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OpenRiskNet SIGNED

OpenRiskNet: Open e-Infrastructure to Support Data Sharing, Knowledge Integration and in silico Analysis and Modelling in Risk Assessment

Total Cost €

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EC-Contrib. €

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Partnership

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 OpenRiskNet project word cloud

Explore the words cloud of the OpenRiskNet project. It provides you a very rough idea of what is the project "OpenRiskNet" about.

toxicokinetics    cosmetic    service    validation    hazard    supporting    integration    stakeholders    interoperability    components    sophisticated    silico    instances    combine    complemented    agents    toxicology    chronic    independently    safer    extrapolations    discipline    prediction    transition    modeling    requiring    standard    generation    risk    templates    options    harmonized    systemic    overcome    earlier    ontologies    applicability    vitro    prototype    guaranteeing    innovation    services    packaging    describe    groups    sharing    workflows    variety    data    risks    virtual    container    generating    communities    file    animal    semantic    vivo    productive    layer    standardized    metadata    toxicity    fragmentation    evaluation    mechanistic    paradigm    databases    therapeutic    ingredients    chemical    alternative    discovery    undergoing    added    run    openrisknet    deployment    ongoing    world    shift    settings    tools    achievements    formats    chemicals    nanomaterials    training    infrastructure    phenomenological    algorithms   

Project "OpenRiskNet" data sheet

The following table provides information about the project.

Coordinator
EDELWEISS CONNECT GMBH 

Organization address
address: HOCHBERGERSTRASSE 60C
city: BASEL
postcode: 4057
website: http://www.douglasconnect.com/

contact info
title: n.a.
name: n.a.
surname: n.a.
function: n.a.
email: n.a.
telephone: n.a.
fax: n.a.

 Coordinator Country Switzerland [CH]
 Project website https://openrisknet.org/
 Total cost 2˙999˙112 €
 EC max contribution 2˙999˙112 € (100%)
 Programme 1. H2020-EU.1.4.1.3. (Development, deployment and operation of ICT-based e-infrastructures)
 Code Call H2020-EINFRA-2016-1
 Funding Scheme RIA
 Starting year 2016
 Duration (year-month-day) from 2016-12-01   to  2019-11-30

 Partnership

Take a look of project's partnership.

# participants  country  role  EC contrib. [€] 
1    EDELWEISS CONNECT GMBH CH (BASEL) coordinator 621˙875.00
2    UNIVERSITEIT MAASTRICHT NL (MAASTRICHT) participant 460˙250.00
3    INFORMATICS MATTERS LIMITED UK (KIDLINGTON) participant 318˙750.00
4    UPPSALA UNIVERSITET SE (UPPSALA) participant 309˙500.00
5    JOHANNES GUTENBERG-UNIVERSITAT MAINZ DE (MAINZ) participant 290˙000.00
6    THE UNIVERSITY OF BIRMINGHAM UK (BIRMINGHAM) participant 243˙500.00
7    FUNDACIO CENTRE DE REGULACIO GENOMICA ES (BARCELONA) participant 181˙875.00
8    NATIONAL TECHNICAL UNIVERSITY OF ATHENS - NTUA EL (ATHINA) participant 180˙500.00
9    FRAUNHOFER GESELLSCHAFT ZUR FOERDERUNG DER ANGEWANDTEN FORSCHUNG E.V. DE (MUNCHEN) participant 149˙137.00
10    STICHTING VU NL (AMSTERDAM) participant 127˙475.00
11    INSTITUT NATIONAL DE L ENVIRONNEMENT ET DES RISQUES INERIS FR (VERNEUIL EN HALATTE) participant 116˙250.00
12    MEDIZINISCHE UNIVERSITAT INNSBRUCK AT (INNSBRUCK) participant 0.00

