bel_parser 1.0.0.alpha.22 → 1.0.0.alpha.23

checksums.yaml

@@ -1,7 +1,7 @@
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-  data.tar.gz: 42a84936274b3cdd6eccdb2918b2b5ad37f49551
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data/.gemspec

@@ -11,7 +11,7 @@ Gem::Specification.new do |spec|
                                  'Anthony Bargnesi',
                                  'Nick Bargnesi',
                                ]
-  spec.date                  = %q{2016-05-02}
+  spec.date                  = %q{2016-05-03}
   spec.email                 = %q{abargnesi@selventa.com}
   spec.files                 = [
                                  Dir.glob('lib/**/*.{rb,rl}'),

data/VERSION

@@ -1 +1 @@
-1.0.0.alpha.22
+1.0.0.alpha.23

data/lib/bel/translator/plugins/bel_script/bel_citation_serialization.rb

@@ -1,13 +1,13 @@
-require_relative 'evidence_serialization.rb'
+require_relative 'nanopub_serialization.rb'
 
-# BEL Script evidence serialization that groups evidence by citation scoped to
+# BEL Script nanopub serialization that groups nanopub by citation scoped to
 # individual statement groups (i.e. BEL Script's +SET STATEMENT_GROUP+ and
 # +UNSET STATEMENT_GROUP+).
 #
-# @example Citation serialization for a group of evidence
+# @example Citation serialization for a group of nanopub
 #   SET STATEMENT_GROUP = 12857727
 #   SET Citation = {"PubMed", "Journal...", "12857727", "2003-08-11", "", ""}
-#   SET Evidence = "USF1 and USF2 bound the IGF2R promoter in vitro, ..."
+#   SET Support = "USF1 and USF2 bound the IGF2R promoter in vitro, ..."
 #   SET CellLine = "MCF 10A"
 #   SET TextLocation = Abstract
 #   complex(p(HGNC:USF1),g(HGNC:IGF2R))
@@ -18,41 +18,41 @@ require_relative 'evidence_serialization.rb'
 #
 #   tscript(p(HGNC:USF1)) causesNoChange r(HGNC:IGF2R)
 #
-#   SET Evidence = "c-Myc was present on the CDK4 promoter to the ..."
+#   SET Support = "c-Myc was present on the CDK4 promoter to the ..."
 #   complex(p(HGNC:MYC),g(HGNC:CDK4))
 #   UNSET STATEMENT_GROUP
 module BEL::Translator::Plugins::BelScript::BelCitationSerialization
-  include BEL::Translator::Plugins::BelScript::EvidenceSerialization
+  include BEL::Translator::Plugins::BelScript::NanopubSerialization
 
-  # Serialize the {BEL::Model::Evidence evidence} to a BEL Script string.
+  # Serialize the {BEL::Nanopub::Nanopub nanopub} to a BEL Script string.
   #
   # Includes +SET AnnotationName+ and +UNSET AnnotationName+ where needed in
   # order to remove duplicating annotations.
   #
-  # @param  [BEL::Model::Evidence] evidence the evidence to serialize
+  # @param  [BEL::Nanopub::Nanopub] nanopub the nanopub to serialize
   # @return [String]               the BEL Script string
-  def to_bel(evidence)
+  def to_bel(nanopub)
     bel = ''
 
-    citation     = citation_value(evidence)
-    summary_text = summary_text_value(evidence)
-    annotations  = annotation_values(evidence)
+    citation     = citation_value(nanopub)
+    summary_text = summary_text_value(nanopub)
+    annotations  = annotation_values(nanopub)
 
     current_annotations            = {}.merge(annotations)
     current_annotations[:Citation] = citation if citation
-    current_annotations[:Evidence] = summary_text if summary_text
+    current_annotations[:Support]  = summary_text if summary_text
 
-    if !evidence.citation.id || evidence.citation.id.empty?
+    if !nanopub.citation.id || nanopub.citation.id.empty?
       citation_id = quote('')
     else
-      citation_id = quote_if_needed(evidence.citation.id)
+      citation_id = quote_if_needed(nanopub.citation.id)
     end
 
