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Please provide your service description in the form below. Fields marked with * are mandatory.
Service description
Service name:
*
Tagline:
Description:
Origin:
Third party application
Provided by OpenRiskNet partner(s)
Implementation Challenge
Category:
Ontology services
Omics database
Toxicology, chemical properties and bioassay databases
Site management
API Definitions for OpenRiskNet applications and data
Processing and analysis
Workflow, visualisation and reporting
Knowledge bases and data mining
Predictive toxicology
Service type:
Database / data source
Application
Visualisation tool
Helper tool
Software
Analysis tool
Processing tool
Trained model
Model generation tool
Model
Data mining tool
Service
Workflow tool
Implementation status:
Graphical user interface available
API documentation available (Swagger-OpenAPI v2)
Application programming interface available
Available as web service
Containerised
OAS v3
Technology readiness level:
---------
TRL 1 – basic principles observed
TRL 2 – technology concept formulated
TRL 3 – experimental proof of concept
TRL 4 – technology validated in lab
TRL 5 – technology validated in relevant environment (industrially relevant environment in the case of key enabling technologies)
TRL 6 – technology demonstrated in relevant environment (industrially relevant environment in the case of key enabling technologies)
TRL 7 – system prototype demonstration in operational environment
TRL 8 – system complete and qualified
TRL 9 – actual system proven in operational environment (competitive manufacturing in the case of key enabling technologies; or in space)
Applicability domain:
Ontology
Predictive toxicology
Bioinformatics
Toxicology
Computational modelling
Topic:
Identifier mapping
Bioassay
Chemical properties
Nano safety
Risk assessment
Kinetics
Structure-activity relationship (SAR / QSAR)
Biokinetics
Predictive modelling
Information extraction
Biological area:
Transcriptomics
Omics
Skin sensitisation
Toxicokinetics
Genotoxicity
Mutagenicity
NOAEL/LOAEL
Carcinogenicity
Blood brain barrier
Acute toxicity
Type of users:
Developers
End-users
System admins
Targeted industry:
Other consumer products
Food
Cosmetics
Drugs
Nanotechnology
Chemicals
Targeted users:
Informed public
Regulators
Data managers
Software Developers
Students
Researchers
Risk assessors
Relevant OpenRiskNet case studies:
AOPLink
DataCure
MetaP
ModelRX
RevK
SysGroup
TGX
Licence type:
---------
Open source
Licence:
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Attribution-ShareAlike 4.0 International (CC BY-SA 4.0)
Attribution 4.0 International (CC BY 4.0)
Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)
Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)
Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)
Apache 2.0
GNU Lesser General Public License (LGPL) 2 (LGPLv2.0)
GNU Lesser General Public License 3 (LGPLv3.0)
Is login required:
Service location
Service URL:
Service API URL:
API Type:
OpenAPI
REST
REST under OpenAPI2 specification
Based on Jaqpot API that uses REST under OpenAPI2 specification
SPARQL
REST under OAS3 specification
OAS3
Based on Jaqpot API that uses REST under OpenAPI3 specification
Integration status
Integration status:
---------
Integrated application
Integration in progress
Integration details:
Utilises the OpenRiskNet APIs to ensure that each service is accessible to our proposed interoperability layer:
Unknown
Yes
No
Is annotated according to the semantic interoperability layer concept using defined ontologies:
Unknown
Yes
No
Is containerised for easy deployment in virtual environments of OpenRiskNet instances:
Unknown
Yes
No
Has documented scientific and technical background:
Unknown
Yes
No
Is deployed into the OpenRiskNet reference environment:
Unknown
Yes
No
Is listed in the OpenRiskNet discovery services:
Unknown
Yes
No
Is listed in other central repositories like eInfraCentral, bio.tools and TeSS (ELIXIR):
Unknown
Yes
No
Provides legal and ethical statements on how the service can be used:
Unknown
Yes
No
Provider
Organisation:
*
Name:
Contact details:
Documentation and support
Link to user support service:
User support contact:
Link to documentation:
References:
Resources & training:
ToxicoDB: an integrated database to mine and visualize large-scale toxicogenomic datasets
Final report on the management process (Deliverable 5.2)
Report of the Service Integration with OpenRiskNet - Final Report (Deliverable 4.3)
Final data management, maintenance and sustainability plan (Deliverable 3.6)
Dissemination & Training Activities - Final Report (Deliverable 3.5)
Reference OpenRiskNet system available online (Deliverable 2.6)
Report on the results of the Implementation Challenge (Deliverable 1.4)
Finalization of case studies and analysis of remaining weaknesses (Deliverable 1.5)
Case Study report - Reverse dosimetry and PBPK prediction [RevK]
Case Study report - Toxicogenomics-based prediction and mechanism identification [TGX]
Case Study report - A systems biology approach for grouping compounds [SysGroup]
Case Study report - Identification and Linking of Data related to AOPs of AOP-Wiki [AOPLink]
Case Study report - Data curation and creation of pre-reasoned datasets and searching [DataCure]
Case Study report - Modelling for Prediction or Read Across [ModelRX]
Case Study report - Metabolism Prediction [MetaP]
OpenRiskNet application (Lazar) deployment from the OpenShift Command-Line
OpenRiskNet final workshop report in NanoSafety Cluster Newsletter
Site-of-metabolism prediction in OpenRiskNet
OpenRiskNet Part III: Modelling Services in Chemical/Nano-safety, Environmental Science and Pharmacokinetics
OpenRiskNet Part IV: WEKA Machine Learning Services for the Prediction of Half-Lifes of Chemicals and Nanoparticle Transport
OpenRiskNet Part II: Predictive Toxicology based on Adverse Outcome Pathways and Biological Pathway Analysis
OpenRiskNet Part I: Development of an open e-infrastructure predictive toxicology and risk assessment
