diff options
| author | Christoph Helma <helma@in-silico.ch> | 2015-11-09 13:22:19 +0100 |
|---|---|---|
| committer | Christoph Helma <helma@in-silico.ch> | 2015-11-09 13:22:19 +0100 |
| commit | 79c43bed16febf66a613b93fa67793a1315c72c5 (patch) | |
| tree | c0b63b08c5fea940a142ba82305bb5045d360b65 | |
| parent | f6030b1c159e22165a854d71ba05835b0e62f033 (diff) | |
swiss LOALs added
| -rw-r--r-- | create_nestec_models.rb | 9 | ||||
| -rw-r--r-- | dump/production/compounds.bson | bin | 853904 -> 2276280 bytes | |||
| -rw-r--r-- | dump/production/crossvalidations.bson | bin | 210252 -> 360266 bytes | |||
| -rw-r--r-- | dump/production/datasets.bson | bin | 2087363 -> 3807049 bytes | |||
| -rw-r--r-- | dump/production/features.bson | bin | 567 -> 744 bytes | |||
| -rw-r--r-- | dump/production/models.bson | bin | 43927 -> 93248 bytes | |||
| -rw-r--r-- | dump/production/open_tox_model_predictions.bson | bin | 817 -> 1504 bytes | |||
| -rw-r--r-- | dump/production/repeatedcrossvalidations.bson | bin | 444 -> 888 bytes | |||
| -rw-r--r-- | dump/production/validations.bson | bin | 227376 -> 395167 bytes | |||
| -rw-r--r-- | mg2mmol.rb | 17 | ||||
| -rw-r--r-- | regression/swissMouse_chron_LOAEL_mmol.csv | 394 | ||||
| -rw-r--r-- | regression/swissMouse_chron_LOAEL_mmol.json | 5 | ||||
| -rw-r--r-- | regression/swissMultigen_LOAEL_mmol.csv | 399 | ||||
| -rw-r--r-- | regression/swissMultigen_LOAEL_mmol.json | 5 | ||||
| -rw-r--r-- | regression/swissRat_chron_LOAEL_mmol.csv | 494 | ||||
| -rw-r--r-- | regression/swissRat_chron_LOAEL_mmol.json | 5 |
16 files changed, 1325 insertions, 3 deletions
diff --git a/create_nestec_models.rb b/create_nestec_models.rb index 0717ce0..8467826 100644 --- a/create_nestec_models.rb +++ b/create_nestec_models.rb @@ -1,12 +1,15 @@ require_relative '../lazar/lib/lazar' include OpenTox -#$mongo.database.drop -#$gridfs = $mongo.database.fs # recreate GridFS indexes +$mongo.database.drop +$gridfs = $mongo.database.fs # recreate GridFS indexes #=begin [ "Rat_TD50.csv", "Mouse_TD50.csv", - "LOAEL_mmol_corrected_smiles.csv" + "LOAEL_mmol_corrected_smiles.csv", + "swissMouse_chron_LOAEL_mmol.csv", + "swissMultigen_LOAEL_mmol.csv", + "swissRat_chron_LOAEL_mmol.csv", ].each do |file| file = File.join(File.dirname(__FILE__),"regression",file) Model::Prediction.from_csv_file