bel_parser 1.0.0.alpha.27-java

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

@@ -0,0 +1,59 @@
+require_relative '../../version2_0'
+require_relative '../../relationship'
+
+module BELParser
+  module Language
+    module Version2_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/version2_0/relationships/increases.rb

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+require_relative '../../version2_0'
+require_relative '../../relationship'
+
+module BELParser
+  module Language
+    module Version2_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/version2_0/relationships/is_a.rb

@@ -0,0 +1,48 @@
+require_relative '../../version2_0'
+require_relative '../../relationship'
+
+module BELParser
+  module Language
+    module Version2_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

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

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+require_relative '../../version2_0'
+require_relative '../../relationship'
+
+module BELParser
+  module Language
+    module Version2_0
+      module Relationships
+        # NegativeCorrelation:  +A negativeCorrelation B+ -  For terms
+        # A and B, +A negativeCorrelation B+ indicates that changes in A
+        # and B have been observed to be negatively correlated. The order
+        # of the subject and object does not affect the interpretation
+        # of the statement, thus B negativeCorrelation A is equivalent
+        # to A negativeCorrelation B.
+        class NegativeCorrelation
+          extend Relationship
+
+          SHORT       = :negativeCorrelation
+          LONG        = :negativeCorrelation
+          DESCRIPTION = ' +A negativeCorrelation B+ -  For terms A and B,
+          A negativeCorrelation B+ indicates that changes
+          n A and B have been observed to be negatively
+          orrelated. The order of the subject and object does
+          ot affect the interpretation of the statement,
+          hus B negativeCorrelation A is equivalent to A
+          egativeCorrelation B.'.freeze
+
+          def self.short
+            SHORT
+          end
+
+          def self.long
+            LONG
+          end
+
+          def self.description
+            DESCRIPTION
+          end
+
+          def self.correlative?
+            true
+          end
+
+          def self.decreasing?
+            true
+          end
+        end
+      end
+    end
+  end
+end

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

@@ -0,0 +1,48 @@
+require_relative '../../version2_0'
+require_relative '../../relationship'
+
+module BELParser
+  module Language
+    module Version2_0
+      module Relationships
+        # Orthologous:  +A orthologous B+ -  For geneAbundance terms A
+        # and B, +A orthologousTo B+ indicates that A and B represent
+        # abundances of genes in different species which are sequence
+        # similar and which are therefore presumed to share a common
+        # ancestral gene. For example, +g(HGNC:AKT1) orthologousTo
+        # g(MGI:AKT1)+ indicates that the mouse and human AKT1 genes
+        # are orthologous.
+        class Orthologous
+          extend Relationship
+
+          SHORT       = :orthologous
+          LONG        = :orthologous
+          DESCRIPTION = ' +A orthologous B+ -  For geneAbundance terms
+           and B, +A orthologousTo B+ indicates that A
+          nd B represent abundances of genes in different
+          pecies which are sequence similar and which are
+          herefore presumed to share a common ancestral
+          ene. For example, +g(HGNC:AKT1) orthologousTo
+          (MGI:AKT1)+ indicates that the mouse and human
+          KT1 genes are orthologous.'.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/version2_0/relationships/positive_correlation.rb

@@ -0,0 +1,46 @@
+require_relative '../../version2_0'
+require_relative '../../relationship'
+
+module BELParser
+  module Language
+    module Version2_0
+      module Relationships
+        # PositiveCorrelation:  +A positiveCorrelation B+ -  For terms
+        # A and B, +A positiveCorrelation B+ indicates that changes in
+        # A and B have been observed to be positively correlated, thus B
+        # positiveCorrelation A is equivalent to A positiveCorrelation B.
+        class PositiveCorrelation
+          extend Relationship
+
+          SHORT       = :positiveCorrelation
+          LONG        = :positiveCorrelation
+          DESCRIPTION = ' +A positiveCorrelation B+ -  For terms A and B,
+          A positiveCorrelation B+ indicates that changes
+          n A and B have been observed to be positively
+          orrelated, thus B positiveCorrelation A is
+          quivalent to A positiveCorrelation B.'.freeze
+
+          def self.short
+            SHORT
+          end
+
+          def self.long
+            LONG
+          end
+
+          def self.description
+            DESCRIPTION
+          end
+
+          def self.increasing?
+            true
+          end
+
+          def self.correlative?
+            true
+          end
+        end
+      end
+    end
+  end
+end

