Lazar Toxicity Predictions

Toxicity predictions
Lazar (Lazy Structure-Activity Relationships ) takes a chemical structure as input and provides predictions for a variety of toxic properties. Lazar uses an automated and reproducible read across procedure to calculate predictions. Rationales for predictions, applicability domain estimations and validation results are presented in a clear graphical interface for the critical examination by toxicological experts.

For developers
For end-users
Type:
Application, Helper tool, Trained model, Model, Service
API Type:
REST, OpenAPI, REST under OAS3 specification, OAS3
Categories:
Toxicology, chemical properties and bioassay databases, Visualisation and reporting, Processing and analysis
Applicability domain:
Toxicology, Predictive toxicology
Topic:
Chemical properties, Risk assessment, Structure-activity relationship (SAR / QSAR)
Biological area:
Acute toxicity, Blood brain barrier, Carcinogenicity, NOAEL/LOAEL, Mutagenicity
Targeted industry:
Drugs, Cosmetics, Food, Other consumer products, Chemicals
Targeted users:
Risk assessors, Researchers, Students, Software Developers, Informed public
Relevant OpenRiskNet case study:
ModelRX - Modelling for Prediction or Read Across
Support contact:

Provided by:
in silico toxicology gmbh, Johannes Gutenberg Univertity
Licence:
GNU Lesser General Public License 3 (LGPLv3.0)
Login required:
Yes
Implementation status:
Containerised, Graphical user interface available, Available as web service, OAS v3, Application programming interface available
Technology readiness level:
TRL 8 – system complete and qualified
Integration status:
Integrated application
Service integration operations completed:
Utilises the OpenRiskNet APIs to ensure that each service is accessible to our proposed interoperability layer.
Is annotated according to the semantic interoperability layer concept using defined ontologies.
Is containerised for easy deployment in virtual environments of OpenRiskNet instances.
Has documented scientific and technical background.
Is deployed into the OpenRiskNet reference environment.
Is listed in the OpenRiskNet discovery services.
Is listed in other central repositories like eInfraCentral, bio.tools and TeSS (ELIXIR).
Provides legal and ethical statements on how the service can be used.

Resources & Training

Poster
OpenRiskNet Part III: Modelling Services in Chemical/Nano-safety, Environmental Science and Pharmacokinetics
Stefan Kramer, Philip Doganis, Denis Gebele, Atif Raza, Pantelis Karatzas, Haralambos Sarimveis, Jonathan Alvarsson, Ola Spjuth, Staffan Arvidsson, Thomas Exner, Lucian Farcal, Barry Hardy
28 Aug 2019
Abstract:
The OpenRiskNet project (https://openrisknet.org/) is funded by the H2020-EINFRA-22-2016 Programme and its main objective is the development of an open e-infrastructure providing data and software resources and services to a variety of industries requiring risk assessment (e.g. chemicals, cosmetic ingredients, pharma or nanotechnologies). The concept of case studies was followed in order to test and evaluate proposed solutions and is described in https://openrisknet.org/e-infrastructure/development/case-studies/. Two case studies, namely ModelRX and RevK, focus on modelling within risk assessment. The ModelRX – Modelling for Prediction or Read Across case study provides computational methods for predictive modelling and support of existing data suitability assessment. It supports final risk assessment by providing calculations of theoretical descriptors, gap filling of incomplete datasets. computational modelling (QSAR) and predictions of adverse effects. Services are offered through Jaqpot (UI/API), JGU WEKA (API), Lazar (UI) and Jupyter & Squonk Notebooks. In the RevK – Reverse dosimetry and PBPK prediction case study, physiologically based pharmacokinetic (PBPK) models are made accessible for the purpose of risk assessment-relevant scenarios. The PKSim software, the httk R package and custom-made PBPK models have been integrated. RevK offers services through Jaqpot (UI/API).
Related services:
Lazar Toxicity Predictions

Target audience: Risk assessors, Researchers, Students, Nanosafety community, Data modellers, Bioinformaticians
Open access: yes
Licence: Attribution-ShareAlike 4.0 International (CC BY-SA 4.0)
Organisations involved: EwC, JGU, NTUA, UU
Poster
Report
Case Study description - Modelling for Prediction or Read Across [ModelRX]
28 Jun 2019
Abstract:
A training data set will be obtained from an OpenRiskNet data source. The model has then to be trained with OpenRiskNet modelling tools and the resulting model has to be packaged into a container, documented and ontologically annotated. The model will be validated using OECD guidelines. Finally, a prediction can be run.
Additional materials:
Case Study report

Target audience: OpenRiskNet stakeholders
Open access: yes
Licence: Attribution-ShareAlike 4.0 International (CC BY-SA 4.0)
Organisations involved: NTUA
Report
Webinar recording
Demonstration on OpenRiskNet approach on modelling for prediction or read across (ModelRX case study)
Philip Doganis and Haralambos Sarimveis (National Technical University of Athens, Greece)
25 Jun 2019
Related services:
Lazar Toxicity Predictions

Target audience: Risk assessors, Researchers, Data modellers, Bioinformaticians
Open access: yes
Licence: Attribution-ShareAlike 4.0 International (CC BY-SA 4.0)
Organisations involved: NTUA
Webinar recording
Webinar recording
Deploying Applications to an OpenRiskNet Virtual Environment
Tim Dudgeon and Alan Christie (Informatics Matters Ltd, UK)
25 Jun 2019
Related services:
Lazar Toxicity Predictions

