EdelweissData serving ToxCast, ToxRefDB and TG-GATEs data

Collection of toxicological data sources exposed via OpenTox
Three of the most popular toxicologic open data sources are already publically available: the EPA's in vitro ToxCast/Tox21 database, the EPA's in vivo ToxRefDB database and the NIBIOHN's toxicogenomics Open TG-Gates database. We have made the data accessible online via the internet in real time as a REST style API. Such APIs can easily be consumed by a wide range of workflow tools (e.g. KNIME, Garuda) and programming languages (e.g. R, Python or Javascript).

For end-users
Database / data source, Application, Service
API Type:
Omics database, Toxicology, chemical properties and bioassay databases
Applicability domain:
Computational modelling, Toxicology, Bioinformatics, Predictive toxicology
Chemical properties, Risk assessment
Biological area:
Omics, NOAEL/LOAEL, Acute toxicity
Targeted industry:
Drugs, Chemicals
Targeted users:
Risk assessors, Researchers, Students
Relevant OpenRiskNet case study:
DataCure - Data curation and creation of pre-reasoned datasets and searching

Provided by:
Edelweiss Connect
Attribution 4.0 International (CC BY 4.0)
Login required:
Implementation status:
API documentation available (Swagger-OpenAPI v2), Graphical user interface available, Available as web service
Technology readiness level:
TRL 6 – technology demonstrated in relevant environment (industrially relevant environment in the case of key enabling technologies)
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

Webinar recording
Demonstration on data curation and creation of pre-reasoned datasets in the OpenRiskNet framework
Noffisat Oki (Edelweiss Connect GmbH, Switzerland), Danyel Jennen (Department of Toxicogenomics, Maastricht University, The Netherlands), Marc Jacobs (Fraunhofer Institute, Germany) and Tim Dudgeon (Informatics Matters Ltd, UK)
26 Mar 2019

Publisher: OpenRiskNet
Target audience: Risk assessors, Researchers, Students, Data managers, Data owners, Data modellers, Bioinformaticians, Data providers
Open access: yes
Licence: Attribution-ShareAlike 4.0 International (CC BY-SA 4.0)
Organisations involved: EwC, UM, Fraunhofer, IM
Webinar recording
Workflow: Access TG-GATEs data for selected compounds, select differentially expressed genes and identifier relevant pathways
Thomas Exner
13 Sep 2018
Example workflow based on OpenRiskNet tools - Pathway identification workflow related to DataCure and AOPlink case studies. This notebook downloads TG-Gates data of 4 compounds and selects genes overexpressed in all sample. The Affymetrix probe sets are then translated into Ensembl gene identifiers using the BridgeDB service and pathways associated with the genes are identified using the WikiPathways service.

Publisher: OpenRiskNet
Target audience: Risk assessors, Researchers, Data modellers
Open access: yes
Licence: Attribution-ShareAlike 4.0 International (CC BY-SA 4.0)
Organisations involved: EwC