Lera-Ramírez, Manuel;
Bähler, Jürg;
Mata, Juan;
Rutherford, Kim;
Hoffman, Charles S;
Lambert, Sarah;
Oliferenko, Snezhana;
... Wood, Valerie; + view all
(2023)
Revised fission yeast gene and allele nomenclature guidelines for machine readability.
Genetics
10.1093/genetics/iyad143.
(In press).
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Abstract
Standardized nomenclature for genes, gene products, and isoforms is crucial to prevent ambiguity and enable clear communication of scientific data, facilitating efficient biocuration and data sharing. Standardized genotype nomenclature, which describes alleles present in a specific strain that differ from those in the wild-type reference strain, is equally essential to maximize research impact and ensure that results linking genotypes to phenotypes are Findable, Accessible, Interoperable, and Reusable (FAIR). In this publication, we extend the fission yeast clade gene nomenclature guidelines to support the curation efforts at PomBase (www.pombase.org), the Schizosaccharomyces pombe Model Organism Database. This update introduces nomenclature guidelines for noncoding RNA genes, following those set forth by the Human Genome Organisation Gene Nomenclature Committee. Additionally, we provide a significant update to the allele and genotype nomenclature guidelines originally published in 1987, to standardize the diverse range of genetic modifications enabled by the fission yeast genetic toolbox. These updated guidelines reflect a community consensus between numerous fission yeast researchers. Adoption of these rules will improve consistency in gene and genotype nomenclature, and facilitate machine-readability and automated entity recognition of fission yeast genes and alleles in publications or datasets. In conclusion, our updated guidelines provide a valuable resource for the fission yeast research community, promoting consistency, clarity, and FAIRness in genetic data sharing and interpretation.
| Type: | Article |
|---|---|
| Title: | Revised fission yeast gene and allele nomenclature guidelines for machine readability |
| Open access status: | An open access version is available from UCL Discovery |
| DOI: | 10.1093/genetics/iyad143 |
| Publisher version: | https://doi.org/10.1093/genetics/iyad143 |
| Language: | English |
| Additional information: | © The Author(s) 2023. Published by Oxford University Press on behalf of The Genetics Society of America. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/). |
| Keywords: | nomenclature, allele, genotype, standardization, FAIR, model organism, fission yeast, database, gene variant, knowledge base |
| UCL classification: | UCL UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences > Genetics, Evolution and Environment |
| URI: | https://discovery-pp.ucl.ac.uk/id/eprint/10178098 |
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