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

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

@@ -5,13 +5,33 @@ module BELParser
   module Language
     module Version1_0
       module Relationships
-        # SubProcessOf:  +A subProcessOf B+ -  For process, activity, or transformation term A and process term B, +A subProcessOf B+ indicates that instances of process B, by default, include one or more instances of A in their composition. For example, the reduction of HMG-CoA to mevalonate is a subprocess of cholesterol biosynthesis: <pre> <code> rxn(reactants(a(CHEBI:"(S)-3-hydroxy-3-methylglutaryl-CoA"),\ a(CHEBI:NADPH), a(CHEBI:hydron)), products(a(CHEBI:Mevalonate),\ a(CHEBI:"CoA-SH"), a(CHEBI:"NADP+"))) subProcessOf bp(GO:"cholesterol\ biosynthetic process") </code> </pre>
+        # SubProcessOf:  +A subProcessOf B+ -  For process, activity, or
+        # transformation term A and process term B, +A subProcessOf B+
+        # indicates that instances of process B, by default, include
+        # one or more instances of A in their composition. For
+        # example, the reduction of HMG-CoA to mevalonate is
+        # a subprocess of cholesterol biosynthesis: <pre> <code>
+        # rxn(reactants(a(CHEBI:"(S)-3-hydroxy-3-methylglutaryl-CoA"),\
+        # a(CHEBI:NADPH), a(CHEBI:hydron)), products(a(CHEBI:Mevalonate),\
+        # a(CHEBI:"CoA-SH"), a(CHEBI:"NADP+"))) subProcessOf
+        # bp(GO:"cholesterol\ biosynthetic process") </code> </pre>
         class SubProcessOf
           extend Relationship
 
           SHORT       = :subProcessOf
           LONG        = :subProcessOf
-          DESCRIPTION = ' +A subProcessOf B+ -  For process, activity, or transformation term A and process term B, +A subProcessOf B+ indicates that instances of process B, by default, include one or more instances of A in their composition. For example, the reduction of HMG-CoA to mevalonate is a subprocess of cholesterol biosynthesis: <pre> <code> rxn(reactants(a(CHEBI:"(S)-3-hydroxy-3-methylglutaryl-CoA"),\ a(CHEBI:NADPH), a(CHEBI:hydron)), products(a(CHEBI:Mevalonate),\ a(CHEBI:"CoA-SH"), a(CHEBI:"NADP+"))) subProcessOf bp(GO:"cholesterol\ biosynthetic process") </code> </pre>'.freeze
+          DESCRIPTION = ' +A subProcessOf B+ -  For process, activity,
+          r transformation term A and process term B,
+          A subProcessOf B+ indicates that instances
+          f process B, by default, include one or more
+          nstances of A in their composition. For example,
+          he reduction of HMG-CoA to mevalonate is a
+          ubprocess of cholesterol biosynthesis: <pre> <code>
+          xn(reactants(a(CHEBI:"(S)-3-hydroxy-3-methylglutaryl-CoA"),\
+          (CHEBI:NADPH), a(CHEBI:hydron)),
+          roducts(a(CHEBI:Mevalonate),\ a(CHEBI:"CoA-SH"),
+          (CHEBI:"NADP+"))) subProcessOf bp(GO:"cholesterol\
+          iosynthetic process") </code> </pre>'.freeze
 
           def self.short
             SHORT

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

@@ -5,13 +5,23 @@ module BELParser
   module Language
     module Version1_0
       module Relationships
-        # TranscribedTo:  +G :> R+ -  For rnaAbundance term R and geneAbundance term G, +G transcribedTo R+ or +G :> R+ indicates that members of R are produced by the transcription of members of G. For example: +g(HGNC:AKT1) :> r(HGNC:AKT1)+ indicates that the human AKT1 RNA is transcribed from the human AKT1 gene.
+        # TranscribedTo:  +G :> R+ -  For rnaAbundance term R and
+        # geneAbundance term G, +G transcribedTo R+ or +G :> R+ indicates
+        # that members of R are produced by the transcription of members
+        # of G. For example: +g(HGNC:AKT1) :> r(HGNC:AKT1)+ indicates
+        # that the human AKT1 RNA is transcribed from the human AKT1 gene.
         class TranscribedTo
           extend Relationship
 
