Class: PubannotationEvaluator

Inherits:
Object
  • Object
show all
Defined in:
lib/pubannotation_evaluator/pubannotation_evaluator.rb

Constant Summary collapse

SOFT_MATCH_CHARACTERS = 
20
SOFT_MATCH_WORDS = 
2
EXACT_TYPE_MATCH = 
'study_type == reference_type ? 1 : 0'

Instance Method Summary collapse

Constructor Details

#initialize(soft_match_chatacters = SOFT_MATCH_CHARACTERS, soft_match_words = SOFT_MATCH_WORDS, denotation_type_match = EXACT_TYPE_MATCH, relation_type_match = EXACT_TYPE_MATCH) ⇒ PubannotationEvaluator

Returns a new instance of PubannotationEvaluator.



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# File 'lib/pubannotation_evaluator/pubannotation_evaluator.rb', line 6

def initialize(soft_match_chatacters = SOFT_MATCH_CHARACTERS, soft_match_words = SOFT_MATCH_WORDS, denotation_type_match = EXACT_TYPE_MATCH, relation_type_match = EXACT_TYPE_MATCH)
	@soft_match_chatacters = soft_match_chatacters
	@soft_match_words = soft_match_words
	@denotation_type_match = eval <<-HEREDOC
		Proc.new do |study_type, reference_type|
			#{denotation_type_match}
		end
	HEREDOC
	@relation_type_match = eval <<-HEREDOC
		Proc.new do |study_type, reference_type|
			#{relation_type_match}
		end
	HEREDOC
end

Instance Method Details

#compare(study_annotations, reference_annotations) ⇒ Object

To compare two sets of annotations

Attributes

  • study_annotations : annotations to be studied

  • reference_annotations : annotations to be compared against



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# File 'lib/pubannotation_evaluator/pubannotation_evaluator.rb', line 27

def compare(study_annotations, reference_annotations)
	study_annotations[:denotations] ||= []
	study_annotations[:relations] ||= []
	study_annotations[:modifications] ||= []
	reference_annotations[:denotations] ||= []
	reference_annotations[:relations] ||= []
	reference_annotations[:modifications] ||= []

	comparison_denotations, mmatches_denotations = compare_denotations(study_annotations[:denotations], reference_annotations[:denotations], reference_annotations[:text])
	comparison_relations = compare_relations(study_annotations[:relations], reference_annotations[:relations], mmatches_denotations)
	comparison_modifications = compare_modifications(study_annotations[:modofications], reference_annotations[:modofications], comparison_denotations, comparison_relations)

	comparison = comparison_denotations.collect{|a| a.merge(type: :denotation)} +
							 comparison_relations.collect{|a| a.merge(type: :relation)} +
							 comparison_modifications.collect{|a| a.merge(type: :modification)}

	docspec = {sourcedb:study_annotations[:sourcedb], sourceid:study_annotations[:sourceid]}
	docspec[:divid] = study_annotations[:divid] if study_annotations.has_key?(:divid)
	comparison.collect{|d| d.merge(docspec)}
end

#evaluate(comparison) ⇒ Object

To produce evaluations based on comparison.

Attributes

  • comparison : the mapping between study and reference annotations



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# File 'lib/pubannotation_evaluator/pubannotation_evaluator.rb', line 53

def evaluate(comparison)
	counts = count(comparison)
	measures = measure(counts)
	{counts:counts, measures:measures}
end

#get_false_negatives(comparison, project_name) ⇒ Object 



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# File 'lib/pubannotation_evaluator/pubannotation_evaluator.rb', line 63

def get_false_negatives(comparison, project_name)
	comparison.select{|m| m[:study].nil? && m[:reference]}
end

#get_false_positives(comparison, project_name) ⇒ Object 



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# File 'lib/pubannotation_evaluator/pubannotation_evaluator.rb', line 59

def get_false_positives(comparison, project_name)
	comparison.select{|m| m[:study] && m[:reference].nil?}
end