STRING's REST-API doesn't return the same info with the Web interface

Question

[arronar]

Hi,

I want to create a script that will check if specific pairs of genes have an interaction. So let's say for example that we want to check if these genes/proteins ACTA1, TNNC2 interact each other.

Through STRING's WEB interface, and by choosing multiple proteins on the left menu, the results show that these two proteins might interact.

Since that the web interface is not accessible through a script, I tried to use the REST API to retrieve this info but without any success. REST-API always returns a NULL table when trying

http://string-db.org/api/tsv/interactionsList?species=9606&identifiers=ACTA1%TNNC2

OR

http://string-db.org/api/tsv/interactorsList?species=9606&identifiers=ACTA1%TNNC2

Am I doing something wrong?

Answer 1

[Jean-Karim Heriche]

The STRING API works with STRING identifiers, e.g.:

http://string-db.org/api/tsv/interactionsList?identifiers=9606.ENSP00000304895%0D9606.ENSP00000303830

[arronar]

And is there any way to automatically retrieve these identifiers for a list of gene/protein names?

[Jean-Karim Heriche]

Use the resolve API:

http://string-db.org/api/tsv-no-header/resolve?species=9606&identifier=ACTA1

If you want only the ID (for example to reuse in a script) then:

http://string-db.org/api/tsv-no-header/resolve?species=9606&format=only-ids&identifier=ACTA1

[arronar]

I realized that some genes/proteins have more than one string identifier. Should check for every one of them if there is a result of interaction with the other identifier or checking one identifier is enough?

[Jean-Karim Heriche]

You have a list of genes and a gene can produce more than one protein. The question is what level of resolution do you need: gene level or protein isoform level ? If all you need is check if a given gene pair interacts via any of their proteins then you can stop as soon as you've found an interacting protein pair.

[arronar]

Thank you very much Jean.