bel_parser 1.0.0.alpha.1 → 1.0.0.alpha.2

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

@@ -0,0 +1,31 @@
+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+ 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")+'.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/negative_correlation.rb

@@ -0,0 +1,31 @@
+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 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.'.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/orthologous.rb

@@ -0,0 +1,31 @@
+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 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.'.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/positive_correlation.rb

@@ -0,0 +1,31 @@
+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 in A and B have been observed to be positively correlated, thus B positiveCorrelation A is equivalent to A positiveCorrelation B.'.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/prognostic_biomarker_for.rb

@@ -0,0 +1,31 @@
+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 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.'.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/rate_limiting_step_of.rb

@@ -0,0 +1,31 @@
+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, 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>'.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/reactant_in.rb

@@ -0,0 +1,31 @@
+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), 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.'.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/sub_process_of.rb

@@ -0,0 +1,31 @@
+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, 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>'.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/transcribed_to.rb

@@ -0,0 +1,31 @@
+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 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.'.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/translated_to.rb

@@ -0,0 +1,31 @@
+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 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.'.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/translocates.rb

@@ -0,0 +1,31 @@
+require_relative '../../version1_0'
+require_relative '../../relationship'
+
+module BELParser
+  module Language
+    module Version1_0
+      module Relationships
+        # Translocates:  +translocation(A, ns1:v1, ns2:v2) translocates A+ -  This relationship links the abundance term in a +translocation()+ to the translocation. This relationship is direct because it is a _self_ relationship. The translocated abundance is directly acted on by the translocation process. This relationship is introduced by the BEL Compiler and may not be used by statements in BEL documents.
+        class Translocates
+          extend Relationship
+
+          SHORT       = :translocates
+          LONG        = :translocates
+          DESCRIPTION = ' +translocation(A, ns1:v1, ns2:v2) translocates A+ -  This relationship links the abundance term in a +translocation()+ to the translocation. This relationship is direct because it is a _self_ relationship. The translocated abundance is directly acted on by the translocation process. This relationship is introduced by the BEL Compiler and may not be used by statements in BEL documents.'.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/{version2 → version1_0}/return_types/abundance.rb

@@ -2,7 +2,7 @@ require_relative 'any'
 
 module BELParser
   module Language
-    module Version2
+    module Version1_0
       module ReturnTypes
         # Abundance return type.
         class Abundance < Any

data/lib/bel_parser/language/{version1 → version1_0}/return_types/any.rb

@@ -2,7 +2,7 @@ require 'English'
 
 module BELParser
   module Language
-    module Version1
+    module Version1_0
       module ReturnTypes
         # The any type.
         class Any

data/lib/bel_parser/language/{version1 → version1_0}/return_types/biological_process.rb

@@ -2,7 +2,7 @@ require_relative 'any'
 
 module BELParser
   module Language
-    module Version1
+    module Version1_0
       module ReturnTypes
         # Biological process return type.
         class BiologicalProcess < Any

data/lib/bel_parser/language/{version1 → version1_0}/return_types/catalytic_activity.rb

@@ -2,7 +2,7 @@ require_relative 'molecular_activity'
 
 module BELParser
   module Language
-    module Version1
+    module Version1_0
       module ReturnTypes
         # CatalyticActivity return type.
         class CatalyticActivity < MolecularActivity

data/lib/bel_parser/language/{version1 → version1_0}/return_types/chaperone_activity.rb

@@ -2,7 +2,7 @@ require_relative 'molecular_activity'
 
 module BELParser
   module Language
-    module Version1
+    module Version1_0
       module ReturnTypes
         # ChaperoneActivity return type.
         class ChaperoneActivity < MolecularActivity

data/lib/bel_parser/language/{version2 → version1_0}/return_types/complex_abundance.rb

@@ -2,7 +2,7 @@ require_relative 'abundance'
 
 module BELParser
   module Language
-    module Version2
+    module Version1_0
       module ReturnTypes
         # Complex abundance return type.
         class ComplexAbundance < Abundance

data/lib/bel_parser/language/{version1 → version1_0}/return_types/fusion.rb

@@ -2,7 +2,7 @@ require_relative 'any'
 
 module BELParser
   module Language
-    module Version1
+    module Version1_0
       module ReturnTypes
         # Fusion return type.
         class Fusion < Any

data/lib/bel_parser/language/{version2 → version1_0}/return_types/gene_abundance.rb

@@ -2,7 +2,7 @@ require_relative 'abundance'
 
 module BELParser
   module Language
-    module Version2
+    module Version1_0
       module ReturnTypes
         # Gene abundance return type.
         class GeneAbundance < Abundance

data/lib/bel_parser/language/{version1 → version1_0}/return_types/gtp_bound_activity.rb

@@ -2,7 +2,7 @@ require_relative 'molecular_activity'
 
 module BELParser
   module Language
-    module Version1
+    module Version1_0
       module ReturnTypes
         # GTP return type.
         class GTPBoundActivity < MolecularActivity

data/lib/bel_parser/language/{version1 → version1_0}/return_types/kinase_activity.rb

@@ -2,7 +2,7 @@ require_relative 'molecular_activity'
 
 module BELParser
   module Language
-    module Version1
+    module Version1_0
       module ReturnTypes
         # KinaseActivity return type.
         class KinaseActivity < MolecularActivity

data/lib/bel_parser/language/{version1 → version1_0}/return_types/list.rb

@@ -2,7 +2,7 @@ require_relative 'any'
 
 module BELParser
   module Language
-    module Version1
+    module Version1_0
       module ReturnTypes
         # List return type.
         class List < Any

data/lib/bel_parser/language/{version1 → version1_0}/return_types/micro_rna_abundance.rb

