Abstract
Motivation: The field of toxicogenomics (the application of ‘-omics’ technologies to risk assessment of compound toxicities) has expanded in the last decade, partly driven by new legislation, aimed at reducing animal testing in chemical risk assessment but mainly as a result of a paradigm change in toxicology towards the use and integration of genome wide data. Many research groups worldwide have generated large amounts of such toxicogenomics data. However, there is no centralized repository for archiving and making these data and associated tools for their analysis easily available.Results: The Data Infrastructure for Chemical Safety Assessment (diXa) is a robust and sustainable infrastructure storing toxicogenomics data. A central data warehouse is connected to a portal with links to chemical information and molecular and phenotype data. diXa is publicly available through a user-friendly web interface. New data can be readily deposited into diXa using guidelines and templates available online. Analysis descriptions and tools for interrogating the data are available via the diXa portal.Availability and implementation: http://www.dixa-fp7.euContact: d.hendrickx@maastrichtuniversity.nl; info@dixa-fp7.euSupplementary information: Supplementary data are available at Bioinformatics online.
Highlights
During the last decade, technology developments as well as new legislation, ethical considerations and concerns about the reliability and relevance of traditional animal experimentation for toxicity testing, have led to the expansion of the field of toxicogenomics (Hartung, 2009; Sycheva, et al, 2013)
To make sure data are accessible and do not disappear over time, we developed the Data Infrastructure for Chemical Safety Assessment, a database and web interface providing access to toxicogenomics datasets and analysis
Toxicogenomics data are generally deposited in isolation, not as structured sets
Summary
Technology developments as well as new legislation, ethical considerations and concerns about the reliability and relevance of traditional animal experimentation for toxicity testing, have led to the expansion of the field of toxicogenomics (Hartung, 2009; Sycheva, et al, 2013). DiXa aims to overcome these drawbacks by defining standard workflows for data (pre)processing and standard formats for metadata annotation. These standards are applied to the diXa data through servicing. Combining data sets from different sources centrally can provide important information about experimental design and mechanistic interpretations. We describe diXa, a database providing access to toxicogenomics data from different sources and data analysis tools. The ChemAgora portal provides direct access for each compound in the diXa data warehouse to chemical information available on third-party resources (see Supplementary Table S2): the portal, through an on-the-fly search, informs whether a compound has data in each of the external resources, and offers links leading to the exact third-party website pages where information about the compound can be found. Through ChemAgora a search is performed in such third-party repositories, after the mapping of the InChiKey received from the diXa data warehouse into the corresponding CAS Registry Number
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