Class: OpenTox::Download

Inherits:
Object show all
Defined in:
lib/download.rb

Constant Summary collapse

DATA = 
File.join(File.dirname(__FILE__),"..","data")

Class Method Summary collapse

Class Method Details

.blood_brain_barrier ⇒ Object

Download Blood Brain Barrier Penetration dataset into the data folder



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# File 'lib/download.rb', line 203

def self.blood_brain_barrier
  url =  "http://cheminformatics.org/datasets/li/bbp2.smi"
  name = "Blood_Brain_Barrier_Penetration-Human"
  $logger.debug name
  map = {"n" => "non-penetrating", "p" => "penetrating"}
  table = CSV.parse RestClientWrapper.get(url).to_s, :col_sep => "\t"
  File.open(File.join(DATA,name+".csv"),"w+") do |f|
    f.puts "ID,SMILES,#{name}"
    table.each do |row|
      f.puts [row[1],row[0],map[row[3]]].join(",")
    end
  end
  meta = {
    :species => "Human",
    :endpoint => "Blood Brain Barrier Penetration",
    :source => url,
    :qmrf => {"name": "QMRF 5.4. Toxicokinetics.Blood-brain barrier penetration", "group": "QMRF 5. Toxicokinetics"},
  }
  File.open(File.join(DATA,name+".json"),"w+"){|f| f.puts meta.to_json}
end

.daphnia ⇒ Object

Download Daphnia dataset from www.michem.unimib.it/download/data/acute-aquatic-toxicity-to-daphnia-magna/ into the public folder The original file requires an email request, this is a temporary workaround



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# File 'lib/download.rb', line 250

def self.daphnia
  #url = "https://raw.githubusercontent.com/opentox/lazar-public-data/master/regression/daphnia_magna_mmol_log10.csv"
  src = File.join(DATA,"parts","toxicity_data.xlsx")
  name = "Acute_toxicity-Daphnia_magna"
  $logger.debug name
  File.open(File.join(DATA,name+".csv"),"w+") do |f|
    i = 0
    CSV.parse(`xlsx2csv #{src}`) do |row|
      i == 0 ? v = "-log[LC50_mmol/L]" : v = -Math.log10(10**-row[3].to_f*1000)
      f.puts [row[0],row[1],v].join(",")
      i += 1
    end
  end
  meta = { "species": "Daphnia magna",
    "endpoint": "Acute toxicity",
    "source": "http://www.michem.unimib.it/download/data/acute-aquatic-toxicity-to-daphnia-magna/",
    "unit": "mmol/L",
    "qmrf": {
      "group": "QMRF 3.1. Short-term toxicity to Daphnia (immobilisation)",
      "name": "EC C. 2. Daphnia sp Acute Immobilisation Test"
    }
  }
  File.open(File.join(DATA,name+".json"),"w+"){|f| f.puts meta.to_json}
end

.loael ⇒ Object

Download the combined LOAEL dataset from Helma et al 2018 into the data folder



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# File 'lib/download.rb', line 225

def self.loael
  # TODO: fix url??
  url = "https://raw.githubusercontent.com/opentox/loael-paper/revision/data/training_log10.csv"
  name = "Lowest_observed_adverse_effect_level-Rats"
  $logger.debug name
  File.open(File.join(DATA,name+".csv"),"w+") do |f|
    CSV.parse(RestClientWrapper.get(url).to_s) do |row|
      f.puts [row[0],row[1]].join ","
    end
  end
  meta = {
    :species => "Rat",
    :endpoint => "Lowest observed adverse effect level",
    :source => url,
    :unit => "mmol/kg_bw/day",
    :qmrf => {
      "name": "QMRF 4.14. Repeated dose toxicity",
      "group": "QMRF 4.Human Health Effects"
    }
  }
  File.open(File.join(DATA,name+".json"),"w+"){|f| f.puts meta.to_json}
end

.mutagenicity ⇒ Object

Combine mutagenicity data from Kazius, Hansen and EFSA and download into the data folder



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# File 'lib/download.rb', line 123

def self.mutagenicity
  $logger.debug "Mutagenicity"
  hansen_url = "http://doc.ml.tu-berlin.de/toxbenchmark/Mutagenicity_N6512.csv"
  kazius_url = "http://cheminformatics.org/datasets/bursi/cas_4337.zip"
  efsa_url = "https://data.europa.eu/euodp/data/storage/f/2017-07-19T142131/GENOTOX data and dictionary.xls"
  
  parts = File.join(DATA, "parts")
  FileUtils.mkdir_p parts
  Dir[File.join(parts,"hansen.*")].each{|f| FileUtils.rm f }
  Dir[File.join(parts,"cas_4337.*")].each{|f| FileUtils.rm f }
  Dir[File.join(parts,"efsa.*")].each{|f| FileUtils.rm f }
  File.open(File.join(parts,"hansen-original.csv"),"w+"){|f| f.puts RestClientWrapper.get(hansen_url).to_s }

