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Re: [HCLS] Bridging Ontologies - with Foundational Ontologies

From: William Bug <William.Bug@DrexelMed.edu>
Date: Tue, 22 Aug 2006 07:54:31 -0400
Message-Id: <3F7B67F4-5A2C-4005-9A6B-5E114A6DE022@DrexelMed.edu>
Cc: Chimezie Ogbuji <ogbujic@bio.ri.ccf.org>, Donald Doherty <donald.doherty@brainstage.com>, Matthias Samwald <samwald@gmx.at>
To: w3c semweb hcls <public-semweb-lifesci@w3.org>
Hi All,

I think Chimezie and Matthias are definitely on the right path here.

As I see it, the bottom-up approach to semantic KE/KR that SemWebTech  
is so suited to must be wedded to the top-down approach using an  
upper level ontology such as DOLCE or OBR (version of BFO designed  
for use in biology**).

As Matthias and Chemezie have both pointed out, if you have two data  
repositories covering overlapping domains of knowledge, if they don't  
use the same fundamental formalized expression for those core  
entities they have in common - say, for instance, a continuant (or  
perdurant) - an entity whose existence extends over some time  
interval - then it won't be possible to automatically determine which  
entities they describe are in fact related in a fundamental way.  I  
most definitely agree with them based on the work we are doing on the  
BIRN Ontology Task Force.  We are trying to import the FuGO ontology  
- recently expanded to cover all biomedical experimental domains at a  
"generic" level and to be re-christened - likely to Ontology of  
Biomedical Investigation (OBI) [don't quote me on that].  We need to  
make certain the collection of "Biomaterial Entities" we specifically  
define for annotating data in BIRN are ontologically equivalent at  
the base level.  The only way for us to do this is for OBI and the  
BIRNLex knowledge representation framework we are building to both  
import and reference the same upper level ontology.  Unfortunately,  
at this time, there is no published version of UBO (see below), so we  
both end up recapitulating the upper level ontology elements in our  
individual OWL files.  Ultimately - and hopefully very soon - there  
will be a UBO for us both to reference externally.

If you don't approach the task of semantic interoperability with a  
shared ontological graph where all the nodes are very clearly defined  
according to a set of empirically derived "best practices" (e.g., the  
OBO Foundry Principles - http://obofoundry.org/) - say you were to do  
a single "bridge" between NeuronDB and CocoDat - there is no  
guarantee that bridge will be of any use beyond linking NeuronDB to  
CocoDat.  In other words, it won't necessarily follow the mapping can  
link either NeuronDB or CocoDat to any other knowledge repository  
covering overlapping domains - even if you use terms from the UMLS.   
As we discussed before - and as Olivier from the NLM UMLS research  
staff mentioned - UMLS is not an ontology, it is a unified thesaurus  
of the medical lexicon as described by several dozen popular,  
overlapping controlled vocabularies.  There are all sorts of ontology  
construction "best practices" it's underlying semantic graphs do not  
obey (e.g., do not combine distinct mereotopological "part of  
relations" and subsuptive "is a" relations all in the same graph).   
This is even true of the UMLS Semantic Network - the closest thing  
UMLS has to an ontology.  Olivier mentioned work is underway to  
review the SN and consider how to bring it closer in line with  
ontology construction "best practices" without breaking existing  
systems (http://mor.nlm.nih.gov/snw/).

I would add I don't see this approach as being incompatible with  
bottom-up approaches to KE/KR.  Along the lines Vipul mentioned in  
response to Don, it certainly is possible to refine and improve the  
underlying semantic graph based on observed statistical correlations  
amongst related entities.  One can also put complex network  
dependencies in place with weights adjusted according to periodic  
reduction of the accruing semantically formalized repository. At this  
point in time, it difficult to imagine how the underlying ontology  
could auto-adjust to such feedback.  An ontology is a bit less  
flexible that the sort of classification and summarization methods  
used by Google - no matter how sophisticated the algorithmic  
implementation of such a system may be.  However, periodic review  
could certainly help point out emerging logical inconsistencies (and  
novel consistencies).  Still, devising a means to "evolve" the  
ontological graph based on statistical analysis of semantically  
formal representation of phenotype observations (and commensurate  
formal descriptions of the investigative procedures used to make  
those observations) is really what will provide the greatest payoff,  
I believe.  It will help tie together several important threads:
	- deriving a deeper understanding of the emergent higher level  
activities such as neurodevelopment, learning, memory, and cognitive  
processing TO genetic networks, enzymatic pathways, receptor-mediated  
cellular events, and ion-channel triggered cell physiological events;
	- linking observations made in animal models to clinical practice.


**OBR (http://ontology.buffalo.edu/medo/biomedo.htm) will likely be  
re-christened UBO and be associated with the OBO Foundry effort.  In  
fact, use of UBO will likely become one of the OBO Foundry "Principles"

On Aug 22, 2006, at 5:11 AM, Matthias Samwald wrote:

> I also think that smaller foundational ontologies like DOLCE are  
> the key to interoperability between ontologies. It seems like the  
> only way to ensure good interoperability is the agreement on some  
> basic structures and design patterns. When two OWL ontologies are  
> based on two totally different world-views to start with, it  
> becomes almost impossible to build a bridge between the two that  
> serves some practical use. Maybe we should look more into the use  
> of foundational ontologies and best-practices of their use and  
> extension, and less on the alignment of ontologies that have  
> already developed into totally different directions
> In metaphoric words: Our task is not to build brigdes between stray  
> villages on different islands. Our task is to find the most livable  
> island and tell all of the villagers to settle there.
>>  Unfortunately, bio-zen was more oriented to concepts at the
>>  molecular
>>  level than for my needs, but any connection made to DOLCE would
>>  automatically orient themselves with bio-zen (or any other
>>  derivatives).
> 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?
> kind regards,
> Matthias Samwald

Bill Bug
Senior Research Analyst/Ontological Engineer

Laboratory for Bioimaging  & Anatomical Informatics
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

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Received on Tuesday, 22 August 2006 11:55:11 UTC

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