[Data-modeling] Hormone type in the Medicine domain

[Faye Li]

Ah, thanks for pointing me to this source, Benjamin and Kavitha. I'll 
look into it today.

-- Faye

Kavitha Srinivas wrote:
> 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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