diff options
| author | helma@in-silico.ch <helma@in-silico.ch> | 2018-11-12 17:08:51 +0100 |
|---|---|---|
| committer | helma@in-silico.ch <helma@in-silico.ch> | 2018-11-12 17:08:51 +0100 |
| commit | 6d68a1ca94937a0553f61ebbbbd317dae54ce4e6 (patch) | |
| tree | 02df42992b8ec3bcd8230826b8ccde5820c35359 | |
| parent | cf80ed17102a0368df8d65037d113b521cdf6f0c (diff) | |
PubChem classification download
| -rw-r--r-- | data/Carcinogenicity-Mouse.csv | 979 | ||||
| -rw-r--r-- | data/Carcinogenicity-Mouse.json | 1 | ||||
| -rw-r--r-- | data/Carcinogenicity-Rat.csv | 1196 | ||||
| -rw-r--r-- | data/Carcinogenicity-Rat.json | 1 | ||||
| -rw-r--r-- | data/Carcinogenicity-Rodents.csv | 1119 | ||||
| -rw-r--r-- | data/Carcinogenicity-Rodents.json | 1 | ||||
| -rw-r--r-- | lib/download.rb | 55 | ||||
| -rw-r--r-- | lib/lazar.rb | 1 | ||||
| -rw-r--r-- | test/download.rb | 22 | ||||
| -rw-r--r-- | test/use_cases.rb | 84 |
10 files changed, 3445 insertions, 14 deletions
diff --git a/data/Carcinogenicity-Mouse.csv b/data/Carcinogenicity-Mouse.csv new file mode 100644 index 0000000..c297f54 --- /dev/null +++ b/data/Carcinogenicity-Mouse.csv @@ -0,0 +1,979 @@ +SID,SMILES,Carcinogenicity-Mouse +48413127,C1=CC=C2C(=C1)C3=C(N2)N=C(C=C3)N,carcinogen +48413128,CC1=CC(=O)[N-]S(=O)(=O)O1.[K+],non-carcinogen +48413130,CC=NN(C)C=O,carcinogen +48413132,CC(=O)N,carcinogen +48413133,CC(=O)NC1=CC=C(C=C1)O,carcinogen +48413134,CC(=O)C1=CC=C(C=C1)S(=O)(=O)NC(=O)NC2CCCCC2,non-carcinogen +48413136,CC#N,non-carcinogen +48413138,CC(=O)OC(C=C)C1=CC2=C(C=C1)OCO2,non-carcinogen +48413139,CC(=O)NNC1=CC=C(C=C1)CO,carcinogen +48413140,CC(=O)NNC(=O)C1=CC=NC=C1,carcinogen +48413141,CC1=CC(=O)C(C(=O)O1)C(=O)C,non-carcinogen +48413142,CC(=O)NNC1=CC=CC=C1,carcinogen +48413145,CC(=O)NC1=CC2=C(C=C1)C3=CC=CC=C3C2,carcinogen +48413147,CC(=O)NC1=CC=C(C=C1)CC(=O)O,non-carcinogen +48413149,C1=CC(=C(C=C1C(F)(F)F)Cl)OC2=CC(=C(C=C2)[N+](=O)[O-])C(=O)O,carcinogen +48413150,C=CC=O,non-carcinogen 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+{"species":"Mouse","endpoint":"Carcinogenicity","source":"https://pubchem.ncbi.nlm.nih.gov/rest/pug/assay/aid/1199","qmrf":null,"warnings":["Ignoring CID 345512/ SMILES CC1(C=CC2=C3C(=C(C=C2O1)OC)C(=O)C4=CC=CC=C4N3C)C, because PubChem activity is 'Unspecified'.","Could not retrieve SMILES for CID '345512', all entries are ignored.","Could not retrieve SMILES for CID '', all entries are ignored.","Could not retrieve SMILES for CID '', all entries are ignored.","Could not retrieve SMILES for CID '', all entries are ignored.","Could not retrieve SMILES for CID '', all entries are ignored.","Could not retrieve SMILES for CID '', all entries are ignored.","Could not retrieve SMILES for CID '', all entries are ignored.","Could not retrieve SMILES for CID '', all entries are ignored.","Ignoring CID 3068143/ SMILES CCC1CN2CCC3=CC(=C(C=C3C2CC1CC4C5=CC(=C(C=C5CCN4)OC)OC)OC)OC.Cl.Cl, because PubChem activity is 'Unspecified'.","Could not retrieve SMILES for CID '', all entries are ignored.","Could not retrieve SMILES for CID '', all entries are ignored.","Could not retrieve SMILES for CID '', all entries are ignored.","Could not retrieve SMILES for CID '3068143', all entries are ignored.","Ignoring CID 441411/ SMILES CNCC(C1=CC(=C(C=C1)O)O)O.Cl, because PubChem activity is 'Unspecified'.","Could not retrieve SMILES for CID '', all entries are ignored.","Could not retrieve SMILES for CID '441411', all entries are ignored.","Could not retrieve SMILES for CID '', all entries are ignored.","Could