Worm Breeder's Gazette 14(5): 12 (February 1, 1997)

These abstracts should not be cited in bibliographies. Material contained herein should be treated as personal communication and should be cited as such only with the consent of the author.

CGC Genetic Map and Nomenclature Subcontract

Jonathan Hodgkin1, Richard Durbin2, Sylvia Martinelli2

1 MRC-LMB, Hills Road, Cambridge CB2 2QH, England
2 The Sanger Centre, Hinxton, Cambridge CB10 1SA, England

1997 Genetic Map
     The deadline for new genetic map data to be incorporated into the 
1997 Genetic Map of Caenorhabditis elegans (Printed Version) is 30 April 
1997.  Data can be sent:
(preferably) by e-mail to: cgc@mrc-lmb.cam.ac.uk.  Forms for data 
submission are available by e-mail or fax, on request to this address.

(or alternatively) by fax or mail, to: Jonathan Hodgkin, MRC-LMB, Hills 
Road, Cambridge CB2 2QH, England [fax (+44) 1223 412142] 

Genetic Nomenclature
     Recommendations for genetic nomenclature have been based on the 
original paper by Horvitz et al. (1979), plus further recommendations 
published in The Worm Breeder's Gazette.  Summaries of current 
recommendations can be found in Trends in Genetics (1995) and C. elegans 
II (1997) and will be added to websites at the GSA (Genetics Society of 
America), the Sanger Centre, and the UTSW C. elegans WWW site.  As 
indicated in the original paper, these recommendations should be 
regarded as flexible guidelines, to be extended and modified when 

Laboratory Designations
     At the end of 1996, 216 laboratories had strain and allele 
designations registered with the CGC.  New Principal Investigators 
should seek approval for proposed new designations, by e-mail to: 
     In 1994, 18 new labs desginations were assigned; in 1995, 29; in 
1996, 24.  At this rate of growth, there is no danger of running short 
of 2-letter strain and allele designations until well into the next 
century.  We have, however, established a 3-letter strain category, for 
use by nematologists who like the idea of systematized strain names for 
isolates of other nematode species.  Also, there is an increasing number 
of laboratories who are making only minor use of C. elegans as an 
experimental tool, and are therefore unlikely to generate more than a 
few strains or alleles.  For these we have established a group 
designation, "XA" (for strains) and "qa" (for alleles).  Successive 
blocks of 100 XA and qa numbers are assigned to separate laboratories in 
the "minor user" category.

Gene Names
     Recommendations for new 3-letter gene names are included in the 
Nomenclature Guidelines.  We appreciate notification of proposed new 
gene names before publication or submission to databases, especially for 
genes inferred from the genomic sequence data.  Consultation on proposed 
names also helps sort out potential problems with multiple names for the 
same gene, or with the same name being used for different genes.  
Occasionally, we are asked to approve a new name in confidence, which we 
are willing to do.  Otherwise, new gene names will be added to the 
"Gene_Class" list in ACeDB.  A total of 40 new gene names were 
registered in 1995, and 41 in 1996.

Genetic Map
     Data for new genes and rearrangements are solicited from the 
community, and also obtained from the published literature.  E-mail 
forms for the efficient communication of data are available from us, and 
have been used successfully by many researchers.  All such data are 
scrutinized before entry into ACeDB, because some correction or 
modification is often necessary.  For many genes, no data are 
communicated, which means that the relevant information must be 
extracted by us from publications.  For example, the following numbers 
apply to 135 genes added to the map over the past year:
                  Genes defined by mutation       Genes defined by
E-mail submission            24                              3
 (no revision needed)

E-mail submission            30                              4
 (revision needed)

Extracted from publications  28                             46

     The genetic map available through ACeDB is periodically updated 
and corrected, ideally (though not always) with every new data release.  
This process is partly manual, since there is no computer program 
capable of generating the entire map de novo from the available data.  
Assessing contradictions within the genetic data, resolving conflicts 
between the genetic and physical map data, and optimizing the 
representations of the genetic map, are all difficult and time-consuming 
tasks.  A full revision and updating of the map is carried out every two 
years, and a printed version of the ACeDB map is then published and 
distributed as an issue of The Worm Breeder's Gazette.  This issue also 
includes full lists of laboratory designations, gene names and 
definitions, and all registered genes, rearrangements and balancers.
     As more and more genes are included on the map, it has become 
increasingly difficult to provide representations that will please 
everyone.  Using ACeDB, it is possible for any user to generate a 
customized map incorporating only the features desired.  S.M. can 
provide instructions for doing this on request to: sylvia@sanger.ac.uk.  
For the printed map, our options are necessarily more limited.  
Nevertheless, we have been encouraged, by various members of the 
Caenorhabditis research community, to remove from the printed map all 
lethals, all poorly mapped genes, all rearrangements, and all genes 
defined only from physical map data.  These suggestions have been noted, 
but not implemented, since we believe in incorporating the maximum 
amount of information into the printed map, in so far as this is 
possible.  We have also been asked to improve the aesthetic properties 
of the map, but have received few useful suggestions as to how this 
might be achieved.
     Corrections to the map and to the data in ACeDB, however minor, 
are always appreciated, and we would like to thank the many researchers 
who have noticed errors and communicated them to us.