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Re: [HCLS] Bridging Ontology...An Automated Approach?

From: William Bug <William.Bug@DrexelMed.edu>
Date: Tue, 22 Aug 2006 10:27:55 -0400
Message-Id: <5F05387B-CA6E-48AF-8126-1F0B1788AA0F@DrexelMed.edu>
Cc: "Kashyap, Vipul" <VKASHYAP1@PARTNERS.ORG>, <donald.doherty@brainstage.com>, <public-semweb-lifesci@w3.org>
To: "Mork, Peter D.S." <pmork@mitre.org>

On Aug 22, 2006, at 9:04 AM, Mork, Peter D.S. wrote:

> I second the request for specific examples because, in my  
> experience, most mediators rely on a logical data model with  
> queries (SQL or XQuery) mapping the underlying data models into the  
> mediated model.
In performing the cross-model mapping, at some point, one needs to  
specify the semantic relatedness of the attributes in the entities  
being inter-related.  For example, if in one data model you are  
storing the descriptions about the shape organ sub-regions and  
descriptions about the shape of cells in the same entity called  
"biomaterial_shape" with attributes "biomaterial entity" and "shape",  
while in another source data model these are stored in separate  
entities called "organ_subregion_shape" and "cell_shape", these two  
different models need to map in different ways into the "global"  
mediator schema, and the ways will mainly differ based on the  
semantic means used to specify different levels of anatomical  
resolution.
> In some cases (e.g., TAMBIS), the mediating model is actually an  
> ontology, but this is rare.
[BB] It's been rare to date, because so few ontologies have been  
created with commensurate foundations.  That is beginning to change.
> The mappings themselves are expressed in a language with  
> sophisticated transformative capabilities because of the myriad  
> incompatibilities that exist.
[BB] Absolutely.  These languages are very powerful, but many of the  
transformational grammars require mixing lexical manipulations and  
semantic manipulations, as is quite common when using UMLS.  This  
again can introduce inconsistencies in interpretation, as you attempt  
to build on the first level of semantic correlations you derive from  
the mappings.
>  For example, aggregation is not supported by many rule or ontology  
> languages.
[BB] Again, I completely agree, aggregation is not necessarily  
supported by some ontological structures, though lexically-oriented  
graphs are quite good at dealing with aggregations.  The Wordnet  
SynSets are a good example of this.  TopicMaps (XTM) also have some  
advantages to provide in this arena.  These derive from the field of  
text summarization and set theoretical approaches to knowledge  
organization, which can differ somewhat from the graph theory based  
methods used in the XML world and often used in ontological  
formalisms.  That's why it can be valuable to keep lexical and  
semantic formalisms distinct, though the must definitely interoperate.

>  Neither are regular expressions.
[BB]: Regex's are an extremely valuable tool in the lexical analysis  
toolkit, but they have nothing to do with ontologies.  One would hope  
the results of a Regex-based analysis would be linked to an ontology,  
but if things are constructed in the proper manner, there is no need  
for Regex-capability within the ontological framework.

>
>
> Peter Mork
>
>
>
> From: Kashyap, Vipul [mailto:VKASHYAP1@PARTNERS.ORG]
> Sent: Tuesday, August 22, 2006 8:57 AM
> To: William Bug; Mork, Peter D.S.
> Cc: donald.doherty@brainstage.com; public-semweb-lifesci@w3.org
> Subject: RE: [HCLS] Bridging Ontology...An Automated Approach?
>
>
>
> We are using mediation technology within the BIRN project as well.   
> It has many ways in which it can solve some of the problems we're  
> discussing.
>
>
>
> My fear is every new repository requires an new mapping/ 
> registration to the mediator and/or shared ontology.  This can be a  
> very fragile system over time, and - as you point out, Peter, tacit  
> assumptions in the source data models (and their use of semantics)  
> - which of course can also change - may greatly limit the depth and  
> breadth with which queries can be mapped to all the data sources.
>
>
>
> Semantic web approaches appear to circumvent some of the technical  
> frailties, though I don't think they can necessarily overcome the  
> requirement for shared foundational and generic ontology layers.
>
>
>
> [VK] It will be great if you could give some use cases on how  
> Semantic web approaches can help circumvent the fragility of the  
> system, requiring mappings and registrations…
>
>
>
>
>
> On Aug 22, 2006, at 7:52 AM, Mork, Peter D.S. wrote:
>
>
>
>
>>> Creating explicit connections between all similar and/or identical
>> entries
>>> in two schemas is an arduous task that is impractical to do
> manually.
>>
>>
>> [VK] Will mapping each of these schemas to an ontology and then using
> the
>> ontology to mediate further queries help alleviate the problem?
>>
>>
>>
>> ---Vipul
>>
>>
>>
>>
>
>
> This is the approach adopted by caBIG.  Individual data models (or
>
> schemata) are related to a common ontology.  By itself, this doesn't
>
> allow one to rewrite queries (because of tacit assumptions present in
>
> the respective data models?), but the hope is that development of
>
> query-mediators will be facilitated by the existence of a loose
>
> mapping.
>
>
>
> Peter
>
>
>
>
>
> 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)
>
> 610 457 0443 (mobile)
>
> 215 843 9367 (fax)
>
>
>
>
>
> Please Note: I now have a new email - William.Bug@DrexelMed.edu
>
>
>
>
>
>
>
>
>
> This email and any accompanying attachments are confidential.
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>

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)
610 457 0443 (mobile)
215 843 9367 (fax)


Please Note: I now have a new email - William.Bug@DrexelMed.edu







This email and any accompanying attachments are confidential. 
This information is intended solely for the use of the individual 
to whom it is addressed. Any review, disclosure, copying, 
distribution, or use of this email communication by others is strictly 
prohibited. If you are not the intended recipient please notify us 
immediately by returning this message to the sender and delete 
all copies. Thank you for your cooperation.
Received on Tuesday, 22 August 2006 14:28:29 GMT

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