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

Xiaoshu wrote:
-----------
In short, a Profile is an ontology that only handles the merging of
ontologies but do not create concepts under its own namespace.  All
ontologies shall be deployed as a local ontology, i.e, ontologies without
using foreign concepts. And complext ontologies, i.e., those import foreign
concepts should be normalized into local ontologies and profile.  Such a
separation will increase ontology reuse and system's robustness because all
ontology is disjoint from each other.  In addition, it maximize overall
system expressiveness.  Now, ontology creator shall try to develop ontology
without thinking how it relates to others.  On the other hand, using
o3:Profile allows all ontologies be combined according to a users' viewpoint
or an application profile. The separation, IMHO, is very important.  And
this is a concrete engineer principle that everyone can follow without
subjective debate.
-------------

It is always good to have suggestions and approaches.
I have some questions though:

1. In a Profile - how can it merge ontologies without having "concepts" 
under its namespace -- what good will this bring us??  When you say "merge" 
I assume merge and not integrate.  For example, A "protein_name" and 
"protein_length" can be in one ontology and another ontology has 
"protein_state" and "protein_distance".  Now merging is putting all four 
attributes in a name_space but doesn't create a dependency between the 
attributes -- correct?  This means if I have a protein name I will not be 
able to know its state.  If yes, than what is the benefit of merging them? 
Merge is a useful term and activity when two sets of identical form and 
shape or semantically the same attributes are merged - e.g. proteins from 
Exp1 and proteins from Exp2 when merged will provide me with list of 
proteins I worked on.  Each ontology is different so will the "merge" work??

2. Complex ontologies should be "normalized" into local ontologies.  Hmm, .. 
How do you normalize an ontology and why?  What are the rules according to 
which a normalization "level" is achieved and what are the benefits of a 
normalized ontology.  In a relational database normalization is clear 
according to a set of rules and it is an exercise that is iterated until a 
desired normalization level is achieved (the 5 levels known).  The benefits 
of normalization is to eliminate redundancies, ensure correctness in a 
schema, etc....  Please clarify how does this transfer to ontologies.

I agree with Robert Stevens that more TOOLS are needed so a scientist 
doesn't have to spend few days or months working on normalizing a set of 
ontologies for example.

Thanks
-Wafik


----- Original Message ----- 
From: "wangxiao" <wangxiao@musc.edu>
To: <public-semweb-lifesci@w3.org>
Sent: Wednesday, October 12, 2005 12:58 PM
Subject: RE: Antwort: RE: Semantic web article in Nature Biotechnology


>
> - Robert Stevens,
>
>> My point of substance was about modularisation. I hope that
>> someone will show me how to do it in OWL, after telling me
>> what the behaviour of a module is.
>
> I have came up to this idea. Please see
> http://www.charlestoncore.org/ont/2005/08/o3.html , the ontology's 
> namespace
> URI is http://www.charlestoncore.org/ontology/2005/08/o3#.
>
> In short, a Profile is an ontology that only handles the merging of
> ontologies but do not create concepts under its own namespace.  All
> ontologies shall be deployed as a local ontology, i.e, ontologies without
> using foreign concepts. And complext ontologies, i.e., those import 
> foreign
> concepts should be normalized into local ontologies and profile.  Such a
> separation will increase ontology reuse and system's robustness because 
> all
> ontology is disjoint from each other.  In addition, it maximize overall
> system expressiveness.  Now, ontology creator shall try to develop 
> ontology
> without thinking how it relates to others.  On the other hand, using
> o3:Profile allows all ontologies be combined according to a users' 
> viewpoint
> or an application profile. The separation, IMHO, is very important.  And
> this is a concrete engineer principle that everyone can follow without
> subjective debate.
>
> Of course, how to partition content (not the engineer artifacts) into 
> local
> ontologies is subjective.  Detailed ontology needs a top ontology to help
> them.  For instance, if when MGED is designed with a top experimental
> ontology in mind (something like BOSS.
> http://www.charlestoncore.org/ontology/boss#), content decomposition will 
> be
> easier.
>
> If an ontology developer doesn't know what the system is supposed to run 
> and
> what it can possibly achieve, how can they do things right.  To help them
> "comprehend" is much more important than let them simply "know".
>
> Xiaoshu
>
>
>

Received on Wednesday, 12 October 2005 19:21:23 UTC