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Updated the AMES ds models. Now all Kazius compounds pass.
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@olas
olas committed Sep 7, 2012
1 parent 1781b14 commit b1e973e
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28 changes: 0 additions & 28 deletions plugins/net.bioclipse.ds.models.ames/data/bursiApproved.txt
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28 changes: 0 additions & 28 deletions plugins/net.bioclipse.ds.models.ames/data/bursiApprovedCDKCorrected.txt
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37 changes: 0 additions & 37 deletions plugins/net.bioclipse.ds.models.ames/data/bursiApprovedInclExcl.txt
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37 changes: 0 additions & 37 deletions plugins/net.bioclipse.ds.models.ames/data/bursiApprovedInclExclCDKCorrected.txt
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4 changes: 0 additions & 4 deletions plugins/net.bioclipse.ds.models.ames/data/sample.txt
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28 changes: 28 additions & 0 deletions plugins/net.bioclipse.ds.models.ames/models/bursiSmartsSchymanskiCorrected.txt
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[$(O=N(~O)a);!$(O=N(O)c[$(aS(=O)=O),$(aaS(=O)=O),$(aaaS(=O)=O),$(aC(F)(F)F),$(aaC(F)(F)F),$(aaaC(F)(F)F)])] Specific arom nitro
[$([NH2]a);!$([NH2]a[$(aC(F)(F)F),$(aaC(F)(F)F),$(aaaC(F)(F)F),$(aS(=O)=O),$(aaS(=O)=O),$(aaaS(=O)=O),$(aC(=O)O),$(aaC(=O)O),$(aaaC(=O)O)])] Specific arom amine
a[N;X2]=O Aromatic nitroso
CO[N;X2]=O Alkyl nitrite
N[N;X2]=O Nitrosamine
O1[c,C]-[c,C]1 Epoxide
C1NC1 Aziridine
N=[N+]=[N-] Azide
C=[N+]=[N-] Diazo
N=N-N Triazine
[$(c[N;X2]!@;=[N;X2]c);!$([$([N;X2]([$(acS(=O)(=O)),$(aacS(=O)(=O)),$(aaacS(=O)(=O)),$(aaaacS(=O)(=O))])=[N;X2][$(acS(=O)(=O)),$(aacS(=O)(=O)),$(aaacS(=O)(=O)),$(aaaacS(=O)(=O))])])] Aromatic azo
[$([OH,NH2][N,O]);!$(O=N(O)[O-])] Unsubstituted heteroatombonded heteroatom
[OH]N-a Aromatic hydroxylamine
[Cl,Br,I]C Aliphatic halide
[Cl,Br,I]C=O Carboxylic acid halide
[N,S]!@[C;X4]!@[CH2][Cl,Br,I] Nitrogen or sulphur mustard
[cH]1[cH]ccc2c1c3c(cc2)cc[cH][cH]3 Bay-region in polycyclic aromatic hydrocarbons
[cH]1cccc2c1[cH][cH]c3c2ccc[cH]3 K-region in polycyclic aromatic hydrocarbons
[$(a13~a~a~a~a~2~a~1~a(~a~a~a~3)~a~a~a~2),$(a1~a~a~a2~a~1~a~a3~a(~a~2)~a~a~a~3),$(a1~a~a~a2~a~1~a~a~a3~a~2~a~a~a~3),$(a1~a~a~a~a2~a~1~a3~a(~a~2)~a~a~a~a~3),$(a1~a~a~a~a2~a~1~a~a3~a(~a~2)~a~a~a~3),$(a1~a~a~a~a2~a~1~*~a3~a(~*~2)~a~a~a~a~3),$(a1~a~a~a~a2~a~1~a~a~a3~a~2~a~a~a~3),$(a1~a~a~a~a2~a~1~a~a~a3~a~2~a~a~a~a~3),$(a13~a~a~a~a2~a~1~a(~a~a~a~3)~a~a~2)] Polycyclic aromatic and planar systems
[$([C,c]OS(=O)(=O)O!@[c,C]),$([c,C]S(=O)(=O)O!@[c,C])] Sulphonatebonded carbon (alkyl alkane sulphonate or dialkyl sulphate)
O=N(~O)N Aliphatic N-nitro
[$(O=[CH]C=C),$(O=[CH]C=O);!$(O=[CH]C([N,O,S])=C);!$(O=[CH]C=C[N,O,S]);!$(O=[CH]C=Ca)] Alpha, beta unsaturated aldehyde
[N;v4]#N Diazonium
O=C1CCO1 Beta-propiolactone
[CH]=[CH]O Alpha, beta unsaturated alkoxy group
[NH;!R][NH;!R]a 1-aryl-2-monoalkyl hydrazine
[$([CH3][NH]a);!$([CH3][NH]a[$(a(S=O)),$(aa(S=O)),$(aaa(S=O)),$(aC(=O)O),$(aaC(=O)O),$(aaaC(=O)O),$(aC(F)(F)F),$(aaC(F)(F)F),$(aaaC(F)(F)F)])] Aromatic methylamine
[$(aN([OH])[$([H]),$(C(=O)[CH3]),$([CH3]),$([OH]),$(O*=O)]),$(aN(O*=O)[$([H]),$(C(=O)[CH3]),$([CH3]),$([OH]),$(O*=O)])] Ester derivative of aromatic hydroxylamine
44 changes: 5 additions & 39 deletions plugins/net.bioclipse.ds.models.ames/plugin.xml
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Expand Up @@ -70,15 +70,15 @@

