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OpenTox Prototype Demonstration Server

Posted by Barry Hardy at Mar 08, 2011 09:40 PM |

OpenTox provides an interoperable, standards-based framework for the support of predictive toxicology data management, algorithms, modelling, validation and reporting. OpenTox provides end-user oriented tools to non-computational specialists, risk assessors, and toxicological experts in addition to Application Programming Interfaces (APIs) for developers of new applications.

OpenTox includes services for compounds, datasets, features, algorithms, models, ontologies, tasks, validation, and reporting which may be combined into multiple applications satisfying a variety of different user needs. OpenTox applications are based on a set of distributed, interoperable OpenTox API-compliant REST web services. The services are operated on a network of publicly accessible prototype demonstration servers that are distributed over multiple locations and organisations. Every provider responsible for service contributions has a server running that contributes to the distributed OpenTox system. In the OpenTox report Prototype Demonstration Server available at http://www.opentox.org/data/documents/development/opentoxreports/opentoxreportd23 we take a closer look at three example server implementations to describe the whole distributed prototype system. The report also provides insight into the technical details, e.g., what programming languages and technologies have been used. It provides example usages of the distributed system, so that potential contributors to the system have a key overview guidance at their hands that will, in addition to further online information on the OpenTox web resources (www.opentox.org), enable easy access to the system itself and make contributions easier. 

Two initial OpenTox applications were prototyped as an illustration of the potential impact of OpenTox for high-quality and consistent structure-activity relationship modelling of REACH-relevant endpoints: ToxPredict which predicts and reports on toxicities for endpoints for an input chemical structure, and ToxCreate which builds and validates a predictive toxicity model based on an input toxicology dataset. Because of the extensible nature of the standardised framework design, barriers of interoperability between applications and content are removed, as the user may combine data, models and validation from multiple sources in a dependable and time-effective way.

Taverna (www.taverna.org.uk) has been used to provide a user friendly workflow system to access and combine OpenTox web services. It provides a user interface which can be used to generate arbitrary workflows from combinations of single OpenTox web services. The web services are combined by importing single web services and connecting their inputs and outputs using a point-and-click user interface.

Continuing effort will be carried out by OpenTox developers to meet current academic and industry challenges regarding interoperability of software components and integration of data, algorithm and model services within the context of tested Use Cases. The experience we have gained during this work should help speed up the development process towards this direction.

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