bel_parser 1.0.0.alpha.27-java

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

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

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

@@ -0,0 +1,46 @@
+require_relative '../../version1_0'
+require_relative '../../relationship'
+
+module BELParser
+  module Language
+    module Version1_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/version1_0/relationships/prognostic_biomarker_for.rb

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

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

@@ -0,0 +1,53 @@
+require_relative '../../version1_0'
+require_relative '../../relationship'
+
+module BELParser
+  module Language
+    module Version1_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/version1_0/relationships/reactant_in.rb

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

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

@@ -0,0 +1,55 @@
+require_relative '../../version1_0'
+require_relative '../../relationship'
+
+module BELParser
+  module Language
+    module Version1_0
+      module Relationships
+        # SubProcessOf:  +A subProcessOf B+ -  For process, activity, or
+        # transformation term A and process term B, +A subProcessOf B+
+        # indicates that instances of process B, by default, include
+        # one or more instances of A in their composition. For
+        # example, the reduction of HMG-CoA to mevalonate is
+        # a subprocess of cholesterol biosynthesis: <pre> <code>
+        # rxn(reactants(a(CHEBI:"(S)-3-hydroxy-3-methylglutaryl-CoA"),\
+        # a(CHEBI:NADPH), a(CHEBI:hydron)), products(a(CHEBI:Mevalonate),\
+        # a(CHEBI:"CoA-SH"), a(CHEBI:"NADP+"))) subProcessOf
+        # bp(GO:"cholesterol\ biosynthetic process") </code> </pre>
+        class SubProcessOf
+          extend Relationship
+
+          SHORT       = :subProcessOf
+          LONG        = :subProcessOf
+          DESCRIPTION = ' +A subProcessOf B+ -  For process, activity,
+          r transformation term A and process term B,
+          A subProcessOf B+ indicates that instances
+          f process B, by default, include one or more
+          nstances of A in their composition. For example,
+          he reduction of HMG-CoA to mevalonate is a
+          ubprocess of cholesterol biosynthesis: <pre> <code>
+          xn(reactants(a(CHEBI:"(S)-3-hydroxy-3-methylglutaryl-CoA"),\
+          (CHEBI:NADPH), a(CHEBI:hydron)),
+          roducts(a(CHEBI:Mevalonate),\ a(CHEBI:"CoA-SH"),
+          (CHEBI:"NADP+"))) subProcessOf bp(GO:"cholesterol\
+          iosynthetic process") </code> </pre>'.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/transcribed_to.rb

@@ -0,0 +1,53 @@
+require_relative '../../version1_0'
+require_relative '../../relationship'
+
+module BELParser
+  module Language
+    module Version1_0
+      module Relationships
+        # TranscribedTo:  +G :> R+ -  For rnaAbundance term R and
+        # geneAbundance term G, +G transcribedTo R+ or +G :> R+ indicates
+        # that members of R are produced by the transcription of members
+        # of G. For example: +g(HGNC:AKT1) :> r(HGNC:AKT1)+ indicates
+        # that the human AKT1 RNA is transcribed from the human AKT1 gene.
+        class TranscribedTo
+          extend Relationship
+
+          SHORT       = :':>'
+          LONG        = :transcribedTo
+          DESCRIPTION = ' +G :> R+ -  For rnaAbundance term R and
+          eneAbundance term G, +G transcribedTo R+ or +G :>
+          + indicates that members of R are produced by
+          he transcription of members of G. For example:
+          g(HGNC:AKT1) :> r(HGNC:AKT1)+ indicates that
+          he human AKT1 RNA is transcribed from the human
+          KT1 gene.'.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.genomic?
+            true
+          end
+        end
+      end
+    end
+  end
+end

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

@@ -0,0 +1,54 @@
+require_relative '../../version1_0'
+require_relative '../../relationship'
+
+module BELParser
+  module Language
+    module Version1_0
+      module Relationships
+        # TranslatedTo:  +R >> P+ -  For rnaAbundance term R and
+        # proteinAbundance term P, +R translatedTo P+ or +R >> P+
+        # indicates that members of P are produced by the translation
+        # of members of R. For example: +r(HGNC:AKT1) >> p(HGNC:AKT1)+
+        # indicates that AKT1 protein is produced by translation of
+        # AKT1 RNA.
+        class TranslatedTo
+          extend Relationship
+
+          SHORT       = :>>
+          LONG        = :translatedTo
+          DESCRIPTION = ' +R >> P+ -  For rnaAbundance term R and
+          roteinAbundance term P, +R translatedTo P+ or
+          R >> P+ indicates that members of P are produced
+          y the translation of members of R. For example:
+          r(HGNC:AKT1) >> p(HGNC:AKT1)+ indicates that
+          KT1 protein is produced by translation of AKT1
+          NA.'.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.genomic?
+            true
+          end
+        end
+      end
+    end
+  end
+end