</test>

<test
<test
id="ames.smarts"
name="Ames Structural Alerts"
name="Kazius Structural Alerts"
endpoint="net.bioclipse.ds.mutagenicity"
consensus="net.bioclipse.ds.consensus.majority.emptynegative"
propertycalculator="Ames Toxicophores"
class="net.bioclipse.ds.matcher.SmartsMatcher">
class="net.bioclipse.ds.matcher.SmartsAlertMatcher">
<resource name="file"
path="data/bursiApprovedCDKCorrected.txt">
path="models/bursiSmartsSchymanskiCorrected.txt">
</resource>

<parameter name="Model type" value="SMARTS matching" />
Expand All @@ -91,7 +91,7 @@

<test
id="ames.signatures"
name="Ames Signature Significance"
name="Ames QSAR"
class="net.bioclipse.ds.libsvm.SignaturesLibSVMPrediction"
endpoint="net.bioclipse.ds.mutagenicity"
propertycalculator="Ames Signature Significance">
Expand Down Expand Up @@ -120,40 +120,6 @@
<parameter name="URL" value="http://pubs.acs.org/doi/abs/10.1021/jm040835a" />
<parameter name="Dataset name" value="Bursi Mutagenicity Dataset" />
</test>

<!--test
id="ames.signatures"
name="Ames Signature Significance"
class="net.bioclipse.ds.libsvm.SignaturesLibSVMPrediction"
endpoint="net.bioclipse.ds.mutagenicity"
propertycalculator="Ames Signature Significance">
<resource name="file" path="data/bursi_nosalts_inchi.sdf" />
<parameter name="responseProperty" value="Ames test categorisation" />
<resource name="trainFile" path="models/ames.train" />
<parameter name="positiveValue" value="mutagen" />
<parameter name="negativeValue" value="nonmutagen" />
<resource name="modelfile" path="models/ames.model.old" />
<resource name="signaturesfile" path="models/ames.signatures.old" />
<parameter name="signatures.min.height" value="0" />
<parameter name="signatures.max.height" value="3" />
<parameter name="Model type" value="QSAR" />
<parameter name="Model choice" value="Maximal accuracy, with 5-fold cross-validated accuracy as objective function" />
<parameter name="Model validation" value="Accuracy measued on an external test set" />
<parameter name="Model performance" value="0.85" />
<parameter name="Learning model" value="SVM" />
<parameter name="Learning parameters" value="kernel=RBF, c=10, gamma=0.002" />
<parameter name="Descriptors" value="Signatures (height 0-3)" />
<parameter name="Observations" value="4337" />
<parameter name="Variables" value="23226" />
<parameter name="URL" value="http://pubs.acs.org/doi/abs/10.1021/jm040835a" />
<parameter name="Dataset name" value="Bursi Mutagenicity Dataset" />
</test-->

<test
id="ames.consensus"
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