Comparative Toxicogenomics Database (CTD): update 2021

By Allan Peter Davis, Cynthia J. Grondin, Robin J. Johnson, Daniela Sciaky, Jolene Wiegers, Thomas C. Wiegers, Carolyn J. Mattingly. Nucleic Acids Res., 2020

933 citations recorded by the source corpus.

Abstract The public Comparative Toxicogenomics Database (CTD; http://ctdbase.org/) is an innovative digital ecosystem that relates toxicological information for chemicals, genes, phenotypes, diseases, and exposures to advance understanding about human health. Literature-based, manually curated interactions are integrated to create a knowledgebase that harmonizes cross-species heterogeneous data for chemical exposures and their biological repercussions. In this biennial update, we report a 20% increase in CTD curated content and now provide 45 million toxicogenomic relationships for over 16 300 chemicals, 51 300 genes, 5500 phenotypes, 7200 diseases and 163 000 exposure events, from 600 comparative species. Furthermore, we increase the functionality of chemical–phenotype content with new data-tabs on CTD Disease pages (to help fill in knowledge gaps for environmental health) and new phenotype search parameters (for Batch Query and Venn analysis tools). As well, we introduce new CTD Anatomy pages that allow users to uniquely explore and analyze chemical–phenotype interactions from an anatomical perspective. Finally, we have enhanced CTD Chemical pages with new literature-based chemical synonyms (to improve querying) and added 1600 amino acid-based compounds (to increase chemical landscape). Together, these updates continue to augment CTD as a powerful resource for generating testable hypotheses about the etiologies and molecular mechanisms underlying environmentally influenced diseases.

Subfields: Computational Theory and Mathematics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/60410ec07fe7dfcec71cd6eacd8cb75caa27fabd

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Comparative Toxicogenomics Database (CTD): update 2023 (2022, background): “4 million evidence-based manually curated chemical–gene, chemical–phenotype, chemical–disease, gene–disease and chemical–exposure interactions, reflecting a 20% increase in curated content since our last update (7).”