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

[Chris M. <cj...@fr...>]

On May 25, 2007, at 8:44 AM, sa...@gm... 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".
>
> 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:
>
> 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 some *experimental* code that does a reasonable job of  
harmonizing the following 3 styles of annotationprops: bfo, birn and  
nci. see

http://www.berkeleybop.org/obo-conv.cgi

it is primarily for owl<->obo -
to harmonize from owl to owl you'd have to do a double transform  -  
and it would all be harmonized to the oboinowl style - but this could  
potentially be modified if there was interest

> 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.
>
> 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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