Module: BEL::Translator::Plugins::BelScript::BelCitationSerialization

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

Overview

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).

Examples:

Citation serialization for a group of nanopub

SET STATEMENT_GROUP = 12857727
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))

complex(p(HGNC:USF2),g(HGNC:IGF2R))

tscript(p(HGNC:USF2)) directlyIncreases r(HGNC:IGF2R)

tscript(p(HGNC:USF1)) causesNoChange r(HGNC:IGF2R)

SET Support = "c-Myc was present on the CDK4 promoter to the ..."
complex(p(HGNC:MYC),g(HGNC:CDK4))
UNSET STATEMENT_GROUP

Instance Method Summary collapse

Instance Method Details

#to_bel(nanopub) ⇒ String

Serialize the nanopub to a BEL Script string.

Includes SET AnnotationName and UNSET AnnotationName where needed in order to remove duplicating annotations.

Parameters:

  • nanopub (BEL::Nanopub::Nanopub) —

    the nanopub to serialize

Returns:

  • (String) —

    the BEL Script string



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# File 'lib/bel/translator/plugins/bel_script/bel_citation_serialization.rb', line 34

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

  if !nanopub.citation.id || nanopub.citation.id.empty?
    citation_id = quote('')
  else
    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 nanopub.citation != cumulative_citation
    bel << %Q{UNSET STATEMENT_GROUP\n}
    bel << "\n\n"
    bel << %Q{SET STATEMENT_GROUP = #{citation_id}\n}
    cumulative_annotations.clear
  end

  # Hang on to the last citation.
  self.cumulative_citation = nanopub.citation

  # 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 nanopub.
  Hash[
    cumulative_annotations.to_a & current_annotations.to_a
  ].each do |same_k, _|
    current_annotations.delete(same_k)
  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