Resources & Training
This page contains resources and training materials to support OpenRiskNet users in getting familiar with the services and tools available in the e-infrastructure. On top of tutorials and video demonstrations, you will also find information on our publications (e.g. peer-review articles, presentations, posters) that may help you further in learning about OpenRiskNet concepts and implementations.
To ensure the usability of the infrastructure, alignment with the community needs as well as pursuing complete coverage of important tools incorporated into the e-infrastructure and available to Users, OpenRiskNet will work with a continuously expanding network of partners. To make the interaction with the OpenRiskNet consortium, to give feedback and to contribute to the developments and case study work as simple as possible but also give the opportunity to share confidential information, foster collaborative developments between consortium and associated partners and even allow integration of tools as in-kind work, three different ways to associate with the project as a third party are available: 1) testing the infrastructure as a early adopter and give feedback and state requirements via the online surveys (see also updated deliverable report D1.1), 2) become an official associated partner allowing the exchange of confidential information like source code with examples of service integration and 3) applying to the implementation challenge, which will provide additionally to the technical support also financial support for service integration. This updated deliverable report describes these options organised in the Associated Partner Programme.
This report describes the first updated version of the data management plan (DMP) for the OpenRiskNet e-infrastructure projects. The current DMP covers the general aspects of the OpenRiskNet data management based on the FAIR (findable, accessible, interoperable and reusable) guidelines, ethics considerations for re-sharing of public datasets and the first examples of shared data sources including diXa, BridgeDb, WikiPathways, AOP-Wiki and ToxCast/Tox21. More specific data source and clearly-defined measures will be added in parallel to their integration into the infrastructure, which will follow the time plan enforced by the case study requirements on data availability.
This report describes the results obtained from the survey, interviews and interactions with associated partners and project stakeholders as part of the requirements analysis. The requirements analysis included surveys sent out to a large number of experts and designed to address issues relevant to: End users (e.g. members of academia, industry and regulatory agencies), and Developers (tools developers, infrastructure provider and data managers.
OpenRiskNet is developing an e-infrastructure for predictive toxicology and safety assessment (of chemicals, pharmaceuticals, nanomaterials etc.) in the form of virtual research environments (VREs) and data, analysis and modelling services coming from the consortium but also from third parties, which can be deployed to these. This deliverable describes the support functions set up and how they were customised for specific user groups. Due to its specific purpose of being an infrastructure where public and commercial services are offered to the community, OpenRiskNet services different types of users and roles, which can be grouped into: End users (e.g. members of academia, industry, and regulatory agencies) who are defined as users who log into an OpenRiskNet VRE and consume one or more services or applications; Developers who are involved in developing or setting up parts of the OpenRiskNet VRE, such as middleware, frameworks, data, or tools packaged as services or applications; in the latter case also referred to as tool provider; System administrators, who are in charge of creating and managing the OpenShift environment for the VRE and deploying the basic services.
A paradigm shift is taking place in risk assessment to replace animal models, reduce the number of economic resources, and refine the methodologies to test the growing number of chemicals and nanomaterials. Therefore, approaches such as transcriptomics, proteomics, and metabolomics have become valuable tools in toxicological research, and are finding their way into regulatory toxicity. One promising framework to bridge the gap between the molecular-level measurements and risk assessment is the concept of Adverse Outcome Pathways (AOPs). These pathways comprise mechanistic knowledge and connect biological events from a molecular level towards an adverse effect outcome after exposure to a chemical. However, the implementation of omics-based approaches in the AOPs and their acceptance by the risk assessment community is still a challenge.
WikiPathways SPARQL Endpoint
This report summarises the management process adopted within the OpenRiskNet project. This process envisaged the implementation of best project management practices to ensure the effective execution of the work plan, tracking and documentation of task progress, an effective communication between partners on technical and administrative matters, as well as the communication with the EC office and external stakeholders.
Tis report describes the status of selection of services of high priority for the OpenRiskNet infrastructure and their integration including active services provided by the consortium, associated partners and other third parties.
This report describes the first documentation of the core OpenRisknet e-infrastructure with examples of an initial development status implementation. This report forms part of this documentation, along with other parts located in the OpenRiskNet GitHub repository. This documentation describes the creation of the e-infrastructure and the deployment of the first partner application to the e-infrastructure.
This report cover the possible risks with respect to security, privacy and re-identification of personal data as well as present the private by design risk management concept.
