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Re: SenseLab note: some updates

From: Kei Cheung <kei.cheung@yale.edu>
Date: Tue, 20 May 2008 13:56:39 -0400
To: "Kashyap, Vipul" <VKASHYAP1@PARTNERS.ORG>
Cc: Alan Ruttenberg <alanruttenberg@gmail.com>, Matthias Samwald <samwald@gmx.at>, public-semweb-lifesci@w3.org
Message-id: <483310D7.2070003@yale.edu>

In addition to data at the phenotype/molecular level, there are public 
clinical data available for different stages (e.g., mild, moderate, ...) 
of Alzheimer's disease, for example.

The following are a couple of examples from clinicaltrials.gov.

http://clinicaltrials.gov/ct2/show/NCT00432081?term=alzheimer&rank=27
http://clinicaltrials.gov/ct2/show/NCT00679627?term=alzheimer&rank=42

Best,

-Kei


Kei Cheung wrote:
> Hi Vipul,
>
> Take the snomed term "Alzheimer's disease" (AD), for example. One axis 
> may be used to indicate the progression of the disease. For example, 
> http://www.memorystudy.org/alzheimers_stages.htm lists 7 stages of 
> Alzheimer's disease: no memory loss symptom, very mild, mild, 
> moderate, moderately severe, severe, and very severe.
>
> In gene ontology (GO), "memory" (or "learning") is a term under 
> biological process, one may want to give it a modifier such as 
> "impaired" if we want to use GO in combination with some modifier 
> ontology to describe an AD phenotype (e.g., "impaired memory").
>
> Just want to give some examples to illustrate the post-coordinated 
> approach.
>
> Cheers,
>
> -Kei
>
> Kashyap, Vipul wrote:
>
>> Kei,
>>
>> It's interesting that you bring up this notion.
>>
>> Most of the vocabularies in healthcare tend to be pre-coordinated, 
>> e.g., ICD9,
>> CPT4.
>> However there some compositional terminologies such as RxNorm and 
>> LOINC which
>> has an underlying model with 6 axes. Snomed tries to be a 
>> post-coordinated terminology, but in
>> reality it is partially
>> pre-coordinated and partially post-coordinated.
>>
>> Cheers,
>>
>> ---Vipul
>>
>>  
>>
>>> -----Original Message-----
>>> From: public-semweb-lifesci-request@w3.org 
>>> [mailto:public-semweb-lifesci-request@w3.org] On Behalf Of Kei Cheung
>>> Sent: Tuesday, May 13, 2008 12:51 PM
>>> To: Alan Ruttenberg
>>> Cc: Matthias Samwald; public-semweb-lifesci@w3.org
>>> Subject: Re: SenseLab note: some updates
>>>
>>>
>>> Sounds to me like an ontology exercise. For example, pre-coordinated 
>>> approach (knowledgebase) vs. post-coordinated approach (knowledge 
>>> base)? May not be a good analogy since I'm not an ontology expert. :-)
>>> However, I wonder to what extent these two ontology approaches have 
>>> been (or have not been) applied to the construction of ontologies 
>>> involved in the "knowledge base" or "knowledgebase" that we are 
>>> talking about here.
>>>
>>> -Kei
>>>
>>> Alan Ruttenberg wrote:
>>>   
>>>> Knowledge base is generally written as two words. Try a     
>>> google fight   
>>>> on scholar.google.com.
>>>> -Alan
>>>>
>>>> On May 13, 2008, at 8:31 AM, Matthias Samwald wrote:
>>>>
>>>>     
>>>>> I have made some small updates to the draft SenseLab conversion 
>>>>> document based on feedback from members of the group. See
>>>>> http://www.w3.org/2001/sw/hcls/notes/senselab/
>>>>>
>>>>> Some added text is highlighted in green. Several minor changes are 
>>>>> not highlighted.
>>>>>
>>>>> Cheers,
>>>>> Matthias Samwald
>>>>> DERI Galway, Ireland // Semantic Web Company, Austria
>>>>> http://www.deri.ie/
>>>>> http://www.semantic-web.at/
>>>>>
>>>>>
>>>>>
>>>>>       
>>>>     
>>>
>>>
>>>   
>>
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>>  
>>
>
>
Received on Tuesday, 20 May 2008 17:57:38 UTC

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