Ontologies

Controlled toxicological vocabularies and interrelations (ontologies) have been developed for several toxicological endpoints with the objective of improving the integration of experimental data from different sources in the QSAR Toolbox and facilitating grouping, read-across and data gap filling.

The developed toxicological ontologies can also be used for the creation of new databases aiming to  harmonise terms including the description of organs and effects.

Two projects were funded by the European Chemicals Agency (ECHA), conducted in cooperation with the Organisation for Economic Co-operation and Development (OECD), and executed by Instituto Superiore di Sanita (ISS) and the Fraunhofer Institute between 2012 and 2013.

Controlled toxicological vocabularies have been developed for the following regulatory endpoints:

  • Carcinogenicity
  • Repeated Dose Toxicity
  • Reproductive/Developmental Toxicity
  • Skin irritation/corrosion
  • Eye irritation/corrosion
  • Skin sensitisation

All related experimental toxicological databases included in the QSAR Toolbox (RepDose DB, HESSDB, ToxRef DB, ILSI-Devtox DB, ISSCAN DB, CPDB, Databases for skin/eye irritation corrosion and skin sensitisation) were associated with the controlled toxicological vocabularies including relationships and restriction rules. For each of the above regulatory endpoints, the following tasks were performed:

  • Definition of classes and hierarchical relationships in the ontology structure
  • Compilation of terms related to the endpoint (including terms for organs, effects)
  • Definition of synonymous and homonymous
  • Establishment of relationships, interactions and hierarchies between classes, object and numeric properties for each term and rules when existing (internal rules and restriction rules)
  • Association of each attribute in a toxicological dataset of the QSAR Toolbox with an entry in the ontology

This work on ontologies could enhance the use of standardised vocabulary for data searches within toxicological datasets and facilitate the exchange and integration of databases within platforms such as the QSAR Toolbox. The standardised toxicological ontologies can also be seen as a backbone to the building of Mode of Action/Adverse Outcome Pathway databases in a consistent manner.

Within the process of developing the toxicological ontologies a critical evaluation of all existing related projects was performed including freely available ontologies at the Bioportal Ontology depository, the OpenTox Ontology project and the INHAND initiative.

The OECD Harmonised Templates available as xml schema were used as the basis for the development of the toxicological ontologies and the Web Ontology Language (OWL DL) supported by the Protégé OWL editor was used for the ontology implementation.

The details of the development and content of the ontologies are described in the Final reports:

The ontologies are freely downloadable below for use according to the disclaimer on this website. The Protégé software needs to be installed to view the Ontologies.

For questions regarding the content of this web page you can send an email to:   qsar-toolbox (at) echa.europa.eu

All results or rights in the Ontology Project, including copyright and other intellectual or industrial property rights are owned solely by the European Chemicals Agency (ECHA). For more information, please consult ECHA’s legal notice on this website.