           SHORT       = :':>'
           LONG        = :transcribedTo
-          DESCRIPTION = ' +G :> R+ -  For rnaAbundance term R and geneAbundance term G, +G transcribedTo R+ or +G :> R+ indicates that members of R are produced by the transcription of members of G. For example: +g(HGNC:AKT1) :> r(HGNC:AKT1)+ indicates that the human AKT1 RNA is transcribed from the human AKT1 gene.'.freeze
+          DESCRIPTION = ' +G :> R+ -  For rnaAbundance term R and
+          eneAbundance term G, +G transcribedTo R+ or +G :>
+          + indicates that members of R are produced by
+          he transcription of members of G. For example:
+          g(HGNC:AKT1) :> r(HGNC:AKT1)+ indicates that
+          he human AKT1 RNA is transcribed from the human
+          KT1 gene.'.freeze
 
           def self.short
             SHORT

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

@@ -5,13 +5,24 @@ module BELParser
   module Language
     module Version1_0
       module Relationships
-        # TranslatedTo:  +R >> P+ -  For rnaAbundance term R and proteinAbundance term P, +R translatedTo P+ or +R >> P+ indicates that members of P are produced by the translation of members of R. For example: +r(HGNC:AKT1) >> p(HGNC:AKT1)+ indicates that AKT1 protein is produced by translation of AKT1 RNA.
+        # TranslatedTo:  +R >> P+ -  For rnaAbundance term R and
+        # proteinAbundance term P, +R translatedTo P+ or +R >> P+
+        # indicates that members of P are produced by the translation
+        # of members of R. For example: +r(HGNC:AKT1) >> p(HGNC:AKT1)+
+        # indicates that AKT1 protein is produced by translation of
+        # AKT1 RNA.
         class TranslatedTo
           extend Relationship
 
           SHORT       = :>>
           LONG        = :translatedTo
-          DESCRIPTION = ' +R >> P+ -  For rnaAbundance term R and proteinAbundance term P, +R translatedTo P+ or +R >> P+ indicates that members of P are produced by the translation of members of R. For example: +r(HGNC:AKT1) >> p(HGNC:AKT1)+ indicates that AKT1 protein is produced by translation of AKT1 RNA.'.freeze
+          DESCRIPTION = ' +R >> P+ -  For rnaAbundance term R and
+          roteinAbundance term P, +R translatedTo P+ or
+          R >> P+ indicates that members of P are produced
+          y the translation of members of R. For example:
+          r(HGNC:AKT1) >> p(HGNC:AKT1)+ indicates that
+          KT1 protein is produced by translation of AKT1
+          NA.'.freeze
 
           def self.short
             SHORT

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

@@ -5,13 +5,27 @@ module BELParser
   module Language
     module Version1_0
       module Relationships
-        # Translocates:  +translocation(A, ns1:v1, ns2:v2) translocates A+ -  This relationship links the abundance term in a +translocation()+ to the translocation. This relationship is direct because it is a _self_ relationship. The translocated abundance is directly acted on by the translocation process. This relationship is introduced by the BEL Compiler and may not be used by statements in BEL documents.
+        # Translocates:  +translocation(A, ns1:v1, ns2:v2) translocates
+        # A+ -  This relationship links the abundance term in a
+        # +translocation()+ to the translocation. This relationship is
+        # direct because it is a _self_ relationship. The translocated
+        # abundance is directly acted on by the translocation
+        # process. This relationship is introduced by the BEL Compiler
+        # and may not be used by statements in BEL documents.
         class Translocates
           extend Relationship
 
           SHORT       = :translocates
           LONG        = :translocates
-          DESCRIPTION = ' +translocation(A, ns1:v1, ns2:v2) translocates A+ -  This relationship links the abundance term in a +translocation()+ to the translocation. This relationship is direct because it is a _self_ relationship. The translocated abundance is directly acted on by the translocation process. This relationship is introduced by the BEL Compiler and may not be used by statements in BEL documents.'.freeze
+          DESCRIPTION = ' +translocation(A, ns1:v1, ns2:v2) translocates
+          + -  This relationship links the abundance term
+          n a +translocation()+ to the translocation. This
+          elationship is direct because it is a _self_
+          elationship. The translocated abundance
+          s directly acted on by the translocation
+          rocess. 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/syntax/function.rb

@@ -8,7 +8,6 @@ module BELParser
         # {BELParser::Parsers::AST::Function} nodes that do not have a valid
         # BEL 1.0 functon name.
         class Function
-
           private_class_method :new
 