  # convert hansen
  hansen = CSV.read File.join(parts,"hansen-original.csv")
  hansen.shift

  map = {"0" => "non-mutagenic","1" => "mutagenic"}
  File.open(File.join(parts,"hansen.csv"),"w+") do |f|
    f.puts "ID,SMILES,Mutagenicity"
    hansen.each do |row|
      f.puts [row[0],row[5],map[row[2]]].join "," 
    end
  end
  File.open(File.join(parts,"cas_4337.zip"),"w+"){|f| f.puts RestClientWrapper.get(kazius_url).to_s }
  `cd #{parts} && unzip cas_4337.zip`
  `cd #{parts} && wget #{URI.escape efsa_url} -O efsa.xls`
  `cd #{parts} && xls2csv -s cp1252 -d utf-8 -x -c "	" efsa.xls > efsa.tsv`

  # convert EFSA data to mutagenicity classifications
  i = 0
  db = {}
  CSV.foreach(File.join(parts,"efsa.tsv"), :encoding => "UTF-8", :col_sep => "\t", :liberal_parsing => true) do |row|
    if i > 0 and row[11] and !row[11].empty? and row[24].match(/Salmonella/i) and ( row[25].match("TA 98") or row[25].match("TA 100") ) and row[33]
      begin
        c = OpenTox::Compound.from_smiles(row[11].gsub('"','')).smiles
      rescue
        c = OpenTox::Compound.from_inchi(row[12]).smiles # some smiles (row[11]) contain non-parseable characters
      end
      db[c] ||= {}
      db[c][:id] ||= row[2]
      if row[33].match(/Positiv/i)
        db[c][:value] = "mutagenic" # at least one positive result in TA 98 or TA 100
      elsif row[33].match(/Negativ/i)
        db[c][:value] ||= "non-mutagenic"
      end
    end
    i += 1
  end
  File.open(File.join(parts,"efsa.csv"),"w+") do |f|
    f.puts "ID,SMILES,Mutagenicity"
    db.each do |s,v|
      f.puts [v[:id],s,v[:value]].join ","
    end
  end

  # merge datasets
  hansen = Dataset.from_csv_file File.join(parts,"hansen.csv")
  efsa = Dataset.from_csv_file File.join(parts,"efsa.csv")
  kazius = Dataset.from_sdf_file File.join(parts,"cas_4337.sdf")
  datasets = [hansen,efsa,kazius]
  map = {"mutagen" => "mutagenic", "nonmutagen" => "non-mutagenic"}
  dataset = Dataset.merge datasets: datasets, features: datasets.collect{|d| d.bioactivity_features.first}, value_maps: [nil,nil,map], keep_original_features: false, remove_duplicates: true
  dataset.merged_features.first.name = "Mutagenicity"
  File.open(File.join(DATA,"Mutagenicity-Salmonella_typhimurium.csv"),"w+"){|f| f.puts dataset.to_training_csv}
  meta = {
    :species => "Salmonella typhimurium",
    :endpoint => "Mutagenicity",
    :source => [kazius_url,hansen_url,efsa_url].join(", "),
    :qmrf => { "group": "QMRF 4.10. Mutagenicity", "name": "OECD 471 Bacterial Reverse Mutation Test"},
  }
  File.open(File.join(DATA,"Mutagenicity-Salmonella_typhimurium.json"),"w+"){|f| f.puts meta.to_json}
  
  # cleanup
  datasets << dataset
  datasets.each{|d| d.delete }
  File.join(DATA,"Mutagenicity-Salmonella_typhimurium.csv")
end

.pubchem_classification(aid:, active:, inactive:, species:, endpoint:, qmrf: nil) ⇒ Object

Download classification dataset from PubChem into the data folder

Parameters:

  • aid (Integer) —

    PubChem Assay ID

  • active (String) —

    Name for the “Active” class

  • inactive (String) —

    Name for the “Inactive” class

  • species (String) —

    Species name

  • endpoint (String) —

    Endpoint name

  • qmrf (Hash) (defaults to: nil) —

    Name and group for QMRF reports (optional)



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# File 'lib/download.rb', line 14

def self.pubchem_classification aid: , active: , inactive: , species: , endpoint:, qmrf: nil
  aid_url = File.join PUBCHEM_URI, "assay/aid/#{aid}"
  
