bel_parser 1.0.0.alpha.7 → 1.0.0.alpha.8

data/lib/bel_parser/language/version1_0/functions/rna_abundance.rb

@@ -37,7 +37,7 @@ module BELParser
           end
 
           module Signatures
-  
+            # RNAAbundanceWithFusionSignature
             class RNAAbundanceWithFusionSignature
               extend BELParser::Language::Signature
 
@@ -45,24 +45,24 @@ module BELParser
 
               AST = BELParser::Language::Semantics::Builder.build do
                 term(
-                function(
-                  identifier(
-                    function_of(RNAAbundance))),
-                argument(
-                  parameter(
-                    prefix(
-                      identifier(
-                        has_namespace,
-                        namespace_of(:*))),
-                    value(
-                      value_type(
-                        has_encoding,
-                        encoding_of(:RnaAbundance))))),
-                argument(
-                  term(
-                    function(
-                      identifier(
-                        return_type_of(BELParser::Language::Version1_0::ReturnTypes::Fusion))))))              
+                  function(
+                    identifier(
+                      function_of(RNAAbundance))),
+                  argument(
+                    parameter(
+                      prefix(
+                        identifier(
+                          has_namespace,
+                          namespace_of(:*))),
+                      value(
+                        value_type(
+                          has_encoding,
+                          encoding_of(:RnaAbundance))))),
+                  argument(
+                    term(
+                      function(
+                        identifier(
+                          return_type_of(BELParser::Language::Version1_0::ReturnTypes::Fusion))))))
               end
               private_constant :AST
 
@@ -77,7 +77,8 @@ module BELParser
                 STRING_FORM
               end
             end
-  
+
+            # RNAAbundanceSignature
             class RNAAbundanceSignature
               extend BELParser::Language::Signature
 
@@ -85,19 +86,19 @@ module BELParser
 
               AST = BELParser::Language::Semantics::Builder.build do
                 term(
-                function(
-                  identifier(
-                    function_of(RNAAbundance))),
-                argument(
-                  parameter(
-                    prefix(
-                      identifier(
-                        has_namespace,
-                        namespace_of(:*))),
-                    value(
-                      value_type(
-                        has_encoding,
-                        encoding_of(:RnaAbundance))))))              
+                  function(
+                    identifier(
+                      function_of(RNAAbundance))),
+                  argument(
+                    parameter(
+                      prefix(
+                        identifier(
+                          has_namespace,
+                          namespace_of(:*))),
+                      value(
+                        value_type(
+                          has_encoding,
+                          encoding_of(:RnaAbundance))))))
               end
               private_constant :AST
 
@@ -112,7 +113,6 @@ module BELParser
                 STRING_FORM
               end
             end
-  
           end
 
           SIGNATURES = Signatures.constants.map do |const|

data/lib/bel_parser/language/version1_0/functions/substitution.rb

@@ -7,14 +7,16 @@ module BELParser
   module Language
     module Version1_0
       module Functions
-        # Substitution: Indicates the abundance of proteins with amino acid substitution sequence
+        # Substitution: Indicates the abundance of proteins with amino
+        # acid substitution sequence
         class Substitution
           extend Function
 
           SHORT       = :sub
           LONG        = :substitution
           RETURN_TYPE = BELParser::Language::Version1_0::ReturnTypes::Substitution
-          DESCRIPTION = 'Indicates the abundance of proteins with amino acid substitution sequence'.freeze
+          DESCRIPTION = 'Indicates the abundance of proteins with amino
+          cid substitution sequence'.freeze
 
           def self.short
             SHORT
@@ -37,7 +39,7 @@ module BELParser
           end
 
           module Signatures
-  
+            # SubstitutionWithReferencePositionVariantSignature
             class SubstitutionWithReferencePositionVariantSignature
               extend BELParser::Language::Signature
 
@@ -45,30 +47,30 @@ module BELParser
 
               AST = BELParser::Language::Semantics::Builder.build do
                 term(
-                function(
-                  identifier(
-                    function_of(Substitution))),
-                argument(
-                  parameter(
-                    prefix(
-                      any),
-                    value(
-                      value_type(
-                        encoding_of(:*))))),
-                argument(
-                  parameter(
-                    prefix(
-                      any),
-                    value(
-                      value_type(
-                        encoding_of(:*))))),
-                argument(
-                  parameter(
-                    prefix(
-                      any),
-                    value(
-                      value_type(
-                        encoding_of(:*))))))              
+                  function(
+                    identifier(
+                      function_of(Substitution))),
+                  argument(
+                    parameter(
+                      prefix(
+                        any),
+                      value(
+                        value_type(
+                          encoding_of(:*))))),
+                  argument(
+                    parameter(
+                      prefix(
+                        any),
+                      value(
+                        value_type(
+                          encoding_of(:*))))),
+                  argument(
+                    parameter(
+                      prefix(
+                        any),
+                      value(
+                        value_type(
+                          encoding_of(:*))))))
               end
               private_constant :AST
 
