MultiomicsBigGIM_DrugResponse_KP

Summary

BigGIM-DrugResponse KP is provided by the Multiomic KP team. BigGIM-DrugResponse KP includes both empirical findings from datasets with large datasets, as well as aggregated public knowledge resources or literatures. It expands the previous BigGIM from only gene_gene_interactions to more biological concepts, such as disease, drugs, and tissue types, etc.

The categories of nodes include: Genes, Drugs (SmallMolecules), Diseases; and the categories of edges (predicates) include Gene ~ gene_associated_with_condition ~ Disease, Gene (aspect qualifier: Genetic variants) ~ associated_with_sensitivity_to ~ SmallMolecule (aspect qualifier: IC50) etc.

gene_associated_with_condition_Disease

Part 1: We used TCGA data to quantify the gene mutation frequency at the patient level. Genes with mutation frequency greater than 5% and has mutated samples greater than 5 samples were selected. To further narrow down the genes, we further filtered the gene list according to the identification of cancer driver genes as published in PMID:29625053. Only driver genes were exposed to the MultiomicsBigGIM_DrugResponse_KP as of the version updated in Sep 2022.

API development

knowledge graph standardization and transformation
Parser updated in Aug 2022
Parser updated in Apr 2022