file diff --git a/dump/production/compounds.bson b/dump/production/compounds.bson Binary files differindex bdabca8..cbd8111 100644 --- a/dump/production/compounds.bson +++ b/dump/production/compounds.bson diff --git a/dump/production/crossvalidations.bson b/dump/production/crossvalidations.bson Binary files differindex 7f07356..e92990e 100644 --- a/dump/production/crossvalidations.bson +++ b/dump/production/crossvalidations.bson diff --git a/dump/production/datasets.bson b/dump/production/datasets.bson Binary files differindex 9e1bbc4..c2a869a 100644 --- a/dump/production/datasets.bson +++ b/dump/production/datasets.bson diff --git a/dump/production/features.bson b/dump/production/features.bson Binary files differindex ef731e1..3145641 100644 --- a/dump/production/features.bson +++ b/dump/production/features.bson diff --git a/dump/production/models.bson b/dump/production/models.bson Binary files differindex d3afba4..9331b89 100644 --- a/dump/production/models.bson +++ b/dump/production/models.bson diff --git a/dump/production/open_tox_model_predictions.bson b/dump/production/open_tox_model_predictions.bson Binary files differindex cef5b5d..0551c0e 100644 --- a/dump/production/open_tox_model_predictions.bson +++ b/dump/production/open_tox_model_predictions.bson diff --git a/dump/production/repeatedcrossvalidations.bson b/dump/production/repeatedcrossvalidations.bson Binary files differindex 8a44f6a..fe7dc5f 100644 --- a/dump/production/repeatedcrossvalidations.bson +++ b/dump/production/repeatedcrossvalidations.bson diff --git a/dump/production/validations.bson b/dump/production/validations.bson Binary files differindex bee7f7e..e5da146 100644 --- a/dump/production/validations.bson +++ b/dump/production/validations.bson diff --git a/mg2mmol.rb b/mg2mmol.rb new file mode 100644 index 0000000..dc6b953 --- /dev/null +++ b/mg2mmol.rb @@ -0,0 +1,17 @@ +#!/usr/bin/env ruby +require_relative '../lazar/lib/lazar' +include OpenTox +newfile = ARGV[0].sub(/.csv/,"_mmol.csv") +p newfile +CSV.open(newfile, "wb") do |csv| + CSV.read(ARGV[0]).each do |line| + smi,mg = line + if mg.numeric? + c = Compound.from_smiles smi + mmol = c.mg_to_mmol mg.to_f + csv << [smi, mmol] + else + csv << [smi, mg.gsub(/mg/,'mmol')] + end + end +end