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Re: [HCLS] Bridging Ontologies - with Foundational Ontologies

From: William Bug <William.Bug@DrexelMed.edu>
Date: Tue, 22 Aug 2006 10:00:10 -0400
Message-Id: <7146A295-8234-475E-A715-ADBF256AF1C4@DrexelMed.edu>
Cc: "Matthias Samwald" <samwald@gmx.at>, <ogbujic@bio.ri.ccf.org>, "Donald Doherty" <donald.doherty@brainstage.com>, <public-semweb-lifesci@w3.org>
To: "Kashyap, Vipul" <VKASHYAP1@PARTNERS.ORG>
Yes - as you and Amit point out, there are many very successful  
applications and meta-analyses that have been performed with  
"isolated" ontologies.

Where the difficultly comes in is when you want to:
	a) interlink the results from these separate studies
	b) formulate additional hypotheses based on these studies

What you begin to confront is the fact that if the ontologies were  
isolated both in terms of not using a shared foundational ontology,  
there were likely also isolated in the sense of not sharing "best  
practices" for ontology construction:
		- many definitions are imprecise, circular, or - in fact - non- 
existent
		- the same is true for relations - they are used in an imprecise,  
inconsistent, or incommensurate manner (a big problem initially for  
GO) - mixing "is_a" with the MANY KINDS of "part of" can be a  
semantic data integration nightmare**.
		- loosely defined and used lexical facets associated with nodes in  
the ontology - e.g., acronyms, abbreviations, and misspellings may  
get used indiscriminately as synonyms - sometimes that's valid, and  
sometimes its not.
		- plurals and pre-coordinated descriptions cutting across knowledge  
domains may appear in the graph - which can limit computability at  
fine-grained levels.

I know this sounds like I'm speaking in the abstract but believe me,  
I'm not.  There are specific examples where all of these issues have  
come up for us on the BIRN ontology efforts.  As Peter Mork mentioned  
for caBIG, registering with a query mediator requires mapping source  
data models to ontology-base semantic declarations.  The problems  
above can be a big problem if more than one ontology is required that  
have overlapping domains.  These inconsistencies need to be  
disambiguated or reconciled in some way, and in doing so, you may  
invalidate mappings made to data model elements.

This means you no longer have an explicit statement about semantics,  
but an implied one based on the knowledge in the head of the  
annotator.  This is also true if you are using algorithmic lexical  
parsing of some sort, as you are eventually parsing against terms  
applied by a human in a "loose" manner.

Don't get me wrong.  It may sound like I'm slamming GO here.  I'm  
not.  I've great admiration and respect for their experience and  
their efforts.  Most commendable of all is the fact that they've  
gradually learned a lot - both from the school of hard knocks and  
from the C.S., library science, and ontological philosophy fields  
that can helped them to develop better shared practices both for  
ontology creation, curation, and use.  To my mind, the 25 slides  
prepared by Suzi Lewis & Michael Ashburner (slides 11 - 37) in the  
following presentation summing up the hard won lessons of the GO  
Consortium do a better job at establishing such guidelines than  
anything else I've seen anywhere:

Principles for Building Biomedical Ontologies http:// 
www.geneontology.org/teaching_resources/presentations/ 
2005-10_ISMB_Ontology-Building_various.ppt

I'd specifically draw attention to the procedural flowchart on slide  
19 as being an excellent foundation from which to build more specific  
guidelines, some of which can be culled from other portions of the  
presentation.  There have also been many successes that have made it  
very clear, ontologies are an extremely important part of biomedical  
KE/KR/KD and semantically-driven data federation.

Cheers,
Bill


**As an example of


On Aug 22, 2006, at 8:51 AM, Kashyap, Vipul wrote:

>
>
> But - it's not clear to me whether we'll be able to evolve highly  
> automated semantically-formal neuroinformatics analysis systems.   
> I'm not thinking of reasoning oriented systems, but simply analysis  
> of semantic info a la the ubiquitious use of Gene Ontology in the  
> bio-molecular informatics world.
>
>
>
> [VK] Itís interesting to see the ground covered by Gene Ontology  
> without the use of foundational ontologies
>
>
>
> Cheers,.
>
> Bill
>
>
>
> On Aug 22, 2006, at 7:49 AM, Kashyap, Vipul wrote:
>
>
>
>
>
>
>
>> Great to hear that! It really seems that most of the promises of  
>> semantic
>>
>> web ontologies are only realised when top-level ontologies like  
>> DOLCE are
>>
>> used. Maybe we should evaluate the potential use of DOLCE or BFO  
>> for the
>>
>> BioRDF tasks?
>
>
> [VK] Whereas I agree with the use of foundational ontologies, I may  
> not agree
>
> with the sweeping generalization above. Significant potential can  
> be realized by
>
> using not so formally organized resources such as the UMLS for  
> instance.
>
>
>
> ---Vipul
>
>
>
>
>
> 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 
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Received on Tuesday, 22 August 2006 14:00:58 GMT

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