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updated DS model documentation.
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olas committed Sep 7, 2012
1 parent b1e973e commit 06892e7
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Showing 10 changed files with 88 additions and 11 deletions.
2 changes: 1 addition & 1 deletion plugins/net.bioclipse.ds.models.ahr/plugin.xml
Expand Up @@ -88,7 +88,7 @@

<test
id="ahr.signatures"
name="AHR Signature Significance"
name="AHR QSAR"
class="net.bioclipse.ds.libsvm.SignaturesLibSVMPrediction"
propertycalculator="AHR Signature Significance"
endpoint="net.bioclipse.ds.ahr"
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2 changes: 1 addition & 1 deletion plugins/net.bioclipse.ds.models.cpdb/plugin.xml
Expand Up @@ -126,7 +126,7 @@

<test
id="cpdb.signatures.classification"
name="CPDB Signature Significance"
name="CPDB QSAR"
class="net.bioclipse.ds.libsvm.SignaturesLibSVMPrediction"
endpoint="net.bioclipse.ds.carcinogenicity"
informative="false"
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4 changes: 3 additions & 1 deletion plugins/net.bioclipse.ds.models.daphnia/build.properties
Expand Up @@ -4,4 +4,6 @@ bin.includes = META-INF/,\
.,\
models/,\
plugin.xml,\
data/
data/,\
html/,\
toc.xml
28 changes: 28 additions & 0 deletions plugins/net.bioclipse.ds.models.daphnia/html/daphnia.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>
14 changes: 11 additions & 3 deletions plugins/net.bioclipse.ds.models.daphnia/plugin.xml
Expand Up @@ -3,8 +3,8 @@
<plugin>
<extension point="net.bioclipse.decisionsupport">
<endpoint
id="net.bioclipse.ds.models.daphnia"
name="Daphnia">
id="net.bioclipse.ds.endpoints.aquatic"
name="Aquatic Toxicity">
</endpoint>
<!--test id="daphnia.qsar" name="daphnia QSAR" endpoint="net.bioclipse.ds.models.daphnia"
class="net.bioclipse.ds.libsvm.SignaturesLibSVMPrediction"
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<test
id="daphnia.smarts"
name="Daphnia SMARTS"
endpoint="net.bioclipse.ds.models.daphnia"
endpoint="net.bioclipse.ds.endpoints.aquatic"
consensus="net.bioclipse.ds.consensus.majority.emptynegative"
class="net.bioclipse.ds.matcher.SmartsAlertMatcher">

Expand All @@ -74,8 +74,16 @@

<parameter name="Model type" value="SMARTS matching" />
<parameter name="Observations" value="18" />
<parameter name="URL" value="http://pubs.acs.org/doi/abs/10.1021/tx0497954" />

</test>
</extension>

<extension
point="org.eclipse.help.toc">
<toc
file="toc.xml"
primary="false"/>
</extension>

</plugin>
6 changes: 6 additions & 0 deletions plugins/net.bioclipse.ds.models.daphnia/toc.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#ContributedEndpoints" label="Aquatic Toxicity" >
<topic label="Aquatic Toxicity" href="html/daphnia.html" />
</toc>
4 changes: 2 additions & 2 deletions plugins/net.bioclipse.ds.models.herg/build.properties
Expand Up @@ -2,6 +2,6 @@ bin.includes = META-INF/,\
icons/,\
plugin.xml,\
toc.xml,\
models/
jars.compile.order =
models/,\
html/

30 changes: 30 additions & 0 deletions plugins/net.bioclipse.ds.models.herg/html/herg.html
@@ -0,0 +1,30 @@
<!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>hERG</title>
<link rel="stylesheet" href="../../PRODUCT_PLUGIN/narrow_book.css" type="text/css">
</head>

<body>
<h1>hERG</h1>
<a href="http://en.wikipedia.org/wiki/Herg">Human Ether-a-go-go-Related Gene (hERG)</a> encodes the the alpha subunit of a potassium ion channel,
best known for its contribution to the electrical activity of the heart that coordinates the heart's beating.
If inhibited or compromised, such as by a drug, it can result in a potentially fatal disorder called long QT syndrome.
hERG inhibition is hence an important antitarget that must be avoided during drug development.

<h2>Data source</h2>
The dataset has 806 molecules of the hERG activities in total, collected from literature.<br>
Data kindly provided by the <a href=""http://cadd.suda.edu.cn/admet/downloads/hERG">PharmacoKinetics KnowledgeBase</a>.

<h2>References</h2>

Thai KM, Ecker GF.<br>
<a href="http://www.sciencedirect.com/science/article/pii/S0968089608000345">A binary QSAR model for classification of hERG potassium channel blockers.</a><br>
<i>Bioorg Med Chem.</i> 2008 Apr 1;16(7):4107-19. Epub 2008 Jan 16.<br>



</body>
</html>
3 changes: 3 additions & 0 deletions plugins/net.bioclipse.ds.models.herg/plugin.xml
Expand Up @@ -46,6 +46,9 @@
(height 0-3)"/>
<parameter name="Observations" value="806"/>
<parameter name="Variables" value="10360"/>

<parameter name="URL" value="http://cadd.suda.edu.cn/admet/downloads/hERG"/>

</test>
</extension>

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6 changes: 3 additions & 3 deletions plugins/net.bioclipse.ds.models.herg/toc.xml
@@ -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="Carcinogenicity" >
<topic label="Carcinogenicity" href="html/carcinogenicity.html" />
</toc>
<toc link_to="../net.bioclipse.ds.ui/toc.xml#ContributedEndpoints" label="hERG" >
<topic label="hERG" href="html/herg.html" />
</toc>

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