bel_parser 1.0.0.alpha.1 → 1.0.0.alpha.2

data/lib/bel_parser/language/{version1 → version2_0}/functions/products.rb

@@ -1,11 +1,11 @@
-require_relative '../../version1'
+require_relative '../../version2_0'
 require_relative '../../function'
 require_relative '../../signature'
-require_relative '../../semantic_ast'
+require_relative '../../semantics'
 
 module BELParser
   module Language
-    module Version1
+    module Version2_0
       module Functions
         # Products: Denotes the products of a reaction
         class Products
@@ -13,7 +13,7 @@ module BELParser
 
           SHORT       = :products
           LONG        = :products
-          RETURN_TYPE = BELParser::Language::Version1::ReturnTypes::Products
+          RETURN_TYPE = BELParser::Language::Version2_0::ReturnTypes::Products
           DESCRIPTION = 'Denotes the products of a reaction'.freeze
 
           def self.short
@@ -52,7 +52,7 @@ module BELParser
                   term(
                     function(
                       identifier(
-                        return_type_of(BELParser::Language::Version1::ReturnTypes::Abundance))))))              
+                        return_type_of(BELParser::Language::Version2_0::ReturnTypes::Abundance))))))              
               end
               private_constant :AST
 

data/lib/bel_parser/language/{version2 → version2_0}/functions/protein_abundance.rb

@@ -1,11 +1,11 @@
-require_relative '../../version1'
+require_relative '../../version2_0'
 require_relative '../../function'
 require_relative '../../signature'
-require_relative '../../semantic_ast'
+require_relative '../../semantics'
 
 module BELParser
   module Language
-    module Version2
+    module Version2_0
       module Functions
         # ProteinAbundance: Denotes the abundance of a protein
         class ProteinAbundance
@@ -13,7 +13,7 @@ module BELParser
 
           SHORT       = :p
           LONG        = :proteinAbundance
-          RETURN_TYPE = BELParser::Language::Version2::ReturnTypes::ProteinAbundance
+          RETURN_TYPE = BELParser::Language::Version2_0::ReturnTypes::ProteinAbundance
           DESCRIPTION = 'Denotes the abundance of a protein'.freeze
 
           def self.short
@@ -97,7 +97,7 @@ module BELParser
                   term(
                     function(
                       identifier(
-                        return_type_of(BELParser::Language::Version2::ReturnTypes::Fragment))))))              
+                        return_type_of(BELParser::Language::Version2_0::ReturnTypes::Fragment))))))              
               end
               private_constant :AST
 
@@ -137,7 +137,7 @@ module BELParser
                   term(
                     function(
                       identifier(
-                        return_type_of(BELParser::Language::Version2::ReturnTypes::Fusion))))))              
+                        return_type_of(BELParser::Language::Version2_0::ReturnTypes::Fusion))))))              
               end
               private_constant :AST
 
@@ -177,7 +177,7 @@ module BELParser
                   term(
                     function(
                       identifier(
-                        return_type_of(BELParser::Language::Version2::ReturnTypes::Location))))))              
+                        return_type_of(BELParser::Language::Version2_0::ReturnTypes::Location))))))              
               end
               private_constant :AST
 
@@ -217,7 +217,7 @@ module BELParser
                   term(
                     function(
                       identifier(
-                        return_type_of(BELParser::Language::Version2::ReturnTypes::ProteinModification))))))              
+                        return_type_of(BELParser::Language::Version2_0::ReturnTypes::ProteinModification))))))              
               end
               private_constant :AST
 
@@ -257,7 +257,7 @@ module BELParser
                   term(
                     function(
                       identifier(
-                        return_type_of(BELParser::Language::Version2::ReturnTypes::Variant))))))              
+                        return_type_of(BELParser::Language::Version2_0::ReturnTypes::Variant))))))              
               end
               private_constant :AST
 

data/lib/bel_parser/language/{version2 → version2_0}/functions/protein_modification.rb