     # Reset cumulative annotations if new citation.
     if cumulative_citation == nil
       bel << %Q{SET STATEMENT_GROUP = #{citation_id}\n}
       cumulative_annotations.clear
-    elsif evidence.citation != cumulative_citation
+    elsif nanopub.citation != cumulative_citation
       bel << %Q{UNSET STATEMENT_GROUP\n}
       bel << "\n\n"
       bel << %Q{SET STATEMENT_GROUP = #{citation_id}\n}
@@ -60,22 +60,22 @@ module BEL::Translator::Plugins::BelScript::BelCitationSerialization
     end
 
     # Hang on to the last citation.
-    self.cumulative_citation = evidence.citation
+    self.cumulative_citation = nanopub.citation
 
-    # UNSET unused annotations from previous evidence.
+    # UNSET unused annotations from previous nanopub.
     (cumulative_annotations.keys - current_annotations.keys).each do |unset_key|
       bel << "UNSET #{unset_key}\n"
       cumulative_annotations.delete(unset_key)
     end
 
-    # Remove annotation if key/value was SET by a previous evidence.
+    # Remove annotation if key/value was SET by a previous nanopub.
     Hash[
       cumulative_annotations.to_a & current_annotations.to_a
     ].each do |same_k, _|
       current_annotations.delete(same_k)
     end
 
-    # Retain the current evidence's annotation in cumulative set.
+    # Retain the current nanopub's annotation in cumulative set.
     cumulative_annotations.merge!(current_annotations)
 
     # SET Citation
@@ -84,10 +84,10 @@ module BEL::Translator::Plugins::BelScript::BelCitationSerialization
       bel << "SET Citation = {#{citation}}\n"
     end
 
-    # SET Evidence
-    summary_text = current_annotations.delete(:Evidence)
+    # SET Support
+    summary_text = current_annotations.delete(:Support)
     if summary_text
-      bel << %Q{SET Evidence = "#{summary_text}"\n}
+      bel << %Q{SET Support = "#{summary_text}"\n}
     end
 
     # SET new or modified annotations
@@ -96,9 +96,9 @@ module BEL::Translator::Plugins::BelScript::BelCitationSerialization
     end
 
     # Assert BEL statement
-    bel << "#{evidence.bel_statement}\n"
+    bel << "#{nanopub.bel_statement}\n"
 
-    # Separate evidence by new line.
+    # Separate nanopub by new line.
     bel << "\n"
 
     bel
@@ -106,12 +106,12 @@ module BEL::Translator::Plugins::BelScript::BelCitationSerialization
 
   private
 
-  # The cumulative citation that is active for the current evidence. This is
+  # The cumulative citation that is active for the current nanopub. This is
   # tracked in order to decide when to begin a new statement group.
   attr_accessor :cumulative_citation
 
   # Returns the cumulative +Hash+ of annotations. This *state* is used to keep
-  # track of the active, scoped annotations as evidence is serialized.
+  # track of the active, scoped annotations as nanopub is serialized.
   def cumulative_annotations
     @cumulative_annotations ||= {}
   end

data/lib/bel/translator/plugins/bel_script/bel_discrete_serialization.rb

@@ -1,69 +1,69 @@
-require_relative 'evidence_serialization'
+require_relative 'nanopub_serialization'
 
