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Re: [ontolog-forum] Topic maps and the "wheel" of "logical semantics": w

To: "Smith, Barry" <phismith@xxxxxxxxxxx>
Cc: "[ontolog-forum]" <ontolog-forum@xxxxxxxxxxxxxxxx>
From: Patrick Durusau <patrick@xxxxxxxxxxx>
Date: Tue, 01 May 2007 16:42:49 -0400
Message-id: <4637A649.4050503@xxxxxxxxxxx>
Barry,    (01)

Smith, Barry wrote:    (02)

>> patrick durusau wrote:
>> Let's take another specific example: The gene for the chemokine
>> lymphotactin was was discovered by by three different groups, who
>> promptly named it SCM1, ATAC and LTN. It is also known as LPTN and has
>> an "official" name of XCL1.
>> There are at least two ways that we could devise a mapping that would
>> result in a "merging of those different identifications.
>> 1) A researcher reading the literature notices that ATAC identifies the
>> same subject as XCL1 and enters that mapping in a topic map. (I am
>> grossly over simplifying, the string "ATAC" is obviously inadequate for
>> identifying this gene. A google search today  returnds some
>> 4,900,000,000 "hits" and not all of them are about this gene.
>> 2) Assuming the existence of an ontology upon which to base inferencing
>> (yes, I know gene ontologies exist) and assuming that all these terms
>> havebeen mappped to that  (note singular) ontology, then you could use
>> an inferencing engine to produce the same result.
>> As I said above, topic maps are not constrained to use only one or the
>> other.
>> So, why would I ever want to use #1 and not #2? Well, let's look at :
>> "The success (or not) of HUGO nomenclature," Genome Biology 2006, 7:402.
>> (http://genomebiology.com/2006/7/5/402) That is the source of the
>> foregoing example. The authors found that there is no clear tendency for
>> authors to adopt official symbols. And that 14% of genes are never
>> referenced using the official symbols.
>> That doesn't bode well for any system, such as an inferencing engine,
>> that depends upon a particular nomenclature mapping for success. That is
>> *not* a dig at logic or  inferencing  engines, just recognition that the
>> initial condition for sucess, a common ontology to which genes are
>> mapped, is highly unlikely.
>> So, it isn't really logic-phobia but facing what I think you would call
>> an "objective fact," that is that people are going to identify the same
>> subject differently and that includes the ontologies that they will
>> choose (or not) to use. If you have the information necessary to support
>> an inferencing engine, by all means, use one in your topic map.
>> Or to put it another way, if you can support an "intelligent agent,"
>> then do so. But don't overlook "intelligent users" while waiting for
>> "intelligent agents" to arrive on the scene.
> It might perhaps be useful to record how these problems are in fact 
> being solved. Expert (PhD biologist) curators, working for model 
> organism databases, curate biological literature by creating 
> annotations linking (e.g.) gene and gene product names from standard 
> nomenclatures to terms in ontologies (such as the Gene Ontology). 
> Naturally the curators use standard names for genes and gene products, 
> just as they use terms from standardized vocabularies. The fact that 
> biological literature is full of non-standard designations calls for 
> hard work on the part of these curators. Attempts to short circuit 
> this hard work via automatic reasoning, e.g. via dynamic statistical 
> clustering of the sort predominantly associated with topic maps, have 
> not, thus far, been successful.    (03)

Thanks for the update!    (04)

One quibble: Why do you say that "dynamic statistical clustering of the 
sort predominantly associated with topic maps..."? I am unaware of that 
association. Can you point to some topic map project using that technique?    (05)

Yes, I agree that any solution will require hard work by curators (if 
not the entire community). And by curators (or others) in other communities.    (06)

Hope you are having a great day!    (07)

Patrick    (08)

> BS
>    (09)

Patrick Durusau
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    (010)

Topic Maps: Human, not artificial, intelligence at work!     (011)

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