The ToxBank Data Warehouse

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

Pekka Kohonen, Emilio Benfenati, David Bower, Rebecca Ceder, Michael Crump, Kevin Cross, Roland C. Grafström, Lyn Healy, Christoph Helma, Nina Jeliazkova, Vedrin Jeliazkov, Silvia Maggioni, Scott Miller, Glenn Myatt, Michael Rautenberg, Glyn Stacey, Egon Willighagen, Jeff Wiseman, Barry Hardy

ToxBank is the cross-cluster infrastructure project whose activities include the development of the ToxBank Data Warehouse (TBDW), the selection of reference gold compounds to support the mode-of-action framework, a physical compounds repository, and resources to support the reliable use of qualified biomaterials and protocols.

ToxBank Data Warehouse

The ToxBank data warehouse provides a web-accessible shared repository of know-how and experimental results to support the SEURAT-1 cluster. The information within the TBDW is uploaded from the research activities of the cluster partners as well as relevant data and protocols from other sources, such as public databases containing toxicogenomics data. You can apply for access >> HERE <<.

Gold Compounds Wiki

The underlying assumption of the SEURAT-1 strategy is that we can identify MOAs that are demonstrably relevant to human toxicity based on existing knowledge such as from adverse events of marketed drugs in humans. To tackle the enormous breadth of chemical space in compound selection, we concentrate on a limited number of basic MOAs of toxicity. The SEURAT-1 goal then becomes to establish in vitro assays to characterize and represent these MOAs. Other issues such as prediction of exposure or absorption, distribution, metabolism, and excretion properties although critical to predicting human toxicity, are not determining factors per se for compound selection. A limitation of an MOA-based strategy is that our understanding of MOAs for even the best-known toxicants is incomplete. The challenge and the opportunity are to select compounds that will enable us to increase our understanding of MOAs. Approved compound-related information is made publically available through the ToxBank wiki.

Physical compound repository

ToxBank is also responsible for the collection of all chemicals and physical properties for the evaluated standards. A framework for data quality control was followed in order to guarantee the reliability and uniformity of the collected data and their sources.

Biomaterials resources

The ToxBank cell and tissue bank will provide an important open source service to specifically enable SEURAT-1 to identify suitable sources of cell lines that will meet scientific criteria, ensure compliance with EU and national regulations and provide assays which can be taken up by industry without delays or blocks due to adverse constraints on commercial exploitation. This work utilizes standards recently developed as consensus amongst stem cell scientists and biobanks. The standards established will be used in ToxBank to develop evaluation criteria for suppliers of stem cell lines. Data from these suppliers will be used to demonstrate compliance with best practices.


In developing infrastructure, such as the data warehouse, the project is taking advantage of existing open standards, particularly the OpenTox project. OpenTox developed a standard framework for interoperable predictive toxicology support. It makes extensive use of REpresentational State Transfer (REST)-based web services for interaction with different geographically distributed services necessary to support predictive toxicology data management, algorithms, modeling, validation, and reporting. Extensions were made to the OpenTox framework to support additional activities needing services by ToxBank within SEURAT-1.

Open standards and the semantic web

ToxBank uses the Investigation/Study/Assay (ISA) infrastructure open source desktop software suite. Ontologies and a domain-specific ToxBank keyword hierarchy are used to enrich datasets by adding enough experimental metadata to make the archives comprehensible and reusable. The ISA2RDF tool developed by ToxBank builds on the ISA-Tab framework and facilitates conversion of investigation meta-data into the semantic web standard RDF format.

Integrated data analysis

The data in the TBDW is being collected to enable a cross-cluster integrated data analysis leading to the prediction of repeated dose toxicity within an MOA framework, based on a detailed understanding of the technologies, requirements and work practices developed across the cluster. Semantic web technologies are likely to be useful for integration of internal information from SEURAT-1 with external information from database resources around the world.

Our goal is to enable our partners and customers to develop and market smarter products contributing to a sustainable and safer society and environment.


The research leading to these results has received funding from the European Community’s Seventh Framework Programme (FP7/2007–2013) under Grant Agreement n° [267042]. The research leading to these results has received financing from Cosmetics Europe. We would like to thank Dr. Scott Auerbach from the NIEHS for providing information on the DrugMatrix database and Drs. Susanna-Assunta Sansone, Philippe Rocca-Serra and Eamonn Maguire for their help with the ISA-Tab and ISAcreator software. We would also like to acknowledge our appreciation of SEURAT-1 partners who collaborated on the requirements gathering, Dr. Brigitte Landesmann, and the Gold Compound Working Group.