Map

 Project objective

Toxicology and risk assessment are undergoing a paradigm shift, from a phenomenological to a mechanistic discipline based on in vitro and in silico approaches that represent an important alternative to classical animal testing applied to the evaluation of chronic and systemic toxicity risks. Large databases and highly sophisticated methods, algorithms and tools are available for different tasks such as hazard prediction, toxicokinetics, and in vitro – in vivo extrapolations to support this transition. However, since these services are developed independently and provided by different groups world-wide, there is no standardized way how to access the data or run modelling workflows. To overcome the fragmentation of data and tools, OpenRiskNet will provide open e-Infrastructure resources and services to a variety of communities requiring chemical risk assessment, including chemicals, cosmetic ingredients, therapeutic agents, and nanomaterials. OpenRiskNet will combine the achievements from earlier projects for generating modeling and validation workflows, knowledge integration and data management as well as include all ongoing projects and important stakeholders through an associated partner programme. The main components of the infrastructure will be an interoperability layer added to every service to describe the functionality and guaranteeing technical and semantic interoperability, a discovery service, deployment options based on container technology, and packaging of the infrastructure into virtual instances. This will be complemented by training and support on integration of specific services based on prototype implementation, usage of standard file formats for data sharing including the generation of templates for data and metadata, as well as the harmonized usage of ontologies. Case studies will demonstrate the applicability of the infrastructure in productive settings supporting research and innovation in safer product design and risk assessment.

 Deliverables

List of deliverables.
Final report on the management process Documents, reports 2020-04-25 00:24:00
Report on the results of the Implementation Challenge Documents, reports 2020-04-25 00:19:36
Fully functional support infrastructure Demonstrators, pilots, prototypes 2020-04-25 00:24:56
Associated partner program is established Other 2020-04-25 00:24:37
Initial version of data management plan Open Research Data Pilot 2020-04-25 00:24:16
Reference OpenRiskNet system available online Demonstrators, pilots, prototypes 2020-04-25 00:21:15
Data management, maintenance and sustainability plan Documents, reports 2020-04-25 00:23:29
Report of the Service Integration with OpenRiskNet (Intermediate Report) Documents, reports 2020-04-25 00:18:50
Finalization of case studies and analysis of remaining weaknesses Other 2020-04-25 00:20:35
Final API available for internal and external service providers Demonstrators, pilots, prototypes 2020-04-25 00:18:35
Compute and data federation Other 2020-04-25 00:19:16
Dissemination & Training Activities (Final Report) Documents, reports 2020-04-25 00:21:57
Report on requirement analysis and recommendations for WP2-4 including Data Management Plan Documents, reports 2020-04-25 00:21:35
Report of the Service Integration with OpenRiskNet (Final Report) Documents, reports 2020-04-25 00:23:45
Final definition of case studies Other 2020-02-19 16:31:30
Report on Re-Identification Risks and Private by Design Risk Management Documents, reports 2020-02-19 16:31:30
Report on deployment of virtual infrastructures with service discovery and container orchestration Demonstrators, pilots, prototypes 2020-02-19 16:31:30
Dissemination & Training Activities (Intermediate Report) Documents, reports 2020-02-19 16:31:30
Development infrastructure online Demonstrators, pilots, prototypes 2020-02-19 16:31:30
First documentation of the core e-infrastructure Documents, reports 2020-02-19 16:31:30
First report on the management process Documents, reports 2020-02-19 16:31:30
Initial API version provided to providers of services Demonstrators, pilots, prototypes 2020-02-19 16:31:30
Report of the Service Integration with OpenRiskNet (Initial Deployment) Documents, reports 2020-02-19 16:31:30

Take a look to the deliverables list in detail:  detailed list of OpenRiskNet deliverables.

