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   Re: Ontologies

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  • From: Jonathan Borden <jborden@mediaone.net>
  • To: Ronald Bourret <rpbourret@rpbourret.com>,"W. E. Perry" <wperry@fiduciary.com>
  • Date: Wed, 20 Dec 2000 18:16:29 -0500

Ronald Bourret wrote:

> Could you explain at a technical level what is happening? It sounds like
> a node contains code to extract whatever it needs from the input, but
> that this code must be written explicitly. That is:
>    "The point is that in all these cases there is processing
>     code--unique to each node--to be written, and nothing will
>     magically obviate that chore."
> Is this correct?

    This is not my view of things. An ontology defined in RDF e.g. by an RDF
Schema or derivative is simply an XML document whose QNames can be expanded
into a URI (e.g. see http://www.openhealth.org/RDF/QNameToURI.htm). No
processing need occur. Of course the process of resolving a URL e.g. HTTP
GET may involve processing on the part of the HTTP server etc. but this is
all completely straightforward web stuff. To reiterate, RDF provides for the
XML serialization of a directed graph. An ontology places constraints on the
arcs and nodes of a particular graph.

    An ontology itself does not define a processing mechanism. Rather
ontologies are *used* by processing mechanisms.

    The nodes of a directed graph representing an ontology (e.g. a semantic
network) do not require unique processing code. Certainly the resolution of
a URI into a resource *may* involve processing of unique code (e.g. a
servlet) but this is not required by nor central to the definition of an

    I think Walter is proposing a model whereby code is attached to a node
and by all means this may indeed be a useful way to do things, to wire up
the semantic web. My view of the semantic web, on the other hand, is one
where custom code exists in the form of a smart "user agent" that navigates
a web of URIs. Will this actually occur by a plethora of HTTP requests and
responses, or rather will the semantic web be sucked into a central arc
store ala Google, and processing occur in this fashion isn't one I can say,
but the reality will likely be a combination of all the above.