This Deliverable describes the computational infrastructure, frameworks and systems for the development and testing of the Virtual Research Environments, APIs and data and software integration of the OpenRiskNet project. Development tools selected for source code control, issue tracking, continuous integration and deployment, and containerization and container orchestration are discussed and guideline for service development are outlined. Finally the current development environment is described and its operation is demonstrated with a simple example.
This document reports the work towards the first version of the OpenRiskNet application programming interfaces (APIs) to be released to all partners of the consortium and associated partners for feedback and usage. Based on the diversity of the requirement foreseeable when developing the case studies to validate the infrastructure with real-world applications across all areas of predictive toxicology and risk assessment, a bottom-up approach to start with existing APIs and then harmonize them and bring them collectively to higher levels by integrating richer scientific annotation (semantic interoperability layer) was adopted in contrast to a top-down approach, where the API specification is defined by the consortium first and then all services have to be changed to comply to this specification.
This report describes the dissemination and training activities undertaken by the OpenRiskNet partners in the first half of the project. These activities were gathered formally within WP3 (Training, Support and Dissemination) but they cover aspects related to all WPs. Details and links to the various activities developed in the first half of the project were included, e.g. organisation of workshops, training events and hackathons, participation at conferences and workshops, peer-review publications, tutorials, public communication activities, the project website and visual identity development as well as the interactions initiated with other EU initiatives. The main dissemination activities related to OpenRiskNet are summarised on the project website at: https://openrisknet.org/library/. The report, follows the agreed Plan for the Exploitation and Dissemination of Results (PEDR).
This report documents the Demonstrator for the Deliverable 2.3, describing the deployment of virtual infrastructure and applications making up the OpenRiskNet Virtual Research Environment (VRE). It outlines the system analysis, deployment fundamentals, service discovery, and a list of the currently available services. The production reference instance is deployed on the Swedish Science Cloud (SSC), and end user access is available at https://home.prod.openrisknet.org.
OpenRiskNet case studies are used to test and evaluate solutions provided by the project to the predictive toxicology and risk assessment community, especially regarding the usability of the developed Application Programming Interfaces (APIs) and the interoperability layer. These case studies will demonstrate the capabilities to satisfy the requirements of the different stakeholder groups, including researchers, risk assessors and regulators and present real-world applications such as 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 for compounds lacking any previous knowledge from animal experiments (ab initio case).
Ligand-based models can be used in drug discovery to obtain an early indication of potential off-target interactions that could be linked to adverse effects. Another application is to combine such models into a panel, allowing to compare and search for compounds with similar profiles. Most contemporary methods and implementations however lack valid measures of confidence in their predictions, and only providing point predictions. We here describe the use of conformal prediction for predicting off-target interactions with models trained on data from 31 targets in the ExCAPE dataset, selected for their utility in broad early hazard assessment. Chemicals were represented by the signature molecular descriptor and support vector machines were used as the underlying machine learning method. By using conformal prediction, the results from predictions come in the form of confidence p-values for each class. The full pre-processing and model training process is openly available as scientific workflows on GitHub, rendering it fully reproducible. We illustrate the usefulness of the methodology on a set of compounds extracted from DrugBank. The resulting models are published online and are available via a graphical web interface and an OpenAPI interface for programmatic access.
Case studies 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. Associated services are demonstrated. Within the implementation challenge, external tools, especially in areas of risk assessment not completely covered by the OpenRiskNet consortium are selected for prioritized integration partial financially and strongly technically supported by researchers of OpenRiskNet partners.
Case studies 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.
The main concept of the OpenRiskNet infrastructure are virtual research environments (VRE) integrating data, analysis, modelling and simulation services for all areas of risk assessment, which can be deployed to workstations as well as public and in-house cloud infrastructures.
OpenRiskNet is a 3 year project funded by the European Commission within Horizon2020 EINFRA-22-2016 Programme (Grant Agreement 731075). Full project name: Open e-Infrastructure to Support Data Sharing, Knowledge Integration and in silico Analysis and Modelling in Predictive Toxicology and Risk Assessment. The main objective is to develop an open e-Infrastructure providing resources and services to a variety of communities requiring risk assessment, including chemicals, cosmetic ingredients, therapeutic agents and nanomaterials. OpenRiskNet is working with a network of partners, organized within an Associated Partners Programme.
This document is addressed to OpenRiskNet and associated partners. Version 1 contains the following topics: How do I access the admin interface of the OpenRiskNet website?, How do I add and describe a new publication, training material or other resources?, How do I add and describe my services? and How do I add and describe a new event?
