bel_parser 1.0.0.alpha.27-java

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

@@ -0,0 +1,80 @@
+require_relative '../../version2_0'
+require_relative '../../function'
+require_relative '../../signature'
+require_relative '../../semantics'
+
+module BELParser
+  module Language
+    module Version2_0
+      module Functions
+        # Variant: Denotes a sequence variant of the specified abundance.
+        class Variant
+          extend Function
+
+          SHORT       = :var
+          LONG        = :variant
+          RETURN_TYPE = BELParser::Language::Version2_0::ReturnTypes::Variant
+          DESCRIPTION = 'Denotes a sequence variant of the specified
+          bundance.'.freeze
+
+          def self.short
+            SHORT
+          end
+
+          def self.long
+            LONG
+          end
+
+          def self.return_type
+            RETURN_TYPE
+          end
+
+          def self.description
+            DESCRIPTION
+          end
+
+          def self.signatures
+            SIGNATURES
+          end
+
+          module Signatures
+            # VariantSignature
+            class VariantSignature
+              extend BELParser::Language::Signature
+
+              private_class_method :new
+
+              # TODO: More strict prefix validation for variant namespace?
+              AST = BELParser::Language::Semantics::Builder.build do
+                term(
+                  function(
+                    identifier(
+                      function_of(Variant))),
+                  argument(
+                    parameter(
+                      prefix(any),
+                      value(any))))
+              end
+              private_constant :AST
+
+              STRING_FORM = 'variant(E:hgvsVariantDescription)variant'.freeze
+              private_constant :STRING_FORM
+
+              def self.semantic_ast
+                AST
+              end
+
+              def self.string_form
+                STRING_FORM
+              end
+            end
+          end
+
+          SIGNATURES = Signatures.constants.map do |const|
+            Signatures.const_get(const)
+          end.freeze
+        end
+      end
+    end
+  end
+end

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

@@ -0,0 +1,61 @@
+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
+          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
+          end
+
+          def self.long
+            LONG
+          end
+
+          def self.description
+            DESCRIPTION
+          end
+
+          def self.direct?
+            true
+          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/relationships/analogous.rb

@@ -0,0 +1,45 @@
+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
+          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
+          end
+
+          def self.long
+            LONG
+          end
+
+          def self.description
+            DESCRIPTION
+          end
+
+          def self.deprecated?
+            true
+          end
+
+          def self.genomic?
+            true
+          end
+        end
+      end
+    end
+  end
+end

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

@@ -0,0 +1,42 @@
+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+
+          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
+          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 +1,46 @@
+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
+          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
+          end
+
+          def self.long
+            LONG
+          end
+
+          def self.description
+            DESCRIPTION
+          end
+
+          def self.deprecated?
+            true
+          end
+
+          def self.directed?
+            true
+          end
+        end
+      end
+    end
+  end
+end

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

@@ -0,0 +1,50 @@
+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
+          ausesNoChange B+ indicates that B was observed not
+          o change in response to changes in A. Statements
+          sing this relationship correspond to cases where
+          xplicit measurement of B demonstrates lack of
+          ignificant change, not for cases where the state
+          f B is unknown.'.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/decreases.rb

@@ -0,0 +1,63 @@
+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
+          r A -| B+ indicates that increases in A have been
+          bserved to cause decreases in B. +A decreases
+          + also represents cases where decreases in A
+          ave been observed to cause increases in B, for
+          xample, in recording the results of gene deletion
+          r other inhibition experiments. A is a BEL Term
+          nd B is either a BEL Term or a BEL Statement. The
+          elationship does not indicate that the changes
+          n A are either necessary for changes in B, nor
+          oes it indicate that changes in A are sufficient
+          o cause changes in B.'.freeze
+
+          def self.short
+            SHORT
+          end
+
+          def self.long
+            LONG
+          end
+
+          def self.description
+            DESCRIPTION
+          end
+
+          def self.causal?
+            true
+          end
+
+          def self.decreasing?
+            true
+          end
+
+          def self.directed?
+            true
+          end
+        end
+      end
+    end
+  end
+end

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

@@ -0,0 +1,56 @@
+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
+          ecreases B and that the mechanism of the causal
+          elationship is based on physical interaction
+          f entities related to A and B. This is a direct
+          ersion of the decreases relationship.'.freeze
+
+          def self.short
+            SHORT
+          end
+
+          def self.long
+            LONG
+          end
+
+          def self.description
+            DESCRIPTION
+          end
+
+          def self.causal?
+            true
+          end
+
+          def self.decreasing?
+            true
+          end
+
+          def self.direct?
+            true
+          end
+
+          def self.directed?
+            true
+          end
+        end
+      end
+    end
+  end
+end