OpenTox Algorithm
=================

- An [OpenTox](http://www.opentox.org) REST Webservice
- Implements the OpenTox algorithm API for
    - fminer
    - lazar

REST operations
---------------

    Get a list of all algorithms  GET   /               -                           URIs of algorithms        200
    Get a representation of the   GET   /fminer/        -                           fminer representation     200,404
     fminer algorithms
    Get a representation of the   GET   /fminer/bbrc    -                           bbrc representation       200,404
    bbrc algorithm
    Get a representation of the   GET   /fminer/last    -                           last representation       200,404
     last algorithm
    Get a representation of the   GET   /lazar          -                           lazar representation      200,404
     lazar algorithm
    Create bbrc features          POST  /fminer/bbrc    dataset_uri,                URI for feature dataset   200,400,404,500
                                                        feature_uri,
                                                        [min_frequency=5 per-mil],
                                                        [feature_type=trees],
                                                        [backbone=true],
                                                        [min_chisq_significance=0.95]
    Create last features          POST  /fminer/last    dataset_uri,                URI for feature dataset   200,400,404,500
                                                        feature_uri,
                                                        [min_frequency=8 %],
                                                        [feature_type=trees],
                                                        [max_hops=25],
    Create lazar model            POST  /lazar          dataset_uri,                URI for lazar model       200,400,404,500
                                                        prediction_feature,
                                                        feature_generation_uri

Supported MIME formats
----------------------

- application/rdf+xml (default): read/write OWL-DL
- application/x-yaml: read/write YAML

Examples
--------

NOTE: http://webservices.in-silico.ch hosts the stable version that might not have complete functionality yet. **Please try http://ot-test.in-silico.ch** for latest versions.

### Get the OWL-DL representation of fminer

    curl http://webservices.in-silico.ch/algorithm/fminer

### Get the OWL-DL representation of lazar

    curl http://webservices.in-silico.ch/algorithm/lazar

* * * 

The following creates datasets with backbone refinement class representatives or latent structure patterns, using supervised graph mining, see http://cs.maunz.de. These features can be used e.g. as structural alerts, as descriptors (fingerprints) for prediction models or for similarity calculations.

### Create the full set of frequent and significant subtrees

    curl -X POST -d dataset_uri={datset_uri} -d prediction_feature={feature_uri} -d min_frequency={min_frequency} -d "backbone=false" http://webservices.in-silico.ch/algorithm/fminer/bbrc

feature_uri specifies the dependent variable from the dataset.
backbone=false reduces BBRC mining to frequent and correlated subtree mining (much more descriptors are produced).

### Create [BBRC](http://bbrc.maunz.de) features, recommended for large and very large datasets.

    curl -X POST -d dataset_uri={datset_uri} -d prediction_feature={feature_uri} -d min_frequency={min_frequency} http://webservices.in-silico.ch/algorithm/fminer/bbrc

feature_uri specifies the dependent variable from the dataset.   
Please click [here](http://bbrc.maunz.de#usage) for more guidance on usage.

### Create [LAST-PM](http://last-pm.maunz.de) descriptors, recommended for small to medium-sized datasets.

    curl -X POST -d dataset_uri={datset_uri} -d prediction_feature={feature_uri} -d min_frequency={min_frequency} http://webservices.in-silico.ch/algorithm/fminer/last

feature_uri specifies the dependent variable from the dataset.   
Please click [here](http://last-pm.maunz.de#usage) for guidance for more guidance on usage.

* * * 

### Create lazar model

    curl -X POST -d dataset_uri={datset_uri} -d prediction_feature={feature_uri} -d feature_generation_uri=http://webservices.in-silico.ch/algorithm/fminer http://webservices.in-silico.ch/test/algorithm/lazar

feature_uri specifies the dependent variable from the dataset

[API documentation](http://rdoc.info/github/opentox/algorithm)
--------------------------------------------------------------

Copyright (c) 2009-2011 Christoph Helma, Martin Guetlein, Micha Rautenberg, Andreas Maunz, David Vorgrimmler, Denis Gebele. See LICENSE for details.