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Re: Clarity in naming genes (Was RE: A precedent suggesting ...)

From: kei cheung <kei.cheung@yale.edu>
Date: Tue, 15 Aug 2006 13:01:49 -0400
To: drew.mcdermott@yale.edu
Cc: public-semweb-lifesci@w3.org
Message-id: <44E1FDFD.20206@yale.edu>


Drew McDermott wrote:

>  
>
>>[wangxiao@musc.edu]
>>
>>Quoting "Miller, Michael D (Rosetta)" <Michael_Miller@Rosettabio.com>:
>>
>>    
>>
>>>You're correct here but it is the state of the art.  Interestingly
>>>enough, I've found that in general the biology-based scientists and
>>>investigators are not all that bothered by this confusion and despite
>>>the confusion seem to make their way through it.
>>>      
>>>
>>The problem is that semantic web is intended to make machine to 
>>understand.  And
>>the clarity is a prerequisite to instruct machine unambigously.
>>    
>>
>
>Naming genes is an interesting case where proper names shade into
>generic names.  However, I think on balance genes tend to have so many
>idiosyncratic properties that their names are never going to fit into
>a systematic naming scheme very well.  But remember, the key
>contribution of the semantic-web methodology is to use URIs as names
>--- period.  So long as a URI means only one gene, and everyone agrees
>what gene it means, there is no ambiguity problem.  It's also a good
>idea to avoid having more than one name for a gene, but multiple names
>do not constitute ambiguity, merely inefficiency.
>
>  
>
Hi Drew et al.,

I agree that gene names are interesting use cases for URI/LSID. In 
addition to synonyms (different terms may be used to refer to the same 
concept), we need to deal with homonyms (the same term may mean 
different things). As discussed in the BioRDF call yesterday, I promised 
to come up with some neuroscience examples for URI/LSID, here is one 
such example for looking up the definition of "spine" in wikipedia. 
Notice that this term has different meanings in different contexts 
(biological vs. anatomical). It looks like we might want to think about 
the possibility of providing such a context in LSID for disambiguation.

http://en.wikipedia.org/wiki/Spine_(biology)

http://en.wikipedia.org/wiki/Spine_(anatomy),

Cheers,

-Kei
Received on Tuesday, 15 August 2006 17:02:00 GMT

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