Class: BEL::Model::Statement

Inherits:
Object
  • Object
show all
Defined in:
lib/bel/evidence_model/bel_statement.rb,
lib/bel/extensions/rdf/rdf.rb

Overview

A Statement captures a BEL statement composed of a subject Term, relationship, and object Term. A Statement may be one of the following common forms:

  • SUBJECT

    • complex(p(HGNC:F3),p(HGNC:F7))

  • SUBJECT RELATIONSHIP OBJECT(Term)

    • pep(complex(p(HGNC:F3),p(HGNC:F7))) => pep(p(HGNC:F9))

  • SUBJECT RELATIONSHIP OBJECT(Statement)

    • p(HGNC:VHL) -> (p(HGNC:TNF) -> bp(GOBP:“cell death”))

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(subject = nil, relationship = nil, object = nil, comment = nil) ⇒ Statement

Creates a BEL::Model::Statement with subject, relationship, and object.

Parameters:

  • subject (Term) (defaults to: nil) —

    the subject term that is perturbed within an experiment

  • relationship (#to_s) (defaults to: nil) —

    the observed relationship between the subject and object (either Term or BEL::Model::Statement).

  • object (Term|Statement) (defaults to: nil) —

    the object term that is measured for change within an experiment



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# File 'lib/bel/evidence_model/bel_statement.rb', line 25

def initialize(subject = nil, relationship = nil, object = nil, comment = nil)
  @subject      = subject
  @relationship = relationship
  @object       = object
  @comment      = comment
  @annotations  = annotations
end

Instance Attribute Details

#comment ⇒ Object

Returns the value of attribute comment.



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# File 'lib/bel/evidence_model/bel_statement.rb', line 15

def comment
  @comment
end

#object ⇒ Object

Returns the value of attribute object.



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# File 'lib/bel/evidence_model/bel_statement.rb', line 15

def object
  @object
end

#relationship ⇒ Object

Returns the value of attribute relationship.



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# File 'lib/bel/evidence_model/bel_statement.rb', line 15

def relationship
  @relationship
end

#subject ⇒ Object

Returns the value of attribute subject.



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# File 'lib/bel/evidence_model/bel_statement.rb', line 15

def subject
  @subject
end

Instance Method Details

#==(other) ⇒ Object Also known as: eql? 



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# File 'lib/bel/evidence_model/bel_statement.rb', line 57

def ==(other)
  return false if other == nil
  @subject == other.subject &&
  @relationship == other.relationship &&
  @object == other.object
end

#annotations ⇒ Object 



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# File 'lib/bel/evidence_model/bel_statement.rb', line 33

def annotations
  @annotations ||= []
end

#annotations=(annotations) ⇒ Object 



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# File 'lib/bel/evidence_model/bel_statement.rb', line 37

def annotations=(annotations)
  @annotations = annotations
end

#hash ⇒ Object 



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# File 'lib/bel/evidence_model/bel_statement.rb', line 53

def hash
  [@subject, @relationship, @object].hash
end

#nested? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/bel/evidence_model/bel_statement.rb', line 49

def nested?
  @object and @object.is_a? Statement
end

#simple? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/bel/evidence_model/bel_statement.rb', line 45

def simple?
  @object and @object.is_a? Term
end

#subject_only? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/bel/evidence_model/bel_statement.rb', line 41

def subject_only?
  !@relationship
end

#to_bel ⇒ Object Also known as: to_s 



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# File 'lib/bel/evidence_model/bel_statement.rb', line 65

def to_bel
  lbl = case
  when subject_only?
    @subject.to_s
  when simple?
    "#{@subject.to_s} #{@relationship} #{@object.to_s}"
  when nested?
    "#{@subject.to_s} #{@relationship} (#{@object.to_s})"
  else
    ''
  end
  comment ? lbl + ' //' + comment : lbl
end

#to_rdf ⇒ Object 



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# File 'lib/bel/extensions/rdf/rdf.rb', line 218

def to_rdf
  uri = to_uri
  statements = []

  case
  when subject_only?
    (sub_uri, sub_statements) = @subject.to_rdf
    statements << [uri, BEL::RDF::BELV.hasSubject, sub_uri]
    statements += sub_statements
  when simple?
    (sub_uri, sub_statements) = @subject.to_rdf
    statements += sub_statements