@@ -83,7 +85,6 @@ module BELParser
                 STRING_FORM
               end
             end
-  
           end
 
           SIGNATURES = Signatures.constants.map do |const|

data/lib/bel_parser/language/version1_0/functions/transcriptional_activity.rb

@@ -7,14 +7,18 @@ module BELParser
   module Language
     module Version1_0
       module Functions
-        # TranscriptionalActivity: Denotes the frequency or abundance of events in which a member directly acts to control transcription of genes
+        # TranscriptionalActivity: Denotes the frequency or abundance of
+        # events in which a member directly acts to control transcription
+        # of genes
         class TranscriptionalActivity
           extend Function
 
           SHORT       = :tscript
           LONG        = :transcriptionalActivity
           RETURN_TYPE = BELParser::Language::Version1_0::ReturnTypes::TranscriptionalActivity
-          DESCRIPTION = 'Denotes the frequency or abundance of events in which a member directly acts to control transcription of genes'.freeze
+          DESCRIPTION = 'Denotes the frequency or abundance of events
+          n which a member directly acts to control
+          ranscription of genes'.freeze
 
           def self.short
             SHORT
@@ -37,7 +41,7 @@ module BELParser
           end
 
           module Signatures
-  
+            # TranscriptionalActivityOfComplexAbundanceSignature
             class TranscriptionalActivityOfComplexAbundanceSignature
               extend BELParser::Language::Signature
 
@@ -45,14 +49,14 @@ module BELParser
 
               AST = BELParser::Language::Semantics::Builder.build do
                 term(
-                function(
-                  identifier(
-                    function_of(TranscriptionalActivity))),
-                argument(
-                  term(
-                    function(
-                      identifier(
-                        return_type_of(BELParser::Language::Version1_0::ReturnTypes::ComplexAbundance))))))              
+                  function(
+                    identifier(
+                      function_of(TranscriptionalActivity))),
+                  argument(
+                    term(
+                      function(
+                        identifier(
+                          return_type_of(BELParser::Language::Version1_0::ReturnTypes::ComplexAbundance))))))
               end
               private_constant :AST
 
@@ -67,7 +71,8 @@ module BELParser
                 STRING_FORM
               end
             end
-  
+
+            # TranscriptionalActivityOfProteinAbundanceSignature
             class TranscriptionalActivityOfProteinAbundanceSignature
               extend BELParser::Language::Signature
 
@@ -75,14 +80,14 @@ module BELParser
 
               AST = BELParser::Language::Semantics::Builder.build do
                 term(
-                function(
-                  identifier(
-                    function_of(TranscriptionalActivity))),
-                argument(
-                  term(
-                    function(
-                      identifier(
-                        return_type_of(BELParser::Language::Version1_0::ReturnTypes::ProteinAbundance))))))              
+                  function(
+                    identifier(
+                      function_of(TranscriptionalActivity))),
+                  argument(
+                    term(
+                      function(
+                        identifier(
+                          return_type_of(BELParser::Language::Version1_0::ReturnTypes::ProteinAbundance))))))
               end
               private_constant :AST
 
@@ -97,7 +102,6 @@ module BELParser
                 STRING_FORM
               end
             end
-  
           end
 
           SIGNATURES = Signatures.constants.map do |const|

data/lib/bel_parser/language/version1_0/functions/translocation.rb

@@ -7,14 +7,16 @@ module BELParser
   module Language
     module Version1_0
       module Functions
-        # Translocation: Denotes the frequency or abundance of events in which members move between locations
+        # Translocation: Denotes the frequency or abundance of events
+        # in which members move between locations
         class Translocation
           extend Function
 
           SHORT       = :tloc
           LONG        = :translocation
           RETURN_TYPE = BELParser::Language::Version1_0::ReturnTypes::Abundance
-          DESCRIPTION = 'Denotes the frequency or abundance of events in which members move between locations'.freeze
+          DESCRIPTION = 'Denotes the frequency or abundance of events
+          n which members move between locations'.freeze
 
           def self.short
             SHORT
@@ -37,7 +39,7 @@ module BELParser
           end
 
           module Signatures
-  
+            # TranslocationSignature
             class TranslocationSignature
               extend BELParser::Language::Signature
 
