bel_parser 1.0.0.alpha.27-java

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

@@ -0,0 +1,51 @@
+require_relative '../../version2_0'
+require_relative '../../relationship'
+
+module BELParser
+  module Language
+    module Version2_0
+      module Relationships
+        # Regulates:  +A regulates B+ - For terms A and B, A regulates
+        # B or A reg B indicate that A is reported to have an effect on
+        # B, but information is missing about whether A increases B or
+        # A decreases B. This relationship provides more information
+        # than association, because the upstream entity (source term)
+        # and downstream entity (target term) can be assigned.
+        class Regulates
+          extend Relationship
+
+          SHORT       = :reg
+          LONG        = :regulates
+          DESCRIPTION = '+A regulates B+ - For terms A and B, A regulates
+           or A reg B indicate that A is reported to
+          ave an effect on B, but information is missing
+          bout whether A increases B or A decreases
+          . This relationship provides more information
+          han association, because the upstream entity
+          source term) and downstream entity (target term)
+          an be assigned.'.freeze
+
+          def self.short
+            SHORT
+          end
+
+          def self.long
+            LONG
+          end
+
+          def self.description
+            DESCRIPTION
+          end
+
+          def self.causal?
+            true
+          end
+
+          def self.directed?
+            true
+          end
+        end
+      end
+    end
+  end
+end

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

@@ -0,0 +1,55 @@
+require_relative '../../version2_0'
+require_relative '../../relationship'
+
+module BELParser
+  module Language
+    module Version2_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>
+        class SubProcessOf
+          extend Relationship
+
+          SHORT       = :subProcessOf
+          LONG        = :subProcessOf
+          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
+          end
+
+          def self.long
+            LONG
+          end
+
+          def self.description
+            DESCRIPTION
+          end
+
+          def self.directed?
+            true
+          end
+        end
+      end
+    end
+  end
+end

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

@@ -0,0 +1,53 @@
+require_relative '../../version2_0'
+require_relative '../../relationship'
+
+module BELParser
+  module Language
+    module Version2_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.
+        class TranscribedTo
+          extend Relationship
+
+          SHORT       = :':>'
+          LONG        = :transcribedTo
+          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
+          end
+
+          def self.long
+            LONG
+          end
+
+          def self.description
+            DESCRIPTION
+          end
+
+          def self.direct?
+            true
+          end
+
+          def self.directed?
+            true
+          end
+
+          def self.genomic?
+            true
+          end
+        end
+      end
+    end
+  end
+end

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

@@ -0,0 +1,54 @@
+require_relative '../../version2_0'
+require_relative '../../relationship'
+
+module BELParser
+  module Language
+    module Version2_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.
+        class TranslatedTo
+          extend Relationship
+
+          SHORT       = :>>
+          LONG        = :translatedTo
+          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
+          end
+
+          def self.long
+            LONG
+          end
+
+          def self.description
+            DESCRIPTION
+          end
+
+          def self.direct?
+            true
+          end
+
+          def self.directed?
+            true
+          end
+
+          def self.genomic?
+            true
+          end
+        end
+      end
+    end
+  end
+end

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

@@ -0,0 +1,57 @@
+require_relative '../../version2_0'
+require_relative '../../relationship'
+
+module BELParser
+  module Language
+    module Version2_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.
+        class Translocates
+          extend Relationship
+
+          SHORT       = :translocates
+          LONG        = :translocates
+          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
+          end
+
+          def self.long
+            LONG
+          end
+
+          def self.description
+            DESCRIPTION
+          end
+
+          def self.directed?
+            true
+          end
+
+          def self.injected?
+            true
+          end
+
+          def self.self?
+            true
+          end
+        end
+      end
+    end
+  end
+end

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

@@ -0,0 +1,20 @@
+require_relative 'any'
+
+module BELParser
+  module Language
+    module Version2_0
+      module ReturnTypes
+        # Abundance return type.
+        class Abundance < Any
+          # Return the {Symbol} value.
+          #
+          # @note This method should be overridden in subclasses.
+          def self.to_sym
+            raise_not_implemented(__method__) if self != Abundance
+            :abundance
+          end
+        end
+      end
+    end
+  end
+end