@@ -1,11 +1,11 @@
-require_relative '../../version1'
+require_relative '../../version2_0'
 require_relative '../../function'
 require_relative '../../signature'
-require_relative '../../semantic_ast'
+require_relative '../../semantics'
 
 module BELParser
   module Language
-    module Version2
+    module Version2_0
       module Functions
         # ProteinModification: Denotes a covalently modified protein abundance
         class ProteinModification
@@ -13,7 +13,7 @@ module BELParser
 
           SHORT       = :pmod
           LONG        = :proteinModification
-          RETURN_TYPE = BELParser::Language::Version2::ReturnTypes::ProteinModification
+          RETURN_TYPE = BELParser::Language::Version2_0::ReturnTypes::ProteinModification
           DESCRIPTION = 'Denotes a covalently modified protein abundance'.freeze
 
           def self.short
@@ -38,7 +38,7 @@ module BELParser
 
           module Signatures
   
-            class ProteinModificationWithType
+            class ProteinModificationWithTypeSignature
               extend BELParser::Language::Signature
 
               private_class_method :new
@@ -71,7 +71,7 @@ module BELParser
               end
             end
   
-            class ProteinModificationWithTypeAmino
+            class ProteinModificationWithTypeAminoSignature
               extend BELParser::Language::Signature
 
               private_class_method :new
@@ -110,7 +110,7 @@ module BELParser
               end
             end
   
-            class ProteinModificationWithTypeAminoPosition
+            class ProteinModificationWithTypeAminoPositionSignature
               extend BELParser::Language::Signature
 
               private_class_method :new

data/lib/bel_parser/language/{version1 → version2_0}/functions/reactants.rb

@@ -1,11 +1,11 @@
-require_relative '../../version1'
+require_relative '../../version2_0'
 require_relative '../../function'
 require_relative '../../signature'
-require_relative '../../semantic_ast'
+require_relative '../../semantics'
 
 module BELParser
   module Language
-    module Version1
+    module Version2_0
       module Functions
         # Reactants: Denotes the reactants of a reaction
         class Reactants
@@ -13,7 +13,7 @@ module BELParser
 
           SHORT       = :reactants
           LONG        = :reactants
-          RETURN_TYPE = BELParser::Language::Version1::ReturnTypes::Reactants
+          RETURN_TYPE = BELParser::Language::Version2_0::ReturnTypes::Reactants
           DESCRIPTION = 'Denotes the reactants of a reaction'.freeze
 
           def self.short
@@ -52,7 +52,7 @@ module BELParser
                   term(
                     function(
                       identifier(
-                        return_type_of(BELParser::Language::Version1::ReturnTypes::Abundance))))))              
+                        return_type_of(BELParser::Language::Version2_0::ReturnTypes::Abundance))))))              
               end
               private_constant :AST
 

data/lib/bel_parser/language/{version2 → version2_0}/functions/reaction.rb

@@ -1,11 +1,11 @@
-require_relative '../../version1'
+require_relative '../../version2_0'
 require_relative '../../function'
 require_relative '../../signature'
-require_relative '../../semantic_ast'
+require_relative '../../semantics'
 
 module BELParser
   module Language
-    module Version2
+    module Version2_0
       module Functions
         # Reaction: Denotes the frequency or abundance of events in a reaction
         class Reaction
@@ -13,7 +13,7 @@ module BELParser
 
