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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
Applicability domain:
Chemical properties, Risk assessment, Information extraction
Biological area:
Carcinogenicity, Mutagenicity, Genotoxicity, Acute toxicity
Targeted industry:
Food, Cosmetics, Drugs, Chemicals
Targeted users:
Software Developers
Relevant OpenRiskNet case study:
DataCure - Data curation and creation of pre-reasoned datasets and searching
Support contact:

Provided by:
Login required:
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 description - Data curation and creation of pre-reasoned datasets and searching [DataCure]
10 May 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 or other endpoint of interest. The datasets can be curated using an OpenRiskNet services developed for this case study and re-submitted to the data source. Text mining facilities and workflows are also included for the purposes of data searching, extraction and annotation. A first step in this process was to define APIs and provide the semantic annotation for selected databases (e.g. diXa, FDA datasets, ToxCast 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. Therefore, ontology development and design of the annotation process as an online or an offline/preprocessing step form an ancillary part of this case study.
Additional materials:
Case Study report
Related services:
ToxCast/Tox21 V3.2

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, UoB, NTUA, Fraunhofer, IM