Table 1. The biological knowledge graph sources.

Relation	Relation database source	Source type	Target type
has function	Uniprot	Gene (Entrez)	Function (Gene Ontology)
has disease annotation	DisGeNet	Gene (Entrez)	Disease (Disease Ontology)
has interaction	STRING	Gene (Entrez)	Gene (Entrez)
has sideeffect	SIDER	Drug (PubChem)	Phenotype (Human phenotype)
has indication	SIDER	Drug (PubChem)	Disease (Disease Ontology)
has target	STITCH	Gene (Entrez)	Drug (PubChem)
has gene phenotype	HPO annotations	Gene (Entrez)	Phenotype (Human Phenotype Ontology)
has disease phenotype	Hoehndorf, Schofield & Gkoutos (2015b)	Disease (Disease ontology)	Phenotype (Human Phenotype Ontology)