Skip to content

Commit

Permalink
Browse files Browse the repository at this point in the history
Model documentations
  • Loading branch information
olas committed Nov 21, 2012
1 parent f71ff60 commit 7145d75
Show file tree
Hide file tree
Showing 36 changed files with 474 additions and 69 deletions.
33 changes: 28 additions & 5 deletions features/net.bioclipse.ds.models_feature/feature.xml
Expand Up @@ -21,7 +21,22 @@
id="net.bioclipse.ds.models.ames"
download-size="0"
install-size="0"
version="0.0.0"/>
version="0.0.0"
unpack="false"/>

<plugin
id="net.bioclipse.ds.models.ahr"
download-size="0"
install-size="0"
version="0.0.0"
unpack="false"/>

<plugin
id="net.bioclipse.ds.models.chemspider"
download-size="0"
install-size="0"
version="0.0.0"
unpack="false"/>

<plugin
id="net.bioclipse.ds.models.cpdb"
Expand All @@ -31,7 +46,14 @@
unpack="false"/>

<plugin
id="net.bioclipse.ds.models.ahr"
id="net.bioclipse.ds.models.cyp.pcm"
download-size="0"
install-size="0"
version="0.0.0"
unpack="false"/>

<plugin
id="net.bioclipse.ds.models.daphnia"
download-size="0"
install-size="0"
version="0.0.0"
Expand All @@ -45,13 +67,14 @@
unpack="false"/>

<plugin
id="net.bioclipse.ds.models.daphnia"
id="net.bioclipse.ds.models.r.ames"
download-size="0"
install-size="0"
version="0.0.0"/>
version="0.0.0"
unpack="false"/>

<plugin
id="net.bioclipse.ds.models.chemspider"
id="net.bioclipse.ds.models.r.u251"
download-size="0"
install-size="0"
version="0.0.0"
Expand Down
3 changes: 2 additions & 1 deletion plugins/net.bioclipse.ds.models.ahr/build.properties
Expand Up @@ -7,4 +7,5 @@ bin.includes = META-INF/,\
icons/,\
data/,\
html/,\
toc.xml
tocEP.xml,\
tocModels.xml
7 changes: 0 additions & 7 deletions plugins/net.bioclipse.ds.models.ahr/html/ahr.html
Expand Up @@ -10,19 +10,12 @@
<body>
<h1>AhR Endpoint</h1>

<h2>Overview</h2>
The aryl hydrocarbon receptor (AHR) is a ligand-activated transcription factor
involved in the biological response to aromatic hydrocarbons, and regulates the
expression of xenobiotic-metabolizing enzymes such as cytochrome P450, aldehyde
dehydrogenase, quinone reductase, and other phase I and phase II detoxification genes.


<h2>Data source</h2>
Data originates from the <a href="http://pubchem.ncbi.nlm.nih.gov/assay/assay.cgi?aid=2796&loc=ea_ras">PubChem BioAssay 2796</a>,
named <i>Luminescence-based cell-based high throughput confirmation assay for activators of the Aryl Hydrocarbon Receptor</i>.
The data was filtered for unknown CDK atom types,
and contained after this filtering 15951 compounds where
7971 were annotated as <i>Active</i>, and 7980 compounds as <i>Inactive</i>.


</body>
Expand Down
54 changes: 54 additions & 0 deletions plugins/net.bioclipse.ds.models.ahr/html/ahrmodels.html
@@ -0,0 +1,54 @@
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">

<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
<title>AhR Models</title>
<link rel="stylesheet" href="../../PRODUCT_PLUGIN/narrow_book.css" type="text/css">
</head>

<body>
<h1>AhR Models</h1>

<h2>Data source</h2>
Data originates from the <a href="http://pubchem.ncbi.nlm.nih.gov/assay/assay.cgi?aid=2796&loc=ea_ras">PubChem BioAssay 2796</a>,
named <i>Luminescence-based cell-based high throughput confirmation assay for activators of the Aryl Hydrocarbon Receptor</i>.
The data was filtered for unknown CDK atom types,
and contained after this filtering 15951 compounds where
7971 were annotated as <i>Active</i>, and 7980 compounds as <i>Inactive</i>.


