Question: Pulling TSV automatically from STRINGDB
0
gravatar for hakimelakhrass
3.3 years ago by
hakimelakhrass80 wrote:

Hello

So I am trying to automatically get the TSV file with all the interactions of a specific protein from STRINGDB. SInce i have a whole list of proteins I would like to this automatically. So every ID I enter I would like to export the entire TSV interaction file. I cannot seem to find a function that does this in STRINGDB for R. the get_interactions only gets the interactions between the IDs submitted. Thanks.

stringdb • 949 views
ADD COMMENTlink modified 4 months ago by gcasabo20 • written 3.3 years ago by hakimelakhrass80

may someone help with this question please, I am also stuck here as well. Thank you in advance

ADD REPLYlink written 4 months ago by tpm10
1
gravatar for gcasabo
4 months ago by
gcasabo20
Spain
gcasabo20 wrote:

Hi, I think what you want is what the interaction_partners API method does (you can see its documentation here: https://string-db.org/cgi/help.pl?subpage=api%23getting-all-the-string-interaction-partners-of-the-protein-set).

As you want a TSV file you have to use this URL: https://string-db.org/api/tsv/interaction_partners?identifiers=[your_identifiers]&[optional_parameters], being [your_identifiers] a string with all the identifiers separated by "%0d" and [optional_parameters] a string with optional configuration (see the link above for information about the optional parameters avalaible).

However, this method gives you only one TSV file with all the interactions for each protein, if you want to have a different TSV file for each protein you can do a loop calling the API individually for each protein.

Hope it serves. Regards

ADD COMMENTlink written 4 months ago by gcasabo20
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