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

Deliverables

Initial API version provided to providers of services

First version of the OpenRiskNet APIs will be released to all partners of the consortium and associated partners for feedback and usage.

Report on deployment of virtual infrastructures with service discovery and container orchestration

Key components of OpenRiskNet e-infrastructure, including the live virtual instance for testing and the service discovery, will be online and documented in the report.

Fully functional support infrastructure

Support infrastructure will be fully functional and in operation.

Reference OpenRiskNet system available online

The reference OpenRiskNet instance will be fully operable and accessible to demonstrate the functionalities to new users. Additionally, all components will be available in containerized form for easy deployment.

Development infrastructure online

Computational infrastructure for the development and testing of the virtual environments, APIs and data and software integration will be completely set up.

Dissemination & Training Activities (Final Report)

Final report on the dissemination and training activities will be filed.

First report on the management process

First report summarizing the management process will be filed.

Report of the Service Integration with OpenRiskNet (Final Report)

This report will describe the status of the service integration including numbers of active services provided by the consortium, associated partners and other third parties.

Report on requirement analysis and recommendations for WP2-4 including Data Management Plan

The report will describe the results obtained from the interviews and interactions with associated partners and projects as part of the requirement analysis.

Final report on the management process

Final report summarizing the management process will be filed.

Report of the Service Integration with OpenRiskNet (Intermediate Report)

This report will describe the status of the service integration including numbers of active services provided by the consortium, associated partners and other third parties.

Data management, maintenance and sustainability plan

Final data management plan as well as maintenance and sustainability plan will be filed.

Report of the Service Integration with OpenRiskNet (Initial Deployment)

This report will describe the status of the service integration including active services provided by the consortium, associated partners and other third parties.

First documentation of the core e-infrastructure

First documentation of the core e-infrastructure with examples of prototype implementations will be delivered. This documentation will be updated throughout the project.

Report on Re-Identification Risks and Private by Design Risk Management

The report will cover possible risk with respect to security, privacy and re-identification of personal data as well as present the private by design risk management concept.

Report on the results of the Implementation Challenge

This report will summarize the selected data sources and software tools identified by the implementation challenge to be supported by OpenRiskNet partners and the status of their implementation.

Dissemination & Training Activities (Intermediate Report)

Intermediate report on the dissemination and training activities will be filed.

Initial version of data management plan

Initial version of the data management plan will been delivered.

Compute and data federation

Interoperability of data and software tools will be established and applied to the case studies.

Associated partner program is established

Rules for the associated partner program will be defined, formalized, legally approved and accepted by the consortium.

Final definition of case studies

Case studies for testing the usability of the infrastructure in state-of-the-art research will be defined.

Finalization of case studies and analysis of remaining weaknesses

All case studies will have been finalized and remaining challenges will be identified. Measures to solve these challenges, especially with respect to the regulatory usage of the workflows developed in the case studies will be outlined.

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Publications

OpenRiskNet, an open e-infrastructure to support data sharing, knowledge integration and in silico analysis and modelling in risk assessment

Author(s): 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
Published in: SOT 2018 (Society of Toxicology 57th Annual Meeting and ToxExpo), Issue 1, 2018
DOI: 10.5281/zenodo.1199286

Towards Semantic Interoperability of Publicly Available Data

Author(s): Exner, Thomas
Published in: OpenTox USA, 2017
DOI: 10.5281/zenodo.831444

Towards Semantic Interoperability of Publicly Available Data

Author(s): Thomas Exner
Published in: OpenTox Euro 2017, 2017

Nextflow for chemistry - crossing the divide

Author(s): Tim Dudgeon
Published in: Nextflow workshop, 2017

The OpenRiskNet Project

Author(s): Thomas Exner
Published in: OpenTox Euro 2017, 2017

If we all jump together, could we make the earth move?