    (obj_uri, obj_statements) = @object.to_rdf
    statements += obj_statements

    rel = BEL::RDF::RELATIONSHIP_TYPE[@relationship.to_s]
    statements << [uri, BEL::RDF::BELV.hasSubject, sub_uri]
    statements << [uri, BEL::RDF::BELV.hasObject, obj_uri]
    statements << [uri, BEL::RDF::BELV.hasRelationship, rel]
  when nested?
    (sub_uri, sub_statements) = @subject.to_rdf
    (nsub_uri, nsub_statements) = @object.subject.to_rdf
    (nobj_uri, nobj_statements) = @object.object.to_rdf
    statements += sub_statements
    statements += nsub_statements
    statements += nobj_statements
    rel = BEL::RDF::RELATIONSHIP_TYPE[@relationship.to_s]
    nrel = BEL::RDF::RELATIONSHIP_TYPE[@object.relationship.to_s]
    nuri = BEL::RDF::BELR["#{strip_prefix(nsub_uri)}_#{nrel}_#{strip_prefix(nobj_uri)}"]

    # inner
    statements << [nuri, BEL::RDF::BELV.hasSubject, nsub_uri]
    statements << [nuri, BEL::RDF::BELV.hasObject, nobj_uri]
    statements << [nuri, BEL::RDF::BELV.hasRelationship, nrel]

    # outer
    statements << [uri, BEL::RDF::BELV.hasSubject, sub_uri]
    statements << [uri, BEL::RDF::BELV.hasObject, nuri]
    statements << [uri, BEL::RDF::BELV.hasRelationship, rel]
  end

  # common statement triples
  statements << [uri, BEL::RDF::RDF.type, BEL::RDF::BELV.Statement]
  statements << [uri, RDF::RDFS.label, to_s.force_encoding('UTF-8')]

  # evidence
  evidence_bnode = BEL::RDF::RDF::Node.uuid
  statements << [evidence_bnode, BEL::RDF::RDF.type, BEL::RDF::BELV.Evidence]
  statements << [uri, BEL::RDF::BELV.hasEvidence, evidence_bnode]
  statements << [evidence_bnode, BEL::RDF::BELV.hasStatement, uri]

  # citation
  citation = @annotations.delete('Citation')
  if citation
    value = citation.value.map{|x| x.gsub('"', '')}
    if citation and value[0] == 'PubMed'
      pid = value[2]
      statements << [
        evidence_bnode,
        BEL::RDF::BELV.hasCitation,
        BEL::RDF::RDF::URI(BEL::RDF::PUBMED[pid])
      ]
    end
  end

  # evidence
  evidence_text = @annotations.delete('Evidence')
  if evidence_text
    value = evidence_text.value.gsub('"', '').force_encoding('UTF-8')
    statements << [evidence_bnode, BEL::RDF::BELV.hasEvidenceText, value]
  end

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

    if BEL::RDF::const_defined? name
      annotation_scheme = BEL::RDF::const_get name
      [anno.value].flatten.map{|x| x.gsub('"', '')}.each do |val|
        value_uri = BEL::RDF::RDF::URI(Addressable::URI.encode(annotation_scheme[val.to_s]))
        statements << [evidence_bnode, BEL::RDF::BELV.hasAnnotation, value_uri]
      end
    end
  end

  return [uri, statements]
end

#to_uri ⇒ Object 



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# File 'lib/bel/extensions/rdf/rdf.rb', line 183

def to_uri
  case
  when subject_only?
    tid = @subject.to_s.squeeze(')').gsub(/[")\[\]]/, '').gsub(/[(:, ]/, '_')
    BEL::RDF::BELR[URI::encode(tid)]
  when simple?
    sub_id = @subject.to_s.squeeze(')').gsub(/[")\[\]]/, '').gsub(/[(:, ]/, '_')
    obj_id = @object.to_s.squeeze(')').gsub(/[")\[\]]/, '').gsub(/[(:, ]/, '_')
    rel = BEL::RDF::RELATIONSHIP_TYPE[@relationship.to_s]
    if rel
      rel = rel.path.split('/')[-1]
    else
      rel = @relationship.to_s
    end
    BEL::RDF::BELR[URI::encode("#{sub_id}_#{rel}_#{obj_id}")]
  when nested?
    sub_id = @subject.to_s.squeeze(')').gsub(/[")\[\]]/, '').gsub(/[(:, ]/, '_')
    nsub_id = @object.subject.to_s.squeeze(')').gsub(/[")\[\]]/, '').gsub(/[(:, ]/, '_')
    nobj_id = @object.object.to_s.squeeze(')').gsub(/[")\[\]]/, '').gsub(/[(:, ]/, '_')
    rel = BEL::RDF::RELATIONSHIP_TYPE[@relationship.to_s]
    if rel
      rel = rel.path.split('/')[-1]
    else
      rel = @relationship.to_s
    end
    nrel = BEL::RDF::RELATIONSHIP_TYPE[@object.relationship.to_s]
    if nrel
      nrel = nrel.path.split('/')[-1]
    else
      nrel = @object.relationship.to_s
    end
    BEL::RDF::BELR[URI::encode("#{sub_id}_#{rel}_#{nsub_id}_#{nrel}_#{nobj_id}")]
  end
end