Worm Breeder's Gazette 13(5): 89 (February 1, 1995)

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.

Request for gene expression pattern information for ACEDB.

Ian A. Hope (1), Sylvia D. Martinelli (2) and Richard Durbin (2),

(1) Department of Pure & Applied Biology and Department of Genetics, The 
University of Leeds, LS2 9JT, UK and (2) The Sanger Centre, Cambridge, 
CB10 1RQ, UK.

      We want to start large scale collection of gene expression data for 
entry into ACEDB.  First, this is part of the genetic description for 
C.elegans, and part of our understanding of this organism's development 
(arguably as important as a mutant phenotype). Second, an expression 
pattern can provide a valuable marker of differentiation and so this 
information should be conveniently accessible.  A long term objective 
would be a series of images, or even a 4D image, for each expression 
pattern, but that requires considerable work.  For now we are asking for 
simple text descriptions of expression patterns.  These may be placed in 
ACEDB immediately and are also readily computer searchable. To  facilitate
entry of text descriptions into ACEDB we are introducing an  email form,
similar to those used for entry of conventional genetic  data.  This will
help standardise this information within ACEDB.  Our  current proposal is
as follows:

      - the first three fields are all required for each entry 
Author:        - format "Hope IA"
Date:          - of data collection, format "2/95" 
Pattern:       - informative text description, will take several lines   

      - also one of the following is required
In_situ:       - name/brief description of probe 
Antibody:      - name/brief description of antibody 
Reporter:      - name/brief description of reporter construct   

      - the following fields are each optional, but are important to fill 
      - where appropriate because they provide links to other objects, as 
      - well as further information.
Reference:     - preferred format "cgc1234", "wbg12.5p35" or "wm93p72"(CGC 
               - bibliography, gazette or worm meeting), otherwise give  
               - standard reference info
Gene:          - gene name, should be present in most cases 
Clone:         - clone name
Sequence:      - e.g. EMBL/GenBank name, or genome project predicted genes 
               - like ZK643.4
Cell:          - specific cells/cell types identified 
Strain:        - important if the pattern is not in a wild type strain

      The whole of your text description will be searchable using the text 
search option in ACEDB, so you should try to use informative key words  in
that.  All the optional fields can be repeated multiple times, for 
example to indicate multiple cells or references.  You can
also add other field names for links to other types of object  (preferably
ACEDB classes).  Multiple entries can be submitted in one  email message,
separated by blank lines.

      The text of this WBG article, together with additional information 
about how to submit data are available by email from Ian, 
pab6iah@lucs-mac.novell.leeds.ac.uk.  Please also send suggestions for 
improvements to the form.  In order to minimize the burden on Sylvia, 
expression pattern information should be sent to Ian, who will check  that
the entry is complete and consistent. He will then relay it to  Sylvia for
inclusion in ACEDB, following any possible communication  about 
clarification/correction with the author.