Report

Teaser, summary, work performed and final results

Periodic Reporting for period 1 - OpenRiskNet (OpenRiskNet: Open e-Infrastructure to Support Data Sharing, Knowledge Integration and in silico Analysis and Modelling in Risk Assessment)

Teaser

Toxicology and risk assessment are undergoing a paradigm shift, from a phenomenological to a mechanistic discipline based on in vitro and in silico approaches that represent an important alternative to classical animal testing applied to the evaluation of chronic and systemic...

Summary

Toxicology and risk assessment are undergoing a paradigm shift, from a phenomenological to a mechanistic discipline based on in vitro and in silico approaches that represent an important alternative to classical animal testing applied to the evaluation of chronic and systemic toxicity risks. Large databases and highly sophisticated methods, algorithms and tools are available for different tasks such as hazard prediction, toxicokinetics, and in vitro – in vivo extrapolations to support this transition. However, since these services are developed independently and provided by different groups world-wide, there is no standardised way to access the data or run modelling workflows.
To overcome the fragmentation of data and tools, OpenRiskNet aims to develop an open e-infrastructure (easily accessible, standardised, harmonised, scalable and robust) providing resources and services to a variety of industries requiring risk assessment (chemicals, cosmetic ingredients, drugs and nanomaterials). These efforts aim to improve industrial risk assessments, prototyping new services and applications, enabling access to integrated resources within a complete and qualified system, supporting innovative product development.
The OpenRiskNet approach is to work on different case studies to test and evaluate requirements to overcome the fragmentation of data and tools and to provide solutions improving the harmonisation of data, usability and interoperability of application programming interfaces (APIs) and the deployment into virtual infrastructure. Therefore, OpenRiskNet e--infrastructure supports many aspects of risk assessment by allowing for the integration of toxicology--related data sources, for the implementation and execution of processing and analysis pipelines and for the execution of modelling workflows.

Work performed

Following an initial analysis addressing the requirements of end users (e.g. members of academia, industry and regulatory agencies), as well as of developers (tools developers, infrastructure provider and data managers), a set of case studies were defined. These are used to test and evaluate the solutions provided by OpenRiskNet to the predictive toxicology and risk assessment community, especially regarding the usability of the developed APIs and the interoperability layer.

To ensure the usability of the infrastructure, alignment with the community as well as to pursue complete coverage of important tools, OpenRiskNet works with a network of partners, organised in the Associated Partners Programme: service providers, early adopters and technology 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.

Within the case studies we are demonstrating the capabilities to satisfy the requirements of the different stakeholder groups including researchers, risk assessors and regulators and present real-world applications. They cover systems biology approaches for grouping compounds, read-across applications using chemical and biological similarity, and identifying areas of concern based on in vitro and in silico approaches. The case studies are also guiding the prioritisation of data sources and tools to be integrated in the infrastructure.

In order to achieve these objectives, the computational infrastructure and systems for the development and testing of the Virtual Research Environments (VREs), APIs, data and software integration of the OpenRiskNet project were established. The deployment process for the OpenRiskNet VREs include a virtual infrastructure, an OpenShift cluster, OpenRiskNet infrastructure services, and operational container orchestration using the underlying Kubernetes cluster. The OpenRiskNet e-infrastructure is currently used for service and tool integration and user access to the deployed services. The project has progressed to the stage that the core components of a VRE have been defined and created. Tools for chemical risk assessment from the partners are now easily deployable to this e-infrastructure, providing a secure environment in which the organisations can perform their work.

In parallel, the selection of services for further integration of high priority for the OpenRiskNet infrastructure (based on case studies) was performed. The services prioritised for integration include active services provided by the OpenRiskNet partners, associated partners and other third parties. The services selected cover areas like toxicology, chemical properties, bioassays and omics, and include databases, knowledge bases and data mining tools, ontology services, processing and analysis tools, predictive toxicology tools and workflows, visualisation and reporting tools. Additionally, OpenRiskNet provide a virtual helpdesk, a wiki and an issue tracker for technical matters and an option for feature requests, addressed to both end users (researchers, risk assessors, etc.) as well associated partners (service providers and early adopters).

Moreover, the developments follow the FAIR (Findable, Accessible, Interoperable and Reusable) data principles aligned with the solutions implemented to guarantee security and privacy for public and commercial data sources and to prevent re-identification of individuals based on the provided data.

In order to foster the worldwide adoption of OpenRiskNet, a wide range of dissemination and networking activities (training sessions, workshops and hackathons) were organised with further iterations planned for the future. These activities are also guiding the definition of project priorities for sustaining a European risk assessment e-infrastructure and to ensure direct exposure to the user communities. OpenRiskNet partners active

Final results

OpenRiskNet is developing and deploying an integrated, secure, service-driven and sustainable infrastructure for data managing, data sharing, processing, analysis, information mining and modelling. Development and sharing of analysis workflows, visualisation and reporting are also supported. These developments will serve the communities in the areas of toxicology, risk assessment and chemical, pharmaceutical, cosmetic and nanomaterial product development, including safety-by-design. OpenRiskNet e-infrastructure supports all aspects of risk assessment by allowing for the integration of all toxicology-related data sources, for the implementation and execution of processing and analysis pipelines and for the execution of modelling workflows for pharmacokinetics or pharmacodynamics. The approach taken in OpenRiskNet supports the overall goal of the targeted communities (i.e. industry, academia and regulatory bodies) on the implementation of 3Rs principles. OpenRiskNet aims to play an important role and have an impact on the mentioned communities by developing an innovation-driven knowledge infrastructure, enabling the access to data and modelling tools, supporting scientific advancements in risk assessment, as well as having an impact on the related and required standards, ontologies and scientific community.

Website & more info

More info: https://openrisknet.org/.