Create miRecords RegIN files

1. Download current miRecords target information

• Go to http://mirecords.biolead.org/download.php
• Download the latest release of miRecords.
• Open the .xls file in Excel and save it as a tab-delimited file (.tab).

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2. Download the identifier mapping databases from BridgeDb

• Download the database for gene products for the relevant species from http://bridgedb.org/data/gene_database/
  • Hs_Derby_xxxxxxxx.bridge = Homo sapiens
  • Mm_Derby_xxxxxxxx.bridge = Mus musculus
  • Rn_Derby_xxxxxxxx.bridge = Rattus norvegicus
  • ...
• Download the microRNA mapping database (maps from miRBase id to accession) from https://github.com/mkutmon/rin-creation/blob/master/mirna-mapping/mirbase-v19.bridge

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3. Download the conversion tool

• You can build the tool yourself:

  • git clone https://github.com/mkutmon/rin-creation.git
  • cd RINCreator
  • Run 'ant' to create the jar file
  • You can find the jar file in the newly created 'dist' directory

• Download the latest uploaded conversion.jar file from https://github.com/mkutmon/rin-creation - check conversion-xxxx-xx-xx.jar. If you are using this jar, you also need to download the dependencies.zip file which contains the lib directory with all the dependencies that are needed to run the jar.

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4. Run the tool with all required arguments

For example,

java -cp conversion.jar cytargetlinker.conversion.MiRecords -i miRecords_version4.tab --bridgeDbFile Hs_Derby_20120602.bridge mirbase-v19.bridge -o mirecords-hsa-2013-04-27.xgmml --organism "Homo sapiens" -v "2013-04-27"

or,

java -cp conversion.jar cytargetlinker.conversion.MirTarBase -i hsa_MTI.tab --bridgeDbFile Hs_Derby_Ensembl_83.bridge mirbase-v19.bridge -o mirtarbase-hsa-6.1.xgmml --organism "Homo sapiens" -v "2016-05-02

• -i -> input file downloaded in step 1
• --bridgeDbFile -> list both bridge files downloaded in step 2 (adapt if you have another version or species)
• -o -> output file, should always end with .xgmml
• --organism -> defines which interactions should be extracted
• -v -> database version - which version of miRecords are you using