Accessing String-Db Through Psicquic

Question

[Woa]

I'm trying to access the String DB through PSICQUIC for fetching protein-protein interaction data of a particular model organism.

The typical output from PSICQUIC is like this

Where the last field contains the score e.g score:507(free-text). However, this score is different from what String-DB web site reports, which has a fractional value.

Can anyone tell me what typical cut off score I can use for PSICQUIC derived STRING data?

Thanks

WoA

[Woa]

I think the score that is available with downloadable files from StringDB is the confidence score multiplied by 1000. As the confidence score lies between zero and one it cant't exceed 1000, but I'm having score like 76000 !!!

[Michael Kuhn]

Hello, as noted below, the bug in STRING should be fixed now.

[Woa]

Thanks a lot for the update

Answer 1

[Michael Kuhn]

In this case, the score is multiplied by 1000, so the actual score is 0.507. In your example, the last interaction (ARF5 and CAPNS1) has "score:452(free-text)", and the STRING web interface gives a score of 0.452.

[Woa]

Thanks Michael, but if you retrieve the following list http://string.uzh.ch/psicquic/webservices/current/search/query/species:10090?firstResult=0&maxResults=100

the 8th entry from the bottom Gnai3 <-> Adcy9 interaction has a score of 'score:76000(free-text)'

[Michael Kuhn]

indeed, there seems to be a bug here. I'll forward this.

[Woa]

Sorry that was the 11th Entry and NOT 8th

[User 8255]

that was my mistake, a bug in the score calculation, only for database transferred scores. have a look again now

[Michael Kuhn]

(the unknown Googler was a member of the STRING development team)

[Michael Kuhn]

(the unknown Googler is a member of the STRING development team)