Lots of databases have disease information, but unfortunately, there is no 'hub" to integrate them like PubChem for chemicals, Uniprot for proteins. Without a controlled vocabulary, many diseases are poorly presented as free text. Human disease ontology as far as I am aware, made the first effort to build controlled vocabulary and link to other identifier such as OMIM ID, MESH, NCI, UMLS and SNOMEDCT. Here I summarize several popular disease related databases and show how they are integrated.

PharmGKB: provides MESH
CTD: provides MESH, OMIM ID
Diseasome: Provides some OMIM ID in the disorder column, but you have to do some manual work.
Drug Disease: provides disease name, need manual mapping.
TTD: provides disease name, need manual mapping