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

Research output: Contribution to journalArticle

Abstract

The aim of the SEURAT-1 (Safety Evaluation Ultimately Replacing Animal Testing-1) research cluster, comprised of seven EU FP7 Health projects co-financed by Cosmetics Europe, is to generate a proof-of-concept to show how the latest technologies, systems toxicology and toxicogenomics can be combined to deliver a test replacement for repeated dose systemic toxicity testing on animals. The SEURAT-1 strategy is to adopt a mode-of-action framework to describe repeated dose toxicity, combining in vitro and in silico methods to derive predictions of in vivo toxicity responses. ToxBank is the cross-cluster infrastructure project whose activities include the development of a data warehouse to provide a web-accessible shared repository of research data and protocols, a physical compounds repository, reference or "gold compounds" for use across the cluster (available via wiki.toxbank.net), and a reference resource for biomaterials. Core technologies used in the data warehouse include the ISA-Tab universal data exchange format, REpresentational State Transfer (REST) web services, the W3C Resource Description Framework (RDF) and the OpenTox standards. We describe the design of the data warehouse based on cluster requirements, the implementation based on open standards, and finally the underlying concepts and initial results of a data analysis utilizing public data related to the gold compounds.

Original languageEnglish
Pages (from-to)47-63
Number of pages17
JournalMolecular Informatics
Volume32
Issue number1
DOIs
Publication statusPublished - Jan 2013

Keywords

  • Alternative Testing Strategies
  • Bioinformatics
  • Cellular models
  • Cheminformatics
  • Data warehouse
  • Databases
  • Electron transport
  • Gene expression
  • OpenTox
  • Oxidation
  • Predictive toxicology
  • Redox chemistry
  • Reference compounds
  • Repeated-dose toxicity testing
  • Semantic web
  • SEURAT-1
  • ToxBank
  • Toxicogenomics
  • Toxicology
  • Wikis

ASJC Scopus subject areas

  • Organic Chemistry
  • Computer Science Applications
  • Drug Discovery
  • Molecular Medicine
  • Structural Biology

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  • Cite this

    Kohonen, P., Benfenati, E., Bower, D., Ceder, R., Crump, M., Cross, K., Grafström, R. C., Healy, L., Helma, C., Jeliazkova, N., Jeliazkov, V., Maggioni, S., Miller, S., Myatt, G., Rautenberg, M., Stacey, G., Willighagen, E., Wiseman, J., & Hardy, B. (2013). The ToxBank data warehouse: Supporting the replacement of in vivo repeated dose systemic toxicity testing. Molecular Informatics, 32(1), 47-63. https://doi.org/10.1002/minf.201200114