SGD Help: Gene Registry

The SGD Gene Registry is the system used by the S. cerevisiae community and SGD to reserve standard names for newly characterized genes. The Gene Naming Guidelines describe how to choose a gene name and how to use the Gene Name Registry to reserve it. See the Nomenclature Conventions page for details on conventions for naming S. cerevisiae genes and chromosomal features.

Contents

  1. About SGD Gene Registry
  2. Gene Naming Guidelines and Procedures
    1. Purpose of Reserving a Gene Name
    2. Reserving a Gene Name With SGD
    3. Gene Name Reservation Procedures
  3. Policies With Respect to Reserved Gene Names
    1. Overview
    2. Expiration of a gene name reservation
    3. Renewing a reserved gene name
    4. Transition from a reserved name to a standard locus name
    5. Revisions to Gene Naming Guidelines
  4. Resolution of Gene Name Conflicts

About SGD Gene Registry

The task of maintaining a comprehensive list of yeast gene names was transferred to the SGD project by Bob Mortimer in early 1994. In subsequent discussions at yeast meetings, the research community conferred upon SGD the authority to mediate S. cerevisiae genetic nomenclature. SGD curators do not choose gene names, but rather work with yeast researchers to ensure that any proposed new gene names are unique, in the correct format, and consistent with those of other related genes. SGD curators resolve nomenclature conflicts or requests to change gene names by surveying researchers and working towards community consensus.

We have developed a set of Gene Naming Guidelines and Procedures in order to assist researchers in gene naming and to inform them about our policies for resolving gene name conflicts. The most common problems encountered are gene names that are not in the standard S. cerevisiae format, names that are used for more than one gene, or multiple names in use for a single gene. The curators at SGD attempt to resolve these problems according to the guidelines section on Resolution of Gene Name Conflicts.

To avoid conflicts, researchers should search for candidate gene names using the Global Gene Hunter tool. We urge researchers to contact SGD prior to the publication of a new gene name (even if they have previously reserved it) to ensure that the gene name they wish to use is still appropriate. The SGD curators are happy to help researchers reserve a gene name or to determine whether a gene name is appropriate.

Please note that all information submitted to SGD is made public. SGD cannot accept and does not maintain any confidential information.

Please do not hesitate to contact SGD curators if you have comments or questions about the SGD Gene Registry.

SGD Gene Naming Guidelines and Procedures

Purpose of Reserving a Gene Name

To avoid gene naming conflicts, SGD accepts reservations for gene names that will be published soon. These names are unique identifiers for genes that are under active study and are intended for publication in a scientific journal. To make a reservation, researchers submit a name to SGD along with at least one piece of scientific information regarding the gene or its product (i.e., a description, phenotype, localization, or function). After a gene name is reserved, SGD curators will act as advocates for usage of the reserved 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 publish a different name for that gene, or use the reserved gene name for a different gene. However, reserving a gene name will make it less likely that the name will be used inappropriately.

Once a gene name is published in a scientific journal, it becomes a standard gene name. Any other published names for that gene are "Not Standard" names, or aliases.

Reserving a Gene Name With SGD

You may reserve a gene name with SGD at any time before 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) as well as systematic names in the abstracts of any relevant papers. This simplifies the task of identifying yeast gene names that are already in use.

Gene Name Reservation Procedure

    1. Step 1: Choose a name, following the S. cerevisiae gene name guidelines
      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. 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 function. For more information please refer to the Nomenclature Conventions page, or the guide to S. cerevisiae nomenclature published in Trends in Genetics (download PDF). Before deciding on a gene name, please search SGD for any gene name beginning with that 3-letter symbol. To do this, enter the 3-letter name followed by an asterisk, e.g., "ADE*", in the SGD Search box located near the top of most SGD pages. 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.
    2. Step 2: Make sure that the proposed name is unique among S. cerevisiae standard gene names
      Researchers should first check using Global Gene Hunter to ensure that their chosen gene name is not already in use for S. cerevisiae. In addition, it is a good idea to avoid using gene names from other organisms, unless you are naming the S. cerevisiae ortholog. See the pombe to cerevisiae gene name mapping page provided by the Forsburg lab for examples of the confusion this can cause.
    3. Step 3: Submit to SGD, via the Gene Registry Form
      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.
    4. Step 4: SGD will confirm the proposed name
      At the time of registration, SGD curators will check PubMed, GenBank/EMBL/DDBJ and the SGD Gene Name Registry to verify that 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 continue to check these databases to avoid name conflicts. If your chosen gene name is not acceptable, you will be contacted and asked to select a new name.
    5. Step 5: SGD will enter the reservation
      A reserved gene name is displayed on the Locus Summary page of the relevant gene; the reservation date and any other information submitted along with the reservation are displayed on the Locus History page. Reservations expire one year from the date of submission; you will be contacted before this time and given the opportunity to extend the reservation if desired.

Policies With Respect to Reserved Gene Names

Overview

  • 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.
  • 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 "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 reservation may be renewed upon meeting certain criteria (see "Renewing a reserved gene name").

Expiration of a gene name reservation

  • 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. 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.

Renewing a reserved gene name

  • To renew a gene name reservation, you must indicate that you are continuing to study the gene. If this is the case, your gene name reservation will be extended by 1 more year.
  • Please use the Gene Registry form to submit a renewal or email us.

Transition from a reserved name to a standard locus name

  • 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 for the locus.
  • Likewise, in the unlikely event that during the reservation period your chosen gene name was published referring to a different gene, then a compromise specific to the situation will be made.

Revisions to Gene Naming Guidelines

These policies were agreed upon by the community of yeast researchers at the 2003 Cold Spring Harbor Yeast Cell Biology meeting:

  • 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.

These policies were agreed upon by the community of yeast researchers at the 1997 Cold Spring Harbor Yeast Cell Biology meeting:

  • 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 will be increased from 6 months to one year.

Resolution of gene name conflicts

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:

      1. 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.
      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 favor the more predominant name usage.
      3. Priority: In the absence of either researcher or literature consensus, we will favor the gene name usage that was first published.
      4. 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.
      5. 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 may cause some pain and inconvenience. This is why it is especially important to check SGD and to use Global Gene Hunter to find any previous usage of a desired gene name. The SGD curators are happy to check a potential gene name for you. Do not hesitate to contact SGD if you would like our assistance.

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 SGD gene naming policies.

Go to SGD Gene Registry