not retrieve SMILES for CID '', all entries are ignored.","Could not retrieve SMILES for CID '', all entries are ignored.","Could not retrieve SMILES for CID '', all entries are ignored.","Could not retrieve SMILES for CID '', all entries are ignored.","Ignoring CID 5284449/ SMILES C1=CC(=CC2=NC3=C(C=CC(=C3)N)C=C21)N.C1=CC(=CC2=NC3=C(C=CC(=C3)N)C=C21)N.O.Cl.Cl, because PubChem activity is 'Unspecified'.","Could not retrieve SMILES for CID '', all entries are ignored.","Could not retrieve SMILES for CID '', all entries are ignored.","Could not retrieve SMILES for CID '', all entries are ignored.","Could not retrieve SMILES for CID '', all entries are ignored.","Could not retrieve SMILES for CID '5284449', all entries are ignored.","Could not retrieve SMILES for CID '', all entries are ignored.","Could not retrieve SMILES for CID '', all entries are ignored.","Could not retrieve SMILES for CID '', all entries are ignored.","Ignoring CID 3000603/ SMILES C1C(C(OC1N2C=NC3=C2NC(=NC3=S)N)CO)O, because PubChem activity is 'Unspecified'.","Could not retrieve SMILES for CID '3000603', all entries are ignored.","Could not retrieve SMILES for CID '', all entries are ignored."]} diff --git a/data/Carcinogenicity-Rat.csv b/data/Carcinogenicity-Rat.csv new file mode 100644 index 0000000..5bf782e --- /dev/null +++ b/data/Carcinogenicity-Rat.csv @@ -0,0 +1,1196 @@ +SID,SMILES,Carcinogenicity-Rat +48413129,CC=O,carcinogen +48413131,CC=NO,non-carcinogen 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'Unspecified'.","Could not retrieve SMILES for CID '', all entries are ignored.","Could not retrieve SMILES for CID '7850', all entries are ignored.","Could not retrieve SMILES for CID '', all entries are ignored.","Could not retrieve SMILES for CID '', all entries are ignored.","Ignoring CID 2347/ SMILES CCCCOC(=O)C1=CC=CC=C1C(=O)OCC2=CC=CC=C2, because PubChem activity is ''.","Could not retrieve SMILES for CID '', all entries are ignored.","Could not retrieve SMILES for CID '2347', all entries are ignored.","Ignoring CID 6423/ SMILES C([N+](=O)[O-])(Cl)(Cl)Cl, because PubChem activity is 'Unspecified'.","Could not retrieve SMILES for CID '', all entries are ignored.","Could not retrieve SMILES for CID '', all entries are ignored.","Could not retrieve SMILES for CID '', all entries are ignored.","Could not retrieve SMILES for CID '', all entries are ignored.","Could not retrieve SMILES for CID '', all entries are ignored.","Could not retrieve SMILES for CID '6423', all entries are ignored.","Could not retrieve SMILES for CID '', all entries are ignored.","Could not retrieve SMILES for CID '', all entries are ignored.","Could not retrieve SMILES for CID '', all entries are ignored.","Could not retrieve SMILES for CID '', all entries are ignored.","Could not retrieve SMILES for CID '', all entries are ignored.","Could not retrieve SMILES for CID '', all entries are ignored.","Ignoring CID 3068143/ SMILES CCC1CN2CCC3=CC(=C(C=C3C2CC1CC4C5=CC(=C(C=C5CCN4)OC)OC)OC)OC.Cl.Cl, because PubChem activity is 'Unspecified'.","Ignoring CID 441411/ SMILES CNCC(C1=CC(=C(C=C1)O)O)O.Cl, because PubChem activity is 'Unspecified'.","Could not retrieve SMILES for CID '', all entries are ignored.","Could not retrieve SMILES for CID '', all entries are ignored.","Could not retrieve SMILES for CID '', all entries are ignored.","Could not retrieve SMILES for CID '3068143', all entries are ignored.","Could not retrieve SMILES for CID '', all entries are ignored.","Could not retrieve SMILES for CID '441411', all