bel_parser 1.0.0.alpha.27-java

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

@@ -0,0 +1,56 @@
+require_relative '../../version2_0'
+require_relative '../../relationship'
+
+module BELParser
+  module Language
+    module Version2_0
+      module Relationships
+        # DirectlyIncreases:  +A => B+ -  For terms A and B, +A
+        # directlyIncreases B or A => B+ indicate A increases 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 increases relationship.
+        class DirectlyIncreases
+          extend Relationship
+
+          SHORT       = :'=>'
+          LONG        = :directlyIncreases
+          DESCRIPTION = ' +A => B+ -  For terms A and B,
+          A directlyIncreases B or A => B+ indicate A
+          ncreases 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 increases relationship.'.freeze
+
+          def self.short
+            SHORT
+          end
+
+          def self.long
+            LONG
+          end
+
+          def self.description
+            DESCRIPTION
+          end
+
+          def self.causal?
+            true
+          end
+
+          def self.increasing?
+            true
+          end
+
+          def self.direct?
+            true
+          end
+
+          def self.directed?
+            true
+          end
+        end
+      end
+    end
+  end
+end

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

@@ -0,0 +1,62 @@
+require_relative '../../version2_0'
+require_relative '../../relationship'
+
+module BELParser
+  module Language
+    module Version2_0
+      module Relationships
+        # HasComponent:  +A hasComponent A1+ -  For complexAbundance
+        # term A and abundance term B, +A hasComponent B+ designates
+        # B as a component of A, that complexes that are instances of
+        # A have instances of B as possible components. Note that, the
+        # stoichiometry of A is not described, nor is it stated that B is
+        # a required component. The use of hasComponent relationships is
+        # complementary to the use of functionally composed complexes and
+        # is intended to enable the assignment of components to complexes
+        # designated by names in external vocabularies. The assignment
+        # of components can potentially enable the reconciliation of
+        # equivalent complexes at knowledge assembly time.
+        class HasComponent
+          extend Relationship
+
+          SHORT       = :hasComponent
+          LONG        = :hasComponent
+          DESCRIPTION = ' +A hasComponent A1+ -  For complexAbundance
+          erm A and abundance term B, +A hasComponent B+
+          esignates B as a component of A, that complexes
+          hat are instances of A have instances of B as
+          ossible components. Note that, the stoichiometry
+          f A is not described, nor is it stated that B
+          s a required component. The use of hasComponent
+          elationships is complementary to the use of
+          unctionally composed complexes and is intended to
+          nable the assignment of components to complexes
+          esignated by names in external vocabularies. The
+          ssignment of components can potentially enable
+          he reconciliation of equivalent complexes at
+          nowledge assembly time.'.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
+        end
+      end
+    end
+  end
+end

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

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+require_relative '../../version2_0'
+require_relative '../../relationship'
+
+module BELParser
+  module Language
+    module Version2_0
+      module Relationships
+        # HasComponents:  +A hasComponents (B, C, D)+ -  The hasComponents
+        # relationship is a special form which enables the assignment
+        # of multiple complex components in a single statement where
+        # the object of the statement is a set of abundance terms. A
+        # statement using hasComponents is exactly equivalent to multiple
+        # hasComponent statements. A term may not appear in both the
+        # subject and object of the same hasComponents statement. For
+        # the abundance terms A, B, C and D, +A hasComponents B, C, D+
+        # indicates that A has components B, C and D.
+        class HasComponents
+          extend Relationship
+
+          SHORT       = :hasComponents
+          LONG        = :hasComponents
+          DESCRIPTION = ' +A hasComponents (B, C, D)+ -  The hasComponents
+          elationship is a special form which enables
+          he assignment of multiple complex components
+          n a single statement where the object of the
+          tatement is a set of abundance terms. A statement
+          sing hasComponents is exactly equivalent to
+          ultiple hasComponent statements. A term may not
+          ppear in both the subject and object of the same
+          asComponents statement. For the abundance terms A,
+          , C and D, +A hasComponents B, C, D+ indicates
+          hat A has components B, C and D.'.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.listable?
+            true
+          end
+        end
+      end
+    end
+  end
+end

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

@@ -0,0 +1,48 @@
+require_relative '../../version2_0'
+require_relative '../../relationship'
+
+module BELParser
+  module Language
+    module Version2_0
+      module Relationships
+        # HasMember:  +A hasMember A1+ -  For term abundances A and B,
+        # +A hasMember B+ designates B as a member class of A. A member
+        # class is a distinguished sub-class. A is defined as a group
+        # by all of the members assigned to it. The member classes may
+        # or may not be overlapping and may or may not entirely cover
+        # all instances of A. A term may not appear in both the subject
+        # and object of the same hasMember statement.
+        class HasMember
+          extend Relationship
+
+          SHORT       = :hasMember
+          LONG        = :hasMember
+          DESCRIPTION = ' +A hasMember A1+ -  For term abundances A and B,
+          A hasMember B+ designates B as a member class of
+          . A member class is a distinguished sub-class. A is
+          efined as a group by all of the members assigned to
+          t. The member classes may or may not be overlapping
+          nd may or may not entirely cover all instances
+          f A. A term may not appear in both the subject
+          nd object of the same hasMember statement.'.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/has_members.rb

