I have been trying to use datasets in education, I think conceptually it is an excellent idea but the implementation and interfaces are inefficient, limited, and tedious to the extreme.
It promotes an awkward, verbose, free text-based parameters scheme, fundamentally unlike how command-line tools are supposed to work!
It is as if the implementers never used the UNIX command-line themselves. Reminds me of the incredible awkwardness of GATK that, in the end, had to also be rewritten into proper Unix parameters format (by version 4). For example, take this command
datasets summary genome accession GCF_000001405.39
The above formalism does not match the way scientists and bioinformaticians use command-line tools.
In the world of data integration, why can't a tool figure out from GCF_000001405.39 that it is a genome accession???? I know this even without having to do a search. How come NCBI datasets is unable to figure out what it is without someone explicitly typing "genome accession"?
Here is what the tool should look like:
datasets GCF_000001405.39 --summary
or if I want a fasta file I should do:
datasets GCF_000001405.39 --fasta
and so on, if I wanted the metadata for the accession number in csv format this is how it should work:
datasets GCF_000001405.39 --metadata --format csv
In the current implementation every invocation of the datasets tool downloads gigantic gzipped blob files, that when unpacked will contain files and directories all named the same way ncbi_data that, prots.fa etc ... a nightmare in data management. The same "blob" mentality that permeates SRA is now in datasets.
To extract the metadata from the "blob" I will need to understand, download and run another tool dataformats that will operate on some obtuse named file data_table.json (or whatever)?
I could go on, but suffice to say I consider datasets an excellent idea being ruined by a terrible interface and desing.
I look at datasets and I see a tool designed by "programmers" that work by the hour, to implement "features" listed on a whiteboard - it is not a tool designed by scientists trying to perform a scientific analysis.
