Class: BioChEMBL::Target

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

Overview

ChEMBL Target

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>

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 



77
78
79
 
# File 'lib/bio-chembl/target.rb', line 77

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

.find_by_refseq(refseq_id) ⇒ Object 



85
86
87
 
# File 'lib/bio-chembl/target.rb', line 85

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

.find_by_uniprot(uniprot_id) ⇒ Object 



81
82
83
 
# File 'lib/bio-chembl/target.rb', line 81

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

.parse(str) ⇒ Object 



37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
 
# File 'lib/bio-chembl/target.rb', line 37

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

Raises:

  • (NotImplementedError) 


69
70
71
 
# File 'lib/bio-chembl/target.rb', line 69

def self.parse_json(str)
  raise NotImplementedError
end

.parse_list_xml(str) ⇒ Object

XML <list><target> …



62
63
64
65
66
67
 
# File 'lib/bio-chembl/target.rb', line 62

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

Raises:

  • (NotImplementedError) 


73
74
75
 
# File 'lib/bio-chembl/target.rb', line 73

def self.parse_rdf(str)
  raise NotImplementedError
end

.parse_xml(str) ⇒ Object 



53
54
55
56
57
58
 
# File 'lib/bio-chembl/target.rb', line 53

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

Instance Method Details

#bioactivities ⇒ Object

bioactivities => [aBioactivity, …]



90
91
92
 
# File 'lib/bio-chembl/target.rb', line 90

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

#resolve ⇒ Object

Resolve the target data by given ChEMBL ID => aTarget



95
96
97
98
99
100
 
# File 'lib/bio-chembl/target.rb', line 95

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