[Data-modeling] Hormone type in the Medicine domain

[Dan Ruderman]

I think this is a great discussion.  Ben's suggestion that existing
ontologies be ported to the MW is an important one.  By doing
so we will end up with a one-stop database which bridges
a number of currently disjoint data sets and ontologies.  The
fact that the MW allows co-typing is central to this.  The price
we pay is the added effort of piecing together the jigsaw puzzle.

I might suggest that the notion of a hormone receptor might
best be captured as a biological function ascribed to a protein
(and, in turn, to its gene).  In the existing data in the biology
domain there is an example of this.  The Gene Ontology group
"steroid hormone receptor activity"
(http://www.freebase.com/view/guid/9202a8c04000641f8000000005213ec5)
is an annotation on a number of genes, e.g. estrogen receptor 1
(http://www.freebase.com/view/guid/9202a8c04000641f800000000419c5ad).
This annotation was made by the Gene Ontology Consortium, and
I doubt anyone would argue with them about it and I doubt
this would change.  But keeping track of who said it is important because
not everyone agrees on these annotations, and they may change
over time (which might be nice to track).

So rather than simply co-typing a protein (or gene) as a hormone receptor,
one could instead define hormone receptor as a type and link to proteins
(or genes) though a membership type which has properties like who said
it, when, and what was the evidence.  This follows the model that the
Gene Ontology Consortium itself uses.  What's nice is that it allows us
to talk about these functional annotations not as a hard fact but as a 
statement
made at a given time by a given organization or person.


Regards,
Dan




>> *From: *"Faye Li" <faye at metaweb.com <mailto:faye at metaweb.com>>
>> *Date: *April 16, 2008 12:03:52 PM PDT
>> *To: *"Freebase data modeling mailing list" 
>> <data-modeling at freebase.com <mailto:data-modeling at freebase.com>>
>> *Subject: **Re: [Data-modeling] Hormone type in the Medicine domain*
>> *Reply-To: *"Freebase data modeling mailing list" 
>> <data-modeling at freebase.com <mailto:data-modeling at freebase.com>>
>>
>> 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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