Class: BEL::Nanopub::Nanopub

Inherits:
Object
  • Object
show all
Defined in:
lib/bel/nanopub/nanopub.rb,
lib/bel/translator/plugins/rdf/monkey_patch.rb

Overview

Nanopub represents an asserted biological interaction with associated constituents:

  • BEL Statement

  • Citation

  • Support

  • Experiment Context

  • References

  • Metadata

Class Method Summary collapse

Instance Method Summary collapse

Class Method Details

.create(hash) ⇒ Object 



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# File 'lib/bel/nanopub/nanopub.rb', line 23

def self.create(hash)
  nanopub = Nanopub.new
  # Order-dependent; metadata/references must be set first in order for
  # _parse_statement to reference specification and namespaces.
  nanopub.metadata           = Metadata.new(hash[:metadata] || {})
  nanopub.references         = References.new(hash[:references] || {})
  nanopub.bel_statement      = hash[:bel_statement] || nil
  nanopub.citation           = Citation.new(hash[:citation] || {})
  nanopub.support.value      = hash[:support] || nil
  nanopub.experiment_context = ExperimentContext.new(hash[:experiment_context] || [])
  nanopub
end

Instance Method Details

#bel_statement ⇒ Object 



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# File 'lib/bel/nanopub/nanopub.rb', line 36

def bel_statement
  @bel_statement
end

#bel_statement=(bel_statement) ⇒ Object 



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# File 'lib/bel/nanopub/nanopub.rb', line 40

def bel_statement=(bel_statement)
  @bel_statement =
    case bel_statement
    when String
      _parse_statement(bel_statement)
    when BELParser::Expression::Model::Statement
      bel_statement
    when nil
      nil
    else
      raise ArgumentError, %(expected String, Statement, actual: #{bel_statement.class})
    end
end

#citation ⇒ Object 



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# File 'lib/bel/nanopub/nanopub.rb', line 54

def citation
  (@citation ||= Citation.new)
end

#citation=(citation) ⇒ Object 



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# File 'lib/bel/nanopub/nanopub.rb', line 58

def citation=(citation)
  @citation = citation
end

#experiment_context ⇒ Object 



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# File 'lib/bel/nanopub/nanopub.rb', line 70

def experiment_context
  (@experiment_context ||= ExperimentContext.new)
end

#experiment_context=(experiment_context) ⇒ Object 



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# File 'lib/bel/nanopub/nanopub.rb', line 74

def experiment_context=(experiment_context)
  @experiment_context = experiment_context
end

#metadata ⇒ Object 



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# File 'lib/bel/nanopub/nanopub.rb', line 86

def metadata
  (@metadata ||= Metadata.new)
end

#metadata=(metadata) ⇒ Object 



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# File 'lib/bel/nanopub/nanopub.rb', line 90

def metadata=(metadata)
  @metadata = metadata
end

#references ⇒ Object 



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# File 'lib/bel/nanopub/nanopub.rb', line 78

def references
  (@references ||= References.new)
end

#references=(references) ⇒ Object 



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# File 'lib/bel/nanopub/nanopub.rb', line 82

def references=(references)
  @references = references
end

#support ⇒ Object 



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# File 'lib/bel/nanopub/nanopub.rb', line 62

def support
  (@support ||= Support.new)
end

#support=(support) ⇒ Object 



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# File 'lib/bel/nanopub/nanopub.rb', line 66

def support=(support)
  @support = support
end

#to_h(hash = {}) ⇒ Object 



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# File 'lib/bel/nanopub/nanopub.rb', line 94

def to_h(hash = {})
  hash.merge!(
    {
      :bel_statement      => bel_statement,
      :citation           => citation.to_h,
      :support            => support.value,
      :experiment_context => experiment_context.values,
      :references         => references.to_h,
      :metadata           => metadata.to_a
    }
  )
  hash
end

#to_rdf(remap = nil) ⇒ Object 



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# File 'lib/bel/translator/plugins/rdf/monkey_patch.rb', line 346

def to_rdf(remap = nil)
  uri                       = to_uri

  # parse BEL statement if necessary
  unless self.bel_statement.is_a?(::BEL::Nanopub::Statement)
    self.bel_statement = self.class.parse_statement(self)
  end

