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Protege transmutes gold into lead. Was: Re: introduction to OA of pharmacogenomics in product labeling

From: Bob Morris <morris.bob@gmail.com>
Date: Fri, 15 Mar 2013 11:28:07 -0400
Message-ID: <CADUi7O4+AR7GKfpF5RaKD6ka20BA8y8O_OVO8eD4q79r=7vmDw@mail.gmail.com>
To: Paolo Ciccarese <paolo.ciccarese@gmail.com>
Cc: Richard Boyce <rdb20@pitt.edu>, public-openannotation@w3.org
On Fri, Mar 15, 2013 at 10:34 AM, Paolo Ciccarese
<paolo.ciccarese@gmail.com> wrote:
> Dear Richard,
> The first thing I notice right away are the OA definitions as
> AnnotationProperty such as:
> <AnnotationProperty rdf:about="&oa;annotatedBy"/>
> While they are defined as ObjectProperties in OA:
> http://www.w3.org/ns/oa#objectproperties

There is a fair chance that Richard is a Protege victim in this case.
(His RDF was generated by the OWL API according to its comment at the
bottom, and that probably was Protege).  OWL2 direct semantics
declares
    rdfs:label rdf:type owl:AnnotationProperty .
See http://www.w3.org/TR/owl2-rdf-based-semantics/ Table 6.5.

Similarly for rdfs:comment.

As soon as you put one of those on an oa object, as far as Protege is
concerned, it seems to become an owl:Annotation property, no matter
what else it is. (Perhaps this is configurable, and perhaps it is also
mainly a consequence of choices the OWL API makes in serializing as
XML).

We are often nailed by this.  Protege is rather unfriendly to
Individuals.  Alas, I've never found a good free tool that isn't.  My
own practice for hand generation of annotations ---for us as
examples---is to use N3, which is anyway more readable than RDF/XML.

There are some benefits of examining oa:Annotation individuals in
Protege, but I almost always have to clean up if I am tempted to edit
and save with Protege.

>[...]
>
-- 
Robert A. Morris

Emeritus Professor  of Computer Science
UMASS-Boston
100 Morrissey Blvd
Boston, MA 02125-3390

IT Staff
Filtered Push Project
Harvard University Herbaria
Harvard University

email: morris.bob@gmail.com
web: http://efg.cs.umb.edu/
web: http://wiki.filteredpush.org
http://www.cs.umb.edu/~ram
===
The content of this communication is made entirely on my
own behalf and in no way should be deemed to express
official positions of The University of Massachusetts at Boston or
Harvard University.
Received on Friday, 15 March 2013 15:28:42 GMT

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