           SHORT       = :rxn
           LONG        = :reaction
-          RETURN_TYPE = BELParser::Language::Version2::ReturnTypes::Abundance
+          RETURN_TYPE = BELParser::Language::Version2_0::ReturnTypes::Abundance
           DESCRIPTION = 'Denotes the frequency or abundance of events in a reaction'.freeze
 
           def self.short
@@ -52,12 +52,12 @@ module BELParser
                   term(
                     function(
                       identifier(
-                        return_type_of(BELParser::Language::Version2::ReturnTypes::Reactants))))),
+                        return_type_of(BELParser::Language::Version2_0::ReturnTypes::Reactants))))),
                 argument(
                   term(
                     function(
                       identifier(
-                        return_type_of(BELParser::Language::Version2::ReturnTypes::Products))))))              
+                        return_type_of(BELParser::Language::Version2_0::ReturnTypes::Products))))))              
               end
               private_constant :AST
 

data/lib/bel_parser/language/{version2 → version2_0}/functions/rna_abundance.rb

@@ -1,11 +1,11 @@
-require_relative '../../version1'
+require_relative '../../version2_0'
 require_relative '../../function'
 require_relative '../../signature'
-require_relative '../../semantic_ast'
+require_relative '../../semantics'
 
 module BELParser
   module Language
-    module Version2
+    module Version2_0
       module Functions
         # RNAAbundance: Denotes the abundance of a gene
         class RNAAbundance
@@ -13,7 +13,7 @@ module BELParser
 
           SHORT       = :r
           LONG        = :rnaAbundance
-          RETURN_TYPE = BELParser::Language::Version2::ReturnTypes::GeneAbundance
+          RETURN_TYPE = BELParser::Language::Version2_0::ReturnTypes::GeneAbundance
           DESCRIPTION = 'Denotes the abundance of a gene'.freeze
 
           def self.short
@@ -38,7 +38,7 @@ module BELParser
 
           module Signatures
   
-            class RNAAbundance
+            class RNAAbundanceSignature
               extend BELParser::Language::Signature
 
               private_class_method :new
@@ -73,7 +73,7 @@ module BELParser
               end
             end
   
-            class RNAAbundanceWithFusion
+            class RNAAbundanceWithFusionSignature
               extend BELParser::Language::Signature
 
               private_class_method :new
@@ -87,7 +87,7 @@ module BELParser
                   term(
                     function(
                       identifier(
-                        return_type_of(BELParser::Language::Version2::ReturnTypes::Fusion))))))              
+                        return_type_of(BELParser::Language::Version2_0::ReturnTypes::Fusion))))))              
               end
               private_constant :AST
 
@@ -103,7 +103,7 @@ module BELParser
               end
             end
   
-            class RNAAbundanceWithLocation
+            class RNAAbundanceWithLocationSignature
               extend BELParser::Language::Signature
 
               private_class_method :new
@@ -127,7 +127,7 @@ module BELParser
                   term(
                     function(
                       identifier(
-                        return_type_of(BELParser::Language::Version2::ReturnTypes::Location))))))              
+                        return_type_of(BELParser::Language::Version2_0::ReturnTypes::Location))))))              
               end
               private_constant :AST
 
@@ -143,7 +143,7 @@ module BELParser
               end
             end
   
-            class RNAAbundanceWithVariant
+            class RNAAbundanceWithVariantSignature
               extend BELParser::Language::Signature
 
               private_class_method :new
@@ -167,7 +167,7 @@ module BELParser
                   term(
                     function(
                       identifier(
-                        return_type_of(BELParser::Language::Version2::ReturnTypes::Variant))))))              
+                        return_type_of(BELParser::Language::Version2_0::ReturnTypes::Variant))))))              
               end
               private_constant :AST
 

data/lib/bel_parser/language/{version2 → version2_0}/functions/to_location.rb

@@ -1,11 +1,11 @@
-require_relative '../../version1'
+require_relative '../../version2_0'
 require_relative '../../function'
 require_relative '../../signature'
-require_relative '../../semantic_ast'
+require_relative '../../semantics'
 
 module BELParser
   module Language
-    module Version2
+    module Version2_0
       module Functions
         # ToLocation: Denotes the to cellular location of the abundance.
         class ToLocation
@@ -13,7 +13,7 @@ module BELParser
 
