Begin forwarded message:
From: Mark Blaxter <mark.blaxter@ed.ac.uk>
Date: Thu Oct 23, 2003 5:27:12 AM US/Pacific
To: Paul Sternberg <pws@caltech.edu>
Subject: Re: nomenclature, non-elegans
Hi Paul
additional comment from me about the naming plan is that as we already
have a stystem in place for non-Caeno parasites, we should continue to
use it, and be forgiving about changes.
Thus
1 we use a two letter species designator, eg bm for brugia malayi
This shouldnt sstop a mix of two-letter and three letter species
designators as long as each is unique. Ralf already uses Cel and Ppa!
2 I would like to make a call for needing the first letter in caps (ie
Bm not bm) and for separating the taxon name from the gene name by a
dash (ie Bm-col-1 NOT Bmcol-1)
3 My preference is for the species name to be italic (makes it obvious
by convention its a taxon name, like italicising species linnean
names) - but obv. theres no italics in scribbles on plates or most
mails, so this is cosmetic.
4 We do need a central registry of these names: we have one we use and
have agreed with nemagene; theres one in our FUNK paper on the
filarial genome project, and theres the original Bird and Riddle set.
I would suggest that Nembase hosts this!
5 There is unfortunately a historical legacy of parasitic gene names
that have been in wide use but which DO NOT match Ce names, for
example "alt" is "axons lose track" in Ce but "abundant larval
transcript" in parasitic datasets. This can be changed, but the
parasite community will be very loath to rescind names it has been
using for years where the Ce gene is robustly obscure. These will have
to stand, and be confusing!
Mark
On Thursday, October 16, 2003, at 10:57 pm, Paul Sternberg wrote:
Dear friends,
I think we have reasonable convergence on a nomenclature plan. (The
immediate motivation is to get briggsae genetic information into
wormbase; there are now many mutations and loci). (Some of you have
already bought on in Spring-Summer 2002 when this first came up).
One briggsae-specific question is what we want to use for species
identifiers (dpy-cb1 rather than dpy-b1, etc.)
Comments?
After dealing with your comments, this will get posted on WormBase,
Society of Nematology, etc.
Thanks
Paul
Revised genetic nomenclature for non-C. elegans nematode species
DRAFT 2003-10-16
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 that 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, but with a species-specific
identifier.
The proposal:
1. Orthologs will be given the same name but with a species prefix.
For example, cb-tra-1 is 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. For paralogs, a “dot and number”
can be appended to distinguish paralogs, e.g., hsp-16.1, hsp-16.2.
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 as a postfix to
the number. 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-CAENORHABDITISBRIGGSAE000000001 etc. The organism’s community
should decide on the exact implementation; this choice will be
tracked by the CGC or WormBase. A species prefix could be added but
will be redundant, e.g., cb-dpy-cb1 OR cb-dpy-B1. OR ce-dpy-1.
C. briggsae gene tra-cb1 does not necessarily correspond to C.
elegans tra-1, tra-2 and tra-3.
2a. We propose that dpy-cb1 be the form for C. briggsae since lower
case is easier to type. (Paul Sternberg, Bhagwati Gupta have so far
expressed this preference.)
3. Gene classes with no equivalent in C. elegans or other species
will be given unique three-letter-number names.
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, “syIs802” is an integrated transgene in C.
briggsae from the Sternberg laboratory; it could be referred to as
cb-syIs802. syIs802will never be used for something else,
especially a C. elegans transgene.
Existing gene classes used in other species could be retained since
there are not too many of them (e.g., ped), but should be retired if
possible.
4a. We propose that the C. briggsae classes be retired
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
another laboratory.)
Notes.
Bird and Riddle (1994 J. Nematol.) proposed nomenclature for
parasitic nematodes. They suggested following the C. elegans
guidelines but with designations in parallel. It would be desirable
for one source (CGC/Wormbase) to enforce uniqueness of lab and allele
designations.
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
uniqueness.
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). Sub-communities
(e.g., those working on Pristionchus or C. briggsae) would tend to
drop lengthy identifiers.
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 known.
e. From a molecular geneticist’s point of view, orthology should be
obvious from the name. There can multiple homologs for a gene, and
orthology might not be clear, especially if full genome sequence is
not available.
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. Depending on the researcher, (b,d) or maximizing (e) and
minimizing (f) is more important.
N. B. There are millions of nematode species.
Paul W. Sternberg
HHMI and Division of Biology 156-29, Caltech
1200 E. Calif Blvd., Pasadena CA 91125
tel 626-395-2181 fax 626-568-8012 email pws@caltech.edu
Admin. Assistant Mary Alvarez 626-395-3990 alvarezm@caltech.edu
Lab webpage: http://wormlab.caltech.edu
WormBase: http://www.wormbase.org
Worm Literature Search Engine: http://www.textpresso.org
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Mark Blaxter
Institute of Cell, Animal and Population Biology
Ashworth Laboratories, King's Buildings
Edinburgh, EH9 3JT, UK
phone: +44 131 650 6760 (lab) +44 131 650 6761
fax: +44 131 650 7489
email: mark.blaxter@ed.ac.uk http://www.nematodes.org
http://www.earthworms.org http://www.tardigrades.org
"I hope there's an animal somewhere that nobody has ever seen.
And I hope nobody ever sees it".
Wendell Berry
Paul W. Sternberg
HHMI and Division of Biology 156-29, Caltech
1200 E. Calif Blvd., Pasadena CA 91125
tel 626-395-2181 fax 626-568-8012 email
pws@caltech.edu
Admin. Assistant Mary Alvarez 626-395-3990
alvarezm@caltech.edu
Lab webpage:
http://wormlab.caltech.edu
WormBase:
http://www.wormbase.org
Worm Literature Search Engine:
http://www.textpresso.org