W3C home > Mailing lists > Public > public-semweb-lifesci@w3.org > May 2008

RE: SenseLab note: some updates

From: Kashyap, Vipul <VKASHYAP1@PARTNERS.ORG>
Date: Wed, 28 May 2008 15:47:10 -0400
Message-ID: <DBA3C02EAD0DC14BBB667C345EE2D124029483EB@PHSXMB20.partners.org>
To: "Kei Cheung" <kei.cheung@yale.edu>
Cc: "Alan Ruttenberg" <alanruttenberg@gmail.com>, "Matthias Samwald" <samwald@gmx.at>, <public-semweb-lifesci@w3.org>


There is an interesting trade-off between post-coordinated and pre-coordinated
vocabularies in the clinical context.

For instance if you have the following concept fracture (site = femur,
laterality = left) this can be used in two contexts:
- In a search and exploration context, where post-coordination makes sense,
e.g., get me all diseases with site = X and laterality = Y
- In a patient encounter context, however, it would be too much to expect a
physician to document each of these (disease, site, laterality) separately in
the patient record --- requires too many clicks. A physician is perfectly happy
to click once and document "left femur fracture" ... Saves him time and
aggravation.

Cheers,

---Vipul 

> -----Original Message-----
> From: Kei Cheung [mailto:kei.cheung@yale.edu] 
> Sent: Thursday, May 15, 2008 7:40 PM
> To: Kashyap, Vipul
> Cc: Alan Ruttenberg; Matthias Samwald; public-semweb-lifesci@w3.org
> Subject: Re: SenseLab note: some updates
> 
> 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/
> >>>>
> >>>>
> >>>>
> >>>>        
> >>>>
> >>>      
> >>>
> >>
> >>
> >>    
> >>
> >
> >The information transmitted in this electronic communication 
> is intended only
> >for the person or entity to whom it is addressed and may 
> contain confidential
> >and/or privileged material. Any review, retransmission, 
> dissemination or other
> >use of or taking of any action in reliance upon this 
> information by persons or
> >entities other than the intended recipient is prohibited. If 
> you received this
> >information in error, please contact the Compliance HelpLine 
> at 800-856-1983 and
> >properly dispose of this information.
> >
> >
> >
> >  
> >
> 
> 
Received on Wednesday, 28 May 2008 19:47:53 UTC

This archive was generated by hypermail 2.3.1 : Wednesday, 7 January 2015 14:52:36 UTC