diff --git a/regression/swissMouse_chron_LOAEL_mmol.csv b/regression/swissMouse_chron_LOAEL_mmol.csv new file mode 100644 index 0000000..102a8b5 --- /dev/null +++ b/regression/swissMouse_chron_LOAEL_mmol.csv @@ -0,0 +1,394 @@ +SMILES,LOAEL parental as dose (mmol/kg bw per day) +O=P(OCC)(SC(C)CC)SC(C)CC,0.0005214647946645646 +C1CNC(=S)NC1,0.0017213967807490692 +CC(C(O)=O)OC2=CC=C(C=C2)OC1=C(Cl)C=C(C(F)(F)F)C=N1,0.0016588317479976395 +FC(F)(F)C1=CC(NC(N(C)C)=O)=CC=C1,0.0032299414713072455 +CC(OC1=CC=C(OC2=CC=C(Cl)C=C2Cl)C=C1)C(OC)=O,0.0022568337247128047 +CCSCSP(OCC)(OCC)=S,0.0034565205655226585 +S=P(OCC)(OCC)SCSC(C)(C)C,0.003120334583633435 +ClC(C(SCC(O)=O)=C3)=CC(F)=C3\N=C2/SC(N1CCCCN12)=O,0.0025650712402365693 +O=C(N(COCC)C1=C(CC)C=CC=C1C)CCl,0.004077591462568489 +S=P(OCC)(OCC)SCSP(OCC)(OCC)=S,0.003043101917348465 +ClC(C=C(C=C1Cl)C(F)(F)F)=C1N2N=C(C(S(C(F)(F)F)=O)=C2N)C#N,0.0027016035498978173 +CCS(CCSP(OC)(OC)=O)(=O)=O,0.004765825265934956 +[O-][N+]2=NC(N3C=CN=C3)=NC1=CC=C(Cl)C=C12,0.005653355368059447 +ClC1(C(Cl)=C2Cl)C(C3Cl)C(C=C3)C2(Cl)C(Cl)1Cl,0.00401802539767067 +FC(F)C1=NC(C(F)(F)F)=C(C2=NCCS2)C(CC(C)C)=C1C(OC)=O,0.004036577506681444 +FC1=CC=CC(F)=C1C(NC(NC2=CC(Cl)=C(C(Cl)=C2F)F)=O)=O,0.005510230739958609 +CCOP(OCC)(SCN1C(OC2=C1C=CC(Cl)=C2)=O)=S,0.006253252921346584 +O=S3OCC1C(CO3)C2(Cl)C(Cl)=C(Cl)C(Cl)1C(Cl)2Cl,0.006143636148899525 +O=P(OC)(OC)SCCS(CC)=O,0.010150855518163414 +CC(C)(C)C1=CC=C(CSC2=C(Cl)C(N(C(C)(C)C)N=C2)=O)C=C1,0.007617844970248671 +FC(F)(F)C1=CC(Cl)=C(OC2=CC=C([N+]([O-])=O)C(OCC)=C2)C=C1,0.007741214384548647 +[O][N](N=C(NC)NCC1COCC1)=O,0.014835983748861215 +BrC1=CC=C(NC(N(C)OC)=O)C=C1,0.01157854825383142 +[O-][N+](C(C(Cl)=C(Cl)C(Cl)=C1Cl)=C1Cl)=O,0.010157966537626632 +BrC1=CC(C#N)=CC(Br)=C1O,0.011194858745191247 +O=P(SC)(OC)N,0.024799974037970036 +O=P(OC)(OC)SCCSCC,0.01563278476717342 +S=P(OC)(OC)SCC(NC)=O,0.01570287055736368 +S=P(OC)(OC)SCN1N=NC(C=CC=C2)=C2C1=O,0.011975129144887783 +O=C2C(N)=C(Cl)C(C1=CC=CC=C12)=O,0.018399605792016827 +O=P(SCCC)(OCC)SCCC,0.016505802491072218 +C1CNC(=S)NC1,0.034427935101965214 +O=C1OC3(CCCCC3)C(OC(C(C)(C)CC)=O)=C1C2=C(Cl)C=C(Cl)C=C2,0.00996793559291828 +N#CC1=C(Cl)C(Cl)=C(Cl)C(C#N)=C1Cl,0.015757152044181925 +O=C(CCC1)C(C(C2=CC=C(S(=O)(C)=O)C(COCC(F)(F)F)=C2Cl)=O)C1=O,0.00952772928740213 +CCOP(OC2=NN(C=N2)C1=CC=CC=C1)(OCC)=S,0.01340514601002239 +O=C(OCC)NCCOC1=CC=C(OC2=CC=CC=C2)C=C1,0.014601589646382791 +CC1(CNC(=NC1)NN=C(C=CC2=CC=C(C=C2)C(F)(F)F)C=CC3=CC=C(C=C3)C(F)(F)F)C,0.00899943837286495 +CCC(C)C1C(C=CC2(O1)CC3CC(O2)CC=C(C(C(C=CC=C4COC5C4(C(C=C(C5O)C)C(=O)O3)O)C)OC6CC(C(C(O6)C)OC7CC(C(C(O7)C)NC)OC)OC)C)C.C1=CC=C(C=C1)C(=O)O,0.0049591365167366295 +O=C(N(OC)C)NC1=CC=C(Cl)C=C1,0.02608912260896714 +C[N+](C=C2)=CC=C2C1=CC=[N+](C)C=C1,0.030174016485746483 +CCN(CCCC)C1=C([N+]([O-])=O)C=C(C(F)(F)F)C=C1[N+]([O-])=O,0.01789554104260317 +O[Sn](C2CCCCC2)(C3CCCCC3)C1CCCCC1,0.015577821917247702 +OC(C2=CC=C(F)C=C2)(C3=C(F)C=CC=C3)CN1C=NC=N1,0.0199475112589154 +S=P(OC1=NC(Cl)=C(Cl)C=C1Cl)(OCC)OCC,0.017399424634198683 +S=P(OC)(OC)SCN1C(SC(OC)=N1)=O,0.02312033114374251 +O=C2C(CCCCCCCCCCCC)=C(OC(C)=O)C(C1=CC=CC=C12)=O,0.01820506013287405 +S=C(S)NC,0.06716555572283331 +FC(F)(F)C(S2)=NN=C2OCC(N(C(C)C)C1=CC=C(F)C=C1)=O,0.020367129884095975 +ClC1=CC=C(C(C(C)C)C(OC(C#N)C2=CC(OC3=CC=CC=C3)=CC=C2)=O)C=C1,0.017861392167393728 +ClC1=CC=C2C(N=CC(OC3=CC=C(OC(C)C(OCCO/N=C(C)/C)=O)C=C3)=N2)=C1,0.01689645165053326 +N4(N=CN=C4)[Sn](C2CCCCC2)(C3CCCCC3)C1CCCCC1,0.017376831785632364 +CC(C(OCCCC)=O)OC1=CC=C(OC2=CC=C(C(F)(F)F)C=N2)C=C1,0.02011156004417597 +ClC1C(Cl)C(Cl)C(Cl)C(Cl)C1Cl,0.026819807041584386 +CCC(C)C1C(C=CC2(O1)CC3CC(O2)CC=C(C(C(C=CC=C4COC5C4(C(C=C(C5O)C)C(=O)O3)O)C)OC6CC(C(C(O6)C)OC7CC(C(C(O7)C)O)OC)OC)C)C.CC1C=CC=C2COC3C2(C(C=C(C3O)C)C(=O)OC4CC(CC=C(C1OC5CC(C(C(O5)C)OC6CC(C(C(O6)C)O)OC)OC)C)OC7(C4)C=CC(C(O7)C(C)C)C)O,0.004618598502680387 +CC2(C)OC1=CC=CC(OC(NC)=O)=C1O2,0.03610703315519948 +CNC(ON=C(SC)C(N(C)C)=O)=O,0.0396786621616568 +CCOP(=S)(OCC)OC1=CC=C(C=C1)[N+](=O)[O-],0.030900160825037038 +S=P(OC)(OC)OC1=NC(N(CC)CC)=NC(C)=C1,0.02947596065103358 +CN(C)C(S[Zn]SC(N(C)C)=S)=S,0.029429761100971286 +CC(C(C1C(OC(C2=CC=CC(OC3=CC=CC=C3)=C2)C#N)=O)/C=C(C(F)(F)F)\Cl)1C,0.020451257925257496 +O=C(OC(C(C)(C)C)=N2)N2C1=CC(OC(C)C)=C(Cl)C=C1Cl,0.026939263984374007 +S=P(OC)(OC)OC1=CC(C)=C(SC)C=C1,0.03384495288148076 +C[N+](C=C2)=CC=C2C1=CC=[N+](C)C=C1,0.050630069477423496 +CN(/C=N/C(C=CC(C)=C2)=C2C)/C=N/C(C=CC(C)=C1)=C1C,0.032719166367035445 +CC(C)C(C2=CN=CN=C2)(O)C1=CC=C(OC(F)(F)F)C=C1,0.03138138916099924 +ClC1=CC(C(F)(F)F)=CC=C1OC2=CC=C([N+]([O-])=O)C(C(NS(C)(=O)=O)=O)=C2,0.022563437776748883 +O=C(OC(C)(C)C)C1=CC=C(CO/N=C/C2=C(OC3=CC=CC=C3)N(C)N=C2C)C=C1,0.0237254183313211 +FC(F)(F)C1=CC=C(N[C@@H]([C@H](C)C)C(OC(C#N)C2=CC(OC3=CC=CC=C3)=CC=C2)=O)C(Cl)=C1,0.01988416717024977 +CS/C(C)=N/OC(N(SN(C(O/N=C(SC)\C)=O)C)C)=O,0.02821118623185781 +N#CC1=CC(F)=C(OC2=CC=C(OC(C)C(OCCCC)=O)C=C2)C=C1,0.028149664483482217 +CC(C(=O)OCC1CCCO1)OC2=CC=C(C=C2)OC3=CN=C4C=C(C=CC4=N3)Cl,0.02378367776824666 +O=C1N(P(OCC)(SC(C)CC)=O)CCS1,0.03642165840388218 +CCOC1=CC=C(C(C)(C)COCC2=CC(OC3=CC=CC=C3)=CC=C2)C=C1,0.02762371992216459 +ClC1=C([N+]([O-])=O)C(NC2=NC=C(C(F)(F)F)C=C2Cl)=C([N+]([O-])=O)C=C1C(F)(F)F,0.02304921960123819 +BrC(C3)COC(CN2C=NC=N2)3C1=C(Cl)C=C(Cl)C=C1,0.028642362113111712 +CC(C(OCC#C)=O)OC1=CC=C(OC2=C(F)C=C(Cl)C=N2)C=C1,0.03145186198168118 +BrC(C3)COC(CN2C=NC=N2)3C1=C(Cl)C=C(Cl)C=C1,0.029968397372707515 +S=P(OC)(OC)OC1=CC=C([N+]([O-])=O)C=C1,0.04331184085181438 +[N+]12=CC=CC=C1C3=[N+](C=CC=C3)CC2,0.06513346824645723 +O=C(NC1=CC(Cl)=C(Cl)C=C1)N(C)OC,0.04817460403486396 +FC(C(F)(OCC(C2=CC=C(C=C2Cl)Cl)CN1C=NC=N1)F)F,0.03224544805117245 +NC#N,0.28782126874155745 +CC(C(CN2C=NC=N2)(C3=CC=C(C=C3)Cl)O)C1CC1,0.04215563844588306 +ClC1=CC=C(C(C(C)C)C(OC(C#N)C2=CC(OC3=CC=CC=C3)=CC=C2)=O)C=C1,0.029292683608764497 +CCOC(C(OC3=CC=C(C=C3)OC2=NC1=CC=C(Cl)C=C1N=C2)C)=O,0.03299336095995684 +FC(F)(F)C(C(F)(F)F)OC(/C=C\C1C(C)(C)C1C(OC(C#N)C2=CC=C(OC3=CC=CC=C3)C=C2)=O)=O,0.02327131770188449 +S=P(OC)(OC)OC1=CC(C)=C([N+]([O-])=O)C=C1,0.04544896572394105 +BrC1=CC(C#N)=CC(Br)=C1O,0.04694618327891067 +C1CC1(C(CC2=CC=CC=C2Cl)(CN3C=NC=N3)O)Cl,0.041640721294167994 +FC(F)(F)/C(Cl)=C/C1C(C)(C)C1C(OCC2=C(F)C(F)=C(C)C(F)=C2F)=O,0.031284802267325856 +CS(C1=CC(C(F)(F)F)=CC=C1C(C2=C(O)N(C)N=C2C)=O)(=O)=O,0.03753544272065299 +ClC1=CC=C(C2=NN(C(N(C(OC)=O)C4=CC=C(OC(F)(F)F)C=C4)=O)COC(C(OC)=O)2C3)C3=C1,0.026144559425692136 +O=C(NS(N(C(C)C)C)(=O)=O)C1=CC(N2C(C=C(C(F)(F)F)N(C)C2=O)=O)=C(F)C=C1Cl,0.027553034030721714 +O=C(NC(C)(C)C#C)C1=CC(Cl)=CC(Cl)=C1,0.05466020406059724 +O=C(N(CC)CC)SCC1=CC=C(Cl)C=C1,0.05430997355337045 +O=C(NC)OC1=C(OC(C)(C)C2)C2=CC=C1,0.06368292571103364 +O=P(OCC)(SCCC)OC1=C(Cl)C=C(Br)C=C1,0.03800543565863019 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+} diff --git a/regression/swissMultigen_LOAEL_mmol.csv b/regression/swissMultigen_LOAEL_mmol.csv