News and Announcements
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. The meeting was attended by 16 people from 8 European partners. A large focus was discussions on how we can develop interoperable services with semantic APIs, and there were also practical hands-on sessions on our OpenShift recipes.
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.
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 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”.
OpenRiskNet Kick-off Meeting
We kicked off the project with a meeting at the Technology Park in Basel 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”. In these discussions it became clear that all partners agree that the only success criterion is the adoption of the infrastructure by the toxicology community. This can only be reached by integrating as many services as possible in the most accessible way and not by limiting it to the services developed by the partners. Additionally, usability testing by external users is needed during the complete development cycle. Therefore, if you are interested in providing your tool and make it interoperable with other state-of-the-art databases and analysis, modeling and visualization services or if you would like to become an early user of the infrastructure please contact us regarding the OpenRiskNet associated partner programme.