@@ -2,7 +2,7 @@ require_relative 'abundance'
 
 module BELParser
   module Language
-    module Version1
+    module Version1_0
       module ReturnTypes
         # Micro RNA abundance return type.
         class MicroRNAAbundance < Abundance

data/lib/bel_parser/language/{version1 → version1_0}/return_types/molecular_activity.rb

@@ -2,7 +2,7 @@ require_relative 'molecular_activity'
 
 module BELParser
   module Language
-    module Version1
+    module Version1_0
       module ReturnTypes
         # MolecularActivity return type.
         class MolecularActivity < Any

data/lib/bel_parser/language/{version1 → version1_0}/return_types/pathology.rb

@@ -2,7 +2,7 @@ require_relative 'biological_process'
 
 module BELParser
   module Language
-    module Version1
+    module Version1_0
       module ReturnTypes
         # Pathology return type.
         class Pathology < BiologicalProcess

data/lib/bel_parser/language/{version1 → version1_0}/return_types/peptidase_activity.rb

@@ -2,7 +2,7 @@ require_relative 'molecular_activity'
 
 module BELParser
   module Language
-    module Version1
+    module Version1_0
       module ReturnTypes
         # PeptidaseActivity return type.
         class PeptidaseActivity < MolecularActivity

data/lib/bel_parser/language/{version1 → version1_0}/return_types/phosphatase_activity.rb

@@ -2,7 +2,7 @@ require_relative 'molecular_activity'
 
 module BELParser
   module Language
-    module Version1
+    module Version1_0
       module ReturnTypes
         # PhosphataseActivity return type.
         class PhosphataseActivity < MolecularActivity

data/lib/bel_parser/language/{version2 → version1_0}/return_types/products.rb

@@ -2,7 +2,7 @@ require_relative 'any'
 
 module BELParser
   module Language
-    module Version2
+    module Version1_0
       module ReturnTypes
         # Products return type.
         class Products < Any

data/lib/bel_parser/language/{version2 → version1_0}/return_types/protein_abundance.rb

@@ -2,7 +2,7 @@ require_relative 'abundance'
 
 module BELParser
   module Language
-    module Version2
+    module Version1_0
       module ReturnTypes
         # Protein abundance return type.
         class ProteinAbundance < Abundance

data/lib/bel_parser/language/{version1 → version1_0}/return_types/protein_modification.rb

@@ -2,7 +2,7 @@ require_relative 'any'
 
 module BELParser
   module Language
-    module Version1
+    module Version1_0
       module ReturnTypes
         # Protein modification return type.
         class ProteinModification < Any

data/lib/bel_parser/language/{version2 → version1_0}/return_types/reactants.rb

@@ -2,7 +2,7 @@ require_relative 'any'
 
 module BELParser
   module Language
-    module Version2
+    module Version1_0
       module ReturnTypes
         # Reactants return type.
         class Reactants < Any

data/lib/bel_parser/language/{version1 → version1_0}/return_types/ribosylation_activity.rb

@@ -2,7 +2,7 @@ require_relative 'molecular_activity'
 
 module BELParser
   module Language
-    module Version1
+    module Version1_0
       module ReturnTypes
         # RibosylationActivity return type.
         class RibosylationActivity < MolecularActivity

data/lib/bel_parser/language/{version1 → version1_0}/return_types/rna_abundance.rb

@@ -2,7 +2,7 @@ require_relative 'abundance'
 
 module BELParser
   module Language
-    module Version1
+    module Version1_0
       module ReturnTypes
         # RNA abundance return type.
         class RNAAbundance < Abundance

data/lib/bel_parser/language/{version1 → version1_0}/return_types/substitution.rb

@@ -2,7 +2,7 @@ require_relative 'any'
 
 module BELParser
   module Language
-    module Version1
+    module Version1_0
       module ReturnTypes
         # Substitution return type.
         class Substitution < Any

data/lib/bel_parser/language/{version1 → version1_0}/return_types/transcriptional_activity.rb

@@ -2,7 +2,7 @@ require_relative 'molecular_activity'
 
 module BELParser
   module Language
-    module Version1
+    module Version1_0
       module ReturnTypes
         # TransportActivity return type.
         class TranscriptionalActivity < MolecularActivity

data/lib/bel_parser/language/{version1 → version1_0}/return_types/transport_activity.rb

@@ -2,7 +2,7 @@ require_relative 'molecular_activity'
 
 module BELParser
   module Language
-    module Version1
+    module Version1_0
       module ReturnTypes
         # TransportActivity return type.
         class TransportActivity < MolecularActivity

data/lib/bel_parser/language/{version1 → version1_0}/return_types/truncation.rb

@@ -2,7 +2,7 @@ require_relative 'any'
 
 module BELParser
   module Language
-    module Version1
+    module Version1_0
       module ReturnTypes
         # Truncation return type.
         class Truncation < Any

data/lib/bel_parser/language/version1_0/syntax/function.rb

@@ -0,0 +1,29 @@
+require 'bel_parser/parsers/ast/node'
+
+module BELParser
+  module Language
+    module Version1_0
+      module Syntax
+        # Function will add syntax errors to
+        # {BELParser::Parsers::AST::Function} nodes that do not have a valid
+        # BEL 1.0 functon name.
+        class Function
+
+          private_class_method :new
+
+          V1 = ::BELParser::Language::Version1_0::Specification.new
+
+          def self.match(input_ast)
+            input_ast.traverse do |node|
+              next unless node.is_a?(BELParser::Parsers::AST::Function)
+              function_name = node.identifier.string_literal
+              unless V1.function(function_name.to_sym)
+                node.add_syntax_error(:FunctionV1)
+              end
+            end
+          end
+        end
+      end
+    end
+  end
+end