Class: BioChEMBL::Assay

Inherits:
Object
  • Object
show all
Extended by:
DataModel
Defined in:
lib/bio-chembl/assay.rb

Overview

ChEMBL Assay Data parser and container.

Data XML

<assay>
  <chemblId>CHEMBL1217643</chemblId>
  <assayType>B</assayType>
  <journal>Bioorg. Med. Chem. Lett.</journal>
  <assayOrganism>Homo sapiens</assayOrganism>
  <assayStrain>Unspecified</assayStrain>
  <assayDescription>Inhibition of human hERG</assayDescription>
  <numBioactivities>1</numBioactivities>
</assay>

Usage

assay = BioChEMBL::Assay.find("CHEMBL1217643")
assay.assayType
assay.assayOrganism
ba = assay.bioactivities

assay = BioChEMBL::Assay.new("CHEMBL1217643")
assay.assayType #=> nil
assay.resolve
assay.assayType #=> "B"

xml = BioChEMBL::REST.new.assays("CHEMBL1217643")
assay = BioChEMBL::Assay.parse_xml(xml)

Constant Summary collapse

ATTRIBUTES = 
[
:chemblId,
:assayType,
:journal,
:assayOrganism,
:assayStrain,
:assayDescription,
:numBioactivities
]

Class Method Summary collapse

Instance Method Summary collapse

Methods included from DataModel

set_attr_accessors, set_attr_values

Constructor Details

#initialize(chemblId = nil) ⇒ Assay

Create a blank Assay instance.



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# File 'lib/bio-chembl/assay.rb', line 94

def initialize(chemblId = nil)
  @chemblId = chemblId
end

Class Method Details

.find(chemblId) ⇒ Object

Find the assay data by ChEMBL ID via the web service.



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# File 'lib/bio-chembl/assay.rb', line 88

def self.find(chemblId)
  self.parse_xml(REST.new.assays(chemblId))
end

.parse(str) ⇒ Object

Parse the assay data.



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# File 'lib/bio-chembl/assay.rb', line 53

def self.parse(str)
  case str
  when /^</
    format = 'xml'
  when /^\{/
    format = 'json'
  else
    raise ArgumentError, "Unexpected file format: #{str.inspect}" 
  end
  begin
    eval "self.parse_#{format}(str)"
  rescue 
    raise NoMethodError
  end  
end

.parse_json(str) ⇒ Object

Parse the assay data in JSON format.

Raises:

  • (NotImplementedError) 


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# File 'lib/bio-chembl/assay.rb', line 78

def self.parse_json(str)
  raise NotImplementedError
end

.parse_rdf(str) ⇒ Object

Parse the assay data in RDF format.

Raises:

  • (NotImplementedError) 


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# File 'lib/bio-chembl/assay.rb', line 83

def self.parse_rdf(str)
  raise NotImplementedError
end

.parse_xml(str) ⇒ Object

Parse the assay data in XML format.



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# File 'lib/bio-chembl/assay.rb', line 70

def self.parse_xml(str)
  xml = Nokogiri::XML(str)
  this = new  
  eval set_attr_values(ATTRIBUTES)
  this
end

Instance Method Details

#bioactivities ⇒ Object

Find the Bioactivity data by the assay.



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# File 'lib/bio-chembl/assay.rb', line 107

def bioactivities
  BioChEMBL::Bioactivity.parse_list_xml(REST.new.assays(@chemblId, 'bioactivities'))
end

#resolve ⇒ Object

Resolve the assay data by given ChEMBL ID



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# File 'lib/bio-chembl/assay.rb', line 99

def resolve
  resolved = self.class.find(@chemblId)
  ATTRIBUTES.each do |attr|
    eval "@#{attr} = resolved.#{attr}"
  end
end