Procedure for naming genes
dictyBase acts as the centralized clearinghouse for Dictyostelium discoideum genes names.
Scientific curators at dictyBase verify proposed names to
encourage the application of the Nomenclature Guidelines
and to ensure that names are not duplicated. The present document explains the procedures that dictyBase applies to name genes
and how conflicts with gene names are resolved.
- Choosing a gene name
New gene names should conform to established nomenclature. If there is no established nomenclature,
the conventions derived from Demerec et al. (1966) should be used. A gene description consisting of three lower-case, italicized letters,
followed by a capital italicized letter to distinguish genes with the same descriptor
that are related in a significant way.
Examples: rdeA, rdeB and rdeC; or
tagA, tagB and tagC.
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 Dictyostelium Nomenclature Guidelines.
- Ensuring that your gene name is unique
Before deciding on your choice of gene name, please search dictyBase
for any gene name beginning with the 3-letter
symbol. To do this, enter the 3-letter name followed by an asterisk
in the query box on the top right corner. Example: abc*.
We encourage you to search PubMed
and GenBank/
EMBL/
DDBJ to ensure that the gene name has not been used
previously. Please note that dictyBase curators routinely perform such
searches before a gene name is entered into the database, and would
be happy to check a potential gene name for you at any time.
- Ensuring that your gene has not already been named
Use the dictyBase BLAST server to
search the Dictyostelium genes. Genes that have Sequencing Center Gene Prediction names or
dictyBase IDs in the "Gene Name" field of the Gene Page have probably not yet been named.
- Naming a gene
Upon publication in a peer-reviewed journal or submission of the sequence to GenBank/EMBL/DDBJ,
the gene name will be automatically imported in dictyBase, provided that the name is mentioned in the abstract
of the paper and/or in the description of the GenBank record.
Genes can also be named prior to publication by writing to dictyBase curators with the dictyBase ID and the
proposed name of the gene.
Gene names will be reserved for one year, as long as there are no naming conflicts. Once your gene
name reservation has expired, dictyBase 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. If you do not respond to dictyBase's attempts to contact you within 6 months, the gene name
reservation will be removed. If the name is still available, the
gene name reservation may be renewed if you are
continuing to study the gene.
We urge you to include your gene name(s) in the abstracts of
any relevant papers. This simplifies the task of identifying
gene names that are already in use.
We occasionally must resolve gene name conflicts where 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. Whenever possible, we try to engage the participation of
all interested parties in the resolution of the conflict. We use the
following guidelines when resolving gene name conflicts:
- Researcher consensus: Above all else, if the
researchers involved in the name conflict agree to a solution, 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 points apply, we may favor a particular name
usage that more accurately describes a phenotype, gene product
or gene function.
- Unmapped/unsequenced genes: If there is a duplicate name for a
mapped/sequenced gene and a gene that has never been mapped on the genome, the name
for the latter may be removed in favor of the mapped gene.
Updated on
October 20, 2004
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