Jonathan Borden
The Open Healthcare Group

> If so, why doesn't this contradict your earlier statement that:
>    "It is just as futile to try solving this problem by creating
>     a separate API for each class of node-to-node pair interactions."
> since the node would need to contain different processing code for each
> node from which it could possibly extract useful data to use as input?
> -- Ron
> "W. E. Perry" wrote:
> >
> > Martin Bryan wrote:
> >
> > > Walter Perry wrote:
> > >
> > > >In fact, aren't we ready to go the whole
> > > way and acknowledge that the ontologies addressable at the nodes of a
> > > semantic
> > > web must in fact *be* executable against the various inputs we put to
> > >
> > > Not unless we agree a fixed API for returning node data in a given
> >
> > No. As I argue regularly at length (and will spare you a full version of
> > the scalability and adaptability of a semantic web (or whatever we call
> > network of autonomous nodes) depends in the first instance on each
> > ability to handle a significant variation of input presentation.
Considered from
> > its own point of view, each node implements one or more processes.
Within its
> > autonomous black box, that node knows what input it requires at the
threshold of
> > executing a process and it knows the output which successful completion
of that
> > process produces. From the node's viewpoint, the forms of both its input
> > output are semantically fixed. That is, both input and output
> > exhibit some structure, and such structure necessarily implies some
> > understanding of the internal relationships of its constituent data and
> > epistemological perspective on that body of data as a whole. That is,
the form
> > of the data, together with such incidentals as what is included or not,
> > significant semantics. A 'fixed API', in exhibiting such a structure,
> > necessarily conveys such semantics of its own. Those API semantics,
however, are
> > unlikely to be the 'native' semantic understanding which both sender and
> > receiver bring to the data that is the substance of any specific
> > between them. In a sufficiently complex network, an agreed fixed API is
> > to represent fully and accurately the semantic understanding of either
> > This has immediate and devastating consequences for the scalability and
> > adaptability of the system as a whole.
> >
> > If there is a single API across the entire semantic web, then as each
node grows
> > more specialized and the interactions among them more complex, an
> > percentage of each node's work will be wasted on conversions in and out
of the
> > API with each process it executes. The maintainer or designer of
> > implementation at each node will face a similarly increasing percentage
> > effort squandered in figuring out how to get from the data presented to
the data
> > required in building the ever more complex functionality required at
> > specialized node. This problem should look very familiar:  those of us
who have
> > been harnessing processes distributed across different enterprises,
> > practices and regulations, time zones, hardware and operating system
> > and interchange protocols have already lived through three generations
> > proposed solutions just since 1980. Need I point out that it is just
> > problem which the semantic web proposes to solve with nodes that
understand the
> > substance of their interaction at a semantic, rather than a purely
> > level (all of it based on the underlying ability of markup to assure
> > self-describing data)? Fine; then get on with it, but don't introduce
> > eventually fatal bottleneck of conversion in every case through a static
> > intermediate level.
> >
> > It is just as futile to try solving this problem by creating a separate
API for
> > each class of node-to-node pair interactions. This is the flaw in the
> > vertical market data vocabularies (ESteel, FpML, etc.--more than 2000 of
> > when I last gave up trying to do an accurate count, as well as to
> > whether even one of them operated from a different premise). To the
extent that
> > a particular node is truly expert--that is, that within the semantic web
> > introduction or application of its unique ontology facilitates a
> > outcome more elaborate, more nuanced, or in some other way more than the
> > denominator of the vertical market vocabulary--that node requires a
> > semantic vocabulary to express the output of its process. To my mind,
this is
> > precisely why we use *extensible* markup as our basic syntax. For any
node to
> > make use of the particular expertise of another surely means using
> > what is unique to the output of that node. This means using as an input
what is
> > outside the standard API in the output of that node. So, in order both
to have
> > access to the particular expertise of other nodes, and also to avoid in
> > general case the proliferating waste of constant conversions into and
out of
> > standard APIs, why don't we try a different premise entirely:  that it
is the
> > responsibility of each node to instantiate for its own purposes (and
> > in its unique native semantics) whatever it might take as input from the
> > output of another node.
> >
> > Not only does this put the solution to the problem in the right place
> > philosophically, but as a practical matter it correctly factors the
> > design, implementation and maintenance tasks incumbent on the expertise
of each
> > node. The node's expectations for input data necessarily reflect its
> > understanding of the process it is to perform, the unique ontological
> > it instantiates. Part of what is unique about that node is the process
by which
> > it gets data from a form in currency outside of it into the unique
internal form
> > which directly expresses its epistemology. To share that form with an
> > data provider might well mean sharing, for example, the algorithmic
processes by
> > which that form is achieved, which may be the very raison d'etre of this
> > Why undo the useful factoring of a problem which incorporates this node
into its
> > solution? It may also be that the data provider's understanding of its
output is
> > fundamentally at odds with this node's understanding of that same data
as input.
> > This touches directly upon the very nature of reuse. Surely one crucial
> > of a semantic web is that different nodes may take the output product of
any one
> > and do vastly different things with it, predicated on entirely different
> > of how, within their individual ontologies, the product of that node
should be
> > understood. This is why it is a semantic web and not a semantic
pipeline, though
> > the thread of any sequence of processes within it might be most easily
> > understood as a unidimensional pipe. And, finally, the practical
business of
> > instantiating input data afresh to fit the ontology of each node just
isn't that
> > difficult in most cases. The node already knows what it needs, so the
> > side of the 'transform' (both contentious terms here, I know) is already
> > To the extent it is looking for some component of the input which is
unique to
> > the data source node, behavior which utilitizes that unique element has
> > been built into this receiver and with it, presumably, some hints to
> > what it is looking for. To the extent that it has some previous
experience with
> > this data source node, this receiver has previous familiarity with the
forms of
> > data which it has received and with how it has previously instantiated
that data
> > for its own purposes. Finally, even where input data may appear at first
> > incomprehensible, it is often possible for the receiver to instantiate
it by
> > brute force into something usable. The receiver knows, after all, the
> > semantics which its own processes require. If by working the
permutations of
> > instantiating what it receives into possible versions of what it needs,
and then
> > by performing its unique processes upon one of those versions, the
receiver is
> > able to achieve a useful--for it--outcome, no one else has the standing
to say
> > that this was not a correct instantiation of the input data. The point
is that
> > in all these cases there is processing code--unique to each node--to be
> > and nothing will magically obviate that chore. This is why I agreed so
> > wholehearted with Jonathan Borden's analogy of the specification of an
> > to source code. If the 'ontological node' is going to *do* anything
useful then
> > yes, of course, executable code is what is required.
> >
> > >
> > >
> > > >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
> > > > 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.
> > > 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
> > > want it adminstered to your grandchildren?
> >
> > As I hope I have very nearly exhaustively covered above (and I said that
> > would not be the version in full!--sorry), this is simply a task
fulfilled by
> > the proper factoring of the problem at each node, based upon the unique
> > expertise of that node. In the example case, if a constellation of
symptoms is
> > submitted to multiple diagnostic nodes (good practice), there must then
be a
> > node which effectively proxies for this particular patient, or perhaps
for this
> > particular patient as treated under the philosophy of his trusted
primary care
> > physician, which then evaluates the various diagnoses and prescriptives
from the
> > unique perspective which none of the diagnostic nodes can have--that of
> > unique individual who will implement the next step of the process.
> >
> > Respectfully,
> >
> > Walter Perry
> --
> Ronald Bourret
> Programming, Writing, and Training
> XML, Databases, and Schemas
> http://www.rpbourret.com

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