is Cb-tra-1 or Cbtra-1 preferable?
Cb-tra-1, definitely. It puts a separator between different types
of information. Also, if the day ever arises when we need
>3-letter gene classes, Cb-trac-1 can still be parsed, whereas
Cbtrac-1 could be Cb-trac-1 or Cbt-rac-1.
(214) 648-4931 (voice)
Department of Molecular
University of Texas Southwestern Medical Center
6000 Harry Hines
At 07:21 AM 10/29/2002 -0800, Paul Sternberg wrote:
an attempt at convergence based on all the nice arguments. I am
particularly swayed by the wishes of those practicing intense classical
genetics on other species (Ralf, Marie-Anne, Takao, Bhagwati, Eric), and
thus think we need to use a dpy-LETTERSnumbers scheme for
I propose that we submit a draft guidelines to the WBG, and call for
comments, since I am sure we have not run this by all interested
parties. A final version will then be sent to the next Gazette, and
submitted for publication.
We still need some guidelines for orthologs.
Revised genetic nomenclature for non-C. elegans nematode
species DRAFT 2002-10-29
Under the current nomenclature system for non-C. elegans nematode
species, each gene class in a given species has a unique three-letter
gene class name which does not overlap with other species. e.g.
the C. briggsae equivalent of dpy is cby, and the
equivalent of unc is mip. However, with over 1100 gene
classes in C. elegans and an increasing number of species under
study, this will soon become unmanageable. We therefore propose an
alternative nomenclature system that will allow genes with similar mutant
phenotypes in other species to keep the same gene class name.
****Philosophy and constraints:
a. From an informatician’s perspective, each genetic entity should have a
unique name, and there should be an authority to maintain
b. From a researcher’s 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 geneticist’s point of view, there should be names
that can be used for decades before the molecular identity of a locus is
e. From a molecular geneticist’s 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.
N. B. There are millions of species.
1. Orthologs will be given the same name but with a species prefix.
For example, Cb-tra-1 for the C. briggsae ortholog of C.
elegans tra-1. In some cases, there will be paralogs and some
confusion; we expect this to be minor compared to the convenience of
having orthologs having the same names. (question: is
Cb-tra-1 or Cbtra-1 preferable?)
2. When a gene is identified in another species that belongs to a gene
class with a clear equivalent in C. elegans, it should be given
the same gene class name, but with a unique symbol. The symbol will
include one or more letters followed by a number.
For example, C. briggsae genes could be dpy-cb1 OR
dpy-B1 OR dpy-CAENORHABDITIISBRIGGSAE000000001 etc. The
organism’s community should decide on the exact implementation; this
choice will be tracked by the CGC or WormBase. A species prefix can
be added but will be redundant, e.g., Cb-dpy-cb1 OR
3. Gene classes with no equivalent in C. elegans or other
species will be given unique three-letter-number names. There could
be a standard name class for “classically-defined genes” such as cdg- or
gen- or ?
4. For alleles, strains, polymorphisms, rearrangements, transgenes,
and other variants, unique numbers (unique across all species) will be
assigned by the relevant laboratory using the standard C. elegans
nomenclature. In all cases, a species prefix can be used, but is
redundant. For example, “syIs701” is an integrated transgene
in C. briggsae from the Sternberg laboratory; it could be referred
to as Cb-syIs701. In this case, syIs701 will never be used
for something else, especially a C. elegans transgene.
Responsibility for the numbering of a gene class will reside with the
assigning laboratory, unless transferred by them to WormBase and the
Caenorhabditis Genetics Center. (As in the present practice,
in some cases, if desirable, a small block of numbers can be assigned to
Jonathan Hodgkin, Paul Sternberg, Ralf Sommer, David Baillie, Marie-Anne
Felix, Donald Riddle, Takao Inoue, Bhagwati Gupta, Eric Haag, Erik
Jorgensen, Iva Greenwald, Susan Strome, Victor Ambros, ….
TO BE CONSULTED: Ronald Ellis, David Fitch, Mark Viney, Mark
Blaxter, Jim McCarter,….others?
A. Should we allow more letters?
****Arguments (not for inclusion in the draft):
dpy(e1111)(e1112) is not viable for the e1112 allele of dpy(e1111).
Subcommunities can still talk in shorthand.
For example, would use dpy-1 rather than
dpy-CAENORHABDITIISBRIGGSAE000000001 just as I might write ‘d1’ on a
An alternative to the letter/number scheme is to start with dpy-1000 for
If someone has a particularly nice example of real alleles, that would be