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The Comparative Toxicogenomics Database: update 2019.

Allan Peter Davis1, Cynthia J Grondin1, Robin J Johnson1

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The Comparative Toxicogenomics Database (CTD) now features a chemical-phenotype module for exploring chemical effects on health. This update enhances data integration and provides new tools for understanding environmentally influenced diseases.

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Area of Science:

  • Toxicogenomics
  • Environmental Health Sciences
  • Computational Biology

Background:

  • The Comparative Toxicogenomics Database (CTD) is a vital resource for manually curated, literature-based associations.
  • It links chemicals, gene products, phenotypes, diseases, and environmental exposures.
  • CTD supports research into environmentally influenced diseases.

Purpose of the Study:

  • To report biennial updates to the CTD resource.
  • To introduce a new chemical-phenotype module for exploring chemical-induced effects.
  • To enhance data content, functionality, and user accessibility.

Main Methods:

  • Manual curation of literature-based associations using controlled vocabularies.
  • Development of a new chemical-phenotype module.
  • Integration of new data, including an updated MEDIC disease vocabulary.
  • Upgrades to computational infrastructure.

Main Results:

  • A new chemical-phenotype module enables exploration of pre-disease states and adverse outcome pathways.
  • A 46% increase in CTD manually curated content, resulting in over 38 million toxicogenomic relationships.
  • Enhanced chemical-exposure science module with improved querying and display features.
  • An updated MEDIC disease vocabulary with over 1700 new terms.

Conclusions:

  • CTD updates significantly expand its data content and functionality.
  • The new module and enhanced features facilitate deeper understanding of chemical-environment-disease interactions.
  • CTD continues to evolve as a critical resource for generating testable hypotheses on disease etiology and mechanisms.