News and Announcements
How to identify and link of data related to AOPWiki to support the Adverse Outcome Pathway approach
The Adverse Outcome Pathway (AOP) concept has been introduced to support risk assessment . An AOP comprises a number of biological events: a molecular initiating event (MIE) is followed by one or more key events (KEs), leading to the adverse outcome (AO). The AOPWiki  is a collaborative platform to exchange AOP-related knowledge.
The use of AOPs for regulatory purposes requires detailed validation and linking to existing knowledge [3; 4]. Part of the development of AOPs is the search for data that supports the occurrence and biological plausibility of KEs and their relationships (KERs). This data can be found in literature and increasingly in databases.
Data curation workflows using OpenRiskNet approach ready for demonstration
In the process of utilising the analysis tools available in the OpenRiskNet e-infrastructure, data needs to be accessed from different sources and various formats. Thus, the users should be able to access different data sources and specific entries. This are then being curated using an OpenRiskNet service and re-submitted to the data source.
Within DataCure case study, we aimed to establish a process for data curation and annotation that makes use of APIs and semantic annotations for a more systematic and reproducible data curation workflow. The development of semantic annotations and API definition for selected databases are also desired.
OpenRiskNet and NanoCommons at SOT 2019
The two sister infrastructure projects OpenRiskNet and NanoCommons will present the two complementary approaches to provide users with risk assessment data, software and workflows at the ToxExpo part of the SOT 58th Annual Meeting in Baltimore (10-14 March 2019).
New deliverables reports are publicly available
OpenRiskNet case studies enter final, test phase
OpenRiskNet’s work on case studies is entering the final phase with the focus on demonstrating infrastructure capabilities and on testing different risk assessment scenarios. The case studies provide examples and prototypes for solutions provided to the predictive toxicology and risk assessment community and demonstrate usage of the developed APIs and the interoperability features to build integrated workflows.
OpenRiskNet e-infrastructure listed to EOSC and eInfraCentral catalogues
OpenRiskNet e-infrastructure is listed as a service under the catalogues of European Open Science Cloud (EOSC) and European E-Infrastructure Services Gateway (eInfraCentral).
Additional services, part of OpenRiskNet e-infrastructure, will be also listed.
Update 2019-Feb-26: News posted by eInfraCentral http://einfracentral.eu/news/openrisknet-joined-eosc-catalogue
Ontology meeting by OpenRiskNet and NanoCommons
The goal of this meeting is to get a picture of the ongoing ontology activities in the toxicology area, harmonize these efforts and the developed ontologies therein, and extend the existing toxicology ontology to support OpenRiskNet and NanoCommons tasks. Part of this will be the ontological annotation of OpenRiskNet Application Programming Interfaces (APIs) as used on their cloud.
General assembly and consortium meeting 2018
The next annual meeting of the OpenRiskNet Consortium will be held in Brussels from 12 to 14 December 2018. The progress on project tasks and case studies will be presented and demonstrated by the project members. The event will include also an ontology meeting.
A new OpenRiskNet introduction session to stakeholders
Following the successful introduction and demo sessions organised in September and beginning of October, OpenRiskNet consortium is organising a new session on 30 October 2018, at 4 pm CEST. During the 1-hour demonstration session you'll get a general and technical introduction to OpenRiskNet e-infrastructure and the case studies. The log-in information were submitted to the registrants by email. However, if you did not get them or you still want to register please contact us at email@example.com before the start of the session.
Major updates to the OpenRiskNet website
The OpenRiskNet website was first released in June 2017, to enable presentation of project work to its stakeholders (end-users and developers), the scientific community and to the general public. The website contains information on project objectives and partners, detailed information on the Associate Partner Programme and a list of dissemination activities (events, publications and other resources). On the technical development side, the website provides information on case studies and associated use cases.
On 19 October 2018, a new version of the website was released including major changes on its structure and the information provided. The new features of the websites (e.g. catalogue of services, resources & training, list of events, etc.) released recently aim to support even more all project stakeholders in browsing and accessing the information on the available services and resources addressed to users.
Implementation challenge deadline extended to 31 October 2018
The deadline for the first implementation challenge was extended to 31 October 2018. For more information see https://openrisknet.org/associated-partner-programme/implementation-challenge/.