-# BEL Script evidence serialization that writes each evidence with their full
+# BEL Script nanopub serialization that writes each nanopub with their full
 # set of annotations (i.e. includes all `SET` and necessary `UNSET` records).
 # This style is more readable because it groups all set annotations near the
 # BEL statement.
 #
-# @example Discrete serialization for a group of evidence
+# @example Discrete serialization for a group of nanopub
 #   SET Citation = {"PubMed", "Journal...", "12857727", "2003-08-11", "", ""}
-#   SET Evidence = "USF1 and USF2 bound the IGF2R promoter in vitro, ..."
+#   SET Support = "USF1 and USF2 bound the IGF2R promoter in vitro, ..."
 #   SET CellLine = "MCF 10A"
 #   SET TextLocation = Abstract
 #   complex(p(HGNC:USF1),g(HGNC:IGF2R))
 #
 #   SET Citation = {"PubMed", "Journal...", "12857727", "2003-08-11", "", ""}
-#   SET Evidence = "USF1 and USF2 bound the IGF2R promoter in vitro, ..."
+#   SET Support = "USF1 and USF2 bound the IGF2R promoter in vitro, ..."
 #   SET CellLine = "MCF 10A"
 #   SET TextLocation = Abstract
 #   complex(p(HGNC:USF2),g(HGNC:IGF2R))
 #
 #   SET Citation = {"PubMed", "Journal...", "12857727", "2003-08-11", "", ""}
-#   SET Evidence = "USF1 and USF2 bound the IGF2R promoter in vitro, ..."
+#   SET Support = "USF1 and USF2 bound the IGF2R promoter in vitro, ..."
 #   SET CellLine = "MCF 10A"
 #   SET TextLocation = Abstract
 #   tscript(p(HGNC:USF2)) directlyIncreases r(HGNC:IGF2R)
 #
 #   SET Citation = {"PubMed", "Journal...", "12857727", "2003-08-11", "", ""}
-#   SET Evidence = "USF1 and USF2 bound the IGF2R promoter in vitro, ..."
+#   SET Support = "USF1 and USF2 bound the IGF2R promoter in vitro, ..."
 #   SET CellLine = "MCF 10A"
 #   SET TextLocation = Abstract
 #   tscript(p(HGNC:USF1)) causesNoChange r(HGNC:IGF2R)
 #
 #   SET Citation = {"PubMed", "Journal...", "12857727", "2003-08-11", "", ""}
-#   SET Evidence = "c-Myc was present on the CDK4 promoter to the ..."
+#   SET Support = "c-Myc was present on the CDK4 promoter to the ..."
 #   SET CellLine = "MCF 10A"
 #   SET TextLocation = Abstract
 #   complex(p(HGNC:MYC),g(HGNC:CDK4))
 #
 #   UNSET CellLine
 module BEL::Translator::Plugins::BelScript::BelDiscreteSerialization
-  include BEL::Translator::Plugins::BelScript::EvidenceSerialization
+  include BEL::Translator::Plugins::BelScript::NanopubSerialization
 
-  # Serialize the {BEL::Model::Evidence evidence} to a BEL Script string.
+  # Serialize the {BEL::Nanopub::Nanopub nanopub} to a BEL Script string.
   # Includes all necessary +SET AnnotationName+ and +UNSET AnnotationName+
   # records around the BEL statement.
   #
-  # @param  [BEL::Model::Evidence] evidence the evidence to serialize
+  # @param  [BEL::Nanopub::Nanopub] nanopub the nanopub to serialize
   # @return [String]               the BEL Script string
-  def to_bel(evidence)
+  def to_bel(nanopub)
     bel = ''
 
-    citation     = citation_value(evidence)
-    summary_text = summary_text_value(evidence)
-    annotations  = annotation_values(evidence)
+    citation     = citation_value(nanopub)
+    summary_text = summary_text_value(nanopub)
+    annotations  = annotation_values(nanopub)
 
     current_annotations            = {}.merge(annotations)
     current_annotations[:Citation] = citation if citation
-    current_annotations[:Evidence] = summary_text if summary_text
+    current_annotations[:Support]  = summary_text if summary_text
 
-    # UNSET unused annotations from previous evidence.
+    # UNSET unused annotations from previous nanopub.
     (cumulative_annotations.keys - current_annotations.keys).each do |unset_key|
       bel << "UNSET #{unset_key}\n"
       cumulative_annotations.delete(unset_key)
     end
 
-    # Retain the current evidence's annotation in cumulative set.
+    # Retain the current nanopub's annotation in cumulative set.
     cumulative_annotations.merge!(current_annotations)
 
     # SET Citation
@@ -72,10 +72,10 @@ module BEL::Translator::Plugins::BelScript::BelDiscreteSerialization
       bel << "SET Citation = {#{citation}}\n"
     end
 
-    # SET Evidence
-    summary_text = current_annotations.delete(:Evidence)
+    # SET Support
+    summary_text = current_annotations.delete(:Support)
     if summary_text
-      bel << %Q{SET Evidence = "#{summary_text}"\n}
+      bel << %Q{SET Support = "#{summary_text}"\n}
     end
 
     # SET new or modified annotations
@@ -84,9 +84,9 @@ module BEL::Translator::Plugins::BelScript::BelDiscreteSerialization
     end
 
