[Data-modeling] Hormone type in the Medicine domain

[Benjamin Good]

Hi Faye (and others interested in modeling biological and medical  
concepts in freebase),

I'm curious why you don't seem to take advantage of the many existing,  
public formal models of biological systems.  You may or may not want  
to follow them exactly, but a search on the National Center for  
Biomedical Ontology portal (http://www.bioontology.org/tools/portal/bioportal.html 
) or in the Unified Medical Language System (http://www.nlm.nih.gov/research/umls/umlsmain.html 
) would certainly be an informative place to start looking when you  
are considering what and how to model in these domains.

Somehow aligning freebase with these efforts would also be very  
valuable - though a different objective.

regards
-Ben


On Apr 16, 2008, at 12:03 PM, Faye Li wrote:

> Thanks -- that was one of the things that confused me. Hormone  
> receptors
> were defined as proteins on most online sources I consulted, but I was
> influenced in the opposite direction by the existing Gene type and
> instances in the Biology domain and the muddy use of both terms in
> Wikipedia. Sounds like using Protein (again, in Biology) as an  
> included
> type would make sense here.
>
> The point of the explicit naming of "Human" in front of "Hormone" is  
> to
> drive home the fact that the Medicine domain will be limited to the
> scope of human instead of encompassing plant or animal. It doesn't  
> mean
> that these hormones are limited to the human species; it does mean,
> however, that hormones that don't apply to humans shouldn't be added  
> to
> this type -- a situation that's been happening with the Disease type
> that I'd like to avoid. Hormone will be linked to Disease, which has
> properties like causes and treatments, both of which can be very
> different depending on the species of the patient. These and other
> things I want to model require that the reciprocating type be Human  
> Hormone.
>
> I could, however, create a separate type of Hormone (perhaps best in  
> the
> Biology domain) for all hormones in the world (and add Human Hormone  
> as
> an included type). Would that be an acceptable solution to you?
>
> -- Faye
>
>
> Brian Karlak wrote:
>>
>> On Apr 15, 2008, at 5:07 PM, Faye Li wrote:
>>> Also, is a Hormone Receptor always or pretty much always a Gene?  
>>> We have
>>> a Gene type in the Biology domain that I'd be more than happy to  
>>> add as
>>> an Included Type if it makes sense. Medical review of the type and
>>> property names would also be appreciated.
>>
>> Hi Faye --
>>
>> Hormone Receptors are all proteins, which in turn are encoded for by
>> genes.  However, the distinction is often blurred in common usage
>> since there is a rough one-to-one correspondence between a gene and
>> and its protein product.  Furthermore, genes often share the same  
>> name
>> as their protein product.
>>
>> Even though common usage often confuses the two concepts, it would
>> probably be incorrect to cotype all Hormone Receptors as Genes.  It
>> would be more correct to cotype them as Proteins.
>>
>> Unfortunately, it seems that Wikipedia usually confuses the two
>> concepts in their articles.  For instance, the A2a Receptor
>> <http://sandbox.freebase.com/view/guid/9202a8c04000641f8000000006bd15e1 
>> > blurb
>> starts with:
>>
>>    The adenosine A receptor, also known as ADORA2A, is an adenosine
>>    receptor, but also denotes the human gene encoding it.
>>
>>
>> It appears that we have continued this conflation of Gene and Protein
>> in freebase.  I see instances where we (automatically) type these
>> entries as a Gene.  This irks the bio geek in me.  For common use  
>> this
>> will work, but any biological application that tries to use this info
>> will get tangled up pretty quick.
>>
>> Because of this, I'd recommend against the automatic cotyping of
>> Hormone Receptor with Gene, unless we're comfortable propagating this
>> issue.
>>
>> One final suggestion: you should probably name your type "Hormone",
>> instead of "Human Hormone".  Most (if not all) of your entries are
>> hormones in a wide variety of species.  Dogs, mice and deer all
>> produce prolactin and insulin, all for pretty much the same purpose.
>>
>> Brian
>>
>> ------------------------------------------------------------------------
>>
>> _______________________________________________
>> Data-modeling mailing list
>> Data-modeling at freebase.com
>> http://lists.freebase.com/mailman/listinfo/data-modeling
>>
>
> _______________________________________________
> Data-modeling mailing list
> Data-modeling at freebase.com
> http://lists.freebase.com/mailman/listinfo/data-modeling