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Re: [hcls] Harmonization of labels, descriptions and definitions

From: William Bug <William.Bug@DrexelMed.edu>
Date: Mon, 28 May 2007 23:58:21 -0400
Message-Id: <F7F1389A-95E6-4CA5-9151-2C2B8FDA28A8@DrexelMed.edu>
To: public-semweb-lifesci hcls <public-semweb-lifesci@w3.org>
This is exactly the point I've been making for over a year now  
regarding use of SKOS in biomedical ontology development, and it is  
why we use SKOS:prefLabel for all classes in BIRNLex (as well as  
having the redundant rdfs:label for interoperability purposes).  The  
"altLabel" provides a means not only to associate lexical variants  
but ultimately to create "namespace qualified" term sets or "views"  
of a single ontology with the terms tailored to the needs of a  
specific community.  There would need to be an expansion of  
annotation support in OWL to fully implement this, but SKOS can  
provide a means to standard that method in the lexical domain, once  
the required annotation capabilities have been added to OWL.

SKOS is not perfect and is still a work-in-progress, but my sense  
from my experience in the life science literature database/library  
science community is SKOS has made an excellent effort to incorporate  
many of the lessons learned by that community over the last 30 years  
- and "prefLabel" is one of them.  It's also being moved forward  
rapidly via its association with the W3C SWeb Best Practices and  
Deployment WG and recently published a compendium of Use Cases they  
started collecting last winter, amongst which are many life science  
examples (thanks to the participation of Daniel Rubin from NCBO and  


On May 27, 2007, at 12:59 PM, Alan Ruttenberg wrote:

> In think in the short term, in context of the HCLS demo, we can use  
> SPARUL rules to convert various forms of definitions and labels to  
> the usual rdfs:comment and rdfs:label. The only issue I see is that  
> there is a need for secondary labels (or conversely primary  
> labels), so we might want to borrow skos:prefLabel for cases where  
> we need this. Still, I would have that be redundant with rdfs:label.
> Course there is a problem with, e.g. multiple synonyms - how does  
> one choose the rdfs:label to use in display if there are so many  
> that are not distinguished?
> -Alan
> On May 25, 2007, at 11:44 AM, samwald@gmx.at wrote:
>> I and some other people have already nagged Chris about the  
>> representation of defintions and synonyms in the OWL versions of  
>> OBO ontologies.
>> This is partly related to a larger problem, namely the  
>> inhomogeneous representation of labels, descriptions and  
>> definitions among biomedical Semantic Web ontologies. I have  
>> started a Wiki page on this topic:

Bill Bug
Senior Research Analyst/Ontological Engineer

Laboratory for Bioimaging  & Anatomical Informatics
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

Received on Tuesday, 29 May 2007 03:55:58 UTC

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