From eed7d6a164229d4ba4bffd56103088d7f2bb8249 Mon Sep 17 00:00:00 2001 From: Manuel Lera Ramirez Date: Fri, 29 Sep 2023 09:54:11 +0100 Subject: [PATCH] add references to nomenclature paper --- src/docs/about/published-by-pombase.PomBase.md | 11 +++++++++++ src/docs/submit-data/gene-naming-guidelines.md | 13 +++++++------ 2 files changed, 18 insertions(+), 6 deletions(-) diff --git a/src/docs/about/published-by-pombase.PomBase.md b/src/docs/about/published-by-pombase.PomBase.md index 096ff1019..896d21201 100644 --- a/src/docs/about/published-by-pombase.PomBase.md +++ b/src/docs/about/published-by-pombase.PomBase.md @@ -7,6 +7,17 @@ Canto, FYPO, annotations and Compara. ### Journal articles +
+ +
+Manuel Lera-Ramírez, Jürg Bähler, Juan Mata, Kim Rutherford, Charles S Hoffman, Sarah Lambert, Snezhana Oliferenko, Sophie G Martin, Kathleen L Gould, Li-Lin Du, Sarah A Sabatinos, Susan L Forsburg, Olaf Nielsen, Paul Nurse, Valerie Wood \ +Revised fission yeast gene and allele nomenclature guidelines for machine readability \ +*Genetics*, September 2023, iyad031 \ +
+[10.1093/genetics/iyad143](https://doi.org/10.1093/genetics/iyad143) + +
+
diff --git a/src/docs/submit-data/gene-naming-guidelines.md b/src/docs/submit-data/gene-naming-guidelines.md index dab544257..ba5e9c02b 100644 --- a/src/docs/submit-data/gene-naming-guidelines.md +++ b/src/docs/submit-data/gene-naming-guidelines.md @@ -34,27 +34,28 @@ will attempt to notify all parties. 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](http://www.yeastgenome.org/). -4. Please include your gene name(s) in the abstracts of any relevant +4. For non-coding RNA genes, follow [these rules](https://academic.oup.com/genetics/advance-article/doi/10.1093/genetics/iyad143/7283026#419163545) from [Lera-Ramirez et al. 2023](https://doi.org/10.1093/genetics/iyad143). +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. -5. At the time of registration, the *${species_abbrev}* curator will check +6. At the time of registration, the *${species_abbrev}* curator will check PubMed, GenBank/EMBL/DDBJ and the Gene Name Registry to ensure the gene name is unique. If your chosen gene name is not unique, you will be contacted and asked to select a new name. -6. Please check that the reserved gene name is still unique, and that +7. Please check that the reserved gene name is still unique, and that the gene still has no other name used for it, before submitting a publication. -7. If it is discovered that your gene has been previously named, your +8. 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. -8. If you reserve a gene name prior to publication, and your reserved +9. If you reserve a gene name prior to publication, and your reserved name is published referring to a different gene before your name usage is published, 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" below). -9. If no conflicts arise, your gene name will become the standard +10. If no conflicts arise, your gene name will become the standard name, and will appear on the gene page and elsewhere in ${database_name}.