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.
Case studies defined within the OpenRiskNet projects and their mutual relationships within the context of a risk assessment framework.
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.
Associated Partner Programme and the Implementation Challenge
The infrastructure can only be as good as the services it provides. Therefore, OpenRiskNet is working with an steadily increasing network of partners, organised within an Associated Partners Programme. On one hand, this allows for direct testing and getting early feedback on the developed concepts and the usability of the infrastructure and, on the other hand, only in this way all important areas, data sources and software tools can be covered by integrating services from these partners.
The programme is open for application to any organisation such as a university, institute, consortium, non-governmental organisation (NGO), small or medium sized enterprises (SME) and large commercial companies. Benefits are extended technical and partly financial support (in form of the implementation challenge with deadlines in September and December 2018 as well as April 2019) on how to integrate services into the infrastructure and premium user support on how to use the services. Associated partners are also involve in the work on the case studies and in this way can directly influence further development of the infrastructure and the prioritisation of features.
The e-infrastructure is developed by the OpenRiskNet project (https://openrisknet.org/) and its associated partners and is funded by the European Commission within Horizon 2020 EINFRA-22-2016 Programme (Project No. 731075).
- Main website: https://openrisknet.org/
- E-infrastructure: https://home.prod.openrisknet.org/
- Associated Partner Programme and Implementation Challenge: https://openrisknet.org/associated-partner-programme/