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Pulling TSV automatically from STRINGDB

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
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updated by gcasabo • gcasabo • written by hakimelakhrass hakimelakhrass

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

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written by tpm • tpm

1 answer

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

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written by gcasabo • gcasabo

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