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

Question

[nicole]

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.

Thanks for any suggestions!

Answer 1

[Scooter]

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

[nicole]

thanks, much appreciated!

[Scooter]

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