Author(s): Chris Evelo
Published in: OpenTox Euro 2017, 2017

Characterisation of intrinsic and extrinsic nanomaterial characteristics: the need for relevant exposure media supplemented with appropriate biomolecules

Author(s): Iseult Lynch
Published in: OpenTox Euro 2017, 2017

The future of regulatory toxicity assessment: Adverse Outcome Pathways

Author(s): Marvin Martens, Chris Evelo, Egon Willighagen
Published in: ByteMAL (Bioinformatics for Young inTernational researchers Expo: Maastricht-Aachen-Liège), 2017

Enriching Key Events in Adverse Outcome Pathways with links to biomolecular databases to allow experimental data analysis for regulatory risk assessment

Author(s): Marvin Martens
Published in: OpenTox Euro 2017, 2017

Data-intensive bioinformatics on HPC and Cloud

Author(s): Ola Spjuth
Published in: COST-CHARME 'Big Data Training School for Life Sciences', 2017

Data-intensive applications on cloud computing resources: Applications in life sciences

Author(s): Ola Spjuth
Published in: 2nd international de.NBI symposium, 2017

Jaqpot: an open source web platform for modelling and model publishing integrated into a safety assessment e-infrastructure

Author(s): Philip Doganis, Georgia Tsiliki, Charalampos Chomenidis, Angelos Valsamis, George Drakakis, Evangelia Anagnostopoulou, Haralambos Sarimveis
Published in: Open Science Fair 2017, 2017

Semantic prioritization of novel causative genomic variants

Author(s): 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
Published in: PLOS Computational Biology, Issue 13/4, 2017, Page(s) e1005500, ISSN 1553-7358
DOI: 10.1371/journal.pcbi.1005500

A confidence predictor for logD using conformal regression and a support-vector machine

Author(s): Maris Lapins, Staffan Arvidsson, Samuel Lampa, Arvid Berg, Wesley Schaal, Jonathan Alvarsson, Ola Spjuth
Published in: Journal of Cheminformatics, Issue 10/1, 2018, ISSN 1758-2946
DOI: 10.1186/s13321-018-0271-1

OpenRiskNet, an open e-infrastructure to support data sharing, knowledge integration and in silico analysis and modelling in risk assessment

Author(s): 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
Published in: Toxicology Letters, Issue 295, 2018, Page(s) S104, ISSN 0378-4274
DOI: 10.1016/j.toxlet.2018.06.617

Meta-analysis for genotoxicity prediction using data from multiple human in vitro cell models

Author(s): J.R. Bayjanov, J.C. Kleinjans, D.G.J. Jennen
Published in: Toxicology Letters, Issue 295, 2018, Page(s) S100-S101, ISSN 0378-4274
DOI: 10.1016/j.toxlet.2018.06.608

Introducing WikiPathways to link molecular pathways to adverse outcome pathways to support regulatory risk assessment

Author(s): M. Martens, E. Willighagen, P. Nymark, R. Grafström, L.D. Burgoon, H.T. Aladjov, F. Torres Andón, C.T. Evelo
Published in: Toxicology Letters, Issue 295, 2018, Page(s) S227-S228, ISSN 0378-4274
DOI: 10.1016/j.toxlet.2018.06.962

Predicting Off-Target Binding Profiles With Confidence Using Conformal Prediction

Author(s): Samuel Lampa, Jonathan Alvarsson, Staffan Arvidsson Mc Shane, Arvid Berg, Ernst Ahlberg, Ola Spjuth
Published in: Frontiers in Pharmacology, Issue 9, 2018, ISSN 1663-9812
DOI: 10.3389/fphar.2018.01256

OligoPVP: Phenotype-driven analysis of individual genomic information to prioritize oligogenic disease variants

Author(s): Imane Boudellioua, Maxat Kulmanov, Paul N. Schofield, Georgios V. Gkoutos, Robert Hoehndorf
Published in: Scientific Reports, Issue 8/1, 2018, ISSN 2045-2322
DOI: 10.1038/s41598-018-32876-3

DeepPVP: phenotype-based prioritization of causative variants using deep learning.

Author(s): Boudellioua, Imane; Kulmanov, Maxat; Schofield, Paul N.; Gkoutos, Georgios V.; Hoehndorf, Robert
Published in: BMC Bioinformatics, Vol 20, Iss 1, Pp 1-8 (2019), Issue 4, 2019, ISSN 1471-2105
DOI: 10.17863/CAM.36763

Development infrastructure online (Deliverable D2.1)

Author(s): Dudgeon, Tim; Spjuth, Ola; Bois, Frederic; Bachler, Daniel
Published in: Issue 1, 2018
DOI: 10.5281/zenodo.1479138

Final definition of case studies (Deliverable 1.3)

Author(s): 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
Published in: Issue 1, 2018
DOI: 10.5281/zenodo.1479127

