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.

Presentation
WP1 Requirement Analysis, Outreach and Case Studies
13 Dec 2018
Additional materials:
WP1 presentation

Target audience: OpenRiskNet stakeholders
Open access: yes
Licence: Attribution-ShareAlike 4.0 International (CC BY-SA 4.0)
Organisations involved: CRG, DC, Fraunhofer, IM, INERIS, JGU, NTUA, UM, UU, UoB, VU
Presentation
Presentation
WP3 Training, Support, Dissemination
13 Dec 2018
Additional materials:
WP3 presentation

Open access: yes
Licence: Attribution-ShareAlike 4.0 International (CC BY-SA 4.0)
Organisations involved: CRG, DC, Fraunhofer, IM, INERIS, JGU, NTUA, UM, UU, UoB, VU
Presentation
Presentation
WP4 Service Integration
13 Dec 2018
Additional materials:
WP4 presentation

Open access: yes
Licence: Attribution-ShareAlike 4.0 International (CC BY-SA 4.0)
Organisations involved: CRG, DC, Fraunhofer, IM, INERIS, JGU, NTUA, UM, UU, UoB, VU
Presentation
Presentation
WP2 Interoperability, Deployment and Security
13 Dec 2018
Additional materials:
WP2 presentation

Open access: yes
Licence: Attribution-ShareAlike 4.0 International (CC BY-SA 4.0)
Organisations involved: CRG, DC, Fraunhofer, IM, INERIS, JGU, NTUA, UM, UU, UoB, VU
Presentation
Public communication
OpenRiskNet factsheet
11 Dec 2018
Additional materials:
Fact-sheet

Target audience: General public, OpenRiskNet stakeholders
Open access: yes
Licence: Attribution-ShareAlike 4.0 International (CC BY-SA 4.0)
Organisations involved: DC
Public communication
Peer-reviewed publication
Introducing WikiPathways as a data-source to support Adverse Outcome Pathways for regulatory risk assessment of chemicals and nanomaterials
Marvin Martens, Tim Verbruggen, Penny Nymark, Roland Grafström, Lyle D. Burgoon, Hristo Aladjov, Fernando Torres Andón, Chris T. Evelo, Egon L. Willighagen
4 Dec 2018
Abstract:
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.

Published in: Frontiers in Genetics
Publisher: Frontiers
Target audience: Risk assessors, Researchers, Regulators, Bioinformaticians
Organisations involved: UM
Peer-reviewed publication
Report
Report of the Service Integration with OpenRiskNet - Initial Deployment (Deliverable 4.1)
Jennen, Danyel; Dudgeon, Tim; Sarimveis, Haralambos; Doganis, Philip; Karatzas, Pantelis; Rautenberg, Micha; Willighagen, Egon; Exner, Thomas
12 Nov 2018
Abstract:
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.

Publisher: OpenRiskNet
Target audience: Risk assessors, Developers, Data modellers
Open access: yes
Licence: Attribution-ShareAlike 4.0 International (CC BY-SA 4.0)
Organisations involved: DC, IM, JGU, NTUA, UM
Report
Report
Report on Re-Identification Risks and Private by Design Risk Management (Deliverable 4.4)
Farcal, Lucian; Exner, Thomas
12 Nov 2018
Abstract:
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.

Publisher: OpenRiskNet
Target audience: Data managers
Open access: yes
Licence: Attribution-ShareAlike 4.0 International (CC BY-SA 4.0)
Organisations involved: DC
Report
Report
First report on the management process (Deliverable 5.1)
Farcal , Lucian; Exner, Thomas; Hardy, Barry
12 Nov 2018
Abstract:
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.

Publisher: OpenRiskNet
Target audience: General public, OpenRiskNet stakeholders
Licence: Attribution-ShareAlike 4.0 International (CC BY-SA 4.0)
Organisations involved: DC
Report
Report
First documentation of the core e-infrastructure (Deliverable 3.2)
Dudgeon, Tim; Christie, Alan; Bachler, Daniel; Farcal, Lucian; Sarimveis, Harry; Doganis, Philip; Karatzas, Pantelis; Spjuth, Ola; Lynch, Iseult; Hardy, Barry
12 Nov 2018
Abstract:
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.

