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Public data sources to support systems toxicology applications.

Allan Peter Davis1, Jolene Wiegers1, Thomas C Wiegers1

  • 1Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27695, United States.

Current Opinion in Toxicology
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Summary

Standardizing data from public databases enables systems toxicology by integrating diverse information on chemicals, genes, and diseases to build chemical-induced outcome pathways.

Keywords:
ChemicalData standardDiseaseGenePublic databaseSystems toxicology

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Area of Science:

  • Toxicology
  • Bioinformatics
  • Data Science

Background:

  • Public databases offer extensive data on chemicals, genes, proteins, biological networks, phenotypes, diseases, and exposure science.
  • Integrating this disparate information for systems toxicology is challenging due to varied data representation and access methods across repositories.

Purpose of the Study:

  • To explore public data sources for systems toxicology.
  • To demonstrate the value of data standardization in constructing chemical-induced outcome pathways.

Main Methods:

  • Review and identification of relevant public data repositories.
  • Analysis of data representation and accessibility challenges.
  • Application of standardized vocabularies for data annotation and integration.

Main Results:

  • Identified numerous public data sources applicable to systems toxicology.
  • Highlighted the difficulties in combining data from heterogeneous sources.
  • Showcased how data standardization facilitates pathway construction.

Conclusions:

  • Standardizing data is crucial for effective integration of public information in systems toxicology.
  • This approach aids in the discovery of new findings and the construction of chemical-induced outcome pathways.