Re: Action-166 Draft sketch of how to serialize rdf annotation spaces - separate files

From: Alan Ruttenberg <>
Subject: Re: Action-166 Draft sketch of how to serialize rdf annotation spaces - separate files
Date: Thu, 17 Jul 2008 02:37:55 -0400

> On Jul 16, 2008, at 5:11 PM, Peter F. Patel-Schneider wrote:
> >> I was worried that was a lot more mechanism, and that given where we
> >> were in the process, the desire to get something in to this release of
> >> OWL, and the desire to keep to schedule and move quickly towards last
> >> call, the amount of work associated with doing that might have been
> >> considered too much. I didn't want to have proposing that much change
> >> put the possibility of getting *something* in this space out of reach.
> >
> > More mechanism than using a separate file?  I view using a separate file
> > as a *very* heavyweight mechanism.
> I'm curious why.

It's and entirely new kind of association.  Although there already is
imports, to me this second file is a very different thing with
unexplored potential ramifications.

> >> In addition there were two technical details which I wasn't sure were
> >> covered by the paper. The first is annotations on annotations. I did
> >> want to make sure some version of this is possible as I am aware of
> >> several use cases in current projects that need it.
> >
> > But your proposal only allows a particular kind of very simple
> > annotations on annotations.  I don't see how that is adequate.  If you
> > think otherwise please put forward the use cases.
> All of the cases I've seen SKOS, OBO, OBI, have essentially boiled
> down to provenance information for the annotations - where a synonym
> came from, who supplied a definition, etc. This proposal covers those
> cases. All I've thought I've ruled out are annotations on annotations
> on annotations (and further levels of same). Do you have use cases in
> mind that go beyond the ones the proposal allows? Could you share
> them? 

I'm guilty of not understanding your proposal here.  I thought that you
only allowed annotations on the annotations in EntityAnnotation axioms.
I see now that you probably allow annotations on just about any
annotation, albeit using an entirely diffferent mechanism -
reification.  Why not reuse the same mechanism?

(I do note that your example here seems to be wrong.)

> In the paper the Annotations are fairly limited as well, but could be
> extended. Having a look at the metaontology
> have AnnotationByEntity and
> AnnotationByConstant. Annotations are not Axioms and so can't have
> annotations themselves. 
> The proposed use of SELF and Annotations (bundles) can do more.

Probably, but this part of your proposal is not developed.

> >> The second was the
> >> issue of how to view that proposal from an RDF point of view.
> >
> > Well, one could just say that the current situation (plus the obvious
> > extension to annotations on annotations) is the RDF point of view for
> > the treatment in the paper.
> We would need more if we were to allow SELF and bundles.

Perhaps. I haven't thought about this much yet.  it appears to me that
bundles can be handled by reification.

> >> I did note that the reification of the axioms and associated ontology of
> >> OWL axioms proposed by the paper seems to not be incompatible with what
> >> I've proposed- in the sense that I can see how one could script the
> >> creation of the reified axioms, and then import that into the second
> >> file.

> > Surely it is easier to do this without having to invoke a
> > special-purpose file-handling mechanism. 
> The file was intended to be OWL-DL, so that the exact same file
> handling that would apply to O would apply to m(O). The sole
> restriction was that ontologies that were imported into it shouldn't
> have annotations themselves, so as to avoid generation of further
> files.  A (perceived) advantage of having the separate file was that
> there was less need for multiple levels of reification to keep the
> annotation facts out of the domain (in the case of
> bundles). Correspondingly, if there is a single file, there is more
> mechanism needed to extract out the two ontologies for reasoning
> separately. 

I meant the file-handling mechanism needed to generate the second file.
> However, one thing I hadn't thought through was interaction with
> imports. Quickthink suggest that if O imports O', m(O) would need to
> import m(O'), but I've added this to the known issues. 

> >> However, I like that paper and its approach and if the WG were wiling to
> >> seriously consider what it proposes I'd certainly support that.

> > Me too.
> >
> > Here is a quick summary of what I see as the gist of the proposal in the
> > paper.  I'm leaving out a few details.
> >
> > Regular reasoning on an ontology proceeds as normal in OWL 2 DL.
> > Annotation reasoning on an ontology O is done by constructing a
> > meta-ontology m(O) containing facts corresponding to the annotations in
> > O plus facts corresponding to the structure of the axioms in O.
> >
> > One could envision a stripped-down version that doesn't include all of
> > the last bit - only individuals corresponding to each axiom in O.
> >
> > It seems to me that the two-file solution has all the machinery of this
> > stripped-down version, plus the complications involved with having two
> > files.
> That's my take as well, subject to the question about where the
> complications arise. It seems that it is a tradeoff of where the
> mechanism is - more files or more specialized encoding/decoding (which
> might complicate use in OWL-R). Solely based on the services
> described, the two file approach might be more appealing to some
> because of the lack of reifications on reifications in the RDF, and
> the implemented (if not standard) means for working with named
> graphs. 
> Something else to consider is whether a two file solution for RDF
> necessitates that the XML syntax do the same thing. I would hope that
> if we did land up with two files in RDF, we could still leave the XML
> version in a single file but haven't thought through how this would
> work. I've added this to the known issues as well. 
> What I found appealing about the paper is the part that goes further -
> the definition of the metaontology, the clearer statement of
> semantics, and the query language. 
> -Alan
> > There are some "extras" that would be useful to have in this proposal,
> > including the ability to put arbitrary axioms into m(O).


Received on Thursday, 17 July 2008 10:31:36 UTC