xml-dev - Reification, was Re: Ontologies

[Jonathan Borden <jborden@mediaone.net>]

Martin Bryan wrote:


> Walter Perry wrote:
> >
> >Let us submit the same body
> > of input simultaneously to various different diagnostic
> methodologies--each
> > expressed as an ontology to which we can form a nexus at an addressable
> > node--and, provided that we can retrieve or address the output of each,
we
> can
> > ignore the particulars of what happens in those opaque boxes.
>
> Works OK for short term data, but try looking at medical records over the
90
> year life of a patient on this basis and you will run into problems. Even
> Jonathon will admit that drugs get reclassified in their life-time. You
need
> to know the classification at the time they were administered, not the
> classification today. Opium was de rigour in our grandparents time. Do you
> want it adminstered to your grandchildren?

    Since you mention it, "Opium" is the archetypical "opiate" which is a
class of molecules which bind to "opiate receptors" within the brain and
spinal cord.

    More refined agents such as "morphine", "demerol", "codeine", "fentanyl"
and on and on share the property of opiate receptor binding with their more
natural predecessors. These agents continue in common usage today as pain
relievers.

    Unless our genetics drastically changes I presume our grandchildren's
opiate receptors will remain nearly identical to our grandparent's and there
remains an excellent chance that in the event of  a surgical procedure, a
drug within the "opiate" category would indeed be administered.

    In any case one of the activities of the ASTM XML Healthcare committee
will be to issue an XML DTD for the codification of medical guidelines in
which many of the raised issues are addressed (for example, the authority
issuing the guideline, links to evidence/articles supporting the guideline,
the time period in which the guideline applies, etc. etc.).

    These issues are indeed important, and are readily dealt with by making
assertions regarding the document which defines the relevent portion of the
particular ontology. As I have intimated before, the process of making
assertions (or statements) about statements involves reification. To try to
briefely explain reification:

(note the RDF Interest Group mailing list has had a recent and lengthy
thread regarding the statement [Bush, wonThe, election])

Suppose we have the document:

<RDF>
    <Description about=".../Bush">
        <s:wonThe ID="S1" resource=".../election"/>
    </Description>
</RDF>

    or more compactly:

    <s:wonThe ID="S1" about=".../Bush" resource=".../election" />

    which parses to the following RDF triple:

    (s:wonThe, Bush, election)

    Yet the ID on the statement in the document provides a URI pointing to
*where* this statement was made:

    http://.../somedoc.rdf#S1 (well call this S1 for short)

    Reification of the statement creates the four triples:

    [S1, rdf:type, rdf:Statement]
    [S1, rdf:predicate, s:wonThe]
    [S1, rdf:subject, Bush]
    [S1, rdf:object, election]

    What this says is that:

1) S1 is an RDF Statement stating "Bush won the election"

One can now make assertions regarding this statement:

    "Al Gore asserts on December 13, 2000 that Bush won the election "
<RDF>
   <asserts ID="S2" about="../AlGore">
        <wonThe ID="S1" about="../Bush" resource="../election"/>
    </asserts>

    <date about="#S2">December 13,2000</date>
<RDF>

S1: [Bush, wonThe, election]
S2: [AlGore, asserts, S1]
S3: [S2, date, "December 13, 2000"]

Jonathan Borden
The Open Healthcare Group
http://www.openhealth.org