Ontology

OpenTox Ontology Description

An ontology is a formal representation of a set of concepts within a domain, and the relationships between those concepts. Within this practical perspective the construction of an ontology consists of: a) selection of entities or objects to be included; b) definition of a controlled vocabulary; c) recognition of hierarchies, when existing.

The definition of ontology and controlled vocabulary in OpenTox is an imperative so as to standardize and organize high-level concepts, chemical information and toxicological data. Distributed OpenTox services exchanging communications need to have unambiguous interpretations of the meaning of any terminology and data that they exchange between each other.

The definition of ontology and controlled vocabulary is also extremely important to the construction of the OpenTox data access and integration services. It contributes to the necessary standardization and rational organization of data, thus facilitating both vertical (e.g., within one toxicological endpoint) and horizontal (e.g., through different endpoints) retrievals.

OpenTox is supporting the creation and curation of OpenToxipedia, a community-based predictive toxicology knowledge resource. All members of the community are welcome to provide term entries and suggested edits or additions to entries in the resource.

OpenTox is working on the evaulation, support and extensions of XML Schema for data management required for computer-based predictive toxicology modelling and reporting.

Endpoints for the OpenTox Ontology are described in the Endpoints section.

The goal of OpenTox is to develop an interoperable predictive toxicology framework with multiple web services providing users access to distributed toxicological resources including data, computer models, validation and reporting. OpenTox applications are based on use cases that satisfy user needs in predictive toxicology. The definition of ontology and controlled vocabulary is extremely important to the construction of the OpenTox data infrastructure. It contributes to the necessary standardization and rational organization of data, describing and linking toxicological endpoints information in a formal way, suitable for being processed automatically by the software, with minimal human interaction.

Besides a ontology for toxicological endpoints and Organs and Effects Ontology, a formal OWL representation of modeling algorithms is available on the OpenTox website http://www.opentox.org/dev/apis/api-1.1/Algorithms.

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.

The toxicological endpoints ontology and Organs and Effects Ontology ontology are also available in OWL from OWL files repository.

Protégé, a free, open source visual ontology editor could be used to open, browse and edit these OWL files.

References:

OpenTox Predictive Toxicology Framework: toxicological ontology and semantic media wiki-based OpenToxipedia, Bio-ontologies 2011. 15-16 July, Vienna, Austria
OpenTox-Bio-ontologies 2011
Bio-ontology 2011

Collaborative Ontology Design and Implementation for the OpenTox Predictive Toxicology Framework, Bio-ontologies 2010, 9-10 July, Boston MA
Poster: Collaborative Ontology Design and Implementation for the Open- Tox Predictive Toxicology Framework
Abstract: Collaborative Ontology Design and Implementation for the Open- Tox Predictive Toxicology Framework