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---
layout: post
title: "Development: Vanilla Version"
description: ""
category: development
tags: [Lazar, Fminer, 4store, BBRC, LAST-PM, Tutorials]
---
{% include JB/setup %}
[Install development](http://opentox.github.com/setup/2012/08/09/install-opentox-development-environment/) version, using `bash`. Make sure ot-tools are available (insert `ot` and press `<TAB>`).
Source from `$HOME`:
# configure
otconfig
otstart all
lh="http://localhost"
# util
function get_result {
task=$1
while [ 1 ]; do
result=`curl -H "accept:text/uri-list" $task 2>/dev/null`
[ $result == $task ] && sleep 1 || break
done
echo $result
}
Load dataset.
# load ds
cd
task=`curl -X POST \
-F "file=@opentox-ruby/opentox-test/test/data/hamster_carcinogenicity.csv;type=text/csv" \
$lh:8083/dataset`
ds=`get_result "$task"`
echo "hamster: $ds"
<br>
<br>
<hr>
<br>
Calculate benzene PC descriptors, constrained by `lib`:
curl \
--data-urlencode "pc_type=geometrical" \
-X POST http://localhost:8082/compound/InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H/pc
Constrained by `lib` and `pc_type`:
curl \
--data-urlencode "lib=joelib" \
--data-urlencode "pc_type=geometrical" \
-X POST http://localhost:8082/compound/InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H/pc
As RDF/XML:
curl -H "accept:application/rdf+xml" \
--data-urlencode "pc_type=geometrical" \
-X POST http://localhost:8082/compound/InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H/pc
Calculate dataset PC descriptors, constrained by `lib`:
task=`curl \
--data-urlencode "pc_type=geometrical" \
-X POST $ds/pc`
pc_fds=`get_result "$task"`
echo "pc feature ds: $pc_fds"
<br>
<br>
<hr>
<br>
Mine subgraphs.
# bbrc feature ds
task=`curl -X POST --data-urlencode "dataset_uri=$ds" $lh:8081/algorithm/fminer/bbrc`
bbrc_fds=`get_result "$task"`
echo "bbrc feature ds: $bbrc_fds"
# last-pm feature ds
task=`curl -X POST --data-urlencode "dataset_uri=$ds" $lh:8081/algorithm/fminer/last`
last_fds=`get_result "$task"`
echo "last-pm feature ds: $last_fds"
Make Lazar models with substructural descriptors.
# create lazar m w/ bbrc
task=`curl -X POST --data-urlencode "dataset_uri=$ds" $lh:8081/algorithm/lazar`
lazar_m_bbrc=`get_result "$task"`
echo "Hamster model with bbrc: $lazar_m_bbrc"
# create lazar m w/ last-pm
task=`curl -X POST \
--data-urlencode "dataset_uri=$ds" \
--data-urlencode "feature_generation_uri=$lh:8081/algorithm/fminer/last" \
$lh:8081/algorithm/lazar`
lazar_m_last=`get_result "$task"`
echo "Hamster model with last-pm: $lazar_m_last"
Make predictions with BBRC (LAST-PM would also work).
# make benzene prediction w lazar m w/ bbrc
task=`curl -X POST \
--data-urlencode "compound_uri=$lh:8082/compound/InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H" \
$lazar_m_bbrc`
lazar_p_bbrc=`get_result "$task"`
echo "Benzene prediction with bbrc model: $lazar_p_bbrc"
# make a database prediction
task=`curl -X POST \
--data-urlencode "compound_uri=$lh:8082/compound/InChI=1S/C12H12N2O3/c1-2-12(8-6-4-3-5-7-8)9(15)13-11(17)14-10(12)16/h3-7H,2H2,1H3,(H2,13,14,15,16,17)" \
$lazar_m_bbrc`
lazar_p_bbrc=`get_result "$task"`
echo "Benzene prediction with bbrc model: $lazar_p_bbrc"
The result dataset does not yet contain verbose information (neighbors etc).
The example below demonstrates how much time each step approximately consumes during prediction. Call is:
curl -X POST --data-urlencode "compound_uri=$lh:8082/compound/InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H" $lazar_m_bbrc
i.e. predict benzene for hamster carcinogenicity.
10:23:34 :: Inited p dataset :: /lazar.rb:135
10:23:35 :: Loaded t dataset :: /lazar.rb:139
10:23:44 :: Loaded f dataset :: /lazar.rb:143
10:23:44 :: Calced q fps :: /lazar.rb:149
10:23:44 :: Custom model :: /lazar.rb:20
10:23:45 :: Filled m data :: /lazar.rb:163
10:23:45 :: F: 11x54; R: 54 :: /transform.rb:402
10:23:45 :: Sims: 11, Acts: 11 :: /transform.rb:403
10:23:45 :: Transformed m :: /lazar.rb:166
10:23:45 :: Weighted Majority Vote :: /algorithm.rb:30
10:23:45 :: Prediction is: '2'. :: /algorithm.rb:56
10:23:45 :: Confidence is: '0.25281 :: /algorithm.rb:58
10:23:45 :: Predicted q :: /lazar.rb:174
Time total: 11s, Time Dataset loading: 10s
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