mapTableColumn / idmapper no longer working at all

[Pierre Klemmer]

Hello,

I have been using mapTableColumn from RCy3 to map identifiers between databases without any issues for the past 6 months or so, but since 05/04 no identifier mapping works anymore. This is the case when using mapTableColumn, the GUI (clicking on a column and selecting 'Map column'), and the command line (idmapper map column) which all use idmapper I believe. When using mapTableColumn, Cytoscape shows a brief error stating that 'networkTable not found', though I'm unsure what this really means.

No other parameters have changed at all (for network, device, or script) and I have tested this on both Cytoscape 3.10.1 and 3.10.2 on multiple devices. I'm using the feature to map Entrez Gene IDs to Ensembl IDs though I have unsuccessfully also tried to map other ID types from other columns.

Best wishes,

Pierre

[Kristina Hanspers]

Hi Pierre,

The BridgeDB web service that Cytoscape id mapping uses is down right now. Please check back later. 

Kristina

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[Pierre Klemmer]

Hi Kristina,

Thanks for the swift reply! I will keep retrying. Is it possible to see the status of the service somewhere online without running idmapper?

Best wishes,

Pierre

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[Kristina Hanspers]

https://webservice.bridgedb.org/

Kristina

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[Ronan M.T. Fleming]

https://beta.metanetx.org/cgi-bin/mnxweb/id-mapper
there is also a SPARQL endpoint. For metabolites only.

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Mr. Ronan MT Fleming B.V.M.S. Dip. Math. Ph.D.
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Associate Professor,
School of Medicine,
University of Galway,

Ireland.

Coordinator of the Horizon Europe project "Reconstruction and Computational Modelling for Inherited Metabolic Diseases" (Recon4IMD)

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Peer-reviewed publications: https://goo.gl/FZPG23
Mobile:  +353 852 109 806
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