Publisher: OpenRiskNet
Open access: yes
Licence: Attribution-ShareAlike 4.0 International (CC BY-SA 4.0)
Organisations involved: DC, IM, NTUA, UU, UoB
Report
Webinar recording
OpenRiskNet webinar: introduction, case studies and demo (Nano WG - Part 1)
9 Nov 2018

Publisher: OpenRiskNet
Target audience: Risk assessors, Researchers, Students, Developers, Nanosafety community, Data modellers, Software developers
Open access: yes
Licence: Attribution-ShareAlike 4.0 International (CC BY-SA 4.0)
Organisations involved: DC, IM, NTUA, UU
Webinar recording
Webinar recording
OpenriskNet webinar: demonstration on services (Nano WG - Part 2)
9 Nov 2018

Publisher: OpenRiskNet
Target audience: Risk assessors, Researchers, Nanosafety community, OpenRiskNet stakeholders, Data modellers, Bioinformaticians, Software developers
Organisations involved: DC, IM, UU
Webinar recording
Report
Development infrastructure online (Deliverable D2.1)
Dudgeon, Tim; Spjuth, Ola; Bois, Frederic; Bachler, Daniel
7 Nov 2018
Abstract:
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.

Publisher: OpenRiskNet
Target audience: Developers, Software developers
Open access: yes
Licence: Attribution-ShareAlike 4.0 International (CC BY-SA 4.0)
Organisations involved: DC, IM, INERIS, UU
Report
Report
Initial API version provided to providers of services (Deliverable 2.2)
Rautenberg, Micha; Karwath, Andreas; Kramer, Stefan; Dudgeon, Tim; Spjuth, Ola; Bachler, Daniel; Exner, Thomas; Dokler, Joh; Sarimveis, Haralambos; Valsamis, Angelos; Doganis, Philip; Willighagen, Egon; Bois, Frederic
7 Nov 2018
Abstract:
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.

Publisher: OpenRiskNet
Target audience: Developers, Software developers
Open access: yes
Licence: Attribution-ShareAlike 4.0 International (CC BY-SA 4.0)
Organisations involved: DC, IM, INERIS, JGU, NTUA, UM, UU
Report
Report
Dissemination & Training Activities - Intermediate Report (Deliverable 3.4)
Doganis, Philip; Karatzas, Pantelis; Sarimveis, Harry; Dudgeon, Tim; Spjuth, Ola; Farcal, Lucian; Exner, Thomas; Lynch, Iseult; Hardy, Barry
7 Nov 2018
Abstract:
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).

Publisher: OpenRiskNet
Target audience: General public, OpenRiskNet stakeholders
Open access: yes
Licence: Attribution-ShareAlike 4.0 International (CC BY-SA 4.0)
Organisations involved: DC, IM, NTUA, UU, UoB
Report
Report
Report on deployment of virtual infrastructures with service discovery and container orchestration (Deliverable 2.3)
Spjuth, Ola; Dudgeon, Tim; Bachler, Daniel; Gebele, Denis; Rautenberg, Micha; Alvarsson, Jonathan; Karatzas, Pantelis; Willighagen, Egon; Evelo, Chris; Martens, Marvin; Exner, Thomas
7 Nov 2018
Abstract:
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.

Publisher: OpenRiskNet
Target audience: Developers, Software developers
Open access: yes
Licence: Attribution-ShareAlike 4.0 International (CC BY-SA 4.0)
Organisations involved: DC, IM, JGU, NTUA, UM, UU
Report
Report
Final definition of case studies (Deliverable 1.3)
Jennings, Paul; Exner, Thomas; Farcal, Lucian; Oki, Noffisat; Sarimveis, Harry; Doganis, Philip; Jennen, Danyel; Geerke, Daan; Willighagen, Egon; Bois, Frederic; Rautenberg, Micha; Dudgeon, Tim; Hardy, Barry
7 Nov 2018
Abstract:
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).

