[Data-modeling] Thoughts on disease/treatment

[Dan Ruderman]

Hi Faye,

Faye Li wrote:
> I have a to-do item regarding anatomical structures affected by diseases 
> on my whiteboard but didn't get to it this time. The type "Anatomical 
> structure" exists today without any properties (see 
> http://www.freebase.com/tools/schema/medicine/anatomical_structure) and 
> the plan was to try to flesh out the schema there. Any properties you'd 
> suggest?
>   
The fundamental concept I would add is a
contains/part-of hierarchy to the structures.  I found
this web site which has thought a lot of this through and
may have an ontology which is importable (e.g. they
have an OWL version):
http://sig.biostr.washington.edu/projects/fm/AboutFM.html
Populating the hierarchy might be tricky, though, unless
the anatomical names are consistent with the freebase ones.
My biggest concern would be that the hierarchy would be
different in different organisms (e.g. cerebral cortex is part of the
mammalian brain but not part of the reptilian brain), and
I'm not sure if there is a ready source for that information.
Because of these complexities I'd probably leave the properties
as they are.


> As for "Disease Cause" (which will be renamed etiology shortly, with the 
> original name saved as an alias), I was thinking about refactoring the 
> type. Each cause needs to be qualified with evidence level, something 
> along the lines of "evident, probable, possible". I was also considering 
> adding an enumeration property/new type for etiology category that would 
> list, "bacterial, viral, chemical, parasitic", etc. I would appreciate 
> your expertise if you have time to talk about this offline.
>   
My knowledge is somewhat limited, but I enjoy thinking about
these things and would be glad to chat about them.

Dan