Question: STRING's REST-API doesn't return the same info with the Web interface
0
gravatar for arronar
18 months ago by
arronar200
Austria
arronar200 wrote:

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?

rest-api stringdb • 431 views
ADD COMMENTlink modified 18 months ago by Jean-Karim Heriche20k • written 18 months ago by arronar200
3
gravatar for Jean-Karim Heriche
18 months ago by
EMBL Heidelberg, Germany
Jean-Karim Heriche20k wrote:

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

http://string-db.org/api/tsv/interactionsList?identifiers=9606.ENSP00000304895%0D9606.ENSP00000303830
ADD COMMENTlink written 18 months ago by Jean-Karim Heriche20k

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

ADD REPLYlink written 18 months ago by arronar200
1

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
ADD REPLYlink written 18 months ago by Jean-Karim Heriche20k

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?

ADD REPLYlink modified 18 months ago • written 18 months ago by arronar200
1

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.

ADD REPLYlink written 18 months ago by Jean-Karim Heriche20k

Thank you very much Jean.

ADD REPLYlink written 18 months ago by arronar200
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