Question: Retrieving protein protein interaction database using STRING database
gravatar for sharmatina189059
2.2 years ago by
United States
sharmatina18905940 wrote:

Deal all Has anyone used the STRING database for retrieving bacterial strains's protein protein interactions. I have all the identifiers list (mentioned below) and I need to retrieve their interacting partners with the information and annotation of gene neighborhood, gene fusion, co-occurences along with their scores. 575584.HMPREF0010_01182 575584.HMPREF0010_02823 575584.HMPREF0010_03718 575584.HMPREF0010_02943 575584.HMPREF0010_01100 575584.HMPREF0010_00178 575584.HMPREF0010_02785 575584.HMPREF0010_01244 and so on ... while using API for this purpose I am using, but it doesnt show any information for gene neighborhood and fusion and nothing has been mentioned in the tutorial. As I have 2500 entries like this, can anyone tell me how can I retrieve it pragmatically by using these identifiers... Please do the needful..

sequence gene • 1.0k views
ADD COMMENTlink modified 2.2 years ago by Jean-Karim Heriche20k • written 2.2 years ago by sharmatina18905940

I don't have a proper answer for you because you provide limited information (an example of expected/ desired information would be helpful as that makes searching easier without having to know exactly what the STRING database(s) contain).

Their very poorly documented REST API shows all other options that you have for retrieving data, but I wonder if you could get all relevant information in a single request (I'm very sure you can't). Therefor you probably need to create multiple requests, first getting the interacting partners, then requesting information for each found entry, etc.

For example, finding the interacting partners as text: (this should obviously also work with JSON output format, but that gives a 404 - definitely not a proper RESTful API)

ADD REPLYlink written 2.2 years ago by Fukusahachi20

Have u used package STRINGdb to retrieve this data which runs o R platform.

ADD REPLYlink written 2.2 years ago by sharmatina18905940
gravatar for Jean-Karim Heriche
2.2 years ago by
EMBL Heidelberg, Germany
Jean-Karim Heriche20k wrote:

You could download the data here.

ADD COMMENTlink written 2.2 years ago by Jean-Karim Heriche20k

As Fukusahachi said, you did not add too many details, I have done something similar. First downloading the 500 1st grade interactors of my protein of interest and 500 2ndgrade interactors (maximum download allowed using the webpage) if you want to use the full STRING Db you need to download it). If you were using the webtool, you can download not only the picture of interactors but the files going to the tab "export" if you download the file ...TSV: tab separated values -you will be able to get that info. The annotation is in a different file (. protein annotations), you will need to intercept it with the tsv file using R or bash should be simple. Hope it helps

ADD REPLYlink written 2.2 years ago by munizmom60
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