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.
OpenRiskNet webinar series
A series of webinars are organised by OpenRiskNet in order to introduce the project and demonstrate on the e-infrastructure services and case studies.
First sessions are scheduled for 24 Sep 2018 (4 pm CEST) and 27 Sep 2018 (4 pm CEST). Additional dates will be selected based on the registrants preference.
Please sign up for these meeting using the doodle poll. The registrants will receive the login information by email.
All presentations and webinars recordings will be available in the Resources & Training page.
Implementation challenge announced
The Implementation Challenge was created to select external tools especially in areas of risk assessment not completely covered by the OpenRiskNet consortium to be prioritized for their integration into the e-infrastructure. Third parties can apply for partial financially and strongly technically support by researchers and developers of OpenRiskNet partners. If you want to make your tool visible to a large community and make it interoperable with other OpenRiskNet services, please apply at https://goo.gl/forms/D90Uxa7ZhvkGeBV72 before one of the three deadlines. More information on the selection criteria and the available funding can be found at https://openrisknet.org/associated-partner-programme/implementation-challenge/.
The OpenRiskNet Approach towards a Semantic Interoperability Layer - Part One: Problem Definition for Datasets
Harmonization and interoperability between data and computational services, the facilitation of their easy discovery, the sharing and usage of data sources as well as of the processing, analysis and modelling tools and finally a better documentation and reproducibility of the risk assessment workflows are major challenges that OpenRiskNet tries to address. The approach adopted by us to tackle these challenges is the development of a semantic interoperability layer to organize the communication between the user and the services or between two services. The blog post describes the taken approach and the first steps to describe data sources in this layer.
OpenRiskNet reveals concepts of harmonised APIs and semantic interoperability, provides first training units, and launches Associate Partner Program
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.
OpenRiskNet Workshop in Uppsala
On 25-26 Sept 2017 the Pharmaceutical Bioinformatics research group at Uppsala University organised a workshop on microservices development with a large focus on Kubernetes/OpenShift and how we can establish a CICD system within the OpenRiskNet project.
OpenTox Euro Conference featuring the first OpenRiskNet training
OpenRiskNet is proud to co-organize OpenTox Euro 2017 taking place at the Hotel Stücki in Basel, 21-23 November 2017. The program starts with training sessions given by OpenRiskNet partners with topics like online modeling services, workflow management and ontology annotation of datasets and software services. This will be followed by a data as well as API hackathon. In the second, the concept of semantic annotation of services will be presented and applied to a biokinetics modeling tool. Finally, the OpenTox conference will run over two days with sessions on the following topics:
- Defined approaches towards regulatory acceptance
- Simulations of exposure and transport
- Integration and interoperability: software
- Integration and interoperability: data
- High-content imaging
- Characterization of experimental conditions
OpenRiskNet Story on EURESEARCH
OpenRiskNet as EU Research Success Story: “Our world is awash with chemicals, many of which still need risk and safety testing. The Horizon 2020 project OpenRiskNet aims to provide a global infrastructure and network to integrate and harmonise data from experiments and computer models of toxicology…”. Read the full article and watch the video on EURESEARCH website.
OpenRiskNet at OpenTox USA
The OpenRiskNet concepts of harmonized APIs and the semantic interoperability layer will be presented at the OpenTox USA 2017 conference, 12-13 July 2017 at the Searle Conference Center, Duke University. The talk given by Thomas Exner will have the title “Semantic Interoperability of Public Available Data”.
The OpenRiskNet partner CRG is organizing the workshop Nextflow: Reproducible In Silico Genomics, 14-15 October 2017, CRG – Centre for Genomic Regulation, Barcelona with contributions by Jordi Rambla and Tim Dudgeon.
OpenRiskNet Kick-off Meeting
We kicked off the project with a meeting at the Technology Park in Basel on 15th and 16th December with scientific presentations and planning sessions for the different work packages. “WP1: Requirement Analysis, Outreach and Case Studies“, “WP2: Interoperability, Deployment and Security”, “WP3: Training, Support, Dissemination” and “WP4: Service Integration”.