Publisher: OpenRiskNet
Target audience: Risk assessors, Researchers, Nanosafety community, OpenRiskNet stakeholders, Regulators
Open access: yes
Licence: Attribution-ShareAlike 4.0 International (CC BY-SA 4.0)
Organisations involved: DC, IM, INERIS, JGU, NTUA, UM, VU
Report
Webinar recording
OpenRiskNet case studies and the implementation challenge explained
6 Nov 2018
Abstract:
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.

Publisher: OpenRiskNet
Target audience: Risk assessors, Researchers, Students, OpenRiskNet stakeholders, Data modellers, Bioinformaticians
Open access: yes
Licence: Attribution-ShareAlike 4.0 International (CC BY-SA 4.0)
Organisations involved: DC, IM, NTUA, UU
Webinar recording
Peer-reviewed publication
Predicting off-target binding profiles with confidence using Conformal Prediction
Samuel Lampa, Jonathan Alvarsson, Staffan Arvidsson Mc Shane, Arvid Berg, Ernst Ahlberg, and Ola Spjuth
6 Nov 2018
Abstract:
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.

Published in: Frontiers in Pharmacology
Target audience: Researchers, Developers, Data modellers, Bioinformaticians, Software developers, Data providers
Open access: yes
Licence: Attribution 4.0 International (CC BY 4.0)
Organisations involved: UU
Peer-reviewed publication
Presentation
OpenRiskNet Case Studies
Thomas Exner
2 Nov 2018
Abstract:
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.
Additional materials:
OpenRiskNet_Case_Studies.pdf

Target audience: Risk assessors, OpenRiskNet stakeholders
Open access: yes
Licence: Attribution-ShareAlike 4.0 International (CC BY-SA 4.0)
Organisations involved: CRG, DC, Fraunhofer, IM, INERIS, JGU, NTUA, UM, UU, UoB, VU
Presentation
Presentation
Introduction to OpenRiskNet
Thomas Exner
2 Nov 2018
Additional materials:
OpenRiskNet_Introduction.pdf

Target audience: OpenRiskNet stakeholders
Open access: yes
Licence: Attribution-ShareAlike 4.0 International (CC BY-SA 4.0)
Organisations involved: DC
Presentation
Presentation
Introduction to OpenRiskNet e-infrastructure
Tim Dudgeon
2 Nov 2018

Target audience: Developers, OpenRiskNet stakeholders
Open access: yes
Licence: Attribution-ShareAlike 4.0 International (CC BY-SA 4.0)
Organisations involved: IM
Presentation
Presentation
Implementation Challenge and Associated Partner Programme
Thomas Exner
2 Nov 2018

Target audience: OpenRiskNet stakeholders
Open access: yes
Licence: Attribution-ShareAlike 4.0 International (CC BY-SA 4.0)
Organisations involved: DC
Presentation
Webinar recording
Introduction to OpenRiskNet e-infrastructure
1 Nov 2018
Abstract:
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.

Target audience: Developers, OpenRiskNet stakeholders
Open access: yes
Licence: Attribution-ShareAlike 4.0 International (CC BY-SA 4.0)
Organisations involved: IM
Webinar recording
Webinar recording
Introduction to OpenRiskNet project
31 Oct 2018
Abstract:
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.

Publisher: OpenRiskNet
Target audience: General public, OpenRiskNet stakeholders
Open access: yes
Licence: Attribution-ShareAlike 4.0 International (CC BY-SA 4.0)
Organisations involved: DC
Webinar recording
Tutorial
Tutorials OpenRiskNet public website
30 Oct 2018
Abstract:
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?
Additional materials:
Tutorial

Publisher: OpenRiskNet
Organisations involved: DC
Tutorial
Tutorial
REVK Pharmacokinetics OpenRiskNet Case study using Jaqpot web modelling platform
Philip Doganis
15 Oct 2018
Related services:
Jaqpot API
Jaqpot GUI

