Open notebook - what's a disease again?

Is there a super-semantic-web-enabled phenotype database out there*? I want to ask a question like 'give a list of monogenic disorders whose locus has been confirmed by at least two labs, broken down by type of causative mutation type' and get an answer.

(* on a tangent: is 23andMe's gene book thing freely available?)

OMIM falls quite a long way short of this... it never set out to be a resource for programmatic access so you can't really blame them. The morbid map is available for download and contains all of the gene -> disorder mappings in their database.

A couple of issues:

• OMIM's weird entry categorization system (#*%+...) is very confusing. There are 2229 'phenotypes' (note: not 'Mendelian phenotypes') with a known molecular basis in the database, apparently, but only 386 genes with a phenotype associated with them? Some of those phenotypes are going to be caused by gross insertions / deletions / whatever and not small mutations in single genes, multiple phenotypes might arise from different mutations in the same genes but even so... what's with the disparity?
  
• It contains polygenic disorders (diabetes, schizophrenia) as well as monogenic ones
  
• You can't tell which is which - you could count the number of genes associated with the disorder but a 'monogenic' disorder might be a complex one whose OMIM entry hasn't been updated yet
  
• It's not a disease database - it has other phenotypes in it too. Longevity? Wet or dry ear wax? Novelty seeking personality?
  

The last point is interesting, really. When is a phenotype a disease? If you have a novelty seeking personality and so are relatively impulsive and prone to climbing mountains, swimming with sharks, cycling without a helmet etc. then are you ill?

Well, no, is the obvious answer. But where do you draw the line? Is autism a disease?

Neh. Beyond our remit. For us a monogenic disease = a clinically recognized disorder with a single, genetic cause.