           V1 = ::BELParser::Language::Version1_0::Specification.new

data/lib/bel_parser/language/version1_0.rb

@@ -9,7 +9,14 @@ module BELParser
         include BELParser::Language::Specification
         def initialize
           @version = '1.0'.freeze
+          load_return_types
+          load_functions
+          load_relationships
+          load_syntax
+          freeze
+        end
 
+        def load_return_types
           # Collect return types
           ret_classes = Version1_0::ReturnTypes.constants.collect do |symbol|
             const = Version1_0::ReturnTypes.const_get(symbol)
@@ -17,7 +24,9 @@ module BELParser
           end
           @return_types         = ret_classes.compact
           @indexed_return_types = index_sym(@return_types)
+        end
 
+        def load_functions
           # Collect functions
           function_classes = Version1_0::Functions.constants.collect do |symbol|
             const = Version1_0::Functions.const_get(symbol)
@@ -27,7 +36,9 @@ module BELParser
           end
           @functions         = function_classes.compact
           @indexed_functions = index_long_short(@functions)
+        end
 
+        def load_relationships
           # Collect relationships
           rel_classes = Version1_0::Relationships.constants.collect do |symbol|
             const = Version1_0::Relationships.const_get(symbol)
@@ -37,15 +48,15 @@ module BELParser
           end
           @relationships         = rel_classes.compact
           @indexed_relationships = index_long_short(@relationships)
+        end
 
+        def load_syntax
           # Collect syntax checkers.
           syntax_classes = Version1_0::Syntax.constants.collect do |symbol|
             const = Version1_0::Syntax.const_get(symbol)
             const if const.respond_to?(:match)
           end
           @syntax = syntax_classes.compact
-
-          freeze
         end
       end
     end

data/lib/bel_parser/language/version2_0/functions/abundance.rb

@@ -37,7 +37,7 @@ module BELParser
           end
 
           module Signatures
-  
+            # AbundanceSignature
             class AbundanceSignature
               extend BELParser::Language::Signature
 
@@ -45,19 +45,19 @@ module BELParser
 
               AST = BELParser::Language::Semantics::Builder.build do
                 term(
-                function(
-                  identifier(
-                    function_of(Abundance))),
-                argument(
-                  parameter(
-                    prefix(
-                      identifier(
-                        has_namespace,
-                        namespace_of(:*))),
-                    value(
-                      value_type(
-                        has_encoding,
-                        encoding_of(:Abundance))))))              
+                  function(
+                    identifier(
+                      function_of(Abundance))),
+                  argument(
+                    parameter(
+                      prefix(
+                        identifier(
+                          has_namespace,
+                          namespace_of(:*))),
+                      value(
+                        value_type(
+                          has_encoding,
+                          encoding_of(:Abundance))))))
               end
               private_constant :AST
 
@@ -72,7 +72,8 @@ module BELParser
                 STRING_FORM
               end
             end
-  
+
+            # AbundanceWithLocationSignature
             class AbundanceWithLocationSignature
               extend BELParser::Language::Signature
 
@@ -80,24 +81,24 @@ module BELParser
 
               AST = BELParser::Language::Semantics::Builder.build do
                 term(
-                function(
-                  identifier(
-                    function_of(Abundance))),
-                argument(
-                  parameter(
-                    prefix(
-                      identifier(
-                        has_namespace,
-                        namespace_of(:*))),
-                    value(
-                      value_type(
-                        has_encoding,
-                        encoding_of(:Abundance))))),
-                argument(
-                  term(
-                    function(
-                      identifier(
-                        return_type_of(BELParser::Language::Version2_0::ReturnTypes::Location))))))              
+                  function(
+                    identifier(
+                      function_of(Abundance))),
+                  argument(
+                    parameter(
+                      prefix(
+                        identifier(
+                          has_namespace,
+                          namespace_of(:*))),
+                      value(
+                        value_type(
+                          has_encoding,
+                          encoding_of(:Abundance))))),
+                  argument(
+                    term(
+                      function(
+                        identifier(
+                          return_type_of(BELParser::Language::Version2_0::ReturnTypes::Location))))))
               end
               private_constant :AST
 
@@ -112,7 +113,8 @@ module BELParser
                 STRING_FORM
               end
             end
-  
+
+            # AbundanceWithMolecularActivitySignature
             class AbundanceWithMolecularActivitySignature
               extend BELParser::Language::Signature
 