           SHORT       = :toLoc
           LONG        = :toLocation
-          RETURN_TYPE = BELParser::Language::Version2::ReturnTypes::ToLocation
+          RETURN_TYPE = BELParser::Language::Version2_0::ReturnTypes::ToLocation
           DESCRIPTION = 'Denotes the to cellular location of the abundance.'.freeze
 
           def self.short

data/lib/bel_parser/language/{version2 → version2_0}/functions/translocation.rb

@@ -1,11 +1,11 @@
-require_relative '../../version1'
+require_relative '../../version2_0'
 require_relative '../../function'
 require_relative '../../signature'
-require_relative '../../semantic_ast'
+require_relative '../../semantics'
 
 module BELParser
   module Language
-    module Version2
+    module Version2_0
       module Functions
         # Translocation: Denotes the frequency or abundance of events in which members move between locations
         class Translocation
@@ -13,7 +13,7 @@ module BELParser
 
           SHORT       = :tloc
           LONG        = :translocation
-          RETURN_TYPE = BELParser::Language::Version2::ReturnTypes::Abundance
+          RETURN_TYPE = BELParser::Language::Version2_0::ReturnTypes::Abundance
           DESCRIPTION = 'Denotes the frequency or abundance of events in which members move between locations'.freeze
 
           def self.short
@@ -38,7 +38,7 @@ module BELParser
 
           module Signatures
   
-            class Translocation
+            class TranslocationSignature
               extend BELParser::Language::Signature
 
               private_class_method :new
@@ -52,17 +52,17 @@ module BELParser
                   term(
                     function(
                       identifier(
-                        return_type_of(BELParser::Language::Version2::ReturnTypes::Abundance))))),
+                        return_type_of(BELParser::Language::Version2_0::ReturnTypes::Abundance))))),
                 argument(
                   term(
                     function(
                       identifier(
-                        return_type_of(BELParser::Language::Version2::ReturnTypes::FromLocation))))),
+                        return_type_of(BELParser::Language::Version2_0::ReturnTypes::FromLocation))))),
                 argument(
                   term(
                     function(
                       identifier(
-                        return_type_of(BELParser::Language::Version2::ReturnTypes::ToLocation))))))              
+                        return_type_of(BELParser::Language::Version2_0::ReturnTypes::ToLocation))))))              
               end
               private_constant :AST
 

data/lib/bel_parser/language/{version2 → version2_0}/functions/variant.rb

@@ -1,11 +1,11 @@
-require_relative '../../version1'
+require_relative '../../version2_0'
 require_relative '../../function'
 require_relative '../../signature'
-require_relative '../../semantic_ast'
+require_relative '../../semantics'
 
 module BELParser
   module Language
-    module Version2
+    module Version2_0
       module Functions
         # Variant: Denotes a sequence variant of the specified abundance.
         class Variant
@@ -13,7 +13,7 @@ module BELParser
 
           SHORT       = :var
           LONG        = :variant
-          RETURN_TYPE = BELParser::Language::Version2::ReturnTypes::Variant
+          RETURN_TYPE = BELParser::Language::Version2_0::ReturnTypes::Variant
           DESCRIPTION = 'Denotes a sequence variant of the specified abundance.'.freeze
 
