W3C home > Mailing lists > Public > public-semweb-lifesci@w3.org > May 2008

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

From: Samson Tu <swt@stanford.edu>
Date: Fri, 16 May 2008 13:21:19 -0700
Message-ID: <482DECBF.8010609@stanford.edu>
To: Matthias Samwald <samwald@gmx.at>
CC: public-semweb-lifesci@w3.org


I don't think there is any reason not to report honest opinions as long 
as the sources of problems are clearly identified.

I am curious about the problems you encountered. Had they been reported 
to the protege-owl mailing list? That's the most constructive way to 
help improving the tool.

With best regard,
Samson Tu


Matthias Samwald wrote:
>
>> However, how _exactly_ can the process of "editing the complex, 
>> expressive ontologies" be improved? Concrete suggestions welcome.
>
> The process is not the problem. It would be a good start if the 
> ontology editors would work as advertised, without introducing logical 
> or syntactic errors into the ontologies during normal work procedure; 
> and if they would adhere to the respective standards and not some 
> specific interpretation thereof. I would estimate that 50% of the time 
> editing the SenseLab ontologies was actually spent on fixing problems 
> caused by Protege 3.x. Don't get me wrong, I like Protege, but it can 
> have its downsides in certain scenarios. Swoop also caused me some 
> troubles, and Protege 4 was/is still in Alpha version...
>
> Cheers,
> Matthias Samwald
> Semantic Web Company, Austria // DERI Galway, Ireland
> http://www.semantic-web.at/
> http://www.deri.ie/
>
>
> ----- Original Message ----- From: "Michel_Dumontier" 
> <Michel_Dumontier@carleton.ca>
> To: <public-semweb-lifesci@w3.org>
> Sent: Friday, May 16, 2008 4:05 PM
> 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
>
>
>
>

-- 
---------
Samson Tu                                   email: swt@stanford.edu 
Senior Research Scientist                   web: www.stanford.edu/~swt/
Center for Biomedical Informatics Research  phone: 1-650-725-3391
Stanford University                         fax: 1-650-725-7944
Received on Friday, 16 May 2008 20:21:58 UTC

This archive was generated by hypermail 2.3.1 : Wednesday, 7 January 2015 14:52:36 UTC