@@ -120,24 +122,24 @@ module BELParser
 
               AST = BELParser::Language::Semantics::Builder.build do
                 term(
-                function(
-                  identifier(
-                    function_of(Abundance))),
-                argument(
-                  parameter(
-                    prefix(
-                      identifier(
-                        has_namespace,
-                        namespace_of(:*))),
-                    value(
-                      value_type(
-                        has_encoding,
-                        encoding_of(:Abundance))))),
-                argument(
-                  term(
-                    function(
-                      identifier(
-                        return_type_of(BELParser::Language::Version2_0::ReturnTypes::MolecularActivity))))))              
+                  function(
+                    identifier(
+                      function_of(Abundance))),
+                  argument(
+                    parameter(
+                      prefix(
+                        identifier(
+                          has_namespace,
+                          namespace_of(:*))),
+                      value(
+                        value_type(
+                          has_encoding,
+                          encoding_of(:Abundance))))),
+                  argument(
+                    term(
+                      function(
+                        identifier(
+                          return_type_of(BELParser::Language::Version2_0::ReturnTypes::MolecularActivity))))))
               end
               private_constant :AST
 
@@ -152,7 +154,6 @@ module BELParser
                 STRING_FORM
               end
             end
-  
           end
 
           SIGNATURES = Signatures.constants.map do |const|

data/lib/bel_parser/language/version2_0/functions/activity.rb

@@ -7,14 +7,17 @@ module BELParser
   module Language
     module Version2_0
       module Functions
-        # Activity: Denotes the frequency or abundance of events in which a member acts as a causal agent at the molecular scale.
+        # Activity: Denotes the frequency or abundance of events in
+        # which a member acts as a causal agent at the molecular scale.
         class Activity
           extend BELParser::Language::Function
 
           SHORT       = :act
           LONG        = :activity
           RETURN_TYPE = BELParser::Language::Version2_0::ReturnTypes::Activity
-          DESCRIPTION = 'Denotes the frequency or abundance of events in which a member acts as a causal agent at the molecular scale.'.freeze
+          DESCRIPTION = 'Denotes the frequency or abundance of events
+          n which a member acts as a causal agent at the
+          olecular scale.'.freeze
 
           def self.short
             SHORT
@@ -37,7 +40,7 @@ module BELParser
           end
 
           module Signatures
-  
+            # ActivitySignature
             class ActivitySignature
               extend BELParser::Language::Signature
 
@@ -67,7 +70,8 @@ module BELParser
                 STRING_FORM
               end
             end
-  
+
+            # ActivityWithSpecificActivityTypeSignature
             class ActivityWithSpecificActivityTypeSignature
               extend BELParser::Language::Signature
 
@@ -102,7 +106,6 @@ module BELParser
                 STRING_FORM
               end
             end
-  
           end
 
           SIGNATURES = Signatures.constants.map do |const|

data/lib/bel_parser/language/version2_0/functions/biological_process.rb

@@ -14,7 +14,8 @@ module BELParser
           SHORT       = :bp
           LONG        = :biologicalProcess
           RETURN_TYPE = BELParser::Language::Version2_0::ReturnTypes::BiologicalProcess
-          DESCRIPTION = 'Denotes a process or population of events.'.freeze
+          DESCRIPTION = 'Denotes a process or population of
+          vents.'.freeze
 
           def self.short
             SHORT
@@ -37,7 +38,7 @@ module BELParser
           end
 
           module Signatures
-  
+            # BiologicalProcessSignature
             class BiologicalProcessSignature
               extend BELParser::Language::Signature
 
@@ -45,19 +46,19 @@ module BELParser
 
               AST = BELParser::Language::Semantics::Builder.build do
                 term(
-                function(
-                  identifier(
-                    function_of(BiologicalProcess))),
-                argument(
-                  parameter(
-                    prefix(
-                      identifier(
-                        has_namespace,
-                        namespace_of(:*))),
-                    value(
-                      value_type(
-                        has_encoding,
-                        encoding_of(:BiologicalProcess))))))              
+                  function(
+                    identifier(
+                      function_of(BiologicalProcess))),
+                  argument(
+                    parameter(
+                      prefix(
+                        identifier(
+                          has_namespace,
+                          namespace_of(:*))),
+                      value(
+                        value_type(
+                          has_encoding,
+                          encoding_of(:BiologicalProcess))))))
               end
               private_constant :AST
 