This workshop aims at providing the users with experience on using the OpenRiskNet infrastructure for risk assessment. Users investigate a problem from nanosafety, studying a panel of nanoparticles (including dry powders of oxides of titanium, zinc, cerium and silicon, dry powders of silvers, suspensions of polystyrene latex beads and dry particles of carbon black, nanotubes and fullerene, as well as diesel exhaust particles). The OpenRiskNet infrastructure is employed to generate models on the toxicity of studied nanoparticles, more specifically the Jaqpot platform for modelling, available at http://www.jaqpot.org. Event pages available at http://www.opentox.net/events/opentox-euro-2018/s6 .
OpenRiskNet (https://openrisknet.org/) is an EU funded infrastructure project with the main objective to develop an open e-infrastructure providing resources and services to a variety of industries requiring risk assessment, including chemicals, cosmetic ingredients, drugs and nanomaterials. 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 harmonization of data, usability and interoperability of application programming interfaces (APIs) and the deployment into virtual infrastructure. The cases present real-world settings such as systems biology approaches for grouping compounds, read-across applications using chemical and biological similarity, and identifying areas of concern based only on alternative methods approaches. We discuss our progress on the OpenRiskNet goal of harmonizing data and metadata within APIs that can be added to already existing analysis and modeling services and data warehouses. We also demonstrate how these APIs can easily be used towards the generation of full risk assessment workflows either using scripting languages or workflow managers. Finally, we show the first approaches to make these APIs semantically rich by annotating data with human- and computer-readable data schemata. OpenRiskNet has initiated the Associated Partners Programme strengthening the working ties between the OpenRiskNet members and other organizations within the scientific community.
Aim: understanding the use, form, inputs and outputs of physiologically based (PBPK) pharmacokinetic models. Presentation of software applications for developing PBPK models. Customising PBPK to individual time-drug concentration data. Creating optimal drug dosage regimens
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.
Example workflow based on OpenRiskNet tools - Pathway identification workflow related to DataCure and AOPlink case studies. This notebook downloads TG-Gates data of 4 compounds and selects genes overexpressed in all sample. The Affymetrix probe sets are then translated into Ensembl gene identifiers using the BridgeDB service and pathways associated with the genes are identified using the WikiPathways service.
BridgeDb identifier mapping service (Homo sapiens, Mus musculus and Rattus norvegicus)
BridgeDb identifier mapping service (variety of species)
Whole genome transcriptional profiling allows global measurement of gene expression changes induced by particular experimental conditions. Toxic treatments of biological systems, such as cell models, may perturb interactions among genes and, in toxicogenomics, such perturbations assessed by transcriptional profiling are used to predict impact of toxic compounds. Form early days on, this toxicogenomics-based approach for predicting apical toxicities, has been dedicated to the purpose of improving predictions of genotoxicity and carcinogenicity in vivo. Over the past decade large amounts of transcriptional profiling data have been generated for in vitro study models using various chemical compounds, across different doses and time points as well as different organisms. As part of the H2020 EU project OpenRiskNet, we propose a large-scale integrative analysis approach using these data sets for predicting genotoxicity and carcinogenicity in vivo. From the diXa Data Warehouse, NCBI GEO, and EBI ArrayExpress we collected gene expression data for human in vitro liver cell models exposed to 125 compounds with known genotoxicity information at different time points and dosages resulting in 822 experiments. We analyzed these data sets using ten different classification algorithms, thereby using 80% of the data for training and 20% for testing. Support Vector Machines algorithm had the best accuracy for predicting genotoxicity in vivo at 92.5% with 95% specificity and 87% sensitivity. Upon identifying deregulated gene-gene interaction networks by applying ConsensusPathDB, the top 5 of affected pathways are related to p53-centered pathways. The results from our meta-analysis demonstrate both high accuracy and robustness of transcriptomic profiling of genotoxicity hazards across a large set of genotoxicants and across multiple human liver cell models. We propose that these assays can be used for regulatory purposes, certainly when applied in combination with the traditional genotoxicity in vitro test battery. Next, we want to perform similar analyses on rat and mouse data and identify core orthologous genes among the three different species that are potential predictive targets for assessing genotoxicity and carcinogenicity across different biological systems.
Get familiar with the eNanoMapper solutions for data management and data access.
