OpenRiskNet e-infrastructure available to end-users
The e-infrastructure project OpenRiskNet developing a platform providing data and modelling tools for predictive toxicology and risk assessment, is entering its second stage, in which the platform is made accessible to everyone. In the first phase, we developed advanced concepts and implemented these into the first version of the platform including building and deploying of virtual research environments (VREs) and integrating the first services for different task in risk assessment accessible by everyone for testing. The platform includes harmonised and partly semantically annotated data and modelling services, corresponding training material as well as seven risk assessment case studies, which are used to evaluate and optimize the infrastructure.
Current implementations and tools integrated
The reference environment is available at https://home.prod.openrisknet.org/. There is a continuously updated list of integrated services and example workflows, which show how to combine services to fully exploit the benefits of the harmonisation and interoperability concepts.
Besides this reference instance, OpenRiskNet provides resources to enable users to instantiate their own virtual infrastructures populated with the applications and middleware making up the VRE on public or private cloud resources, as well as in-house server/workstations.
The currently available services and tools include:
- OpenRiskNet and Third-Party Workflow Managers and Scripting Tools: Squonk Computational Notebook, Jupyter Notebooks
- Graphical User Interface Access to OpenRiskNet Applications: Lazar Toxicity Predictions, Jaqpot Modeling and Analysis Services
- OpenRiskNet Data Sources: Nanomaterial database (eNanoMapper), Data Explorer serving ToxCast, ToxRefDB and TG-Gates data
- Example Workflows based on OpenRiskNet Tools: Jupyter Notebook: Access TG-Gates data for selected compounds, select differentially expressed genes and identifier relevant pathways
- API Definitions for OpenRiskNet Applications and Data: Model Generation (Lazar Toxicity Predictions, JGU WEKA REST Service, Jaqpot Modeling and Analysis Services), Trained Models (LogP Predictor, Metabolic Site Predictor) and Helper Tools (Chemical ID Converter Service), Data and Knowledge Sources (BridgeDb identifier mapping service, eNanoMapper database, ToxCast, ToxRefDB)
The OpenRiskNet e-infrastructure aims to support many aspects of risk assessment by allowing the integration of toxicology-related data sources, for the implementation and execution of processing and analysis pipelines and for the execution of modelling workflows.