Debbie, (01)
Thanks! No, I hadn't seen that one, but had seen "The Success (or not)
of HUGO Nomenclature" by Javier Tamames and Alfonso Valencia,
http://genomebiology.com/2006/7/5/402, which is along similar lines. (02)
Hope you are having a great day! (03)
Patrick (04)
Deborah MacPherson wrote: (05)
> Hi Patrick -
>
> Interesting. Have you seen the paper "What Gene Do You Mean" by Barend
> Mons? http://www.biomedcentral.com/1471-2105/6/142
>
> Debbie
>
> On 3/12/07, Patrick Durusau <patrick@xxxxxxxxxxx> wrote:
>
>> Deborah,
>>
>> Deborah MacPherson wrote:
>>
>> > Right - but - when you are drawing, for example in AutoCAD, there are
>> > however many underlying strings of codes, positions, and lengths
>> > relative to an arbitrary 0,0....the act of drawing simply happens to
>> > figure out relationships in a methodical fashion and the operators
>> > never see the bottom level the computer uses to capture or regenerate
>> > the drawing. There is no reason for a CAD operator to look at at that
>> > level to see what they are drawing. Adrian Walker shows this as a blue
>> > line - tasks and decisions that happen above or below the line.
>> >
>> I assume you mean the "blue line" on Adrian's slide 28 for example?
>>
>> I am not sure that is a helpful distinction other than to illustrate
>> that most users don't consider that there may be a semantic disconnect
>> between their use of a term and the term used by others. Adrian says
>> "model" and I suppose that is fair since neither users uses a term in
>> isolation from all the other terms in their environment.
>>
>> > Where this distinction occurs in the subject maps you refer to are
>> > what I will be looking for in the link below. Honestly, I don't care
>> > about naming, I prefer numbers. I only really care about proportions
>> > and putting things that belong together next to each other for easy
>> > access and a flow or planned unfolding of a story - as if conceptual
>> > or digital structures could be like visiting a museum and feel like
>> > you are discovering and seeing but actually being led through by
>> > someone who loves the materials.
>> >
>> Well, it is certainly possible to construct a subject map that results
>> in the type of goo that is the result of a Google search. Nothing in
>> that paradigm guarantees that authors are going to make sensible or even
>> useful choices. I suspect that is rather difficult for any abstract
>> formal model to enforce.
>>
>> What subject maps do recognize is that you and I may have completely
>> different ways to identify the same subject. What is more, either one of
>> us or even a third person, take Jack in this case, can create a rule
>> that adds the same third identification to both of our proxies along
>> with a rule that says in the presence of that third identification,
>> these proxies merge. (That is one model of merging, there are others.)
>> The result is a single representative for the same subject.
>>
>> Note that each of our identifications persist (at least under the model
>> I have suggested), which means that we have not arrived at a common
>> identification (one of the failing goals of the SW) and that we can in
>> fact find the "foreign" identifications when we arrive at the proxy by
>> our identifications.
>>
>> While it is possible in some situations to write inference rules to
>> result in that sort of merging, what puzzles me is the apparent
>> adversion to using the currently best inference engine that is
>> available, people. Granted there is a lot of data already and more
>> appearing everyday but surely the authors of that data thought it meant
>> something in some particular domain.
>>
>> In a following post you make the point that simply knowing the domain
>> would be a big step in terms of dealing with ambiguity. Take gene names
>> for example. Simply knowing that a term is used for a gene would at
>> least reduce the problem to one of ambiguity in the domain of gene
>> names. And there are distinctions within that domain that are almost as
>> simple and that would further reduce the ambiguity. All without
>> constructing ontologies or other mechanisms to assist in the research
>> problem of "intelligent" agents. Not that I am unsympathetic to that
>> problem, but I would rather have useful results sooner than later. Or in
>> the case of "intelligent" agents as envisioned by TBL, much later (if
>> ever).
>>
>> Hope you are at the start of a great week!