In the last decade, omics-based approaches such as transcriptomics, proteomics and metabolomics have become valuable tools in toxicological research, and are finding their way into regulatory toxicity. A promising framework to bridge the gap between the molecular-level measurements and risk assessment is the concept of Adverse Outcome Pathways (AOPs). These pathways comprise mechanistic knowledge and connect biological events from a molecular level towards an adverse effect after exposure to a chemical or nanomaterial. However, the implementation of omics-based approaches in the AOPs and acceptance by the risk assessment community is still a challenge. Therefore, tools are required for omics-based data analysis and visualization, and to link the data to the traditional AOPs. Here we show how WikiPathways, an open science pathway database, can serve as a viable tool for this purpose. Therefore, an AOP Portal (aop.wikipathways.org)has been created with a rapidly growing collection of molecular-level AOPs on which omics datasets can be mapped an analyzed, currently consisting of 15 pathways by 14 authors that are structured in various ways. Besides that, we are making WikiPathways more interoperable with aopwiki.org, the main knowledge-base that collects and stores AOPs. The open and collaborative nature makes WikiPathways a fast growing platform that is applicable in a wide range of biomedical research fields in which omics-based approaches are used. Also, its use of ontologies, OpenAPI documentation and FAIR (Findable, Accessible, Interoperable, Reusable) approaches makes WikiPathways interoperable with many other data sources. By introducing AOPs in WikiPathways and linking these with the AOPs in aopwiki.org, we aimed to make WikiPathways a useful tool for the regulatory toxicity community and for toxicological research in general. Eventually this could lead to implementation of WikiPathways as a data-source for decision-making in REACH (Registration, Evaluation, Authorization, and restriction of Chemicals) dossiers for risk assessment of chemicals. This project has received funding from the European Union’s Horizon 2020 research and innovation programme project EU-ToxRisk under grant agreement No. 681002 and EINFRA-22-2016 programme project OpenRiskNet under grant agreement No. 731075.
The eNM ontology might be accessed through three different ways, namely online via BioPortal and AberOWL or locally using the open-source Protégé software. This tutorial focusses on browsing through the eNM ontology when one would be interested in finding a Unique Resource Identifier (URI) for mapping a term originating from for example a database schema. Using URIs for database schemas will facilitate the harmonization of data originating from different sources and will make them more comparable.
Lipophilicity is a major determinant of ADMET properties and overall suitability of drug candidates. We have developed large-scale models to predict water–octanol distribution coefficient (logD) for chemical compounds, aiding drug discovery projects. Using ACD/logD data for 1.6 million compounds from the ChEMBL database, models are created and evaluated by a support-vector machine with a linear kernel using conformal prediction methodology, outputting prediction intervals at a specified confidence level. The resulting model shows a predictive ability of Q2=0.973 and with the best performing nonconformity measure having median prediction interval of ± 0.39 log units at 80% confidence and ± 0.60 log units at 90% confidence. The model is available as an online service via an OpenAPI interface, a web page with a molecular editor, and we also publish predictive values at 90% confidence level for 91 M PubChem structures in RDF format for download and as an URI resolver service.
cpLogD confidence predictor for logD
This ontology describes how terms can be added to the eNanoMapper ontology.
OpenRiskNet (https://openrisknet.org/) is an EU funded infrastructure project with the main objective to develop an open e-infrastructure providing resources and services to a variety of industries requiring risk assessment, including chemicals, cosmetic ingredients, drugs and nanomaterials. 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 harmonization of data, usability and interoperability of application programming interfaces (APIs) and the deployment into virtual infrastructure. The cases present real-world settings such as systems biology approaches for grouping compounds, read-across applications using chemical and biological similarity, and identifying areas of concern based only on alternative methods approaches.
The “OpenRiskNet: Open e-Infrastructure to Support Data Sharing, Knowledge Integration and in silico Analysis and Modelling in Risk Assessment” project, funded by the European Commission within Horizon2020 Programme, intends to improve the harmonization and interoperability (i.e. the ability to work together, be combined to workflows and transfer data between each other without manual intervention) of data and software tools used in predictive toxicology and risk assessment. This includes (1) in vivo, in vitro and in silico data and derived knowledge sources, (2) the processing, analysis, modeling and visualization services, in order to facilitate their easy discovery, sharing and usage. The vision is that knowledge management, including a better documentation and reproducibility, will lead finally to validated risk assessment approaches for safe-by-design studies and regulatory setting supporting the goals of replacement, reduction and refinement (3R). The approach taken by OpenRiskNet to tackle these challenges is based on the development of a semantic interoperability layer responsible for the communication between the user and the services or between two services. This semantic layer will provide detailed annotations on (1) the scientific background and the meaningful usage of the services and their limitations, (2) the required input as well as (3) the obtainable results including possible output formats and standards used. In order to generate the technical solutions for this layer, some domain specific standards have first to be developed to describe the data sources and computer services in this metadata-rich fashion. This first part of a multi-part post is intended to provide background information on the current status of data sharing efforts and guidelines enforced by funding agencies and publishers’ and describes the problems we are additionally facing with respect to the interoperability layer. Additional posts will follow whenever we have at least partly solved a problem.
