Pathway

Biocarta
EHMN (Edinburgh Human Metabolic Network)
HumnCyc
INOH (Integrating Network Objects with Hierarchies)
NetPath
PID (Pathway Interaction Database)
Reactome
Wikipathways

Disease/Phenotype

CancerGenes
KEGG Disease
HPO (Human Phenotype Ontology)
MethCancerDB
MethyCancer
MPO (Mammalian Phenotype Ontology)
SIDER (SIDe Effect Resource)

Drug/Chemical

CTD (Comparative Toxicogenomics Database)
DrugBank
MATADOR (Manually Annotated Targets and Drugs Online Resource)
SMPDB (Small Molecular Pathway DataBase)
STITCH (Search Tool for Interactions of Chemicals)
T3DB (Toxin and Toxin Target Database)

Gene Regulation

MicroCosm Targets
miRTarBase
TFactS
Rel/NF-kappaB target genes

Gene Ontology

Gene Ontology