mirBase-mature-v21.bridge

[Rajalekshmi N]

Dear BridgeDb Team,

I hope you are doing well.

I am reaching out regarding an issue I’ve been encountering while using CyTargetLinker’s Linkset Creator to generate a miRNA–target interaction linkset for Mus musculus (mouse), based on the latest miRTarBase v10.0 dataset.

I have been in contact with Prof. Martina Kutmon (CyTargetLinker developer) regarding this issue, and after several troubleshooting attempts, it appears that the problem might be related to the source_bridgedb file, specifically, the mirBase-mature-v21.bridge file, which I have been unable to locate in the BridgeDb repository.

Here is a summary of what I’ve tried so far:

1. Data preparation

   • Downloaded the Mus musculus interactions file (mmu_MTI.tsv) from miRTarBase.

   • Converted the provided CSV file to TSV format for use in Linkset Creator.

2. Configuration setup

   • Created a configuration file based on the hsa_mirtarbase.config example provided with Linkset Creator.

   • Initially used target_bridgedb=databases/Hs_Derby_Ensembl_83.bridge, which was later replaced with the correct Mouse bridge file downloaded from BridgeDb.

3. Issue

   • The linkset creation completes successfully, producing a large output.xgmml file (~450 MB).

   • However, when I load this linkset in Cytoscape, no mapped interactions appear, suggesting a mapping issue between miRNA identifiers and gene targets.

4. Suspected cause

   • In all attempts, I used the example source_bridgedb file path (databases/mirBase-mature-v21.bridge), but I do not have this file locally and could not find it in the BridgeDb repository/MirBase.

Could you please advise:

• Whether a mirBase-mature-v21.bridge file is available or has been replaced by a newer equivalent?

• If available, where can I download the latest version for use with Linkset Creator?

• Alternatively, whether there is an updated pipeline for generating a miRBase bridge file compatible with the current BridgeDb and CyTargetLinker releases?

I would greatly appreciate any guidance or resources you could provide to help resolve this issue.

Thank you very much for your time and support.

Best regards,
Rajalekshmi N.
Doctoral Researcher
Max Planck Institute for Evolutionary Biology, Plön