test_description
+      assert_equal("", @obj.description)
+    end
+
+    def test_keggclass
+      expected = "Metabolism; Biosynthesis of Other Secondary Metabolites"
+      assert_equal(expected, @obj.keggclass)
+    end
+
+    def test_pathways_as_strings
+      expected = ["ko00312  beta-Lactam resistance"]
+      assert_equal(expected, @obj.pathways_as_strings)
+    end
+
+    def test_modules_as_strings
+      assert_equal([], @obj.modules_as_strings)
+    end
+
+    def test_diseases_as_strings
+      assert_equal([], @obj.diseases_as_strings)
+    end
+
+    def test_diseases_as_hash
+      assert_equal({}, @obj.diseases_as_hash)
+    end
+
+    def test_dblinks_as_strings
+      assert_equal([], @obj.dblinks_as_strings)
+    end
+
+    def test_orthologs_as_strings
+      expected =
+        [ "K02172  bla regulator protein blaR1",
+          "K02171  penicillinase repressor",
+          "K01467  beta-lactamase [EC:3.5.2.6]",
+          "K02352  drp35",
+          "K02547  methicillin resistance protein",
+          "K02546  methicillin resistance regulatory protein",
+          "K02545  penicillin-binding protein 2 prime"
+        ]
+      assert_equal(expected, @obj.orthologs_as_strings)
+    end
+
+    def test_organism
+      assert_equal("", @obj.organism)
+    end
+
+    def test_genes_as_strings
+      assert_equal([], @obj.genes_as_strings)
+    end
+
+    def test_enzymes_as_strings
+      assert_equal([], @obj.enzymes_as_strings)
+    end
+
+    def test_reactions_as_strings
+      assert_equal([], @obj.reactions_as_strings)
+    end
+
+    def test_reactions_as_hash
+      assert_equal({}, @obj.reactions_as_hash)
+    end
+
+    def test_compounds_as_strings
+      expected = ["C00039  DNA", "C03438  beta-Lactam antibiotics"]
+      assert_equal(expected, @obj.compounds_as_strings)
+    end
+
+    def test_compounds_as_hash
+      expected = {"C03438"=>"beta-Lactam antibiotics", "C00039"=>"DNA"}
+      assert_equal(expected, @obj.compounds_as_hash)
+    end
+
+    def test_rel_pathways_as_strings
+      expected = ["ko00311  Penicillin and cephalosporin biosynthesis"]
+      assert_equal(expected, @obj.rel_pathways_as_strings)
+    end
+
+    def test_rel_pathways_as_hash
+      expected = {"ko00311"=>"Penicillin and cephalosporin biosynthesis"}
+      assert_equal(expected, @obj.rel_pathways_as_hash)
+    end
+
+    def test_ko_pathway
+      assert_equal("", @obj.ko_pathway)
+    end
+
+  end #class TestBioKEGGPATHWAY_ko00312
+
+end #module Bio