connection timeout in importing protein network

[michela riba]

Hi,

I'm trying to retrieve a network starting from 1360 IDs (Uniprot Ids) using 

import network from public database.

I'd like to use STRING data

but the results panel is all red and seems that there are no interactions

next to the database name  the "connection timeout, try again" comes

I'm surprised because some months ago this does not happen, and at that time I used IntAct database

with the same staring list and al was fairly simple 

I do not understand what could be the problem.

I have tried with a subste of the list (50 IDs or more) and that seems functioning, but I do not know waht is the problem

and how to solve.

Are there any limitations (new because before the summer everything was OK) in the number of IDs 

or other parameters for example in the preferences that I should control?

Thanks a lot,

Michela

[Kei]

Hi.

Probably, the query size is too big for remote data import, but there is an alternative.

1. Download STRING DB dump (it is available as text)

2. Load network for the species you are interested in (import as table)

3. Use your list of gene IDs for selection

4. From the selection, create new subnetwork

Kei

2014年3月12日水曜日 13時35分20秒 UTC-7 michela riba:

[IgorRodchenkov]

I suspect it's a core bug or design issue with Cy3 (we had a similar one fixed for the biopax reader only).

Please see tickets: https://code.cytoscape.org/redmine/issues/2385 and https://code.cytoscape.org/redmine/issues/2412 

Igor.