  # convert BEL statement to RDF
  statement_uri, statements = bel_statement.to_rdf(uri, remap)

  statements << ::RDF::Statement.new(uri,           BELRDF::RDF.type,          BELRDF::BELV.Nanopub, :graph_name => uri)
  statements << ::RDF::Statement.new(statement_uri, BELRDF::BELV.hasNanopub,  uri,                     :graph_name => uri)
  statements << ::RDF::Statement.new(uri,           BELRDF::BELV.hasStatement, statement_uri,           :graph_name => uri)

  annotations = bel_statement.annotations

  # citation
  citation = annotations.delete('Citation')
  if citation
    value = citation.value.map{|x| x.gsub('"', '')}
    if citation and value[0] == 'PubMed'
      pid = value[2]
      statements << ::RDF::Statement.new(uri, BELRDF::BELV.hasCitation, BELRDF::PUBMED[pid], :graph_name => uri)
    end
  end

  # support
  support = annotations.delete('Support')
  if support
    value = support.value.gsub('"', '').force_encoding('UTF-8')
    statements << ::RDF::Statement.new(uri, BELRDF::BELV.hasSupport, value, :graph_name => uri)
  end

  # annotations
  annotations.each do |_, anno|
    name = anno.name.gsub('"', '')

    if BELRDF::const_defined? name
      annotation_scheme = BELRDF::const_get name
      [anno.value].flatten.map{|x| x.gsub('"', '')}.each do |val|
        value_uri = BELRDF::RDF::URI(URI.encode(annotation_scheme + val.to_s))
        statements << ::RDF::Statement.new(uri, BELRDF::BELV.hasAnnotation, value_uri, :graph_name => uri)
      end
    end
  end

  [uri, statements]
end

#to_uri ⇒ Object 



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# File 'lib/bel/translator/plugins/rdf/monkey_patch.rb', line 342

def to_uri
  BELRDF::BELE[BELRDF.generate_uuid]
end

#to_void_dataset(void_dataset_uri) ⇒ Object 



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# File 'lib/bel/translator/plugins/rdf/monkey_patch.rb', line 396

def to_void_dataset(void_dataset_uri)
  document_header = self.metadata[:document_header]
  return nil if !document_header || !document_header.is_a?(Hash)

  triples = ::RDF::Repository.new
  triples << ::RDF::Statement.new(void_dataset_uri, ::RDF.type, BELRDF::VOID.Dataset)

  name = version = nil
  document_header.each do |property, value|
    case property
      when /name/i
        name     = value.to_s
        triples << ::RDF::Statement.new(void_dataset_uri, BELRDF::DC.title, name)
      when /description/i
        triples << ::RDF::Statement.new(void_dataset_uri, BELRDF::DC.description, value.to_s)
      when /version/i
        version  = value.to_s
      when /copyright/i
        waiver = RDF::Vocabulary.new('http://vocab.org/waiver/terms/').waiver

        value = value.to_s
        uri   = RDF::URI(value)
        value = if uri.valid?
                  uri
                else
                  value
                end
        triples << ::RDF::Statement.new(void_dataset_uri, waiver, value)
      when /authors/i
        if value.respond_to?(:each)
          value.each do |v|
            triples << ::RDF::Statement.new(void_dataset_uri, BELRDF::DC.creator, v.to_s)
          end
        else
          triples << ::RDF::Statement.new(void_dataset_uri, BELRDF::DC.creator, value.to_s)
        end
      when /licenses/i
        value = value.to_s
        uri   = RDF::URI(value)
        value = if uri.valid?
                  uri
                else
                  value
                end
        triples << ::RDF::Statement.new(void_dataset_uri, BELRDF::DC.license, value)
      when /contactinfo/i
        triples << ::RDF::Statement.new(void_dataset_uri, BELRDF::DC.publisher, :publisher)
        triples << ::RDF::Statement.new(:publisher,       ::RDF.type,           BELRDF::FOAF.Person)
        triples << ::RDF::Statement.new(:publisher,       BELRDF::FOAF.mbox,    value.to_s)
    end
  end

  if name && version
    identifier = "#{name}/#{version}"
    triples << ::RDF::Statement.new(void_dataset_uri, BELRDF::DC.identifier, identifier)
  end

  triples
end