Module: BEL::Translator::Plugins::BelScript::BelDiscreteSerialization

Includes:
NanopubSerialization
Defined in:
lib/bel/translator/plugins/bel_script/bel_discrete_serialization.rb

Overview

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.

Examples:

Discrete serialization for a group of nanopub

SET Citation = {"PubMed", "Journal...", "12857727", "2003-08-11", "", ""}
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 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 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 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 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

Instance Method Summary collapse

Instance Method Details

#to_bel(nanopub) ⇒ String

Serialize the nanopub to a BEL Script string. Includes all necessary SET AnnotationName and UNSET AnnotationName records around the BEL statement.



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# File 'lib/bel/translator/plugins/bel_script/bel_discrete_serialization.rb', line 49

def to_bel(nanopub)
  bel = ''

  citation     = citation_value(nanopub)
  support = support_value(nanopub)
  annotations  = annotation_values(nanopub)

  current_annotations            = {}.merge(annotations)
  current_annotations[:Citation] = citation if citation
  current_annotations[:Support]  = support if support

  # 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 nanopub's annotation in cumulative set.
  cumulative_annotations.merge!(current_annotations)

  # SET Citation
  citation = current_annotations.delete(:Citation)
  if citation
    bel << "SET Citation = {#{citation}}\n"
  end

  # SET Support
  support = current_annotations.delete(:Support)
  if support
    bel << %Q{SET Support = "#{support}"\n}
  end

  # SET new or modified annotations
  current_annotations.sort.each do |(name, value)|
    bel << "SET #{name} = #{value}\n"
  end

  # Assert BEL statement
  bel << "#{nanopub.bel_statement}\n"

  # Separate nanopub by new line.
  bel << "\n"

  bel
end