Subject: Fwd: nomenclature, non-elegans
From: Paul Sternberg
Date: Thu, 23 Oct 2003 08:18:07 -0700
CC: Paul Sternberg

Begin forwarded message:

From: Mark Blaxter <>
Date: Thu Oct 23, 2003  5:27:12 AM US/Pacific
To: Paul Sternberg <>
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.

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!


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.)


After dealing with your comments, this will get posted on WormBase, Society of Nematology, etc.

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.)


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
Admin. Assistant Mary Alvarez 626-395-3990
Lab webpage:
Worm Literature Search Engine:
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

"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
Admin. Assistant Mary Alvarez 626-395-3990
Lab webpage:
Worm Literature Search Engine: