Class: BioChEMBL::Target

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

Overview

ChEMBL Target parser and container.

Data XML

<target>
  <chemblId>CHEMBL1785</chemblId>
  <targetType>PROTEIN</targetType>
  <preferredName>Endothelin receptor ET-B</preferredName>
  <proteinAccession>P24530</proteinAccession>
  <synonyms>Endothelin B receptor; Endothelin receptor non-selective type; ET-B; ET-BR</synonyms>
  <organism>Homo sapiens</organism>
  <description>Endothelin B receptor</description>
  <geneNames>EDNRB; ETRB</geneNames>
</target>

Usage

target = BioChEMBL::Target.find("CHEMBL1785")
target.geneNames
BioChEMBL.to_array(target.geneNames)[0] #=> "EDNRB"

bioactivities = target.bioactivities

target = BioChEMBL::Target.find_by_uniprot("P24530")

Constant Summary collapse

ATTRIBUTES = 
[
  :chemblId,
  :targetType,
  :preferredName,
  :proteinAccession,
  :synonyms,
  :organism,
  :description,
  :geneNames
]

Class Method Summary collapse

Instance Method Summary collapse

Methods included from DataModel

set_attr_accessors, set_attr_values

Class Method Details

.find(chemblId) ⇒ Object

Find the Target data by the ChEMBL ID.



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# File 'lib/bio-chembl/target.rb', line 93

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

.find_by_refseq(refseq_id) ⇒ Object

Find the Target data by the RefSeq ID.



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# File 'lib/bio-chembl/target.rb', line 103

def self.find_by_refseq(refseq_id)
  self.parse_xml(REST.new.targets_refseq(refseq_id))            
end

.find_by_uniprot(uniprot_id) ⇒ Object

Find the Target data by the UniProt ID.



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# File 'lib/bio-chembl/target.rb', line 98

def self.find_by_uniprot(uniprot_id)
  self.parse_xml(REST.new.targets_uniprot(uniprot_id))      
end

.parse(str) ⇒ Object

Parse the Target data.



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# File 'lib/bio-chembl/target.rb', line 49

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 Target data in JSON format.

Raises:

  • (NotImplementedError) 


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

def self.parse_json(str)
  raise NotImplementedError
end

.parse_list_xml(str) ⇒ Object

Parse the Target data list in XML format. data lsit: <list><target/></list>



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# File 'lib/bio-chembl/target.rb', line 75

def self.parse_list_xml(str)
  xmls = Nokogiri::XML(str)
  xmls.xpath("/list/target").map do |cpd|
    self.parse_xml(cpd.to_s)
  end
end

.parse_rdf(str) ⇒ Object

Parse the Target data in RDF format.

Raises:

  • (NotImplementedError) 


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

def self.parse_rdf(str)
  raise NotImplementedError
end

.parse_xml(str) ⇒ Object

Parse the Target data in XML format.



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# File 'lib/bio-chembl/target.rb', line 66

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

Instance Method Details

#bioactivities ⇒ Object

Get the bioactivity data list.



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# File 'lib/bio-chembl/target.rb', line 108

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

#resolve ⇒ Object

Resolve the Target data by the ChEMBL ID



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# File 'lib/bio-chembl/target.rb', line 113

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