           def self.short

data/lib/bel_parser/language/version2_0/relationships/acts_in.rb

@@ -0,0 +1,31 @@
+require_relative '../../version2_0'
+require_relative '../../relationship'
+
+module BELParser
+  module Language
+    module Version2_0
+      module Relationships
+        # ActsIn:  +A actsIn f(A)+ -  This relationship links an abundance term to the activity term for the same abundance. This relationship is direct because it is a _self_ relationship, the abundance acts in its own activity. For protein abundance p(A) and its molecular activity kin(p(A), +p(A) actsIn kin(p(A))+. This relationship is introduced by the BEL Compiler and may not be used by statements in BEL documents.
+        class ActsIn
+          extend Relationship
+
+          SHORT       = :actsIn
+          LONG        = :actsIn
+          DESCRIPTION = ' +A actsIn f(A)+ -  This relationship links an abundance term to the activity term for the same abundance. This relationship is direct because it is a _self_ relationship, the abundance acts in its own activity. For protein abundance p(A) and its molecular activity kin(p(A), +p(A) actsIn kin(p(A))+. This relationship is introduced by the BEL Compiler and may not be used by statements in BEL documents.'.freeze
+
+          def self.short
+            SHORT
+          end
+
+          def self.long
+            LONG
+          end
+
+          def self.description
+            DESCRIPTION
+          end
+        end
+      end
+    end
+  end
+end

data/lib/bel_parser/language/version2_0/relationships/analogous.rb

@@ -0,0 +1,35 @@
+require_relative '../../version2_0'
+require_relative '../../relationship'
+
+module BELParser
+  module Language
+    module Version2_0
+      module Relationships
+        # Analogous:  +A analogous B+ -  For terms A and B, +A analogousTo B+ indicates that A and B represent abundances or molecular activities in different species which function in a similar manner.
+        class Analogous
+          extend Relationship
+
+          SHORT       = :analogous
+          LONG        = :analogous
+          DESCRIPTION = ' +A analogous B+ -  For terms A and B, +A analogousTo B+ indicates that A and B represent abundances or molecular activities in different species which function in a similar manner.'.freeze
+
+          def self.short
+            SHORT
+          end
+
+          def self.long
+            LONG
+          end
+
+          def self.description
+            DESCRIPTION
+          end
+
+          def self.deprecated?
+            true
+          end
+        end
+      end
+    end
+  end
+end

data/lib/bel_parser/language/version2_0/relationships/association.rb

@@ -0,0 +1,31 @@
+require_relative '../../version2_0'
+require_relative '../../relationship'
+
+module BELParser
+  module Language
+    module Version2_0
+      module Relationships
+        # Association:  +A -- B+ -  For terms A and B, +A association B+ or +A -- B+ indicates that A and B are associated in an unspecified manner. This relationship is used when not enough information about the association is available to describe it using more specific relationships, like increases or positiveCorrelation.
+        class Association
+          extend Relationship
+
+          SHORT       = :'--'
+          LONG        = :association
+          DESCRIPTION = ' +A -- B+ -  For terms A and B, +A association B+ or +A -- B+ indicates that A and B are associated in an unspecified manner. This relationship is used when not enough information about the association is available to describe it using more specific relationships, like increases or positiveCorrelation.'.freeze
+
+          def self.short
+            SHORT
+          end
+
+          def self.long
+            LONG
+          end
+
+          def self.description
+            DESCRIPTION
+          end
+        end
+      end
+    end
+  end
+end

data/lib/bel_parser/language/version2_0/relationships/biomarker_for.rb

@@ -0,0 +1,35 @@
+require_relative '../../version2_0'
+require_relative '../../relationship'
+
+module BELParser
+  module Language
+    module Version2_0
+      module Relationships
+        # BiomarkerFor:  +A biomarkerFor P+ -  For term A and process term P, +A biomarkerFor P+ indicates that changes in or detection of A is used in some way to be a biomarker for pathology or biological process P.
+        class BiomarkerFor
+          extend Relationship
+
+          SHORT       = :biomarkerFor
+          LONG        = :biomarkerFor
+          DESCRIPTION = ' +A biomarkerFor P+ -  For term A and process term P, +A biomarkerFor P+ indicates that changes in or detection of A is used in some way to be a biomarker for pathology or biological process P.'.freeze
+
+          def self.short
+            SHORT
+          end
+
+          def self.long
+            LONG
+          end
+
+          def self.description
+            DESCRIPTION
+          end
+
+          def self.deprecated?
+            true
+          end
+        end
+      end
+    end
+  end
+end