  # Get assay data in chunks
  # Assay record retrieval is limited to 10000 SIDs
  # https://pubchemdocs.ncbi.nlm.nih.gov/pug-rest-tutorial$_Toc458584435
  list = JSON.parse(RestClientWrapper.get(File.join aid_url, "sids/JSON?list_return=listkey").to_s)["IdentifierList"]
  listkey = list["ListKey"]
  size = list["Size"]
  start = 0
  csv = []
  while start < size
    url = File.join aid_url, "CSV?sid=listkey&listkey=#{listkey}&listkey_start=#{start}&listkey_count=10000"
    csv += CSV.parse(RestClientWrapper.get(url).to_s).select{|r| r[0].match /^\d/} # discard header rows
    start += 10000
  end
  warnings = []
  name = endpoint.gsub(" ","_")+"-"+species.gsub(" ","_")
  $logger.debug name
  table = [["SID","SMILES",name]]
  csv.each_slice(100) do |slice| # get SMILES in chunks, size limit is 100
    cids = slice.collect{|s| s[2]}
    pubchem_cids = []
    JSON.parse(RestClientWrapper.get(File.join(PUBCHEM_URI,"compound/cid/#{cids.join(",")}/property/CanonicalSMILES/JSON")).to_s)["PropertyTable"]["Properties"].each do |prop|
      i = cids.index(prop["CID"].to_s)
      value = slice[i][3]
      if value == "Active"
        table << [slice[i][1].to_s,prop["CanonicalSMILES"],active]
        pubchem_cids << prop["CID"].to_s
      elsif value == "Inactive"
        table << [slice[i][1].to_s,prop["CanonicalSMILES"],inactive]
        pubchem_cids << prop["CID"].to_s
      else
        warnings << "Ignoring CID #{prop["CID"]}/ SMILES #{prop["CanonicalSMILES"]}, because PubChem activity is '#{value}'."
      end
    end
    (cids-pubchem_cids).each { |cid| warnings << "Could not retrieve SMILES for CID '#{cid}', all entries are ignored." }
  end
  File.open(File.join(DATA,name+".csv"),"w+"){|f| f.puts table.collect{|row| row.join(",")}.join("\n")}
  meta = {
    :species => species,
    :endpoint => endpoint,
    :source => "https://pubchem.ncbi.nlm.nih.gov/bioassay/#{aid}",
    :qmrf => qmrf,
    :warnings => warnings
  }
  File.open(File.join(DATA,name+".json"),"w+"){|f| f.puts meta.to_json}
  File.join(DATA,name+".csv")
end

.pubchem_regression(aid:, species:, endpoint:, qmrf: nil) ⇒ Object

Download regression dataset from PubChem into the data folder Uses -log10 transformed experimental data in mmol units

Parameters:

  • aid (String) —

    PubChem Assay ID

  • species (String) —

    Species name

  • endpoint (String) —

    Endpoint name

  • qmrf (Hash) (defaults to: nil) —

    Name and group for QMRF reports (optional)



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# File 'lib/download.rb', line 70

def self.pubchem_regression aid: , species: , endpoint:, qmrf: nil
  aid_url = File.join PUBCHEM_URI, "assay/aid/#{aid}"
  
