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For developers
Database / data source, Data mining tool, Service
API Type:
REST under OpenAPI2 specification, REST, OpenAPI, REST under OAS3 specification, OAS3
Toxicology, chemical properties and bioassay databases, Knowledge bases and data mining
Applicability domain:
Chemical properties, Risk assessment, Information extraction
Biological area:
Genotoxicity, Mutagenicity, Carcinogenicity, Acute toxicity
Targeted industry:
Drugs, Cosmetics, Food, Chemicals
Targeted users:
Software Developers
Relevant OpenRiskNet case studies:
  • DataCure - Data curation and creation of pre-reasoned datasets and searching
  • SysGroup - A systems biology approach for grouping compounds
  • TGX - Toxicogenomics-based prediction and mechanism identification
Support contact:

Provided by:
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Implementation status:
API documentation available (Swagger-OpenAPI v2), OAS v3, Available as web service, Application programming interface available
Technology readiness level:
TRL 7 – system prototype demonstration in operational environment
Integration status:
Integration in progress
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, and TeSS (ELIXIR).
Provides legal and ethical statements on how the service can be used.

Resources & Training

Case Study report - Data curation and creation of pre-reasoned datasets and searching [DataCure]
Noffisat Oki (EwC), Thomas Exner (EwC), Tim Dudgeon (IM), Danyel Jennen (UM), Marc Jacobs (Fraunhofer), Marvin Martens (UM), Philip Doganis, Pantelis Karatzas (NTUA)
11 Dec 2019
DataCure establishes a process for data curation and annotation that makes use of APIs (eliminating the need for manual file sharing) and semantic annotations for a more systematic and reproducible data curation workflow. In this case study, users are provided with capabilities to allow access to different OpenRiskNet data sources and target specific entries in an automated fashion for the purpose of identifying data and metadata associated with a chemical in general to identify possible areas of concern or for a specific endpoint of interest (Figure 1B). The datasets can be curated using OpenRiskNet workflows developed for this case study and, in this way, cleansed e.g. for their use in model development (Figure 1A). Text mining facilities and workflows are also included for the purposes of data searching, extraction and annotation (Figure 1C). A first step in this process was to define APIs and provide the semantic annotation for selected databases (e.g. FDA datasets, ToxCast/Tox21 and ChEMBL). During the preparation for these use cases, it became clear that the existing ontologies do not cover all requirements of the semantic interoperability layer. Nevertheless, the design of the annotation process as an online or an offline/preprocessing step forms an ancillary part of this case study even though the ontology development and improvement cannot be fully covered by OpenRiskNet and is instead organized as a collaborative activity of the complete chemical and nano risk assessment community.
Additional materials:

Target audience: Risk assessors, Researchers, Data managers, Data owners, OpenRiskNet stakeholders, Data modellers, Bioinformaticians, Data providers
Open access: yes
Licence: Attribution-ShareAlike 4.0 International (CC BY-SA 4.0)
Organisations involved: EwC, UM, NTUA, Fraunhofer, IM