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The GFF3 format is a common, flexible tab-delimited format representing thestructure and function of genes or other mapped features(https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md).However, with increasing re-use of annotation data, this flexibility has becomean obstacle for standardized downstream processing. Common software packagesthat export annotations in GFF3 format model the same data and metadata indifferent notations, which puts the burden on end-users to interpret the datamodel. The AgBioData consortium is a group of genomics, genetics and breedingdatabases and partners working towards shared practices and standards.Providing concrete guidelines for generating GFF3, and creating a standardrepresentation of the most common biological data types would provide a majorincrease in efficiency for AgBioData databases and the genomics researchcommunity that use the GFF3 format in their daily operations. The AgBioDataGFF3 working group has developed recommendations to solve common problems inthe GFF3 format. We suggest improvements for each of the GFF3 fields, as wellas the special cases of modeling functional annotations, and standardprotein-coding genes. We welcome further discussion of these recommendations.We request the genomics and bioinformatics community to utilize the githubrepository (https://github.com/NAL-i5K/AgBioData_GFF3_recommendation) toprovide feedback via issues or pull requests.

Recommendations for extending the GFF3 specification for improved interoperability of genomic data