 Publications

year authors and title journal last update
List of publications.
2018 Jennen, Danyel; Dudgeon, Tim; Sarimveis, Haralambos; Doganis, Philip; Karatzas, Pantelis; Rautenberg, Micha; Willighagen, Egon; Exner, Thomas
Report of the Service Integration with OpenRiskNet - Initial Deployment (Deliverable 4.1)
published pages: , ISSN: , DOI: 10.5281/zenodo.1484309
2 2020-02-19
2018 Farcal , Lucian; Exner, Thomas; Hardy, Barry
First report on the management process (Deliverable 5.1)
published pages: , ISSN: , DOI: 10.5281/zenodo.1484358
5 2020-02-19
2018 Spjuth, Ola; Farcal, Lucian; Lynch, Iseult; Dudgeon, Tim; Exner, Thomas
Fully functional support infrastructure (Deliverable 3.3)
published pages: , ISSN: , DOI: 10.5281/zenodo.2558121
2 2020-02-19
2019 Boudellioua, Imane; Kulmanov, Maxat; Schofield, Paul N.; Gkoutos, Georgios V.; Hoehndorf, Robert
DeepPVP: phenotype-based prioritization of causative variants using deep learning.
published pages: , ISSN: 1471-2105, DOI: 10.17863/CAM.36763
BMC Bioinformatics, Vol 20, Iss 1, Pp 1-8 (2019) 4 2020-02-19
2018 Farcal, Lucian; Bachler, Daniel; Dokler, Joh; Exner, Thomas
Report on requirements analysis and recommendations for WP2-4 (Deliverable 1.1)
published pages: , ISSN: , DOI: 10.5281/zenodo.2557731
4 2020-02-19
2018 Farcal, Lucian; Exner, Thomas
Report on Re-Identification Risks and Private by Design Risk Management (Deliverable 4.4)
published pages: , ISSN: , DOI: 10.5281/zenodo.1484319
5 2020-02-19
2018 Danyel, Jennen; Bayjanov, Jumamurat; Farcal, Lucian; Oki, Noffisat; Geerke, Daan; Doganis, Philip; Martens, Marvin; Willighagen, Egon; Gebele, Denis; Jacobs, Marc; Dudgeon, Tim; Lynch, Iseult; Exner, Thomas
Report of the Service Integration with OpenRiskNet (Intermediate Report) (Deliverable 4.2)
published pages: , ISSN: , DOI: 10.5281/zenodo.2596998
5 2020-02-19
2017 Philip Doganis, Georgia Tsiliki, Charalampos Chomenidis, Angelos Valsamis, George Drakakis, Evangelia Anagnostopoulou, Haralambos Sarimveis
Jaqpot: an open source web platform for modelling and model publishing integrated into a safety assessment e-infrastructure
published pages: , ISSN: , DOI:
Open Science Fair 2017 2020-02-19
2017 Ola Spjuth
Data-intensive bioinformatics on HPC and Cloud
published pages: , ISSN: , DOI:
COST-CHARME \'Big Data Training School for Life Sciences\' 2020-02-19
2018 Maris Lapins, Staffan Arvidsson, Samuel Lampa, Arvid Berg, Wesley Schaal, Jonathan Alvarsson, Ola Spjuth
A confidence predictor for logD using conformal regression and a support-vector machine
published pages: , ISSN: 1758-2946, DOI: 10.1186/s13321-018-0271-1
Journal of Cheminformatics 10/1 2020-02-19
2017 Exner, Thomas
Towards Semantic Interoperability of Publicly Available Data
published pages: , ISSN: , DOI: 10.5281/zenodo.831444
OpenTox USA 2020-02-19
2017 Iseult Lynch
Characterisation of intrinsic and extrinsic nanomaterial characteristics: the need for relevant exposure media supplemented with appropriate biomolecules
published pages: , ISSN: , DOI:
OpenTox Euro 2017 2020-02-19
2017 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
Semantic prioritization of novel causative genomic variants
published pages: e1005500, ISSN: 1553-7358, DOI: 10.1371/journal.pcbi.1005500
PLOS Computational Biology 13/4 2020-02-19
2017 Thomas Exner
Towards Semantic Interoperability of Publicly Available Data
published pages: , ISSN: , DOI:
OpenTox Euro 2017 2020-02-19
2017 Thomas Exner
The OpenRiskNet Project
published pages: , ISSN: , DOI:
OpenTox Euro 2017 2020-02-19
2017 Tim Dudgeon
Nextflow for chemistry - crossing the divide
published pages: , ISSN: , DOI:
Nextflow workshop 2020-02-19
2017 Ola Spjuth
Data-intensive applications on cloud computing resources: Applications in life sciences
published pages: , ISSN: , DOI:
2nd international de.NBI symposium 2020-02-19
