Data Import for Chemical-Gene Interactions
|RGD automated import pipeline for gene-chemical interactions
Data is imported from the Comparative Toxicogenomics Database (CTD, http://ctdbase.org/). Data is extracted from the file CTD_chemicals.tsv.gz to map chemical designations from CTD to ChEBI IDs using the CasRN IDs. Gene-chemical interaction data is extracted from the file CTD_chem_gene_ixns.tsv.gz. Genes are matched to RGD genes using the Entrez Gene ID in the file. Annotations are loaded onto the gene corresponding to the species designated in the file as "EXP" or "inferred from experimental evidence" annotations, and propagated to the orthologs using the "ISO" or "inferred from sequence orthology" evidence code. RGD stores and presents the PubMed ID of the original reference, and also shows as a note the interaction statement contained in the CTD file.