@@ -72,7 +73,6 @@ module BELParser
                 STRING_FORM
               end
             end
-  
           end
 
           SIGNATURES = Signatures.constants.map do |const|

data/lib/bel_parser/language/version2_0/functions/cell_secretion.rb

@@ -7,14 +7,18 @@ module BELParser
   module Language
     module Version2_0
       module Functions
-        # CellSecretion: Denotes the frequency or abundance of events in which members of an abundance move from cells to regions outside of the cells.
+        # CellSecretion: Denotes the frequency or abundance of events
+        # in which members of an abundance move from cells to regions
+        # outside of the cells.
         class CellSecretion
           extend Function
 
           SHORT       = :sec
           LONG        = :cellSecretion
           RETURN_TYPE = BELParser::Language::Version2_0::ReturnTypes::Abundance
-          DESCRIPTION = 'Denotes the frequency or abundance of events in which members of an abundance move from cells to regions outside of the cells.'.freeze
+          DESCRIPTION = 'Denotes the frequency or abundance of events
+          n which members of an abundance move from cells
+          o regions outside of the cells.'.freeze
 
           def self.short
             SHORT
@@ -37,7 +41,7 @@ module BELParser
           end
 
           module Signatures
-  
+            # CellSecretionSignature
             class CellSecretionSignature
               extend BELParser::Language::Signature
 
@@ -45,14 +49,14 @@ module BELParser
 
               AST = BELParser::Language::Semantics::Builder.build do
                 term(
-                function(
-                  identifier(
-                    function_of(CellSecretion))),
-                argument(
-                  term(
-                    function(
-                      identifier(
-                        return_type_of(BELParser::Language::Version2_0::ReturnTypes::Abundance))))))              
+                  function(
+                    identifier(
+                      function_of(CellSecretion))),
+                  argument(
+                    term(
+                      function(
+                        identifier(
+                          return_type_of(BELParser::Language::Version2_0::ReturnTypes::Abundance))))))
               end
               private_constant :AST
 
@@ -67,7 +71,6 @@ module BELParser
                 STRING_FORM
               end
             end
-  
           end
 
           SIGNATURES = Signatures.constants.map do |const|

data/lib/bel_parser/language/version2_0/functions/cell_surface_expression.rb

@@ -7,14 +7,18 @@ module BELParser
   module Language
     module Version2_0
       module Functions
-        # CellSurfaceExpression: Denotes the frequency or abundance of events in which members of an abundance move to the surface of cells.
+        # CellSurfaceExpression: Denotes the frequency or abundance of
+        # events in which members of an abundance move to the surface
+        # of cells.
         class CellSurfaceExpression
           extend Function
 
           SHORT       = :surf
           LONG        = :cellSurfaceExpression
           RETURN_TYPE = BELParser::Language::Version2_0::ReturnTypes::Abundance
-          DESCRIPTION = 'Denotes the frequency or abundance of events in which members of an abundance move to the surface of cells.'.freeze
+          DESCRIPTION = 'Denotes the frequency or abundance of events in
+          hich members of an abundance move to the surface
+          f cells.'.freeze
 
           def self.short
             SHORT
@@ -37,7 +41,7 @@ module BELParser
           end
 
           module Signatures
-  
+            # CellSurfaceExpressionSignature
             class CellSurfaceExpressionSignature
               extend BELParser::Language::Signature
 
@@ -45,14 +49,14 @@ module BELParser
 
               AST = BELParser::Language::Semantics::Builder.build do
                 term(
-                function(
-                  identifier(
-                    function_of(CellSurfaceExpression))),
-                argument(
-                  term(
-                    function(
-                      identifier(
-                        return_type_of(BELParser::Language::Version2_0::ReturnTypes::Abundance))))))              
+                  function(
+                    identifier(
+                      function_of(CellSurfaceExpression))),
+                  argument(
+                    term(
+                      function(
+                        identifier(
+                          return_type_of(BELParser::Language::Version2_0::ReturnTypes::Abundance))))))
               end
               private_constant :AST
 
@@ -67,7 +71,6 @@ module BELParser
                 STRING_FORM
               end
             end
-  
           end
 
           SIGNATURES = Signatures.constants.map do |const|