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Proteomicslab57357 / UniprotR

Retrieving Information of Proteins from Uniprot
GNU General Public License v3.0
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HTTP status was '400 Bad Request' #20

Closed JorgeVindelAlfageme closed 2 years ago

JorgeVindelAlfageme commented 2 years ago

Hi: I've been using UniprotR for a while and everything has been well until today. The thing is every time I try to connect to UniProtKB using functions such as "GetProteinGOInfo" or "GetSubcellular_location", I can't get anything from them. For example, using a random accession code (e. g., Q9HCE5), if I execute: GetProteinGOInfo(ProteinAccList = "Q9HCE5", directorypath = NULL) I get the next messages: "Please wait we are processing your accessions ... data frame with 0 columns and 0 rows Warning message: In file(file, "rt") : cannot open URL 'http://www.uniprot.org/uniprot/?query=accession:Q9HCE5&format=tab&columns=go-id,go,go(biological%20process),go(molecular%20function),go(cellular%20component)': HTTP status was '400 Bad Request'" It seems that now I can't retrieve information from the web. What has happened? Is there any problem with my code or is this package now obsolete due to a change in UniProtKB? Thanks for your time. Regards.

donumanimae commented 2 years ago

I'm having the same issue. I suspect it's because Uniprot recently went through a redesign and change their programmatic access. Any idea if/when the package will be updated?

JorgeVindelAlfageme commented 2 years ago

If you had the same problem, then it has to do with the UniProt platform. Since it's the first time I'm facing this issue, I don't know how long it will last. But if it is a problem only due to programmatic access, and information retrieval from the web doesn't have to be changed, I assume the package will be updated soon. Until then, I'll try to find an alternative to extract information from UniProt.

donumanimae commented 2 years ago

I contacted the authors and they expect to have an update "within the next few days"

AliYoussef96 commented 2 years ago

Hi @JorgeVindelAlfageme @donumanimae

The problems with the package are due to the recent changes in Uniprot. We are going to work on solving the issues this week.

MohmedSoudy commented 2 years ago

Dears @donumanimae, and @JorgeVindelAlfageme The new version is now available on CRAN https://cran.r-project.org/web/packages/UniprotR/index.html and also on GitHub. We are waiting for your valuable feedback.

JorgeVindelAlfageme commented 2 years ago

Everything is working perfectly again. Thank you, @AliYoussef96, @MohmedSoudy.