@@ -0,0 +1,57 @@
+require_relative '../../version2_0'
+require_relative '../../relationship'
+
+module BELParser
+  module Language
+    module Version2_0
+      module Relationships
+        # HasMembers:  +A hasMembers (B, C, D)+ -  The hasMembers
+        # relationship is a special form which enables the assignment of
+        # multiple member classes in a single statement where the object
+        # of the statement is a set of abundance terms. A statement
+        # using hasMembers is exactly equivalent to multiple hasMember
+        # statements. A term may not appear in both the subject and
+        # object of a of the same hasMembers statement. For the abundance
+        # terms A, B, C and D, +A hasMembers B, C, D+ indicates that A
+        # is defined by its member abundance classes B, C and D.
+        class HasMembers
+          extend Relationship
+
+          SHORT       = :hasMembers
+          LONG        = :hasMembers
+          DESCRIPTION = ' +A hasMembers (B, C, D)+ -  The hasMembers
+          elationship is a special form which enables the
+          ssignment of multiple member classes in a single
+          tatement where the object of the statement is a set
+          f abundance terms. A statement using hasMembers
+          s exactly equivalent to multiple hasMember
+          tatements. A term may not appear in both the
+          ubject and object of a of the same hasMembers
+          tatement. For the abundance terms A, B, C and D,
+          A hasMembers B, C, D+ indicates that A is defined
+          y its member abundance classes B, C and D.'.freeze
+
+          def self.short
+            SHORT
+          end
+
+          def self.long
+            LONG
+          end
+
+          def self.description
+            DESCRIPTION
+          end
+
+          def self.directed?
+            true
+          end
+
+          def self.listable?
+            true
+          end
+        end
+      end
+    end
+  end
+end

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

@@ -0,0 +1,54 @@
+require_relative '../../version2_0'
+require_relative '../../relationship'
+
+module BELParser
+  module Language
+    module Version2_0
+      module Relationships
+        # HasModification:  +p(A) hasModification p(A, pmod(P, S, 473))+
+        # -  This relationship links abundance terms modified by the
+        # +pmod()+ function to the unmodified abundance term. This is a
+        # direct relationship because it is a _self_ relationship. This
+        # relationship is introduced by the BEL Compiler and may not be
+        # used by statements in BEL documents.
+        class HasModification
+          extend Relationship
+
+          SHORT       = :hasModification
+          LONG        = :hasModification
+          DESCRIPTION = ' +p(A) hasModification p(A, pmod(P, S, 473))+ -
+          his relationship links abundance terms modified by
+          he +pmod()+ function to the unmodified abundance
+          erm. This is a direct relationship because it
+          s a _self_ relationship. This relationship is
+          ntroduced by the BEL Compiler and may not be used
+          y statements in BEL 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
+        end
+      end
+    end
+  end
+end

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

@@ -0,0 +1,60 @@
+require_relative '../../version2_0'
+require_relative '../../relationship'
+
+module BELParser
+  module Language
+    module Version2_0
+      module Relationships
+        # HasProduct:  +reaction(reactants(A), products(B))
+        # hasProduct B+ -  This relationship links abundance
+        # terms from the +products(<list>)+ in a reaction to the
+        # reaction. This is a direct relationship because it is a _self_
+        # relationship. Products are produced directly by a reaction. This
+        # relationship is introduced by the BEL Compiler and may not be
+        # used by statements in BEL documents.
+        class HasProduct
+          extend Relationship
+
+          SHORT       = :hasProduct
+          LONG        = :hasProduct
+          DESCRIPTION = ' +reaction(reactants(A), products(B)) hasProduct
+          + -  This relationship links abundance terms
+          rom the +products(<list>)+ in a reaction to the
+          eaction. This is a direct relationship because it
+          s a _self_ relationship. Products are produced
+          irectly by a reaction. This relationship is
+          ntroduced by the BEL Compiler and may not be used
+          y statements in BEL 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/has_variant.rb

@@ -0,0 +1,54 @@
+require_relative '../../version2_0'
+require_relative '../../relationship'
+
+module BELParser
+  module Language
+    module Version2_0
+      module Relationships
+        # HasVariant:  +p(A) hasVariant p(A, sub(G, 12, V))+ -
+        # This relationship links abundance terms modified by the
+        # +substitution()+, +fusion()+, or +truncation()+ functions to
+        # the unmodified abundance term. This relationship is introduced
+        # by the BEL Compiler and does not need to be used by statements
+        # in BEL documents.
+        class HasVariant
+          extend Relationship
+
+          SHORT       = :hasVariant
+          LONG        = :hasVariant
+          DESCRIPTION = ' +p(A) hasVariant p(A, sub(G, 12, V))+ -  This
+          elationship links abundance terms modified by the
+          substitution()+, +fusion()+, or +truncation()+
+          unctions to the unmodified abundance term. This
+          elationship is introduced by the BEL Compiler
+          nd does not need to 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
+        end
+      end
+    end
+  end
+end