Subject: nema genetic nomenclature-2
From: Thomas Burglin
Date: Tue, 29 Oct 2002 19:37:24 +0100
To: Paul Sternberg , , Bhagwati Gupta , Eric Haag , , , , Marie-Anne Felix , Victor Ambros , CGC advisory , , , , , , , , (Richard Durbin), Lincoln Stein ,, spieth John ,

nema genetic nomenclature-2
We should also consider that we want to make our results understandable  people in other research areas
(flies, vertebrates...etc.) thus keeping it as simple as possible would be good (e/f).
In particular, for briggsae and other closely related nematodes, it would be good to make every  effort to
apply point 1 (Orthologs will be given the same name but with a species prefix), rather than 2.

****Philosophy and constraints: 
a. From an informaticianıs perspective, each genetic entity should have a unique name, and there should be an authority to maintain uniqueness. 
b. From a researcherıs perspective, the names should be easy-to-use and intuitive, and not generate confusing nicknames (think about what you would write on the side of your Petri plate). Subcommunities (e.g., those working on Pristionchus or briggsae) would tend to drop
c. If possible, the names should not stifle creativity.
d. From a classical geneticistıs point of view, there should be names that can be used for decades before the molecular identity of a locus is known.
e. From a molecular geneticistıs point of view, orthology should be obvious from the name.  f. However the name should not confuse relationships among genes.
g. Other species names should not crowd out those in C. elegans.

Uniqueness (a) is the overriding concern.  Ease of use is the second priority.  Dependingo n the researcher, (b,d)  or maximizing (e) and minimizing (f) is more important.
Thomas Bürglin, lecturer (Associate Prof.)
Dept. of Biosciences at Novum             
and Center for Genomics and Bioinformatics
Karolinska Institutet                       
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Thomas Bürglin
Dept. of Natural Sciences
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