entries are ignored.","Could not retrieve SMILES for CID '', all entries are ignored.","Could not retrieve SMILES for CID '', all entries are ignored.","Could not retrieve SMILES for CID '', all entries are ignored.","Could not retrieve SMILES for CID '', all entries are ignored.","Could not retrieve SMILES for CID '', all entries are ignored.","Could not retrieve SMILES for CID '', all entries are ignored.","Could not retrieve SMILES for CID '', all entries are ignored.","Could not retrieve SMILES for CID '', all entries are ignored.","Could not retrieve SMILES for CID '', all entries are ignored.","Ignoring CID 3032604/ SMILES CCN(CC)C(=O)C(=C(C)OP(=O)(OC)OC)Cl, because PubChem activity is 'Unspecified'.","Ignoring CID 5284449/ SMILES C1=CC(=CC2=NC3=C(C=CC(=C3)N)C=C21)N.C1=CC(=CC2=NC3=C(C=CC(=C3)N)C=C21)N.O.Cl.Cl, because PubChem activity is 'Unspecified'.","Could not retrieve SMILES for CID '3032604', all entries are ignored.","Could not retrieve SMILES for CID '', all entries are ignored.","Could not retrieve SMILES for CID '5284449', all entries are ignored.","Could not retrieve SMILES for CID '', all entries are ignored.","Could not retrieve SMILES for CID '', all entries are ignored.","Could not retrieve SMILES for CID '', all entries are ignored.","Could not retrieve SMILES for CID '', all entries are ignored.","Could not retrieve SMILES for CID '', all entries are ignored.","Could not retrieve SMILES for CID '', all entries are ignored.","Ignoring CID 5284462/ SMILES COP(=O)(OC)OC(=CCl)C1=CC(=C(C=C1Cl)Cl)Cl, because PubChem activity is ''.","Could not retrieve SMILES for CID '5284462', all entries are ignored.","Ignoring CID 7499/ SMILES C=CC1CCC=CC1, because PubChem activity is 'Unspecified'.","Could not retrieve SMILES for CID '7499', all entries are ignored.","Could not retrieve SMILES for CID '', all entries are ignored."]} diff --git a/data/Carcinogenicity-Rodents.csv b/data/Carcinogenicity-Rodents.csv new file mode 100644 index 0000000..d8c5c82 --- /dev/null +++ b/data/Carcinogenicity-Rodents.csv @@ -0,0 +1,1119 @@ +SID,SMILES,Carcinogenicity-Rodents +48413127,C1=CC=C2C(=C1)C3=C(N2)N=C(C=C3)N,carcinogen +48413128,CC1=CC(=O)[N-]S(=O)(=O)O1.[K+],non-carcinogen +48413129,CC=O,carcinogen +48413130,CC=NN(C)C=O,carcinogen +48413132,CC(=O)N,carcinogen +48413133,CC(=O)NC1=CC=C(C=C1)O,carcinogen +48413134,CC(=O)C1=CC=C(C=C1)S(=O)(=O)NC(=O)NC2CCCCC2,non-carcinogen +48413136,CC#N,non-carcinogen +48413139,CC(=O)NNC1=CC=C(C=C1)CO,carcinogen +48413140,CC(=O)NNC(=O)C1=CC=NC=C1,carcinogen +48413141,CC1=CC(=O)C(C(=O)O1)C(=O)C,non-carcinogen +48413142,CC(=O)NNC1=CC=CC=C1,carcinogen +48413145,CC(=O)NC1=CC2=C(C=C1)C3=CC=CC=C3C2,carcinogen +48413147,CC(=O)NC1=CC=C(C=C1)CC(=O)O,non-carcinogen +48413149,C1=CC(=C(C=C1C(F)(F)F)Cl)OC2=CC(=C(C=C2)[N+](=O)[O-])C(=O)O,carcinogen +48413150,C=CC=O,non-carcinogen +48413151,CCOC(C=C)OCC,non-carcinogen +48413152,C=CC=NO,non-carcinogen 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+48414670,CC(=O)NC1=CC2=C(C=C1)C3=C(C2)C=C(C=C3)NC(=O)C,non-carcinogen +48414671,CC1C(C(CC(O1)OC2CC(CC3=C(C4=C(C(=C23)O)C(=O)C5=C(C4=O)C=CC=C5OC)O)(C(=O)CO)O)N)O,non-carcinogen +48414672,C[N+](=NCOC1C(C(C(C(O1)CO)O)O)O)[O-],carcinogen diff --git a/data/Carcinogenicity-Rodents.json b/data/Carcinogenicity-Rodents.json new file mode 100644 index 0000000..92caeb7 --- /dev/null +++ b/data/Carcinogenicity-Rodents.json @@ -0,0 +1 @@ +{"species":"Rodents","endpoint":"Carcinogenicity","source":"https://pubchem.ncbi.nlm.nih.gov/rest/pug/assay/aid/1205","qmrf":null,"warnings":["Could