[Data-modeling] Hormone type in the Medicine domain

[Kavitha Srinivas]

Agree.  The Open Biological Ontologies effort and the NCBO are great  
starting points for re-use.
Kavitha

On Apr 17, 2008, at 12:59 PM, Benjamin Good wrote:

> 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
>>>
>>> -------------------------------------------------------------------- 
>>> ----
>>>
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