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Re: HL7 RIM Designtime OWL Runtime RDF

From: Jim McCusker <mccusj@rpi.edu>
Date: Wed, 16 Jan 2013 15:00:04 -0500
Message-ID: <CAAtgn=TkkDW9-LCs39ky_5PT-9HrN8aMaFWVfkDWQgWMg2G-8Q@mail.gmail.com>
To: David Booth <david@dbooth.org>
Cc: Peter.Hendler@kp.org, "Mead, Charlie (NIH/NCI) [C]" <meadch@mail.nih.gov>, Conor Dowling <conor-dowling@caregraf.com>, d.rebholz.schuhmann@gmail.com, Joanne Luciano <jluciano@gmail.com>, Michel Dumontier <michel.dumontier@gmail.com>, w3c semweb HCLS <public-semweb-lifesci@w3.org>, Renato Iannella <ri@semanticidentity.com>, rmrich5@gmail.com, tfmorris@gmail.com
If you would like to validate that an RDF graph hasn't changed, you can
assert it's graph digest. Any new assertions would change the digest hash,
invalidating the asserted graph. The digest can then be signed by the
creator. That would close the (explicit) graph in a very real, computable
way. Here's some howto and implementation:

https://github.com/timrdf/csv2rdf4lod-automation/wiki/frbr:mccusker2012parallel

Related papers:
http://tw.rpi.edu/web/doc/parallelIdentitiesOGD
https://github.com/timrdf/DataFAQs/raw/master/doc/papers/mccusker2012ipaw.pdf

Jim


On Wed, Jan 16, 2013 at 2:46 PM, David Booth <david@dbooth.org> wrote:

> Hi Peter,
>
> On Wed, 2013-01-16 at 08:39 -0800, Peter.Hendler@kp.org wrote:
> > Eric et al,
> > Is there any material on the idea of "design time OWL runtime RDF"?
> >
> > Is it Kosher, once you are done with your reasoners, to convert to RDF
> > and then treat it as if it were closed world like a database?
>
> Absolutely.  Almost all applications use a closed world assumption at
> some point.
> >
> > RIM which is OO, is of course closed world and can be represented in a
> > database. Nothing can change, no new assertions can be made. When an
> > HL7 message is sent, we assume it can't be changed by a reasoner or
> > anything else. It is set in stone. In fact, there are laws. You are
> > not allowed to edit a message once it's been sent.
> >
> > In open world, anyone can add to the triple store at any time, and
> > meanings can change. But in an HL7 message, once you make the message,
> > you are not allowed to amend or add to it.
>
> It should be monotonic, so even though all of the existing statements
> still hold, additional statements may be true also.  When talking about
> "changing" some data, it's important to distinguish between
> (monotonically) adding more data to it and (non-monotonically) modifying
> the existing data.
> >
> > On a related note.  We have different ways of expressing negation to
> > Acts. Much of the complication comes from whether the negation is done
> > in the vocabulary (SNOMED) or the OO part of the model (RIM).
> > How can we tell if two different representations where the is negation
> > expressed on different parts in the model, are semantically the same?
>
> Can you give an example?
> >
> > The terminology (SNOMED open world, OK to use reasoners) and the RIM
> > (OO closed world) can not be mixed (I think).
>
> Why do you say that they cannot be mixed?  You do have to be careful to
> know which data is making what closed world assumption.
>
> > But my question is this.
> > Can you reduce the whole representation of the RIM part of the model
> > and the terminology part (SNOMED) into one set of triples, and then
> > could you reduce two  instances of the these mixed models to graphs of
> > triplets that you can compare?
>
> In principle, yes, I think so.  But let me turn it around the other way.
> I think it is important to design the RDF models such that they can be
> mixed and instances can be compared.  If there are problems in doing so,
> then we need to correct the models to fix them.
> >
> > If you did reduce/normalize the mixed model of the OO RIM and the EL+
> > logic SNOMED into one set of triples.  Could you consider these, for
> > your comparisons, as if they are closed world and simply compare the
> > graph patterns?
> >
> > This is another way to ask.  At any point in the life of a model (HL7
> > message or clinical statement for example), can you just declare "from
> > this point forward, no one is allowed to add to or change this graph
> > in any way", and then treat the whole graph as if it is closed world,
> > even though at an earlier point in the graphs life cycle it did
> > consist of SNOMED (open) and RIM (closed)?  Does it become closed by
> > agreement not to add to it after it is final?
> >
> I think it is critical that the RDF models be designed to be monotonic,
> so that you can always add more information without invalidating
> previous information.  This means that you cannot just say something
> like "Mary is pregnant".  It has to be qualified to a particular context
> or time period, such as "On 1-Jan-2013 Mary's pregnancy test was
> negative".  (Sorry for such an obvious example, but hopefully you see
> what I mean.)
>
> To my mind, monotonicity is the key.  I normally think of "closed world"
> and "open world" as being more about what you *do* with the data, than
> being about the data itself.  If the data is designed to be monotonic,
> then for specific uses you can use closed world reasoning.
>
> With all that said, I'm not certain that I'm really hitting on the
> question that you're raising, so if you can show a more concrete example
> it may help.
>
> Thanks!
>
> --
> David Booth, Ph.D.
> http://dbooth.org/
>
> Loss of web prodigy Aaron Swartz: http://tinyurl.com/ahe2k8c
>
> Opinions expressed herein are those of the author and do not necessarily
> reflect those of his employer.
>
>
>


-- 
Jim McCusker
Programmer Analyst
Krauthammer Lab, Pathology Informatics
Yale School of Medicine
james.mccusker@yale.edu | (203) 785-4436
http://krauthammerlab.med.yale.edu

PhD Student
Tetherless World Constellation
Rensselaer Polytechnic Institute
mccusj@cs.rpi.edu
http://tw.rpi.edu
Received on Wednesday, 16 January 2013 20:00:53 GMT

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