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

Peter,

Yes, totally agree -- methodologies are good, or at least good 
methodologies are good. Our methodologies and principles need to get a 
little further than "do it properly". I also think there are many lessons 
to be learnt from software engineering -- there are many good methodologies 
and most people still hack. However, the only way software engineering 
methodologies work is by having tools.

All this was, if I remember correctly, from a call for modular ontologies. 
certainly in the OWL world there isn't much support and we haven't decided 
what it means anyway. So how can we call for decently modular ontologies 
when we don't really know ourselves.

there was a notion of a module should mean that no one re-using that module 
would ever need to edit said module. I suspect this means one axiom per 
module. such a tool would, I think, result in what is popularly known as an 
editor.

Nevertheless, we're largely agreeing furiously.

robert.
At 12:17 11/10/2005, Peter Karp wrote:
>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 Tuesday, 11 October 2005 19:43:51 UTC