Question

STRINGdb R package reference class instantiation with v12.0

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Abhishek • 0

@e3a7a4dc

Last seen 4 months ago

Australia

Hi all,

I've obtained the latest StringDB file : 9606.protein.links.full.v12.0.txt, from the downloads section of the website. I intend to use this data to obtain list of protein pairs that are from databases and experimentally verified.

To map some genes of interest which I have, to corresponding protein STRING Id, I had previously used,

string_db <- STRINGdb::STRINGdb$new(version = "11.5", species = 9606, score_threshold = 400, input_directory = "data/stringdb")    
string_db$map(genes_of_interest, "gene", removeUnmappedRows = TRUE)

Now that I'm using v12 string db data, I installed the latest version of the package available for me,STRINGdb_2.8.4, and thought it makes sense to use version = "12" while instantiating this class. i.e.

string_db <- STRINGdb::STRINGdb$new(version = "12.0", species = 9606, score_threshold = 400, input_directory = "data/stringdb")

But this gave the error :

cannot open URL 'https://stringdb-static.org/download/protein.aliases.v12.0/9606.protein.aliases.v12.0.txt.gz'

I have found that protein.aliases.v12.0 entry is not present in https://stringdb-static.org/download/, and only protein.aliases.v11.5 is present.

Should I use version = "11.5" to instantiate the class while using 9606.protein.links.full.v12.0.txt ?

STRINGdb • 1.0k views

ADD COMMENT • link updated 23 days ago by damian.szk ▴ 80 • written 5 months ago by Abhishek • 0

score 2 · Accepted Answer · 2023-11-22

2

Entering edit mode

James W. MacDonald 65k

@james-w-macdonald-5106

Last seen 1 day ago

United States

Dear Abhishek,

In order to use STRING version 12.0 you'll have update the package to the latest version.

Best, Damian.

ADD COMMENT • link 5 months ago James W. MacDonald 65k

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Thank you for the response. I had to update my R version to get the latest StringDB package STRINGdb_2.14.0 Unfortunately, as of now

string_db <- STRINGdb::STRINGdb$new(version = "11.5", species = 9606, score_threshold = 400, input_directory = "data/stringdb")

gives me

Error in open.connection(file, "rt") : 
  cannot open the connection to 'https://string-db.org/api/tsv-no-header/version'
In addition: Warning message:
In open.connection(file, "rt") :
  cannot open URL 'https://string-db.org/api/tsv-no-header/version': HTTP status was '400 Bad Request'

Searching this link on the browser gives

Service Unavailable Sorry, our system is currently overloaded with requests. Please try again later.

I hope the issue is temporary. I'll try again later

ADD REPLY • link 5 months ago Abhishek • 0

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Its working now. Thank you :)

ADD REPLY • link 5 months ago Abhishek • 0

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Hi Damian, I've updated the STRINGdb package to the latest one, STRINGdb_2.14.3. I then try this to run this:

string_db <- STRINGdb$new(version = "12", species = 9606, score_threshold = 700, input_directory="")

I do some steps to get the input_genes_mapped_vector and try to get the interactions

interactions <- string_db$get_interactions(input_genes_mapped_vector)
head(interactions)

But I get this error:

trying URL 'https://stringdb-static.org/download/protein.links.v12.0/9606.protein.links.v12.0.txt.gz'
Error in download.file(urlStr, temp) : 
  cannot open URL 'https://stringdb-static.org/download/protein.links.v12.0/9606.protein.links.v12.0.txt.gz'
In addition: Warning message:
In download.file(urlStr, temp) :
  cannot open URL 'https://stringdb-static.org/download/protein.links.v12.0/9606.protein.links.v12.0.txt.gz': HTTP status was '404 Not Found'

It thinks there is a directory called static.org/download/protein.links.v12.0 but there isn't one. Should it be looking for this file /downloads/9606.protein.links.v12.0.txt.gz ?

ADD REPLY • link 23 days ago marta • 0

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Dear Marta,

There is no reference to "stringdb-static.org" within the STRINGdb 2.14.3 code base. After updating Bioconductor make sure you are using the updated package.

library(STRINGdb)
packageVersion('STRINGdb')
[1] '2.14.3'

Older versions work only with v11.5 and return the error that you see when trying to access v12.0

Best, Damian.

ADD REPLY • link 23 days ago damian.szk ▴ 80