Guidelines for gene and genome assembly nomenclature

Area of Science:

• Genomics
• Bioinformatics
• Data Science

Background:

• The proliferation of high-quality genome assemblies offers new research avenues.
• Lack of standardized naming conventions for genome assemblies and annotations creates significant challenges in data integration and identification.
• Inconsistent naming hinders bioinformatics pipeline integration and cross-resource assembly linking.

Purpose of the Study:

• To develop a specification for standardizing reference genome assembly naming.
• To enhance data consistency, interoperability, and adherence to FAIR principles.
• To ensure compatibility with major genomic data repositories.

Main Methods:

• Developed a specification for standardized genome assembly naming.
• Incorporated FAIR (Findable, Accessible, Interoperable, Reusable) principles.
• Designed for compliance with primary genomic data repositories.

Main Results:

• A new specification for standardizing reference genome assembly names has been created.
• The specification promotes consistency, findability, and interoperability across datasets.
• It ensures compatibility with major genomic databases and facilitates cross-species analyses.

Conclusions:

• Widespread adoption of standardized nomenclature will streamline assembly management and improve research reproducibility.
• Enhanced natural language processing applications for genomic literature are expected.
• The specification is adaptable across taxa, benefiting diverse research communities.