new file mode 100644 index 0000000..204b1ae --- /dev/null +++ b/regression/swissMultigen_LOAEL_mmol.csv @@ -0,0 +1,399 @@ +SMILES,LOAEL parental as dose (mmol/kg bw per day) +O=P(OCC)(SC(C)CC)SC(C)CC,0.0009689629134850461 +CCSCSP(OCC)(OCC)=S,0.0013057967064131171 +O=P(OC)(OC)SCCSCC,0.001519854088965729 +CCC(C)C1C(C=CC2(O1)CC3CC(O2)CC=C(C(C(C=CC=C4COC5C4(C(C=C(C5O)C)C(=O)O3)O)C)OC6CC(C(C(O6)C)OC7CC(C(C(O7)C)O)OC)OC)C)C.CC1C=CC=C2COC3C2(C(C=C(C3O)C)C(=O)OC4CC(CC=C(C1OC5CC(C(C(O5)C)OC6CC(C(C(O6)C)O)OC)OC)C)OC7(C4)C=CC(C(O7)C(C)C)C)O,0.00023092992857514307 +[O-][N+]2=NC(N3C=CN=C3)=NC1=CC=C(Cl)C=C12,0.0016556255143997062 +O=P(OCC)(OCC)O/C(C1=CC=C(Cl)C=C1Cl)=C/Cl,0.001390550132780851 +O=P(OC)(OC)O/C(C)=C/C(OC)=O,0.0022306662357614343 +CCOP(=S)(OCC)OC1=CC=C(C=C1)[N+](=O)[O-],0.0017166756013909466 +CS(C(C=C2Cl)=CC=C2C(C(C(CCC1)=O)C1=O)=O)(=O)=O,0.0015208291852717307 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"endpoint": "Lowest observed adverse effect level (parental)", + "unit": "mmol/kg_bw/day" +} diff --git a/regression/swissRat_chron_LOAEL_mmol.csv b/regression/swissRat_chron_LOAEL_mmol.csv new file mode 100644 index 0000000..997d8a4 --- /dev/null +++ b/regression/swissRat_chron_LOAEL_mmol.csv @@ -0,0 +1,494 @@ +SMILES,LOAEL parental as dose (mmol/kg bw per day) +[O-][N+]2=NC(N3C=CN=C3)=NC1=CC=C(Cl)C=C12,0.00020190555530632425 +ClC(C=C(C=C1Cl)C(F)(F)F)=C1N2N=C(C(S(C(F)(F)F)=O)=C2N)C#N,0.00013496580117055152 +CC(C(O)=O)OC2=CC=C(C=C2)OC1=C(Cl)C=C(C(F)(F)F)C=N1,0.0002764719511333511 +S=P(OCC)(OCC)SCSC(C)(C)C,0.00034670385697674235 +CCSCSP(OCC)(OCC)=S,0.0006144925475253195 +CC(OC1=CC=C(OC2=CC=C(Cl)C=C2Cl)C=C1)C(OC)=O,0.0005861906011027885 +S=P(OC)(OC)SCC(NC)=O,0.000872381733741038 +S=P(OC)(OC)OC1=CC(C)=C(SC)C=C1,0.0007185764991867223 +O=P(OC)(OC)SCCS(CC)=O,0.0008932752807580748 +O=P(OCC)(SC(C)CC)SC(C)CC,0.0008210296720157477 +O=P(SC)(OC)N,0.0020548549325897737 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a/regression/swissRat_chron_LOAEL_mmol.json b/regression/swissRat_chron_LOAEL_mmol.json new file mode 100644 index 0000000..10b52ac --- /dev/null +++ b/regression/swissRat_chron_LOAEL_mmol.json @@ -0,0 +1,5 @@ +{ + "species": "Rat", + "endpoint": "Lowest observed adverse effect level (LOAEL)", + "unit": "mmol/kg_bw/day" +} |