OpenTox Datasets
=================

* An OpenTox REST Webservice
* Stores associations between compounds and features in datasets
* Implements a subset of the OpenTox dataset API (http://opentox.org/wiki/opentox/Dataset).
* Current version runs at http://webservices.in-silico.ch/dataset/v0

REST API

Description               Method  URI                         Parameters      Result                Status codes

Get a list of all         GET     /                                           List of URIs          200, 500
datasets

Get a YAML representation GET     /{id}                                       YAML representation    200, 404, 500
of a dataset                                                                  of a dataset

Get the dataset name      GET     /{id}/name                                  Dataset name          200, 404, 500

Get all compound URIs     GET     /{id}/compounds                             List of compound      200, 404, 500
from a dataset                                                                URIs

Get all feature URIs      GET     /{id}/features                              List of features      200, 404, 500

Get all features with     GET     /{id}/features/compounds                    YAML with features     200, 404, 500
corresponding compounds                                                       and compounds

Get all compounds and     GET     /{id}/compounds/features                    YAML with compounds    200, 404, 500
their features                                                                and featues

Get all features for a    GET     /{id}/compound/                             List of feature URIs  200, 404, 500
compound URI                      {compound_uri}/features

Get all features for a    GET     /{id}/feature/                              List of compound URIs 200, 404, 500
feature URI                       {feature_uri}/compounds

Create a new dataset      POST    /                           name            Dataset URI           200, 500

Create a new dataset      POST    /                           name, file      Dataset URI           200, 500
from a csv file

Add a new association to  POST    /{id}                       compound_uri,   Dataset URI           200, 404, 500
a dataset                                                     feature_uri

Delete a dataset          DELETE  /{id}                                                             200, 404, 500

EXAMPLES

Create a dataset from a csv file:

  curl -X POST -F name="Hamster carcinogenicity" -F file=@hamster_carcinogenicity.csv  http://webservices.in-silico.ch/dataset/v0/

  returns a dataset_uri

Show a list of all compounds:

  curl {dataset_uri}/compounds

Show a list of all features:

  curl {dataset_uri}/features

Show all compounds and their features:

  curl {dataset_uri}/compounds/features

INSTALLATION

Run 'rake install' to install the required gems and openbabel

Copyright (c) 2009 Christoph Helma. See LICENSE for details.