<h2>Models</h2>

<table>
<td bgcolor="cccccc" width=150>Model type</td>
<td bgcolor="cccccc">Model implementation</td>
<td bgcolor="cccccc">Comment</td>
<tr>

<td>Exact Match</td>
<td>Molecular Signature</td>
<td></td>
<tr>

<td>Near Neighbor</td>
<td>CDK Fingerprint</td>
<td>Tanimoto distance > 0.7</td>
<tr>

<td>Structural alerts</td>
<td>Signatures</td>
<td></td>
<tr>

<td>QSAR</td>
<td>SVM model with Signature descriptor height 0-3</td>
<td></td>
<tr>

</table>



</body>
</html>
5 changes: 4 additions & 1 deletion plugins/net.bioclipse.ds.models.ahr/plugin.xml
Expand Up @@ -5,7 +5,10 @@
<extension
point="org.eclipse.help.toc">
<toc
file="toc.xml"
file="tocEP.xml"
primary="false"/>
<toc
file="tocModels.xml"
primary="false"/>
</extension>

Expand Down
File renamed without changes.
6 changes: 6 additions & 0 deletions plugins/net.bioclipse.ds.models.ahr/tocModels.xml
@@ -0,0 +1,6 @@
<?xml version="1.0" encoding="UTF-8"?>
<?NLS TYPE="org.eclipse.help.toc"?>

<toc link_to="../net.bioclipse.ds.ui/toc.xml#ContributedModels" label="AhR" >
<topic label="AhR" href="html/ahrmodels.html" />
</toc>
5 changes: 3 additions & 2 deletions plugins/net.bioclipse.ds.models.ames/build.properties
Expand Up @@ -6,5 +6,6 @@ bin.includes = META-INF/,\
data/,\
html/,\
icons/,\
toc.xml,\
models/
tocModels.xml,\
models/,\
tocEP.xml
71 changes: 71 additions & 0 deletions plugins/net.bioclipse.ds.models.ames/html/ames.html
@@ -0,0 +1,71 @@
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">

<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
<title>Ames Mutagenicity Models</title>
<link rel="stylesheet" href="../../PRODUCT_PLUGIN/narrow_book.css" type="text/css">
</head>

<body>
<h1>Ames Mutagenicity Models</h1>

<h2>Overview</h2>
These mutagenicity models are built on data from Ames <i>Salmonella</i> microsome mutagenicity assays
(AMES test) [1].


<h2>Data source</h2>
The AMES dataset published by Kazius et al. [2] was downloaded from
<a href="http://cheminformatics.org/datasets/bursi/">
http://cheminformatics.org/datasets/bursi/</a>.
The dataset contained 4337 chemical structures of which 2401 were
classified as <i>mutagen</i>, and 1936 <i>nonmutagen</i>.

<h2>Models</h2>

<table>
<td bgcolor="cccccc" width=150>Model type</td>
<td bgcolor="cccccc">Model implementation</td>
<td bgcolor="cccccc">Comment</td>
<tr>

<td>Exact Match</td>
<td>Molecular Signature</td>
<td></td>
<tr>

<td>Near Neighbor</td>
<td>CDK Fingerprint</td>
<td>Tanimoto distance > 0.7</td>
<tr>

<td>Structural alerts</td>
<td>SMARTS</td>
<td>List of SMARTS defined in [2]</td>
<tr>

<td>QSAR</td>
<td>SVM model with Signature descriptor height 0-3</td>
<td></td>
<tr>

</table>



<h2>References</h2>

[1] K. Mortelmans and E. Zeiger<br>
The ames salmonella/microsome mutagenicity assay<br>
<i>Mutat Res</i>, 455(1-2):29-60, Nov 2000<br>