Report on deployment of virtual infrastructures with service discovery and container orchestration (Deliverable 2.3)

Author(s): Spjuth, Ola; Dudgeon, Tim; Bachler, Daniel; Gebele, Denis; Rautenberg, Micha; Alvarsson, Jonathan; Karatzas, Pantelis; Willighagen, Egon; Evelo, Chris; Martens, Marvin; Exner, Thomas
Published in: Issue 1, 2018
DOI: 10.5281/zenodo.1479475

Dissemination & Training Activities - Intermediate Report (Deliverable 3.4)

Author(s): Doganis, Philip; Karatzas, Pantelis; Sarimveis, Harry; Dudgeon, Tim; Spjuth, Ola; Farcal, Lucian; Exner, Thomas; Lynch, Iseult; Hardy, Barry
Published in: Issue 2, 2018
DOI: 10.5281/zenodo.1479648

Initial API version provided to providers of services (Deliverable 2.2)

Author(s): 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
Published in: Issue 3, 2018
DOI: 10.5281/zenodo.1479444

Final API available for internal and external service providers (Deliverable 2.4)

Author(s): Bachler, Daniel; Dokler, Joh; Dudgeon, Tim; Willighagen, Egon; Karatzas, Pantelis; Lynch, Iseult; Hardy, Barry; Exner, Thomas
Published in: Issue 2, 2019
DOI: 10.5281/zenodo.2597061

Fully functional support infrastructure (Deliverable 3.3)

Author(s): Spjuth, Ola; Farcal, Lucian; Lynch, Iseult; Dudgeon, Tim; Exner, Thomas
Published in: Issue 2, 2018
DOI: 10.5281/zenodo.2558121

Report of the Service Integration with OpenRiskNet (Intermediate Report) (Deliverable 4.2)

Author(s): 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
Published in: Issue 5, 2018
DOI: 10.5281/zenodo.2596998

First documentation of the core e-infrastructure (Deliverable 3.2)

Author(s): Dudgeon, Tim; Christie, Alan; Bachler, Daniel; Farcal, Lucian; Sarimveis, Harry; Doganis, Philip; Karatzas, Pantelis; Spjuth, Ola; Lynch, Iseult; Hardy, Barry
Published in: Issue 1, 2018
DOI: 10.5281/zenodo.1483397

Compute and data federation (Deliverable 2.5)

Author(s): Floden, Evan; Lloret-Villas, Audald; Di Tommaso, Paolo; Spjuth, Ola; Farcal, Lucian; Dudgeon, Tim; Jennen, Danyel
Published in: Issue 2, 2019
DOI: 10.5281/zenodo.3256306

Initial version of data management plan (Deliverable 3.1)

Author(s): Farcal, Lucian; Florean, Oana; Doganis, Philip; Jennen, Danyel; Willighagen, Egon; Martens, Marvin; Bachler, Daniel; Oki, Noffisat; Exner, Thomas
Published in: Issue 1, 2018
DOI: 10.5281/zenodo.2558116

Associated partner program is established (Deliverable 1.2)

Author(s): Farcal, Lucian; Lynch, Iseult; Exner, Thomas
Published in: Issue 5, 2018
DOI: 10.5281/zenodo.2557741

Report of the Service Integration with OpenRiskNet - Initial Deployment (Deliverable 4.1)

Author(s): Jennen, Danyel; Dudgeon, Tim; Sarimveis, Haralambos; Doganis, Philip; Karatzas, Pantelis; Rautenberg, Micha; Willighagen, Egon; Exner, Thomas
Published in: Issue 2, 2018
DOI: 10.5281/zenodo.1484309

First report on the management process (Deliverable 5.1)

Author(s): Farcal , Lucian; Exner, Thomas; Hardy, Barry
Published in: Issue 5, 2018
DOI: 10.5281/zenodo.1484358

Report on Re-Identification Risks and Private by Design Risk Management (Deliverable 4.4)

Author(s): Farcal, Lucian; Exner, Thomas
Published in: Issue 5, 2018
DOI: 10.5281/zenodo.1484319

Report on requirements analysis and recommendations for WP2-4 (Deliverable 1.1)

Author(s): Farcal, Lucian; Bachler, Daniel; Dokler, Joh; Exner, Thomas
Published in: Issue 4, 2018
DOI: 10.5281/zenodo.2557731