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

@@ -0,0 +1,20 @@
+require_relative 'any'
+
+module BELParser
+  module Language
+    module Version2_0
+      module ReturnTypes
+        # Activity return type.
+        class Activity < Any
+          # Return the {Symbol} value.
+          #
+          # @note This method should be overridden in subclasses.
+          def self.to_sym
+            raise_not_implemented(__method__) if self != Activity
+            :activity
+          end
+        end
+      end
+    end
+  end
+end

data/lib/bel_parser/language/version2_0/return_types/any.rb

@@ -0,0 +1,74 @@
+require 'English'
+
+module BELParser
+  module Language
+    module Version2_0
+      module ReturnTypes
+        # The any type.
+        class Any
+          # Return the {Symbol} value.
+          #
+          # @note This method should be overridden in subclasses.
+          def self.to_sym
+            raise_not_implemented(__method__) if self != Any
+            :*
+          end
+
+          # Returns +true+ if I am a subtype of +other_return_type+; otherwise
+          # return +false+.
+          #
+          # @param  [Class]   other_return_type to compare to
+          # @return [Boolean] +true+ if I am a subtype; +false+ if not
+          def self.subtype_of?(other_return_type)
+            self <= other_return_type
+          end
+
+          # Retrieve my immediate subtypes.
+          #
+          # @return [Array<Class>] my immediate subtypes
+          def self.subtypes
+            (@subtypes ||= []).freeze
+          end
+
+          # Retrieve my transitive subtypes.
+          #
+          # @return [Array<Class>] my transitive subtypes
+          def self.transitive_subtypes
+            transitive_subtypes =
+              (@subtypes ||= []).flat_map do |subtype|
+                [subtype, subtype.subtypes]
+              end.flatten
+            transitive_subtypes << self
+            transitive_subtypes.freeze
+          end
+
+          # Inherited hook overridden to keep track of descendants. This method
+          # is inherited by all descendants.
+          #
+          # @param [Class] cls the subclass that is inheriting me
+          # @see .subtypes
+          def self.inherited(cls)
+            (@subtypes ||= []) << cls
+          end
+          private_class_method
+
+          # Raise {NotImplementedError} for +method+. Alters the exception
+          # backtrace to exclude this method.
+          #
+          # @param [#to_s] the method name
+          # @raise [NotImplementedError] for +method+
+          def self.raise_not_implemented(method)
+            msg = "#{name} must implement the #{method} method"
+            raise NotImplementedError, msg
+          rescue StandardError
+            raise(
+              $ERROR_INFO.class,
+              $ERROR_INFO.message,
+              $ERROR_INFO.backtrace[1..-1])
+          end
+          private_class_method
+        end
+      end
+    end
+  end
+end

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

@@ -0,0 +1,17 @@
+require_relative 'any'
+
+module BELParser
+  module Language
+    module Version2_0
+      module ReturnTypes
+        # Biological process return type.
+        class BiologicalProcess < Any
+          def self.to_sym
+            raise_not_implemented(__method__) if self != BiologicalProcess
+            :biologicalProcess
+          end
+        end
+      end
+    end
+  end
+end

data/lib/bel_parser/language/version2_0/return_types/complex_abundance.rb

@@ -0,0 +1,17 @@
+require_relative 'abundance'
+
+module BELParser
+  module Language
+    module Version2_0
+      module ReturnTypes
+        # Complex abundance return type.
+        class ComplexAbundance < Abundance
+          def self.to_sym
+            raise_not_implemented(__method__) if self != ComplexAbundance
+            :complexAbundance
+          end
+        end
+      end
+    end
+  end
+end

data/lib/bel_parser/language/version2_0/return_types/fragment.rb

@@ -0,0 +1,20 @@
+require_relative 'any'
+
+module BELParser
+  module Language
+    module Version2_0
+      module ReturnTypes
+        # Fragment return type.
+        class Fragment < Any
+          # Return the {Symbol} value.
+          #
+          # @note This method should be overridden in subclasses.
+          def self.to_sym
+            raise_not_implemented(__method__) if self != Fragment
+            :fragment
+          end
+        end
+      end
+    end
+  end
+end