Bashing file formats is a favorite pastime in bioinformatics, and annotation file formats such as GFF and BED seem to get special attention. A lot of this frustration stems from community's shockingly inconsistent adherence to specifications and conventions, but there are also some (dare I say objectively) problematic design choices in each of these formats.
GFF (and its more common derivatives GTF and GFF3) use 1-based closed interval notation, which optimizes for human comprehension but is far inferior to 0-based half-open interval notation (such as used by BED) for computations involving interval arithmetic.
Although BED and GTF were designed for very specific use cases (visualization and gene prediction, respectively), they have been used and abused in a much wider set of contexts. For example, the BED fields related to the thick part are irrelevant if you're not plotting them in a genome browser.
BED supports a single level of feature decomposition (a feature can be broken up into blocks). GTF supports two levels (exons grouped by transcript_id, transcripts grouped by gene_id). In contrast, GFF3 supports an arbitrary number of levels, and uses parent/child relationships defined by
Parentattributes to declare a directed acyclic graph of features.
Data that does not fit into mandatory pre-defined fields must be relegated to optional fields or free-form attribute key/value pairs. While this flexibility is powerful, a common complaint is that "all the action" happens in these optional/free-form fields.
There is a dearth of validation tools, and those that do exist focus primarily on validating syntax and not semantics. To use an aging analogy, it's one thing to say an XML file is valid, but it's completely different to validate it against a schema. There are essentially no widely used tools that do the latter for annotation files.
If we were tasked with creating a new annotation format, and if we were guaranteed the resources needed to develop it, and interest and wide adoption from the wider community (one can dream!), what design criteria should be considered in the development of this new format? What, if anything, makes an objectively good annotation data format?