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

From: Chris Mungall <cjm@fruitfly.org>
Date: Fri, 25 May 2007 14:28:33 -0700
Message-Id: <93EAFDAE-BB41-4BDD-A186-04408BE80C80@fruitfly.org>
Cc: William Bug <William.Bug@DrexelMed.edu>, public-semweb-lifesci hcls <public-semweb-lifesci@w3.org>, obo-format@lists.sourceforge.net
To: samwald@gmx.at

On May 25, 2007, at 8:44 AM, samwald@gmx.at wrote:

>> [2] For instance, definitions in the PATO OWL file (quality.owl) are
>> not visible in Protege.  The OWL version of PATO has an
>> AnnotationProperty called "oboInOwl:hasDefintion" that has the value
>> "@_:A4843".

note there is a protege3 plugin that has oboinowl aware displays

..but of course this doesn't help if you're using  p4, swoop, lsw,  
triple20 on any other sw tool

> I and some other people have already nagged Chris about the  
> representation of defintions and synonyms in the OWL versions of  
> OBO ontologies.

nagging me directly won't do much, it's a collaborative effort. the  
best place to comment is probably here:

my own preferred way of doing this is to use simple class-label  
annotprops and reify them to attach provenance info. this would  
probably be even less popular (even *less* support in owl tools), but  
it makes sense to me. See also the reif/NG discussion on this list -  
NGs would seem clunky here

> This is partly related to a larger problem, namely the  
> inhomogeneous representation of labels, descriptions and  
> definitions among biomedical Semantic Web ontologies.

++ to that

> I have started a Wiki page on this topic:
> http://esw.w3.org/topic/HCLS/Labels_and_Definitions
> The page is intended to contain the following (please add to it /  
> discuss!):
> * Examples from biomedical ontologies of non-standard constructs to  
> represent Labels, names, descriptions and definitions of entities.
> * An analysis of the motivations behind the creation of these  
> constructs
> *A description of the problems that arise through a lack of  
> harmonization (e.g. for queries and user interfaces)
> * A review of the basic constructs in the RDF, RDFS and OWL  
> vocabularies and their intended usage for labels, descriptions and  
> definitions
> * An informal recommendation for the representation of labels,  
> descriptions and definitions and suggestions for the harmonization  
> of biomedical ontologies in this regard.
> I have started comparing the constructs from a few ontologies, but  
> there are many additional ontologies that have created their own  
> style for the representation of this information. We should try to  
> find the smallest common denominator between all these approaches,  
> because this really is a large hindrance to practical  
> interoperability between our ontologies.

seems worthwhile. but if you want it to take off why restrict it to  
the HCLS?

> cheers,
> Matthias Samwald
> ----------
> Yale Center for Medical Informatics, New Haven /
> Section on Medical Expert and Knowledge-Based Systems, Vienna /
> http://neuroscientific.net
> .
> -- 
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Received on Friday, 25 May 2007 21:28:48 UTC

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