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

Dear Robert,  We certainly do need to enable, but I do see preaching
as critical as well.  I see it happen far too often in our field that
people jump into large projects and "just do it" without proper
design and deliberation up front.  They end up wasting huge amounts
of effort, and creating artifacts that waste the time of others
as well.

Biologists learn the importance of designing their experiments
carefully; I think it is imperative for the computer scientists
among us to also teach them the importance of designing their
software carefully.

P


Robert Stevens wrote:
> 
> Principles are all well and good, but we should know from decades of 
> software engineering that saying "do it properly" isn't a solution. We 
> need tooling and methdologies that do not in themselves hinder a domain 
> specialist. In many cases it is easier to re-develop than re-use or even 
> cut-and-paste from an existing ontology than it is to muck around "doing 
> it properly".
> 
> Of course, I'd love a world of ontologies done properly, but 
> realistically, life is often too short. As a comunity we need to enable 
> rather than preach.
> 
> Robert.
> At 03:38 30/09/2005, wangxiao wrote:
> 
>> To Helen Chen,
>>
>> > 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.
>>
>> Of course, it is not the job of SW to well-coordinated ontology creation.
>> But we need to have a common vision how ontology is going to evolve over
>> time.  For instance, when I design a 2D gel ontology.  When I want to
>> specify that "spot shape Ellipse".  I would put Ellipse in a separate
>> namespace because the existence of Ellipse has no effects on the
>> conceptualization of "spot".  By this, if there is a well defined 
>> geometry
>> ontology along with a software library.  I can easiy switch to it without
>> breaking my gel ontology.  Such kind of engineering principle will 
>> help us
>> to build resuable ontology.  The charter shall make such 
>> recommendations to
>> principles like that.
>>
>> > 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.
>>
>> It will help if the "fragmented" means "orthogonal".  If two ontologies
>> overlap, you need to merge or align them, which IMHO is not an easier 
>> task!
>> Again, if everytime I want to use ontologies build by others, I need to
>> manually tweak it a little bit.  We lost the spirit of SW a little 
>> bit.  I
>> am not saying that we can avoid the problem but good engineer 
>> principle can
>> minimize it.
> 
> 
>

Received on Wednesday, 12 October 2005 10:54:17 UTC