AMBIT REST Web services

Explore AMBIT implementation of OpenTox REST API at http://apps.ideaconsult.net:8080/ambit2.

Try ToxPredict - demo application, consuming OpenTox REST services.

Download AMBIT REST Web services 2.4.9

Web application archive: ambit2.war, A&A disabled ?, configured to run under http://
Database content: None. Create an empty database as described in Install your own service guide. Import chemical compounds and data by navigating to http://yourhost:8080/ambit2/dataset and using the web form for upload. Alternatively,use HTTP POST to http://yourhost:8080/ambit2/dataset via OpenTox API.

Download AMBIT REST Web services 2.4.5

Web application archive: ambit2.war, A&A disabled ?, configured to run under http://
Database content: None. Create an empty database as described in Install your own service guide. Import chemical compounds and data by navigating to http://yourhost:8080/ambit2/dataset and using the web form for upload. Alternatively,use HTTP POST to http://yourhost:8080/ambit2/dataset via OpenTox API.

Download AMBIT REST Web services 2.4.3

Web application archive: ambit2.war, A&A enabled ?, configured to run under http://
Web application archive: ambit2.war, A&A enabled ?, configured to run under https://
Database content: None. Create an empty database as described in Install your own service guide. Import chemical compounds and data by navigating to http://yourhost:8080/ambit2/dataset and using the web form for upload. Alternatively,use HTTP POST to http://yourhost:8080/ambit2/dataset via OpenTox API.

Download AMBIT REST Web services 2.4.1

Web application archive: ambit2.war, A&A enabled ?
Web application archive: ambit2.war, A&A disabled ?
Database content (OPTIONAL): SQL dump of the database, used by ambit2.war. 176 MB, unzips into 1GB, MySQL database is 3GB

Deployment

Follow instructions in Install your own service. When installed, the application should be accessible at:
```
 http://localhost:8080/ambit2
```
After installation, the database will be empty, and no compounds or datasets available. You might import your own data, or for version 2.4.1 only use the database content, available as SQL dump above.
Importing the database dump is OPTIONAL. If you decide to use the database dump, follow the next steps:
1. Unzip the database archive.
2. Open a MySQL console. Run
```
 > source ambit2.sql
```

Upon completion, there should be non-empty list of datasets at the following URI http://yourhost:8080/ambit2/dataset

Note: Access to chemical structures and data is assumed to be performed via OpenTox REST web services API, and not via direct database access. Developers may be interested in the ambit2-db module for information about the database schema and related Java classes.

Configuration

After deployment to the servlet container, the following configuration files can be modified:

General configuration:

    WEB-INF/classes/ambit2/rest/config/ambit2.pref

Database

The default database is ambit2 and the default user is guest. These are created automatically, if following the instructions above.

To modify, editing ambit.pref configuration file and restart the service.

Ontology service

A pointer to an OpenTox Ontology service is provided by http://yourhost:8080/ambit2/sparqlendpoint, but not directly used by AMBIT REST services. Setting the pointer may affect external applications (e.g. ToxPredict). The pre-configured Ontology Service at expected at http://yourhost:8080/ontology.

To modify, editing ambit.pref configuration file and restart the service.

Authentication and authorisation: +--------------------------------- WEB-INF/classes/ambit2/rest/config/config.prop. +---------------------------------

AMBIT REST services use OpenTox Authentication and Authorisation infrastructure, which is based on OpenAM. Enable/disable AA, set OpenTox identity and policy service. To modify, editing ambit.pref configuration file and restart the service.

Create models

Upon a fresh install, only Algorithms are available. To create models use the web form, available at each algorithm page, or cURL command:

        curl -X POST http://yourhost:8080/ambit2/algorithm/pKa
        curl -X POST http://yourhost:8080/ambit2/algorithm/toxtreecramer

The commands will return a Model URI, which could be subsequently registered at the Ontology service.

Interesting subsets of algorithms: ToxTree Descriptors

Artifact

<dependency>
  <groupId>ambit</groupId>
  <artifactId>ambit2-www</artifactId>
  <type>war</type>
</dependency>

Repository

   <repository>
        <id>ambit-plovdiv-releases</id>
        <url>http://ambit.uni-plovdiv.bg:8083/nexus/content/repositories/releases</url>
    </repository>

AMBIT

AMBIT REST web services

Support

AMBIT publications

Project Documentation