Revised fission yeast gene and allele nomenclature guidelines for machine readability

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

doi:10.1093/genetics/iyad143

Revised fission yeast gene and allele nomenclature guidelines for machine readability

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^*

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

3 Citations (Scopus)

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.

Original language	English
Article number	iyad143
Journal	Genetics
Volume	225
Issue number	3
DOIs	https://doi.org/10.1093/genetics/iyad143
Publication status	Published - Nov 2023

Keywords

allele
database
FAIR
fission yeast
gene variant
genotype
knowledge base
model organism
nomenclature
standardization

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10.1093/genetics/iyad143

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Lera-Ramírez, M., Bähler, J., Mata, J., Rutherford, K., Hoffman, C. S., Lambert, S., Oliferenko, S., Martin, S. G., Gould, K. L., Du, L. L., Sabatinos, S. A., Forsburg, S. L., Nielsen, O., Nurse, P., & Wood, V. (2023). Revised fission yeast gene and allele nomenclature guidelines for machine readability. Genetics, 225(3), Article iyad143. https://doi.org/10.1093/genetics/iyad143

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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.",

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AU - Lambert, Sarah

AU - Oliferenko, Snezhana

AU - Martin, Sophie G.

AU - Gould, Kathleen L.

AU - Du, Li Lin

AU - Sabatinos, Sarah A.

AU - Forsburg, Susan L.

AU - Nielsen, Olaf

AU - Nurse, Paul

AU - Wood, Valerie

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Revised fission yeast gene and allele nomenclature guidelines for machine readability

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Keywords

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