Revisions to Gene Naming Guidelines
- The
following revisions were agreed upon by the community of yeast researchers at
the Cold Spring Harbor Yeast Cell Biology meeting (August 12-17,
2003):
- In order for a reserved gene name to become a standard gene name,
it must be published in a peer-reviewed journal article.
- Once a gene name reservation has expired, the gene name
reservation will be removed if there is no response from the
researcher for 6 months after the reservation has expired. For
further details, see policies regarding the
expiration of a gene name reservation.
- Gene name conflicts that have arisen in the past have convinced SGD
curators that an "in press" paper can no longer be sufficient to
change a reserved name to a standard locus name. A reserved name
becomes a standard name on the date it is published in a journal
article.
- Two major changes were agreed upon by the community of yeast researchers at the Cold
Spring Harbor Yeast Cell Biology meeting (August 12-17, 1997):
- Submission of a sequence to GenBank/EMBL/DDBJ with a locus
name is no longer sufficient to make that gene name the "Standard"
locus name in the database.
- The length of time that a gene name can be reserved at SGD has
been increased from 6 months to one year.
15 May 1998
To avoid gene naming
conflicts, SGD accepts reservations for gene names that will be
published soon. The SGD curators will act as advocates for your usage
of the gene name. If we become aware of a nomenclature conflict, we
will attempt to notify all parties. Thus, a gene name reservation
with SGD can prevent a serious conflict with your gene name.
Making a gene name reservation does not guarantee that no one else will use
your reserved gene name. However, reserving a gene name will make it
less likely that the name will be used inappropriately.
What is a Reserved Gene Name? A reserved gene name is a unique
identifier for a locus that will be published shortly in a scientific
journal. This name has been submitted to SGD along with at least
one piece of scientific information regarding the gene or its product
(i.e. description, phenotype, gene product, ORF name, mapping
information).
What is a Standard Gene Name?
A standard gene name is a unique gene
name that is published in a scientific journal and is
the primary accepted name for that gene. Other published names for
that gene are "Not Standard" names, or aliases.
Note: Submission of a sequence to GenBank/EMBL/DDBJ with a new gene
name no longer suffices to make that gene name standard. If
you intend to submit a new gene name to GenBank/EMBL/DDBJ, you
should first register that gene name with SGD.
You may reserve a gene name with SGD shortly before submitting your
paper containing the gene name for journal publication. An SGD gene
name reservation informs the research community that this gene name
will be published soon.
We urge you to include your gene name(s) in the abstracts of
any relevant papers. This simplifies the task of identifying yeast
gene names that are already in use.
Note: If at any time you wish to send us any unpublished
information about a gene (even if you do not ever plan to publish it),
it will appear with the locus information (if it is named gene) or
with the sequence information (if it is an un-named ORF) as a personal
communication with your name(s) as author(s).
- The gene name should consist of three letters (the gene
symbol) followed by an integer (e.g. ADE12). Dominant alleles of the
gene (most often wild-type) are denoted by all uppercase letters, while
recessive alleles are denoted by all lowercase letters.
- 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. For more information
please refer to the guide to S. cerevisiae nomenclature,
published in Trends in Genetics.
Before deciding on your choice of gene name, please search SGD
Gene Names for any gene name beginning with the 3-letter
symbol. To do this, enter the 3-letter name followed by an asterisk,
e.g. "ADE*", in the query box.
For instance, if you wanted to register ASM1, the query "ASM*" would
reveal that ASM4 already exists in our database, and therefore the
3-letter symbol "ASM" is already in use and should not be used to
describe a different class of genes.
- The gene name should be unique for S. cerevisiae. In
addition, it is a good idea to avoid using gene names from other
organisms, unless you are naming the cerevisiae ortholog. See the
pombe to cerevisiae gene name mapping page provided by the Forsburg lab for an example of the confusion
this can cause. We
encourage you to use the SGD Global Gene
Hunter to ensure that the gene name has not been used
previously. Please 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.
- Researchers should first check using Global Gene
Hunter to ensure that their chosen gene name is not already in
use.
- Gene names may be reserved using the SGD
Gene Registry Form. You must provide us with your name and
address (including e-mail) as well as the gene name. We
would also appreciate an explanation of the 3-letter gene symbol,
whenever possible.
- At the time of registration, SGD curators will check PubMed,
GenBank/EMBL/DDBJ and the SGD Gene Name Registry to ensure the gene
name is unique. Note that although submission of a sequence to
GenBank/EMBL/DDBJ no longer suffices to make a gene name a standard
name, the curators will also continue to check GenBank/EMBL/DDBJ to
attempt to avoid name conflicts.
- Unique gene names will be entered as a reserved gene name in the
SGD
Gene Name Registry for one year from the date of submission. This
registry includes all gene names, both Standard and Not_Standard. If
your chosen gene name is not unique, you will be contacted and asked
to select a new name.
