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Comparative Toxicogenomics Database (CTD)

CTD is a robust, publicly available database that aims to advance understanding about how environmental exposures affect human health. It provides manually curated information about chemical–gene/protein interactions, chemical–disease and gene–disease relationships. These data are integrated with functional and pathway data to aid in development of hypotheses about the mechanisms underlying environmentally influenced diseases.

Chemical to Disease

This ingest takes only the chemical to disease rows where a direct evidence label is applied, and creates ChemicalEntity and Disease nodes connected by a ChemicalToDiseaseOrPhenotypicFeatureAssociation. The the chemical ID row is expected to need a 'MESH:' prefix added, the disease id is used as-is.

Rows are included only if the direct evidence field is 'therapeutic' and the biolink:affects predicate is used to avoid making too strong a claim.

Biolink Captured

  • ChemicalToDiseaseOrPhenotypicFeatureAssociation
  • id (random uuid)
  • subject (chemical id)
  • predicate (biolink:affects)
  • object (disease id)
  • publication (pubmed ids provided by file)
  • aggregating_knowledge_source (["infores:monarchinitiative"])
  • primary_knowledge_source (infores:ctd)

Citation

Davis AP, Wiegers TC, Johnson RJ, Sciaky D, Wiegers J, Mattingly CJ Comparative Toxicogenomics Database (CTD): update 2023. Nucleic Acids Res. 2022 Sep 28.