Re: A question on the vocabulary for 'persons'

Ditto, Kei!!!

Of course, at the heart of this - in addition to the very important  
issue Chemezie introduced re: ACL at the graph node level, if that is  
practical - is the discussion we've been having regarding URIs - how  
to create them, broadcast/discover them, and guarantee their uniqueness.

The individual tracking issue Kei mentions below is one we've had to  
deal with on the BIRN project, where different research groups are  
passing a given subject (or samples from that subject) amongst  
themselves to perform different sorts of investigation - vital  
imaging with MRI or fMRI, imaging of dead tissue - the brain - at  
high rez either with histo-based LM techniques or for some samples EM  
- also gene expression analysis on matched microdissected tissue  
punches, ELIZA, etc.

There is also the very difficult issue of being able to stream-line  
the IRB paperwork across campuses which to some extent depends on  
being able to "publish" subject/sample level IDs.

This is why we'd started investigating LSID over a year ago, as we  
need an ID franking authority at least at the subject and or  
biomaterial sample level.  To be honest, I think we've only partly  
solved this problem, to the extent required to pass animals back-n- 
forth, and so far we've been using a propriotary authority, which  
will later need to be mapped to some more global authentication  
service, possibly LSID-based, or whatever becomes the "best practice"  
as recommended by the BioRDF group.

Cheers,
Bill

On Sep 14, 2006, at 10:12 AM, kei cheung wrote:

>
> Hi Helen, Vipul, et al.,
>
> I think we are at a significant point of discussion here. That is,  
> we're talking about how to possibly bridge life science and health  
> care through semantic web (not just applying semantic web  
> technologies to health care and life sciences independently/ 
> separately). The person entity can serve as a bridge or linkage (at  
> least at a high level). At a deeper level of connection, we might  
> want to use the person/patient/subject's samples to integrate  
> different types of experimental data associated with the samples.  
> Different types of samples (blood, urine, tissue, etc) may  
> becollected from the same person/paitent/subject over time for  
> different types of studies/lab tests. In other words, how can we  
> make sure all these samples collected at different time points  
> orginate from the same person who might have participated in  
> different studies. Vipul also touches upon the important issue of  
> privacy and confidentiality in the clinical world. In this regard,  
> I wonder how semantic web relates to the work on data encryption  
> and security. For example, certain properties or property values of  
> a person (or its class) may need to be encripted or made visible to  
> certain authorized groups only.
>
> Helen, when you say adding a triple for each role to handle role  
> multiplicity, do you mean this is a meta triple? In RDF, for  
> example, can we use reification or named graph to implement this?
>
> Cheers,
>
> -Kei
>
> Kashyap, Vipul wrote:
>
>> An important issue that is likely to come up soon in healthcare is  
>> the integration of a person’s genetic information in the  
>> electronic medical record.
>>
>> So, would it make sense to extend the person class to hold a  
>> person’s genomic information?
>>
>> Another big issue is one of privacy. How does one specify ACLs  
>> related to what fields of the person class be visible to which  
>> classes of users?
>>
>> Maybe we need another ontology there?
>>
>> ---Vipul
>>
>> --------------------------------------------------------------------- 
>> ---
>>
>> *From:* public-semweb-lifesci-request@w3.org [mailto:public-semweb- 
>> lifesci-request@w3.org] *On Behalf Of *helen.chen@agfa.com
>> *Sent:* Thursday, September 14, 2006 8:08 AM
>> *To:* kei.cheung@yale.edu
>> *Cc:* Marco Brandizi; public-semweb-lifesci@w3.org; public-semweb- 
>> lifesci-request@w3.org
>> *Subject:* Re: A question on the vocabulary for 'persons'
>>
>>
>> Kei
>>
>> You raised a good point here.
>>
>> Indeed, person can have multiple roles in a given organization or  
>> scenario. Capturing this multiplicity in the "person" ontology  
>> should not be a problem - you simply add a triple for each role  
>> the person assumes.
>>
>> These roles are likely to change over time, as you point out in  
>> your email. Such changes should not be a problem, just as one  
>> might change their home addresses. As with your home address, you  
>> can add "effectiveUntil" and "effecitiveOn" to specify the valid  
>> period of this information. In addition, a role is only meaningful  
>> within a scope. In HL7, it uses "scopedRole" and "playedRole" to  
>> set this context. This, too, can be modelled in ontology.
>>
>> My problem is with the so-called "participation". Participation is  
>> similar to "role" but might change in each episode. For example,  
>> Dr. K is a chest specialist (Role) in hospital A. He is sick today  
>> and is treated at hospital A. So in such "patient-encounter"  
>> episode, he is a patient (Participation).
>>
>> I am not sure if the person ontology should concern such  
>> transitional concepts.
>>
>> Helen
>>
>>
>> *kc28 <kei.cheung@yale.edu>*
>> Sent by: public-semweb-lifesci-request@w3.org
>>
>> 09/13/2006 09:45 PM
>>
>> 	
>>
>> To
>>
>> 	
>>
>> Marco Brandizi <brandizi@ebi.ac.uk>
>>
>> cc
>>
>> 	
>>
>> public-semweb-lifesci@w3.org
>>
>> Subject
>>
>> 	
>>
>> Re: A question on the vocabulary for 'persons'
>>
>> 	
>>
>>
>>
>>
>>
>>
>> Hi Marco et al.,
>>
>> It is also possible that a person can have multiple roles (e.g.,
>> researcher and teacher). Are there standard vocabularies that we  
>> can use
>> to describe roles, for example? There might be a temporal aspect as
>> well. For example, a person at one point was a postdoc but later  
>> became
>> a professor. If this is taken into account, we can ask questions like
>> what is the most recent role(s) a person has. This may somewhat  
>> relates
>> to how we should model a paitent/subject involved in a longitudinal
>> studies. Besides relations (how persons relate to each other), we  
>> might
>> also want to think about how persons are grouped for different
>> basic/clinical research purposes. For examples, panels vs. cohorts,
>> population samples vs. pedigrees, etc... This might have been
>> thought/discussed about by other people. I may just reignite such
>> thought and discussion.
>>
>> Cheers,
>>
>> -Kei
>>
>> Marco Brandizi wrote:
>>
>>>
>>> kei cheung wrote:
>>>
>>>> Based on my limited experience, a person in the life science and
>>>> healthcare context can be considered as a subject or patient (which
>>>> can be a subclass of person). Of course, there are other roles a
>>>> person can play (e.g., doctors, researchers, and authors). For
>>>> genetic studies, a group of subjects/indviduals may be a
>>>> family/pedigree. In this case, relationships among these family
>>>> members may include Father_of, Mother_of, Child_of, etc. Other  
>>>> types
>>>
>>>
>>> Hi Kei,
>>>
>>> In addition, I think there is another side as well: science  
>>> community
>>> people, having a role (student, teacher, director of), relations  
>>> with
>>> fields of study ( immunologist, studies TLR signalling),  
>>> relations with
>>> events and scientific production ( has published, has organized
>>> conference ), relations with other people ( works with,  
>>> supervisor of,
>>> ... ).
>>>
>>> I vaguely remember at least one similar case of ontology, does  
>>> anyone
>>> have further details?
>>>
>>> Cheers.
>>>
>>
>>
>
>
>
>

Bill Bug
Senior Research Analyst/Ontological Engineer

Laboratory for Bioimaging  & Anatomical Informatics
www.neuroterrain.org
Department of Neurobiology & Anatomy
Drexel University College of Medicine
2900 Queen Lane
Philadelphia, PA    19129
215 991 8430 (ph)
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215 843 9367 (fax)


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