>>
>> Patrick
>>
>> > Debbie
>> >
>> > On 3/11/07, *Jack Park* <jack.park@xxxxxxx <mailto:jack.park@xxxxxxx>>
>> > wrote:
>> >
>> > Debbie,
>> > There is a bit more at
>> >
>>
>http://www.sciam.com/article.cfm?chanId=sa003&articleId=5021D304-E7F2-99DF-33DDD86F3B3ECA20
>
>>
>> >
>>
><http://www.sciam.com/article.cfm?chanId=sa003&articleId=5021D304-E7F2-99DF-33DDD86F3B3ECA20>
>
>>
>> >
>> >
>> > It's worth reiterating one point in light of your inquiry: subject
>> > proxy
>> > objects are the objects contained in a subject map. A subject
>> proxy,
>> > itself, could be as simple as a database table the columns of
>> > which are
>> > propertyType and propertyValue (in the simplest possible
>> rendition).
>> > Therefore, RDF is a reasonable way to represent the properties
>> > contained
>> > in a subject proxy.
>> >
>> > Among those properties will be "name properties"; every
>> knowable name
>> > for the subject represented by the subject proxy can be gathered
>> > together for each with some metadata such as language or usage
>> or name
>> > type (e.g. acronym). With that organization, you can create a
>> social
>> > bookmarking website such as Tagomizer or Fuzzzy and, at the same
>> > time,
>> > have a name be used without ambiguity in relation to many
>> different
>> > subjects. Some names, e.g. "George Bush" can serve the proxies
>> that
>> > represent both presidents and a tag with the same name. Each
>> actual
>> > proxy carries a locator, the database identity, which, itself,
>> > could be
>> > a URI as has been discussed at length here. By separating names
>> from
>> > identity, we are able to accommodate many uses for the same name
>> > string.
>> > Other properties facilitate disambiguation when a name string is
>> > used as
>> > a query.
>> >
>> > IMHO, with that architecture, or at least attention to what that
>> > architecture offers as one creates ontologies, conceptual
>> graphs, or
>> > other representation systems, one need not write any "design
>> criteria"
>> > or even "building codes" for naming since the identification
>> scheme is
>> > decoupled from naming conventions. Within subject/object
>> > identification
>> > schemes, I have no doubt that "building codes" will be
>> appropriate.
>> > Please note that I am using the term "naming conventions" here in
>> > a way
>> > that seems vastly different from the way everybody else appears to
>> > use
>> > that term; indeed, I suspect that when the term "name" is
>> applied to a
>> > concept, what is meant is "identifier". I use the term "naming
>> > convention" more as an oxymoron: the only naming conventions I
>> have
>> > experienced appear in such contexts as, for example, giving the
>> first
>> > daughter the grandmother's name as a middle name, following the
>> > appending of "jr", "II", etc to children who take a parent's name,
>> > and
>> > other naming practices. I'm waving arms and leaving a lot out
>> > here, but
>> > my intent is to show how I see "naming conventions" in the grand
>> > scheme
>> > of communications.
>> >
>> > In terms of naming subjects, well, those come from everywhere
>> and are
>> > just strings that are often ambiguous, as my experience with
>> homeland
>> > security suggests.
>> >
>> > In terms of identifying conventions, the story is quite different;
>> > names
>> > *can* serve in identification, but they often should not be the
>> sole
>> > property associated with identity. My experience with Philippine
>> > Airlines giving my frequent flyer mileage to someone who was
>> born on a
>> > different date strongly suggests their computer programmers don't
>> > know that.
>> >
>> > Jack
>> >
>> > Deborah MacPherson wrote:
>> > > Thanks John, printing and reading. Actually, I think ambiguity
>> > may be
>> > > what makes the world go around and look forward to reading these
>> > materials.
>> > >
>> > > Thanks Jack, I'm so happy to see you describe the examples as
>> > "crafted"
>> > > and will look at these. It would be interesting to hear the
>> > > author/artist Steve Newcombs views. I realize now after reading
>> > > ontolog-forum that probably homegrown tags and tag gardeners are
>> > what
>> > > I'm interested in mainly to connect these people to their
>> > counterparts
>> > > at museums and other government organizations with public
>> > information.
>> > >
>> > > In my opinoin, what needs to happen is writing or specifying
>> > this design
>> > > criteria, which I don't think is an ontology after all. If there
>> > could
>> > > be what Pat Hayes called a kind of "building code" that would
>> > really let
>> > > the tag gardeners and PhD curators, research scientists and
>> others
>> > > actually connect to each other on a level playing field. Will
>> > look at
>> > > your suggested links and digest them for awhile now. Thanks.