data/lib/bel_parser/language/version2_0/relationships/causes_no_change.rb

@@ -0,0 +1,31 @@
+require_relative '../../version2_0'
+require_relative '../../relationship'
+
+module BELParser
+  module Language
+    module Version2_0
+      module Relationships
+        # CausesNoChange:  +A causesNoChange B+ -  For terms A and B, +A causesNoChange B+ indicates that B was observed not to change in response to changes in A. Statements using this relationship correspond to cases where explicit measurement of B demonstrates lack of significant change, not for cases where the state of B is unknown.
+        class CausesNoChange
+          extend Relationship
+
+          SHORT       = :causesNoChange
+          LONG        = :causesNoChange
+          DESCRIPTION = ' +A causesNoChange B+ -  For terms A and B, +A causesNoChange B+ indicates that B was observed not to change in response to changes in A. Statements using this relationship correspond to cases where explicit measurement of B demonstrates lack of significant change, not for cases where the state of B is unknown.'.freeze
+
+          def self.short
+            SHORT
+          end
+
+          def self.long
+            LONG
+          end
+
+          def self.description
+            DESCRIPTION
+          end
+        end
+      end
+    end
+  end
+end

data/lib/bel_parser/language/version2_0/relationships/decreases.rb

@@ -0,0 +1,31 @@
+require_relative '../../version2_0'
+require_relative '../../relationship'
+
+module BELParser
+  module Language
+    module Version2_0
+      module Relationships
+        # Decreases:  +A -| B+ -  For terms A and B, +A decreases B or A -| B+ indicates that increases in A have been observed to cause decreases in B. +A decreases B+ also represents cases where decreases in A have been observed to cause increases in B, for example, in recording the results of gene deletion or other inhibition experiments. A is a BEL Term and B is either a BEL Term or a BEL Statement. The relationship does not indicate that the changes in A are either necessary for changes in B, nor does it indicate that changes in A are sufficient to cause changes in B.
+        class Decreases
+          extend Relationship
+
+          SHORT       = :'-|'
+          LONG        = :decreases
+          DESCRIPTION = ' +A -| B+ -  For terms A and B, +A decreases B or A -| B+ indicates that increases in A have been observed to cause decreases in B. +A decreases B+ also represents cases where decreases in A have been observed to cause increases in B, for example, in recording the results of gene deletion or other inhibition experiments. A is a BEL Term and B is either a BEL Term or a BEL Statement. The relationship does not indicate that the changes in A are either necessary for changes in B, nor does it indicate that changes in A are sufficient to cause changes in B.'.freeze
+
+          def self.short
+            SHORT
+          end
+
+          def self.long
+            LONG
+          end
+
+          def self.description
+            DESCRIPTION
+          end
+        end
+      end
+    end
+  end
+end

data/lib/bel_parser/language/version2_0/relationships/directly_decreases.rb

@@ -0,0 +1,31 @@
+require_relative '../../version2_0'
+require_relative '../../relationship'
+
+module BELParser
+  module Language
+    module Version2_0
+      module Relationships
+        # DirectlyDecreases:  +A =| B+ -  For terms A and B, +A directlyDecreases B or A =| B+ indicates A decreases B and that the mechanism of the causal relationship is based on physical interaction of entities related to A and B. This is a direct version of the decreases relationship.
+        class DirectlyDecreases
+          extend Relationship
+
+          SHORT       = :'=|'
+          LONG        = :directlyDecreases
+          DESCRIPTION = ' +A =| B+ -  For terms A and B, +A directlyDecreases B or A =| B+ indicates A decreases B and that the mechanism of the causal relationship is based on physical interaction of entities related to A and B. This is a direct version of the decreases relationship.'.freeze
+
+          def self.short
+            SHORT
+          end
+
+          def self.long
+            LONG
+          end
+
+          def self.description
+            DESCRIPTION
+          end
+        end
+      end
+    end
+  end
+end