Class: OpenTox::Download
Constant Summary collapse
Class Method Summary collapse
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.blood_brain_barrier ⇒ Object
Download Blood Brain Barrier Penetration dataset into the data folder.
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.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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.loael ⇒ Object
Download the combined LOAEL dataset from Helma et al 2018 into the data folder.
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.mutagenicity ⇒ Object
Combine mutagenicity data from Kazius, Hansen and EFSA and download into the data folder.
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.pubchem_classification(aid:, active:, inactive:, species:, endpoint:, qmrf: nil) ⇒ Object
Download classification dataset from PubChem into the data folder.
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.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.
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.public_data ⇒ Object
Download all public lazar datasets into the data folder.
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. 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 = { :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 .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 = { "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 .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 = { :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 .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} = { :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 .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
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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(" ","_") $logger.debug name table = [["SID","SMILES",name]] csv.each_slice(100) do |slice| # get SMILES in chunks, size limit is 100 cids = slice.collect{|s| s[2]} pubchem_cids = [] JSON.parse(RestClientWrapper.get(File.join(PUBCHEM_URI,"compound/cid/#{cids.join(",")}/property/CanonicalSMILES/JSON")).to_s)["PropertyTable"]["Properties"].each do |prop| i = cids.index(prop["CID"].to_s) value = slice[i][3] if value == "Active" table << [slice[i][1].to_s,prop["CanonicalSMILES"],active] pubchem_cids << prop["CID"].to_s elsif value == "Inactive" table << [slice[i][1].to_s,prop["CanonicalSMILES"],inactive] pubchem_cids << prop["CID"].to_s else warnings << "Ignoring CID #{prop["CID"]}/ SMILES #{prop["CanonicalSMILES"]}, because PubChem activity is '#{value}'." end end (cids-pubchem_cids).each { |cid| warnings << "Could not retrieve SMILES for CID '#{cid}', all entries are ignored." } end File.open(File.join(DATA,name+".csv"),"w+"){|f| f.puts table.collect{|row| row.join(",")}.join("\n")} = { :species => species, :endpoint => endpoint, :source => "https://pubchem.ncbi.nlm.nih.gov/bioassay/#{aid}", :qmrf => qmrf, :warnings => warnings } File.open(File.join(DATA,name+".json"),"w+"){|f| f.puts .to_json} File.join(DATA,name+".csv") end |
.pubchem_regression(aid:, species:, endpoint:, qmrf: nil) ⇒ Object
Download regression dataset from PubChem into the data folder Uses -log10 transformed experimental data in mmol units
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# File 'lib/download.rb', line 70 def self.pubchem_regression aid: , species: , endpoint:, qmrf: nil aid_url = File.join PUBCHEM_URI, "assay/aid/#{aid}" # Get assay data in chunks # Assay record retrieval is limited to 10000 SIDs # https://pubchemdocs.ncbi.nlm.nih.gov/pug-rest-tutorial$_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")} = { :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 .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. # 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 |