@@ -45,34 +47,34 @@ module BELParser
 
               AST = BELParser::Language::Semantics::Builder.build do
                 term(
-                function(
-                  identifier(
-                    function_of(Translocation))),
-                argument(
-                  term(
-                    function(
-                      identifier(
-                        return_type_of(BELParser::Language::Version1_0::ReturnTypes::Abundance))))),
-                argument(
-                  parameter(
-                    prefix(
-                      identifier(
-                        has_namespace,
-                        namespace_of(:*))),
-                    value(
-                      value_type(
-                        has_encoding,
-                        encoding_of(:Abundance))))),
-                argument(
-                  parameter(
-                    prefix(
-                      identifier(
-                        has_namespace,
-                        namespace_of(:*))),
-                    value(
-                      value_type(
-                        has_encoding,
-                        encoding_of(:Abundance))))))              
+                  function(
+                    identifier(
+                      function_of(Translocation))),
+                  argument(
+                    term(
+                      function(
+                        identifier(
+                          return_type_of(BELParser::Language::Version1_0::ReturnTypes::Abundance))))),
+                  argument(
+                    parameter(
+                      prefix(
+                        identifier(
+                          has_namespace,
+                          namespace_of(:*))),
+                      value(
+                        value_type(
+                          has_encoding,
+                          encoding_of(:Abundance))))),
+                  argument(
+                    parameter(
+                      prefix(
+                        identifier(
+                          has_namespace,
+                          namespace_of(:*))),
+                      value(
+                        value_type(
+                          has_encoding,
+                          encoding_of(:Abundance))))))
               end
               private_constant :AST
 
@@ -87,7 +89,6 @@ module BELParser
                 STRING_FORM
               end
             end
-  
           end
 
           SIGNATURES = Signatures.constants.map do |const|

data/lib/bel_parser/language/version1_0/functions/transport_activity.rb

@@ -7,14 +7,19 @@ module BELParser
   module Language
     module Version1_0
       module Functions
-        # TransportActivity: Denotes the frequency or abundance of events in which a member directs acts to enable the directed movement of substances into, out of, within, or between cells
+        # TransportActivity: Denotes the frequency or abundance of events
+        # in which a member directs acts to enable the directed movement
+        # of substances into, out of, within, or between cells
         class TransportActivity
           extend Function
 
           SHORT       = :tport
           LONG        = :transportActivity
           RETURN_TYPE = BELParser::Language::Version1_0::ReturnTypes::TransportActivity
-          DESCRIPTION = 'Denotes the frequency or abundance of events in which a member directs acts to enable the directed movement of substances into, out of, within, or between cells'.freeze
+          DESCRIPTION = 'Denotes the frequency or abundance of events
+          n which a member directs acts to enable the
+          irected movement of substances into, out of,
+          ithin, or between cells'.freeze
 
           def self.short
             SHORT
@@ -37,7 +42,7 @@ module BELParser
           end
 
           module Signatures
-  
+            # TransportActivityOfComplexAbundanceSignature
             class TransportActivityOfComplexAbundanceSignature
               extend BELParser::Language::Signature
 
@@ -45,14 +50,14 @@ module BELParser
 
               AST = BELParser::Language::Semantics::Builder.build do
                 term(
-                function(
-                  identifier(
-                    function_of(TransportActivity))),
-                argument(
-                  term(
-                    function(
-                      identifier(
-                        return_type_of(BELParser::Language::Version1_0::ReturnTypes::ComplexAbundance))))))              
+                  function(
+                    identifier(
+                      function_of(TransportActivity))),
+                  argument(
+                    term(
+                      function(
+                        identifier(
+                          return_type_of(BELParser::Language::Version1_0::ReturnTypes::ComplexAbundance))))))
               end
               private_constant :AST
 
@@ -67,7 +72,8 @@ module BELParser
                 STRING_FORM
               end
             end
-  
+
+            # TransportActivityOfProteinAbundanceSignature
             class TransportActivityOfProteinAbundanceSignature
               extend BELParser::Language::Signature
 