     # Assert BEL statement
-    bel << "#{evidence.bel_statement}\n"
+    bel << "#{nanopub.bel_statement}\n"
 
-    # Separate evidence by new line.
+    # Separate nanopub by new line.
     bel << "\n"
 
     bel
@@ -95,14 +95,14 @@ module BEL::Translator::Plugins::BelScript::BelDiscreteSerialization
   private
 
   # Returns the cumulative +Hash+ of annotations. This *state* is used to keep
-  # track of the active, scoped annotations as evidence is serialized.
+  # track of the active, scoped annotations as nanopub is serialized.
   def cumulative_annotations
     @cumulative_annotations ||= {}
   end
 
   # Return BEL Script syntax that completes the BEL Script document.
   # The empty string is returned since no ending syntax is necessary when
-  # serializing each evidence discretely.
+  # serializing each nanopub discretely.
   def epilogue
     ""
   end

data/lib/bel/translator/plugins/bel_script/bel_top_down_serialization.rb

@@ -1,12 +1,12 @@
-require_relative 'evidence_serialization.rb'
+require_relative 'nanopub_serialization.rb'
 
-# BEL Script evidence serialization that writes evidence sequentially while
+# BEL Script nanopub serialization that writes nanopubs sequentially while
 # including only the necessary unsetting of annotations (i.e. BEL Script's
 # +UNSET AnnotationName+ syntax).
 #
-# @example Top-down serialization for a group of evidence
+# @example Top-down serialization for a group of nanopubs
 #   SET Citation = {"PubMed", "Journal...", "12857727", "2003-08-11", "", ""}
-#   SET Evidence = "USF1 and USF2 bound the IGF2R promoter in vitro, ..."
+#   SET Support = "USF1 and USF2 bound the IGF2R promoter in vitro, ..."
 #   SET CellLine = "MCF 10A"
 #   SET TextLocation = Abstract
 #   complex(p(HGNC:USF1),g(HGNC:IGF2R))
@@ -17,44 +17,44 @@ require_relative 'evidence_serialization.rb'
 #
 #   tscript(p(HGNC:USF1)) causesNoChange r(HGNC:IGF2R)
 #
-#   SET Evidence = "c-Myc was present on the CDK4 promoter to the ..."
+#   SET Support = "c-Myc was present on the CDK4 promoter to the ..."
 #   complex(p(HGNC:MYC),g(HGNC:CDK4))
 #
 #   UNSET CellLine
 module BEL::Translator::Plugins::BelScript::BelTopDownSerialization
-  include BEL::Translator::Plugins::BelScript::EvidenceSerialization
+  include BEL::Translator::Plugins::BelScript::NanopubSerialization
 
-  # Serialize the {BEL::Model::Evidence evidence} to a BEL Script string.
+  # Serialize the {BEL::Nanopub::Nanopub nanopub} to a BEL Script string.
   # Includes all necessary +SET AnnotationName+ and +UNSET AnnotationName+
   # records within the scope of a citation's statement group.
   #
-  # @param  [BEL::Model::Evidence] evidence the evidence to serialize
+  # @param  [BEL::Nanopub::Nanopub] nanopub the nanopub to serialize
   # @return [String]               the BEL Script string
-  def to_bel(evidence)
+  def to_bel(nanopub)
     bel = ''
 
-    citation     = citation_value(evidence)
-    summary_text = summary_text_value(evidence)
-    annotations  = annotation_values(evidence)
+    citation     = citation_value(nanopub)
+    summary_text = summary_text_value(nanopub)
+    annotations  = annotation_values(nanopub)
 
     current_annotations            = {}.merge(annotations)
     current_annotations[:Citation] = citation if citation
-    current_annotations[:Evidence] = summary_text if summary_text
+    current_annotations[:Support] = summary_text if summary_text
 
-    # UNSET unused annotations from previous evidence.
+    # UNSET unused annotations from previous nanopub.
     (cumulative_annotations.keys - current_annotations.keys).each do |unset_key|
       bel << "UNSET #{unset_key}\n"
       cumulative_annotations.delete(unset_key)
     end
 