Target audience: Risk assessors, Researchers, OpenRiskNet stakeholders, Data modellers
Open access: yes
Licence: Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)
Organisations involved: NTUA
Tutorial
Tutorial
Model RX OpenRiskNet - Case study using Jaqpot web modelling platform
Philip Doganis
15 Oct 2018
Related services:
Jaqpot API
Jaqpot GUI

Target audience: Risk assessors, Researchers, OpenRiskNet stakeholders, Data modellers
Open access: yes
Licence: Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)
Organisations involved: NTUA
Tutorial
Tutorial
Building risk assessment workflows with OpenRiskNet
Philip Doganis, Thomas Exner
11 Oct 2018
Abstract:
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 .

Publisher: OpenRiskNet
Target audience: Risk assessors, Researchers, Students, Developers, Data owners, Nanosafety community, General public, OpenRiskNet stakeholders, Regulators, Data modellers
Open access: yes
Licence: Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
Organisations involved: DC, NTUA
Tutorial
Poster
OpenRiskNet, an open e-infrastructure to support data sharing, knowledge integration and in silico analysis and modelling in risk assessment
Thomas Exner, Joh Dokler, Daniel Bachler, Lucian Farcal, Chris Evelo, Egon Willighagen, Danyel Jennen, Marc Jacobs, Philip Doganis, Haralambos Sarimveis, Iseult Lynch, Georgios Gkoutos, Stefan Kramer, Cedric Notredame, Ola Spjuth, Paul Jennings, Tim Dudgeon, Frederic Bois, Barry Hardy
10 Oct 2018
Abstract:
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.
Additional materials:
20180810_ORN_Poster_EuroTox.pdf

Published in: Toxicology Letters
Publisher: Elsevier
Target audience: Risk assessors, Researchers, Students, OpenRiskNet stakeholders, Regulators, Data modellers, Bioinformaticians
Organisations involved: CRG, DC, Fraunhofer, IM, INERIS, JGU, NTUA, UM, UU, UoB, VU
Poster
Public communication
OpenRiskNet e-infrastructure available to end-users
Lucian Farcal
9 Oct 2018
Abstract:
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.

Published in: NSC Newsletter Issue No. 13, Autumn 2018 (pg. 19)
Publisher: EU NanoSafety Cluster
Target audience: Nanosafety community
Open access: yes
Organisations involved: DC
Public communication
Tutorial
Biokinetics Modelling: use, form, inputs and outputs of PBPK models
Harry Sarimveis, Aris Dokoumetzidis, Pantelis Karatzas, Philip Doganis, Periklis Tsiros, Nikolas-Marios Katritsis, Georgia Tsiliki
9 Oct 2018
Abstract:
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

Target audience: Risk assessors, Researchers, Developers, Data owners, Nanosafety community, OpenRiskNet stakeholders, Regulators, Data modellers
Open access: yes
Licence: Attribution-ShareAlike 4.0 International (CC BY-SA 4.0)
Organisations involved: NTUA
Tutorial
Tutorial
Workflow: Access TG-GATEs data for seleted compounds, select differentially expressed genes and identifier relevant pathways
Thomas Exner
13 Sep 2018
Abstract:
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.
Related services:
Jupyter Notebooks

Publisher: OpenRiskNet
Target audience: Risk assessors, Researchers, Data modellers
Open access: yes
Licence: Attribution-ShareAlike 4.0 International (CC BY-SA 4.0)
Organisations involved: DC
Tutorial
Public communication
OpenRiskNet roll-up banner
12 Sep 2018
Additional materials:
ORN-roll-up.pdf

Target audience: General public, OpenRiskNet stakeholders
Open access: yes
Licence: Attribution-ShareAlike 4.0 International (CC BY-SA 4.0)
Organisations involved: DC
Public communication
Poster
Meta-analysis for genotoxicity prediction using data from multiple human in vitro cell models
Jumamurat R. Bayjanov Jos Kleinjans Danyel Jennen
12 Sep 2018
Abstract:
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.

