Complete SGD Gene-naming guidelines
curator at GENOME.STANFORD.EDU
Fri Mar 29 15:56:42 EST 1996
This message is for anyone naming genes in S. cerevisiae. It contains
a detailed "guide" to gene naming in S. cerevisiae, and to "reserving"
S. cerevisiae gene names.
The Saccharomyces Genome Database project has created and is actively
maintaining a database containing all S. cerevisiae publicly-available
nucleotide sequence information, as well as protein information (the
Yeast Protein Database (YPD) of J. Garrels; links to SwissProt and
PIR), physical mapping data (the Olson/Riles Clone Map and Restriction
Map) and genetic mapping data (Mortimer et al. 1992 Yeast 8:817-902).
In addition, the SGD maintains a complete list of all S. cerevisiae
gene names (the "Gene Name Registry"). The task of maintaining the
Registry was transferred to the SGD project by Bob Mortimer in early
1994. The Registry (as well as all other facets of the SGD) is
available via the Web (see below). Among other things, we explore the
literature and GenBank/EMBL/DDBJ/SwissProt/PIR entries to find new
gene names, and then work to resolve any gene nomenclature conflicts.
Below is the first of two installments detailing, respectively, the
SGD's guidelines for (1) Naming genes in S. cerevisiae and (2)
Resolving gene name conflicts.
For further information:
Web site: http://genome-www.stanford.edu/
e-mail: yeast-curator at genome.stanford.edu
*Gene naming in S. cerevisiae*
There are several guidelines to keep in mind when naming
S. cerevisiae genes:
1.) The gene name should consist of three letters (the gene
symbol) followed by an integer.
2.) The 3-letter gene symbol should stand for a description of
a phenotype, gene product or gene function. In addition, we strongly
prefer that a given gene symbol have only one associated description,
i.e., all genes which use a given 3-letter symbol should have a
related phenotype, gene product or gene function.
3.) The gene name should be unique for S. cerevisiae. We
encourage you to search Medline, GenBank/EMBL/DDBJ, and our own SGD
Gene Name Registry (both the Reserved Name list and the Locus Name
list) to ensure that neither the gene name nor the 3-letter symbol
have been used previously. It is prudent to perform searches using
the 3-letter symbol alone, as well as the gene name itself. Note that
SGD curators routinely perform such searches before a gene name is
entered into the database, and we would be happy to check a potential
gene name for you at any time.
When you are close to submitting your gene name for journal
publication and/or to GenBank/EMBL/DDBJ, you may "reserve" the name
with SGD to let other researchers know that the name will be publicly
released soon. See *Reserving a gene name with the SGD* below.
*Reserving a gene name with the SGD*
We encourage you to "reserve" a gene name with the SGD before
submitting it for publication. The purpose of this is to help
Saccharomyces researchers avoid gene name conflicts by including in
the database gene names which will be published soon. The "Reserved
Names" will be included within the Gene Name Registry, which will also
include all "Standard" and "Not-Standard" locus names. Please note
that inclusion of a gene name as a "Reserved Name" is not considered
to be a public release of the name for priority purposes.
To reserve a gene name you need to provide us with your name
and address (including e-mail if possible), as well as the gene name.
We would also appreciate an explanation of the 3-letter gene symbol,
whenever possible. This information, along with the reservation date
(called "Last-Update") and a note to the effect that this is a
"Reserved" name, will be available as part of the SGD database within
the Locus (or "Named-Genes") class, as well as within the
Gene Name Registry. At the time of reservation SGD curators will
check Medline, GenBank/EMBL/DDBJ and the SGD Gene Name Registry to
make sure the name is unique. If it is not unique, you will be
contacted and asked to choose a new name. If unique, it will be
entered into the Gene Name Registry and held there for up to 6 months,
renewable upon petition.
Upon public release of your gene name (defined by publication
of a journal article and/or release of sequence by GenBank/EMBL/DDBJ),
the name will become a "Standard" locus name in the database, provided
that the gene itself and the gene name are still unique at the time of
public release. However, if your gene was shown to be identical to a
previously-named gene, your gene name would become a
"Not-Standard-Name" for the locus, and it and any associated
references would be searchable and linked to the original "Standard"
locus name). Likewise, if during the reservation period your gene
name was publicly used to name a different gene, then a compromise
specific to the situation would have to be worked out. Hopefully this
latter case will be fairly rare.
If at any time you furnish us with data demonstrating that the
gene is novel (such as genetic or physical mapping, or its identity as
an un-named systematically-sequenced ORF), we will consider that the
gene has been uniquely identified and it will be listed as a
"Standard" locus name in the database. If the data have not been
published, a note that you have personally communicated the data to us
will appear with the locus information. We would appreciate being
notified by you of any subsequent publication of the data so that we
can include it in the database.
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