-    # Remove annotation if key/value was SET by a previous evidence.
+    # Remove annotation if key/value was SET by a previous nanopub.
     Hash[
       cumulative_annotations.to_a & current_annotations.to_a
     ].each do |same_k, _|
       current_annotations.delete(same_k)
     end
 
-    # Retain the current evidence's annotation in cumulative set.
+    # Retain the current nanopub's annotation in cumulative set.
     cumulative_annotations.merge!(current_annotations)
 
     # SET Citation
@@ -63,10 +63,10 @@ module BEL::Translator::Plugins::BelScript::BelTopDownSerialization
       bel << "SET Citation = {#{citation}}\n"
     end
 
-    # SET Evidence
-    summary_text = current_annotations.delete(:Evidence)
+    # SET Support
+    summary_text = current_annotations.delete(:Support)
     if summary_text
-      bel << %Q{SET Evidence = "#{summary_text}"\n}
+      bel << %Q{SET Support = "#{summary_text}"\n}
     end
 
     # SET new or modified annotations
@@ -75,9 +75,9 @@ module BEL::Translator::Plugins::BelScript::BelTopDownSerialization
     end
 
     # Assert BEL statement
-    bel << "#{evidence.bel_statement}\n"
+    bel << "#{nanopub.bel_statement}\n"
 
-    # Separate evidence by new line.
+    # Separate nanopub by new line.
     bel << "\n"
 
     bel
@@ -86,7 +86,7 @@ module BEL::Translator::Plugins::BelScript::BelTopDownSerialization
   private
 
   # Returns the cumulative +Hash+ of annotations. This *state* is used to keep
-  # track of the active, scoped annotations as evidence is serialized.
+  # track of the active, scoped annotations as nanopub is serialized.
   def cumulative_annotations
     @cumulative_annotations ||= {}
   end

data/lib/bel/translator/plugins/bel_script/{evidence_serialization.rb → nanopub_serialization.rb}

@@ -1,19 +1,19 @@
 require 'bel/quoting'
 
-# Serializing of common {BEL::Model::Evidence evidence} components to BEL
+# Serializing of common {BEL::Nanopub::Nanopub nanopub} components to BEL
 # Script syntax.
 #
 # @abstract
-module BEL::Translator::Plugins::BelScript::EvidenceSerialization
+module BEL::Translator::Plugins::BelScript::NanopubSerialization
   include BEL::Quoting
 
-  # Serialize the {BEL::Model::Evidence evidence} to a BEL Script string.
+  # Serialize the {BEL::Nanopub::Nanopub nanopub} to a BEL Script string.
   #
-  # @param  [BEL::Model::Evidence] evidence the evidence to serialize
+  # @param  [BEL::Nanopub::Nanopub] nanopub the nanopub to serialize
   # @return [String]               the BEL Script string
   # @abstract Include and override {#to_bel} to implement serialization
-  #           {BEL::Model::Evidence evidence} to BEL Script
-  def to_bel(evidence)
+  #           {BEL::Nanopub::Nanopub nanopub} to BEL Script
+  def to_bel(nanopub)
   end
 
   # Return BEL Script syntax that completes the BEL Script document.
@@ -25,8 +25,8 @@ module BEL::Translator::Plugins::BelScript::EvidenceSerialization
 
   protected
 
-  def citation_value(evidence)
-    citation = evidence.citation
+  def citation_value(nanopub)
+    citation = nanopub.citation
 
     return nil unless citation && citation.valid?
 
@@ -42,8 +42,8 @@ module BEL::Translator::Plugins::BelScript::EvidenceSerialization
     values.join(', ')
   end
 
-  def summary_text_value(evidence)
-    summary_text = evidence.summary_text
+  def summary_text_value(nanopub)
+    summary_text = nanopub.summary_text
 
     return nil unless summary_text && summary_text.value
 
@@ -53,8 +53,8 @@ module BEL::Translator::Plugins::BelScript::EvidenceSerialization
     value
   end
 