Target audience: Developers, Software developers
Open access: yes
Licence: Attribution-ShareAlike 4.0 International (CC BY-SA 4.0)
Organisations involved: IM
Webinar recording
Presentation
Deploying Applications to an OpenRiskNet Virtual Environment
Tim Dudgeon and Alan Christie (Informatics Matters Ltd, UK)
24 Jun 2019
Additional materials:
Slides
Related services:
Lazar Toxicity Predictions

Publisher: OpenRiskNet
Target audience: Developers, Software developers
Open access: yes
Licence: Attribution-ShareAlike 4.0 International (CC BY-SA 4.0)
Organisations involved: IM
Presentation
Presentation
Demonstration on OpenRiskNet approach on modelling for prediction or read across (ModelRX case study)
Philip Doganis and Haralambos Sarimveis (National Technical University of Athens, Greece)
24 Jun 2019
Additional materials:
Slides
Related services:
Lazar Toxicity Predictions

Publisher: OpenRiskNet
Target audience: Risk assessors, Researchers, Students, Data modellers, Bioinformaticians
Open access: yes
Licence: Attribution-ShareAlike 4.0 International (CC BY-SA 4.0)
Organisations involved: NTUA
Presentation
Webinar recording
How to describe OpenRiskNet services and their functionality by semantic annotation
Thomas Exner (Edelweiss Connect GmbH, Switzerland)
15 May 2019
Related services:
Lazar Toxicity Predictions

Publisher: OpenRiskNet
Target audience: Developers, Software developers
Open access: yes
Licence: Attribution-ShareAlike 4.0 International (CC BY-SA 4.0)
Organisations involved: EwC
Webinar recording
Presentation
How to describe OpenRiskNet services and their functionality by semantic annotation
Thomas Exner (EwC)
13 May 2019
Additional materials:
Slides
Related services:
Lazar Toxicity Predictions

Target audience: Developers, Software developers, Data providers
Open access: yes
Licence: Attribution-ShareAlike 4.0 International (CC BY-SA 4.0)
Organisations involved: EwC
Presentation
Presentation
WP4 Service Integration
13 Dec 2018
Additional materials:
WP4 presentation

Open access: yes
Licence: Attribution-ShareAlike 4.0 International (CC BY-SA 4.0)
Organisations involved: EwC, JGU, CRG, UM, UoB, NTUA, Fraunhofer, UU, VU, IM, INERIS
Presentation
Report
Report of the Service Integration with OpenRiskNet - Initial Deployment (Deliverable 4.1)
Jennen, Danyel; Dudgeon, Tim; Sarimveis, Haralambos; Doganis, Philip; Karatzas, Pantelis; Rautenberg, Micha; Willighagen, Egon; Exner, Thomas
12 Nov 2018
Abstract:
Tis report describes the status of selection of services of high priority for the OpenRiskNet infrastructure and their integration including active services provided by the consortium, associated partners and other third parties.
Related services:
Lazar Toxicity Predictions

Publisher: OpenRiskNet
Target audience: Risk assessors, Developers, Data modellers
Open access: yes
Licence: Attribution-ShareAlike 4.0 International (CC BY-SA 4.0)
Organisations involved: EwC, JGU, UM, NTUA, IM
Report
Report
Initial API version provided to providers of services (Deliverable 2.2)
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
7 Nov 2018
Abstract:
This document reports the work towards the first version of the OpenRiskNet application programming interfaces (APIs) to be released to all partners of the consortium and associated partners for feedback and usage. Based on the diversity of the requirement foreseeable when developing the case studies to validate the infrastructure with real-world applications across all areas of predictive toxicology and risk assessment, a bottom-up approach to start with existing APIs and then harmonize them and bring them collectively to higher levels by integrating richer scientific annotation (semantic interoperability layer) was adopted in contrast to a top-down approach, where the API specification is defined by the consortium first and then all services have to be changed to comply to this specification.

Publisher: OpenRiskNet
Target audience: Developers, Software developers
Open access: yes
Licence: Attribution-ShareAlike 4.0 International (CC BY-SA 4.0)
Organisations involved: EwC, JGU, UM, NTUA, UU, IM, INERIS
Report
Report
Report on deployment of virtual infrastructures with service discovery and container orchestration (Deliverable 2.3)
Spjuth, Ola; Dudgeon, Tim; Bachler, Daniel; Gebele, Denis; Rautenberg, Micha; Alvarsson, Jonathan; Karatzas, Pantelis; Willighagen, Egon; Evelo, Chris; Martens, Marvin; Exner, Thomas
7 Nov 2018
Abstract:
This report documents the Demonstrator for the Deliverable 2.3, describing the deployment of virtual infrastructure and applications making up the OpenRiskNet Virtual Research Environment (VRE). It outlines the system analysis, deployment fundamentals, service discovery, and a list of the currently available services. The production reference instance is deployed on the Swedish Science Cloud (SSC), and end user access is available at https://home.prod.openrisknet.org.
Related services:
Lazar Toxicity Predictions

Publisher: OpenRiskNet
Target audience: Developers, Software developers
Open access: yes
Licence: Attribution-ShareAlike 4.0 International (CC BY-SA 4.0)
Organisations involved: EwC, JGU, UM, NTUA, UU, IM
Report