Connecting Adverse Outcome Pathways, knowledge and data with AOPLink workflows
Connecting Adverse Outcome Pathways, knowledge and data with AOPLink workflows
AOP-Wiki Resource Description Framework
Compute and data federation (Deliverable 2.5)
Deploying Applications to an OpenRiskNet Virtual Environment
Demonstration on OpenRiskNet approach on modelling for prediction or read across (ModelRX case study)
Deploying Applications to an OpenRiskNet Virtual Environment
Demonstration on OpenRiskNet approach on modelling for prediction or read across (ModelRX case study)
Use Nextflow for toxicogenomics-based prediction
Use Nextflow for toxicogenomics-based prediction
How to describe OpenRiskNet services and their functionality by semantic annotation
How to describe OpenRiskNet services and their functionality by semantic annotation
OpenRiskNet Case Studies report into NanoSafety Cluster Newsletter
AOP-DB: The Adverse Outcome Pathway Database
OpenRiskNet, an open e-infrastructure to support data sharing, knowledge integration and in silico analysis and modelling in predictive toxicology and risk assessment
AOP-DB: The Adverse Outcome Pathway Database
Population pharmacokinetic reanalysis of a Diazepam PBPK model: a comparison of Stan and GNU MCSim
AOPLink - Linking experimental data to Adverse Outcome Pathways
Identification and linking of data related to AOPWiki
Demonstration on data curation and creation of pre-reasoned datasets in the OpenRiskNet framework
Final API available for internal and external service providers (Deliverable 2.4)
Report of the Service Integration with OpenRiskNet (Intermediate Report) (Deliverable 4.2)
Demonstration on data curation
Learn how to deploy the OpenRiskNet virtual research environment
OpenRiskNet e-infrastructure Deployment
Expanding Adverse Outcome Pathway knowledge by creating AOP-Wiki RDF with semantic annotations to facilitate risk assessment of chemicals.
Report on requirements analysis and recommendations for WP2-4 (Deliverable 1.1)
Initial version of data management plan (Deliverable 3.1)
Fully functional support infrastructure (Deliverable 3.3)
Associated partner program is established (Deliverable 1.2)
DeepPVP: phenotype-based prioritization of causative variants using deep learning
WP2 Interoperability, Deployment and Security
WP1 Requirement Analysis, Outreach and Case Studies
WP3 Training, Support, Dissemination
WP4 Service Integration
OpenRiskNet factsheet
Introducing WikiPathways as a data-source to support Adverse Outcome Pathways for regulatory risk assessment of chemicals and nanomaterials
First report on the management process (Deliverable 5.1)
Report on Re-Identification Risks and Private by Design Risk Management (Deliverable 4.4)
Report of the Service Integration with OpenRiskNet - Initial Deployment (Deliverable 4.1)
First documentation of the core e-infrastructure (Deliverable 3.2)
OpenRiskNet webinar: introduction, case studies and demo (Nano WG - Part 1)
OpenriskNet webinar: demonstration on services (Nano WG - Part 2)
Final definition of case studies (Deliverable 1.3)
Initial API version provided to providers of services (Deliverable 2.2)
Dissemination & Training Activities - Intermediate Report (Deliverable 3.4)
Development infrastructure online (Deliverable D2.1)
Report on deployment of virtual infrastructures with service discovery and container orchestration (Deliverable 2.3)
OpenRiskNet case studies and the implementation challenge explained
Predicting off-target binding profiles with confidence using Conformal Prediction
Introduction to OpenRiskNet e-infrastructure
Implementation Challenge and Associated Partner Programme
OpenRiskNet Case Studies
Introduction to OpenRiskNet
Introduction to OpenRiskNet e-infrastructure
Introduction to OpenRiskNet project
Tutorials OpenRiskNet public website
RevK Pharmacokinetics OpenRiskNet Case study using Jaqpot web modelling platform
Model RX OpenRiskNet - Case study using Jaqpot web modelling platform
Building risk assessment workflows with OpenRiskNet
OpenRiskNet, an open e-infrastructure to support data sharing, knowledge integration and in silico analysis and modelling in risk assessment
Biokinetics Modelling: use, form, inputs and outputs of PBPK models
OpenRiskNet e-infrastructure available to end-users
OligoPVP: Phenotype-driven analysis of individual genomic information to prioritize oligogenic disease variants
Workflow: Access TG-GATEs data for selected compounds, select differentially expressed genes and identifier relevant pathways
OpenRiskNet roll-up banner
Meta-analysis for genotoxicity prediction using data from multiple human in vitro cell models
Entering and analysing nano safety data
Introducing WikiPathways to support Adverse Outcome Pathways for regulatory risk assessment
Approaches for containerized scientific workflows in cloud environments with applications in life science
OpenRiskNet flyer
Big Data in Toxicogenomics: Towards FAIR predictions
Browsing the eNM ontology with BioPortal, AberOWL and Protégé
A confidence predictor for logD using conformal regression and a support-vector machine
Adding ontology terms
OpenRiskNet, an open e-infrastructure to support data sharing, knowledge integration and in silico analysis and modelling in risk assessment
The OpenRiskNet Approach towards a Semantic Interoperability Layer - Part One: Problem Definition for Datasets
OpenRiskNet reveals concepts of harmonised APIs and semantic interoperability, provides first training units, and launches Associate Partner Program
Integration and interoperability (conference session)
OpenRiskNet case studies to support data and tools integration from NanoSafety Cluster
Horizon 2020 Research Success Story | OpenRiskNet
A global harmonized basis for testing chemical safety
Semantic prioritization of novel causative genomic variants
Introduction to OpenRiskNet
OpenRiskNet Kicked off
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