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

To: patrick@xxxxxxxxxxx, "[ontolog-forum] " <ontolog-forum@xxxxxxxxxxxxxxxx>, Pat Hayes <phayes@xxxxxxx>
Cc: "[ontolog-forum]" <ontolog-forum@xxxxxxxxxxxxxxxx>
From: "Smith, Barry" <phismith@xxxxxxxxxxx>
Date: Tue, 01 May 2007 16:27:10 -0400
Message-id: <20070501203213.LCQB14403.mta9.adelphia.net@xxxxxxxxxxxxxxxxxxxxxxxxxxx>

>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
>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.    (01)

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.
BS    (02)

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