Re: scientific publishing task force update

Ditto to Kei's note at the bottom - with a few qualifiers added in  
the interstices.

BTW - I'd really appreciate hearing from folks what tool they prefer  
for viewing, editing, and creating graphical representations of OWL  
instances.  I've tried several tools from oXygen through Protégé, and  
several other Open Source tools in between and am not completely  
satisfied with any one solution.  There a a few tools available from  
Dr. Hendler's MindSwap site (http://www.mindswap.org) which I like,  
particularly, the OWL SVG Viewer (when I can get it to work right on  
my PowerBook).  It would be very helpful to hear what others have  
found to be the most useful GUI-based tool(s) for human-based OWL doc  
manipulation.

Cheers,
Bill

On Jun 12, 2006, at 1:02 PM, kei cheung wrote:

>
> Jim Hendler wrote:
>
>> At 9:36 -0700 6/12/06, Miller, Michael D (Rosetta) wrote:
>>
>>> Hi Kei,
>>>
>>> Once an OWL ontology is published there are no typos!

Huh?  If you are being facetious, please include a smiley.  :-)

>>> If one wants to
>>> use the ontology, one must conform to the definitions.

term strings are not definitions, they are merely a specific lexical  
tag (likely one of many) for communicating with others (humans or  
algorithms) you are referring to a specific entity.  From the  
algorithm vantage, there had better be a unique identifier  
(preferably a URI) for that entity - from which you could derive a  
definition, if the ontology curator(s) have given one.

>>>
>>> cheers,
>>> Michael
>>>
>>
>> or produce a new, backward compatible version which makes the  
>> change...
>> (or inform the author of the original to fix it in his next release)

Communication with the curating authority is critical.

>>
>> One thing this does teach us is the importance of having the  
>> ontology name space document be at a set URI - this packaging up  
>> OWL in zip files is very harmful to the whole idea of the Seamntic  
>> Web, since the "same" ontology in two different places is really  
>> two different ontologies in actuality, since the URIs are difference.

Absolutely, yes!  It is also extremely harmful to the more top-down  
effort to build a constellation of biomedical ontologies covering  
distinct knowledge domains which are meant to be shared throughout  
the community.

The effort to consolidate/coordinate these efforts via NCBO (aka  
cBiO) and the ontologies themselves within the OBO Foundary will help  
greatly in promoting this approach - both having a unique URI/ 
namespace for each ontology, as well as providing the community a  
communication channel for correcting mistakes, completing incomplete  
entity descriptions, and generally posting requests to expand and/or  
contract knowledge domain coverage in a particular sub-domain of a  
given ontology.  The OBO user-oriented mailing lists set up for each  
specific ontology - in particular, those for PATO & FuGO, are very  
active and can be used quite effectively to ensure the additional  
value any user seeks to add to an ontology can - via the curation  
process for that ontology - can eventually become available to us all  
from a single, canonical source.

>> I've actually suggested to some folks in the OWL community an easy  
>> fix for this, am hoping it will get into one of the notes...
>>  -JH
>>
> I think this are very good points, trying to identify (legal,  
> technical, and social) impediments to semantic web technologies. :-)
>
> -Kei
>
>

Bill Bug
Senior Analyst/Ontological Engineer

Laboratory for Bioimaging  & Anatomical Informatics
www.neuroterrain.org
Department of Neurobiology & Anatomy
Drexel University College of Medicine
2900 Queen Lane
Philadelphia, PA    19129
215 991 8430 (ph)
610 457 0443 (mobile)
215 843 9367 (fax)


Please Note: I now have a new email - William.Bug@DrexelMed.edu







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Received on Monday, 12 June 2006 20:15:34 UTC