>> > >
>> > > This things have been bothering me and I appreciate the pointers
>> > and
>> > > explanations.
>> > >
>> > > Sincerely,
>> > >
>> > > Debbie
>> > >
>> > > On 3/10/07, *John F. Sowa* < sowa@xxxxxxxxxxx
>> > <mailto:sowa@xxxxxxxxxxx> <mailto: sowa@xxxxxxxxxxx
>> > <mailto:sowa@xxxxxxxxxxx>>>
>> > > wrote:
>> > >
>> > > Debbie,
>> > >
>> > > Ambiguity is inevitable.
>> > >
>> > > It sometimes causes trouble. For certain special cases,
>> > > it is possible to create artificial languages that
>> > > eliminate ambiguity -- but *only* for those special cases.
>> > >
>> > > It is not possible to eliminate ambiguity, because that
>> > > would also freeze science, engineering, business, art, and
>> > > *life* in a static, unalterable toy universe that endlessly
>> > > repeats its preset moves -- like a computer program.
>> > >
>> > > See the following abstract and paper.
>> > >
>> > > John
>> > > ________________________________________________
>> > >
>> > > Source: http://www.jfsowa.com/pubs/dynonto.htm
>> > >
>> > > A Dynamic Theory of Ontology
>> > >
>> > > John F. Sowa
>> > >
>> > > Abstract. Natural languages are easy to learn by infants,
>> > they can
>> > > express any thought that any adult might ever conceive,
>> and they
>> > > accommodate the limitations of human breathing rates and
>> > short-term
>> > > memory. The first property implies a finite vocabulary, the
>> > second
>> > > implies infinite extensibility, and the third implies a
>> > small upper
>> > > bound on the length of phrases. Together, they imply that
>> > most words in
>> > > a natural language will have an open-ended number of senses
>> > — ambiguity
>> > > is inevitable. Peirce and Wittgenstein are two
>> philosophers who
>> > > understood that vagueness and ambiguity are not defects in
>> > language, but
>> > > essential properties that enable it to accommodate
>> anything and
>> > > everything that people need to say. In analyzing the
>> > ambiguities,
>> > > Wittgenstein developed his theory of language games, which
>> > allow words
>> > > to have different senses in different contexts,
>> > applications, or modes
>> > > of use. Recent developments in lexical semantics, which are
>> > remarkably
>> > > compatible with the views of Peirce and Wittgenstein, are
>> > based on the
>> > > recognition that words have an open-ended number of
>> > dynamically changing
>> > > and context-dependent microsenses. The resulting flexibility
>> > enables
>> > > natural languages to adapt to any possible subject from any
>> > perspective
>> > > for any humanly conceivable purpose. To achieve a comparable
>> > level of
>> > > flexibility with formal ontologies, this paper proposes an
>> > organization
>> > > with a dynamically evolving collection of formal theories,
>> > systematic
>> > > mappings to formal concept types and informal lexicons of
>> > natural
>> > > language terms, and a modularity that allows independent
>> > distributed
>> > > development and extension of all resources, formal and
>> informal.
>> > >
>> > >
>> >
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>> >
>> >
>> > --
>> >
>> > *************************************************
>> >
>> > Deborah MacPherson
>> > www.accuracyandaesthetics.com <http://www.accuracyandaesthetics.com>
>> > www.deborahmacpherson.com <http://www.deborahmacpherson.com>
>> >
>> > The content of this email may contain private
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>> >
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>>
>> --
>> Patrick Durusau
>> Patrick@xxxxxxxxxxx
>> Chair, V1 - Text Processing: Office and Publishing Systems Interface
>> Co-Editor, ISO 13250, Topic Maps -- Reference Model
>> Member, Text Encoding Initiative Board of Directors, 2003-2005
>>
>> Topic Maps: Human, not artificial, intelligence at work!
>>
>>
>>
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>
> (06)
--
Patrick Durusau
Patrick@xxxxxxxxxxx
Chair, V1 - Text Processing: Office and Publishing Systems Interface
Co-Editor, ISO 13250, Topic Maps -- Reference Model
Member, Text Encoding Initiative Board of Directors, 2003-2005 (07)
Topic Maps: Human, not artificial, intelligence at work! (08)
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