Test Web Services
Descriptions and links to OpenTox web services
Please note that initial alpha-test services listed here are early development services and work in progress. They may be unavailable or not working! Also such test services may require technical QSAR or developer experience to use.
Alpha-Test Services
Entry Format:
Provider Name
Description Summary of Service Functionality:
Location:
Guidance:
Contact:
Date:
Version:
Bug Reporting:
PLEASE ADD YOUR NEW SERVICES TO THE INDIVIDUAL SERVICE TYPE PAGES (e.g., algorithm, model, integrated, etc.)
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Below is a list of the first iteration for current historical purposes only!
Services (Iteration 1.0)
Technical University of Munich
Description Summary of Service Functionality:
Location:
The web-browser readable entry page is located at: http://opentox.informatik.tu-muenchen.de:8080/OpenTox/Some of the available HTTP GET methods are also linked on that page.
Download:
The standalone version, tested on Linux and Windows XP, can be downloaded at
https://opentox.informatik.tu-muenchen.de/trac/TUMOpenTox/wiki/Download
Wiki and Bugtracker:
A documentation wiki and a bug tracker is available at
https://opentox.informatik.tu-muenchen.de/trac/TUMOpenTox/
Guidance:
A Linux example call (command line) to retrieve a list of available algorithm URIs would be:
curl -X GET -H 'Accept:text/uri-list' http://opentox.informatik.tu-muenchen.de:8080/OpenTox/algorithm
Changing this to:
curl -X GET -H 'Accept:text/xml' http://opentox.informatik.tu-muenchen.de:8180/OpenTox/algorithm
will give you the same information as above but formatted as XML.
You also can build (or train) models with the available classification and regression algorithms. Classification and regression algorithms at this stage of development only take WEKA arff files (URI to the file) as input, e.g.:
curl -X POST -d "dataset_id=http://someserver.com/files/iris.arff" http://opentox.informatik.tu-muenchen.de:8080/OpenTox/algorithm/kNNclassification
Calculate descriptors: Momentarily the descriptor calculation services accept only SDF/MOL files as input for calculating descriptors. An example curl call would look like this:
curl -X POST -d "dataset_id=http://test.server.com/dataset/234/compound" -H 'Accept:text/xml' http://opentox.informatik.tu-muenchen.de:8080/OpenTox/algorithm/CDKPhysChem
Here you can see that the HTTP media type that we expect in the response from the server is explicitly stated with text/xml.
Contact:
Tobias Girschick (TUM), Fabian Buchwald (TUM), Jörg Wicker (TUM)
in silico toxicology
Description Summary of Service Functionality:
Location:
Documentation, examples and source code on github account of Christoph Helma:
http://github.com/helma/opentox-compound
http://github.com/helma/opentox-feature
http://github.com/helma/opentox-dataset
http://github.com/helma/opentox-fminer
http://github.com/helma/opentox-lazar
The services run under the following base URIs (see github READMEs for
details):
http://webservices.in-silico.ch/compound/v0/
http://webservices.in-silico.ch/feature/v0/
http://webservices.in-silico.ch/dataset/v0/
http://webservices.in-silico.ch/fminer/v0/
http://webservices.in-silico.ch/lazar/v0/
Guidance:
At present, the servies provide YAML output and a few chemical structure
representations. XML output will come with the next update.
Please use the issue tracker on gihub to report problems and feature
requests.
Contact:
Christoph Helma (IST)
ALU-FR
Description Summary of Service Functionality:
Location:
http://opentox.informatik.uni-freiburg.de/validation
Guidance:
See
http://opentox.informatik.uni-freiburg.de/validation/examples
for curl examples.
Source code and some more documentation on github account of Martin Gütlein:
http://github.com/mguetlein/opentox-validation
Contact:
Martin Gütlein
Please use issue tracker to report bugs, request changes, etc:
http://github.com/mguetlein/opentox-validation/issues
Ideaconsult
Description Summary of Service Functionality:
OpenTox Web services based on Ambit.
Location:
Guidance:
Contact:
Nina Jeliazkova (IDEA)
National Technical Univeristy of Athens
Description Summary of Service Functionality:
1. Get XML representations of available algorithms
2. Build a classification model (SVM)
3. Build a regression model (SVM, MLR)
4. Validate a regression model (MLR)
5. Validate a classification model (SVM)
These service were built as a Java Web Application using the RESTlet 1.1.5
framework (http://www.restlet.org )
Location:
Home: http://opentox.ntua.gr:3000
Source Code: http://github.com/sopasakis/yaqp
Guidance:
You can find detailed instructions at http://opentox.ntua.gr:3000/guide
Contact:
Sopasakis Pantelis (NTUA) - chvng@mail.ntua.gr
Seascape Learning & Jawaharlal Nehru University
Description Summary of Service Functionality:
Guidance:
Contact:
Date:
Version:
Bug Reporting:
IBMC
Description Summary of Service Functionality:
IBMC - OpenTox Web services includes:
1) Caculation of MNA descritpors
2) Caculation of QNA descriptors
3) Build a regression model (SCR)
Location:
http://195.178.207.160/opentox/Guidance:
Contact:
Alexey Zakharov (IBMC)
