Table 1.

ReproTox-KG node and edge sources and enumeration.

Assertion edge type	Name	Relationship	Reference	Nodes/nodes/edges
Birth defect–gene	HPO	Genes known to be associated with a birth defect	Human Phenotype Ontology	599/5093/127,023
	Geneshot	Genes co-mentioned with birth-defect terms in publications	Geneshot	32/1091/1565
Birth defect–drug	FDA Adverse Event Reporting System (Female/Male)	Drugs with reported adverse events related to birth defects	FDA Adverse Event Reporting System	32/94/372
	Drugshot	Drugs co-mentioned with birth-defect terms in publications	Drugshot	679/2207/13,000
Drug–gene	IDG (Drug Target)	Drugs with known human gene targets	Target Central Resource Database	1363/1034/7326
	SigCom LINCS Drug-to-Gene (upregulates/ downregulates)	Drugs that up- or down-regulate genes across the LINCS L1000 signatures	SigCom LINCS	4523/4419/225,509
Drug–drug	LINCS Drugs Cosine Similarity	Drugs that induce similar gene expression patterns across LINCS L1000 signatures based on cosine similarity	SigCom LINCS	4523/3449/20,785
Gene–gene	ARCHS4 (positively/ negatively correlated)	Genes positively or negatively correlated across ARCHS4 gene expression samples	ARCHS4	17,964/12,185/ 170,801

The ReproTox-KG is made of entities (nodes) representing birth defects, genes, and drugs that are connected based on semantic assertions (edges/relationships) extracted from different sources. The table lists the type of assertion, the nature of the relationship, the original source from where the assertion was extracted from, and the number of entities and relations for each entry in the table.