Where to download a curated dataframe of the full archive of UniProt?

Question

[johnnytam100]

I want to download a curated dataframe of the full archive of UniProt.

Any format as long as it is a table (.csv, .tsv, SQL etc.).

Solution 1: Download the .fasta and do the formating myself -> very slow + information incomplete.

Solution 2: Use API like BioServices -> still very slow but more information.

Do we have an already-curated dataframe containing as complete as possible the entry + metadata of UniProt that can be downloaded right away?

[Michael]

See also Importing Uniprot into BioSQL using BioPython takes years (nearly literally!)

Answer 1

[Michael]

The closest you get is UniProtKB's Download page. If you download SwissProt and TrEMBL databases you will get a lot of data. I don't think a public complete database dump of UniProtKB exists containing everything from the underlying SQL databases. I further do not think loading everything into a large dataframe would make much sense, it would be redundant and likely not fit into memory where R objects reside. The gzip compressed TrEMBL data are already 140GB to download.

Answer 2

[Eugenio]

you can also set a direct connection via ftp ftp://ftp.uniprot.org/