bel_parser 1.0.0.alpha.27-java

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

@@ -0,0 +1,48 @@
+require_relative '../../version1_0'
+require_relative '../../relationship'
+
+module BELParser
+  module Language
+    module Version1_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/version1_0/relationships/has_members.rb

@@ -0,0 +1,57 @@
+require_relative '../../version1_0'
+require_relative '../../relationship'
+
+module BELParser
+  module Language
+    module Version1_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/version1_0/relationships/has_modification.rb

@@ -0,0 +1,54 @@
+require_relative '../../version1_0'
+require_relative '../../relationship'
+
+module BELParser
+  module Language
+    module Version1_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/version1_0/relationships/has_product.rb

@@ -0,0 +1,60 @@
+require_relative '../../version1_0'
+require_relative '../../relationship'
+
+module BELParser
+  module Language
+    module Version1_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/version1_0/relationships/has_variant.rb

@@ -0,0 +1,54 @@
+require_relative '../../version1_0'
+require_relative '../../relationship'
+
+module BELParser
+  module Language
+    module Version1_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

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

@@ -0,0 +1,59 @@
+require_relative '../../version1_0'
+require_relative '../../relationship'
+
+module BELParser
+  module Language
+    module Version1_0
+      module Relationships
+        # Includes:  +compositeAbundance(A,B) includes A+ -  This
+        # relationship links each individual abundance term in a
+        # +compositeAbundance(<list>)+ to the compositeAbundance. For
+        # example, +compositeAbundance(A, B) includes A+ and
+        # +compositeAbundance(A, B) includes B+. This relationship is
+        # direct 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 Includes
+          extend Relationship
+
+          SHORT       = :includes
+          LONG        = :includes
+          DESCRIPTION = ' +compositeAbundance(A,B) includes A+ -  This
+          elationship links each individual abundance
+          erm in a +compositeAbundance(<list>)+
+          o the compositeAbundance. For example,
+          compositeAbundance(A, B) includes A+ and
+          compositeAbundance(A, B) includes B+. This
+          elationship is direct because it is a _self_
+          elationship. This relationship is introduced by
+          he BEL Compiler and may not be used by statements
+          n BEL 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/version1_0/relationships/increases.rb

@@ -0,0 +1,63 @@
+require_relative '../../version1_0'
+require_relative '../../relationship'
+
+module BELParser
+  module Language
+    module Version1_0
+      module Relationships
+        # Increases:  +A -> B+ -  For terms A and B, +A increases B or
+        # A -> B+ indicates that increases in A have been observed to
+        # cause increases in B. +A increases B+ also represents cases
+        # where decreases in A have been observed to cause decreases 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 Increases
+          extend Relationship
+
+          SHORT       = :'->'
+          LONG        = :increases
+          DESCRIPTION = ' +A -> B+ -  For terms A and B, +A increases B
+          r A -> B+ indicates that increases in A have been
+          bserved to cause increases in B. +A increases
+          + also represents cases where decreases in A
+          ave been observed to cause decreases 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.directed?
+            true
+          end
+
+          def self.increasing?
+            true
+          end
+        end
+      end
+    end
+  end
+end

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

@@ -0,0 +1,48 @@
+require_relative '../../version1_0'
+require_relative '../../relationship'
+
+module BELParser
+  module Language
+    module Version1_0
+      module Relationships
+        # IsA:  +A isA B+ -  For terms A and B, +A isA B+ indicates
+        # that A is a subset of B. All terms in BEL represent classes,
+        # but given that classes implicitly have instances, one can
+        # also interpret +A isA B+ to mean that any instance of A must
+        # also be an instance of B. This relationship can be used to
+        # represent GO and MeSH hierarchies: +pathology(MESH:Psoriasis)
+        # isA pathology(MESH:"Skin Diseases")+
+        class IsA
+          extend Relationship
+
+          SHORT       = :isA
+          LONG        = :isA
+          DESCRIPTION = ' +A isA B+ -  For terms A and B, +A isA B+
+          ndicates that A is a subset of B. All terms in BEL
+          epresent classes, but given that classes implicitly
+          ave instances, one can also interpret +A isA B+ to
+          ean that any instance of A must also be an instance
+          f B. This relationship can be used to represent
+          O and MeSH hierarchies: +pathology(MESH:Psoriasis)
+          sA pathology(MESH:"Skin Diseases")+'.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