Accessing older version of STRINGdb using Cytoscape

[Pranavathiyani G]

Dear community,

I am currently using the latest version of Cytoscape (v3.8.2) and StringApp (v1.6.0), is there a possible way to access the STRING database version v10.5 directly from the tool? The tool can access only the current available version(v11.0) of STRING DB, and even the Bioconductor package 'STRINGdb' supports the recent version.

I can get the interaction data directly from the download page from the older version of STRINGdb. Still, the retrieval or mapping of enrichment/annotation or STRINGifying the network doesn't seem to work. Hoping for some suggestions or alternative ways.

Thank you.

Regards,
Pranavathiyani G.

[Scooter Morris]

Hi Pranavathiyani,

   It might be possible, but definitely not easy.  I would have to check with the database owner to see if the older API is still available.  One thing to try would be to installer an older version of the stringApp (1.4.0) to see if that works for you.  It will try to connect to the pre-version 11 API, but there's no guarantee that it will still work.

-- scooter

[Nadezhda Doncheva]

Hi,

We discussed this question yesterday, but I did not manage to write the answer yet. Unfortunately, it is not possible to access older versions of STRING through the stringApp. It doesn't matter which version of the stringApp is used.

The only possible workaround would be to go to the older web version of STRING, search for the desired network there and download the network file. This file can then be imported into Cytoscape as a network and the edges will correspond to the edges of the STRING version from which the file came. However, you would need to play some more with the visual styles if you would like the network to look as stringApp networks look. Also none of the functionalities like Change confidence, Expand, etc. will be available.

Could you maybe explain why you need an older version and what for? Maybe we can provide better help if we know that.

Best wishes,

Nadya

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[Pranavathiyani G]

Thank you for the reply.

In the new version of STRING DB, the reference organism strain considered for PPI data is different from the older version in some microbes. However, I can proceed with orthology-based PPI mapping. But will miss out on some interactions specific to a particular strain as the proteins may not be present in the organism considered in the newer version. 

Regards,

Pranavathiyani G.

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