STRING API

Question

[kamalika]

Hi,

I am using the Stringdb api to retrieve all the interaction partners of the given input proteins. I am giving a list of input proteins. However, I am unable to know whether the output consists of all the proteins given as input. Eg: if my list is protein A, B and C - ['A', 'B', 'C'] in which the api does not return any output for protein 'B', it does not throw any error. Please tell me how to know if any protein is missing in the output file.

Thanks in advance.

[Jean-Karim Heriche]

I don't know what you expect. You're asking it to give you interaction partners for some proteins and this is what it does. If it doesn't find anything for a query protein then it won't report anything for it, that is it won't be in the output file. If you don't trust the API or want to do things in a different way, you can download the data and write a script to deal with it the way you want. If your question is about a known interaction partner not being reported, this situation can occur either because you've set a score threshold too high or simply because the interaction is not in the database.

[kamalika]

Thank you for your response. You are right, it's better I download the data and do the processing.