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cytoscape Stringdb identifiers can't be mapped to uniprot or ensembl

Hi - I am following a cytoscape tutorial on networks.

Using String disease query, I imported the ovarian cancer network and need to integrate the network with a datatable that uses uniprot identifiers. In the Ovarian cancer network, I am trying to map the string identifiers to uniprot but keep getting the error message "failed to map ## identifiers".

The "Map From" column automatically selects "Ensembl", I selected "Uniprot" for the "To" column. The error message indicates: "Failed to may any of 78 identifiers.Mapped:Ensembl -> Uniprot TrEMBL"

I am using cytoscape Version: 3.10.3 on a Mac (OS Sequia 15.4) with Java version: openjdk version "23.0.2" 2025-01-21.

image of column mapping

error message

Thanks for any suggestions!

map stringdb cytoscape

1 answer

You are correct, when we switched to the new backend, we switched to a different canonical name. I'll raise this as an issue.

thanks, much appreciated!

Well, unfortunately, it's not something that we can change easily. You could probably use the Display name and map it to Uniprot, though.

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