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Toxicological Ontology

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We develop the OpenTox toxicological endpoints ontology using the DL species of the Web Ontology Language (OWL DL) and the Protégé OWL editor

Several OWL ontology classes are needed to describe different toxicological studies. Each attribute in a toxicological dataset can be associated with an entry in the ontology.

The main OWL classes are “ToxicityStudyType”, “TestSystem” (includes such subclasses as strains, species, sex, route of explosions, etc), “TestResult” (includes such subclasses as toxicity measure, test call, mode of action, etc), “Organs”. 

Our ontology currently possesses 5 toxicity study types: carcinogenicity, mutagenicity, in vivo micronucleus, repeated dose toxicity and aquatic toxicity. One of the more challenging ontology classes is the detailed description of organs starting from organs systems up to up to histological components. Organs ontology is very important for repeated dose toxicity and carcinogenicity endpoints.

It has been decided to follow the OBO Foundry principles  of ontology development that could open a perspective for a fruitful external collaboration in the future. However it is important to say that our domain of interest (Ontology of Toxicological Endpoints) is not yet covered by any existing ontology of OBO Foundry.. There are several neighboring onlologies (such as several anatomy and pathology ontologies) and we could consider to use some parts of them.

We try to integrate the ToxML scheme. It has been proposed to keep the ToxML terminology for giving names to the main classes of OpenTox endpoints ontology. The last Leadscope ToxML release has a very structured scheme for many toxicity studies. After mapping of several databases (carcinogenicity, in vitro mutagenicity, in vivo micronucleus, repeated dose tossicity) onto ToxML we can confirm that the ToxML is well suitable for accommodation of toxicity data. On the other hand, in order to use the ToxML we will need to fill a gap of free text fields, because the Leadscope schema does not contain a standartized vocalularies for many fields, for example, a standard list of organs for TargetSites description is not present in ToxMl. For this reason we started development of organs related subontology as a part of OpenTox toxicological endpoints ontology.


The collaborative work on the project is curated using the Collaborative Protégé Editor Collaborative Protege, with different access privileges . The ontology is open for community reviews and annotations.



Methodology of Toxicological Ontology DevelopmentGraphical rapresentation of Toxicological Ontology

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