Gene Naming Guidelines

Purpose of Reserving Gene Names

To avoid gene naming conflicts, the S. pombeGene Naming Committee accepts reservations for gene names that will be published imminently. This does not guarantee that no one else will use your reserved gene name, but the naming committee will actively discourage alternative usage. If we become aware of a nomenclature conflict, we will attempt to notify all parties.

 

Guidelines for naming S. pombe genes

  1. The gene name should consist of three italicized lower case letters (the gene symbol) followed by an integer (e.g. rad26). This will not be italicized in the database. (Note that a few historical gene names with four letters, or without an integer, have been grandfathered into the database, but all new standard gene names must conform to the three-letters-plus-integer pattern.)
  2. Gene names may be reserved using the Gene Name Registration Form. Please provide requested information and an explanation of the 3-letter gene symbol.
  3. 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. If a 3-letter symbol is already in use, it should not be used to describe a different class of genes. Before choosing your gene name, search PomBase for any gene name beginning with the 3-letter symbol, by entering the 3-letter name followed by an asterisk, e.g. "cdc*". Also check the usage of the 3-letter code in S. cerevisiae at SGD.
  4. The length of time that a gene name can be reserved is one year (as for S. cerevisiae names at SGD). After one year, a gene name may be renewed upon meeting certain criteria (see "Renewing a reserved gene name").
  5. Please 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.
  6. 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").
  7. Please check that the reserved gene name is still unique before submitting a publication.
  8. At the time of registration, the S. pombe curator will check PubMed, GenBank/EMBL/DDBJ and the Gene Name Registry to ensure the gene name is unique.
  9. Unique gene names will be entered as reserved gene names in the Gene Name Registry for one year from the date of submission. This registry includes all gene names, both Standard and Synonyms. If your chosen gene name is not unique, you will be contacted and asked to select a new name.
  10. Once a gene name is reserved with the information you have submitted, the reservation date and a note that this is a reserved name will be displayed on the gene page.

 

Renewing a reserved gene name

To renew a gene name reservation, you must submit new data demonstrating continued study of this gene. Please use the Gene Name Registration Form to submit a renewal.

 

Transition from a reserved name to a standard gene name

  1. Upon publication of a journal article that contains the gene name, your reserved gene name will become a standard gene name in GeneDB, as long as the name is still unique and there are still no other published names for the locus.
  2. If it is discovered that your gene has been previously named, your gene name would instead become an alias (Synonym) for the locus, and it and any associated references will remain searchable and linked to the standard locus name.
  3. 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.

 

Resolution of gene name conflicts

Gene name conflicts in which multiple names have been used to describe one gene or, conversely, one name has been applied to multiple genes, will be resolved within 12 months. Whenever possible, all interested parties will be involved in the resolution of the conflict. We recognize that each case is unique, and we will choose the most appropriate solution using the following guidelines:

  1. Researcher Consensus: In the first instance, if the researchers involved in the name conflict agree to a resolution that satisfies our Gene Naming requirements, this solution will be implemented.
  2. 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 favour the predominant name usage.
  3. Priority: In the absence of either researcher or literature consensus, we will favour the gene name usage that was first published if this is significantly earlier. However, if papers are published simultaneously (within 3 months), the pre-registered name will become the primary name.
  4. Relevance of the Name: In rare cases where none of the above guidelines apply, we may favour a particular name usage that more accurately describes a phenotype, gene product or gene function.