<p>

[2] J. Kazius, R. McGuire, and R. Bursi<br>
Derivation and validation of toxicophores for mutagenicity prediction<br>
<i>J Med Chem</i>, 48(1):312-320, Jan 2005<br>


</body>
</html>
35 changes: 11 additions & 24 deletions plugins/net.bioclipse.ds.models.ames/html/mutagenicity.html
Expand Up @@ -11,31 +11,18 @@
<h1>Mutagenicity Endpoint</h1>

<h2>Overview</h2>
Mutagenicity is the ability of a substance to induce mutations to DNA, which
can be measured with the Ames <i>Salmonella</i> microsome mutagenicity assay
(AMES test) [1].


<h2>Data source</h2>
The AMES dataset published by Kazius et al. [2] was downloaded from
<a href="http://cheminformatics.org/datasets/bursi/">
http://cheminformatics.org/datasets/bursi/</a>.
The dataset contained 4337 chemical structures of which 2401 were
classified as <i>mutagen</i>, and 1936 <i>nonmutagen</i>.


<h2>References</h2>

[1] K. Mortelmans and E. Zeiger<br>
The ames salmonella/microsome mutagenicity assay<br>
<i>Mutat Res</i>, 455(1-2):29-60, Nov 2000<br>

Mutagenicity is the ability of a substance to induce mutations to DNA.
<p>
In genetics, a mutagen (Latin, literally origin of change) is a physical or
chemical agent that changes the genetic material, usually DNA, of
an organism and thus increases the frequency of mutations above the natural
background level. As many mutations cause cancer, mutagens are therefore also
likely to be carcinogens. Not all mutations are caused by mutagens: so-called
"spontaneous mutations" occur due to spontaneous hydrolysis, errors in DNA replication,
repair and recombination.
<p>
<a href="http://en.wikipedia.org/wiki/Mutagen">Wikipedia article on Mutagen</a>
<p>

[2] J. Kazius, R. McGuire, and R. Bursi<br>
Derivation and validation of toxicophores for mutagenicity prediction<br>
<i>J Med Chem</i>, 48(1):312-320, Jan 2005<br>


</body>
</html>
5 changes: 4 additions & 1 deletion plugins/net.bioclipse.ds.models.ames/plugin.xml
Expand Up @@ -5,7 +5,10 @@
<extension
point="org.eclipse.help.toc">
<toc
file="toc.xml"
file="tocModels.xml"
primary="false"/>
<toc
file="tocEP.xml"
primary="false"/>
</extension>

Expand Down
@@ -1,6 +1,6 @@
<?xml version="1.0" encoding="UTF-8"?>
<?NLS TYPE="org.eclipse.help.toc"?>

<toc link_to="../net.bioclipse.ds.ui/toc.xml#ContributedEndpoints" label="Mutagenicity EP" >
<toc link_to="../net.bioclipse.ds.ui/toc.xml#ContributedEndpoints" label="Mutagenicity" >
<topic label="Mutagenicity" href="html/mutagenicity.html" />
</toc>
</toc>
6 changes: 6 additions & 0 deletions plugins/net.bioclipse.ds.models.ames/tocModels.xml
@@ -0,0 +1,6 @@
<?xml version="1.0" encoding="UTF-8"?>
<?NLS TYPE="org.eclipse.help.toc"?>

<toc link_to="../net.bioclipse.ds.ui/toc.xml#ContributedModels" label="Ames Mutagenicity" >
<topic label="Ames Mutagenicity" href="html/ames.html" />
</toc>
3 changes: 2 additions & 1 deletion plugins/net.bioclipse.ds.models.daphnia/build.properties
Expand Up @@ -5,4 +5,5 @@ bin.includes = META-INF/,\
plugin.xml,\
data/,\
html/,\
toc.xml
tocEP.xml,\
tocModels.xml
28 changes: 28 additions & 0 deletions plugins/net.bioclipse.ds.models.daphnia/html/aquatictox.html
@@ -0,0 +1,28 @@
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">

