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Re: SenseLab note: some updates

From: Kei Cheung <kei.cheung@yale.edu>
Date: Thu, 15 May 2008 21:57:16 -0400
Message-ID: <482CE9FC.6020500@yale.edu>
To: Chris Mungall <cjm@fruitfly.org>
CC: "Kashyap, Vipul" <VKASHYAP1@PARTNERS.ORG>, Alan Ruttenberg <alanruttenberg@gmail.com>, Matthias Samwald <samwald@gmx.at>, public-semweb-lifesci@w3.org

Chris Mungall wrote:

>
>
> On May 15, 2008, at 4:39 PM, 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").
>
>
> In fact both pre- and post- coordinated description of phenotypes  
> such as "impaired memory" are used. PATO is typically used as the  
> "modifier" ontology (actually an ontology of qualities and  
> dispositions). The mammalian phenotype ontology used implicitly pre- 
> coordinated terms, other groups post-coordinate using PATO + other  
> OBO ontologies. We have retrospectively gone back to the mammalian  
> phenotype ontology and attached class expressions defining their  
> terms to make these approaches comparable. Still very much a work in  
> progess, see:
>
> http://www.bioontology.org/wiki/index.php/PATO:Pre_vs_Post_Coordinating

Thanks for pointing to PATO describing pre- and post-coordination. It 
sounds like one can potentially find the same phenotype in pre- and 
post-coordinated ontologies. Is there an issue of redundancy?

Also, I noticed in the document to which you pointed the following: "A 
phenotype ontology should be orthogonal to an ontology of molecular 
function." For the AD phenotype "impaired memory", researchers may want 
to explore to understand the underlying molecular mechanism. For 
example, there is a "synaptic plasticity and memory" hypothesis studying 
the relationship between synaptic plasticity and memory. In GO, there is 
a term called "regulation of synaptic activity", such a biological 
process and/or its subclasses may be used to annotate at least partly 
the phenotype "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 Friday, 16 May 2008 02:13:26 UTC

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