-  def annotation_values(evidence)
-    experiment_context = evidence.experiment_context
+  def annotation_values(nanopub)
+    experiment_context = nanopub.experiment_context
 
     return {} unless experiment_context
 

data/lib/bel/translator/plugins/bel_script/reader.rb

@@ -1,6 +1,6 @@
 require 'bel_parser'
 require 'bel_parser/resource/resource_url_reader'
-require 'bel/evidence_model'
+require 'bel/nanopub'
 
 module BEL::Translator::Plugins
   module BelScript
@@ -28,7 +28,7 @@ module BEL::Translator::Plugins
             true,
             false
           ).each do |(num, line, ast_node, nanopub_hash)|
-                  yield ::BEL::Model::Evidence.create(nanopub_hash)
+                  yield ::BEL::Nanopub::Nanopub.create(nanopub_hash)
                 end
         else
           enum_for(:each)

data/lib/bel/translator/plugins/bel_script/writer.rb

@@ -9,16 +9,16 @@ module BEL::Translator::Plugins
 
     class Writer
 
-      # Create a {Writer} object that serializes {BEL::Model::Evidence} to
+      # Create a {Writer} object that serializes {BEL::Nanopub::Nanopub} to
       # BEL Script.
       #
-      # @param [Enumerator<BEL::Model::Evidence>] data evidence data iterated
+      # @param [Enumerator<BEL::Nanopub::Nanopub>] data nanopubs iterated
       #        using +each+
       # @option options [Boolean] :write_header +true+ to write the BEL Script
       #         document header; +false+ to not write the BEL Script document
       #         header
       # @option options [Symbol,Module] :serialization the serialization
-      #         technique to use for evidence; a +Module+ type will be used as
+      #         technique to use for nanopub; a +Module+ type will be used as
       #         is; a +Symbol+ type will be mapped as
       #         +:discrete+ => {BelDiscreteSerialization},
       #         +:topdown+ => {BelTopDownSerialization},
@@ -61,27 +61,27 @@ module BEL::Translator::Plugins
         if block_given?
           combiner =
             if @streaming
-              BEL::Model::StreamingEvidenceCombiner.new(@data)
+              BEL::Nanopub::StreamingNanopubCombiner.new(@data)
             elsif @annotation_reference_map && @namespace_reference_map
-              BEL::Model::MapReferencesCombiner.new(
+              BEL::Nanopub::MapReferencesCombiner.new(
                 @data,
-                BEL::Model::HashMapReferences.new(
+                BEL::Nanopub::HashMapReferences.new(
                   @annotation_reference_map,
                   @namespace_reference_map
                 )
               )
             else
-              BEL::Model::BufferingEvidenceCombiner.new(@data)
+              BEL::Nanopub::BufferingNanopubCombiner.new(@data)
             end
 
           header_flag = true
-          combiner.each { |evidence|
+          combiner.each { |nanopub|
 
-            # serialize evidence
-            bel = to_bel(evidence)
+            # serialize nanopub
+            bel = to_bel(nanopub)
 
             if @write_header && header_flag
-              yield document_header(evidence.metadata.document_header)
+              yield document_header(nanopub.metadata.document_header)
               yield namespaces(combiner.namespace_references)
               yield annotations(combiner.annotation_references)
 

data/lib/bel/translator/plugins/bel_script.rb

@@ -5,7 +5,7 @@ module BEL::Translator::Plugins
   module BelScript
     ID          = :bel_script
     NAME        = 'BEL Script Translator'
-    DESCRIPTION = 'A translator that can read/write evidence to BEL Script.'
+    DESCRIPTION = 'A translator that reads/writes BEL nanopubs to BEL Script.'
     MEDIA_TYPES = %i(application/bel)
     EXTENSIONS  = %i(bel)
 

data/lib/bel_parser/script/keywords.rb

@@ -1,14 +1,16 @@
 module BELParser
   module Script
     module Keyword
-      BEL_VERSION_STRING = 'BELVersion'.freeze
-      BEL_VERSION_REGEX  = /\A#{BEL_VERSION_STRING}\Z/i
+      BEL_VERSION_STRING   = 'BELVersion'.freeze
+      BEL_VERSION_REGEX    = /\A#{BEL_VERSION_STRING}\Z/i
 
-      CITATION       = 'Citation'.freeze
-      CITATION_REGEX = /\A#{CITATION}\Z/i
+      CITATION             = 'Citation'.freeze
+      CITATION_REGEX       = /\A#{CITATION}\Z/i
 
