On May 25, 2007, at 8:44 AM, [EMAIL PROTECTED] 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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