Uploading metabolites file

[Jaione Telleria]

Hi everyone,

It is the first time for me using BridgeDbR. I was trying to upload the metabolite database, I have followed the step for proper installation of rJava described in the documentation, but still, this error appears to me when loading the database:

Error in .jcall("RJavaTools", "Ljava/lang/Object;", "invokeMethod", cl,  :
  org.bridgedb.IDMapperException: Could not connect to database: Failed to start database 'jar:(/home/jaione/bridge/metabolites_20220707.bridge)database', see the next exception for details. 

I have checked the rJava issue couple of times but still is generating issue. This are the basic versions:

-rJava: 1.0.6

-BridgeDbR: 2.8.0

-R version: 4.2.2

Sorry for the inconvenience and thank you very much in advance.

Jaione

[Egon Willighagen]

Hi Jalone,

this error message actually suggests a BridgeDb version mismatch between the R package and the .bridge file. And not a rJava version. If that was not set up well, you would not even get this error.

Earlier today I checked a 2023 metabolite ID mapping database with BridgeDbR 2.9.1 and that worked (for me). I need to check later to see if I can reproduce the problem with your combination. What is behind this is a actually often a version mismatch of a dependency of BridgeDb, Apache Derby. 

More as soon as possible,

Egon

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Lipidomics is increasing to be a fascinating new method to look at biology. This Nature Methods article includes how we use WikiPathways and related tools: https://doi.org/10.1038/s41592-022-01710-0 

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[Jaione Telleria]

Hi Egon,

Thank you for your early response. When you know more, please let me know.

Thank you very much

Jaione

To view this discussion on the web visit https://groups.google.com/d/msgid/bridgedb-discuss/CAMPqvY8r%2BpKHu6RcYsdstNEKiuBBrojDReteu8nXd098wS-sKg%40mail.gmail.com.

[Jaione Telleria]

Hi again Egon,

I just found out which was the bug, I have made a beginner's mistake. The point was that once downloaded the file of metabolites I decompress it and that is why bridgeDbR did not detect the database correctly. I have tried again and the file that is now on your page works perfectly with bridgeDbR version 2.8.0.

Really sorry for the inconvenience, thank you very much for your help.

Jaione

[Egon Willighagen]

Ah, okay, happy to hear that.

Egon

To view this discussion on the web visit https://groups.google.com/d/msgid/bridgedb-discuss/CA%2B9Y_PooXUdEVKtR%3DTbThCKOyQ-yoXEUzoF4ECwFGu8gnWMoBQ%40mail.gmail.com.

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Predicting binding affinities can be predicted for each protein variant with a new QSAR model that takes into account the amino acid change: https://jcheminf.biomedcentral.com/articles/10.1186/s13321-023-00701-3