-      SUPPORT       = 'Support'.freeze
-      SUPPORT_REGEX = /\A#{SUPPORT}\Z/i
+      SUPPORT              = 'Support'.freeze
+      SUPPORT_REGEX        = /\A#{SUPPORT}\Z/i
+
+      IMPLICIT_ANNOTATIONS = ['Citation', 'Support', 'STATEMENT_GROUP']
 
       def is_bel_version?(string)
         string =~ BEL_VERSION_REGEX
@@ -21,6 +23,10 @@ module BELParser
       def is_support?(string)
         string =~ SUPPORT_REGEX
       end
+
+      def is_implicit_annotation?(string)
+        IMPLICIT_ANNOTATIONS.any? { |annotation| string == annotation }
+      end
     end
   end
 end

data/lib/bel_parser/script/syntax/undefined_annotation.rb

@@ -4,15 +4,16 @@ require 'bel_parser/language/syntax_error'
 require 'bel_parser/quoting'
 require 'bel_parser/parsers/ast/node'
 require 'concurrent/hash'
+require_relative '../keywords'
 
 module BELParser
   module Script
     module Syntax
       class UndefinedAnnotation
         extend BELParser::Language::Syntax::SyntaxFunction
+        extend BELParser::Script::Keyword
 
         TARGET_NODE       = BELParser::Parsers::AST::Set
-        IMPLICIT_KEYWORDS = ['Citation', 'Evidence', 'STATEMENT_GROUP']
 
         def self.map(ast_node, script_context)
           return nil unless ast_node.is_a?(TARGET_NODE)
@@ -20,7 +21,7 @@ module BELParser
           annotation_definitions =
             script_context[:annotation_definitions] ||= Concurrent::Hash.new
 
-          return nil if IMPLICIT_KEYWORDS.include?(name_string)
+          return nil if is_implicit_annotation?(name_string)
           return nil if annotation_definitions.key?(name_string)
           UndefinedAnnotationError.new(
             ast_node,

data/lib/bel_parser/script/syntax/undefined_annotation_value.rb

@@ -4,6 +4,7 @@ require 'bel_parser/language/syntax_warning'
 require 'bel_parser/quoting'
 require 'bel_parser/parsers/ast/node'
 require 'concurrent/hash'
+require_relative '../keywords'
 
 module BELParser
   module Script
@@ -11,17 +12,17 @@ module BELParser
       class UndefinedAnnotationValue
         extend BELParser::Language::Syntax::SyntaxFunction
         extend BELParser::Quoting
+        extend BELParser::Script::Keyword
 
         TARGET_NODE       = BELParser::Parsers::AST::Set
         LIST_NODE         = BELParser::Parsers::AST::List
-        IMPLICIT_KEYWORDS = ['Citation', 'Evidence', 'STATEMENT_GROUP']
 
         def self.map(ast_node, script_context)
           return nil unless ast_node.is_a?(TARGET_NODE)
           name, value  = ast_node.children
           name_string  = ast_node.name.identifier.string_literal
 
-          return nil if IMPLICIT_KEYWORDS.include?(name_string)
+          return nil if is_implicit_annotation?(name_string)
           dataset = annotation(name_string, script_context)
           return nil unless dataset
 

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: bel_parser
 version: !ruby/object:Gem::Version
-  version: 1.0.0.alpha.22
+  version: 1.0.0.alpha.23
 platform: ruby
 authors:
 - Anthony Bargnesi
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2016-05-02 00:00:00.000000000 Z
+date: 2016-05-03 00:00:00.000000000 Z
 dependencies: []
 description: Implements language versions 1.0 and 2.0.
 email: abargnesi@selventa.com
@@ -30,7 +30,7 @@ files:
 - lib/bel/translator/plugins/bel_script/bel_citation_serialization.rb
 - lib/bel/translator/plugins/bel_script/bel_discrete_serialization.rb
 - lib/bel/translator/plugins/bel_script/bel_top_down_serialization.rb
-- lib/bel/translator/plugins/bel_script/evidence_serialization.rb
+- lib/bel/translator/plugins/bel_script/nanopub_serialization.rb
 - lib/bel/translator/plugins/bel_script/reader.rb
 - lib/bel/translator/plugins/bel_script/translator.rb
 - lib/bel/translator/plugins/bel_script/writer.rb