2017 Marvin Martens, Chris Evelo, Egon Willighagen
The future of regulatory toxicity assessment: Adverse Outcome Pathways
published pages: , ISSN: , DOI:
ByteMAL (Bioinformatics for Young inTernational researchers Expo: Maastricht-Aachen-Liège) 2020-02-19
2017 Marvin Martens
Enriching Key Events in Adverse Outcome Pathways with links to biomolecular databases to allow experimental data analysis for regulatory risk assessment
published pages: , ISSN: , DOI:
OpenTox Euro 2017 2020-02-19
2018 Exner, Thomas; Dokler, Joh; Bachler, Daniel; Farcal, Lucian; Evelo, Chris; Willighagen, Egon; Jacobs, Marc; Doganis, Philip; Sarimveis, Haralambos; Lynch, Iseult; Kramer, Stefan; Notredame, Cedric; Jennen, Danyel; Gkoutos, Georgios; Spjuth, Ola; Jennings, Paul; Dudgeon, Tim; Bois, Frederic; Hardy, Barry
OpenRiskNet, an open e-infrastructure to support data sharing, knowledge integration and in silico analysis and modelling in risk assessment
published pages: , ISSN: , DOI: 10.5281/zenodo.1199286
SOT 2018 (Society of Toxicology 57th Annual Meeting and ToxExpo) 1 2020-02-19
2017 Chris Evelo
If we all jump together, could we make the earth move?
published pages: , ISSN: , DOI:
OpenTox Euro 2017 2020-02-19
2018 J.R. Bayjanov, J.C. Kleinjans, D.G.J. Jennen
Meta-analysis for genotoxicity prediction using data from multiple human in vitro cell models
published pages: S100-S101, ISSN: 0378-4274, DOI: 10.1016/j.toxlet.2018.06.608
Toxicology Letters 295 2020-02-19
2018 Dudgeon, Tim; Spjuth, Ola; Bois, Frederic; Bachler, Daniel
Development infrastructure online (Deliverable D2.1)
published pages: , ISSN: , DOI: 10.5281/zenodo.1479138
1 2020-02-19
2018 Doganis, Philip; Karatzas, Pantelis; Sarimveis, Harry; Dudgeon, Tim; Spjuth, Ola; Farcal, Lucian; Exner, Thomas; Lynch, Iseult; Hardy, Barry
Dissemination & Training Activities - Intermediate Report (Deliverable 3.4)
published pages: , ISSN: , DOI: 10.5281/zenodo.1479648
2 2020-02-19
2018 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
Initial API version provided to providers of services (Deliverable 2.2)
published pages: , ISSN: , DOI: 10.5281/zenodo.1479444
3 2020-02-19
2018 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
Final definition of case studies (Deliverable 1.3)
published pages: , ISSN: , DOI: 10.5281/zenodo.1479127
1 2020-02-19
2018 Samuel Lampa, Jonathan Alvarsson, Staffan Arvidsson Mc Shane, Arvid Berg, Ernst Ahlberg, Ola Spjuth
Predicting Off-Target Binding Profiles With Confidence Using Conformal Prediction
published pages: , ISSN: 1663-9812, DOI: 10.3389/fphar.2018.01256
Frontiers in Pharmacology 9 2020-02-19
2018 Spjuth, Ola; Dudgeon, Tim; Bachler, Daniel; Gebele, Denis; Rautenberg, Micha; Alvarsson, Jonathan; Karatzas, Pantelis; Willighagen, Egon; Evelo, Chris; Martens, Marvin; Exner, Thomas
Report on deployment of virtual infrastructures with service discovery and container orchestration (Deliverable 2.3)
published pages: , ISSN: , DOI: 10.5281/zenodo.1479475
1 2020-02-19
2018 M. Martens, E. Willighagen, P. Nymark, R. Grafström, L.D. Burgoon, H.T. Aladjov, F. Torres Andón, C.T. Evelo
Introducing WikiPathways to link molecular pathways to adverse outcome pathways to support regulatory risk assessment
published pages: S227-S228, ISSN: 0378-4274, DOI: 10.1016/j.toxlet.2018.06.962
Toxicology Letters 295 2020-02-19
2018 T.E. Exner, J. Dokler, D. Bachler, L.R. Farcal, C.T. Evelo, E. Willighagen, D.G.J. Jennen, M. Jabocs, P. Doganis, H. Sarimveis, I. Lynch, G. Gkoutos, S. Kramer, C. Notredame, O. Spjuth, P. Jennings, T. Dudgeon, F. Bois, B. Hardy
OpenRiskNet, an open e-infrastructure to support data sharing, knowledge integration and in silico analysis and modelling in risk assessment
published pages: S104, ISSN: 0378-4274, DOI: 10.1016/j.toxlet.2018.06.617
Toxicology Letters 295 2020-02-19

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