  # Get assay data in chunks
  # Assay record retrieval is limited to 10000 SIDs
  # https://pubchemdocs.ncbi.nlm.nih.gov/pug-rest-tutorial$_Toc458584435
  list = JSON.parse(RestClientWrapper.get(File.join aid_url, "sids/JSON?list_return=listkey").to_s)["IdentifierList"]
  listkey = list["ListKey"]
  size = list["Size"]
  start = 0
  csv = []
  unit = nil
  while start < size
    url = File.join aid_url, "CSV?sid=listkey&listkey=#{listkey}&listkey_start=#{start}&listkey_count=10000"
    # get unit
    unit ||= CSV.parse(RestClientWrapper.get(url).to_s).select{|r| r[0] == "RESULT_UNIT"}[0][8]
    csv += CSV.parse(RestClientWrapper.get(url).to_s).select{|r| r[0].match /^\d/} # discard header rows
    start += 10000
  end
  warnings = []
  name = endpoint.gsub(" ","_")+"-"+species.gsub(" ","_")
  $logger.debug name
  table = [["SID","SMILES","-log10(#{name} [#{unit}])"]]
  csv.each_slice(100) do |slice| # get SMILES in chunks, size limit is 100
    cids = slice.collect{|s| s[2]}
    pubchem_cids = []
    JSON.parse(RestClientWrapper.get(File.join(PUBCHEM_URI,"compound/cid/#{cids.join(",")}/property/CanonicalSMILES/JSON")).to_s)["PropertyTable"]["Properties"].each do |prop|
      i = cids.index(prop["CID"].to_s)
      value = slice[i][8]
      if value
        value = -Math.log10(value.to_f)
        table << [slice[i][1].to_s,prop["CanonicalSMILES"],value]
        pubchem_cids << prop["CID"].to_s
      else
        warnings << "Ignoring CID #{prop["CID"]}/ SMILES #{prop["CanonicalSMILES"]}, because PubChem activity is '#{value}'."
      end
    end
    (cids-pubchem_cids).each { |cid| warnings << "Could not retrieve SMILES for CID '#{cid}', all entries are ignored." }
  end
  File.open(File.join(DATA,name+".csv"),"w+"){|f| f.puts table.collect{|row| row.join(",")}.join("\n")}
  meta = {
    :species => species,
    :endpoint => endpoint,
    :source => "https://pubchem.ncbi.nlm.nih.gov/bioassay/#{aid}",
    :unit => unit,
    :qmrf => qmrf,
    :warnings => warnings
  }
  File.open(File.join(DATA,name+".json"),"w+"){|f| f.puts meta.to_json}
  File.join(DATA,name+".csv")
end

.public_data ⇒ Object

Download all public lazar datasets into the data folder



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# File 'lib/download.rb', line 276

def self.public_data

  # Classification
  [
    {
      :aid => 1205,
      :species => "Rodents",
      :endpoint => "Carcinogenicity",
      :qmrf => {:group => "QMRF 4.12. Carcinogenicity", :name => "OECD 451 Carcinogenicity Studies"}
    },{
      :aid => 1208,
      :species => "Rat",
      :endpoint => "Carcinogenicity",
      :qmrf => {:group => "QMRF 4.12. Carcinogenicity", :name => "OECD 451 Carcinogenicity Studies"}
    },{
      :aid => 1199,
      :species => "Mouse",
      :endpoint => "Carcinogenicity",
      :qmrf => {:group => "QMRF 4.12. Carcinogenicity", :name => "OECD 451 Carcinogenicity Studies"}
    }
  ].each do |assay|
    Download.pubchem_classification aid: assay[:aid], species: assay[:species], endpoint: assay[:endpoint], active: "carcinogenic", inactive: "non-carcinogenic", qmrf: assay[:qmrf]
  end
  Download.mutagenicity
  Download.blood_brain_barrier

  # Regression
  [
    {
      :aid => 1195,
      :species => "Human",
      :endpoint => "Maximum Recommended Daily Dose",
      :qmrf => {
        "group": "QMRF 4.14. Repeated dose toxicity",
        "name": "OECD 452 Chronic Toxicity Studies"
      },
    },{
      :aid => 1208,
      :species => "Rat (TD50)",
      :endpoint => "Carcinogenicity",
      :qmrf => {
        :group => "QMRF 4.12. Carcinogenicity",
        :name => "OECD 451 Carcinogenicity Studies"
      }
    },{
      :aid => 1199,
      :species => "Mouse (TD50)",
      :endpoint => "Carcinogenicity",
      :qmrf => {
        :group => "QMRF 4.12. Carcinogenicity",
        :name => "OECD 451 Carcinogenicity Studies"
      }
    },{
      :aid => 1188,
      :species => "Fathead minnow",
      :endpoint => "Acute toxicity",
      :qmrf => {
        "group": "QMRF 3.3. Acute toxicity to fish (lethality)",
        "name": "EC C. 1. Acute Toxicity for Fish"
      }
    }
  ].each do |assay|
    Download.pubchem_regression aid: assay[:aid], species: assay[:species], endpoint: assay[:endpoint], qmrf: assay[:qmrf]
  end
  
  Download.loael
  Download.daphnia

=begin
    # 1204  estrogen receptor
    # 1259408, # GENE-TOX
    # 1159563 HepG2 cytotoxicity assay
    # 588209 hepatotoxicity
    # 1259333 cytotoxicity
    # 1159569 HepG2 cytotoxicity counterscreen Measured in Cell-Based System Using Plate Reader - 2153-03_Inhibitor_Dose_DryPowder_Activity
    # 2122 HTS Counterscreen for Detection of Compound Cytotoxicity in MIN6 Cells
    # 116724 Acute toxicity determined after intravenal administration in mice
    # 1148549 Toxicity in po dosed mouse assessed as mortality after 7 days
=end
end