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.
(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.