bel_parser 1.0.0.alpha.27-java

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

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+require_relative '../../version1_0'
+require_relative '../../relationship'
+
+module BELParser
+  module Language
+    module Version1_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.genomic?
+            true
+          end
+        end
+      end
+    end
+  end
+end

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

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+require_relative '../../version1_0'
+require_relative '../../relationship'
+
+module BELParser
+  module Language
+    module Version1_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/version1_0/relationships/biomarker_for.rb

@@ -0,0 +1,42 @@
+require_relative '../../version1_0'
+require_relative '../../relationship'
+
+module BELParser
+  module Language
+    module Version1_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.directed?
+            true
+          end
+        end
+      end
+    end
+  end
+end

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

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+require_relative '../../version1_0'
+require_relative '../../relationship'
+
+module BELParser
+  module Language
+    module Version1_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/version1_0/relationships/decreases.rb

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+require_relative '../../version1_0'
+require_relative '../../relationship'
+
+module BELParser
+  module Language
+    module Version1_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/version1_0/relationships/directly_decreases.rb

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+require_relative '../../version1_0'
+require_relative '../../relationship'
+
+module BELParser
+  module Language
+    module Version1_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

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

@@ -0,0 +1,56 @@
+require_relative '../../version1_0'
+require_relative '../../relationship'
+
+module BELParser
+  module Language
+    module Version1_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/version1_0/relationships/has_component.rb

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+require_relative '../../version1_0'
+require_relative '../../relationship'
+
+module BELParser
+  module Language
+    module Version1_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/version1_0/relationships/has_components.rb

@@ -0,0 +1,61 @@
+require_relative '../../version1_0'
+require_relative '../../relationship'
+
+module BELParser
+  module Language
+    module Version1_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