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RE: SenseLab note: should flaws in open source ontology editors be mentioned?

From: Miller, Michael D (Rosetta) <Michael_Miller@Rosettabio.com>
Date: Fri, 16 May 2008 07:50:15 -0700
Message-ID: <C9EDB84D403E654CB78E37A506E406AF01DA64D6@ussemx1101.merck.com>
To: <public-semweb-lifesci@w3.org>
Cc: "Michel_Dumontier" <Michel_Dumontier@carleton.ca>

 
hi all,

i agree with michel's second point ("Concrete suggestions welcome.") but
i also think it is important, since this document can be used as a guide
by others, to point out pitfalls and problems that a new user will face.
in that vein it might be good, as suggested, to provide examples of what
and how issues with the software were worked around (i haven't read the
whole document yet, it is in my to do stack, so perhaps you have) and
how the software could be improved.

cheers,
michael

Michael Miller
Lead Software Developer
Rosetta Biosoftware Business Unit
www.rosettabio.com


> -----Original Message-----
> From: public-semweb-lifesci-request@w3.org 
> [mailto:public-semweb-lifesci-request@w3.org] On Behalf Of 
> Michel_Dumontier
> Sent: Friday, May 16, 2008 7:06 AM
> To: public-semweb-lifesci@w3.org
> Subject: RE: SenseLab note: should flaws in open source 
> ontology editors be mentioned?
> 
> 
> While Xiaoshu brings up an important point of constructive criticism,
> it's not clear from the text that is being done. In the first 
> case, bugs
> happen, and these will get fixed, I don't think it's worth mentioning.
> In the second, I think the topic is much more relevant. However, how
> _exactly_ can the process of "editing the complex, expressive
> ontologies" be improved? Concrete suggestions welcome.
> 
> -=Michel=-
> 
> -----Original Message-----
> From: public-semweb-lifesci-request@w3.org
> [mailto:public-semweb-lifesci-request@w3.org] On Behalf Of 
> Xiaoshu Wang
> Sent: May 16, 2008 6:54 AM
> To: Matthias Samwald
> Cc: public-semweb-lifesci@w3.org
> Subject: Re: SenseLab note: should flaws in open source 
> ontology editors
> be mentioned?
> 
> 
> 
> Matthias Samwald wrote:
> >
> > One feedback I got for the SenseLab conversion note 
> > (http://www.w3.org/2001/sw/hcls/notes/senselab/) was that 
> it might be 
> > inappropriate to mention that flaws in certain popular open source 
> > ontology editors caused problems for our work. To portions 
> of text in 
> > question are:
> I absolutely think it *is* appropriate to mention it.  People takes 
> criticisms too personally, which is not good for the health 
> of science. 
> Truth should be gained through intelligent but authoritarian 
> debate .  
> >
> > """
> > We experienced the following problems while using RDF/OWL:
> >
> > The open-source ontology editors used for this project were 
> relatively
> 
> > unreliable. A lot of time was spent with steering around 
> software bugs
> 
> > that caused instability of the software and errors in the generated 
> > RDF/OWL. Future versions of freely available editors or currently 
> > available commercial ontology editors might be preferable. [...]
> > """
> >
> > and
> >
> > """
> > We experienced clear benefits from using Semantic Web 
> technologies for
> 
> > the integration of SenseLab data with other neuroscientific 
> data in a 
> > consistent, flexible and decentralised manner. The main obstacle in 
> > our work was the lack of mature and scalable open source 
> software for 
> > editing the complex, expressive ontologies we were dealing 
> with. Since
> 
> > the quality of these tools is rapidly improving, this will 
> cease to be
> 
> > an issue in the near future.
> > """
> >
> > In my opinion, the errors in one of the most popular OWL ontology 
> > editors were problematic enough that they need to be mentioned -- I 
> > guess most people working with non-trivial OWL ontologies 
> know what I 
> > mean. What do you think?
> Do it.  I definitely think it should.  In fact, the more popular an 
> ontology, the more stentorian the criticism should be because the 
> potential damage a popular ontology can do is much more than a less 
> popular one.  The problem is the critics but those who is being 
> criticized.  They should take criticism as constructive advise to 
> improve their work but as destructive sense to take them out of their
> job.
> 
> Xiaoshu
> 
> 
> 
Received on Friday, 16 May 2008 14:51:06 UTC

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