not retrieve SMILES for CID '', all entries are ignored.","Could not retrieve SMILES for CID '', all entries are ignored.","Could not retrieve SMILES for CID '', all entries are ignored.","Could not retrieve SMILES for CID '', all entries are ignored.","Could not retrieve SMILES for CID '', all entries are ignored.","Could not retrieve SMILES for CID '', all entries are ignored.","Could not retrieve SMILES for CID '', all entries are ignored.","Could not retrieve SMILES for CID '', all entries are ignored.","Could not retrieve SMILES for CID '', all entries are ignored.","Could not retrieve SMILES for CID '', all entries are ignored.","Could not retrieve SMILES for CID '', all entries are ignored.","Could not retrieve SMILES for CID '', all entries are ignored.","Could not retrieve SMILES for CID '', all entries are ignored.","Could not retrieve SMILES for CID '', all entries are ignored.","Could not retrieve SMILES for CID '', all entries are ignored.","Could not retrieve SMILES for CID '', all entries are ignored.","Could not retrieve SMILES for CID '', all entries are ignored.","Could not retrieve SMILES for CID '', all entries are ignored.","Could not retrieve SMILES for CID '', all entries are ignored.","Could not retrieve SMILES for CID '', all entries are ignored.","Could not retrieve SMILES for CID '', all entries are ignored.","Could not retrieve SMILES for CID '', all entries are ignored.","Could not retrieve SMILES for CID '', all entries are ignored.","Could not retrieve SMILES for CID '', all entries are ignored.","Could not retrieve SMILES for CID '', all entries are ignored.","Could not retrieve SMILES for CID '', all entries are ignored.","Could not retrieve SMILES for CID '', all entries are ignored.","Could not retrieve SMILES for CID '', all entries are ignored.","Could not retrieve SMILES for CID '', all entries are ignored.","Could not retrieve SMILES for CID '', all entries are ignored.","Could not retrieve SMILES for CID '', all entries are ignored.","Could not retrieve SMILES for CID '', all entries are ignored.","Could not retrieve SMILES for CID '', all entries are ignored.","Could not retrieve SMILES for CID '', all entries are ignored."]} diff --git a/lib/download.rb b/lib/download.rb new file mode 100644 index 0000000..9e30790 --- /dev/null +++ b/lib/download.rb @@ -0,0 +1,55 @@ +module OpenTox + + class Download + + 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+"-"+species + table = [["SID","SMILES",name]] + csv.each_slice(100) do |slice| # get SMILES in chunks + 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(File.dirname(__FILE__),"..","data",name+".csv"),"w+"){|f| f.puts table.collect{|row| row.join(",")}.join("\n")} + meta = { + :species => species, + :endpoint => endpoint, + :source => aid_url, + :qmrf => qmrf, + :warnings => warnings + } + File.open(File.join(File.dirname(__FILE__),"..","data",name+".json"),"w+"){|f| f.puts meta.to_json} + end + + end + +end diff --git a/lib/lazar.rb b/lib/lazar.rb index 69a6f15..6f14f67 100644 --- a/lib/lazar.rb +++ b/lib/lazar.rb @@ -97,5 +97,6 @@ CLASSES = ["Feature","Substance","Dataset","CrossValidation","LeaveOneOutValidat "train-test-validation.rb", "leave-one-out-validation.rb", "crossvalidation.rb", + "download.rb" #"import.rb", ].each{ |f| require_relative f } diff --git a/test/download.rb b/test/download.rb new file mode 100644 index 0000000..9fd0f40 --- /dev/null +++ b/test/download.rb @@ -0,0 +1,22 @@ +require_relative "setup.rb" + +class DownloadTest < MiniTest::Test + + def test_pubchem_classification + Download.pubchem_classification aid: 1191, active: "carcinogen", inactive: "non-carcinogen", species: "Hamster", endpoint: "Carcinogen" + csv = File.join(File.dirname(__FILE__),"..","data","Carcinogen-Hamster.csv") + meta_file = File.join(File.dirname(__FILE__),"..","data","Carcinogen-Hamster.json") + assert File.exists?