Re: Antwort: RE: Semantic web article in Nature Biotechnology

Hi Wafik,

One beauty of SW is that the "over-arching layer" doesn't really need to
know any details about the sub-domain ontologies.  This is the classic
contrast between XML and RDF: XML data is tree-structured, while RDF data
is structured as a DAG.  If you combine two different DAGs, the result is
still a DAG.  But if you combine two trees, the result is not necessarily
a tree: if you join on the leaves, you end up with a structure with two
roots.  To turn this into a tree again, you have to go through "XML hell"
and rebuild the whole structure.

The more subtle beauty of SW is that it helps foster over-arching layers
that aren't big and cumbersome.  If data aggregation is difficult, then
data tends to be kept in "monster tables": full of every quantity you
might want, and several you didn't. Except, there's always something else
that want, so you end up joining with another monster table to get it.  
The result: a real monster.  And worse, the data may be inconsistent or
outdated, because when data aggregation is difficult, it tends to be done
infrequently, with the results kept for a long time.  SW helps avoid this
through a framework flexible enough to contain combined ontologies (RDF),
and mechanisms such as LSIDs to serve as unique global identifiers.  So it
becomes easier for us to keep the data distributed, and in small,
lightweight ontologies that we can combine when we need.

Cheers,

Melissa


> Hi Helen,
>   I thought the power of the SW is linking those monolithic fragmented
> domains or sub-domains into one with no over-arching layer.  Maybe I
> am wrong -- please someone correct me here.  The idea of creating
> another over arching layer to connect the sub-domains might seem
> defeating the purpose.  How will this over arching layer react to any
> change in any of the underlying sub-domains -- will it need to be
> changed/adjusted every time one of the underlying sub-domains is
> changed???
> 
> I think the power of the SW is in linking ontologies -- creating RDF
> statements in each ontology to establish a link. Best -Wafik Farag
> 
> 
>   ----- Original Message ----- 
>   From: helen.chen@agfa.com 
>   To: Phillip.Lord@newcastle.ac.uk ; wangxiao@musc.edu 
>   Cc: public-semweb-lifesci@w3.org ; public-semweb-lifesci-request@w3.org ; wangxiao@musc.edu 
>   Sent: Tuesday, September 27, 2005 12:02 PM
>   Subject: RE: Antwort: RE: Semantic web article in Nature Biotechnology
> 
> 
> 
>   Hi, Phil and Xiaoshu 
> 
> 
> 
>   >> (3) All these ontologies are still developed in a monolithic manner.
>   >> No consideration about the granuality and practicality has been
>   >> emphasized.  
> 
>   >There have been many considerations of practicality made. Monolithic
>   >development is a problem, but both OBO and the MGED ontologies have 
>   >been attemping to ensure consistency between ontologies as well as 
>   >minimise overlap. 
> 
>   Even with many considerations and increasing community efforts in developing ontologies to be consumed by semantic web, I am afraid the "monolithic development" problem will be with us for a long time.   Ontologies developed within different specialties and sub-domains will always be fragmented and rather "monolithic" in their own right.   
> 
>   In Healthcare domain, different regulatory bodies may develop ontologies for their practice guidelines, and disease management centers develop their own care plans and protocols.   It is not realistic to hope for a well-coordinated ontology that covers everything nicely under the hood. 
> 
>   What I understand of the power of semantic web technology lays the connecting and inference capability between those "fragmented" knowledge bases.  This connection is to be reached by a thin layer of "over-arching" ontology and a set of basic rules. We have limited experience in linking (mapping) our rather "monolithically developed" RPGOntology (ontology for EU-radiation protection guideline) with SNOMED CT(http://www.snomed.org/snomedct/).  The benefit of such connection can not be over-stated. 
> 
> 
>   Helen 
> 
> 
> 
>   ---------------------------------------------------------------------------------------------
>   Helen Chen, Ph.D
>   Research and Innovation Center for Healthcare
>   Global Architecture and Design Group
>   Agfa Healthcare
> 
>   http://www.agfa.com/healthcare 
>     
> 
> 
>

Received on Wednesday, 28 September 2005 13:46:19 UTC