Target audience: Risk assessors, Researchers, Regulators
Open access: yes
Organisations involved: UM
Poster
Tutorial
Entering and analysing nano safety data
Nina Jeliazkova, Egon Willighagen
9 Sep 2018
Abstract:
Get familiar with the eNanoMapper solutions for data management and data access.

Publisher: eNanoMapper
Target audience: Researchers, Data modellers, Data providers
Open access: yes
Licence: Attribution 4.0 International (CC BY 4.0)
Organisations involved: UM
Tutorial
Poster
Introducing WikiPathways to support Adverse Outcome Pathways for regulatory risk assessment
Marvin Martens, Tim Verbruggen, Penny Nymark, Roland Grafström, Lyle Burgoon, Hristo Aladjov, Fernando Torres Andón, Chris T Evelo, Egon Willighagen
7 Sep 2018
Abstract:
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.

Target audience: Risk assessors, Researchers, Students, Developers, Data managers, Data owners, Regulators, Bioinformaticians, Software developers, Data providers
Open access: yes
Licence: Attribution 4.0 International (CC BY 4.0)
Organisations involved: UM
Poster
Public communication
OpenRiskNet flyer
1 Aug 2018
Additional materials:
OpenRiskNet-Flyer20180801.pdf

Target audience: OpenRiskNet stakeholders
Open access: yes
Licence: Attribution-ShareAlike 4.0 International (CC BY-SA 4.0)
Organisations involved: DC
Public communication
Presentation
Big Data in Toxicogenomics: Towards FAIR predictions
Danyel Jennen
26 Jul 2018

Target audience: Risk assessors, Researchers, Bioinformaticians
Organisations involved: UM
Presentation
Tutorial
Browsing the eNM ontology with BioPortal, AberOWL and Protégé
Linda Rieswijk, Friederike Ehrhart, Egon Willighagen
8 May 2018
Abstract:
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.

Publisher: eNanoMapper
Target audience: Researchers, Data modellers, Data providers
Open access: yes
Licence: Attribution 4.0 International (CC BY 4.0)
Organisations involved: UM
Tutorial
Peer-reviewed publication
A confidence predictor for logD using conformal regression and a support-vector machine
Lapins M, Arvidsson S, Lampa S, Berg A, Schaal W, Alvarsson J, Spjuth O
3 Apr 2018
Abstract:
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.
Related services:
Conformal LogD Predictor

Published in: J. Cheminformatics
Publisher: BMC (Springer Nature)
Target audience: Risk assessors, Researchers, Students, Developers
Open access: yes
Organisations involved: UU
Peer-reviewed publication
Tutorial
Adding ontology terms
Egon Willighagen
28 Mar 2018
Abstract:
This ontology describes how terms can be added to the eNanoMapper ontology.

Publisher: eNanoMapper
Target audience: Researchers, Data modellers, Data providers
Open access: yes
Licence: Attribution 4.0 International (CC BY 4.0)
Organisations involved: UM
Tutorial
Poster
OpenRiskNet, an open e-infrastructure to support data sharing, knowledge integration and in silico analysis and modelling in risk assessment
Exner T, Dokler J, Bachler D, Farcal L, Evelo C, Willighagen E, Jacobs M, Doganis P, Sarimveis H, Lynch I, Kramer S, Notredame C, Jennen D, Gkoutos G, Spjuth S, Jennings P, Dudgeon T, Bois F, Hardy B
12 Mar 2018
Abstract:
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.

Publisher: Society of Toxicology (SOT)
Target audience: Risk assessors, Researchers, Regulators, Data modellers
Open access: yes
Licence: Attribution-ShareAlike 4.0 International (CC BY-SA 4.0)
Organisations involved: CRG, DC, Fraunhofer, IM, INERIS, JGU, NTUA, UM, UU, UoB, VU
Poster
Public communication
The OpenRiskNet Approach towards a Semantic Interoperability Layer - Part One: Problem Definition for Datasets
Thomas Exner, Chris Evelo, Egon Willighagen, Marc Jacobs, Philip Doganis, Haralambos Sarimveis, Iseult Lynch, Stefan Kramer, Cedric Notredame, Danyel Jennen, Georgios Gkoutos, Ola Spjuth, Paul Jennings, Tim Dudgeon, Frederic Bois, Barry Hardy
17 Jan 2018
Abstract:
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.