(csv) + table = CSV.read csv + assert_equal 87, table.size + assert_equal ["48413129", "CC=O", "carcinogen"], table[1] + meta = JSON.parse(File.read(meta_file)) + assert_equal "Hamster", meta["species"] + assert_equal 1, meta["warnings"].size + FileUtils.rm(csv) + FileUtils.rm(meta_file) + end + +end + + diff --git a/test/use_cases.rb b/test/use_cases.rb index 4842a18..59677cb 100644 --- a/test/use_cases.rb +++ b/test/use_cases.rb @@ -50,25 +50,81 @@ class UseCasesTest < MiniTest::Test end def test_public_models - skip + #skip + # TODO clean mongo + # PubChem 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: "carcinogen", inactive: "non-carcinogen", qmrf: qmrf + end + =begin - #classification - aids = [ - 1205, #Rodents (multiple species/sites) - 1208, # rat carc - 1199 # mouse - # Mutagenicity + # Mutagenicity + kazius = Dataset.from_sdf_file "#{DATA_DIR}/cas_4337.sdf" + hansen = Dataset.from_csv_file "#{DATA_DIR}/hansen.csv" + efsa = Dataset.from_csv_file "#{DATA_DIR}/efsa.csv" + datasets = [kazius,hansen,efsa] + map = {"1" => "mutagen", "0" => "nonmutagen"} + training_dataset = Dataset.merge datasets: datasets, features: datasets.collect{|d| d.bioactivity_features.first}, value_maps: [nil,map,map], keep_original_features: false, remove_duplicates: true + # rename merged feature + training_dataset.merged_features.first.name = "Mutagenicity" + training_dataset.merged_features.first.save + Model::Validation.from_dataset training_dataset: training_dataset, prediction_feature: training_dataset.merged_features.first, species: "Salmonella typhimurium", endpoint: "Mutagenicity" + + # Blood Brain Barrier Penetration + bbb = Dataset.from_csv_file "#{DATA_DIR}/bbb.csv" + Model::Validation.from_dataset training_dataset: bbb, prediction_feature: bbb.bioactivity_features.first, species: "Human", endpoint: "Blood Brain Barrier Penetration" + # PubChem Regression + # TODO transformations + [ + { + :aid => 1195, + :species => "Human", + :endpoint => "Maximum Recommended Daily Dose" + },{ + :aid => 1208, + :species => "Rat (TD50)", + :endpoint => "Carcinogenicity" + },{ + :aid => 1199, + :species => "Mouse (TD50)", + :endpoint => "Carcinogenicity" + },{ + :aid => 1188, + :species => "Fathead minnow", + :endpoint => "Acute Toxicity" + } + ].each do |assay| + Model::Validation.from_pubchem_aid aid: assay[:aid], species: assay[;species], endpoint: assay[:endpoint], regression:true + end - 1195 #MRDD - 1188 #FHM - 1208, # rat carc td50 - 1199 # mouse td50 - # daphnia - # Blood Brain Barrier Penetration - # Lowest observed adverse effect level (LOAEL) + daphnia = Dataset.from_csv_file "#{DATA_DIR}/daphnia.csv" + Model::Validation.from_dataset training_dataset: daphnia, prediction_feature: daphnia.bioactivity_features.first, species: "Daphnia magna", endpoint: "Acute toxicity" + # LOAEL + loael = Dataset.from_csv_file "#{DATA_DIR}/loael.csv" + Model::Validation.from_dataset training_dataset: loael, prediction_feature: loael.bioactivity_features.first, species: "Rat", endpoint: "Lowest observed adverse effect level (LOAEL)" +=end + +=begin # 1204 estrogen receptor # 1259408, # GENE-TOX # 1159563 HepG2 cytotoxicity assay |