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

@@ -0,0 +1,48 @@
+require_relative '../../version2_0'
+require_relative '../../relationship'
+
+module BELParser
+  module Language
+    module Version2_0
+      module Relationships
+        # PrognosticBiomarkerFor:  +A prognosticBiomarkerFor P+ -
+        # For term A and process term P, +A prognosticBiomarkerFor P+
+        # indicates that changes in or detection of A is used in some
+        # way to be a prognostic biomarker for the subsequent development
+        # of pathology or biological process P.
+        class PrognosticBiomarkerFor
+          extend Relationship
+
+          SHORT       = :prognosticBiomarkerFor
+          LONG        = :prognosticBiomarkerFor
+          DESCRIPTION = ' +A prognosticBiomarkerFor P+ -  For term A
+          nd process term P, +A prognosticBiomarkerFor P+
+          ndicates that changes in or detection of A is used
+          n some way to be a prognostic biomarker for the
+          ubsequent development of pathology or biological
+          rocess P.'.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/rate_limiting_step_of.rb

@@ -0,0 +1,53 @@
+require_relative '../../version2_0'
+require_relative '../../relationship'
+
+module BELParser
+  module Language
+    module Version2_0
+      module Relationships
+        # RateLimitingStepOf:  +A rateLimitingStepOf B+ -  For process,
+        # activity, or transformation term A and process term B, +A
+        # rateLimitingStepOf B+ indicates +A subProcessOf B+ and +A ->
+        # B+. For example, the catalytic activity of HMG CoA reductase
+        # is a rate-limiting step for cholesterol biosynthesis: <pre>
+        # <code> cat(p(HGNC:HMGCR)) rateLimitingStepOf\ bp(GO:"cholesterol
+        # biosynthetic process") </code> </pre>
+        class RateLimitingStepOf
+          extend Relationship
+
+          SHORT       = :rateLimitingStepOf
+          LONG        = :rateLimitingStepOf
+          DESCRIPTION = ' +A rateLimitingStepOf B+ -  For process,
+          ctivity, or transformation term A and process
+          erm B, +A rateLimitingStepOf B+ indicates
+          A subProcessOf B+ and +A -> B+. For example,
+          he catalytic activity of HMG CoA reductase is a
+          ate-limiting step for cholesterol biosynthesis:
+          pre> <code> cat(p(HGNC:HMGCR)) rateLimitingStepOf\
+          p(GO:"cholesterol biosynthetic process") </code>
+          /pre>'.freeze
+
+          def self.short
+            SHORT
+          end
+
+          def self.long
+            LONG
+          end
+
+          def self.description
+            DESCRIPTION
+          end
+
+          def self.directed?
+            true
+          end
+
+          def self.increasing?
+            true
+          end
+        end
+      end
+    end
+  end
+end

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

@@ -0,0 +1,60 @@
+require_relative '../../version2_0'
+require_relative '../../relationship'
+
+module BELParser
+  module Language
+    module Version2_0
+      module Relationships
+        # ReactantIn:  +A reactantIn reaction(reactants(A),
+        # products(B))+ -  This relationship links abundance
+        # terms from the +reactants(<list>)+ in a reaction to the
+        # reaction. This is a direct relationship because it is a
+        # _self_ relationship. Reactants are consumed directly by a
+        # reaction. This relationship is introduced by the BEL Compiler
+        # and may not be used by statements in BEL documents.
+        class ReactantIn
+          extend Relationship
+
+          SHORT       = :reactantIn
+          LONG        = :reactantIn
+          DESCRIPTION = ' +A reactantIn reaction(reactants(A),
+          roducts(B))+ -  This relationship links abundance
+          erms from the +reactants(<list>)+ in a reaction
+          o the reaction. This is a direct relationship
+          ecause it is a _self_ relationship. Reactants are
+          onsumed directly by a reaction. This relationship
+          s introduced by the BEL Compiler and may not be
+          sed by 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