Publisher: OpenRiskNet
Target audience: Data managers, Data owners
Open access: yes
Licence: Attribution 4.0 International (CC BY 4.0)
Organisations involved: CRG, DC, Fraunhofer, IM, INERIS, JGU, NTUA, UM, UU, UoB, VU
Public communication
Public communication
OpenRiskNet reveals concepts of harmonised APIs and semantic interoperability, provides first training units, and launches Associate Partner Program
Thomas Exner
8 Dec 2017
Abstract:
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.

Publisher: OpenRiskNet
Target audience: Nanosafety community
Open access: yes
Licence: Attribution 4.0 International (CC BY 4.0)
Organisations involved: CRG, DC, Fraunhofer, IM, INERIS, JGU, NTUA, UM, UU, UoB, VU
Public communication
Presentation
Integration and interoperability (conference session)
Chris Evelo, Marvin Martens, Thomas Exner, Herve Menager, Jildau Bouwman, Alessia Bardi
23 Nov 2017
Abstract:
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.

Publisher: OpenTox
Target audience: Researchers, Bioinformaticians, Software developers
Open access: yes
Licence: Attribution-ShareAlike 4.0 International (CC BY-SA 4.0)
Organisations involved: DC, UM
Presentation
Public communication
OpenRiskNet case studies to support data and tools integration from NanoSafety Cluster
Lucian Farcal
2 Nov 2017
Abstract:
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.

Published in: NSC Newsletter Issue No. 10, Autumn 2017 (pg. 7)
Publisher: EU NanoSafety Cluster
Open access: yes
Licence: Attribution-ShareAlike 4.0 International (CC BY-SA 4.0)
Organisations involved: DC
Public communication
Public communication
A global harmonized basis for testing chemical safety
Barry Hardy
9 Aug 2017
Abstract:
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.

Published in: Euresearch INFO
Publisher: Euresearch
Target audience: General public, OpenRiskNet stakeholders
Open access: yes
Organisations involved: DC
Public communication
Public communication
Horizon 2020 Research Success Story | OpenRiskNet
9 Aug 2017

Publisher: Euresearch
Target audience: General public, OpenRiskNet stakeholders
Open access: yes
Licence: Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
Organisations involved: DC
Public communication
Peer-reviewed publication
Semantic prioritization of novel causative genomic variants
Imane Boudellioua, Rozaimi B. Mahamad Razali, Maxat Kulmanov, Yasmeen Hashish, Vladimir B. Bajic, Eva Goncalves-Serra, Nadia Schoenmakers, Georgios V. Gkoutos, Paul N. Schofield, Robert Hoehndorf
17 Apr 2017
Abstract:
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.

Published in: PLoS Computational Biology
Publisher: PLOS
Open access: yes
Organisations involved: UoB
Peer-reviewed publication
Public communication
Introduction to OpenRiskNet
Lucian Farcal
4 Apr 2017
Abstract:
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.

Published in: NSC Newsletter Issue No. 9, Spring 2017 (pg. 15)
Publisher: EU NanoSafety Cluster
Target audience: Nanosafety community
Open access: yes
Licence: Attribution-ShareAlike 4.0 International (CC BY-SA 4.0)
Organisations involved: DC
Public communication
Public communication
OpenRiskNet Kicked off
Thomas Exner
24 Jan 2017
Abstract:
OpenRiskNet kicked off at Technology Park in Basel, Switzerland (on 15 and 16 December 2016). All partners were present on this two-day event.

Publisher: OpenRiskNet
Target audience: OpenRiskNet stakeholders
Open access: yes
Licence: Attribution-ShareAlike 4.0 International (CC BY-SA 4.0)
Organisations involved: CRG, DC, Fraunhofer, IM, INERIS, JGU, NTUA, UM, UU, UoB, VU
Public communication