OpenRiskNet, a pan-European consortium funded by Horizon 2020 to develop open e-infrastructure for predictive toxicology and risk assessment, has demonstrated the results on approaches for harmonised application programming interfaces and semantic interoperability during training sessions and scientific presentations at the OpenTox Euro 2017 Conference in Basel, November 21-23 2017. Prior to these activities, the annual consortium meeting was held on 20 November to discuss the progress after twelve months in the project and plan the next steps. Moreover, the 11 European partners that make up OpenRiskNet are now launching an Associate Partner Programme to build global reach into its work.
Besides new and improved in vitro methods, in silico plays a major role in the endeavor to reach the 3R goals of replacement, reduction and refinement in both toxicodynamics and biokinetics and especially in the interplay with the first mentioned methods in forming integrated approaches to testing and assessment (IATA) and integrated testing strategies (ITS). However, for the most efficient usage of these methods and making them available to all stakeholder, these tools need to be available and accessible not necessarily in an open (not in the sense of free of charge but of open, interpretable and reproducible science), harmonized and interoperable way. This session will present international approaches and platforms providing discovery services and repositories for predictive-toxicology and risk-assessment software solutions and related disciplines, activities to harmonize the description, access and usage of these and ways to combine them into workflows for more complex analysis and modeling task.
OpenRiskNet e-infrastructure aims to provide resources and services to a variety of communities requiring risk assessment, including the NanoSafety Cluster (NSC) as a primary target community customer. Specific needs identified by the nanosafety community will be addressed and defined based on NSC projects requirements, hence identifying the key areas where the OpenRiskNet infrastructure can be deployed and tested. The possibilities to incorporate data and tools developed by other projects and to combine with other type of resources will be evaluated. Alignment and interoperability with the nano-specific ontology, protocols and templates, as initially developed under eNanoMapper, will also be pursued.
Our world is awash with chemicals, many of which still need risk and safety testing. The Horizon 2020 project “OpenRiskNet” (Open e-Infrastructure to Support Data Sharing, Knowledge Integration and in silico Analysis and Modelling in Risk Assessment) aims to provide a global infrastructure and network to integrate and harmonise data from experiments and computer models of toxicology.
Discriminating the causative disease variant(s) for individuals with inherited or de novo mutations presents one of the main challenges faced by the clinical genetics community today. Computational approaches for variant prioritization include machine learning methods utilizing a large number of features, including molecular information, interaction networks, or phenotypes. Here, we demonstrate the PhenomeNET Variant Predictor (PVP) system that exploits semantic technologies and automated reasoning over genotype-phenotype relations to filter and prioritize variants in whole exome and whole genome sequencing datasets. We demonstrate the performance of PVP in identifying causative variants on a large number of synthetic whole exome and whole genome sequences, covering a wide range of diseases and syndromes. In a retrospective study, we further illustrate the application of PVP for the interpretation of whole exome sequencing data in patients suffering from congenital hypothyroidism. We find that PVP accurately identifies causative variants in whole exome and whole genome sequencing datasets and provides a powerful resource for the discovery of causal variants.
Open e-Infrastructure to Support Data Sharing, Knowledge Integration and in silico Analysis and Modelling in Risk Assessment OpenRiskNet is a 3 year project funded under the Horizon 2020 EINFRA-22-2016 Programme (Project Number 731075; start date 1 December 2016). The main objective is to provide an open e-Infrastructure providing resources and services to a variety of communities requiring risk assessment, including chemicals, cosmetic ingredients, therapeutic agents and nanomaterials. OpenRiskNet will work with a network of partners, organized within an Associated Partners Programme. One of the OpenRiskNet case studies will address specific needs identified by the nanosafety community. The case study will be defined based on project partners’ experience in NanoEHS projects and activities within NanoSafety Cluster (NSC) working groups and task forces. Interactions with nanosafety projects have already been established in order to identify the key questions to be addressed, and where the OpenRiskNet infrastructure could be deployed and tested.
OpenRiskNet kicked off at Technology Park in Basel, Switzerland (on 15 and 16 December 2016). All partners were present on this two-day event.