OpenTox predictive toxicology framework: toxicological ontology and semantic media wiki-based OpenToxipedia

Abstract

BackgroundThe OpenTox Framework, developed by the partners in the OpenTox project (http://www.opentox.org), aims at providing a unified access to toxicity data, predictive models and validation procedures. Interoperability of resources is achieved using a common information model, based on the OpenTox ontologies, describing predictive algorithms, models and toxicity data. As toxicological data may come from different, heterogeneous sources, a deployed ontology, unifying the terminology and the resources, is critical for the rational and reliable organization of the data, and its automatic processing.ResultsThe following related ontologies have been developed for OpenTox: a) Toxicological ontology – listing the toxicological endpoints; b) Organs system and Effects ontology – addressing organs, targets/examinations and effects observed in in vivo studies; c) ToxML ontology – representing semi-automatic conversion of the ToxML schema; d) OpenTox ontology– representation of OpenTox framework components: chemical compounds, datasets, types of algorithms, models and validation web services; e) ToxLink–ToxCast assays ontology and f) OpenToxipedia community knowledge resource on toxicology terminology.OpenTox components are made available through standardized REST web services, where every compound, data set, and predictive method has a unique resolvable address (URI), used to retrieve its Resource Description Framework (RDF) representation, or to initiate the associated calculations and generate new RDF-based resources.The services support the integration of toxicity and chemical data from various sources, the generation and validation of computer models for toxic effects, seamless integration of new algorithms and scientifically sound validation routines and provide a flexible framework, which allows building arbitrary number of applications, tailored to solving different problems by end users (e.g. toxicologists).AvailabilityThe OpenTox toxicological ontology projects may be accessed via the OpenTox ontology development page http://www.opentox.org/dev/ontology; the OpenTox ontology is available as OWL at http://opentox.org/api/1 1/opentox.owl, the ToxML - OWL conversion utility is an open source resource available at http://ambit.svn.sourceforge.net/viewvc/ambit/branches/toxml-utils/

The eNanoMapper database for nanomaterial safety information

“…Once a developer (possibly third-party) has prepared a JPDIcompliant web service, they need to register it to the eNanoMapper framework and specify (i) the name of the algorithm, (ii) metadata for the algorithm, such as a description, tags, copyright notice, bibliographic references and any other metadata supported by the Dublin core ontology (http://dublincore.org/) and/or the OpenTox ontology [52], (iii) the URI of their implementation to be used as an endpoint for training, (iv) the corresponding URI for the prediction web service, (v) an ontological characterization of the algorithm according to the OpenTox Algorithms ontology (e.g., "ot:Regression" or "ot:Classification", or "ot:Clustering" (http://www.opentox.org/ dev/apis/api-1.1/Algorithms), and (vi) a set of tuning parameter definitions, optional or mandatory, that the client may provide during training. The algorithm is then registered by POSTing a JSON document containing all this information to "/algorithm".…”

The ToxBank Data Warehouse: Supporting the Replacement of In Vivo Repeated Dose Systemic Toxicity Testing

“…In developing infrastructure, such as the data warehouse, the project is taking advantage of existing open standards, particularly the OpenTox project. [16,17,[27][28][29][30][31] OpenTox developed a standard framework for interoperable predictive toxicology support. [27] It makes extensive use of REpresentational State Transfer (REST)-based web services [32] for interaction with different geographically distributed services necessary to support predictive toxicology data management, algorithms, modeling, validation, and reporting.…”

“…This design is expected to facilitate adding new services of any kind, for example supporting different data types. ToxBank adopts the OpenTox framework design, [27][28][29][30][31] based on the following technological choices (i) the REpresentational State Transfer (REST) [32] software architecture style allowing platform and programming language independence and facilitating the implementation of new data and processing components; (ii) a formally defined common information model, based on the W3C Resource Description Framework (RDF) [45] and communication through well-defined interfaces ensuring interoperability of the web components; (iii) authentication and authorization, allowing defining access policies of REST resources, based on OpenAM; [46] (iv) 4store (http://4store.org) triple store as a backend for the investigation service. The protocol services use MySQL relational database as a backend.…”

“…RDF is the W3C proposed technology to link data on web pages, small resources or large databases, in a unified way. These Linked Resource or Semantic Web approaches are being adopted by the international life sciences community, such as the Health Care & Life Science interest group, [48] and EU projects such as OpenTox [27][28][29][30][31] and Open PHACTS. [49] The standards support many different applications; by adopting them we ensure that ToxBank will be fully interoperable with many other life science projects.…”

Open Source Software and Web Services for Designing Therapeutic Molecules

“…Recent research also suggests that open collaborative drug discovery will be the future paradigm of biomedical research [18][19][20]. In order to overcome the limitations of existing approaches, open source/ freely available software have been developed by different organizations like OpenTox [21], OSDD (Open Source Drug Discovery), CDD [22], Blue Obelisk [23] etc. In past, number of reviews had been published in this area.…”