- Once a gene name is reserved within SGD, the information you
submitted, the reservation date (called Reserved_date), the date when
the reservation expires (called Reserved_expiration), and a note
indicating that this is a reserved name will be available in SGD on
the locus history page and in the Gene Name Registry. Also, following
the S.cerevisiae nomenclature guidelines, the gene name
will be displayed in italics on the locus page at SGD.
- A gene name may be reserved with SGD shortly before its submission
for publication in a scientific journal.
- SGD curators will actively discourage anyone else from using your
reserved gene name. If we become aware of a nomenclature conflict, we
will attempt to notify all parties. Thus, a gene name reservation
with SGD can prevent a serious conflict with your gene name.
- Reserving a gene name DOES NOT GUARANTEE that you will
retain the gene name as it is not considered to be a public release of
the name for priority purposes (see policies regarding the "Transition from a
reserved name to a standard locus name").
- If your reserved gene name is published referring to a different
gene during the reservation period, a compromise specific to the
situation will be made. In most cases, you will NOT retain the use of
the gene name unless you published the name first (see "Resolution of gene name
conflicts").
- It is the responsibility of the researcher reserving the gene name
to ensure that it is still unique PRIOR TO PUBLICATION. Check
to see that the gene name is still unique using Global Gene
Hunter before submitting the paper.
- Gene names may be reserved for up to one year. After one year, a
gene name may be renewed upon meeting certain criteria (see "Renewing a reserved gene
name").
- The gene name reservation is good for one year. Once your gene
name reservation has expired, SGD will search PubMed to see if the
reserved gene name has been published.
- If we are unable to determine if the gene name has been
published, you will be contacted by email or phone.
- Please provide us with the reference if you have published the
gene name and we were unable to find it. If you have not published
the gene name, you have the option to renew your gene name
reservation or request that your gene name reservation be removed.
- If you do not respond to SGD's attempts to contact you within 6 months, the gene name
reservation will be removed.
- All expired gene names will be retained as aliases for the gene.
- Once a reserved gene name has expired and been moved to an 'alias'
status, the gene is available for new gene name reservations from the
yeast community.
- To renew a gene name reservation, you must indicate that you are
continuing to study the gene.
- Your gene name reservation will be extended by 1 more year.
- Please use the Gene
Registry form to submit a renewal or email us.
- Upon publication of a peer-reviewed journal article that contains the gene name,
your reserved gene name will become a standard locus name in SGD as
long as the gene name is still unique and there are still no other
published names for the locus. The transition to a standard name is
effective on the publication date, in print or online, of the journal article in which the
gene name is described. Gene name conflicts that have arisen in the
past have convinced SGD curators that an "in press" paper can no
longer be sufficient to change a reserved name to a standard locus
name.
- If it is discovered that your gene has been previously named,
your gene name would instead become an alias ("Not_Standard_Name") for
the prior (standard name) locus, and it and any associated references
would remain searchable and linked to the standard locus name.
- Likewise, if during the reservation period your chosen gene name was
published referring to a different gene, then a compromise
specific to the situation will have to be made. Hopefully, reserving a
gene name in advance will make this event rare.
We frequently must resolve gene name conflicts in which multiple names
have been used to describe one gene or, conversely, one name has been
applied to multiple genes. We recognize that each case is unique, and
we strive to choose the most appropriate solution using the following
guidelines. We try whenever possible to engage the participation of
all interested parties in the resolution of the conflict. We use the
following parameters when resolving gene name conflicts:
- Researcher Consensus: Above all else, if the
researchers involved in the name conflict agree to a resolution that
satisfies our Gene Naming requirements, we will abide
by it.
- Literature Consensus: In the absence of
researcher consensus, we will examine the literature for the number of
name usages and the number of different research groups utilizing a
particular name usage. If there is a very obvious imbalance, we will
favor the more predominant name usage.
- Priority: In the absence of either researcher or
literature consensus, we will favor the gene name usage that was first
published.
- Relevance of the Name: In rare cases where
none of the above guidelines apply, we may favor a particular name
usage that more accurately describes a phenotype, gene product
or gene function.
- Unmapped/Unsequenced genes: This is a special case that
applies only to situations where one name has been used for
multiple genes. If one of the genes involved in the conflict
has never been mapped (physically or genetically) or
sequenced, and thus cannot be proven to be a previously
uncharacterized and un-named gene, that usage may be passed
over (even if some of the other guidelines above apply) in
favor of a usage for a gene known to be a novel locus.
We understand that resolving gene name conflicts causes some pain and
inconvenience, especially in the situation where one name has been
applied to multiple genes and thus one of these genes will have a
completely new name. This is why it is especially important to check
the SGD
Gene Name Registry and Global Gene
Hunter for previous usage of a desired gene name. The SGD curators
are happy to check a potential gene name for you. Send us an e-mail
message to
yeast-curator@genome.stanford.edu
or call us at (650) 725-8956.
Our overall goal is to serve the yeast community as a repository of
S. cerevisiae information. As such, we strive to reflect the
current community consensus on gene name usages. In order to achieve
these goals we need to hear from you! We welcome your questions,
comments and suggestions regarding the SGD.
Thanks,
the SGD staff.
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