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

From: Drew McDermott <drew.mcdermott@yale.edu>
Date: Tue, 15 Aug 2006 12:05:22 -0400
Message-ID: <17633.61634.132413.743145@drew-mcdermotts-computer.local>
To: public-semweb-lifesci@w3.org

> [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.

   Drew McDermott
   Yale Computer Science Department
Received on Tuesday, 15 August 2006 16:05:42 UTC

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