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Re: [ontolog-forum] ambiguity interferes with

To: Deborah MacPherson <debmacp@xxxxxxxxx>
Cc: "[ontolog-forum]" <ontolog-forum@xxxxxxxxxxxxxxxx>
From: Patrick Durusau <patrick@xxxxxxxxxxx>
Date: Mon, 12 Mar 2007 16:28:44 -0400
Message-id: <45F5B7FC.5090706@xxxxxxxxxxx>
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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>> >
>> >
>>
>> -- 
>> 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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