<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
<title>Aquatic Toxicity</title>
<link rel="stylesheet" href="../../PRODUCT_PLUGIN/narrow_book.css" type="text/css">
</head>

<body>
<h1>Aquatic Toxicity</h1>
<a href="http://en.wikipedia.org/wiki/Aquatic_toxicology">Aquatic toxicology</a> is the study of the effects of manufactured chemicals on aquatic organisms.

<p>
<h2>Daphnid assay</h2>
<a href="http://en.wikipedia.org/wiki/Daphnia">Daphnia</a> are small, planktonic crustaceans widely used in aquatic toxicity testing.
A list of structural alerts (SMARTS) consiting of 18 manually created SMARTS from the publication below was kindly supported by Emma Schymanski.

<p>
<h2>References</h2>
Peter C. von der Ohe, Ralph K&uuml;hne,Ralf-Uwe Ebert, Rolf Altenburger, Matthias Liess, and Gerrit Sch&uuml;&uuml;rmann<br>
<a href="http://pubs.acs.org/doi/abs/10.1021/tx0497954">Structural Alerts: A New Classification Model to Discriminate Excess Toxicity from Narcotic Effect Levels of Organic Compounds in the Acute Daphnid Assay</a><br>
<i>Chemical Research in Toxicology</i> 2005 18 (3), 536-555<br>



</body>
</html>
27 changes: 19 additions & 8 deletions plugins/net.bioclipse.ds.models.daphnia/html/daphnia.html
Expand Up @@ -3,22 +3,33 @@
<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
<title>Aquatic Toxicity</title>
<title>Daphnia</title>
<link rel="stylesheet" href="../../PRODUCT_PLUGIN/narrow_book.css" type="text/css">
</head>

<body>
<h1>Aquatic Toxicity</h1>
<a href="http://en.wikipedia.org/wiki/Aquatic_toxicology">Aquatic toxicology</a> is the study of the effects of manufactured chemicals on aquatic organisms.

<p>
<h2>Daphnid assay</h2>
<h1>Daphnid assay</h1>
<a href="http://en.wikipedia.org/wiki/Daphnia">Daphnia</a> are small, planktonic crustaceans widely used in aquatic toxicity testing.
A list of structural alerts (SMARTS) consiting of 18 manually created SMARTS from the publication below was kindly supported by Emma Schymanski.
A list of structural alerts (SMARTS) consiting of 18 manually created SMARTS from the publication [1] was kindly supported by Emma Schymanski.

<h2>Models</h2>

<table>
<td bgcolor="cccccc" width=150>Model type</td>
<td bgcolor="cccccc">Model implementation</td>
<td bgcolor="cccccc">Comment</td>
<tr>

<td>Structural alerts</td>
<td>SMARTS</td>
<td>List of SMARTS defined in [1]</td>
<tr>

</table>

<p>
<h2>References</h2>
Peter C. von der Ohe, Ralph K&uuml;hne,Ralf-Uwe Ebert, Rolf Altenburger, Matthias Liess, and Gerrit Sch&uuml;&uuml;rmann<br>
[1] Peter C. von der Ohe, Ralph K&uuml;hne,Ralf-Uwe Ebert, Rolf Altenburger, Matthias Liess, and Gerrit Sch&uuml;&uuml;rmann<br>
<a href="http://pubs.acs.org/doi/abs/10.1021/tx0497954">Structural Alerts: A New Classification Model to Discriminate Excess Toxicity from Narcotic Effect Levels of Organic Compounds in the Acute Daphnid Assay</a><br>
<i>Chemical Research in Toxicology</i> 2005 18 (3), 536-555<br>

Expand Down
Empty file.

0 comments on commit 7145d75

Please sign in to comment.