@@ -75,14 +81,14 @@ module BELParser
 
               AST = BELParser::Language::Semantics::Builder.build do
                 term(
-                function(
-                  identifier(
-                    function_of(TransportActivity))),
-                argument(
-                  term(
-                    function(
-                      identifier(
-                        return_type_of(BELParser::Language::Version1_0::ReturnTypes::ProteinAbundance))))))              
+                  function(
+                    identifier(
+                      function_of(TransportActivity))),
+                  argument(
+                    term(
+                      function(
+                        identifier(
+                          return_type_of(BELParser::Language::Version1_0::ReturnTypes::ProteinAbundance))))))
               end
               private_constant :AST
 
@@ -97,7 +103,6 @@ module BELParser
                 STRING_FORM
               end
             end
-  
           end
 
           SIGNATURES = Signatures.constants.map do |const|

data/lib/bel_parser/language/version1_0/functions/truncation.rb

@@ -7,14 +7,16 @@ module BELParser
   module Language
     module Version1_0
       module Functions
-        # Truncation: Indicates an abundance of proteins with truncation sequence variants
+        # Truncation: Indicates an abundance of proteins with truncation
+        # sequence variants
         class Truncation
           extend Function
 
           SHORT       = :trunc
           LONG        = :truncation
           RETURN_TYPE = BELParser::Language::Version1_0::ReturnTypes::Truncation
-          DESCRIPTION = 'Indicates an abundance of proteins with truncation sequence variants'.freeze
+          DESCRIPTION = 'Indicates an abundance of proteins with
+          runcation sequence variants'.freeze
 
           def self.short
             SHORT
@@ -37,7 +39,7 @@ module BELParser
           end
 
           module Signatures
-  
+            # TruncationWithPositionSignature
             class TruncationWithPositionSignature
               extend BELParser::Language::Signature
 
@@ -45,16 +47,16 @@ module BELParser
 
               AST = BELParser::Language::Semantics::Builder.build do
                 term(
-                function(
-                  identifier(
-                    function_of(Truncation))),
-                argument(
-                  parameter(
-                    prefix(
-                      any),
-                    value(
-                      value_type(
-                        encoding_of(:*))))))              
+                  function(
+                    identifier(
+                      function_of(Truncation))),
+                  argument(
+                    parameter(
+                      prefix(
+                        any),
+                      value(
+                        value_type(
+                          encoding_of(:*))))))
               end
               private_constant :AST
 
@@ -69,7 +71,6 @@ module BELParser
                 STRING_FORM
               end
             end
-  
           end
 
           SIGNATURES = Signatures.constants.map do |const|

data/lib/bel_parser/language/version1_0/relationships/acts_in.rb

@@ -5,13 +5,27 @@ module BELParser
   module Language
     module Version1_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.
+        # 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
+          DESCRIPTION = ' +A actsIn f(A)+ -  This relationship links an
+          bundance term to the activity term for the same
+          bundance. This relationship is direct because
+          t is a _self_ relationship, the abundance acts
+          n its own activity. For protein abundance p(A)
+          nd its molecular activity kin(p(A), +p(A) actsIn
+          in(p(A))+. This relationship is introduced by the
+          EL Compiler and may not be used by statements in
+          EL documents.'.freeze
 
           def self.short
             SHORT

data/lib/bel_parser/language/version1_0/relationships/analogous.rb

@@ -5,13 +5,19 @@ module BELParser
   module Language
     module Version1_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.
+        # 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
+          DESCRIPTION = ' +A analogous B+ -  For terms A and B, +A
+          nalogousTo B+ indicates that A and B represent
+          bundances or molecular activities in different
+          pecies which function in a similar manner.'.freeze
 
           def self.short
             SHORT

data/lib/bel_parser/language/version1_0/relationships/association.rb

@@ -5,13 +5,24 @@ module BELParser
   module Language
     module Version1_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.
+        # 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
+          DESCRIPTION = ' +A -- B+ -  For terms A and B, +A association B+
+          r +A -- B+ indicates that A and B are associated
+          n an unspecified manner. This relationship
+          s used when not enough information about the
+          ssociation is available to describe it using
+          ore specific relationships, like increases or
+          ositiveCorrelation.'.freeze
 
           def self.short
             SHORT

data/lib/bel_parser/language/version1_0/relationships/biomarker_for.rb

@@ -5,13 +5,20 @@ module BELParser
   module Language
     module Version1_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.
+        # 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
+          DESCRIPTION = ' +A biomarkerFor P+ -  For term A and process
+          erm P, +A biomarkerFor P+ indicates that changes
+          n or detection of A is used in some way to be
+           biomarker for pathology or biological process
+          .'.freeze
 
           def self.short
             SHORT